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1
Kornieieva, M. O., P. I. Vakulenko, L. S. Andrieieva, and S. M. Tymchychyn. "The potential of adaptivity of sugar beet sterility maintainers to regulated abiotic factors." Faktori eksperimental'noi evolucii organizmiv 27 (September 1, 2020): 107–12. http://dx.doi.org/10.7124/feeo.v27.1311.
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Aim. To determine the expression of the adaptive ability of sterility maintainers of sugar beet under different combination of abiotic factors. Methods. Testing breeding materials against agricultural backgrounds with different combinations of controlled abiotic factors: Normal and Large Growing Space; Normal and Rich Mineral Nutrition Background. Results. Genotypes had a specific interaction with a specific background. The range of variation of the effects of the general adaptive ability of the lines on the yield was -2.9 ... + 3.4 and sugar content -0.6…+0.6. With the increased background of mineral fertilizers and different areas of nutrition, respectively, 11 and 9 sources of valuable genes were selected. The elevated mineral fertilizer background over the usual feeding area was the background that distinguished specific combinations with high SAA effects: Ot1/Ot4 (+2.5), Ot3/Ot4 (+0.9), Ot4/Ot2 (+0.9) and Ot6/Ot5 (0.8). In the extended area, the lines Ot1 and Ot2 combined well with the line Ot 4 (respectively +1.1 and +0.9). Conclusions. O-type lines are characterized by a specific response to the controlled abiotic factors. O-type 4 and O-type 6 lines can be attributed to intensive type. Stable on both grounds include the Ot3 line. For the collection of sugar on the ordinary background of mineral fertilizers GAA were preferred lines Ot6 and Ot4, and on the higher - respectively lines Ot6, Ot3 and Ot4. High differential ability of selective with backgrounds with regulated abiotic factors has been established.
Keywords: sterility maintainers, yield, sugar content, general and specific adaptive ability, the coefficient of plasticity.
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BORDINI, Fábio Luis, Marcelo Alves COSTA, Josiane MEDINA-PAPST, Thiago Viana CAMATA, and Inara MARQUES. "Efeito da oclusão temporal na ação de ataque sobre a tomada de decisão defensiva na modalidade de voleibol." Revista Brasileira de Educação Física e Esporte 29, no. 1 (March 2015): 107–18. http://dx.doi.org/10.1590/1807-55092015000100107.
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O presente estudo analisou o efeito da oclusão temporal na cortada do voleibol sobre a tomada de decisão defensiva em atletas com diferentes níveis de experiência. Os participantes foram divididos em três grupos: adulto (GAD; n = 16), infanto/mirim (GIM; n =16) e adulto novato (GNO; n = 16). Imagens da finalização de jogadas de ataque realizadas por quatro atletas foram editadas em cinco diferentes momentos: (OT1) a 399 ms (12 quadros) antes do contato do atacante com a bola; (OT2) a 266 ms (oito quadros) antes; (OT3) a 133 ms (quatro quadros) antes; (OT4) no momento do contato atacante/bola e; (OT5) a 133 ms (quatro quadros) após o contato do atacante com a bola. Ao assistirem os vídeos editados, os participantes deveriam informar o local de aterrissagem da bola seguido da confiança com a qual emitiam suas respostas. Foi mensurada a precisão na predição da trajetória da bola (acerto/erro) e a confiança da resposta (escala Likert 1-5). Quanto à frequência de acertos, o grupo GAD (X = 63,67 ± 10,38%) apresentou maior frequência de acertos que GIM (X = 55,46 ± 10,17%) em OT2 (p = 0,001). A frequência de acertos de GAD (X = 79,29 ± 10,38%) também foi maior que a de GNO (X = 71,87 ± 10,43%) em OT3 (p = 0,012). As condições mostraram-se diferentes entre si (Bonferroni's p < 0,005), com a frequência de acertos aumentando de OT1 (X = 36,06 ± 12,44%) à OT5 (X = 98,17 ± 4,81%). Para confiança, GAD e GIM apresentaram-se mais confiantes que GNO (Bonferroni's p < 0,016) em OT1, OT2, OT3. Novamente, as condições diferiram entre si (Bonferroni's p < 0,005), com os grupos mostrando-se mais confiantes em OT5. Concluiu-se que, independente da experiência, os grupos se mostraram capazes de predizer a localização de aterrissagem da bola. Contudo, grupos com maior experiência mostraram-se superior quanto à sua capacidade antecipatória.
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Zhang, Meijia, Haiyan Hong, Bo Zhou, Shiying Jin, Chao Wang, Maoyong Fu, Songbo Wang, and Guoliang Xia. "The expression of atrial natriuretic peptide in the oviduct and its functions in pig spermatozoa." Journal of Endocrinology 189, no. 3 (June 2006): 493–507. http://dx.doi.org/10.1677/joe.1.06483.
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Locally synthesized atrial natriuretic peptide (ANP) and its receptors have been found in reproductive tissues of various mammals, and play an important role in the acrosome reaction of human sperm. The objective of the present study was to examine the expression of ANP and its receptors in pig spermatozoa and oviduct, and the effect of ANP on pig spermatozoa function. The expression of ANP and its receptors was analyzed by RT-PCR. Only natriuretic peptide receptors-A (NPRA) mRNA was detected in fresh sperm. While the levels of natriuretic peptide receptors-C (NPRC) mRNA were low with no obvious change among different oviductal phases, the levels of ANP mRNA were high in oviduct(OT)1 , OT3 and OT5, but were very low in OT2. On the other hand, the levels of NPRA mRNA were low in OT1 and OT2, increased in OT3 and reached a maximum in OT4 and OT5. Western blot analysis revealed that the level of ANP was high in OT1, decreased in OT2 and OT3, and arrived at the nadir in OT4 and OT5. The effect of ANP on spermatozoa function was studied by the acrosome reaction and IVF. Incubation with ANP for 1 h significantly induced acrosome reaction of preincubated spermatozoa, and maximal response of acrosome reaction (34.1 ± 2.3%) was achieved at 1 nM ANP treatment. Both C-ANP-(4–23), a selective ligand of NPRC, and caffeine had no effect on the acrosome reaction. The stimulatory effect of ANP on acrosome reaction could be mimicked by the permeable cGMP analog, 8-Br-cGMP. ANP and caffeine had a similar effect on improving the oocytes penetration rate, polyspermy rate and the average number of sperm per penetrated oocyte. Also, ANP treatment had a similar effect on cleavage rate, blastocyst formation rate and the number of cells per blastocyst as that of caffeine treatment. The effects of ANP on the acrosome reaction and the parameters of oocyte penetration could be blocked by cGMP-dependent protein kinase (PKG) inhibitors KT5823 and/or Rp-8-pCPT-cGMPS. These results suggest that the expression of ANP in the oviduct may be involved in the regulation of the acrosome reaction and the fertilising ability of pig spermatozoa, and the PKG pathway possibly participates in the process.
