Journal articles: 'Gene SMART study'

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Purohit, Arpana, Sameeksha Jain, Prakhar Nema, Harshna Vishwakarma, and Prateek Kumar Jain. "Intelligent or Smart Polymers: Advance in Novel Drug Delivery." Journal of Drug Delivery and Therapeutics 12, no. 5 (September 15, 2022): 208–16. http://dx.doi.org/10.22270/jddt.v12i5.5578.

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Novel drug delivery system utilizing smart polymer to get significant and attracting changes in the targeting of drugs, increasing the bioavailability of drugs, enhancement patient compliance and gene therapy. The scientific community tries to mimic nature in the way that living organisms adopt their behavior as a function of environmental conditions to improve survival. In this sense, smart polymers offer materials that respond to numerous stimuli (temperature, pH, electric and magnetic fields, light intensity, biological molecules, etc.), and scientists must devise the best way to apply them in all research areas. Smart polymers are representing promising means for targeted drug delivery, enhanced drug delivery, gene therapy, actuator stimuli and protein folders. Smart polymers are very promising applicants in drug delivery, tissue engineering, cell culture, gene carriers, textile engineering, oil recovery, radioactive wastage and protein purification. The study is focused on the entire features of smart polymers and their most recent and relevant applications. Keywords: Smart polymer, Novel drug delivery system, Stimuli, Gene therapy

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Jacques, Macsue, Jujiao Kuang, David J. Bishop, Xu Yan, Javier Alvarez‐Romero, Fiona Munson, Andrew Garnham, Ioannis Papadimitriou, Sarah Voisin, and Nir Eynon. "Mitochondrial respiration variability and simulations in human skeletal muscle: The Gene SMART study." FASEB Journal 34, no. 2 (January 9, 2020): 2978–86. http://dx.doi.org/10.1096/fj.201901997rr.

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Ishiguro, Nobuhisa, Rikako Sato, Toshihiko Mori, Hiroshi Tanaka, Mitsuo Narita, Takashi Nagano, Masato Owaku, Kensuke Miyajima, and Atsushi Manabe. "Point-of-care molecular diagnosis of Mycoplasma pneumoniae including macrolide sensitivity using quenching probe polymerase chain reaction." PLOS ONE 16, no. 10 (October 14, 2021): e0258694. http://dx.doi.org/10.1371/journal.pone.0258694.

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Objectives Macrolides are generally considered to be the drugs of choice for treatment of patients with Mycoplasma pneumoniae infection. However, macrolide-resistant M. pneumoniae has been emerging since about 2000. The Smart Gene® system (MIZUHO MEDY Co., Ltd., Tosu, Japan) is a novel fully automated system for detection of pathogens using the method of quantitative polymerase chain reaction (qPCR) with QProbe (QProbe PCR). The entire procedure is completed within 50 min and the size of the instrument is small (15 x 34 x 30 cm). The purpose of this study was to evaluate the usefulness of the Smart Gene® system for detection of M. pneumoniae and detection of a point mutation at domain V of the 23S rRNA gene of M. pneumoniae. Materials Pharyngeal swab samples were collected from 154 patients who were suspected of having respiratory tract infections associated with M. pneumoniae. Results Compared with the results of qPCR, the sensitivity and specificity of the Smart Gene® system were 98.7% (78/79) and 100.0% (75/75), respectively. A point mutation at domain V of the 23S rRNA gene was detected from 7 (9.0%) of 78 M. pneumoniae-positive samples by the Smart Gene® system and these results were confirmed by direct sequencing. The minimum inhibitory concentrations of clarithromycin among the 5 isolates of M. pneumoniae with a point mutation at domain V of the 23S rRNA gene were >64 μg/ml and those among the 33 isolates without a mutation in the 23S rRNA gene were <0.0625 μg/ml. Conclusion The Smart Gene® system is a rapid and accurate assay for detection of the existence of M. pneumoniae and a point mutation at domain V of the 23S rRNA gene of M. pneumoniae at the same time. The Smart Gene® system is suitable for point-of-care testing in both hospital and outpatient settings.

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Ishiguro, Nobuhisa, Rikako Sato, Toshihiko Mori, Hiroshi Tanaka, Mitsuo Narita, Takashi Nagano, Masato Owaku, Kensuke Miyajima, and Atsushi Manabe. "Point-of-care molecular diagnosis of Mycoplasma pneumoniae including macrolide sensitivity using quenching probe polymerase chain reaction." PLOS ONE 16, no. 10 (October 14, 2021): e0258694. http://dx.doi.org/10.1371/journal.pone.0258694.

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Objectives Macrolides are generally considered to be the drugs of choice for treatment of patients with Mycoplasma pneumoniae infection. However, macrolide-resistant M. pneumoniae has been emerging since about 2000. The Smart Gene® system (MIZUHO MEDY Co., Ltd., Tosu, Japan) is a novel fully automated system for detection of pathogens using the method of quantitative polymerase chain reaction (qPCR) with QProbe (QProbe PCR). The entire procedure is completed within 50 min and the size of the instrument is small (15 x 34 x 30 cm). The purpose of this study was to evaluate the usefulness of the Smart Gene® system for detection of M. pneumoniae and detection of a point mutation at domain V of the 23S rRNA gene of M. pneumoniae. Materials Pharyngeal swab samples were collected from 154 patients who were suspected of having respiratory tract infections associated with M. pneumoniae. Results Compared with the results of qPCR, the sensitivity and specificity of the Smart Gene® system were 98.7% (78/79) and 100.0% (75/75), respectively. A point mutation at domain V of the 23S rRNA gene was detected from 7 (9.0%) of 78 M. pneumoniae-positive samples by the Smart Gene® system and these results were confirmed by direct sequencing. The minimum inhibitory concentrations of clarithromycin among the 5 isolates of M. pneumoniae with a point mutation at domain V of the 23S rRNA gene were >64 μg/ml and those among the 33 isolates without a mutation in the 23S rRNA gene were <0.0625 μg/ml. Conclusion The Smart Gene® system is a rapid and accurate assay for detection of the existence of M. pneumoniae and a point mutation at domain V of the 23S rRNA gene of M. pneumoniae at the same time. The Smart Gene® system is suitable for point-of-care testing in both hospital and outpatient settings.

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Cheng, Ling-Yi, Yu-Chi Wang, Ming-Hong Chen, Fu-I. Tung, Kuan-Ming Chiu, and Tse-Ying Liu. "An Engineered Gene Nanovehicle Developed for Smart Gene Therapy to Selectively Inhibit Smooth Muscle Cells: An In Vitro Study." International Journal of Molecular Sciences 21, no. 4 (February 24, 2020): 1530. http://dx.doi.org/10.3390/ijms21041530.

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In-stent restenosis is a serious concern for patients treated through the stenting procedure, although this can be solved using drug-eluting stents and/or drug-eluting balloon catheters. However, the chemical agents released from the drug-eluting layer for inhibiting smooth muscle cell (SMC) migration are inevitably associated with damage to vascular endothelial cell (ECs). The present in vitro study used a distinct strategy, in which a smart gene (phEGR1-PKCδ, an engineered plasmid consists of an SMC-specific promoter (human early growth response 1, hEGR1 promoter) ligated with a gene encoding apoptosis-inducing protein (protein kinase C-delta, PKCδ) was incorporated into a novel gene vehicle (Au cluster-incorporated polyethylenimine/carboxymethyl hexanoyl chitosan, PEI-Au/CHC) to form the PEI-Au/CHC/phEGR1-PKCδ complex, which was proposed for the selective inhibition of SMC proliferation. It was found that the cell viability of SMCs receiving the PEI-Au/CHC/phEGR1-PKCδ complex under simulated inflammation conditions was significantly lower than that of the ECs receiving the same treatment. In addition, the PEI-Au/CHC/phEGR1-PKCδ complex did not demonstrate an inhibitory effect on EC proliferation and migration under simulated inflammation conditions. Finally, the PEI-Au/CHC/phEGR1-PKCδ complexes coated onto a balloon catheter used in percutaneous transluminal coronary angioplasty (PTCA) could be transferred to both the ECs and the SMC layer of Sprague Dawley (SD) rat aortas ex vivo. These preliminary in vitro results suggest that the newly developed approach proposed in the present study might be a potential treatment for reducing the incidence rate of in-stent restenosis and late thrombosis in the future.

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Aditama, Redi, Zulfikar Achmad Tanjung, Widyartini Made Sudania, and Toni Liwang. "SMART-RDA: A Galaxy Workflow for RNA-Seq Data Analysis." KnE Life Sciences 3, no. 4 (March 27, 2017): 186. http://dx.doi.org/10.18502/kls.v3i4.703.

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RNA-seq using the Next Generation Sequencing (NGS) approach is a common technology to analyze large-scale RNA transcript data for gene expression studies. However, an appropriate bioinformatics tool is needed to analyze a large amount of transcriptomes data from RNA-seq experiment. The aim of this study was to construct a system that can be easily applied to analyze RNA-seq data. RNA-seq analysis tool as SMART-RDA was constructed in this study. It is a computational workflow based on Galaxy framework to be used for analyzing RNA-seq raw data into gene expression information. This workflow was adapted from a well-known Tuxedo Protocol for RNA-seq analysis with some modifications. Expression value from each transcriptome was quantitatively stated as Fragments Per Kilobase of exon per Million fragments (FPKM). RNA-seq data of sterile and fertile oil palm (Pisifera) pollens derived from Sequence Read Archive (SRA) NCBI were used to test this workflow in local facility Galaxy server. The results showed that differentially gene expression in pollens might be responsible for sterile and fertile characteristics in palm oil Pisifera.Keywords: FPKM; Galaxy workflow; Gene expression; RNA sequencing.

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Hiam, Danielle, Sarah Voisin, Xu Yan, Shanie Landen, Macsue Jacques, Ioannis D. Papadimitriou, Fiona Munson, et al. "The association between bone mineral density gene variants and osteocalcin at baseline, and in response to exercise: The Gene SMART study." Bone 123 (June 2019): 23–27. http://dx.doi.org/10.1016/j.bone.2019.03.015.

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Lolita C, Jenifer. "Cloning and Expression Analysis of bZIP Transcription Factor from Finger Millet (Eleusine coracana L.) Under Abiotic Stress Conditions." International Journal of Advances in Agricultural Science and Technology 9, no. 1 (January 30, 2022): 1–13. http://dx.doi.org/10.47856/ijaast.2022.v09i01.001.

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Basic leucine zipper (bZIP) transcription factors comprise one of the largest gene families in plants. They play a key role in almost every aspect of plant growth and development and also in biotic and abiotic stress tolerance. In this study, we were attempted to study characterization of bZIP, a transcription factor from a climate smart cereal finger millet (Eleusine coracana L.). Seeds of Eleusine coracana (finger millet) was purchase from local market and were grown under field conditions drought and salt stress conditions. In this study, EcbZIP gene was isolated from finger millet, cloned into DH5α cells, screened by using colony PCR and expression analysis in response to two abiotic stresses was carried out by using qRT PCR. EcbZIP coding DNA sequence and protein sequence were retrieved from NCBI Nucleotide Database and Genpept of Accession number KP033192.1 and AJP67539.1 and validated by using SMART (simple modular architecture tool) Domain Tool. Cloning and expression studies were carried out using standardized molecular biology protocol. Results depicted that EcbZIP transcription factor showed significant upregulation under both salt and drought stress conditions, indicating that it plays an important role in tolerance towards these stresses. In conclusion, expression analysis of bZIP gene from finger millet seed cultivar ML-365 showed 5-fold upregulation to salt stress to drought stress and 8-fold upregulation to salt stress. Hence, it can serve as a candidate gene for improving abiotic stress tolerance and can be helpful in enhancing the crop productivity under stress conditions.

