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1
Walker, Sierra A., Jesús S. Aguilar Díaz De león, Sara Busatto, Gregory A. Wurtz, Abba C. Zubair, Chad R. Borges, and Joy Wolfram. "Glycan Node Analysis of Plasma-Derived Extracellular Vesicles." Cells 9, no. 9 (August 22, 2020): 1946. http://dx.doi.org/10.3390/cells9091946.
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Blood plasma is a readily accessible source of extracellular vesicles (EVs), i.e., cell-secreted nanosized carriers that contain various biomolecules, including glycans. Previous studies have demonstrated that glycans play a major role in physiological and pathological processes, and certain plasma glycans have been associated with disease conditions. However, glycome studies have been limited by a lack of analytical techniques with the throughput capacity necessary to study hundreds of clinical samples. This study is the first to characterize the EV plasma glycome based on all major glycan classes. The results based on glycan node analysis revealed, as expected, that plasma-derived EVs have distinct glycan features from donor-matched whole plasma. Specifically, glycan nodes corresponding to those observed in chondroitin sulfate, dermatan sulfate, type I keratan sulfate, and type II keratan sulfate were enriched on EVs. The identification of specific differences in glycan features in plasma vs. plasma-derived EVs is relevant for understanding the physiological role of EVs and as a reference for future diagnostic studies. Additionally, the results indicate that EV glycan nodes do not substantially differ among a small set of healthy donors. These results lay the framework for the further evaluation of all EV glycan classes as diagnostic markers, therapeutic targets, and biologically active components in health and disease.
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Ueno, Takayuki, Fumiaki Sato, Nobuhiko Shinkura, Taichi Aihara, Masao Fukushima, Masaru Sekijima, and Masakazu Toi. "Comprehensive analysis of serum N-glycans as a biomarker for breast cancer." Journal of Clinical Oncology 30, no. 15_suppl (May 20, 2012): e21031-e21031. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.e21031.
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e21031 Background: Early detection of breast cancer is an important aspect to improve therapeutic outcome. Serum biomarkers have a number of advantages including less invasiveness and possible application for monitoring. Glycans are involved in many biological processes including cancer progression and promising candidates for cancer biomarker. Methods: Sera were collected from 54 patients with operable breast cancer and 118 healthy volunteers. N-glycans were isolated by BlotGlyco (Sumitomo Bakelite Co., LTD, Japan) and N-glycan profile was obtained by MALDI-TOF MS. The principal component analysis (PCA) was performed by SIMCA-P+ ver.12 (Umetrics). N-glycan compositions were estimated from mass spectra using 'GlycoMod' database. Results: Fifty-four pts (age: 31-78) and 118 healthy females (age: 29-73) were enrolled. The tumor size was between 9 and 107mm (median 29mm). Twenty six pts (48%) had lymph node involvement. Fifty three peaks of N-glycans were observed in more than 95% of the samples and utilized for the analyses. By PCA, no distinction was observed in sera form breast cancer pts in terms of the tumor size, hormone receptor status and HER2 status. The N-glycan signature to identify cancer pts was created based on the PCA. The signature categorized samples into three groups: cancer, healthy and border groups. Half of the samples (even registration number) were used for training and the rest for validation. In the validation cohort, 18 (66.7%) of 27 pts were categorized into the cancer group and 9 were into the border group. Forty-seven (79.7%) of 59 volunteers were categorized into the healthy group and 11 were into the border group. When the border group was included in the cancer group, the sensitivity was 100% (27 of 27 pts in the cancer group) and the specificity was 79.7% (47 of 59 volunteers in the healthy group). Conclusions: The comprehensive analysis of N-glycans in sera enabled the creation of the N-glycan signature to distinguish between breast cancer pts and healthy females with high sensitivity and high specificity. Confirmative studies are warranted.
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Herrera, Harmin, Tinslee Dilday, Allison Uber, Danielle Scott, Joelle N. Zambrano, Mengjun Wang, Peggi M. Angel, et al. "Core-Fucosylated Tetra-Antennary N-Glycan Containing A Single N-Acetyllactosamine Branch Is Associated with Poor Survival Outcome in Breast Cancer." International Journal of Molecular Sciences 20, no. 10 (May 23, 2019): 2528. http://dx.doi.org/10.3390/ijms20102528.
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(1) Glycoproteins account for ~80% of proteins located at the cell surface and in the extracellular matrix. A growing body of evidence indicates that α-L-fucose protein modifications contribute to breast cancer progression and metastatic disease. (2) Using a combination of techniques, including matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) based in cell and on tissue imaging and glycan sequencing using exoglycosidase analysis coupled to hydrophilic interaction ultra-high performance liquid chromatography (HILIC UPLC), we establish that a core-fucosylated tetra-antennary glycan containing a single N-acetyllactosamine (F(6)A4G4Lac1) is associated with poor clinical outcomes in breast cancer, including lymph node metastasis, recurrent disease, and reduced survival. (3) This study is the first to identify a single N-glycan, F(6)A4G4Lac1, as having a correlation with poor clinical outcomes in breast cancer.
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Smit, Cornelis H., Christiaan L. Kies, Hamish E. G. McWilliam, Els N. T. Meeusen, Cornelis H. Hokke, and Angela van Diepen. "Local Antiglycan Antibody Responses to Skin Stage and Migratory Schistosomula of Schistosoma japonicum." Infection and Immunity 84, no. 1 (October 12, 2015): 21–33. http://dx.doi.org/10.1128/iai.00954-15.
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Schistosomiasis is a tropical disease affecting over 230 million people worldwide. Although effective drug treatment is available, reinfections are common, and development of immunity is slow. Most antibodies raised during schistosome infection are directed against glycans, some of which are thought to be protective. Developing schistosomula are considered most vulnerable to immune attack, and better understanding of local antibody responses raised against glycans expressed by this life stage might reveal possible glycan vaccine candidates for future vaccine research. We used antibody-secreting cell (ASC) probes to characterize local antiglycan antibody responses against migratingSchistosoma japonicumschistosomula in different tissues of rats. Analysis by shotgunSchistosomaglycan microarray resulted in the identification of antiglycan antibody response patterns that reflected the migratory pathway of schistosomula. Antibodies raised by skin lymph node (LN) ASC probes mainly targeted N-glycans with terminal mannose residues, Galβ1-4GlcNAc (LacNAc) and Galβ1-4(Fucα1-3)GlcNAc (LeX). Also, responses to antigenic and schistosome-specific glycosphingolipid (GSL) glycans containing highly fucosylated GalNAcβ1-4(GlcNAcβ1)nstretches that are believed to be present at the parasite's surface constitutively upon transformation were found. Antibody targets recognized by lung LN ASC probes were mainly N-glycans presenting GalNAcβ1-4GlcNAc (LDN) and GlcNAc motifs. Surprisingly, antibodies against highly antigenic multifucosylated motifs of GSL glycans were not observed in lung LN ASC probes, indicating that these antigens are not expressed in lung stage schistosomula or are not appropriately exposed to induce immune responses locally. The local antiglycan responses observed in this study highlight the stage- and tissue-specific expression of antigenic parasite glycans and provide insights into glycan targets possibly involved in resistance toS. japonicuminfection.
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Sun, In-Cheol, SeongHoon Jo, Diego Dumani, Wan Su Yun, Hong Yeol Yoon, Dong-Kwon Lim, Cheol-Hee Ahn, Stanislav Emelianov, and Kwangmeyung Kim. "Theragnostic Glycol Chitosan-Conjugated Gold Nanoparticles for Photoacoustic Imaging of Regional Lymph Nodes and Delivering Tumor Antigen to Lymph Nodes." Nanomaterials 11, no. 7 (June 28, 2021): 1700. http://dx.doi.org/10.3390/nano11071700.
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Lymph node mapping is important in cancer immunotherapy because the morphology of lymph nodes is one of the crucial evaluation criteria of immune responses. We developed new theragnostic glycol-chitosan-coated gold nanoparticles (GC-AuNPs), which highlighted lymph nodes in ultrasound-guided photoacoustic (US/PA) imaging. Moreover, the ovalbumin epitope was conjugated GC-AuNPs (OVA-GC-AuNPs) for delivering tumor antigen to lymph node resident macrophage. In vitro studies proved the vigorous endocytosis activity of J774A.1 macrophage and consequent strong photoacoustic signals from them. The macrophages also presented a tumor antigen when OVA-GC-AuNPs were used for cellular uptake. After the lingual injection of GC-AuNPs into healthy mice, cervical lymph nodes were visible in a US/PA imaging system with high contrast. Three-dimensional analysis of lymph nodes revealed that the accumulation of GC-AuNPs in the lymph node increased as the post-injection time passed. Histological analysis showed GC-AuNPs or OVA-GC-AuNPs located in subcapsular and medullar sinuses where macrophages are abundant. Our new theragnostic GC-AuNPs present a superior performance in US/PA imaging of lymph nodes without targeting moieties or complex surface modification. Simultaneously, GC-AuNPs were able to deliver tumor antigens to cause macrophages to present the OVA epitope at targeted lymph nodes, which would be valuable for cancer immunotherapy.
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Pratheek, H. P., N. Manikanta, K. S. Shashidhara, and M. S. P. Kanavi. "In-silico Analysis of Evolution of Plant Polyamine Oxidases." Research Journal of Biotechnology 16, no. 8 (July 25, 2021): 11–21. http://dx.doi.org/10.25303/168rjbt1121.
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Amino oxidase enzymes have attractive role in programmed cell death. Full length amino acid sequences of 46 polyamino oxidases (PAO) and 8 diamino oxidases (DAO) were retrieved from major sequence repositories. Sequences were obtained using combination of queries based on key terms and BLASTp searches. The PAOs belong to 21 and DAOs belong to 5 families. Multiple sequence alignment of amino-acid sequences identified the conserved residues to be Glycine, Glutamic acid, Alanine, Arginine, Tryptophan, Proline, Valine, Leucine, Phenylalanine, Tyrosine and Lysine. Glycine is most conserved followed by glutamic acid and proline. The phylogenetic analysis revealed the three main nodes/clades A, B and C. Clade C containing highest number of PAO species was followed by clade B. Clade A mostly contains tree species PAOs. Similar trend has been observed for DAOs. PAO and DAO genes of plants including Arabidopsis thaliana, Brachipodium, Glycin max, Oryza sativa present on different chromosomes. Comparative modelling was done to build 3D structure of the PAO and DAO from A. thaliana. In the Ramachandran plot, more than 90% residues were in most allowed regions. DAOs are mostly located in lysosomes and vacuoles in the cell and are in soluble form. PAOs located in cytoplasm and peroxisomes are in soluble form.
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Zou, Hang, Ni-Na Zhang, Qing Pan, Jian-Hua Zhang, Juan Chen, and Ge-Hong Wei. "Hydrogen Sulfide Promotes Nodulation and Nitrogen Fixation in Soybean–Rhizobia Symbiotic System." Molecular Plant-Microbe Interactions® 32, no. 8 (August 2019): 972–85. http://dx.doi.org/10.1094/mpmi-01-19-0003-r.
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The rhizobium–legume symbiotic system is crucial for nitrogen cycle balance in agriculture. Hydrogen sulfide (H2S), a gaseous signaling molecule, may regulate various physiological processes in plants. However, whether H2S has regulatory effect in this symbiotic system remains unknown. Herein, we investigated the possible role of H2S in the symbiosis between soybean (Glycine max) and rhizobium (Sinorhizobium fredii). Our results demonstrated that an exogenous H2S donor (sodium hydrosulfide [NaHS]) treatment promoted soybean growth, nodulation, and nitrogenase (Nase) activity. Western blotting analysis revealed that the abundance of Nase component nifH was increased by NaHS treatment in nodules. Quantitative real-time polymerase chain reaction data showed that NaHS treatment upregulated the expressions of symbiosis-related genes nodA, nodC, and nodD of S. fredii. In addition, expression of soybean nodulation marker genes, including early nodulin 40 (GmENOD40), ERF required for nodulation (GmERN), nodulation signaling pathway 2b (GmNSP2b), and nodulation inception genes (GmNIN1a, GmNIN2a, and GmNIN2b), were upregulated. Moreover, the expressions of glutamate synthase (GmGOGAT), asparagine synthase (GmAS), nitrite reductase (GmNiR), ammonia transporter (GmSAT1), leghemoglobin (GmLb), and nifH involved in nitrogen metabolism were upregulated in NaHS-treated soybean roots and nodules. Together, our results suggested that H2S may act as a positive signaling molecule in the soybean–rhizobia symbiotic system and enhance the system’s nitrogen fixation ability.