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Geyer, P. K., J. S. Patton, C. Rodesch, and R. N. Nagoshi. "Genetic and molecular characterization of P element-induced mutations reveals that the Drosophila ovarian tumor gene has maternal activity and a variable null phenotype." Genetics 133, no. 2 (February 1, 1993): 265–78. http://dx.doi.org/10.1093/genetics/133.2.265.
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Abstract The mutations in the ovarian tumor (otu) gene arrest oogenesis at several stages in development. A series of deletion mutations in the otu region were characterized, each of which causes the absence or reduction of the otu transcript. These alleles range from the most severe class, which results in ovaries lacking egg cysts, to relatively mild mutations that allow the development of late stage oocytes. Heteroallelic combinations of these mutations demonstrate that the phenotypic complexity of otu mutant ovaries is due to a dosage dependent requirement for otu activity. Reciprocal cross and developmental Northern blot studies suggest a maternal requirement for otu in the development of the female germline. In addition we demonstrate that the otu zygotic null phenotype is variable, ranging from the absence of cysts in the most extreme cases, to the presence of tumorous egg chambers.
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Sass, G. L., J. D. Mohler, R. C. Walsh, L. J. Kalfayan, and L. L. Searles. "Structure and expression of hybrid dysgenesis-induced alleles of the ovarian tumor (otu) gene in Drosophila melanogaster." Genetics 133, no. 2 (February 1, 1993): 253–63. http://dx.doi.org/10.1093/genetics/133.2.253.
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Abstract Mutations at the ovarian tumor (otu) gene of Drosophila melanogaster cause female sterility and generate a range of ovarian phenotypes. Quiescent (QUI) mutants exhibit reduced germ cell proliferation; in oncogenic (ONC) mutants germ cells undergo uncontrolled proliferation generating excessive numbers of undifferentiated cells; the egg chambers of differentiated (DIF) mutants differentiate to variable degrees but fail to complete oogenesis. We have examined mutations caused by insertion and deletion of P elements at the otu gene. The P element insertion sites are upstream of the major otu transcription start sites. In deletion derivatives, the P element, regulatory regions and/or protein coding sequences have been removed. In both insertion and deletion mutants, the level of otu expression correlates directly with the severity of the phenotype: the absence of otu function produces the most severe QUI phenotype while the ONC mutants express lower levels of otu than those which are DIF. The results of this study demonstrate that the diverse mutant phenotypes of otu are the consequence of different levels of otu function.
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Pauli, D., B. Oliver, and A. P. Mahowald. "The role of the ovarian tumor locus in Drosophila melanogaster germ line sex determination." Development 119, no. 1 (September 1, 1993): 123–34. http://dx.doi.org/10.1242/dev.119.1.123.
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The locus ovarian tumor (otu) is involved in several aspects of oogenesis in Drosophila melanogaster. The possible role of otu in the determination of the sexual identity of germ cells has not been extensively explored. Some otu alleles produce a phenotype known as ovarian tumors: ovarioles are filled with numerous poorly differentiated germ cells. We show that these mutant germ cells have a morphology similar to primary spermatocytes and that they express male germ line-specific reporter genes. This indicates that they are engaged along the male pathway of germ line differentiation. Consistent with this conclusion, we found that the splicing of Sex-lethal (Sxl) pre-mRNAs occurs in the male-specific mode in otu-transformed germ cells. The position of the otu locus in the regulatory cascade of germ line sex determination has been studied by using mutations that constitutively express the feminizing activity of the Sxl gene. The sexual transformation of the germ cells observed with several combinations of otu alleles can be reversed by constitutive expression of Sxl. This shows that otu acts upstream of Sxl in the process of germ line sex determination. Other phenotypes of otu mutations were not rescued by constitutive expression of Sxl, suggesting that several functions of otu are likely to be independent of sex determination. Finally, we show that the gene dosage of otu modifies the phenotype of ovaries heterozygous for the dominant alleles of ovo, another gene involved in germ line sex determination. One dose of otu+ enhances the ovoD ovarian phenotypes, while three doses partially suppress these phenotypes. Synergistic interaction between ovoD1 and otu alleles leads to the occasional transformation of chromosomally female germ cells into early spermatocytes. These interactions are similar to those observed between ovoD and one allele of the sans fille (snf) locus. Altogether, our results imply that the otu locus acts, along with ovo, snf, and Sxl, in a pathway (or parallel pathways) required for proper sex determination of the female germ line.
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Anderson, Michael, and Joshua Habiger. "Characterization and Identification of Productivity-Associated Rhizobacteria in Wheat." Applied and Environmental Microbiology 78, no. 12 (April 13, 2012): 4434–46. http://dx.doi.org/10.1128/aem.07466-11.
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ABSTRACTThe rhizosphere is populated by a numerous and diverse array of rhizobacteria, and many impact productivity in largely unknown ways. Here we characterize the rhizobacterial community in a wheat variety categorized according to shoot biomass using 16S rRNA pyrosequencing abundance data. Plants were grown in homogenized field soil under greenhouse conditions, and DNA was extracted and pyrosequenced, resulting in 29,007 quality sequences. Operational taxonomic units (OTUs) that were significantly associated with biomass productivity were identified using an exact test adjusted for the false-discovery rate. The productivity deviation expressed as a percentage of the total mean square for regression (PMSR) was determined for each OTU. Out of 719 OTUs, 42 showed significant positive associations and 39 showed significant negative associations (qvalue, ≤0.05). OTUs with the greatest net positive associations, by genus, were as follows:Duganella, OTU 43 and OTU 3;Janthinobacterium, OTU 278;Pseudomonas, OTU 588; andCellvibrio, OTU 1847. Those with negative associations were as follows:Bacteria, OTU 273;Chryseobacterium, OTU 508;Proteobacteria, OTU 249; andEnterobacter, OTU 357. Shoot biomass productivity was strongly correlated with the balance between the overall abundances of positive- and negative-productivity-associated OTUs. High-productivity rhizospheres contained 9.2 significant positives for every negatively associated rhizobacterium, while low-productivity rhizospheres showed 2.3 significant negatives for every positively associated rhizobacterium. Overall rhizobacterial community diversity as measured by the Chao1, Shannon, and Simpson indexes was nonlinearly related to productivity, closely fitting a wavelike cubic equation. We conclude that shoot biomass productivity is strongly related to the ratio of positive- to negative-productivity-associated rhizobacteria in the rhizosphere. This study identifies significant OTUs composing the productive and unproductive rhizobacterial communities.