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Karanikolou, Antonia, Guan Wang, Ioannis D. Papadimitriou, Xu Yan, Andrew Garnham, David J. Bishop, Nir Eynon, and Yannis P. Pitsiladis. "P-86 The use of whole-genome expression to predict exercise training response in the gene smart study: preliminary results." British Journal of Sports Medicine 50, Suppl 1 (November 2016): A79.2—A80. http://dx.doi.org/10.1136/bjsports-2016-097120.139.

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Hajar Yusoff, Siti, Ummi Nur Kamilah Abdullah Din, Hasmah Mansor, Nur Shahida Midi, and Syasya Azra Zaini. "Design of Smart Waste Bin and Prediction Algorithm for Waste Management in Household Area." Indonesian Journal of Electrical Engineering and Computer Science 12, no. 2 (November 1, 2018): 748. http://dx.doi.org/10.11591/ijeecs.v12.i2.pp748-758.

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Maintaining current municipal solid waste management (MSWM) for the next ten years would not be efficient anymore as it has brought many environmental issues such as air pollution. This project has proposed Artificial Neural Network (ANN) based prediction algorithm that can forecast Solid Waste Generation (SWG) based on household size factor. Kulliyyah of Engineering (KOE) in International Islamic University Malaysia (IIUM) has been chosen as the sample size for household size factor. A smart waste bin has been developed that can measure the weight, detect the emptiness level of the waste bin, stores information and have direct communication between waste bin and collector crews. This study uses the information obtained from the smart waste bin for the waste weight while the sample size of KOE has been obtained through KOE’s department. All data will be normalized in the pre-processing stage before proceeding to the prediction using Visual Gene Developer. This project evaluated the performance using R2 value. Two hidden layers with five and ten nodes were used respectively. The result portrayed that the average rate of increment of waste weight is 2.05 percent from week one until week twenty. The limitation to this study is that the amount of smart waste bin should be replicated more so that all data for waste weight is directly collected from the smart waste bin.

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Yan, Xu, Noam Dvir, Macsue Jacques, Luiz Cavalcante, Ioannis D. Papadimitriou, Fiona Munson, Jujiao Kuang, et al. "ACE I/D gene variant predicts ACE enzyme content in blood but not the ACE, UCP2, and UCP3 protein content in human skeletal muscle in the Gene SMART study." Journal of Applied Physiology 125, no. 3 (September 1, 2018): 923–30. http://dx.doi.org/10.1152/japplphysiol.00344.2018.

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Angiotensin-converting enzyme (ACE) is expressed in human skeletal muscle. The ACE I/D polymorphism has been associated with athletic performance in some studies. Studies have suggested that the ACE I/D gene variant is associated with ACE enzyme content in serum, and there is an interaction between ACE and uncoupling proteins 2 and 3 (UCP2 and UCP3). However, no studies have explored the effect of ACE I/D on ACE, UCP2, and UCP3 protein content in human skeletal muscle. Utilizing the Gene SMART cohort ( n = 81), we investigated whether the ACE I/D gene variant is associated with ACE enzyme content in blood and ACE, UCP2, and UCP3 protein content in skeletal muscle at baseline and following a session of high-intensity interval exercise (HIIE). Using a stringent and robust statistical analyses, we found that the ACE I/D gene variant was associated with ACE enzyme content in blood ( P < 0.005) at baseline but not the ACE, UCP2, and UCP3 protein content in muscle at baseline. A single session of HIIE tended (0.005 < P < 0.05) to increase blood ACE content immediately postexercise, whereas muscle ACE protein content was lower 3 h after a single session of HIIE ( P < 0.005). Muscle UCP3 protein content decreased immediately after a single session of HIIE ( P < 0.005) and remained low 3 h postexercise. However, those changes in the muscle were not genotype dependent. In conclusion, The ACE I/D gene variant predicts ACE enzyme content in blood but not the ACE, UCP2, and UCP3 protein content of human skeletal muscle. NEW & NOTEWORTHY This paper describes the association between ACE I/D gene variant and ACE protein content in blood and ACE, UCP2, and UCP3 protein content in skeletal muscle at baseline and after exercise in a large cohort of healthy males. Our data suggest that ACE I/D is a strong predictor of blood ACE content but not muscle ACE content.

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Kozuka, Masahiro, Francesca Battaglin, Priya Jayachandran, Jingyuan Wang, Hiroyuki Arai, Shivani Soni, Wu Zhang, Mitsuharu Hirai, Satoshi Matsusaka, and Heinz-Josef Lenz. "Clinical Significance of Circulating Tumor Cell Induced Epithelial-Mesenchymal Transition in Patients with Metastatic Colorectal Cancer by Single-Cell RNA-Sequencing." Cancers 13, no. 19 (September 28, 2021): 4862. http://dx.doi.org/10.3390/cancers13194862.

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Background: Circulating tumor cells (CTCs) are a prognostic marker in patients with metastatic colorectal cancer (mCRC). However, little is known about the characterization of CTCs in mCRC at the single-cell level using RNA sequencing. The purpose of this study was to validate the capability to detect and isolate single CTCs for single-cell RNA sequencing (scRNA-seq) and to identify clinical significance at a single CTC level. Methods: Single CTCs from 27 mCRC patients were collected by CTC-FIND, which is comprised of filter separation and immunomagnetic depletion to collect ultra-pure CTC samples. To address tumor heterogeneity, CTCs were collected without relying on any traditional CTC markers, such as epithelial and mesenchymal cell antigens, and were undertaken by scRNA-seq using SMART-Seq v4. Results: We identified 59 single CTCs which were classified into four groups by epithelial, epithelial-mesenchymal transition (EMT) and stem cell-related gene expression. Patients receiving second or later-line treatment who had EMT gene expressing CTCs had a significantly shorter PFS and OS. Conclusions: Exploiting CTC-FIND with SMART-Seq v4 showed that scRNA-seq of CTCs may shed new insight into tumor heterogeneity of mCRC and that the presence of CTCs expressing EMT-related genes at the single-cell level could have prognostic value in mCRC patients.

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Hsueh, Po-Ren, Lee-Jene Teng, Chun-Ming Lee, Wen-Kuei Huang, Tsu-Lan Wu, Jen-Hsien Wan, Dine Yang, et al. "Telithromycin and Quinupristin-Dalfopristin Resistance in Clinical Isolates of Streptococcus pyogenes: SMART Program 2001 Data." Antimicrobial Agents and Chemotherapy 47, no. 7 (July 2003): 2152–57. http://dx.doi.org/10.1128/aac.47.7.2152-2157.2003.

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ABSTRACT This study evaluated the current status of antimicrobial resistance in clinical isolates of Streptococcus pyogenes in Taiwan as part of the SMART (Surveillance from Multicenter Antimicrobial Resistance in Taiwan) program. In 2001, 419 different isolates of S. pyogenes, including 275 from respiratory secretions, 87 from wound pus, and 31 from blood, were collected from nine hospitals in different parts of Taiwan. MICs of 23 antimicrobial agents were determined at a central location by the agar dilution method. All of the isolates were susceptible to penicillin (MIC at which 90% of the isolates were inhibited [MIC90], ≤0.03 μg/ml), cefotaxime (MIC90, ≤0.03 μg/ml), cefepime (MIC90, 0.06 μg/ml), meropenem (MIC90, ≤0.03 μg/ml), moxifloxacin (MIC90, 0.25 μg/ml), vancomycin (MIC90, 0.5 μg/ml), and linezolid (MIC90, 1 μg/ml). Overall, 78% of isolates were not susceptible to erythromycin (54% were intermediate, and 24% were resistant), and 5% were not susceptible to clindamycin. Of the 101 erythromycin-resistant isolates, 80.2% exhibited the M phenotype (mefA gene positive), 18.9% exhibited the cMLS (constitutive resistance to macrolides-lincosamides-streptogramin B [MLS]) phenotype (ermB gene positive), and 1% exhibited the iMLS (inducible resistance to MLS) phenotype (ermB gene positive). Fluoroquinolones (sitafloxacin > moxifloxacin > ciprofloxacin = levofloxacin = gatifloxacin > gemifloxacin) demonstrated potent activity against nearly all of the isolates of S. pyogenes tested. Thirty-two isolates (8%) were not susceptible to quinupristin-dalfopristin. Seventeen percent of isolates had telithromycin MICs of ≥1 μg/ml, and all of these isolates exhibited erythromycin MICs of ≥32 μg/ml. The high prevalence of resistance to telithromycin (which is not available in Taiwan) limits its potential use in the treatment of S. pyogenes infections, particularly in areas with high rates of macrolide resistance.

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Ziminska, Monika, Jordan J. Wilson, Emma McErlean, Nicholas Dunne, and Helen O. McCarthy. "Synthesis and Evaluation of a Thermoresponsive Degradable Chitosan-Grafted PNIPAAm Hydrogel as a “Smart” Gene Delivery System." Materials 13, no. 11 (June 2, 2020): 2530. http://dx.doi.org/10.3390/ma13112530.

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Thermoresponsive hydrogels demonstrate tremendous potential as sustained drug delivery systems. However, progress has been limited as formulation of a stable biodegradable thermosensitive hydrogel remains a significant challenge. In this study, free radical polymerization was exploited to formulate a biodegradable thermosensitive hydrogel characterized by sustained drug release. Highly deacetylated chitosan and N-isopropylacrylamide with distinctive physical properties were employed to achieve a stable, hydrogel network at body temperature. The percentage of chitosan was altered within the copolymer formulations and the subsequent physical properties were characterized using 1H-NMR, FTIR, and TGA. Viscoelastic, swelling, and degradation properties were also interrogated. The thermoresponsive hydrogels were loaded with RALA/pEGFP-N1 nanoparticles and release was examined. There was sustained release of nanoparticles over three weeks and, more importantly, the nucleic acid cargo remained functional and this was confirmed by successful transfection of the NCTC-929 fibroblast cell line. This tailored thermoresponsive hydrogel offers an option for sustained delivery of macromolecules over a prolonged considerable period.

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Al-Sayaydeh, Rabea, Khaled Al-Habahbeh, Zahera Akkeh, and Randa N. Albdaiwi. "IN SILICO GENE EXPRESSION ANALYSIS OF THE STRESS-RELATED NAC-A GENE SUBFAMILY TO DISSECT THEIR ROLE IN ABIOTIC STRESS TOLERANCE IN BREAD WHEAT (TRITICUM AESTIVUM L.)." Jordan Journal of Agricultural Sciences 17, no. 3 (September 1, 2021): 341–54. http://dx.doi.org/10.35516/jjas.v17i3.90.

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Wheat is a major staple crop that is largely affected by different abiotic stresses that include heat, drought, and salinity. The main objective of this study was to identify wheat NAC transcription factors that are related to the NAC-a subfamily, which is involved in mediating stress tolerance in different plant species. Furthermore, in silico gene expression analysis was conducted to detect differential changes in wheat NAC-a subfamily members in different organs, developmental stages, and under various abiotic stress. Herein, using phylogenetic analysis for 488 NAC transcription factors, 41 proteins were identified as wheat NAC-a subfamily members. In silico gene expression analysis found that NAC-related wheat transcription factors are expressed exclusively at the anthesis stage till dough development with high expression levels detected in flag leaves. The in-silico gene expression analysis identified SNAC1-related members, which had high expression levels under drought, cold, and heat stresses. The identified stress-induced wheat NAC-a subfamily members can be utilized in the future to develop climate-smart wheat cultivars with improved tolerance against abiotic stresses.