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Saeed, Anwaar Mohammed, Ammar Ali Alkhazna, Betty Herndon, and Daniel Dim. "Triggers in the pathway from lung cell damage to malignancy: The glycans." Journal of Clinical Oncology 31, no. 15_suppl (May 20, 2013): e22189-e22189. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.e22189.
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e22189 Background: It has been reported that carbon nanoparticles (CN) produce mesothelioma as readily as do asbestos fibers. We have studied early CN damage in experimental animals, quantifying toxicity by release from cells of the nuclear chaperone HMGB1. Damage-released HMGB1 binds to receptors (RAGE, CD24) to upregulate cytokines and produce regulatory signals that control cell homeostasis. Further, HMGB1 has recently been shown to form a complex with P53, one of the most commonly mutated genes in human cancers, and HMGB1 is the controlling factor in autophagy, an important new field in translational cancer research. Methods: One HMGB1 receptor, CD24, is the source of a whole-receptor antibody used to determine extent of malignancy during surgery. CD24 is highly glycosylated. We hypothesized that carbohydrate vs protein specificity would show differences in tumor character. Would antibodies to the CD24 carbohydrate moiety reflect a tumor glycan character, and how would this relate to the tumor profile such as metastasis? With cooperation of TMC pathology Dept, blocks (N=15 each) of lung squamous cell, adenocarcinoma, and small cell cancer were sectioned and stained with mouse monoclonals to CD24, IgM –glycan, IgG-protein fraction. Results: Small cell and adenocarcinoma lung tumors showed mostly similar staining by CD24 protein vs CD24 glycan antibodies. Squamous cell CA showed elevated carbohydrate CD24 staining with negative or low protein stain in over half of the cases, and examination of patient records are being studied to determine metastatic character, lung- damage history and tumor chemotherapy response. Conclusions: Squamous cell tumors demonstrate significantly more staining by antibody to the glycan moiety of CD24, p=0.02. There was no relationship between numbers of positive nodes and staining, although other chart information awaits analysis. Research continues into the significance of this glycan CD24 receptor for HMGB1, our marker for nanoparticle lung damage, and its relationship to malignant transformation. [Table: see text]
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Scheel, Julia, and Detlef Keller. "Investigation of the Skin Sensitizing Properties of 5 Osmolytic Prodrugs in a Weight-of-Evidence Assessment, Employing In Silico, In Vivo, and Read Across Analyses." International Journal of Toxicology 31, no. 4 (July 31, 2012): 358–63. http://dx.doi.org/10.1177/1091581812449662.
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The amino acid esters ethyl glycinate (EG), dl-α-tocopheryl-(mono-)betainate hydrochloride (TMB), dl-α-tocopheryl-(mono-)glycinate hydrochloride (TMG), dl-α-tocopheryl-(mono-)prolinate hydrochloride (TMP), and dl-α-tocopheryl-(mono-)sarcosinate hydrochloride (TMS) were previously shown to exert an osmoprotective function to human skin in vitro. Based on literature data, the parent compounds α-tocopherol (vitamin E) and the amino acids glycine, betaine (trimethylated glycine), proline, and sarcosine ( N-methylated glycine) are not considered to be sensitizers. To investigate skin sensitizing properties of the esters, EG, TMG, and TMP were tested in the Local Lymph Node Assay (LLNA). Remaining esters were assessed by read across analysis considering structural similarities and mechanistic aspects. The LLNA results were consistent with in silico outcomes from ToxTree 2.5.0 indicative for protein binding; EG was negative; TMG and TMP were positive. Since TMB and TMS showed structural similarities to TMG and TMP and were also positive in ToxTree, it was concluded that both TMB and TMS can also be expected to have a skin sensitizing potential and therefore animal testing was waived.
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Car, Iris, Sarah Visentin, Davorin Đanić, and Marko Klobučar. "Different expression of lumican glycoforms in non-metastatic and metastatic laryngeal squamous cell carcinoma." Medicina Fluminensis 57, no. 1 (March 1, 2021): 114–21. http://dx.doi.org/10.21860/medflum2021_365329.
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Objective: Association of altered growth factor receptors-mediated intracellular pathways and biological processes associated with extracellular matrix composition and structure in laryngeal squamous cell carcinoma (LSCC) were described previously. In particular, the expression and glycosylation of important extracellular matrix molecules (ECM) such as small leucine rich proteoglycan lumican, may be generally associated with disrupted extracellular matrix integrity and inflammation processes which have a role in tumour invasiveness. In this study, the relative expression of different lumican glycoforms were evaluated in primary tumour and tumour-unaffected tissue samples of ten patients with metastatic and ten non-metastatic LSCC by Western blot and 2D immunoblot analysis. Materials and methods: Tissue samples from the primary tumours and paired adjacent non-tumour tissues were surgically resected from ten untreated LSCC patients with non-metastatic disease and ten LSCC patients with lymph nodes metastases. The relative expression of different lumican glycoforms in primary tumours and paired adjacent non-tumour tissues were evaluated by Western blot and 2D immunoblot analysis. Results: Results of Western blot analysis have revealed elevated expression of the moderately glycosylated lumican form in metastatic (p<0,05) and non-metastatic primary tumour tissues in comparison with tumour unaffected tissues. In addition, moderately glycosylated form of lumican with negatively charged oligosaccharide residues in the N-glycan molecule part was exclusively determined in metastatic primary tumour tissues by 2D immunoblot analysis. Conclusion: We demonstrated elevated expression of the moderately glycosylated lumican form with negatively charged oligosaccharide residues in the N-glycan portion exclusively in primary laryngeal squamous cell carcinoma from patients with metastatic disease.
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Wedhastri, Sri, Dinar Mindrati Fardhani, Siti Kabirun, Jaka Widada, Donny Widianto, Rusdi Evizal, and Irfan Dwidya Prijambada. "Legume Nodulating Bacterium, Achromobacter xylosoxidans Found in Tropical Shrub Agroecosystem, Sumatera, Indonesia." Indonesian Journal of Biotechnology 18, no. 2 (November 9, 2015): 161. http://dx.doi.org/10.22146/ijbiotech.7879.
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Legume nodulating bacteria (LNB), known also as rhizobia, are soil bacteria, which are able to form rootnodules and fi x nitrogen in the leguminous plants. The LNB availability in the soil depends on the type ofagroecosystem, where plant grows. In this study, we isolated LNB from the shrub agroecosystem in Sumatera,Indonesia, and obtained four selected bacterial strains. Among them, the isolate UGM48a formed root nodulein Macroptilium atropurpureum and showed highest number of nitrogenase activity. UGM48a also contains nifHand nodA genes. An analysis of the PCR-amplifi ed 16S rDNA and BLASTn analysis showed that UGM48adisplayed 96% similarity with Achromobacter xylosoxidans. In addition, UGM48a were successfully nodulatedGlycine max (L.) merr var. wilis. This is the fi rst report detecting A. xylosoxidans as nodule-forming species forGlycine max possesing the positive copy of nodA gene. Keywords : Legume Nodulating Bacteria, shrub agroecosystem, Achromobacter xylosoxidans, nodA, Glycine max
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Chachaj, Angelika, Rafał Matkowski, Gerhard Gröbner, Andrzej Szuba, and Ilona Dudka. "Metabolomics of Interstitial Fluid, Plasma and Urine in Patients with Arterial Hypertension: New Insights into the Underlying Mechanisms." Diagnostics 10, no. 11 (November 11, 2020): 936. http://dx.doi.org/10.3390/diagnostics10110936.
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There is growing evidence that lymphatic system plays a pivotal role in the pathogenesis of hypertension. Here, for the first time, the metabolome of interstitial fluid is analyzed in patients with arterial hypertension. Due to ethical issues to obtain human interstitial fluid samples, this study included only oncological patients after axillary lymph node dissection (ALND). These patients were matched into hypertensive (n = 29) and normotensive (n = 35) groups with similar oncological status. Simultaneous evaluation of interstitial fluid, plasma, and urine was obtained by combining high-resolution proton nuclear magnetic resonance (1H NMR) spectroscopy with chemometric analysis. Orthogonal partial least squares discriminant analysis (OPLS-DA) provided a clear differentiation between the hypertension and normotensive group, with the discrimination visible in each biofluid. In interstitial fluid nine potential metabolomic biomarkers for hypertension could be identified (creatinine, proline, pyroglutamine, glycine, alanine, 1-methylhistidine, the lysyl group of albumin, threonine, lipids), seven distinct markers in plasma (creatinine, mannose, isobutyrate, glycine, alanine, lactate, acetate, ornithine), and seven respectively in urine (methylmalonate, citrulline, phenylacetylglycine, fumarate, citrate, 1-methylnicotinamide, trans-aconitate). Biomarkers in plasma and urine allowed for the identification of specific biochemical pathways involved in hypertension, as previously suggested. Analysis of the interstitial fluid metabolome provided additional biomarkers compared to plasma or urine. Those biomarkers reflected primarily alterations in the metabolism of lipids and amino acids, and indicated increased levels of oxidative stress/inflammation in patients with hypertension.
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Li, Qin Qin, En Tao Wang, Yue Li Chang, Yun Zeng Zhang, Yan Ming Zhang, Xin Hua Sui, Wen Feng Chen, and Wen Xin Chen. "Ensifer sojae sp. nov., isolated from root nodules of Glycine max grown in saline-alkaline soils." International Journal of Systematic and Evolutionary Microbiology 61, no. 8 (August 1, 2011): 1981–88. http://dx.doi.org/10.1099/ijs.0.025049-0.
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Thirteen bacterial isolates from root nodules of soybean grown in saline-alkaline soils in the Chinese province of Hebei were identified as a unique group in the genus Ensifer based upon BOX-PCR patterns, sequencing analyses of 16S rRNA and housekeeping genes and DNA–DNA hybridization. Phenotypically, positive tests for acid production and negative results for reduction in litmus milk and sensitivity to 50 µg ampicillin ml−1, as well as some other features, could differentiate the novel group from defined species of the Ensifer–Sinorhizobium group. The novel group had symbiotic gene sequences (nodC and nifH) that were identical or very similar to those of Ensifer (Sinorhizobium) fredii, and formed effective nodules with Glycine max (soybean), Vigna unguiculata and Glycine soja. Based upon the consensus of these analyses, a novel species, Ensifer sojae sp. nov., is proposed, with CCBAU 05684T ( = LMG 25493T = HAMBI 3098T) as the type strain. The DNA G+C content of strain CCBAU 05684T was 60.9 mol% (T m).
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Baumhueter, S., N. Dybdal, C. Kyle, and LA Lasky. "Global vascular expression of murine CD34, a sialomucin-like endothelial ligand for L-selectin." Blood 84, no. 8 (October 15, 1994): 2554–65. http://dx.doi.org/10.1182/blood.v84.8.2554.2554.
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Abstract Extravasation of leukocytes into organized lymphoid tissues and into sites of inflammation is critical to immune surveillance. Leukocyte migration to peripheral lymph nodes (PLN), mesenteric lymph nodes (MLN) and Peyer's patches (PP) depends on L-selectin, which recognizes carbohydrate-bearing, sialomucin-like endothelial cell surface glycoproteins. Two of these ligands have been identified at the molecular level. One is the potentially soluble mucin, GlyCAM 1, which is almost exclusively produced by high endothelial venules (HEV) of PLN and MLN. The second HEV ligand for L-selectin is the membrane-bound sialomucin CD34. Historically, this molecule has been successfully used to purify human pluripotent bone marrow stem cells, and limited data suggest that human CD34 is present on the vascular endothelium of several organs. Here we describe a comprehensive analysis of the vascular expression of CD34 in murine tissues using a highly specific antimurine CD34 polyclonal antibody. CD34 was detected on vessels in all organs examined and was expressed during pancreatic and skin inflammatory episodes. A subset of HEV-like vessels in the inflamed pancreas of nonobese diabetic (NOD) mice are positive for both CD34 and GlyCAM 1, and bind to an L-selectin/immunoglobulin G (IgG) chimeric probe. Finally, we found that CD34 is present on vessels of deafferentiated PLN, despite the fact that these vessels are no longer able to interact with L-selectin or support lymphocyte binding in vitro or trafficking in vivo. Our data suggest that the regulation of posttranslational carbohydrate modifications of CD34 is critical in determining its capability to act as an L-selectin ligand. Based on its ubiquitous expression, we propose that an appropriately glycosylated form of vascular CD34 may act as a ligand for L-selectin-mediated leukocyte trafficking to both lymphoid and nonlymphoid sites.
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Baumhueter, S., N. Dybdal, C. Kyle, and LA Lasky. "Global vascular expression of murine CD34, a sialomucin-like endothelial ligand for L-selectin." Blood 84, no. 8 (October 15, 1994): 2554–65. http://dx.doi.org/10.1182/blood.v84.8.2554.bloodjournal8482554.