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Torok, Valeria A., Gwen E. Allison, Nigel J. Percy, Kathy Ophel-Keller, and Robert J. Hughes. "Influence of Antimicrobial Feed Additives on Broiler Commensal Posthatch Gut Microbiota Development and Performance." Applied and Environmental Microbiology 77, no. 10 (March 25, 2011): 3380–90. http://dx.doi.org/10.1128/aem.02300-10.
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ABSTRACTThe effects of avilamycin, zinc bacitracin, and flavophospholipol on broiler gut microbial community colonization and bird performance in the first 17 days posthatch were investigated. Significant differences in gut microbiota associated with gut section, dietary treatment, and age were identified by terminal restriction fragment length polymorphism (T-RFLP), although no performance-related differences between dietary treatments were detected. Similar age-related shifts in the gut microbiota were identified regardless of diet but varied between the ilea and ceca. Interbird variabilities in ileal bacterial communities were reduced (3 to 7 days posthatch) in chicks fed with feed containing antimicrobial agents. Avilamycin and flavophospholipol had the most consistent effect on gut microbial communities. Operational taxonomic units (OTU) linked to changes in gut microbiota in birds on antimicrobial-supplemented diets were characterized and identified. Some OTUs could be identified to the species level; however, the majority could be only tentatively classified to the genus, family, order, or domain level. OTUs 140 to 146 (Lachnospiraceae), OTU 186/188 (Lactobacillus johnsonii), OTU 220 (Lachnospiraceae), OTUs 284 to 288 (unclassified bacterial spp. orRuminococcaceae), OTU 296/298 (unclassified bacterium orClostridiales), and OTU 480/482 (Oxalobacteraceae) were less prevalent in the guts of chicks fed antimicrobial-supplemented diets. OTU 178/180 (Lactobacillus crispatus), OTU 152 (Lactobacillus reuterior unclassifiedClostridiales), OTU 198/200 (Subdoligranulumspp.), and OTU 490/492 (unclassified bacterium orEnterobacteriaceae) were less prevalent in the gut of chicks raised on the antimicrobial-free diet. The identification of key bacterial species influenced by antimicrobial-supplemented feed immediately posthatch may assist in the formulation of diets that facilitate beneficial gut microbial colonization and, hence, the development of alternatives to current antimicrobial agents in feed for sustainable poultry production.
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Steinhauer, W. R., R. C. Walsh, and L. J. Kalfayan. "Sequence and structure of the Drosophila melanogaster ovarian tumor gene and generation of an antibody specific for the ovarian tumor protein." Molecular and Cellular Biology 9, no. 12 (December 1989): 5726–32. http://dx.doi.org/10.1128/mcb.9.12.5726.
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Sequencing cDNA and genomic DNA from the ovarian tumor gene revealed a gene with seven introns spanning 4.5 kilobases. The proline-rich, hydrophilic otu protein is novel. An antibody prepared to a beta-gal-otu fusion protein recognized a 110-kilodalton ovarian protein which was altered in the ovaries of otu gene mutants.
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Steinhauer, W. R., R. C. Walsh, and L. J. Kalfayan. "Sequence and structure of the Drosophila melanogaster ovarian tumor gene and generation of an antibody specific for the ovarian tumor protein." Molecular and Cellular Biology 9, no. 12 (December 1989): 5726–32. http://dx.doi.org/10.1128/mcb.9.12.5726-5732.1989.
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Sequencing cDNA and genomic DNA from the ovarian tumor gene revealed a gene with seven introns spanning 4.5 kilobases. The proline-rich, hydrophilic otu protein is novel. An antibody prepared to a beta-gal-otu fusion protein recognized a 110-kilodalton ovarian protein which was altered in the ovaries of otu gene mutants.
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Rodesch, C., P. K. Geyer, J. S. Patton, E. Bae, and R. N. Nagoshi. "Developmental analysis of the ovarian tumor gene during Drosophila oogenesis." Genetics 141, no. 1 (September 1, 1995): 191–202. http://dx.doi.org/10.1093/genetics/141.1.191.
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Abstract Severe alleles of the ovarian tumor (otu) and ovo genes result in female sterility in Drosophila melanogaster, producing adult ovaries that completely lack egg chambers. We examined the developmental stage in which the agametic phenotype first becomes apparent. Germ cell development in embryos was studied using a strategy that allowed simultaneous labeling of pole cells with the determination of embryonic genotype. We found that ovo- or otu- XX embryonic germ cells were indistinguishable in number and morphology from those present in wild-type siblings. The effects of the mutations were not consistently manifested in the female germline until pupariation, and there was no evidence that either gene was required for germ cell viability at earlier stages of development. The requirement for otu function in the pupal and adult ovary is supported by temperature-shift experiments using a heat-inducible otu gene construct. We demonstrate that otu activity limited to prepupal stages was not sufficient to support oogenesis, while induction during the pupal and adult periods caused suppression of the otu mutant phenotype.
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Fortunato, Caroline S., David B. Carlini, Evan Ewers, and Karen L. Bushaw-Newton. "Nitrifier and denitrifier molecular operational taxonomic unit compositions from sites of a freshwater estuary of Chesapeake Bay." Canadian Journal of Microbiology 55, no. 3 (March 2009): 333–46. http://dx.doi.org/10.1139/w08-124.