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Wei, Zuzhuang, Bobo Liu, Xiaomin Lin, Jing Wang, Zhi-Shu Huang, and Ding Li. "Development of a Smart Fluorescent Probe Specifically Interacting with C-Myc I-Motif." International Journal of Molecular Sciences 23, no. 7 (March 31, 2022): 3872. http://dx.doi.org/10.3390/ijms23073872.

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I-motifs play key regulatory roles in biological processes, holding great potential as attractive therapeutic targets. In the present study, we developed a novel fluorescent probe G59 with strong and selective binding to the c-myc gene promoter i-motif. G59 had an i-motif-binding carbazole moiety conjugated with naphthalimide fluorescent groups. G59 could differentiate the c-myc i-motif from other DNA structures through selective activation of its fluorescence, with its apparent visualization in solution. The smart probe G59 showed excellent sensitivity, with a low fluorescent detection limit of 154 nM and effective stabilization to the c-myc i-motif. G59 could serve as a rapid and sensitive probe for label-free screening of selective c-myc i-motif binding ligands under neutral crowding conditions. To the best of our knowledge, G59 is the first fluorescent probe with high sensitivity for recognizing the i-motif structure and screening for selective binding ligands.

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Heshmati Aghda, Niloofar, Yu Zhang, Jiawei Wang, Anqi Lu, Amit Raviraj Pillai, and Mohammed Maniruzzaman. "A Novel 3D Printing Particulate Manufacturing Technology for Encapsulation of Protein Therapeutics: Sprayed Multi Adsorbed-Droplet Reposing Technology (SMART)." Bioengineering 9, no. 11 (November 5, 2022): 653. http://dx.doi.org/10.3390/bioengineering9110653.

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Recently, various innovative technologies have been developed for the enhanced delivery of biologics as attractive formulation targets including polymeric micro and nanoparticles. Combined with personalized medicine, this area can offer a great opportunity for the improvement of therapeutics efficiency and the treatment outcome. Herein, a novel manufacturing method has been introduced to produce protein-loaded chitosan particles with controlled size. This method is based on an additive manufacturing technology that allows for the designing and production of personalized particulate based therapeutic formulations with a precise control over the shape, size, and potentially the geometry. Sprayed multi adsorbed-droplet reposing technology (SMART) consists of the high-pressure extrusion of an ink with a well determined composition using a pneumatic 3D bioprinting approach and flash freezing the extrudate at the printing bed, optionally followed by freeze drying. In the present study, we attempted to manufacture trypsin-loaded chitosan particles using SMART. The ink and products were thoroughly characterized by dynamic light scattering, rheometer, Scanning Electron Microscopy (SEM), and Fourier Transform Infra-Red (FTIR) and Circular Dichroism (CD) spectroscopy. These characterizations confirmed the shape morphology as well as the protein integrity over the process. Further, the effect of various factors on the production were investigated. Our results showed that the concentration of the carrier, chitosan, and the lyoprotectant concentration as well as the extrusion pressure have a significant effect on the particle size. According to CD spectra, SMART ensured Trypsin’s secondary structure remained intact regardless of the ink composition and pressure. However, our study revealed that the presence of 5% (w/v) lyoprotectant is essential to maintain the trypsin’s proteolytic activity. This study demonstrates, for the first time, the viability of SMART as a single-step efficient process to produce biologics-based stable formulations with a precise control over the particulate morphology which can further be expanded across numerous therapeutic modalities including vaccines and cell/gene therapies.

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Alwani, Saniya, Raj Rai, Isabella Zittlau, Jonathan Rekve, Deborah Michel, and Ildiko Badea. "Design of Smart Nanodiamonds: Introducing pH Sensitivity to Improve Nucleic Acid Carrier Efficiency of Diamoplexes." Pharmaceutics 14, no. 9 (August 26, 2022): 1794. http://dx.doi.org/10.3390/pharmaceutics14091794.

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The mechanism of cellular uptake and intracellular fate of nanodiamond/nucleic acid complexes (diamoplexes) are major determinants of its performance as a gene carrier. Our group designed lysine-nanodiamonds (K-NDs) as vectors for nucleic acid delivery. In this work, we modified the surface of K-NDs with histidine to overcome endo-lysosomal entrapment diamoplexes, the major rate limiting step in gene transfer. Histidine is conjugated onto the NDs in two configurations: lysyl-histidine-NDs (HK-NDs) where histidine is loaded on 100% of the lysine moieties and lysine/lysyl-histidine-NDs (H50K50-NDs) where histidine is loaded on 50% of the lysine moieties. Both HK-NDs and H50K50-NDs maintained the optimum size distribution (i.e., <200 nm) and a cationic surface (zeta potential > 20 mV), similar to K-NDs. HK-NDs binds plasmid deoxyribonucleic acid (pDNA) and small interfering ribonucleic acid (siRNA) forming diamoplexes at mass ratios of 10:1 and 60:1, respectively. H50K50-NDs significantly improved nucleic acid binding, forming diamoplexes at a 2:1 mass ratio with pDNA and a 30:1 mass ratio with siRNA, which are at values similar to the K-NDs. The amount of histidine on the surface also impacted the interactions with mammalian cells. The HK-NDs reduced the cell viability by 30% at therapeutic concentrations, while H50K50-NDs maintained more than 90% cell viability, even at the highest concentrations. H50K50-NDs also showed highest cellular uptake within 24 h, followed by K-NDs and HK-NDs. Most functionalized NDs show cellular exit after 5 days, leaving less than 10% of cells with internalized diamonds. The addition of histidine to the ND resulted in higher transfection of anti-green fluorescent protein siRNA (anti-GFP siRNA) with the fraction of GFP knockdown being 0.8 vs. 0.6 for K-NDs at a mass ratio of 50:1. H50K50-NDs further improved transfection by achieving a similar fraction of GFP knockdown (0.8) at a lower mass ratio of 30:1. Overall, this study provides evidence that the addition of histidine, a pH-modulating entity in the functionalization design at an optimized ratio, renders high efficiency to the diamoplexes. Further studies will elucidate the uptake mechanism and intracellular fate to build the relationship between physicochemical characteristics and biological efficacy and create a platform for solid-core nanoparticle-based gene delivery.

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Adnindya, Msy Rulan, Indri Seta Septadina, and Muhammad Reagan. "Potential of Sriwijaya Thermal Cycler Smart Controlling-Based as a Tool for DNA Sequence Polymerase Chain Reaction." Bioscientia Medicina : Journal of Biomedicine and Translational Research 5, no. 4 (December 16, 2020): 348–51. http://dx.doi.org/10.32539/bsm.v5i4.208.

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Introduction. Along with the COVID-19 pandemic, the need for a thermal cyclerdevice for examining COVID-19 is getting bigger. Many laboratories have overusedthe use of thermal cyclers due to the limited availability of this tool. This study aimsto test the effectiveness of the Sriwijaya thermal cycler based on a smart controllerin conducting PCR DNA sequences. Methods. The research design was anexperimental study with a posttest control group approach, in order to see anoverview of the results of the polymerase chain reaction (PCR) in the form ofintermediate DNA bands using Sriwijaya Thermal Cycler compared to groups usingfactory-made Thermal cyclers. Results. The PCR results showed precise results fromthe image and band separation, and there was a clear separation of the bands onthe marker. The PCR results from the ACE I / D gene showed quite good and optimalresults in the separation of the PCR results band. Conclusion. Sriwijaya thermalcycler is effective in DNA polymerase chain reaction (PCR) sequences comparable tothat of the manufacturer's Thermal Cycler.

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Wang, Yu-Chieh, Daniel Ramskold, Shujun Luo, Robin Li, Qiaolin Deng, Gregory A. Daniels, Irina Khrebtukova, et al. "Circulating melanoma cells isolated from clinical blood samples and characterized by full-length mRNA sequencing at single-cell level." Journal of Clinical Oncology 30, no. 15_suppl (May 20, 2012): 10539. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.10539.

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10539 Background: Melanoma is the most aggressive type of skin cancer. Late-stage melanoma is highly metastatic and currently lacks effective treatment. This discouraging clinical observation highlights the need for a better understanding of the molecular mechanisms underlying melanoma initiation and progression and for developing new therapeutic approaches based on novel targets. Although genome-wide transcriptome analyses have been frequently used to study molecular alterations in clinical samples, it has been technically challenging to obtain the transcriptomic profiles at single-cell level. Methods: Using antibody-mediated magnetic activated cell separation (MACS), we isolated and individualized putative circulating melanoma cells (CMCs) from the blood samples of the melanoma patients at advance stages. The transcriptomic analysis based on a novel and robust mRNA-Seq protocol (Smart-Seq) was established and applied to the putative CMCs for single-cell profiling. Results: We have discovered distinct gene expression patterns, including new putative markers for CMCs. Meanwhile, the gene expression profiles derived of the CMC candidates isolated from the patient’s blood samples are closely-related to the expression profiles of other cells originated from human melanocytes, including normal melanocytes in primary culture and melanoma cell lines. Compared with existing methods, Smart-Seq has improved read coverage across transcripts, which provides advantage for better analyzing transcript isoforms and SNPs. Conclusions: Our results suggest that the techniques developed in this research for cell isolation and transcriptomic analyses can potentially be used for addressing many biological and clinical questions requiring genomewide transcriptome profiling in rare cells.

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Adnindya, Msy Rulan, Rachmat Hidayat, Indri Seta Septadina, and Muhammad Reagan. "Potential of Sriwijaya Thermal Cycler Smart Controlling-Based as a Tool for DNA Sequence Polymerase Chain Reaction." Bioscientia Medicina : Journal of Biomedicine and Translational Research 5, no. 2 (December 16, 2020): 200–203. http://dx.doi.org/10.32539/bsm.v5i2.208.

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A B S T R A C TIntroduction. Along with the COVID-19 pandemic, the need for a thermal cyclerdevice for examining COVID-19 is getting bigger. Many laboratories have overusedthe use of thermal cyclers due to the limited availability of this tool. This study aimsto test the effectiveness of the Sriwijaya thermal cycler based on a smart controllerin conducting PCR DNA sequences. Methods. The research design was anexperimental study with a posttest control group approach, in order to see anoverview of the results of the polymerase chain reaction (PCR) in the form ofintermediate DNA bands using Sriwijaya Thermal Cycler compared to groups usingfactory-made Thermal cyclers. Results. The PCR results showed precise results fromthe image and band separation, and there was a clear separation of the bands onthe marker. The PCR results from the ACE I / D gene showed quite good and optimalresults in the separation of the PCR results band. Conclusion. Sriwijaya thermalcycler is effective in DNA polymerase chain reaction (PCR) sequences comparable tothat of the manufacturer's Thermal Cycler.

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Radhakrishnan, Arun, and Gowthamarajan Kuppusamy. "Theoretical Formulation Strategies towards Neutralizing Inter-individual Variability Associated with Tacrolimus Immunosuppressant Therapy: A Case Study on Nextgeneration Personalized Medicine." Current Drug Metabolism 22, no. 12 (October 2021): 939–56. http://dx.doi.org/10.2174/1389200222666211015153317.