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Extravasation of leukocytes into organized lymphoid tissues and into sites of inflammation is critical to immune surveillance. Leukocyte migration to peripheral lymph nodes (PLN), mesenteric lymph nodes (MLN) and Peyer's patches (PP) depends on L-selectin, which recognizes carbohydrate-bearing, sialomucin-like endothelial cell surface glycoproteins. Two of these ligands have been identified at the molecular level. One is the potentially soluble mucin, GlyCAM 1, which is almost exclusively produced by high endothelial venules (HEV) of PLN and MLN. The second HEV ligand for L-selectin is the membrane-bound sialomucin CD34. Historically, this molecule has been successfully used to purify human pluripotent bone marrow stem cells, and limited data suggest that human CD34 is present on the vascular endothelium of several organs. Here we describe a comprehensive analysis of the vascular expression of CD34 in murine tissues using a highly specific antimurine CD34 polyclonal antibody. CD34 was detected on vessels in all organs examined and was expressed during pancreatic and skin inflammatory episodes. A subset of HEV-like vessels in the inflamed pancreas of nonobese diabetic (NOD) mice are positive for both CD34 and GlyCAM 1, and bind to an L-selectin/immunoglobulin G (IgG) chimeric probe. Finally, we found that CD34 is present on vessels of deafferentiated PLN, despite the fact that these vessels are no longer able to interact with L-selectin or support lymphocyte binding in vitro or trafficking in vivo. Our data suggest that the regulation of posttranslational carbohydrate modifications of CD34 is critical in determining its capability to act as an L-selectin ligand. Based on its ubiquitous expression, we propose that an appropriately glycosylated form of vascular CD34 may act as a ligand for L-selectin-mediated leukocyte trafficking to both lymphoid and nonlymphoid sites.
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Chazalet, Valerie, Kazuyoshi Uehara, Roberto A. Geremia, and Christelle Breton. "Identification of Essential Amino Acids in theAzorhizobium caulinodans Fucosyltransferase NodZ." Journal of Bacteriology 183, no. 24 (December 15, 2001): 7067–75. http://dx.doi.org/10.1128/jb.183.24.7067-7075.2001.
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ABSTRACT The nodZ gene, which is present in various rhizobial species, is involved in the addition of a fucose residue in an α1-6 linkage to the reducing N-acetylglucosamine residue of lipo-chitin oligosaccharide signal molecules, the so-called Nod factors. Fucosylation of Nod factors is known to affect nodulation efficiency and host specificity. Despite a lack of overall sequence identity, NodZ proteins share conserved peptide motifs with mammalian and plant fucosyltransferases that participate in the biosynthesis of complex glycans and polysaccharides. These peptide motifs are thought to play important roles in catalysis. NodZ was expressed as an active and soluble form in Escherichia coli and was subjected to site-directed mutagenesis to investigate the role of the most conserved residues. Enzyme assays demonstrate that the replacement of the invariant Arg-182 by either alanine, lysine, or aspartate results in products with no detectable activity. A similar result is obtained with the replacement of the conserved acidic position (Asp-275) into its corresponding amide form. The residues His-183 and Asn-185 appear to fulfill functions that are more specific to the NodZ subfamily. Secondary structure predictions and threading analyses suggest the presence of a “Rossmann-type” nucleotide binding domain in the half C-terminal part of the catalytic domain of fucosyltransferases. Site-directed mutagenesis combined with theoretical approaches have shed light on the possible nucleotide donor recognition mode for NodZ and related fucosyltransferases.
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Acker, Rene C. Van, Stephan F. Weise, and Clarence J. Swanton. "Influence of interference from a mixed weed species stand on soybean (Glycine max (L.) Merr.) growth." Canadian Journal of Plant Science 73, no. 4 (October 1, 1993): 1293–304. http://dx.doi.org/10.4141/cjps93-168.
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Field experiments were conducted to examine soybean-weed interactions under Ontario conditions. Trials were conducted at Elora, Ontario in 1990 and 1991 using comparative growth analysis to investigate the aboveground response of soybean to weed interference from a mixed weed species stand. Although season-long weed interference caused a significant decrease in soybean grain yield, weeds could remain in the crop up to 40 d after emergence, between R1 and beginning pod development stage (R3), in 1990 and up to 16 d after emergence, 3rd node development stage (V3), in 1991 without causing more than a 5% yield loss. These critical times of weed removal coincided with the timing of significant effects of weed interference on soybean LAI. Weed interference also significantly reduced total aboveground soybean dry weight and crop growth rate. Pods m−2 was the yield component most affected by season-long weed interference. Although there was no consistent effect of weed interference upon net assimilation rate and leaf weight ratio, weed interference resulted in a decrease in dry weight distribution to branch stems, causing as much as a fivefold reduction in allocation to branch stems. It may be useful to develop early branching soybean varieties, or use narrower row spacing, to enhance soybean competitiveness against weeds. Key words: Soybean (Glycine max), weed interference, growth analysis, leaf area, yield components
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Yu, Xiumei, Sylvie Cloutier, James T. Tambong, and Eden S. P. Bromfield. "Bradyrhizobium ottawaense sp. nov., a symbiotic nitrogen fixing bacterium from root nodules of soybeans in Canada." International Journal of Systematic and Evolutionary Microbiology 64, Pt_9 (September 1, 2014): 3202–7. http://dx.doi.org/10.1099/ijs.0.065540-0.
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Sixteen strains of symbiotic bacteria from root nodules of Glycine max grown in Ottawa, Canada, were previously characterized and placed in a novel group within the genus Bradyrhizobium . To verify their taxonomic status, these strains were further characterized using a polyphasic approach. All strains possessed identical 16S rRNA gene sequences that were 99.79 % similar to the closest relative, Bradyrhizobium liaoningense LMG 18230T. Phylogenetic analysis of concatenated atpD, glnII, recA, gyrB, rpoB and dnaK genes divided the 16 strains into three multilocus sequence types that were placed in a highly supported lineage distinct from named species of the genus Bradyrhizobium consistent with results of DNA–DNA hybridization. Based on analysis of symbiosis gene sequences (nodC and nifH), all novel strains were placed in a phylogenetic group with five species of the genus Bradyrhizobium that nodulate soybeans. The combination of phenotypic characteristics from several tests including carbon and nitrogen source utilization and antibiotic resistance could be used to differentiate representative strains from recognized species of the genus Bradyrhizobium . Novel strain OO99T elicits effective nodules on Glycine max, Glycine soja and Macroptilium atropurpureum, partially effective nodules on Desmodium canadense and Vigna unguiculata, and ineffective nodules on Amphicarpaea bracteata and Phaseolus vulgaris. Based on the data presented, we conclude that our strains represent a novel species for which the name Bradyrhizobium ottawaense sp. nov. is proposed, with OO99T ( = LMG 26739T = HAMBI 3284T) as the type strain. The DNA G+C content is 62.6 mol%.
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Apollonio, Benedetta, Peter Jarvis, Beth Phillips, Andrea Kuhnl, Jon Salisbury, Georgios Zacharioudakis, Lesley-Ann Sutton, et al. "Diffuse Large B-Cell Lymphoma Remodels the Fibroblastic Reticular Network That Acquires Aberrant Immunosuppressive Capabilities; Implications for the Regulation of Anti-Tumor Immunity in the Immuno-Oncology Era." Blood 132, Supplement 1 (November 29, 2018): 675. http://dx.doi.org/10.1182/blood-2018-99-116409.
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Abstract Immunotherapy has demonstrated potential to reactivate or transfer T cell immunity and regress tumors, offering hope to relapsed or refractory diffuse large B-cell lymphoma (DLBCL) patients. However, many DLBCL patients do not experience therapeutic benefit, likely owing to a lack of pre-existing anti-tumor immunity and/or poorly understood immunosuppressive mechanisms in the tumor microenvironment (TME). Understanding the different obstacles that cytotoxic T cells face in the DLBCL TME will help the development of novel therapeutic approaches to overcome them and optimize immunotherapy. Stroma-associated gene signatures reflecting fibroblast and immune cell activity as well as angiogenesis have been associated with outcome in DLBCL but the biology underlying these signatures has been understudied. Here we have examined beyond tumor 'effacement' and hypothesized that, rather than being sparse bystanders, lymph node stromal cells may be important players in driving immune suppression in lymphoma. Multiplex immunofluorescence (IF) confocal microscopy analysis of the major stromal cell subsets revealed a marked expansion and remodeling of podoplanin, PDPN+ fibroblastic reticular cells (FRCs) in DLBCL lymph node tissue TME biopsies across GCB and ABC subtypes (n=40) compared to reactive control tissues (n=10). FRC myofibroblasts were similarly remodeled in tumors from the transgenic mouse model of DLBCL (Iμ-HABCL6, n=10) compared to wild type littermates (n=5). These altered PDPNhigh, αSMAhigh FRC networks were interspersed within effaced lymph node tissues in close proximity to DLBCL tumor cells. To model the interactions between tumor cells and FRCs, we established 2D and 3D co-culture platforms that combined DLBCL cells (or non-malignant control B-cells) and PDPN+ FRCs derived from human or murine lymph node tissues. These quantitative assays have shown that tumor cells activate FRCs promoting their proliferation, increased expression of PDPN, marked elongation/stretching and subsequent reduced ability to contract 3D collagen matrix (non-contractile) (P<.01). Exposure to tumor cells caused uncoupling of PDPN from RHOA signaling and redistribution of PDPN into lipid rafts, permitting FRC stretching. FRCs purified from both human and murine tumor lymph nodes showed the same activated morphology and phenotype, demonstrating that our co-culture systems recapitulate in vivo findings. Screening experiments have shown that lymphoma-expressed membrane and soluble lymphotoxins (LTα1β2, LTα3) as well as TNFα significantly contribute to the remodeling of FRCs (P<.01). Co-culture assays have revealed evidence for mutualistic interaction as FRCs, that express BAFF, promote the survival of DLBCL cells in 3D matrix gels (P<.01). Expanded lymphoma PDPNhigh FRCs in situ co-expressed BAFF compared to a more restricted expression profile (marginal zone FRCs) in reactive lymph node tissues. Flow cytometry revealed that lymphoma FRCs exhibit a cancer-associated fibroblast (CAF)-like immunophenotype including upregulation of fibroblast activation protein (FAP) and αSMA, as well as immunomodulatory MHC class I, PD-L1 and PD-L2 molecules compared to control FRCs (P<.01). An important function of FRCs in regulating immunity is attracting and maintaining T cells by secreting chemokines and promoting their migration along the network. Functional assays revealed that T cells show significantly reduced chemotaxis as well motility (quantitative time-lapse movies) across 2D and 3D lymphoma FRC networks compared to control FRCs (P<.01). Multiplex IF analysis revealed reduced CCL19 and CCL21-expressing FRCs in DLBCL compared to the reactive control FRC network as well as low numbers of tumor-infiltrated CD8+ T cells, which localized closely with remodeled FRCs. We next determined whether lymphoma FRCs (CAFs) could negatively regulate T cell function. Triple culture autologous assays (murine and human) have shown that prior exposure of tumor-infiltrated CD8+ T cells to FRCs significantly decreased their cytolytic killing activity against tumor cells (P<.01). In conclusion our data indicate that DLBCL tumor cells convert FRCs into immunosuppressive CAFs, which exhibit altered immumomodulatory activities at different levels that we believe has important implications for the regulation of anti-tumor immunity as well as response to immunotherapy. Disclosures Vardi: Gilead: Research Funding; Janssen: Honoraria. Ramsay:Roche Glycart AG: Research Funding; MedImmune: Research Funding; Celgene Corporation: Research Funding.
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Baloda, Anila, Seema Madanpotra, and P. K. J. Aiwal. "Transformation of Mungbean Plants for Salt and Drought Tolerance by introducing a gene for an osmoprotectant glycine betaine." Journal of Plant Stress Physiology 3 (February 20, 2017): 5. http://dx.doi.org/10.19071/jpsp.2017.v3.3148.
Full textAbstract:
Mungbean (<em>Vignaradiata</em>L. Wilczek) is an important grain legume widely cultivated in tropical and subtropical regions of the Indian subcontinent and in South East Asian countries. Protein and carbohydrate of Mungbean are easily digestible and create less flatulence than proteins derived from other legumes.Mungbean is very sensitive to salinity, drought, high and low temperature during the flowering and seed/pod development stages resulting in heavy losses to productivity. The development of genetically engineered plants by the introduction and/or over expression of selected abiotic stress tolerant genes seems to be a viable option for obtaining improved plants. Stable transformation and expression of transgene (<em>codA</em> gene) was achieved in mungbean through <em>Agrobacterium tumefaciens</em>mediated system using cotyledonary node explants, under the optimized conditions. Molecular analysis of transgenic plants was done by using PCR, DOT-BLOT, ELISA and Western blotting. The primary transformants were checked for salt tolerance by the leaf disc test.