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Temporal and spatial changes in the molecular operational taxonomic unit (OTU) compositions of bacteria harboring genes for nitrification and denitrification were assessed using denaturing gradient gel electrophoresis (DGGE), clone-based DNA sequencing of selected PCR products, and analyses of ammonium and organic matter concentrations. Sediment, overlying water, and pore-water samples were taken from different vegetated sites of Jug Bay National Estuarine Research Reserve, Maryland, during spring, summer, and fall 2006. OTU richness and the diversities of nitrifiers and denitrifiers were assessed by the presence of bands on DGGE gels, both ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) were seasonally dependent. AOB OTU richness was highest in the summer when NOB richness was decreased, whereas NOB richness was highest in the spring when AOB richness was decreased. The OTU diversities of nitrifiers did not correlate with ammonium concentrations, organic matter concentrations, or the presence of vegetation. The OTU diversities of denitrifiers possessing either the nirK or nosZ genes were not seasonally dependent but were positively correlated with organic matter content (p = 0.0015, r2 = 0.27; p < 0.0001, r2 = 0.39, respectively). Additionally, the presence of vegetation significantly enhanced nosZ species richness (Wilcoxon/Kruskal–Wallis test, p < 0.008), but this trend was not seen for nirK OTU richness. Banding patterns for nirK OTUs were more similar within sites for each season compared with any of the other genes. Over all seasons, nirK OTU richness was highest and AOB and nosZ OTU richness were lowest (Wilcoxon/Kruskal–Wallis test, p < 0.0001). High levels of sequence divergence among cloned nirK PCR products indicate a broad diversity of nirK homologs in this freshwater estuary.
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Lu, J., and B. Oliver. "Drosophila OVO regulates ovarian tumor transcription by binding unusually near the transcription start site." Development 128, no. 9 (May 1, 2001): 1671–86. http://dx.doi.org/10.1242/dev.128.9.1671.
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Evolutionarily conserved ovo loci encode developmentally regulated, sequence-specific, DNA-binding, C(2)H(2)-zinc-finger proteins required in the germline and epidermal cells of flies and mice. The direct targets of OVO activity are not known. Genetic experiments suggest that ovo acts in the same regulatory network as ovarian tumor (otu), but the relative position of these genes in the pathway is controversial. Three OVO-binding sites exist in a compact regulatory region that controls germline expression of the otu gene. Interestingly, the strongest OVO-binding site is very near the otu transcription start, where basal transcriptional complexes must function. Loss-of-function, gain-of-function and promoter swapping constructs demonstrate that OVO binding near the transcription start site is required for OVO-dependent otu transcription in vivo. These data unambiguously identify otu as a direct OVO target gene and raise the tantalizing possibility that an OVO site, at the location normally occupied by basal components, functions as part of a specialized core promoter.
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Sun, Zhi, Zhenhai Chen, Steven R. Lawson, and Ying Fang. "The Cysteine Protease Domain of Porcine Reproductive and Respiratory Syndrome Virus Nonstructural Protein 2 Possesses Deubiquitinating and Interferon Antagonism Functions." Journal of Virology 84, no. 15 (May 26, 2010): 7832–46. http://dx.doi.org/10.1128/jvi.00217-10.
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ABSTRACT Porcine reproductive and respiratory syndrome (PRRS) virus nonstructural protein 2 (nsp2) contains a cysteine protease domain at its N terminus, which belongs to the ovarian tumor (OTU) protease family. In this study, we demonstrated that the PRRSV nsp2 OTU domain antagonizes the type I interferon induction by interfering with the NF-κB signaling pathway. Further analysis revealed that the nsp2 OTU domain possesses ubiquitin-deconjugating activity. This domain has the ability to inhibit NF-κB activation by interfering with the polyubiquitination process of IκBα, which subsequently prevents IκBα degradation. To determine whether the nsp2 protein antagonist function can be ablated from the virus, we introduced point mutations into the OTU domain region by use of reverse genetics. The D458A, S462A, and D465A mutations targeting on a B-cell epitope in the OTU domain region generated the viable recombinant viruses, and the S462A and D465A mutants were attenuated for growth in cell culture. The OTU domain mutants were examined to determine whether mutations in the nsp2 OTU domain region altered virus ability to inhibit NF-κB activation. The result showed that certain mutations lethal to virus replication impaired the ability of nsp2 to inhibit NF-κB activation but that the viable recombinant viruses, vSD-S462A and vSD-D465A, were unable to inhibit NF-κB activation as effectively as the wild-type virus. This study represents a fundamental step in elucidating the role of nsp2 in PRRS pathogenesis and provides an important insight in future modified live-virus vaccine development.
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Lagishetty, Venu, Nerea Arias, Tien Dong, Meg Hauer, William Katzka, Marla Dubinsky, Jonathan Braun, and Jonathan Jacobs. "2 EFFECTS OF AN IBD-ASSOCIATED MICROBIAL COMMUNITY STATE ON INTESTINAL INFLAMMATION IN HUMANIZED GNOTOBIOTIC MICE." Inflammatory Bowel Diseases 26, Supplement_1 (January 2020): S40. http://dx.doi.org/10.1093/ibd/zaa010.103.
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Abstract Background and Aims We previously reported that 20% of unaffected first-degree relatives of pediatric IBD patients share the same microbial community structure (OTU-type) as IBD patients. This suggests that a preexisting dysbiosis can predispose to the development of IBD. The aims of this study were to establish that microbial community types identified in the family cohort could be reconstituted in gnotobiotic mice for further translational studies and to assess for any direct effects of this microbiota on intestinal inflammation. Methods Over 100 germ-free wild-type C57/BL6 mice were colonized for 4 weeks in the UCLA gnotobiotic facility with fecal microbiota from 30 human donors belonging to each of four groups from the pediatric family cohort: unaffected first-degree relatives with OTU-type 1, unaffected first-degree relatives with the IBD-associated OTU-type 2, Crohn’s disease (CD) with OTU-type 1, CD with OTU-type 2. Each group was represented by 8 human donors (n=3–4 mice/donor) with the exception of CD OTU-type 1 (only 5 donors available in the cohort). In addition, 35 eight week old germ-free IL-10-/- C57/BL6 mice were colonized for 12 weeks with fecal microbiota from 4 CD OTU-type 2 donors and 4 unaffected OTU-type 1 donors (n=4–5/donor). Luminal and mucosal microbial composition in the colon and small intestine was evaluated by 16S rRNA sequencing. Intestinal inflammation was assessed in the small intestine and colon by semiquantitative scoring of H&E stained sections. Results Donor-specific microbial composition was observed in the humanized gnotobiotic mice with clear separation between recipients of donor OTU-type 1 vs. OTU-type 2 stool. Parallel differences in differentially abundant microbes and microbial diversity were seen in these gnotobiotic mice as in the original human donors. No histologic evidence was found for colitis, enteritis, or fibrosis in wild-type colonized mice. However, fecal lipocalin was increased two-fold increase in recipients of OTU-type 2 microbiota from CD patients relative to the other three groups. CD humanized IL-10-/- mice exhibited lower microbial diversity and distinct microbial composition compared to non-IBD humanized IL-10-/- mice, mirroring differences in the human donors. Mice colonized with CD microbiota had increased histological disease severity in the colon and cecum (p=0.05) compared to mice colonized with non-IBD microbiota. Conclusion Our results demonstrate that human microbial community states identified in the pediatric IBD cohort could be reconstituted in gnotobiotic mice for translational studies. Moreover, CD-associated dysbiosis exacerbated colitis severity. These data support the concept that dysbiosis plays a direct role in promoting intestinal inflammation and provide an experimental framework for further mechanistic studies of IBD-associated microbial communities.