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: Individualizing drug therapy and attaining maximum benefits of a drug devoid of adverse reactions is the benefit of personalized medicine. One of the important factors contributing to inter-individual variability is genetic polymorphism. As of now, dose titration is the only followed golden standard for implementing personalized medicine. Converting the genotypic data into an optimized dose has become easier now due to technology development. However, for many drugs, finding an individualized dose may not be successful, which further leads to a trial and error approach. These dose titration strategies are generally followed at the clinical level, and so industrial involvement and further standardizations are not feasible. On the other side, technologically driven pharmaceutical industries have multiple smart drug delivery systems which are underutilized towards personalized medicine. Transdisciplinary research with drug delivery science can additionally support the personalization by converting the traditional concept of “dose titration towards personalization” with novel “dose-cum-dosage form modification towards next-generation personalized medicine”; the latter approach is useful to overcome gene-based inter-individual variability by either blocking, to downregulate, or bypassing the biological protein generated by the polymorphic gene. This article elaborates an advanced approach to implementing personalized medicine with the support of novel drug delivery systems. As a case study, we further reviewed the genetic polymorphisms associated with tacrolimus and customized novel drug delivery systems to overcome these challenges factored towards personalized medicine for better clinical outcomes, thereby paving a new strategy for implementing personalized medicine for all other drug candidates.

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Zor, Kasım, Özgür Çelik, Oğuzhan Timur, and Ahmet Teke. "Short-Term Building Electrical Energy Consumption Forecasting by Employing Gene Expression Programming and GMDH Networks." Energies 13, no. 5 (March 2, 2020): 1102. http://dx.doi.org/10.3390/en13051102.

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Over the past decade, energy forecasting applications not only on the grid side of electric power systems but also on the customer side for load and demand prediction purposes have become ubiquitous after the advancements in the smart grid technologies. Within this context, short-term electrical energy consumption forecasting is a requisite for energy management and planning of all buildings from households and residences in the small-scale to huge building complexes in the large-scale. Today’s popular machine learning algorithms in the literature are commonly used to forecast short-term building electrical energy consumption by generating an abstruse analytical expression between explanatory variables and response variables. In this study, gene expression programming (GEP) and group method of data handling (GMDH) networks are meticulously employed for creating genuine and easily understandable mathematical models among predictor variables and target variables and forecasting short-term electrical energy consumption, belonging to a large hospital complex situated in the Eastern Mediterranean. Consequently, acquired results yielded mean absolute percentage errors of 0.620% for GMDH networks and 0.641% for GEP models, which reveal that the forecasting process can be accomplished and formulated simultaneously via proposed algorithms without the need of applying feature selection methods.

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Wu, Hsi-Chin, and Wei-Ting Kuo. "Redox/pH-Responsive 2-in-1 Chimeric Nanoparticles for the Co-Delivery of Doxorubicin and siRNA." Polymers 13, no. 24 (December 13, 2021): 4362. http://dx.doi.org/10.3390/polym13244362.

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The co-delivery of chemotherapy drugs and gene-suppressing small interfering RNA (siRNA) show promise for cancer therapy. The key to the clinical realization of this treatment model will be the development of a carrier system enabling the simultaneous delivery (“co-delivery” instead of combinatorial delivery) of chemotherapy and siRNA agents to cancer. In this study, a co-delivery system was developed from two individual components to form one integrated nanovehicle through a redox-sensitive thiol–disulfide bond for the synergistic delivery of chemotherapy and RNA silencing: doxorubicin (Dox)-loaded N,O-carboxymethyl chitosan (NOCC) complex with a thiolated hyaluronic acid (HA-SH) nanocarrier and dopamine (Dopa)-conjugated thiolated hyaluronic acid (SH-HA-Dopa)-coated calcium phosphate (CaP)-siRNA nanocarrier. The 2-in-1 chimeric nanoparticles (NPs) were structurally stable together in the storage environment and in the circulation. This smart system selectively releases Dox and siRNA into the cytosol. Furthermore, equipped with the tumor-targeting component HA, the co-delivery system shows specific targeting and high cellular uptake efficiency by receptor-mediated endocytosis. In summary, these dual-responsive (redox and pH), tumor-targeting smart 2-in-1 chimeric NPs show promise to be employed in functional co-delivery and tumor therapy.

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Nanda, Satyabrata, Gagan Kumar, Sudheer Kumar Yadav, and Sajid Hussain. "GENOME-WIDE IDENTIFICATION OF THE GATA TRANSCRIPTION FACTOR FAMILY IN Dichanthelium oligosanthes." Journal of Experimental Biology and Agricultural Sciences 9, no. 4 (August 30, 2021): 407–16. http://dx.doi.org/10.18006/2021.9(4).407.416.

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The GATA transcription factors (TFs) play a crucial role in regulating various physiological processes in plants. Identification and characterization of the GATA TF family has been carried out in several important grass species, including rice, maize, and bamboo. However, no information is available on the GATA TFs in the C3 grass species Dichanthelium oligosanthes. In the current study, 31 GATA genes have been identified in the D. oligosanthes genome by stringent bioinformatics analysis. The exon-intron arrangement analysis of the DoGATAs via the Gene Structure Display Server (GSDS 2.0) revealed the redundancy and differences in their gene structural organization. In addition, the sequence comparisons within the DoGATAs via BLAST revealed 11 numbers of putative paralogs. Similarly, the BLAST comparisons among the OsGATAs and DoGATAs resulted in the identification of 21 orthologs. Structural analysis of the identified DoGATAs through Simple Modular Architecture Research Tool (SMART), Conserved Domain Database (CDD), and Multiple Expectation Maximization for Motif Elicitation (MEME) revealed that all of them possess the signature GATA domain and the C-X2-C-X18-C-X2-C consensus sequence. The phylogenetic analysis via MEGA divided the DoGATAs into four groups along with rice and Arabidopsis GATAs. In addition, the subcellular localization, gene ontology, and other peptide functional prediction results further supported the DoGATAs to be putative GATA genes. Moreover, the findings of this study can serve as a basic framework for the isolation and functional characterization of GATA genes in D. oligosanthes.

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Zhao, Xinyi, Bilal Javed, Furong Tian, and Kangze Liu. "Hydrogel on a Smart Nanomaterial Interface to Carry Therapeutics for Digitalized Glioma Treatment." Gels 8, no. 10 (October 17, 2022): 664. http://dx.doi.org/10.3390/gels8100664.

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Glioma is considered the primary brain tumor to cause brain illnesses, and it is difficult to treat and shows resistance to various routine therapeutics. The most common treatments to cure glioma are the surgical removal of tumors followed by adjuvant chemotherapy and radiation therapy. The latest biocompatible interfaces have been incorporated into therapeutic modalities such as the targeted delivery of drugs using hydrogels to treat and manage brain glioma. This review illustrates the applications of the multimodal hydrogel as the carrier of therapeutics, gene therapy, therapeutic tactics, and glioma devices. The scientific articles were retrieved from 2019 to 2022 on Google Scholar and the Scopus database and screened to determine whether they were suitable for review. The 20 articles that fit the study are summarized in this review. These studies indicated that the sizes of the hydrogel range from 28 nm to 500 nm. There are 16 out of 20 articles that also explain the post-surgical application of hydrogels, and 13 out of 20 articles are employed in 3D culture and other structural manifestations of hydrogels. The pros of the hydrogel include the quick formulation for a sufficient filling of irregular damage sites, solubilizing hydrophobic drugs, continuously slowing drug release, provision of a 3D cell growth environment, improving efficacy, targetability of soluble biomolecules, increasing patient compliance, and decreased side effects. The cons of the hydrogel include difficult real-time monitoring, genetic manipulations, the cumbersome synchronized release of components, and lack of safety data. The prospects of the hydrogel may include the development of electronic hydrogel sensors that can be used to enhance guidance for the precise targeting patterns using patient-specific pathological idiosyncrasies. This technology has the potential to revolutionize the precision medicine approaches that would aid in the early detection and management of solid brain tumors.

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Sun, Wenjun, Zhaotang Ma, Hui Chen, and Moyang Liu. "Genome-wide investigation of WRKY transcription factors in Tartary buckwheat (Fagopyrum tataricum) and their potential roles in regulating growth and development." PeerJ 8 (March 5, 2020): e8727. http://dx.doi.org/10.7717/peerj.8727.

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Background The WRKY gene family plays important roles in plant biological functions and has been identified in many plant species. With the publication of the Tartary buckwheat genome, the evolutionary characteristics of the WRKY gene family can be systematically explored and the functions of Fagopyrum tataricum WRKY (FtWRKY) genes in the growth and development of this plant also can be predicted. Methods In this study, the FtWRKY genes were identified by the BLASTP method, and HMMER, SMART, Pfam and InterPro were used to determine whether the FtWRKY genes contained conserved domains. The phylogenetic trees including FtWRKY and WRKY genes in other plants were constructed by the neighbor-joining (NJ) and maximum likelihood (ML) methods. The intron and exon structures of the FtWRKY genes were analyzed by the gene structure display server, and the motif compositions were analyzed by MEME. Chromosome location information of FtWRKY genes was obtained with gff files and sequencing files, and visualized by Circos, and the collinear relationship was analyzed by Dual synteny plotter software. The expression levels of 26 FtWRKY genes from different groups in roots, leaves, flowers, stems and fruits at the green fruit, discoloration and initial maturity stage were measured through quantitative real-time polymerase chain reaction (qRT-PCR) analysis. Results A total of 76 FtWRKY genes identified from the Tartary buckwheat genome were divided into three groups. FtWRKY genes in the same group had similar gene structures and motif compositions. Despite the lack of tandem-duplicated gene pairs, there were 23 pairs of segmental-duplicated gene pairs. The synteny gene pairs of FtWRKY genes and Glycine max WRKY genes were the most. FtWRKY42 was highly expressed in roots and may perform similar functions as its homologous gene AtWRKY75, playing a role in lateral root and hairy root formation. FtWRKY9, FtWRKY42 and FtWRKY60 were highly expressed in fruits and may play an important role in fruit development. Conclusion We have identified several candidate FtWRKY genes that may perform critical functions in the development of Tartary buckwheat root and fruit, which need be verified through further research. Our study provides useful information on WRKY genes in regulating growth and development and establishes a foundation for screening WRKY genes to improve Tartary buckwheat quality.

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Zhu, Bi Yun, Lan Gao, and Hao Ming Li. "Monascus anka Pyruvate Decarboxylase Accounts for the New Candidate Resources of Fuel Ethanol Production." Advanced Materials Research 512-515 (May 2012): 432–38. http://dx.doi.org/10.4028/www.scientific.net/amr.512-515.432.

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In order to study the nature and function of Pyruvate decarboxylase (PDC, E.C.4.1.1.1), which is the key enzyme to produce ethanol by fermentation; full-length cDNA library was constructed with SMART technique from Monascus anka CICC 5031. The pdc gene, including a 1713-bp open reading frame, encoding a 570 amino acid protein, was obtained by screening the constructed M. anka cDNA library. The pdc gene was successfully heterologously expressed in E.coli BL21(DE3), accounting for 32.7% of total cellular proteins. Recombinant PDC was expressed in prokaryotic cells and purified by affinity chromatography, and native PDC was extracted and purified from M. anka through Sephadex G-25 and DEAE-anion exchange resin. The enzymatic characterization of both recombinant and native PDC were studied, respectively. The specific activity of recombinant and native PDC was 20.2 and 30.11U/mg respectively. Kinetic analysis indicated that recombinant and native PDC had the same optimum conditions: pH6.0, 30°C, the Km value for pyruvate of recombinant PDC was 2.6 mmol/L and native PDC was 0.56 mmol/L. The high activity and stable PDC from M. anka accounts for the new candidate resources of fuel ethanol production.

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Tan, Amelia Cheng Wei, Siti Waheeda Mohd-Zin, Nur'Awatif Ishak, Meow-Keong Thong, Azlina Ahmad-Annuar, Abu Bakar Azizi, and Noraishah Mydin Abdul-Aziz. "MTRR gene variant rs1801394 found in Malaysian patients with neural tube defects." Neuroscience Research Notes 3, no. 1 (March 5, 2020): 24–31. http://dx.doi.org/10.31117/neuroscirn.v3i1.41.