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Mora-Vásquez, Soledad, Silverio García-Lara, Edgardo J. Escalante-Vázquez, and Guy A. Cardineau. "IMPROVEMENT OF DIRECT REGENERATION OF MEXICAN SOYBEAN FROM COTYLEDONARY NODES." Agrociencia 54, no. 3 (December 23, 2020): 387–99. http://dx.doi.org/10.47163/agrociencia.v54i3.1914.
Full textAbstract:
Plant tissue culture provides an alternative approach to improve the quality of soybean (Glycine max (L.) Merrill) cultivars. This study was undertaken to analyze the susceptibility of Mexican soybean for direct shoot regeneration and to determine the critical factors that affect in vitro performance. Our hypothesis was that Mexican soybean is suitable for in vitro regeneration using a cotyledonary node as explant. The effects of the seed disinfection procedure, soaking pretreatment before germination, soybean variety, as well as the culture medium composition of the shoot induction medium, were evaluated by two split-plot statistical designs. According to the statistical analysis, the seed disinfection procedure, the soaking pretreatment before germination, and the soybean genotype were the factors that brought about a significant effect (p£0.01), while the hormones composition of the shoot induction medium did not have a significant effect. The best response for multiple shoot formation was observed using a chlorine gas seed disinfection method, 3% hydrogen peroxide soaking pretreatment, and Huasteca-100, Nainari and Suaqui soybean genotypes. A robust protocol was developed, and under these selected conditions, it is possible to obtain more than 10 shoots per explant. Well-developed plantlets were obtained after 60 d of in vitro culture.
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Zhang, Yan Ming, Ying Li, Wen Feng Chen, En Tao Wang, Xin Hua Sui, Qin Qin Li, Yun Zeng Zhang, Yu Guang Zhou, and Wen Xin Chen. "Bradyrhizobium huanghuaihaiense sp. nov., an effective symbiotic bacterium isolated from soybean (Glycine max L.) nodules." International Journal of Systematic and Evolutionary Microbiology 62, Pt_8 (August 1, 2012): 1951–57. http://dx.doi.org/10.1099/ijs.0.034546-0.
Full textAbstract:
In a survey of the biodiversity and biogeography of rhizobia associated with soybean (Glycine max L.) in different sites of the Northern (Huang-Huai-Hai) Plain of China, ten strains were defined as representing a novel genomic species in the genus of Bradyrhizobium . They were distinguished from defined species in restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA gene and the 16S–23S rRNA gene intergenic spacer (IGS). In BOX-PCR, these strains presented two patterns that shared 94 % similarity, demonstrating that they were a homogenous group with limited diversity. In phylogenetic analyses of the 16S rRNA gene, IGS and housekeeping gene sequences, four representative strains formed a distant lineage within the genus Bradyrhizobium , which was consistent with the results of DNA–DNA hybridization. The strains of this novel group formed effective nodules with G. max, Glycine soja and Vigna unguiculata in cross-nodulation tests and harboured symbiotic genes (nodC and nifH) identical to those of reference strains of Bradyrhizobium japonicum , Bradyrhizobium liaoningense and ‘Bradyrhizobium daqingense’ originating from soybean, implying that the novel group may have obtained these symbiotic genes by lateral gene transfer. In analyses of cellular fatty acids and phenotypic features, some differences were found between the novel group and related Bradyrhizobium species, demonstrating that the novel group is distinct phenotypically from other Bradyrhizobium species. Based upon the data obtained, these strains are proposed to represent a novel species, Bradyrhizobium huanghuaihaiense sp. nov., with CCBAU 23303T ( = LMG 26136T = CGMCC 1.10948T = HAMBI 3180T) as the type strain. The DNA G+C content of strain CCBAU 23303T is 61.5 mol% (T m).
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Gauguet, Jean-Marc, Steven D. Rosen, Jamey D. Marth, and Ulrich H. von Andrian. "Core 2 branching β1,6-N-acetylglucosaminyltransferase and high endothelial cell N-acetylglucosamine-6-sulfotransferase exert differential control over B- and T-lymphocyte homing to peripheral lymph nodes." Blood 104, no. 13 (December 15, 2004): 4104–12. http://dx.doi.org/10.1182/blood-2004-05-1986.
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Abstract Blood-borne lymphocyte trafficking to peripheral lymph nodes (PLNs) depends on the successful initiation of rolling interactions mediated by L-selectin binding to sialomucin ligands in high endothelial venules (HEVs). Biochemical analysis of purified L-selectin ligands has identified posttranslational modifications mediated by Core2GlcNAcT-I and high endothelial cell GlcNAc-6-sulfotransferase (HECGlcNAc6ST). Consequently, lymphocyte migration to PLNs of C2GlcNAcT-I-/- and HEC-GlcNAc6ST-/- mice was reduced; however, B-cell homing was more severely compromised than T-cell migration. Accordingly, intravital microscopy (IVM) of PLN HEVs revealed a defect in B-cell tethering and increased rolling velocity (Vroll) in C2GlcNAcT-I-/- mice that was more pronounced than it was for T cells. By contrast, B- and T-cell tethering was normal in HEC-GlcNAc6ST-/- HEVs, but Vroll was accelerated, especially for B cells. The increased sensitivity of B cells to glycan deficiencies was caused by lower expression levels of L-selectin; L-selectin+/- T cells expressing L-selectin levels equivalent to those of B cells exhibited intravascular behavior similar to that of B cells. These results demonstrate distinct functions for C2GlcNAcT-I and HEC-GlcNAc6ST in the differential elaboration of HEV glycoproteins that set a threshold for the amount of L-selectin needed for lymphocyte homing. (Blood. 2004;104:4104-4112)
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Cross, Graciela A. de, Horacio Suarez, Fabián Pitoia, Daniel Moncet, María Vanegas, Oscar D. Bruno, and Hugo Niepomniszcze. "Fatal outcome of a young woman with papillary thyroid carcinoma and graves' disease: possible implication of "cross-signalling" mechanism." Arquivos Brasileiros de Endocrinologia & Metabologia 52, no. 7 (October 2008): 1194–200. http://dx.doi.org/10.1590/s0004-27302008000700018.
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A 29 yrs-old patient was referred to our hospital due to generalized convulsions. She had hyperthyroidism treated with methimazole. Her MRI showed 4 metastatic lesions in the brain. She had a goiter with a "cold" nodule and a palpable ipsilateral lymph node. The FNAB disclosed a papillary thyroid carcinoma. Under 5 mg of MMI treatment, she had a subclinical hyperthyroidism and TRAb were 47.8% (n.v. < 10%). The CT scan also showed lung metastasis. She underwent a total thyroidectomy with a modified neck dissection and she received an accumulated radioiodine dose of 700 mCi during the following two years. She died from the consequences of multiple metastatic lesions. Studies were performed in DNA extracted from paraffin-embedded tissue from the tumor, the metastatic lymph node and the non-tumoral thyroid. The genetic analysis of tumoral DNA revealed point mutations in two different genes: the wild type CAA at codon 61 of N-RAS mutated to CAT, replacing glycine by histidine (G61H) and the normal GCC sequence at codon 623 of the TSHR gene was replaced by TCC, changing the alanine by serine (A623S). In the non-tumoral tissue no mutations were found. In vitro studies showed a constitutive activation of the TSHR. It is very probable that this activating mutation of the TSHR is unable to reach the end point of the PKA cascade in the tumoral tissue. One possibility that could explain this is the presence of a cross-signaling mechanism generating a deviation of the TSH receptor cascade to the more proliferative one involving the MAPKinase, giving perhaps a more aggressive behavior of this papillary thyroid cancer.
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Bernard, Kathryn A., Tamara Burdz, Ana Luisa Pacheco, Deborah Wiebe, Nisha B. Patel, Paul A. Lawson, Marc-Christian Domingo, Jean Longtin, and Anne-Marie Bernier. "Enemella gen. nov., Enemella evansiae sp. nov., Enemella dayhoffiae sp. nov. and Parenemella sanctibonifatiensis gen. nov., sp. nov., novel taxa assignable to the family Propionibacteriaceae and derived from human clinical samples." International Journal of Systematic and Evolutionary Microbiology 70, no. 11 (November 1, 2020): 5676–85. http://dx.doi.org/10.1099/ijsem.0.004461.
Full textAbstract:
Nine Gram-stain-positive cocci, coccobacilli or short, rod-shaped strains recovered from clinical sources from patients located in two Canadian provinces and one environmental source were extensively studied. Clinical sources included blood cultures, cerebral spinal fluid, lymph node, lung biopsy and peritoneal fluid. Through 16S rRNA gene and whole genome sequencing analyses, the strains were found to cluster into three groups, closest to but distinguished from other genera in the family Propionibacteriaceae . The genomes from these bacteria had high G+C content, ranging from 67.8–69.56 mol%, and genome sizes of 3.02–4.52 Mb. Biochemical and chemotaxonomic properties including branched-chain cellular fatty acids, l-lysine diaminopimelic acid (ll-DAP) and cell-wall type A3γ (ll-DAP-gly) containing ll-DAP, alanine, glycine and glutamic acid were found and so the strains were therefore deemed to be consistent with other new genera in this family. Based on this investigation, we propose Enemella gen. nov., Enemella evansiae sp. nov., Enemella dayhoffiae sp. nov. and Parenemella sanctibonifatiensis gen. nov., sp. nov. for these taxa. Misidentified taxon ‘Ponticoccus gilvus’ was found to be assignable to Enemella evansiae based on this study.
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Kebede, Addis T., Suresh K. Raina, and Jacques M. Kabaru. "Structure, Composition, and Properties of Silk from the African Wild Silkmoth, Anaphe panda (Boisduval) (Lepidoptera: Thaumetopoeidae)." International Journal of Insect Science 6 (January 2014): IJIS.S13338. http://dx.doi.org/10.4137/ijis.s13338.
Full textAbstract:
Silk cocoon nests, as well as the fiber structure, compositions, and properties of the African wild silkmoth, Anaphe panda, collected from Kakamega tropical rainforest (western Kenya) were studied using scanning electron microscopy, high-pressureliquid chromatography, tensile tests, and thermogravmetric analysis, and they were compared with the industrial standard, Bombyx mori. Cocoon nests are complex structures made up of inner, middle, and outer layers. The inner hard parchment was found to protect a mass of (20–200) individual soft flossy cocoons that enclose the pupae. The outer surface of the cocoon nests was covered with a mass of hair-like bristles. Fibers contained crescent-shaped and globular cross-sections with nods at regular intervals. Alanine (34%) and glycine (28%) were the dominant fibroin amino acids observed. Total weight loss after degumming the cocoon nest was 25.6%. Degummed fibers showed higher moisture regain of 9% when compared with cocoon nests (8%). The fibers had 0.4 GPa breaking stress and 15.4% breaking strain. Total weight loss values after thermogravimetric analysis were 86% and 90% for degummed fibers and cocoon shells, respectively.
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Vinuesa, Pablo, Milagros León-Barrios, Claudia Silva, Anne Willems, Adriana Jarabo-Lorenzo, Ricardo Pérez-Galdona, Dietrich Werner, and Esperanza Martínez-Romero. "Bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont that nodulates endemic genistoid legumes (Papilionoideae: Genisteae) from the Canary Islands, along with Bradyrhizobium japonicum bv. genistearum, Bradyrhizobium genospecies alpha and Bradyrhizobium genospecies beta." International Journal of Systematic and Evolutionary Microbiology 55, no. 2 (March 1, 2005): 569–75. http://dx.doi.org/10.1099/ijs.0.63292-0.
Full textAbstract:
Highly diverse Bradyrhizobium strains nodulate genistoid legumes (brooms) in the Canary Islands, Morocco, Spain and the Americas. Phylogenetic analyses of ITS, atpD, glnII and recA sequences revealed that these isolates represent at least four distinct evolutionary lineages within the genus, namely Bradyrhizobium japonicum and three unnamed genospecies. DNA–DNA hybridization experiments confirmed that one of the latter represents a new taxonomic species for which the name Bradyrhizobium canariense is proposed. B. canariense populations experience homologous recombination at housekeeping loci, but are sexually isolated from sympatric B. japonicum bv. genistearum strains in soils of the Canary Islands. B. canariense strains are highly acid-tolerant, nodulate diverse legumes in the tribes Genisteae and Loteae, but not Glycine species, whereas acid-sensitive B. japonicum soybean isolates such as USDA 6T and USDA 110 do not nodulate genistoid legumes. Based on host-range experiments and phylogenetic analyses of symbiotic nifH and nodC sequences, the biovarieties genistearum and glycinearum for the genistoid legume and soybean isolates, respectively, were proposed. B. canariense bv. genistearum strains display an overlapped host range with B. japonicum bv. genistearum isolates, both sharing monophyletic nifH and nodC alleles, possibly due to the lateral transfer of a conjugative chromosomal symbiotic island across species. B. canariense is the sister species of B. japonicum, as inferred from a maximum-likelihood Bradyrhizobium species phylogeny estimated from congruent glnII+recA sequence partitions, which resolves eight species clades. In addition to the currently described species, this phylogeny uncovered the novel Bradyrhizobium genospecies alpha and beta and the photosynthetic strains as independent evolutionary lineages. The type strain for B. canariense is BTA-1T (=ATCC BAA-1002T=LMG 22265T=CFNE 1008T).