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Keyes, L. N., and A. C. Spradling. "The Drosophila gene fs(2)cup interacts with otu to define a cytoplasmic pathway required for the structure and function of germ-line chromosomes." Development 124, no. 7 (April 1, 1997): 1419–31. http://dx.doi.org/10.1242/dev.124.7.1419.
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The Drosophila ovarian tumor gene (otu) encodes cytoplasmic proteins that are required in germ-line cells for cyst formation, nurse cell chromosome structure and egg maturation. We have analyzed a gene, fs(2)cup, that participates in many of the same processes and interacts with otu genetically. Both nurse cell and oocyte chromosomes require cup to attain a normal morphology. In addition, the gene is needed for the oocyte to grow normally by taking up materials transported from the nurse cells. The gene encodes a 1132-amino-acid protein containing a putative membrane-spanning domain. Cup protein (but not cup RNA) is transported selectively into the oocyte in germarial cysts, like the p104 Otu protein. It is strongly associated with large structures in the cytoplasm and perinuclear region of nurse cells and, like Otu, moves to the periphery of these cells in stages 9–10. Moreover, cup mutations dominantly disrupt meiotic chromosome segregation. We propose that cup, otu and another interacting gene, fs(2)B, take part in a common cytoplasmic pathway with multiple functions during oogenesis.
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Berhe, Tesfemariam, Richard Ipsen, Eyassu Seifu, Mohamed Y. Kurtu, Angelina Fugl, and Egon Bech Hansen. "Metagenomic analysis of bacterial community composition in Dhanaan: Ethiopian traditional fermented camel milk." FEMS Microbiology Letters 366, Supplement_1 (June 10, 2019): i127—i132. http://dx.doi.org/10.1093/femsle/fnz128s.
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ABSTRACT This study was conducted to evaluate the safety and bacterial profile of Dhanaan (Ethiopian traditional fermented camel milk). The composition of the microbial community in Dhanaan samples was analysed by a metagenomic approach of 16S rRNA gene amplicon sequencing. Metagenomic profiling identified 87 different bacterial microorganisms (OTUs) in six samples analysed. Although the Dhanaan samples contained various lactic acid bacteria (LAB), they also all contained undesirable microorganisms in large proportions. The following LAB genera were identified: Streptococcus, Lactococcus and Weissella. One Streptococcus species represented by OTU-1 (operational taxonomic unit) was found in all Dhanaan samples and the dominating species in four out of six samples. This common isolate was found to be closely related to S. lutetiensis and S. infantarius. Undesirable microorganisms from genera such as Escherichia, Klebsiella, Enterobacter, Acinetobacter and Clostridium were, however, also frequent, or even dominant in Dhanaan samples. Thus, this calls for a change in the Dahnaan manufacturing practice to an improved and safer production system. Starter cultures suitable for Dhanaan production might be developed from the Streptococcus, Weissella and Lactococcus microorganisms identified in this study. However, further safety evaluation and technological characterization need to be conducted on strains defined by OTU-1, OTU-2, OTU-3, OTU-8 and OTU-35 before they can be used as food grade starter cultures.
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Nagoshi, R. N., J. S. Patton, E. Bae, and P. K. Geyer. "The somatic sex determines the requirement for ovarian tumor gene activity in the proliferation of the Drosophila germline." Development 121, no. 2 (February 1, 1995): 579–87. http://dx.doi.org/10.1242/dev.121.2.579.
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Gametogenesis in Drosophila requires sex-specific interactions between the soma and germline to control germ cell viability, proliferation, and differentiation. To determine what genetic components are involved in this interaction, we examined whether changes in the sexual identity of the soma affected the function of the ovarian tumor (otu) and ovo genes. These genes are required cell autonomously in the female germline for germ cell proliferation and differentiation. Mutations in otu and ovo cause a range of ovarian defects, including agametic ovaries and tumorous egg cysts, but do not affect spermatogenesis. We demonstrate that XY germ cells do not require otu when developing in testes, but become dependent on otu function for proliferation when placed in an ovary. This soma-induced requirement can be satisfied by the induced expression of the 98 × 10(3) M(r) OTU product, one of two isoforms produced by differential RNA splicing. These results indicate that the female somatic gonad can induce XY germ cells to become ‘female-like’ because they require an oogenesis-specific gene. In contrast, the requirement for ovo is dependent on a cell autonomous signal derived from the X:A ratio. We propose that differential regulation of the otu and ovo genes provides a mechanism for the female germline to incorporate both somatic and cell autonomous inputs required for oogenesis.
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Dzimianski, John V., Savannah L. Mace, Isabelle L. Williams, Brendan T. Freitas, and Scott D. Pegan. "Flipping the substrate preference of Hazara virus ovarian tumour domain protease through structure-based mutagenesis." Acta Crystallographica Section D Structural Biology 76, no. 11 (October 16, 2020): 1114–23. http://dx.doi.org/10.1107/s2059798320012875.