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Neural tube defects (NTDs) are congenital anomalies resulting from the failure of neural tube closure during embryogenesis. The precise molecular mechanisms underlying this multifactorial disease is poorly understood, although single nucleotide polymorphisms in genes involved in the one-carbon metabolism cycle are believed to contribute towards NTD development. Among them is 5-methyltetrahydrofolate-homocysteine methyltransferase reductase (MTRR). Protein function prediction algorithms (PolyPhen-2, PROVEAN, SIFT, SMART-Ensembl) were employed to evaluate its pathogenicity potential caused by the replacement of isoleucine with methionine. Seven NTD patients and 12 of their parents were recruited for this study. DNA samples were collected through blood or saliva whereby the extracted DNAs were then sent for whole exome sequencing (WES). Zygosity of the variant was confirmed from WES data of each subject and further validated through polymerase chain reaction (PCR) and Sanger sequencing. The results revealed that 57% of patients and 83% of parents carried rs1801394 mutation in their MTRR gene, based on either homozygous (G/G) or heterozygous (A/G) genotypes. Bioinformatics analysis of this missense mutation predicted that this change is damaging to MTRR protein function by 2 of the 3 predictor algorithms and that the change from isoleucine to methionine amino acid affects flavodoxin domain of the protein. This impacts enzyme activity within the one-carbon metabolism pathway, which is linked to the aetiology of NTDs. From population databases, this variant was considered common with a MAF >0.3, however, it was not found in the Singapore Genome Variation Project (SGVP), whose population is a closer representation of the Malaysian subjects investigated here. Hence, we explored the prevalence of this variant in other studies and found that its association with NTDs differed across populations worldwide. Finally, we conclude that rs1801394 may be an NTD risk factor in the Malaysian population and should be further investigated as a potential prenatal screening tool.

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Tsunekawa, Katsuhiko, Yoshimaro Yanagawa, Tomoyuki Aoki, Tadashi Morimura, Osamu Araki, Takao Kimura, Takayuki Ogiwara, Nobuo Kotajima, Masumi Yanagawa, and Masami Murakami. "Frequency and Clinical Implication of the R450H Mutation in the Thyrotropin Receptor Gene in the Japanese Population Detected by Smart Amplification Process 2." BioMed Research International 2014 (2014): 1–7. http://dx.doi.org/10.1155/2014/964635.

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In Japanese pediatric patients with thyrotropin (TSH) resistance, the R450H mutation in TSH receptor gene (TSHR) is occasionally observed. We studied the frequency and clinical implication of the R450H mutation inTSHRin the general population of Japanese adults using smart amplification process 2 (SmartAmp2). We designed SmartAmp2 primer sets to detect this mutation using a drop of whole blood. We analyzed thyroid function, antithyroid antibodies, and this mutation in 429 Japanese participants who had not been found to have thyroid disease. Two cases without antithyroid antibodies were heterozygous for the R450H mutation inTSHR. Thus, the prevalence of this mutation was 0.47% in the general population and 0.63% among those without antithyroid antibodies. Their serum TSH concentrations were higher than the average TSH concentration not only in subjects without antithyroid antibodies but also in those with antithyroid antibodies. The R450H mutation inTSHRis relatively common in the Japanese population and potentially affects thyroid function. The present study demonstrates that the SmartAmp2 method is useful to detect the R450H mutation inTSHR, which is one of the common causes of TSH resistance in the Japanese population.

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Dubey, Kavita, Suneha Goswami, Narendra Kumar, Ranjeet R. Kumar, and Shelly Praveen. "CHARACTERIZATION OF PUTATIVE HEAT SHOCK TRANSCRIPTION FACTOR (Hsf2) GENE INVOLVED IN REGULATING THE EXPRESSION OF HSP90 IN WHEAT UNDER TERMINAL HEAT STRESS." Journal of Experimental Biology and Agricultural Sciences 8, no. 6 (December 30, 2020): 765–73. http://dx.doi.org/10.18006/2020.8(6).765.773.

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Wheat, being staple food grain crop, is highly sensitive to heat stress. The effect is more evident under present threat of global climate change. Very limited information about heat-responsive transcription factor is known in wheat. A putative Heat Shock Factor (HSF) was cloned from wheat under HS. The gene was titled as Hsf2 (acc No. KP063542). The nucleotide sequence was found to be 1551 bp long with open reading frame (ORF) of 1125 bp (5’UTR of 213bp and 3’UTR of 213bp). The amino acid sequence showed the presence of HSF_ DNA binding domain having high degree of similarity (homology) with other HSF coding gene of related species (Aegilops tauschii with 95% homology and 100% homology with Chinese spring cultivar of Triticum aestivum). The protein was observed to be localized in the nucleus. Phosphorylation study showed the presence of phosphorylated threonine at seventeen sites in amino acid sequence. Expression analysis of Hsf2 showed maximum relative fold expression (2.04fold) in the leaves of HD2967 under HS, as compared to control. The transcript abundance was observed maximum in thermotolerant cv., as compared to thermo susceptible. Current study established positive correlation between the expression of Hsf2 and HSP90 under HS. Hsf2, being regulator of HSPs can be used as potential molecular marker for screening wheat germplasm for thermo tolerance. It will pave the way for the development of ‘climate-smart’ wheat crop.

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Qin, Beibei, Tiaoyi Xiao, Chunhua Ding, Yadong Deng, Zhao Lv, and Jianming Su. "Genome-Wide Identification and Expression Analysis of Potential Antiviral Tripartite Motif Proteins (TRIMs) in Grass Carp (Ctenopharyngodon idella)." Biology 10, no. 12 (December 1, 2021): 1252. http://dx.doi.org/10.3390/biology10121252.

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Tripartite motif proteins (TRIMs), especially B30.2 domain-containing TRIMs (TRIMs-B30.2), are increasingly well known for their antiviral immune functions in mammals, while antiviral TRIMs are far from being identified in teleosts. In the present study, we identified a total of 42 CiTRIMs from the genome of grass carp, Ctenopharyngodon idella, an important cultured teleost in China, based on hmmsearch and SMART analysis. Among these CiTRIMs, the gene loci of 37 CiTRIMs were located on different chromosomes and shared gene collinearities with homologous counterparts from human and zebrafish genomes. They possessed intact conserved RBCC or RB domain assemblies at their N-termini and eight different domains, including the B30.2 domain, at their C-termini. A total of 19 TRIMs-B30.2 were identified, and most of them were clustered into a large branch of CiTRIMs in the dendrogram. Tissue expression analysis showed that 42 CiTRIMs were universally expressed in various grass carp tissues. A total of 11 significantly differentially expressed CiTRIMs were found in two sets of grass carp transcriptomes during grass carp reovirus (GCRV) infection. Three of them, including Cibtr40, CiTRIM103 and CiTRIM109, which all belonged to TRIMs-B30.2, were associated with the type I interferon response during GCRV infection by weighted network co-expression and gene expression trend analyses, suggesting their involvement in antiviral immunity. These findings may offer useful information for understanding the structure, evolution, and function of TRIMs in teleosts and provide potential antiviral immune molecule markers for grass carp.

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Bellu, Emanuela, Giuseppe Garroni, Sara Cruciani, Francesca Balzano, Diletta Serra, Rosanna Satta, Maria Antonia Montesu, et al. "Smart Nanofibers with Natural Extracts Prevent Senescence Patterning in a Dynamic Cell Culture Model of Human Skin." Cells 9, no. 12 (November 24, 2020): 2530. http://dx.doi.org/10.3390/cells9122530.

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Natural cosmetic products have recently re-emerged as a novel tool able to counteract skin aging and skin related damages. In addition, recently achieved progress in nanomedicine opens a novel approach yielding from combination of modern nanotechnology with traditional treatment for innovative pharmacotherapeutics. In the present study, we investigated the antiaging effect of a pretreatment with Myrtus communis natural extract combined with a polycaprolactone nanofibrous scaffold (NanoPCL-M) on skin cell populations exposed to UV. We set up a novel model of skin on a bioreactor mimicking a crosstalk between keratinocytes, stem cells and fibroblasts, as in skin. Beta-galactosidase assay, indicating the amount of senescent cells, and viability assay, revealed that fibroblasts and stem cells pretreated with NanoPCL-M and then exposed to UV are superimposable to control cells, untreated and unexposed to UV damage. On the other hand, cells only exposed to UV stress, without NanoPCL-M pretreatment, exhibited a significantly higher yield of senescent elements. Keratinocyte-based 3D structures appeared disjointed after UV-stress, as compared to NanoPCL-M pretreated samples. Gene expression analysis performed on different senescence associated genes, revealed the activation of a molecular program of rejuvenation in stem cells pretreated with NanoPCL-M and then exposed to UV. Altogether, our results highlight a future translational application of NanoPCL-M to prevent skin aging.

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Du, Hongmei, Shah Zaman, Shuiqingqing Hu, and Shengquan Che. "Single-Molecule Long-Read Sequencing of Purslane (Portulaca oleracea) and Differential Gene Expression Related with Biosynthesis of Unsaturated Fatty Acids." Plants 10, no. 4 (March 30, 2021): 655. http://dx.doi.org/10.3390/plants10040655.

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This study aimed to obtain the full-length transcriptome of purslane (Portulaca oleracea); assorted plant samples were used for single-molecule real-time (SMRT) sequencing. Based on SMRT, functional annotation of transcripts, transcript factors (TFs) analysis, simple sequence repeat analysis and long non-coding RNAs (LncRNAs) prediction were accomplished. Total 15.33-GB reads were produced; with 9,350,222 subreads and the average length of subreads, 1640 bp was counted. With 99.99% accuracy, after clustering, 132,536 transcripts and 78,559 genes were detected. All unique SMART transcripts were annotated in seven functional databases. 4180 TFs (including transcript regulators) and 7289 LncRNAs were predicted. The results of RNA-seq were confirmed with qRT–PCR analysis. Illumina sequencing of leaves and roots of two purslane genotypes was carried out. Amounts of differential expression genes and related KEGG pathways were found. The expression profiles of related genes in the biosynthesis of unsaturated fatty acids pathway in leaves and roots of two genotypes of purslane were analyzed. Differential expression of genes in this pathway built the foundation of ω-3 fatty acid accumulation in different organs and genotypes of purslane. The aforementioned results provide sequence information and may be a valuable resource for whole-genome sequencing of purslane in the future.

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Zhou, Jian, Wanchun Wang, Pengxia Song, Lin Wang, Yali Han, Jingjing Guo, Zhen Hao, et al. "Structural predication and antigenic analysis of Toxoplasma gondii ROP20." Acta Parasitologica 63, no. 2 (June 26, 2018): 244–51. http://dx.doi.org/10.1515/ap-2018-0028.

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Abstract Toxoplasma gondii infects almost all the warm-blooded animals. ROP20 protein is expressed in the rhoptry of Toxoplasma gondii. In this study, the secondary structure of ROP20 was analyzed using SMART software. We constructed and analyzed the 3D model of ROP20 protein using SWISS-MODEL online procedure and Visual Molecular Dynamics (VMD) software. The structure analysis fully indicated that ROP20 protein is an important member of the ROP family. Furthermore, We used DNASTAR software and Epitope Database online service to analyze liner-B cell epitopes and T-cell epitopes of ROP20 protein. All the analysis results of ROP20 protein can provide positive information on treatment and vaccine for toxoplasmosis. Moreover, ROP20 gene was obtained from PCR, and a recombinant eukaryotic expression vector (pEGFP-C1-ROP20) was constructed in the following study. After restriction enzyme digestion, the constructed plasmid was transfected into HEK 293-T cells. The RT-PCR result indicated that the recombinant plasmid could transcribe successfully in HEK 293-T cell. The results of western blotting indicated the expressed proteins can be recognized by anti-STAg mouse sera.