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Zhu, Wei, Lin Lin Li, Yiyan Songyang, Zhan Shi, and Dejia Li. "Identification and validation of HELLS (Helicase, Lymphoid-Specific) and ICAM1 (Intercellular adhesion molecule 1) as potential diagnostic biomarkers of lung cancer." PeerJ 8 (March 9, 2020): e8731. http://dx.doi.org/10.7717/peerj.8731.
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Although lung cancer is one of the greatest threats to human health, its signaling pathway and related genes are still unknown. This study integrates data from three groups of people to study potential key candidate genes and pathways related to lung cancer. Expression profiles (GSE18842, GSE19188 and GSE27262), including 162 tumor tissue and 135 adjacent normal lung tissue samples, were integrated and analyzed. Differentially expressed genes (DEGs) and candidate genes were identified, their expression pathways were analyzed, and the diethylene glycol-related protein–protein interaction (PPI) network was analyzed. We identified 232 shared DEGs (40 upregulated and 192 down-regulated) from the three GSE datasets. The DEGs were clustered according to function and signaling pathway for significant enrichment analysis. In total, 129 nodes/DEGs were identified from the DEG PPI network complex. An improved prognosis was associated with increased Helicase, Lymphoid-Specific (HELLS) and decreased Intercellular adhesion molecule 1 (ICAM1) mRNA expression in lung cancer patients. In conclusion, we used integrated bioinformatics analysis to identify candidate genes and pathways in lung cancer to show that HELLS and ICAM1 might be the key genes related to tumorigenesis or tumor progression in lung cancer. Additional studies are needed to further explore the involved functional mechanisms.
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Tsai, I.-Chen, and Chih-Chiang Hung Hung. "Efficacy Of Pegylated Liposomal Doxorubicin-based Neoadjuvant Chemotherapy In Breast Cancer: A Single Center Experience." Clinical and Investigative Medicine 44, no. 1 (March 21, 2021): E7–14. http://dx.doi.org/10.25011/cim.v44i1.35196.
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Purpose: Neoadjuvant chemotherapy using a doxorubicin-based regimen has recently become a common therapeutic option for operable breast cancer. This study aimed to investigate the efficacy of polyethylene glycol-coated liposomal doxorubicin (PLD)-based chemotherapy for breast cancer in neoadjuvant settings.
Methods: A total of 227 female operable breast cancer patients who were diagnosed between January 2009 and December 2017 and completed neoadjuvant PLD-based chemotherapy were retrospectively included. The logistic regression analysis was used to determine the associations between pathologic complete response (pCR) and preoperative clinicopathological characteristics. The breast cancer recurrence rate was estimated using the survival analysis.
Results: A higher pCR rate was found in the patients with clinically negative lymph nodes and HER2-enriched patients. Moreover, the patients who achieved pCR also had a better prognosis outcome. A recurrence rate of 11.5% (n=26) was observed during a median follow-up of 11.63 months, and the recurrence rate of the pCR group (2.04%; 95% CI = 0.29-13.62) was lower than the non-pCR group (14.62%; 95% CI = 10.12-20.87). Higher histological grade was also associated high pCR rate (52.0% vs 40.0%).
Conclusion: The use of PLD-containing chemotherapeutics in neoadjuvant settings might have benefits for non-metastatic operable breast cancer in Taiwanese females.
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Zhang, Yu Jing, Wen Tao Zheng, Isobel Everall, J. Peter W. Young, Xiao Xia Zhang, Chang Fu Tian, Xin Hua Sui, En Tao Wang, and Wen Xin Chen. "Rhizobium anhuiense sp. nov., isolated from effective nodules of Vicia faba and Pisum sativum." International Journal of Systematic and Evolutionary Microbiology 65, Pt_9 (September 1, 2015): 2960–67. http://dx.doi.org/10.1099/ijs.0.000365.
Full textAbstract:
Four rhizobia-like strains, isolated from root nodules of Pisum sativum and Vicia faba grown in Anhui and Jiangxi Provinces of China, were grouped into the genus Rhizobium but were distinct from all recognized species of the genus Rhizobium by phylogenetic analysis of 16S rRNA and housekeeping genes. The combined sequences of the housekeeping genes atpD, recA and glnII for strain CCBAU 23252T showed 86.9 to 95 % similarity to those of known species of the genus Rhizobium. All four strains had nodC and nifH genes and could form effective nodules with Pisum sativum and Vicia faba, and ineffective nodules with Phaseolus vulgaris, but did not nodulate Glycine max, Arachis hypogaea, Medicago sativa, Trifolium repens or Lablab purpureus in cross-nodulation tests. Fatty acid composition, DNA–DNA relatedness and a series of phenotypic tests also separated these strains from members of closely related species. Based on all the evidence, we propose a novel species, Rhizobium anhuiense sp. nov., and designate CCBAU 23252T ( = CGMCC 1.12621T = LMG 27729T) as the type strain. This strain was isolated from a root nodule of Vicia faba and has a DNA G+C content of 61.1 mol% (T m).
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Kenny, L. M., E. Aboagye, P. S. Cohen, M. Miller, F. Turkheimer, A. Al-Nahhas, D. Blunt, and R. C. Coombes. "Imaging of angiogenesis in metastatic breast cancer by positron emission tomography (PET) using [18F]AH11585, an [18F]- labeled alphaVbeta3 (αvβ3) peptide." Journal of Clinical Oncology 25, no. 18_suppl (June 20, 2007): 14067. http://dx.doi.org/10.1200/jco.2007.25.18_suppl.14067.
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14067 Background: In vivo imaging of avβ3 expression in tumors and tumor endothelial cells may be a useful biomarker of angiogenesis. [18F]AH11585 is a novel peptide containing an Arginine-Glycine-Aspartic Acid (RGD) motif that binds to avβ3 with high affinity designed for use in PET studies. Methods: 7 patients with metastatic breast cancer (aged 37–68 years) received intravenous injections of [18F]AH11585 and were scanned dynamically by PET over 61.5 mins. Radioactivity concentrations, derived from regions of interest placed on tumour and normal tissues, were analysed mathematically to determine the net irreversible uptake (Ki), fractional retention (FRT) and standardized uptake at 56.5min (SUV) of the radiotracer. Computed tomography (CT) was performed within 4 weeks of the scan. Results: Tumor lesions were clearly visible on PET images in 6/7 patients. In one patient with a palpable supraclavicular lymph node not visible on CT, we were unsure if a hyperintense region visible by PET was tumor. In total 18/19 tumor lesions were identified on both PET and corresponding CT images. Tumors in areas of low background were hyperintense (lung, bone, breast) whereas those in areas of high background were hypointense regions (liver). Tumors with central necrosis showed high uptake of [18F]AH11585 around the periphery only. Mathematical analysis demonstrated irreversible retention of [18F]AH11585 in tumors. [18F]AH11585-PET discriminated between non-liver lesions (n=10) and normal tissues: Ki (p=0.002), FRT (p=0.0039), SUV (p=0.002). Corresponding comparisons for liver lesions (n=8) were significant for FRT (p=0.0078) and SUV (p=0.0078) only. Conclusions: [18F]AH11585 PET is a promisng method for in vivo imaging of avβ3 integrin expression in metastatic breast cancer. No significant financial relationships to disclose.
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Solivera, J., A. Fuentes Fayos, R. M. Luque, L. Barrios, J. M. Roda, S. Cerdán, and M. L. Gandía-González. "P13.08 1H-MRS metabolomics as a predictor of overall survival in glioma patients." Neuro-Oncology 21, Supplement_3 (August 2019): iii63—iii64. http://dx.doi.org/10.1093/neuonc/noz126.229.
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Abstract BACKGROUND We assess the efficacy of the metabolomic profile from glioma biopsies, in providing estimates of postsurgical Overall Survival in glioma patients. MATERIAL AND METHODS Tumor biopsies from 46 patients bearing gliomas, obtained neurosurgically in the period 1992–1998, were analyzed by high resolution 1H magnetic resonance spectroscopy (HR- 1H MRS), following retrospectively individual postsurgical Overall Survival up to 720 weeks. RESULTS The Overall Survival profile could be resolved in three groups; Short (shorter than 52 weeks, n=19), Intermediate (between 53 and 364 weeks, n=19) or Long (longer than 365 weeks, n=8), respectively. Classical histopathological analysis assigned WHO grades II-IV to every biopsy but notably, some patients with low grade glioma depicted unexpectedly Short Overall Survival, while some patients with high grade glioma, presented unpredictably Long Overall Survival. To explore reasons underlying this behavior, we analyzed HR- 1H MRS spectra from acid extracts of these biopsies, to identify the metabolite patterns underlying OS predictions. Poor prognosis was found in biopsies with higher contents of alanine, acetate, glutamate, total choline, phosphorylcholine and glycine, while more favorable prognosis was achieved in biopsies with larger contents of total creatine, glycerol-phosphorylcholine and myo-inositol. We implemented then a multivariate analysis approach to identify hierarchically the influence of these metabolomic biomarkers on OS predictions, using Classification Regression Trees (CRTs). Metabolomic CRTs grew up to 3 branches and split into 8 nodes, predicting correctly the outcome of 94.7% of the patients in the Short Overall Survival group, 78.9 % of the patients in the Intermediate Overall Survival group, and 75% of the patients in the Long Overall Survival group, respectively. CONCLUSION Present results suggest that metabolic profiling by HR-1H MRS provides more accurate Overall Survival estimates of glioma patients than classical histopathological grading, thus allowing to implement more accurate therapeutic decisions.
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Wang, Yan, Zou, Wang, Xu, Cui, and Qu. "Morphological, Transcriptomic and Hormonal Characterization of Trimonoecious and Subandroecious Pumpkin (Cucurbita maxima) Suggests Important Roles of Ethylene in Sex Expression." International Journal of Molecular Sciences 20, no. 13 (June 28, 2019): 3185. http://dx.doi.org/10.3390/ijms20133185.
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: Sex expression is a complex process, and in-depth knowledge of its mechanism in pumpkin is important. In this study, young shoot apices at the one-true-leaf stage and 10-leaf stage in Cucurbita maxima trimonoecious line ‘2013–12’ and subandroecious line ‘9–6’ were collected as materials, and transcriptome sequencing was performed using an Illumina HiSeqTM 2000 System. 496 up-regulated genes and 375 down-regulated genes were identified between shoot apices containing mostly male flower buds and only female flower buds. Based on gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the differentially expressed genes were mainly enriched in the ethylene and auxin synthesis and signal transduction pathways. In addition, shoot apices at the 4-leaf stage were treated with the ethylene-releasing agent 2-chloroethylphosphonic acid (Ethrel), aminoethoxyvinyl glycine (AVG), AgNO3 and indoleacetic acid (IAA). The number of female flowers up to node 20 on the main stem of ‘2013–12’ increased significantly after Ethrel and IAA treatment and decreased significantly after AVG and AgNO3 treatment. The female flowers in ‘9–6’ showed slight changes after treatment with the exogenous chemicals. The expression of key genes in ethylene synthesis and signal transduction (CmaACS7, CmaACO1, CmaETR1 and CmaEIN3) was determined using quantitative RT-PCR, and the expression of these four genes was positively correlated with the number of female flowers in ‘2013–12’. The variations in gene expression, especially that of CmaACS7, after chemical treatment were small in ‘9–6’. From stage 1 (S1) to stage 7 (S7) of flower development, the expression of CmaACS7 in the stamen was much lower than that in the ovary, stigma and style. These transcriptome data and chemical treatment results indicated that IAA might affect pumpkin sex expression by inducing CmaACS7 expression and indirectly affecting ethylene production, and the ethylene synthesis and signal transduction pathways play crucial roles in pumpkin flower sex expression. A possible reason for the differences in sex expression between pumpkin lines ‘2013–12’ and ‘9–6’ was proposed based on the key gene expression. Overall, these transcriptome data and chemical treatment results suggest important roles for ethylene in pumpkin sex expression.