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Nairoviruses are arthropod-borne viruses with a nearly global geographical distribution. Several are known causative agents of human disease, including Crimean–Congo hemorrhagic fever virus (CCHFV), which has a case fatality rate that can exceed 30%. Nairoviruses encode an ovarian tumour domain protease (OTU) that can suppress the innate immune response by reversing post-translational modifications by ubiquitin (Ub) and/or interferon-stimulated gene product 15 (ISG15). As a result, the OTU has been identified as a potential target for the development of CCHFV therapeutics. Despite sharing the same general fold, nairoviral OTUs show structural and enzymatic diversity. The CCHFV OTU, for example, possesses activity towards both Ub and ISG15, while the Hazara virus (HAZV) OTU interacts exclusively with Ub. Virology studies focused on the OTU have mostly been restricted to CCHFV, which requires BSL-4 containment facilities. Although HAZV has been proposed as a BSL-2 alternative, differences in the engagement of substrates by CCHFV and HAZV OTUs may present complicating factors when trying to model one using the other. To understand the molecular underpinnings of the differences in activity, a 2.78 Å resolution crystal structure of HAZV OTU bound to Ub was solved. Using structure-guided site-directed mutagenesis, HAZV OTUs were engineered with altered or eliminated deubiquitinase activity, including one with an exclusive activity for ISG15. Additionally, analysis of the structure yielded insights into the difference in inhibition observed between CCHFV and HAZV OTUs with a Ub-based inhibitor. These new insights present opportunities to utilize HAZV as a model system to better understand the role of the OTU in the context of infection.
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Bakshi, S., B. Holzer, A. Bridgen, G. McMullan, D. G. Quinn, and M. D. Baron. "Dugbe virus ovarian tumour domain interferes with ubiquitin/ISG15-regulated innate immune cell signalling." Journal of General Virology 94, no. 2 (February 1, 2013): 298–307. http://dx.doi.org/10.1099/vir.0.048322-0.
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The ovarian tumour (OTU) domain of the nairovirus L protein has been shown to remove ubiquitin and interferon-stimulated gene 15 protein (ISG15) from host cell proteins, which is expected to have multiple effects on cell signalling pathways. We have confirmed that the OTU domain from the L protein of the apathogenic nairovirus Dugbe virus has deubiquitinating and deISGylating activity and shown that, when expressed in cells, it is highly effective at blocking the TNF-α/NF-κB and interferon/JAK/STAT signalling pathways even at low doses. Point mutations of the catalytic site of the OTU [C40A, H151A and a double mutant] both abolished the ability of the OTU domain to deubiquitinate and deISGylate proteins and greatly reduced its effect on cell signalling pathways, confirming that it is this enzymic activity that is responsible for blocking the two signalling pathways. Expression of the inactive mutants at high levels could still block signalling, suggesting that the viral OTU can still bind to its substrate even when mutated at its catalytic site. The nairovirus L protein is a very large protein that is normally confined to the cytoplasm, where the virus replicates. When the OTU domain was prevented from entering the nucleus by expressing it as part of the N-terminal 205 kDa of the viral L protein, it continued to block type I interferon signalling, but no longer blocked the TNF-α-induced activation of NF-κB.
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Sekyi-Otu, Ato. "Author’s response – Ato Sekyi-Otu." Journal of the African Literature Association 13, no. 2 (April 9, 2019): 278–82. http://dx.doi.org/10.1080/21674736.2019.1594872.
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Balakirev, Maxim Y., and Keith D. Wilkinson. "OTU takes the chains OUT." Nature Chemical Biology 4, no. 4 (April 2008): 227–28. http://dx.doi.org/10.1038/nchembio0408-227.
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La Duc, Myron T., Parag Vaishampayan, Henrik R. Nilsson, Tamas Torok, and Kasthuri Venkateswaran. "Pyrosequencing-Derived Bacterial, Archaeal, and Fungal Diversity of Spacecraft Hardware Destined for Mars." Applied and Environmental Microbiology 78, no. 16 (June 22, 2012): 5912–22. http://dx.doi.org/10.1128/aem.01435-12.
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ABSTRACTSpacecraft hardware and assembly cleanroom surfaces (233 m2in total) were sampled, total genomic DNA was extracted, hypervariable regions of the 16S rRNA gene (bacteria and archaea) and ribosomal internal transcribed spacer (ITS) region (fungi) were subjected to 454 tag-encoded pyrosequencing PCR amplification, and 203,852 resulting high-quality sequences were analyzed. Bioinformatic analyses revealed correlations between operational taxonomic unit (OTU) abundance and certain sample characteristics, such as source (cleanroom floor, ground support equipment [GSE], or spacecraft hardware), cleaning regimen applied, and location about the facility or spacecraft. National Aeronautics and Space Administration (NASA) cleanroom floor and GSE surfaces gave rise to a larger number of diverse bacterial communities (619 OTU; 20 m2) than colocated spacecraft hardware (187 OTU; 162 m2). In contrast to the results of bacterial pyrosequencing, where at least some sequences were generated from each of the 31 sample sets examined, only 13 and 18 of these sample sets gave rise to archaeal and fungal sequences, respectively. As was the case for bacteria, the abundance of fungal OTU in the GSE surface samples dramatically diminished (9× less) once cleaning protocols had been applied. The presence of OTU representative of actinobacteria, deinococci, acidobacteria, firmicutes, and proteobacteria on spacecraft surfaces suggests that certain bacterial lineages persist even following rigorous quality control and cleaning practices. The majority of bacterial OTU observed as being recurrent belonged to actinobacteria and alphaproteobacteria, supporting the hypothesis that the measures of cleanliness exerted in spacecraft assembly cleanrooms (SAC) inadvertently select for the organisms which are the most fit to survive long journeys in space.
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Barnes, Christopher J., Linett Rasmussen, Maria Asplund, Steen Wilhelm Knudsen, Maja-Lisa Clausen, Tove Agner, and Anders J. Hansen. "Comparing DADA2 and OTU clustering approaches in studying the bacterial communities of atopic dermatitis." Journal of Medical Microbiology 69, no. 11 (November 1, 2020): 1293–302. http://dx.doi.org/10.1099/jmm.0.001256.