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Magnani, Alessandra, Michaela Semeraro, Frédéric ADAM, Claire Booth, Loic Dupre, Emma C. Morris, Aurélie Gabrion, et al. "Long-Term Follow-up Study after Lentiviral Hematopoietic Stem/Progenitor Cell Gene Therapy for Wiskott - Aldrich Syndrome." Blood 138, Supplement 1 (November 5, 2021): 2934. http://dx.doi.org/10.1182/blood-2021-147697.

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Abstract Wiskott Aldrich syndrome (WAS) is a rare X-linked primary immunodeficiency associated with thrombocytopenia, eczema, infectious, autoimmune complications, and lymphomas. Patients lacking an HLA-matched donor may benefit from an alternative therapeutic approach based on the infusion of autologous gene corrected CD34+ cells. We previously reported a non-randomised, open-label, phase 1/2 clinical study applying a lentiviral vector based gene therapy (GT) protocol in 7 paediatric patients with severe WAS (score ≥ 3/5) (S. Hacein-Bey Abina et al, JAMA 2015). One patient died 7 months after GT because of pre-existing severe opportunistic infections, as reported. Two additional patients have been treated since that initial report, with a follow-up of at least 4 years. We here present a comprehensive long-term study on 8 patients with a follow-up from 4 to 9 years (median 7.6). The safety and efficacy of the approach is thoroughly investigated, with a particular focus on the correction of thrombocytopenia and auto-immunity. A stable engraftment of genetically and functionally corrected lymphoid and myeloid cells was reached in all patients, with no serious treatment-associated adverse events or concerning clonal expansion. Corrected lymphoid cells displayed a selective advantage over time with increasing vector copy number (VCN) level. In turn, this led to (i) sustained expression of WAS protein (WASp) in the patients' cells and (ii) clinical resolution of severe eczema and susceptibility to recurrent infections. In line with these results, T-cell function was restored after GT, as shown by the recovery of immune synapse assembly and the normalization of naïve T cell numbers. The T-cell compartment was also reconstituted in the patient treated at the age of 30 years, suggesting that GT for WAS is a treatment option in adult patients. In parallel with the robustness of T-cell reconstitution a normalized B-cell compartment was observed after GT, as shown in particular by increasing levels of WASp + switched memory B cells over time and the age-matched levels of KRECs. Five patients out of 8 were able to discontinue Ig replacement therapy while achieving normal post-vaccination antibody titers. Autoimmune disorders and bleeding episodes were significantly less frequent, despite only partial correction of the platelet compartment. After GT, a few autoimmune manifestations were observed: the persistence of lower extremity vasculitis (P2, very severe prior to GT), the new occurrence of nephrotic syndrome (P9), and the presence of anti-platelet antibodies (P2, P4, P7). The levels of circulating autoantibodies detected before GT (including ANA and vasculitis-related autoantibodies) normalized after treatment. Following GT, platelets were found to express sub-normal levels of WASp and to only partially augment their size. Platelet function studies indicated a partial correction of the platelet compartment achieved by GT, which may be sufficient to prevent occurrence of the hemorrhagic symptoms typical of WAS. Our results suggest that lentiviral GT provides sustained clinical benefits for patients with WAS. Overall clinical remission was observed in our patients despite very severe disease scores before GT. More efficacious and more reliable transduction protocols and conditioning regimen are likely to further improve outcomes, particularly with regard to platelet recovery, where the advantages of intrinsic correction are less apparent. Disclosures Booth: Orchard Therapeutics: Consultancy, Honoraria; SOBI: Consultancy, Honoraria; Takeda: Honoraria; GSK: Honoraria; Rocket Pharmaceuticals, Inc.: Consultancy. Thrasher: Orchard Therapeutics: Consultancy, Current equity holder in publicly-traded company, Membership on an entity's Board of Directors or advisory committees; Generation bio: Consultancy, Current equity holder in publicly-traded company, Membership on an entity's Board of Directors or advisory committees; 4Bio Capital: Consultancy, Membership on an entity's Board of Directors or advisory committees; Rocket Pharmaceuticals: Consultancy, Membership on an entity's Board of Directors or advisory committees. Cavazzana: Smart Immune: Other: co-founder.

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Ida, Hisashi, Sharon A. Boylan, Andrea L. Weigel, and Leonard M. Hjelmeland. "Age-related changes in the transcriptional profile of mouse RPE/choroid." Physiological Genomics 15, no. 3 (November 11, 2003): 258–62. http://dx.doi.org/10.1152/physiolgenomics.00126.2003.

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To evaluate the age-related changes in gene expression occurring in the complex of retinal pigmented epithelium, Bruch’s membrane, and choroid (RPE/choroid), we examined the gene expression profiles of young adult (2 mo) and old (24 mo) male C57BL/6 mice. cDNA probe sets from individual animals were synthesized using total RNA isolated from the RPE/choroid of each animal. Probes were amplified using the Clontech SMART system, radioactively labeled, and hybridized to two different Clontech Atlas mouse cDNA arrays. From each age group, three independent triplicates were hybridized to the arrays. Statistical analyses were performed using the Significance Analysis of Microarrays program (SAM version 1.13; Stanford University). Selected array results were confirmed by semi-quantitative RT-PCR analysis. Of 2,340 genes represented on the arrays, ∼60% were expressed in young and/or old mouse RPE/choroid. A moderate fraction (12%) of all expressed genes exhibited a statistically significant change in expression with age. Of these 150 genes, all but two, HMG14 and carboxypeptidase E, were upregulated with age. Many of these upregulated genes can be grouped into several broad functional categories: immune response, proteases and protease inhibitors, stress response, and neovascularization. RT-PCR results from six of six genes examined confirmed the differential change in expression with age of these genes. Our study provides likely candidate genes to further study their role in the development of age-related macular degeneration and other aging diseases affecting the RPE/choroid.

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Mazzurana, Luca, Paulo Czarnewski, Viktor Jonsson, Leif Wigge, Markus Ringnér, Teresa C. Williams, Avinash Ravindran, et al. "Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing." Cell Research 31, no. 5 (January 8, 2021): 554–68. http://dx.doi.org/10.1038/s41422-020-00445-x.

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AbstractThe impact of the microenvironment on innate lymphoid cell (ILC)-mediated immunity in humans remains largely unknown. Here we used full-length Smart-seq2 single-cell RNA-sequencing to unravel tissue-specific transcriptional profiles and heterogeneity of CD127+ ILCs across four human tissues. Correlation analysis identified gene modules characterizing the migratory properties of tonsil and blood ILCs, and signatures of tissue-residency, activation and modified metabolism in colon and lung ILCs. Trajectory analysis revealed potential differentiation pathways from circulating and tissue-resident naïve ILCs to a spectrum of mature ILC subsets. In the lung we identified both CRTH2+ and CRTH2− ILC2 with lung-specific signatures, which could be recapitulated by alarmin-exposure of circulating ILC2. Finally, we describe unique TCR-V(D)J-rearrangement patterns of blood ILC1-like cells, revealing a subset of potentially immature ILCs with TCR-δ rearrangement. Our study provides a useful resource for in-depth understanding of ILC-mediated immunity in humans, with implications for disease.

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Liu, Fei, Xiao-Long Wei, Hao Li, Ji-Fu Wei, Yong-Qing Wang, and Xiao-Jian Gong. "Molecular Evolution of the Vertebrate FK506 Binding Protein 25." International Journal of Genomics 2014 (2014): 1–9. http://dx.doi.org/10.1155/2014/402603.

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FK506 binding proteins (FKBPs) belong to immunophilins with peptidyl-prolyl isomerases (PPIases) activity. FKBP25 (also known as FKBP3) is one of the nuclear DNA-binding proteins in the FKBPs family, which plays an important role in regulating transcription and chromatin structure. The calculation of nonsynonymous and synonymous substitution rates suggested that FKBP25 undergoes purifying selection throughout the whole vertebrate evolution. Moreover, the result of site-specific tests showed that no sites were detected under positive selection. Only one PPIase domain was detected by searching FKBP25 sequences at Pfam and SMART domain databases. Mammalian FKBP25 possess exon-intron conservation, although conservation in the whole vertebrate lineage is incomplete. The result of this study suggests that the purifying selection triggers FKBP25 evolutionary history, which allows us to discover the complete role of the PPIase domain in the interaction between FKBP25 and nuclear proteins. Moreover, intron alterations during FKBP25 evolution that regulate gene splicing may be involved in the purifying selection.

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Abdi, Jafar, Menad Nait Amar, Masoud Hadipoor, Thomas Gentzis, Abdolhossein Hemmati-Sarapardeh, and Mehdi Ostadhassan. "Modeling of Brine/CO2/Mineral Wettability Using Gene Expression Programming (GEP): Application to Carbon Geo-Sequestration." Minerals 12, no. 6 (June 15, 2022): 760. http://dx.doi.org/10.3390/min12060760.

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Carbon geo-sequestration (CGS), as a well-known procedure, is employed to reduce/store greenhouse gases. Wettability behavior is one of the important parameters in the geological CO2 sequestration process. Few models have been reported for characterizing the contact angle of the brine/CO2/mineral system at different environmental conditions. In this study, a smart machine learning model, namely Gene Expression Programming (GEP), was implemented to model the wettability behavior in a ternary system of CO2, brine, and mineral under different operating conditions, including salinity, pressure, and temperature. The presented models provided an accurate estimation for the receding, static, and advancing contact angles of brine/CO2 on various minerals, such as calcite, feldspar, mica, and quartz. A total of 630 experimental data points were utilized for establishing the correlations. Both statistical evaluation and graphical analyses were performed to show the reliability and performance of the developed models. The results showed that the implemented GEP model accurately predicted the wettability behavior under various operating conditions and a few data points were detected as probably doubtful. The average absolute percent relative error (AAPRE) of the models proposed for calcite, feldspar, mica, and quartz were obtained as 5.66%, 1.56%, 14.44%, and 13.93%, respectively, which confirm the accurate performance of the GEP algorithm. Finally, the investigation of sensitivity analysis indicated that salinity and pressure had the utmost influence on contact angles of brine/CO2 on a range of different minerals. In addition, the effect of the accurate estimation of wettability on CO2 column height for CO2 sequestration was illustrated. According to the impact of wettability on the residual and structural trapping mechanisms during the geo-sequestration of the carbon process, the outcomes of the GEP model can be beneficial for the precise prediction of the capacity of these mechanisms.

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Romanova, Yulia A., and Elena V. Levina. "«Agriculture 4.0» – a project of the future or a platform for responding to major challenges and threats to national security." Market economy problems, no. 3 (2020): 84–94. http://dx.doi.org/10.33051/2500-2325-2020-3-84-94.

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The purpose of the article is to study «Agriculture 4.0» as a project of the future or a platform for responding to major challenges and threats to national security. The methodology of this study was based on the methods of analysis and synthesis, comparison, generalization and systematization, as well as the structural-logical approach, analysis of open empirical statistical data and the graphical method. Results. The article examines the theoretical and practical foundations of the directions of digital development of agriculture. The necessity of transformation of modern techniques and technologies for managing the development of agriculture on the principles of sustainable development into a qualitatively new type – «Agriculture 4.0», digital economy or smart agriculture is substantiated. This paper focuses on four main technologies: the Internet of Things, blockchain, big data and artificial intelligence. Conclusions. The Agriculture 4.0 project is comprised of a variety of existing or emerging technologies such as robotics, nanotechnology, synthetic protein, cell agriculture, gene editing technology, artificial intelligence, blockchain and machine learning, which could have overarching impact on future agricultural and food systems. It can ensure the creation of economic, environmental and social benefits and be a response to challenges and threats to national security.