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Ouyang, Jing, Annette Plütschow, Elke Pogge, Sabine Ponader, Gabriel Rabinovich, Donna S. Neuberg, Andreas Engert, and Margaret A. Shipp. "Galectin-1 Serum Levels Reflect Tumor Burden and Adverse Clinical Features in Hodgkin Lymphoma." Blood 120, no. 21 (November 16, 2012): 51. http://dx.doi.org/10.1182/blood.v120.21.51.51.
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Abstract Abstract 51 Galectin-1 (Gal1) is a member of a highly conserved family of carbohydrate-binding proteins that modulate innate and adaptive immune responses and foster tumor immune escape. Through the selective recognition of specific cell-surface glycans (Gal-beta1-4-NAcGlc [N-acetyllactosamine] units on the branches of N- or O-linked glycans), Gal1 induces the apoptosis of Th1 and cytotoxic T cells. Th2 cells have different patterns of sialylation of cell-surface glycoproteins, lack Gal1 ligands, and resist Gal1-induced cell death. Regulatory T (Treg) cells are also resistant to Gal1-mediated apoptosis. In addition, Gal1 promotes hypoxia-driven tumor angiogenesis. Primary Hodgkin lymphomas (HLs) include small numbers of malignant Reed-Sternberg cells within a Th2/Treg-skewed inflammatory infiltrate. In previous studies, we found that Reed-Sternberg cells overexpress Gal1, which selectively kills Th1 and cytotoxic T cells and promotes the immunosuppressive Th2/Treg-predominant HL microenvironment. In HLs, which exhibit constitutive AP-1 activation, Gal1 overexpression is driven in large part by an AP-1-dependent enhancer. Given the immunosuppressive function of Gal1, we reasoned that the secreted protein might be a potent marker of disease activity and a novel therapeutic target. We previously developed a panel of Gal1 monoclonal antibodies and demonstrated the utility of Gal1 as a diagnostic marker of AP-1-dependent lymphoid malignancies. A potent neutralizing Gal1 antibody also protected Th1 and cytotoxic T cells from Gal1-induced apoptosis, abrogated Gal1-associated tumor angiogenesis and limited the growth of Gal1+ tumors in vivo. We have now developed a sandwich ELISA to assess the utility of Gal1 as a serum marker of disease burden in HL. After establishing the sandwich ELISA with purified recombinant Gal1 and the newly developed Gal1 antibodies, we assessed the levels of serum Gal1 in 15 healthy normal donors and 315 newly diagnosed, previously untreated HL patients from the German Hodgkin Study Group. The HL patients were enrolled on 3 tailored, risk-adapted clinical trials: HD13 for early-stage disease (clinical stage [CS] IA-IIB) with no risk factors, 94 pts); HD 14 for early stage disease with risk factors (CS I-IIA with large mediastinal mass, extranodal disease, elevated ESR or > 3 nodal areas and CS IIB with elevated ESR or > 3 nodal areas, 90 pts); and HD18 for bulky localized or advanced stage disease (CS IIB with bulky mediastinal involvement and/or extranodal involvement and CS III or IV, 131 pts). Serum Gal1 levels were significantly elevated in HL patients in comparison to normal controls (median value 2.3 X higher, p <.0001; 100% specificity and 78% sensitivity with a cut-off value of ∼ 50 ng/ml). HL patients on the clinical trial for early-stage low-risk patients (HD13) had significantly lower Gal1 levels than patients on either HD14 or HD18 (p =.0006). We next evaluated the potential association of Gal1 serum levels with Ann Arbor stage and B-symptoms, two major determinants for assigning HL pts to risk-adapted therapy. Gal1 levels were significantly higher in HL pts with advanced-stage disease (stage I/II vs. III/IV, p <.001) and B symptoms (absence vs. presence, p =.03). We also assessed the potential association of Gal1 levels with individual clinical prognostic factors in the Hodgkin Lymphoma International Prognostic Score (IPS). In univariate analyses, Gal1 levels were highly correlated with the following clinical risk factors: extranodal involvement (p =.01); > 3 lymph node areas (p =.0001); elevated erythrocyte sedimentation rate (ESR) (p =.0015); albumin < 4 g/dl (p =.035); hemoglobin < 10.5 g/dl (p =.035); lymphoma count < 600 per mm or < 8% of white cell count (p =.015). Consistent with these observations, HL patients with an IPS score of >= 2 had significantly higher Gal1 levels than patients with an IPS of 0 or 1 (p =.007). Direct analyses of the association between Gal1 levels and outcome await completion of the ongoing HD18 clinical trial. In conclusion, Gal1 serum levels are significantly associated with tumor burden and additional adverse clinical characteristics in newly diagnosed HL patients. Given the demonstrated role of Gal1 in tumor immune evasion and angiogenesis, analyses of circulating Gal1 levels may inform risk-adapted and targeted treatment strategies for HL patients. Disclosures: No relevant conflicts of interest to declare.
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Oh, Han-Jin, Yei-Ju Park, Jae Hyoung Cho, Min-Ho Song, Bon-Hee Gu, Won Yun, Ji-Hwan Lee, et al. "Changes in Diarrhea Score, Nutrient Digestibility, Zinc Utilization, Intestinal Immune Profiles, and Fecal Microbiome in Weaned Piglets by Different Forms of Zinc." Animals 11, no. 5 (May 11, 2021): 1356. http://dx.doi.org/10.3390/ani11051356.
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Twenty weaned piglets with initial body weight of 6.83 ± 0.33 kg (21 day of age, LYD) were randomly assigned to four treatments for a two-week feeding trial to determine the effects of different dietary zinc on nutrient digestibility, intestinal health, and microbiome of weaned piglets. The dietary treatments included a negative control (CON), standard ZnO (ZnO, 2500 ppm), zinc chelate with glycine (Chelate-ZnO, 200 ppm), and nanoparticle-sized ZnO (Nano-ZnO, 200 ppm). At 0 to 1 week, the diarrhea score was decreased in the CON group compared with the ZnO, Chelate-ZnO, and Nano-ZnO group. In overall period, the ZnO and Nano-ZnO groups exhibited improved diarrhea scores compared to the CON group. The apparent total tract digestibility of dry matter and gross energy was the lowest in the CON group after one week. Compared to the ZnO group, the chelate-ZnO group exhibited higher proportion of T-bet+ and FoxP3+ T cells and the nano-ZnO group had higher numbers of RORgt+ and GATA3+ T cells in the mesenteric lymph nodes. ZnO group increased IL-6 and IL-8 levels in the colon tissues and these positive effects were observed in both chelate ZnO and nano-ZnO groups with lower level. The 16S rRNA gene analysis showed that the relative abundance of Prevotella was higher in the ZnO-treated groups than in the CON group and that of Succinivibrio was the highest in the nano-ZnO group. The relative abundance of Lactobacillus increased in the ZnO group. In conclusion, low nano-ZnO levels have similar effects on nutrient digestibility, fecal microflora, and intestinal immune profiles in weaning pigs; thus, nano-ZnO could be used as a ZnO alternative for promoting ZnO utilization and intestinal immunity.
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Willett, Cammy D., Erin M. Grantz, Jung Ae Lee, Matthew N. Thompson, and Jason K. Norsworthy. "Soybean response to dicamba in irrigation water under controlled environmental conditions." Weed Science 67, no. 3 (April 10, 2019): 354–60. http://dx.doi.org/10.1017/wsc.2019.4.
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AbstractWhile much research has focused on crop damage following foliar exposure to auxin herbicides, reports documenting the risk posed by exposure via root uptake of irrigation water are lacking. Herbicide residues circulated in tailwater recovery systems may pose threats of cross-crop impacts to nonresistant cultivars with known sensitivity to auxins. An auxin-susceptible soybean [Glycine max(L.) Merr.] cultivar was grown in a controlled growth chamber environment and exposed to dicamba dissolved in irrigation water applied to the soil surface, simulating furrow irrigation. Five herbicide treatment concentrations, ranging from 0.05 to 5.0 mg L−1and encompassing estimated field doses of 3.1 to 310g ha−1, were applied to the soil of potted soybean plants at V3/V4 or R1 growth stages. Plant injury (0% to 100%), dry mass, height, number of pods, and number of pod-bearing nodes were measured. Kruskal-Wallis and logistic regression analyses were performed to determine treatment differences and examine dose effects. Yield losses were projected using (1) 14 d after treatment plant injury assessments based on injury–yield relationships described for foliar exposures and (2) pod counts. Dicamba concentration was the main significant factor affecting all growth response metrics, and growth stage was a significant explanatory variable only for the height response metric. A nonlinear response to dicamba dose was observed, with the threshold response dose required to affect 50% of plants being three times greater for 40% crop injury compared with 20% injury. Yield projections derived from plant response to root uptake compared with foliar exposure indicate that soybean may express both magnitude of injury and specific symptomology differently when exposure occurs via root uptake. Drift exposure–based models may be incompatible to predict soybean yield loss when injury results from irrigation. Data are needed to develop correlations for predicting yield losses based on field-scale exposure to dicamba in irrigation water, as well as assessment of real-world concentrations of herbicide residues in tailwater recovery systems.
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Roy, Dipayan, Anupama Modi, and Purvi Purohit. "Interactome Profile of Visceral Adipose Tissue in Obesity Links Key Genes to Cancer Pathogenesis." Journal of the Endocrine Society 5, Supplement_1 (May 1, 2021): A51—A52. http://dx.doi.org/10.1210/jendso/bvab048.102.
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Abstract Obesity increases the risk of the development of several malignancies. The visceral adipose tissue (VAT) depot is one of the pivotal contributors behind the obesity-related pathogenetic mechanisms. In this study, we analyzed the differential gene expression profile in the VAT of obese children using two Gene Expression Omnibus datasets. GSE29718 and GSE9624 were sorted and 68 common differentially expressed genes (DEG) with fold change 1.5 upregulation or downregulation (cutoff |logFC|≥0.58496) were obtained. Gene ontology and functional enrichment and protein-protein interaction (PPI) network for the DEG were analyzed in Search Tool for the Retrieval of Interacting Genes (STRING), which revealed 37 biological processes, 3 cellular components, and 1 molecular function to be significantly associated. Reactome pathway analysis showed the DEG to be involved in- one carbon pool by folate, glycine degradation, transcriptional regulation by TP53, ERK inactivation, G1/S-specific transcription, Fanconi anemia pathway, beta-catenin phosphorylation cascade, RAF activation, and negative regulation of the MAPK pathway. The PPI network was set with a minimum interaction score of 0.400 and a maximum of 10 interactions, and it was significantly enriched (p-value 0.047) with 66 nodes and 46 edges. Target prediction was performed using miRNet. Several miRNA, including hsa-miR-1-3p, hsa-let-7b-5p, hsa-miR-16-5p, hsa-miR-27a-3p and hsa-miR-34a-5p were part of the mRNA-miRNA interaction network. Using the CytoHubba plugin in Cytoscape, the top 10 hub genes from the PPI network were discovered. Thymidine phosphorylase (TYMP) and dihydrofolate reductase (DHFR), essential components of nucleic acid metabolism, have been shown to be involved in angiogenesis and endothelial cell growth, and correlated to p53 mutations, respectively. Protein phosphatase 2, regulatory subunit A & regulatory subunit B (PPP2R1A and PPP2R1B) mutations are involved in ovarian, endometrial, lung and colorectal cancers. HLA-DQA1 mutation is involved cervical cancer, and it is involved in increased immune sensitivity and liver damage in breast cancer patients. The RAB7Ab and RAB7-interacting lysosomal protein (RILP) are regulators of endo-lysosomal trafficking and suppresses breast cancer cell invasion. To conclude, this study identifies several genes and their regulatory pathways in VAT which may contribute to the increased risk of cancer pathogenesis in obese individuals.
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Shan, Z., S. Li, Y. Liu, Z. Yang, C. Yang, A. Sha, H. Chen, S. Chen, and X.-A. Zhou. "First Report of Phomopsis Seed Decay of Soybean Caused by Phomopsis longicolla in South China." Plant Disease 96, no. 11 (November 2012): 1693. http://dx.doi.org/10.1094/pdis-04-12-0401-pdn.