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Introduction. The pathogenesis of atopic dermatitis (AD) is not yet fully understood, but the bacterial composition of AD patients’ skin has been shown to have an increased abundance of Staphylococcus aureus . More recently, coagulase-negative Staphylococcus (CoNS) species were shown to be able to inhibit S. aureus , but further studies are required to determine the effects of Staphylococcus community variation in AD. Aim. Here we investigated whether analysing metabarcoding data with the more recently developed DADA2 approach improves metabarcoding analyses compared to the previously used operational taxonomic unit (OTU) clustering, and can be used to study Staphylococcus community dynamics. Methods. The bacterial 16S rRNA region from tape strip samples of the stratum corneum of AD patients (non-lesional skin) and non-AD controls was metabarcoded. We processed metabarcoding data with two different bioinformatic pipelines (an OTU clustering method and DADA2), which were analysed with and without technical replication (sampling strategy). Results. We found that OTU clustering and DADA2 performed well for community-level studies, as demonstrated by the identification of significant differences in the skin bacterial communities associated with AD. However, the OTU clustering approach inflated bacterial richness, which was worsened by not having technical replication. Data processed with DADA2 likely handled sequencing errors more effectively and thereby did not inflate molecular richness. Conclusion. We believe that DADA2 represents an improvement over an OTU clustering approach, and that biological replication rather than technical replication is a more effective use of resources. However, neither OTU clustering nor DADA2 gave insights into Staphylococcus community dynamics, and caution should remain in not overinterpreting the taxonomic assignments at lower taxonomic ranks.
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Ritter, Camila D., Alexander Zizka, Fabian Roger, Hanna Tuomisto, Christopher Barnes, R. Henrik Nilsson, and Alexandre Antonelli. "High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia." PeerJ 6 (September 25, 2018): e5661. http://dx.doi.org/10.7717/peerj.5661.
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BackgroundKnowledge on the globally outstanding Amazonian biodiversity and its environmental determinants stems almost exclusively from aboveground organisms, notably plants. In contrast, the environmental factors and habitat preferences that drive diversity patterns for micro-organisms in the ground remain elusive, despite the fact that micro-organisms constitute the overwhelming majority of life forms in any given location, in terms of both diversity and abundance. Here we address how the diversity and community turnover of operational taxonomic units (OTU) of organisms in soil and litter respond to soil physicochemical properties; whether OTU diversities and community composition in soil and litter are correlated with each other; and whether they respond in a similar way to soil properties.MethodsWe used recently inferred OTUs from high-throughput metabarcoding of the 16S (prokaryotes) and 18S (eukaryotes) genes to estimate OTU diversity (OTU richness and effective number of OTUs) and community composition for prokaryotes and eukaryotes in soil and litter across four localities in Brazilian Amazonia. All analyses were run separately for prokaryote and eukaryote OTUs, and for each group using both presence-absence and abundance data. Combining these with novel data on soil chemical and physical properties, we identify abiotic correlates of soil and litter organism diversity and community structure using regression, ordination, and variance partitioning analysis.ResultsSoil organic carbon content was the strongest factor explaining OTU diversity (negative correlation) and pH was the strongest factor explaining community turnover for prokaryotes and eukaryotes in both soil and litter. We found significant effects also for other soil variables, including both chemical and physical properties. The correlation between OTU diversity in litter and in soil was non-significant for eukaryotes and weak for prokaryotes. The community compositions of both prokaryotes and eukaryotes were more separated among habitat types (terra-firme, várzea, igapó and campina) than between substrates (soil and litter).DiscussionIn spite of the limited sampling (four localities, 39 plots), our results provide a broad-scale view of the physical and chemical correlations of soil and litter biodiversity in a longitudinal transect across the world’s largest rainforest. Our methods help to understand links between soil properties, OTU diversity patterns, and community composition and turnover. The lack of strong correlation between OTU diversity in litter and in soil suggests independence of diversity drives of these substrates and highlights the importance of including both measures in biodiversity assessments. Massive sequencing of soil and litter samples holds the potential to complement traditional biological inventories in advancing our understanding of the factors affecting tropical diversity.
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McBride, William L. "Fanon's Dialectic of Experience.Ato Sekyi-Otu." Ethics 108, no. 3 (April 1998): 615–16. http://dx.doi.org/10.1086/233835.
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Dai, Mulan, Chantal Hamel, Marc St. Arnaud, Yong He, Cynthia Grant, Newton Lupwayi, Henry Janzen, Sukhdev S. Malhi, Xiaohong Yang, and Zhiqin Zhou. "Arbuscular mycorrhizal fungi assemblages in Chernozem great groups revealed by massively parallel pyrosequencing." Canadian Journal of Microbiology 58, no. 1 (January 2012): 81–92. http://dx.doi.org/10.1139/w11-111.
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The arbuscular mycorrhizal (AM) fungal resources present in wheat fields of the Canadian Prairie were explored using 454 pyrosequencing. Of the 33 dominant AM fungal operational taxonomic units (OTUs) found in the 76 wheat fields surveyed at anthesis in 2009, 14 clustered as Funneliformis – Rhizophagus, 16 as Claroideoglomus, and 3 as Diversisporales. An OTU of Funneliformis mosseae and one OTU of Diversisporales each accounted for approximately 16% of all AM fungal OTUs. The former was ubiquitous, and the latter was mainly restricted to the Black and Dark Brown Chernozems. AM fungal OTU community composition was better explained by the Chernozem great groups (P = 0.044) than by measured soil properties. Fifty-two percent of the AM fungal OTUs were unrelated to measured soil properties. Black Chernozems hosted the largest AM fungal OTU diversity and almost twice the number of AM fungal sequences seen in Dark Brown Chernozems, the great group ranking second for AM fungal sequence abundance. Brown Chernozems hosted the lowest AM fungal abundance and an AM fungal diversity as low as that seen in Gray soils. We concluded that Black Chernozems are most conducive to AM fungal proliferation. AM fungi are generally distributed according to Chernozem great groups in the Canadian Prairie, although some taxa are evenly distributed in all soil groups.
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Gorrasi, Susanna, Marcella Pasqualetti, Andrea Franzetti, Alejandro Gonzalez-Martinez, Jesus Gonzalez-Lopez, Barbara Muñoz-Palazon, and Massimiliano Fenice. "Persistence of Enterobacteriaceae Drawn into a Marine Saltern (Saline di Tarquinia, Italy) from the Adjacent Coastal Zone." Water 13, no. 11 (May 21, 2021): 1443. http://dx.doi.org/10.3390/w13111443.