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Islamov, Rustem I., Michail E. Sokolov, Zufar Z. Safiullov, Maria A. Davleeva, Ravil R. Garifulin, Farid V. Bashirov, Ilnur I. Salafutdinov, et al. "A Simple, Safe and Effective Approach for Personalized Precision Ex Vivo Gene Therapy Based on Autoinfusion of Gene-Modified Leucoconcentrate (GML) Prepared from Routine Unit of Patient's Peripheral Blood." Blood 136, Supplement 1 (November 5, 2020): 31. http://dx.doi.org/10.1182/blood-2020-133805.

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Nowadays gene and cell therapy become the basic methods in regenerative medicine. However only few gene and cell products are currently approved for clinical usage. Biosafety problems, complexity of cell and gene technologies and high cost of manufacturing are the main reasons for the slow introduction of such approaches in practical medicine. Treatment of hereditary diseases of the immune system based on the correction of the mutant gene by delivering functional recombinant gene into WBC is the first successfully employed in the clinical practice approach of cell-mediated or ex vivo gene therapy. Earlier we have reported the strategy of the cell-mediated gene therapy based on umbilical cord blood mononuclear cells transduced with adenoviral vectors carrying recombinant genes encoding neurotrophic factors for treatment neurodegenerative diseases, neurotrauma and stroke. Significant disadvantage of this method is the usage of the umbilical cord blood mononuclear cells as a cell carrier for the therapeutic genes. Considering immunodeficiency treatment and our own data we developed a new approach of recombinant gene delivery for personalized ex vivo gene therapy. The method is based on autoinfusion of patient's WBC transduced with recombinant therapeutic genes for correction of certain pathological conditions. In the present study for the first time the human gene-modified leucoconcentrate (GML) producing recombinant reporter gene encoding green fluorescent protein (GFP) was obtained without culturing WBC in vitro. The routine unit of peripheral blood (450 ml) was collected into the plastic blood bag and the leucocyte- and platelet-rich concentrates (50 ml) were obtained by standard method using Macopress Smart (Macopharma, France). Afterwards the equal volume of hydroxyethyl starch 6% was added into the plastic blood bag which was centrifuged (DP-2065 R PLUS, Centrifugal Presvac RV; Presvac, Buenos Aires, Argentina) at 350 rpm for 10 min at 10°C. The obtained supernatant was transferred into the new plastic blood bag using manual plasma extractor FK-01 (Leadcore, Russia) and 200 ml of saline was added into the bag which was centrifuged at 1300 rpm for 10 min at 10°C and the supernatant was expressed out of the bag so that the remaining solution in the bag (30 ml) contained leucoconcentrate (WBC - 45.56 ± 23.93 × 106/ml and RBC - 1.76 ± 3.33 × 109/ml). Transduction of WBC with chimeric adenoviral vector (Ad5/35) carrying GFP gene was performed in the plastic bag with MOI 5 according to the count of WBC in the leucoconcentrate. After transduction for 12 hours, 200 ml of saline was added to the bag with leucoconcentrate, the mixture was centrifuged at 1000 rpm for 10 min at 10°C and the supernatant was squeezed out of the bag. The remained in the bag solution (30 ml) was considered as gene-modified leucoconcentrate carrying GFP gen (WBC - 22.63 ± 8.90 × 106/ml and RBC - 1.77 ± 1.21 × 109/ml). For in vitro study of GFP gene expression the samples of GML-GFP were cultivated for 60 hours after GML-GFP preparation. Fluorescent microscopy in the cytoplasm of the transduced WBC showed specific intensive green fluorescence. Flow cytometry analysis demonstrated that 2.5% of WBC from the GML-GFP efficiently expressed GFP. Thus leucoconcentrate after 72 h of transduction with Ad5/35-GFP with MOI 5 resulted in 2.5% of the GFP-positive cells. Thus the results of this study represent a simple, safe and effective approach for preparation of GML for personalized ex vivo gene therapy aimed at temporary production of the specific recombinant biologically active molecules for pathogenetic therapy of the varied nosological form, such as trauma, ischemic, degenerative, autoimmune, infection and other diseases. This study was supported by the grant of Russian Science Foundation 19-75-10030. Disclosures No relevant conflicts of interest to declare.

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Shen, Ying, Yuandong Feng, Hongli Chen, Yachun Jia, Yue Peng, Ru Zhang, Yun Yang, et al. "Silencing Long Non-Coding RNA ST3GAL6-AS1 Inhibits Adhesion and Migration of Myeloma Cells in Vitro." Blood 132, Supplement 1 (November 29, 2018): 4470. http://dx.doi.org/10.1182/blood-2018-99-114660.

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Abstract Introduction: Multiple myeloma (MM) is a fatal B-cell malignancy characterized by abnormal proliferation of plasma cells (PCs) in bone marrow (BM). Despite the remarkable improvements have been done in knowledge on the pathobiology of MM, treatment and patients care, MM is still an incurable disease. Long non-coding RNAs (lncRNAs) are a new sort of noncoding RNA longer than 200 nucleotides and without the function of translating into canonical functional proteins. Increasing evidence suggests that lncRNAs have huge impact on adjusting gene expression through the processes of transcription and post-transcription regulation, genomic imprinting, and chromatin modification. We have validated several dysregulated lncRNAs in MM by microarray and bioinformatic analysis. Among them, we focused on the function and mechanism of ST3 beta-galactoside alpha-2,3-sialyltransferase 6 antisense RNA 1(ST3GAL6-AS1), which was upregulated markedly in MM patients. In our previous study, we verified the upregulation level and the co-expression relationship of ST3GAL6-AS1 and ST3 beta-galactoside alpha-2,3-sialyltransferase 6 (ST3GAL6) in bone marrow samples from MM patients. Methods: MM cell lines MM1.S and RPMI-8226 were confirmed to have high expression levels of ST3GAL6-AS1 at RNA level compared with healthy controls. Knockdown of ST3GAL6-AS1 was conducted in MM1.S and RPMI-8226 cells using lncRNA Smart Silencer from Ribobio (Guangzhou, China). ST3GAL6-AS1 knockdown and ST3GAL6 expression were confirmed by quantitative real-time PCR (qRT-PCR) at RNA level. We next evaluated the effects of ST3GAL6-AS1 knockdown on MM cell adhesion to human umbilical vein endothelial cell (HUVEC), fibronectin and collagen I coated plates after MM1.S and RPMI-8226 was labeled by CFSE. Migration and invasion to complete medium were assessed using transwell plates comparing ST3GAL6-AS1 knockdown cells to NC controls. Matrigel matrix was coated at transwell plates in invasion analysis. Cell count in adhesion analysis was conducted by Image J software, while migration and invasion analysis were evaluated by flow cytometer. Results: ST3GAL6-AS1 (Genebank number: NR_046683.1) was a 769bp antisense RNA, which located in chromosome 3. Its expression level was decreased dramatically after transfection of ST3GAL6-AS1 smart silencer or control siRNA into MM1.S and RPMI-8226 cells (Figure 1A). There was a significant reduction in the ability of knockdown MM1.S and RPMI-8226 cells to adhere to HUVEC, fibronectin and collagen I in vitro compared to NC controls (Figure 1B). Migration and invasion ability of MM cells transfected with lncRNA smart silencer in response to complete medium were also decreased obviously (Figure 1C). However, there was no significant difference in the ability of proliferation and apoptosis between ST3GAL6-AS1 knockdown group and NC controls. Furthermore, the expression level of ST3GAL6 was decreased in ST3GAL6-AS1 knockdown MM cells (Figure 1D). Conclusions: Knockdown of ST3GAL6-AS1 in MM cells significantly inhibits adhesion, migration and invasion in vitro, indicating that ST3GAL6-AS1 may play an important role in the malignant behavior of MM cells. The co-expression between ST3GAL6-AS1 and gene ST3GAL6 has been demonstrated in our previous study, which was further confirmed in present study. Researches are ongoing to address the potential mechanism among them in MM. Figure 1. Figure 1. Disclosures No relevant conflicts of interest to declare.

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Poddubskaya, Elena, Anton Buzdin, Andrew Garazha, Maxim Sorokin, Alex Glusker, Alexey Aleshin, Daria Allina, et al. "Oncobox, gene expression-based second opinion system for predicting response to treatment in advanced solid tumors." Journal of Clinical Oncology 37, no. 15_suppl (May 20, 2019): e13143-e13143. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e13143.

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e13143 Background: Anticancer Targeted Drugs (ATDs) specifically target one or a few types of tumor-related molecules in a cell. More than two hundred of ATDs were approved worldwide. They have different mechanisms of action and are effective for different cohorts of patients. However, many individual cases remain poorly responsive and it is of great importance to identify predictive markers of ATD efficacy. Our aim was to develop a platform enabling smart selection of the most efficient ATD therapies. Methods: We generated a second-opinion platform for clinical oncologists termed Oncobox. It is based on the analysis of gene expression profile of a cancer sample in comparison with the corresponding normal tissue biosamples in order to personalize selection of targeted drugs for individual cancer patients. Based on RNA-seq gene expression data, pathway activation levels are calculated and along with the concentrations of molecular target genes products used as predictors of tumor response to ATDs. Results: The Oncobox method was tested first on the retrospective samples of advanced tumors: gastric, renal cell, ovarian and colorectal cancers, thus showing ROC AUC values > 0.7. In currently ongoing prospective trial for advanced solid tumor patients, the Oncobox tests were completed for 239 patients, primary feedback information received for 144 patients. 25 patients (17%) died before prescription of the therapy, 19% received palliative care treatment, 39% received Oncobox-recommended therapies and 25% received other therapies (February 2019). Tumor responses were estimated for 30 patients (breast, colorectal, ovarian and other cancers) receiving therapies, with disease control rate of 71% for Oncobox-recommended ATDs (Bevacizumab, Crizotinib, Trastuzumab and others) and 44% for other therapies. Our results also suggest that cancer metastases and primary tumors may have different gene expression, molecular pathway activation and drug scoring patterns, thus pointing to the importance of testing multiple tumor sites. Conclusions: Our study suggests that profound analysis of gene expression profiles of tumor tissues may be useful for ATDs treatment of advanced and metastatic cancers. Clinical trial information: NCT03724097.

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Karlowsky, James A., Sibylle H. Lob, Krystyna M. Kazmierczak, Robert E. Badal, Katherine Young, Mary R. Motyl, and Daniel F. Sahm. "In Vitro Activity of Imipenem against Carbapenemase-Positive Enterobacteriaceae Isolates Collected by the SMART Global Surveillance Program from 2008 to 2014." Journal of Clinical Microbiology 55, no. 6 (March 15, 2017): 1638–49. http://dx.doi.org/10.1128/jcm.02316-16.