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Phomopsis seed decay of soybean (Glycine max (L.) Merr.) causes poor seed quality and suppresses yield in most soybean-growing areas in the world. The disease is caused primarily by Phomopsis longicolla Hobbs. During the spring of 2010, soybean seeds without symptoms were planted in the fields but emergence was poor and the emergence rates ranged from 30 to 70% in south China. Approximately 3,000 symptomless seeds were randomly collected from seven fields at three locations in Guangzhou, Nanchang, and Wuhan. Seeds were surface disinfected with 1% sodium hypochlorite for 12 min, rinsed in sterile distilled water three to four times, and placed on 2% agar. Plates were then incubated at 26°C under 16/8-h photoperiod for 3 to 4 days. About 10 to 20% of the seeds produced white hyphae that spread rapidly and covered the whole seed. The hyphae from fungal isolates were transferred to potato dextrose agar (PDA) and incubated at 26°C in the dark. After 3 to 4 weeks, conidia were elliptical with two oil drops at both ends and hyaline (6.2 to 7.2 × 2.6 to 3.2 μm). The cultural and morphological characteristics of the isolates corresponded with the description of P. longicolla (2). Colonies on PDA were floccose, dense, and white. Stromata were large, black, and spreading. To confirm the morphological identification, the ribosomal internal transcribed spacers (ITS1-5.8S-ITS2) from three isolates were sequenced (GenBank Accession Nos. JQ899030, JQ899031, and JQ899032). BLAST analysis indicated that the isolates had 99% nucleotide sequence identity with P. longicolla (GenBank Accession Nos. AY857868.1, EF026104, and HQ130441.1). Pathogenicity tests were conducted on 2-week-old soybean seedlings (3). A mycelial plug (3 mm in diameter) from the margin of 1-week-old PDA culture of the Wuhan isolate was individually placed mycelial side down directly on the top of cut stem 1 to 2 cm above cotyledon node of the soybean seedling. PDA plugs without the fungus was used as the negative control. All seedlings were kept in a growth chamber at 26°C with 92 to 94% relative humidity. After 2 weeks, all inoculated seedlings showed browning, stem wilt, and the lesions were 0.3 to 2.0 cm long. No symptoms were observed in the control plants. P. longicolla was reisolated from the infected seedlings. The pathogenicity test was repeated three times. Soybean stem blight caused by P. longicolla has been reported in northeast China (1). To our knowledge, this is the first report of P. longicolla causing Phomopsis seed decay of soybean in south China. This report will establish a foundation for developing a program for screening germplasm for resistance to this disease in south China. References: (1) Y. L. Cui et al. Plant Pathol. 58:799, 2009. (2) T. W. Hobbs et al. Mycologia 77:535,1985. (3) S. Li et al. Plant Dis. 85:1031, 2001.
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Zaare, Sahba, Jesús S. Aguilar, Yueming Hu, Shadi Ferdosi, and Chad R. Borges. "Glycan Node Analysis: A Bottom-up Approach to Glycomics." Journal of Visualized Experiments, no. 111 (May 22, 2016). http://dx.doi.org/10.3791/53961.
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Turkistani, Safaa, Bruna M. Sugita, Paolo Fadda, Rafael Marchi, Ali Afsari, Tammey Naab, Victor Apprey, et al. "A panel of miRNAs as prognostic markers for African-American patients with triple negative breast cancer." BMC Cancer 21, no. 1 (July 27, 2021). http://dx.doi.org/10.1186/s12885-021-08573-2.
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Abstract Background To investigate the global expression profile of miRNAs, their impact on cellular signaling pathways, and their association with poor prognostic parameters in African-American (AA) patients with triple negative breast cancer (TNBC). Methods Twenty-five samples of AA TNBC patients were profiled for global miRNA expression and stratified considering three clinical-pathological parameters: tumor size, lymph node (LN), and recurrence (REC) status. Differential miRNA expression analysis was performed for each parameter, and their discriminatory power was determined by Receiver Operating Characteristic (ROC) curve analysis. KMplotter was assessed to determine the association of the miRNAs with survival, and functional enrichment analysis to determine the main affected pathways and miRNA/mRNA target interactions. Results A panel of eight, 23 and 27 miRNAs were associated with tumor size, LN, and REC status, respectively. Combined ROC analysis of two (miR-2117, and miR-378c), seven (let-7f-5p, miR-1255b-5p, miR-1268b, miR-200c-3p, miR-520d, miR-527, and miR-518a-5p), and three (miR-1200, miR-1249-3p, and miR-1271-3p) miRNAs showed a robust discriminatory power based on tumor size (AUC = 0.917), LN (AUC = 0.945) and REC (AUC = 0.981) status, respectively. Enrichment pathway analysis revealed their involvement in proteoglycans and glycan and cancer-associated pathways. Eight miRNAs with deregulated expressions in patients with large tumor size, positive LN metastasis, and recurrence were significantly associated with lower survival rates. Finally, the construction of miRNA/mRNA networks based in experimentally validated mRNA targets, revealed nodes of critical cancer genes, such as AKT1, BCL2, CDKN1A, EZR and PTEN. Conclusions Altogether, our data indicate that miRNA deregulated expression is a relevant biological factor that can be associated with the poor prognosis in TNBC of AA patients, by conferring to their TNBC cells aggressive phenotypes that are reflected in the clinical characteristics evaluated in this study.
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FAOT, MARIA MONICHA, SITI ZUBAIDAH, and HERU KUSWANTORO. "Genetic correlation and path analysis of agronomical traits of soybean (Glycine max) lines infected by CpMMV." Biodiversitas Journal of Biological Diversity 20, no. 6 (May 2, 2019). http://dx.doi.org/10.13057/biodiv/d200602.
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Abstract. Faot MM, Zubaidah S, Kuswantoro H. 2019. Genetic correlation and path analysis of agronomical traits of soybean (Glycine max) lines infected by CpMMV. Biodiversitas 20: 1496-1503. CpMMV is a virus that can decrease soybean production. The virus vector is an insect where the control is carried out using a chemical insecticide that is less environmentally friendly. Developing a superior variety of soybean that is resistant to CpMMV is one of the solutions to solve such a problem. This research aimed to study the relationship of agronomical traits to the yield of soybean line infected by CpMMV. Ten lines and two varieties of soybean with four replications was used in this study in a randomized complete block design. Bemisia tabaci was used in CpMMV infestation as the vector of the disease. Rearing Bemisia tabaci was done forty days before sowing the main experiment, and it placed surrounding the main experiment plots. The observation variables were disease severity, days to flowering and maturity, plant height, length, width and ratio of the leaf, number of branches and reproductive nodes, number of filled and unfilled pods, number of seeds, 100 seeds weight, and seed yield per plant. The data was analyzed for genotypic and phenotypic correlation, and the path analysis for direct and indirect effects of disease severity, and agronomical characters. The results showed that CpMMV infestation caused disease severity by about 20-28.5%. A significant positive phenotypic correlation to the seed yield per plant was shown by the number of reproductive nodes and the 100 seeds weight. Meanwhile, a significant positive genotypic correlation to the seed yield per plant was shown by the days to maturity and the number of branches. The number of reproductive nodes, the 100 seeds weight, and the number of seeds per plant showed a high direct effect to the seed yield per plant. The high positive indirect effect was also shown by the number of filled pods, days to flowering, plant height, leaf length, leaf width, the number of reproductive nodes, and the number of branches through the number of seeds per plant was also. Therefore, the selection criteria for high yielding CpMMV-resistant soybean lines can be based on the number of reproductive nodes and 100 seeds weight.
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tian, zhongmin, le wang, entai hou, and qiong sun. "Abstract 663: Metabolomics And Correlation Network Analysis Of Hypertension." Hypertension 64, suppl_1 (September 2014). http://dx.doi.org/10.1161/hyp.64.suppl_1.663.
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The awareness, treatment and controls rates of hypertension for people in their 20s and 30s age are much lower than average. In this paper, a GC/MS based metabolomics study was performed in plasma of young hypertensive men and age-matched normal ones. Correlations of the identified metabolites were analyzed and visualized. A systematic correlation network was constructed with the significance of correlation coefficient setting at threshold of 0.6. Glycine, lysine, cystine and beta-alanine were selected as the most important nodes of the network, with high values of degree. A relatively short average path length and high clustering coefficient suggested a small-world property of the network. Moreover, differential metabolites in young hypertensive men were used to construct a core correlation network for further understanding. Four hubs (lysine, glycine, cystine and tryptophan) were confirmed by a comprehensive evaluation of three centrality indices. The statistical and topological parameters of the network indicated that local disturbance to hubs would rapidly transfer to the whole network. These results demonstrated that the distinct metabolic profiles of young hypertensive men might be due to perturbation of the biosynthesis pathway of amino acids. Integrated analyses of metabolomics and correlation networks would provide a broadened window for further understanding of hypertension. Key Words: metabolomics; hypertension; correlation network; amino acids; statistical and topological characteristics; centrality indices; hubs
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Klepa, Milena Serenato, Luisa Caroline Ferraz Helene, Graham O’Hara, and Mariangela Hungria. "Bradyrhizobium agreste sp. nov., Bradyrhizobium glycinis sp. nov. and Bradyrhizobium diversitatis sp. nov., isolated from a biodiversity hotspot of the genus Glycine in Western Australia." International Journal of Systematic and Evolutionary Microbiology 71, no. 3 (June 6, 2019). http://dx.doi.org/10.1099/ijsem.0.004742.
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Strains of the genus Bradyrhizobium associated with agronomically important crops such as soybean (Glycine max) are increasingly studied; however, information about symbionts of wild Glycine species is scarce. Australia is a genetic centre of wild Glycine species and we performed a polyphasic analysis of three Bradyrhizobium strains—CNPSo 4010T, CNPSo 4016T, and CNPSo 4019T—trapped from Western Australian soils with Glycine clandestina, Glycine tabacina and Glycine max, respectively. The phylogenetic tree of the 16S rRNA gene clustered all strains into the Bradyrhizobium japonicum superclade; strains CNPSo 4010T and CNPSo 4016T had Bradyrhizobium yuanmingense CCBAU 10071T as the closest species, whereas strain CNPSo 4019T was closer to Bradyrhizobium liaoningense LMG 18230T. The multilocus sequence analysis (MLSA) with five housekeeping genes—dnaK, glnII, gyrB, recA and rpoB—confirmed the same clusters as the 16S rRNA phylogeny, but indicated low similarity to described species, with nucleotide identities ranging from 93.6 to 97.6% of similarity. Considering the genomes of the three strains, the average nucleotide identity and digital DNA–DNA hybridization values were lower than 94.97 and 59.80 %, respectively, with the closest species. In the nodC phylogeny, strains CNPSo 4010T and CNPSo 4019T grouped with Bradyrhizobium zhanjiangense and Bradyrhizobium ganzhouense , respectively, while strain CNPSo 4016T was positioned separately from the all symbiotic Bradyrhizobium species. Other genomic (BOX-PCR), phenotypic and symbiotic properties were evaluated and corroborated with the description of three new lineages of Bradyrhizobium . We propose the names of Bradyrhizobium agreste sp. nov. for CNPSo 4010T (=WSM 4802T=LMG 31645T) isolated from Glycine clandestina, Bradyrhizobium glycinis sp. nov. for CNPSo 4016T (=WSM 4801T=LMG 31649T) isolated from Glycine tabacina and Bradyrhizobium diversitatis sp. nov. for CNPSo 4019T (=WSM 4799T=LMG 31650T) isolated from G. max.
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Wang, Zhen, Zhongjie Liu, Yingxia Yang, and Lei Kang. "Identification of biomarkers and pathways in hypertensive nephropathy based on the ceRNA regulatory network." BMC Nephrology 21, no. 1 (November 11, 2020). http://dx.doi.org/10.1186/s12882-020-02142-8.
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Abstract Background Hypertensive nephropathy (HTN) is a kind of renal injury caused by chronic hypertension, which seriously affect people’s life. The purpose of this study was to identify the potential biomarkers of HTN and understand its possible mechanisms. Methods The dataset numbered GSE28260 related to hypertensive and normotensive was downloaded from NCBI Gene Expression Omnibus. Then, the differentially expressed RNAs (DERs) were screened using R limma package, and functional analyses of DE-mRNA were performed by DAVID. Afterwards, a ceRNA network was established and KEGG pathway was analyzed based on the Gene Set Enrichment Analysis (GSEA) database. Finally, a ceRNA regulatory network directly associated with HTN was proposed. Results A total of 947 DERs were identified, including 900 DE-mRNAs, 20 DE-lncRNAs and 27 DE-miRNAs. Based on these DE-mRNAs, they were involved in biological processes such as fatty acid beta-oxidation, IRE1-mediated unfolded protein response, and transmembrane transport, and many KEGG pathways like glycine, serine and threonine metabolism, carbon metabolism. Subsequently, lncRNAs KCTD21-AS1, LINC00470 and SNHG14 were found to be hub nodes in the ceRNA regulatory network. KEGG analysis showed that insulin signaling pathway, glycine, serine and threonine metabolism, pathways in cancer, lysosome, and apoptosis was associated with hypertensive. Finally, insulin signaling pathway was screened to directly associate with HTN and was regulated by mRNAs PPP1R3C, PPKAR2B and AKT3, miRNA has-miR-107, and lncRNAs SNHG14, TUG1, ZNF252P-AS1 and MIR503HG. Conclusions Insulin signaling pathway was directly associated with HTN, and miRNA has-miR-107 and lncRNAs SNHG14, TUG1, ZNF252P-AS1 and MIR503HG were the biomarkers of HTN. These results would improve our understanding of the occurrence and development of HTN.
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Shariatifard, Alireza, Emad Hasani Malekshah, and Narges Akbar. "Thermal performance of parabolic-trough solar collector using double-population LBM with single-node/curved scheme and experimental evaluation on properties of SiO2-TiO2/EG nanofluid." International Journal of Numerical Methods for Heat & Fluid Flow ahead-of-print, ahead-of-print (June 10, 2021). http://dx.doi.org/10.1108/hff-02-2021-0130.
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Purpose This paper aims to analyze the effect of absorber’s geometry and operating fluid on the thermal and hydrodynamic behaviors of a solar collector. Two different profiles are proposed for the absorber which is wavy and flat. Also, the inner tube of HTF (i.e. heat transfer fluid) is considered as single and double. The solar collector is filled with hybrid nanofluid of SiO2-TiO2/ ethylene glycol (EG) which its thermal conductivity and dynamic viscosity are measured using KD2 Pro and Brookfield LVDV III Ultra; respectively, in the temperature range of 30°C to 80°C and nanoparticle concentration in the range of 1.5% to 3.5%. Design/methodology/approach Among the solar collector, the parabolic-trough solar collector is one of the most efficient models for extracting solar thermal power. A parabolic trough solar collector with two different models of absorbers and included with two models of inner HTF tube is proposed. Findings The corresponding regression equations are derived versus temperature and volume fraction and used in the numerical process. For the numerical process, the thermal lattice Boltzmann method manipulated with a single-node curved scheme is used. Also, in the final step, the second law analysis is carried out in local and volumetric forms. The influential factors are Rayleigh number, the concentration of hybrid nano-powder and the structure of absorber profile. Originality/value The originality of the present work is combining a modern numerical method (i.e. double-population lattice Boltzmann method) with experimental observation on characteristics of SiO2-TiO2/EG nanofluid to analyze the thermal performance of parabolic trough solar collector.
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López-Cardona, Nathali, YUDY ALEJANDRA GUEVARA, Lederson Gañán-Betancur, and Carol Viviana Amaya Gomez. "First report of Diaporthe ueckerae causing stem canker on soybean (Glycine max L.) in Colombia." Plant Disease, June 28, 2021. http://dx.doi.org/10.1094/pdis-04-21-0718-pdn.
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In October 2018, soybean plants displaying elongated black to reddish-brown lesions on stems were observed in a field planted to the cv. BRS Serena in the locality of Puerto López (Meta, Colombia), with 20% incidence of diseased plants. Symptomatic stems were collected from five plants, and small pieces (∼5 mm2) were surface sterilized, plated on potato dextrose agar (PDA) and incubated for 2 weeks at 25°C in darkness. Three fungal isolates with similar morphology were obtained, i.e., by subculturing single hyphal tips, and their colonies on PDA were grayish-white, fluffy, with aerial mycelium, dark colored substrate mycelium, and produced circular black stroma. Pycnidia were globose, black, occurred as clusters, embedded in tissue, erumpent at maturity, with an elongated neck, and often had yellowish conidial cirrus extruding from the ostiole. Alpha conidia were observed for all isolates after 30 days growth on sterile soybean stem pieces (5 cm) on water agar, under 25ºC and 12 h light/12h darkness photoperiod. Alpha conidia (n = 50) measured 6.0 – 7.0 µm (6.4 ± 0.4 µm) × 2.0 – 3.0 µm (2.5± 0.4 µm), were aseptate, hyaline, smooth, ellipsoidal, often biguttulate, with subtruncate base. Beta conidia were not observed. Observed morphological characteristics of these isolates were similar to those reported in Diaporthe spp. by Udayanga et al. (2015). DNA from each fungal isolate was used to sequence the internal transcribed spacer region (ITS), and the translation elongation factor 1-α (TEF1) gene, using the primer pairs ITS5/ITS4 (White et al. 1990) and EF1-728F/EF1- 986R (Carbone & Kohn, 1999), respectively. Results from an NCBI-BLASTn, revealed that the ITS sequences of the three isolates (GenBank accessions MW566593 to MW566595) had 98% (581/584 bp) identity with D. miriciae strain BRIP 54736j (NR_147535.1), whereas the TEF1 sequences (GenBank accessions MW597410 to MW597412) had 97 to 100% (330-339/339 bp) identity with D. ueckerae strain FAU656 (KJ590747). The species Diaporthe miriciae R.G. Shivas, S.M. Thomps. & Y.P. Tan, and Diaporthe ueckerae Udayanga & Castl. are synonymous, with the latter taking the nomenclature priority (Gao et al. 2016). According to a multilocus phylogenetic analysis, by maximum likelihood, the three isolates clustered together in a clade with reference type strains of D. ueckerae (Udayanga et al. 2015). Soybean plants cv. BRS Serena (growth stages V3 to V4) were used to verify the pathogenicity of each isolate using a toothpick inoculation method (Mena et al. 2020). A single toothpick colonized by D. ueckerae was inserted directly into the stem of each plant (10 plants per isolate) approximately 1 cm below the first trifoliate node. Noncolonized sterile toothpicks, inserted in 10 soybean plants served as the non-inoculated control. Plants were arbitrarily distributed inside a glasshouse, and incubated at high relative humidity (>90% HR). After 15 days, inoculated plants showed elongated reddish-brown necrosis at the inoculated sites, that were similar to symptoms observed in the field. Non-inoculated control plants were asymptomatic. Fungal cultures recovered from symptomatic stems were morphologically identical to the original isolates. This is the first report of soybean stem canker caused by D. ueckerae in Colombia. Due to the economic importance of this disease elsewhere (Backman et al. 1985; Mena et al. 2020), further research on disease management strategies to mitigate potential crop losses is warranted.
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Qi, Yifei, Niwen Zhou, Qing Jiang, Zhi Wang, Yingying Zhang, Bing Li, Wenjuan Xu, Jun Liu, Zhong Wang, and Lixing Zhu. "Dose-Dependent Variation of Synchronous Metabolites and Modules in a Yin/Yang Transformation Model of Appointed Ischemia Metabolic Networks." Frontiers in Neuroscience 15 (August 20, 2021). http://dx.doi.org/10.3389/fnins.2021.645185.
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AimChinese medicine Danhong injection (DHI) is an effective pharmaceutical preparation for treating cerebral infarction. Our previous study shows that DHI can remarkably reduce the ischemic stroke-induced infarct volume in a dose-dependent manner, but the pharmacological mechanism of the DHI dose-dependent relationship is not clear. Therefore, the dose-dependent efficacy of DHI on cerebral ischemia and the underlying mechanisms were further investigated in this study.MethodsA middle cerebral artery occlusion (MCAO) model was established and the rats were randomly divided into six groups: sham, vehicle, DHI dose-1, DHI dose-2, DHI dose-3, and DHI dose-4. Forty-one metabolites in serum were selected as candidate biomarkers of efficacy phenotypes by the Agilent 1290 rapid-resolution liquid chromatography system coupled with the Agilent 6550 Q-TOF MS system. Then, the metabolic networks in each group were constructed using the Weighted Correlation Network analysis (WGCNA). Moreover, the Yang and Yin transformation of six patterns (which are defined by up- and downregulation of metabolites) and synchronous modules divided from a synchronous network were used to dynamically analyze the mechanism of the drug’s effectiveness.ResultsThe neuroprotective effect of DHI has shown a dose-dependent manner, and the high-dose group (DH3 and DH4) effect is better. The entropy of the metabolic network and the Yin/Yang index both showed a consistent dose–response relationship. Seven dose-sensitive metabolites maintained constant inverse upregulation or downregulation in the four dose groups. Three synchronous modules for the DH1–DH4 full-course network were identified. Glycine, N-acetyl-L-glutamate, and tetrahydrofolate as a new emerging module appeared in DH2/DH3 and enriched in glutamine and glutamate metabolism-related pathways.ConclusionThis study takes the DHI metabolic network as an example to provide a new method for the discovery of multiple targets related to pharmacological effects. Our results show that the three conservative allosteric module nodes, taurine, L-tyrosine, and L-leucine, may be one of the basic mechanisms of DHI in the treatment of cerebral infarction, and the other three new emerging module nodes glyoxylate, L-glutamate, and L-valine may participate in the glutamine and glutamate metabolism pathway to improve the efficacy of DHI.
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Faass, Larissa, Saskia C. Stein, Martina Hauke, Madeleine Gapp, Manuel Albanese, and Christine Josenhans. "Contribution of Heptose Metabolites and the cag Pathogenicity Island to the Activation of Monocytes/Macrophages by Helicobacter pylori." Frontiers in Immunology 12 (May 19, 2021). http://dx.doi.org/10.3389/fimmu.2021.632154.
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The human gastric pathogen Helicobacter pylori activates human epithelial cells by a particular combination of mechanisms, including NOD1 and ALPK1-TIFA activation. These mechanisms are characterized by a strong participation of the bacterial cag pathogenicity island, which forms a type IV secretion system (CagT4SS) that enables the bacteria to transport proteins and diverse bacterial metabolites, including DNA, glycans, and cell wall components, into human host cells. Building on previous findings, we sought to determine the contribution of lipopolysaccharide inner core heptose metabolites (ADP-heptose) in the activation of human phagocytic cells by H. pylori. Using human monocyte/macrophage-like Thp-1 cells and human primary monocytes and macrophages, we were able to determine that a substantial part of early phagocytic cell activation, including NF-κB activation and IL-8 production, by live H. pylori is triggered by bacterial heptose metabolites. This effect was very pronounced in Thp-1 cells exposed to bacterial purified lysates or pure ADP-heptose, in the absence of other bacterial MAMPs, and was significantly reduced upon TIFA knock-down. Pure ADP-heptose on its own was able to strongly activate Thp-1 cells and human primary monocytes/macrophages. Comprehensive transcriptome analysis of Thp-1 cells co-incubated with live H. pylori or pure ADP-heptose confirmed a signature of ADP-heptose-dependent transcript activation in monocyte/macrophages. Bacterial enzyme-treated lysates (ETL) and pure ADP-heptose–dependent activation differentiated monocytes into macrophages of predominantly M1 type. In Thp-1 cells, the active CagT4SS was less required for the heptose-induced proinflammatory response than in epithelial cells, while active heptose biosynthesis or pure ADP-heptose was required and sufficient for their early innate response and NF-κB activation. The present data suggest that early activation and maturation of incoming and resident phagocytic cells (monocytes, macrophages) in the H. pylori–colonized stomach strongly depend on bacterial LPS inner core heptose metabolites, also with a significant contribution of an active CagT4SS.
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Zhang, Xiaoli, Wentao Ding, Dong Xue, Xiangnan Li, Yang Zhou, Jiacheng Shen, Jianying Feng, et al. "Genome-wide association studies of plant architecture-related traits and 100-seed weight in soybean landraces." BMC Genomic Data 22, no. 1 (March 6, 2021). http://dx.doi.org/10.1186/s12863-021-00964-5.
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Abstract Background Plant architecture-related traits (e.g., plant height (PH), number of nodes on main stem (NN), branch number (BN) and stem diameter (DI)) and 100-seed weight (100-SW) are important agronomic traits and are closely related to soybean yield. However, the genetic basis and breeding potential of these important agronomic traits remain largely ambiguous in soybean (Glycine max (L.) Merr.). Results In this study, we collected 133 soybean landraces from China, phenotyped them in two years at two locations for the above five traits and conducted a genome-wide association study (GWAS) using 82,187 single nucleotide polymorphisms (SNPs). As a result, we found that a total of 59 SNPs were repeatedly detected in at least two environments. There were 12, 12, 4, 4 and 27 SNPs associated with PH, NN, BN, DI and 100-SW, respectively. Among these markers, seven SNPs (AX-90380587, AX-90406013, AX-90387160, AX-90317160, AX-90449770, AX-90460927 and AX-90520043) were large-effect markers for PH, NN, BN, DI and 100-SW, and 15 potential candidate genes were predicted to be in linkage disequilibrium (LD) decay distance or LD block. In addition, real-time quantitative PCR (qRT-PCR) analysis was performed on four 100-SW potential candidate genes, three of them showed significantly different expression levels between the extreme materials at the seed development stage. Therefore, Glyma.05 g127900, Glyma.05 g128000 and Glyma.05 g129000 were considered as candidate genes with 100-SW in soybean. Conclusions These findings shed light on the genetic basis of plant architecture-related traits and 100-SW in soybean, and candidate genes could be used for further positional cloning.