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ABSTRACT The Study for Monitoring Antimicrobial Resistance Trends (SMART) global surveillance program collected 103,960 isolates of Enterobacteriaceae from 2008 to 2014. From this isolate collection, all ertapenem-nonsusceptible isolates (MIC, ≥1 μg/ml; n = 3,428) and 9,371 isolates of Escherichia coli , Klebsiella pneumoniae , Klebsiella oxytoca , and Proteus mirabilis with an ertapenem-susceptible extended-spectrum-β-lactamase (ESBL)-positive phenotype were assessed for the presence of common carbapenemase genes using a Check-MDR CT101 microarray (Check-Points, Wageningen, the Netherlands) and published multiplex PCR assays. Testing identified 1,493 isolates that harbored a carbapenemase gene (1,485 ertapenem-nonsusceptible isolates and 8 ertapenem-susceptible ESBL-positive isolates) and accounted for 1.4% (1,493/103,960) of all isolates of Enterobacteriaceae . The most frequently identified carbapenemase genes were the KPC ( n = 794), OXA-48-like ( n = 300), and NDM ( n = 290) genes. Carbapenemase genes were most frequently identified in Klebsiella pneumoniae ( n = 1,127), Escherichia coli ( n = 149), and Enterobacter cloacae ( n = 110). Among the carbapenemase-positive isolates, 66.7% (2/3), 37.0% (111/300), 20.0% (8/40), 3.3% (3/92), 2.3% (18/794), and 0% (0/290) of the isolates with genes for GES, OXA-48-like, IMP, VIM, KPC, and NDM, respectively, were susceptible to imipenem (MIC, ≤1 μg/ml). Isolates that tested as susceptible to imipenem were not uncommon among carbapenemase-positive isolates (9.4%, 141/1,493) and most frequently carried OXA-48-like enzymes (78.7%; 111/141); however, overall, these isolates remained rare (0.1%, 141/103,960). The practice of screening clinical isolates of Enterobacteriaceae that test as susceptible to carbapenems in vitro for the presence of carbapenemase genes remains controversial and requires further study.

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Xue, Yunping, Pengfei Xu, Sujuan Xu, Kai Xue, Lingling Xu, Jie Chen, Juan Xu, Xiaoyan Shi, Qian Li, and Lin Gu. "Peptidomic Analysis of Endometrial Tissue from Patients with Ovarian Endometriosis." Cellular Physiology and Biochemistry 47, no. 1 (2018): 107–18. http://dx.doi.org/10.1159/000489753.

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Background/Aims: Ovarian endometriosis (OvE) is ovarian cyst that is lined with endometrial tissue. They are found in 17–44% of women with endometriosis. Their clinical manifestations include pelvic pain, dysmenorrhea, dyspareunia, and infertility. Although the incidence of OvE has increased yearly, the exact pathogenesis of OvE is still unclear. We used peptidomics, an emerging branch of proteomics, to identify differentially expressed peptides in order to determine the possible roles of these peptides in the pathogenesis of OvE. Methods: The ectopic and eutopic endometria of OvE were used to extract peptides with 10-kDa molecular weight cutoff filters, and the peptide precursor proteins were then identified with PEAKS software, followed by quantification with the TMT labeling method and subsequent analysis by liquid chromatography-tandem mass spectrometry. Gene ontology (GO) analysis, pathway analysis, SMART, and SABLE were used to study the possible functions of these peptide according to their precursor proteins’ function. The effects of peptides derived from VCAM-1 (PDFV) on endometrial stromal cell (ESC) migration and invasion were examined with wound healing assays and Transwell assays and the expression of E-cadherin was detected by western blotting. Results: A total of 491 peptides were identified with abundant differences between the two groups of samples (p < 0.05, and absolute fold change ≥ 2). SMART and SABLE database showed that 42 of the 491 peptides were located in the conserved structural domains of their protein precursors and contained secondary structure and, among them, 2 peptides’ precursor proteins were associated with the cell proliferation. Additionally, 5 peptides’ precursor proteins were associated with endometriosis. Our study confirmed that PDFV promoted ESC migration and invasion and reduced E-cadherin expression (p < 0.05). Conclusion: PDFV and its precursor protein VCAM-1 may be involved in the process of OvE formation by reducing the expression of E-cadherin. The peptidomics analysis provides new insight for future studies of the mechanisms of OvE development.

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Wang, Sheliang, Hao Zhang, Lei Shi, Fangsen Xu, and Guangda Ding. "Genome-Wide Dissection of the CRF Gene Family in Brassica napus Indicates that BnaCRF8s Specifically Regulate Root Architecture and Phosphate Homeostasis against Phosphate Fluctuation in Plants." International Journal of Molecular Sciences 21, no. 10 (May 22, 2020): 3660. http://dx.doi.org/10.3390/ijms21103660.

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Phosphorus (P) is an essential macronutrient required for plant growth and development. The involvement of cytokinin response factors (CRFs) in phosphate (Pi) homeostasis and lateral root (LR) initiation in Arabidopsis has been revealed. However, little is known in oil crops. Here, we performed genome-wide dissection of the CRF family in Brassica napus to identify 44 members, which were evolutionally classified into 6 subgroups. Among them, four BnaCRF8 genes were strongly upregulated by P deprivation, and were selected to be further investigated. Time course qRT-PCR analyses showed that four BnaCRF8 genes were enhanced dramatically after 12 h of P stress. Analyses of the subcellular localization in tobacco leaves indicated that BnaA7.CRF8 and BnaC2.CRF8 were localized in the nucleus. The expression of BnaCRF8 genes had constant negative effects on primary root growth and LR initiation and growth, and it reduced Pi acquisition and plant growth in Arabidopsis. Moreover, the expression of Pi homeostasis-related genes was modulated in BnaA7.CRF8 overexpression plants. These results suggest that BnaCRF8 genes might negatively regulate root architecture and plant growth through transcriptional modification of Pi homeostasis-related components. Overall, this study suggests that upregulation of BnaCRF8 genes might be a smart adaptive strategy to cope with continuous Pi deficiency in the environment.

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Lee, Yong Gyun, Mi-Young Song, Hwangeui Cho, Jong Sik Jin, Byung-Hyun Park, and Eun Ju Bae. "Limonium tetragonum Promotes Running Endurance in Mice through Mitochondrial Biogenesis and Oxidative Fiber Formation." Nutrients 14, no. 19 (September 21, 2022): 3904. http://dx.doi.org/10.3390/nu14193904.

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The purpose of this study was to examine whether Limonium tetragonum, cultivated in a smart-farming system with LED lamps, could increase exercise capacity in mice. C57BL/6 male mice were orally administered vehicle or Limonium tetragonum water extract (LTE), either 30 or 100 mg/kg, and were subjected to moderate intensity treadmill exercise for 4 weeks. Running distance markedly increased in the LTE group (100 mg/kg) by 80 ± 4% compared to the vehicle group, which was accompanied by a higher proportion of oxidative fibers (6 ± 6% vs. 10 ± 4%). Mitochondrial DNA content and gene expressions related to mitochondrial biogenesis were significantly increased in LTE-supplemented gastrocnemius muscles. At the molecular level, the expression of PGC-1α, a master regulator of fast-to-slow fiber-type transition, was increased downstream of the PKA/CREB signaling pathway. LTE induction of the PKA/CREB signaling pathway was also observed in C2C12 cells, which was effectively suppressed by PKA inhibitors H89 and Rp-cAMP. Altogether, these findings indicate that LTE treatment enhanced endurance exercise capacity via an improvement in mitochondrial biosynthesis and the increases in the formation of oxidative slow-twitch fibers. Future study is warranted to validate the exercise-enhancing effect of LTE in the human.

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Ghosh, Abhrajyoti, Krishanu Chakrabarti, and Dhrubajyoti Chattopadhyay. "Cloning of feather-degrading minor extracellular protease from Bacillus cereus DCUW: dissection of the structural domains." Microbiology 155, no. 6 (June 1, 2009): 2049–57. http://dx.doi.org/10.1099/mic.0.027573-0.

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Bacterial extracellular proteases play an important role in cell survival and cell–cell communication. A high-molecular-mass minor extracellular protease (Vpr) from a feather-degrading bacterium, Bacillus cereus DCUW, has been reported by our laboratory. In the present study, we cloned and expressed Vpr in Escherichia coli. Complete nucleotide sequencing of this gene predicted that the protease is a member of the serine protease family, and smart domain analysis revealed that the protease consists of an N-terminal signal sequence for secretion, a subtilisin_N sequence that is a signature for N-terminal processing, a catalytic S_8 peptidase domain, and finally a long C-terminal protease-associated (PA) region containing nine intrinsically disordered subdomains. Four truncated constructs of the Vpr protease were cloned and expressed in E. coli. We found that the catalytic domain (amino acid residues 172–583) is sufficient for protease activity. Maturation of the Vpr protease needed both N-terminal and C-terminal processing. We have demonstrated that the oligomerization property is associated with the C-terminal protease-associated domain and also shown that the substrate-binding specificity to raw feather resides in this domain.

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Jiang, Z., E. Gutierrez, H. Ming, B. Foster, L. Gatenby, C. Mak, C. Pinto, and K. Bondioli. "31 Effect of vitrification on global gene expression dynamics of bovine elongating embryos." Reproduction, Fertility and Development 32, no. 2 (2020): 141. http://dx.doi.org/10.1071/rdv32n2ab31.

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The ability to cryopreserve gametes and embryos has been a valuable tool for reproductive management in all mammalian species, especially livestock. Embryo vitrification involves exposure to high concentrations of cryoprotectants and osmotic stress during cooling and warming. These factors have to affect gene expression. The elongating embryo is a stage of embryo development that can be recovered noninvasively in the cow on day (D) 14 and represents a critical stage of development when many embryos die. In this study, we aimed to evaluate the effect of vitrification on the transcriptome dynamics of D14 embryos by RNA sequencing (RNA-seq). Invitro blastocyst-stage embryos were vitrified by exposure to dimethyl sulfoxide and ethylene glycol solution, followed by placing on Cryo Loks and plunging in liquid nitrogen. After warming, embryos were loaded into straws and transferred into eight synchronized recipients, four cows received nonvitrified embryos and four cows received vitrified embryos (20 embryos per cow). Embryo flushing yielded 12 nonvitrified and 9 vitrified viable D14 embryos. Whole embryos (six nonvitrified and two vitrified embryos) or isolated trophectoderm (TE; four nonvitrified and seven vitrified) were processed for RNA-seq. The Smart-sEqn 2 protocol was followed to prepare RNA-seq libraries. Sequencing reads were prefiltered and aligned to the bovine genome, and gene expression values were calculated as fragments per kilobase of transcript per million mapped reads. Genes were deemed differentially expressed between treatments if they showed a false discovery rate P-value<0.05 and fold-change >2. Ingenuity pathway analysis was used to reveal gene ontology and pathways. Expression of 927 genes was changed in D14 embryos as a result of vitrification, with 782 and 145 genes upregulated and downregulated, respectively. In TE, vitrification resulted in 4096 and 280 upregulated or downregulated genes, respectively. Several pathways were upregulated by vitrification in both whole embryos and TE, including epithelial adherens junctions, sirtuin signalling, germ cell-Sertoli cell junction, ATM signalling, nucleotide excision repair, and protein ubiquitination pathways. Downregulated pathways included EIF2 signalling, oxidative phosphorylation, mitochondrial dysfunction, regulation of eIF4 and p70S6K signalling, mammalian target of rapamycin signalling, sirtuin singling, and nucleotide excision repair pathways. In addition, we found 671 and 61 genes upregulated and downregulated in both vitrified whole embryos and TE. Mitochondrial dysfunction and oxidative phosphorylation signalling were upregulated, whereas epithelial adherens junction and sirtuin signalling were downregulated, suggesting mitochondrial function and energy production were impaired in TE after vitrification. Our analysis identified specific pathways and implicated specific genes affected by cryopreservation and potentially affecting embryo developmental competence.

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Journal articles on the topic 'Gene SMART study'

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