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Enterobacteriaceae is present in various niches worldwide (i.e., the gastrointestinal tracts of animals, clinical specimens, and diverse environments) and hosts some well-known pathogens (i.e., salmonellas, shigellas and pathogenic coliforms). No investigation has focused on its occurrence in marine salterns, and it is not clear if these hypersaline environments could be a reservoir for these bacteria including some potentially harmful members. In this study, a two-year metabarcoding survey was carried out on samples collected from different ponds of the “Saline di Tarquinia” salterns and the nearby coastal waters. Enterobacteriaceae was recorded almost constantly in the seawaters feeding the saltern. Its abundance was generally higher in the sea than in the ponds, probably due to the higher anthropic impact. The same trend was evidenced for the key genus (Escherichia/Shigella) and OTU (OTU 5) of the Enterobacteriaceae community. Various parameters affected taxon/OTU abundance: Enterobacteriaceae, Escherichia/Shigella and OTU5 decreased with increasing salinity and rains; moreover, Escherichia/Shigella and OTU 5 were higher in autumn than in spring. Although Enterobacteriaceae did not seem to find the most favourable conditions for a high-abundance persistence in the saltern environment, it did not disappear. These observations suggested this environment as a potential reservoir for bacteria with possible important health implications.
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Bandarupalli, Venkata, and Benoit St- Pierre. "330 Identification and genomic characterization of two novel strains of Prevotella albensis as starch utilizers in the rumen of beef cows." Journal of Animal Science 97, Supplement_2 (July 2019): 132. http://dx.doi.org/10.1093/jas/skz122.234.
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Abstract In cattle fed concentrate diets, rumen amylolytic bacteria digest starch into glucose, which is metabolized for growth. Since metagenomics studies have revealed that uncharacterized ruminal amylolytic bacteria far outnumber known starch utilizers, we have been pursing the identification of novel ruminal amylolytic bacteria. The same Operational Taxonomic Unit (OTU) was enriched independently from the rumen fluid of two beef cows after culturing with starch. Since this identification was performed using the V1–V3 region of the 16S rRNA gene, a metagenomic analysis was conducted to determine whether this OTU represented the same strain or different strains of the same species. A total of 9.25 and 9.16 million sequence reads were respectively generated from a select enriched starch culture from each cow, which had a relative abundance for this OTU of 67.9% and 74.0%, respectively. Contigs were assembled using the publicly available software ABySS, with contigs of at least 2kb in length used for further analysis. Of the enzymes identified by gene annotation of these contigs (using a combination of the online tools RAST and BLASTp), the presence of genes encoding α-amylase and lactate dehydrogenase enzymes further supported this OTU as corresponding to a starch utilizer. The alpha-amylase isoforms from the two rumens differed in amino acid length (538 vs 625) and sequence, with their respective closest affiliation being to an uncultured species of Lachnospiraceae (51% amino acid identity) and to Prevotella albensis (95% amino acid identity), respectively. The lactate dehydrogenase isoforms were also found to be different in length (348 aa vs 335 aa) and sequence (100% amino acid identity to Lactobacillus mucosae and 99% to an uncultured species of the genus Olsonella, respectively). These and other gene comparisons together suggest that two strains of the same starch-utilizing OTU have been identified in the rumen of beef cows.
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Juhel, Jean-Baptiste, Rizkie S. Utama, Virginie Marques, Indra B. Vimono, Hagi Yulia Sugeha, Kadarusman, Laurent Pouyaud, Tony Dejean, David Mouillot, and Régis Hocdé. "Accumulation curves of environmental DNA sequences predict coastal fish diversity in the coral triangle." Proceedings of the Royal Society B: Biological Sciences 287, no. 1930 (July 8, 2020): 20200248. http://dx.doi.org/10.1098/rspb.2020.0248.
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Environmental DNA (eDNA) has the potential to provide more comprehensive biodiversity assessments, particularly for vertebrates in species-rich regions. However, this method requires the completeness of a reference database (i.e. a list of DNA sequences attached to each species), which is not currently achieved for many taxa and ecosystems. As an alternative, a range of operational taxonomic units (OTUs) can be extracted from eDNA metabarcoding. However, the extent to which the diversity of OTUs provided by a limited eDNA sampling effort can predict regional species diversity is unknown. Here, by modelling OTU accumulation curves of eDNA seawater samples across the Coral Triangle, we obtained an asymptote reaching 1531 fish OTUs, while 1611 fish species are recorded in the region. We also accurately predict ( R ² = 0.92) the distribution of species richness among fish families from OTU-based asymptotes. Thus, the multi-model framework of OTU accumulation curves extends the use of eDNA metabarcoding in ecology, biogeography and conservation.
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Komander, David, and David Barford. "Structure of the A20 OTU domain and mechanistic insights into deubiquitination." Biochemical Journal 409, no. 1 (December 11, 2007): 77–85. http://dx.doi.org/10.1042/bj20071399.
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The NF-κB (nuclear factor κB) regulator A20 antagonises IKK [IκB (inhibitor of κB) kinase] activation by modulating Lys63-linked polyubiquitination of cytokine-receptor-associated factors including TRAF2/6 (tumour-necrosis-factor-receptor-associated factor 2/6) and RIP1 (receptor-interacting protein 1). In the present paper we describe the crystal structure of the N-terminal OTU (ovarian tumour) deubiquitinase domain of A20, which differs from other deubiquitinases but shares the minimal catalytic core with otubain-2. Analysis of conserved surface regions allows prediction of ubiquitin-binding sites for the proximal and distal ubiquitin molecules. Structural and biochemical analysis suggests a novel architecture of the catalytic triad, which might be present in a subset of OTU domains including Cezanne and TRABID (TRAF-binding domain). Biochemical analysis shows a preference of the isolated A20 OTU domain for Lys48-linked tetraubiquitin in vitro suggesting that additional specificity factors might be required for the physiological function of A20 in cells.
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Bellikci Koyu, Ezgi. "Diyabette Kullanılan Bitkisel Desteklerin Etkinliği ve Güvenilirliği." Journal of Nutrition and Dietetics 47 (December 31, 2019): 110–17. http://dx.doi.org/10.33076/2019.bdd.1322.
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Bitkiler uzun yüzyıllar boyunca tedavinin en önemli parçası olmuşlardır. On dokuzuncu yüzyılda kimya alanında önemli gelişmelerin olması ve ilaç moleküllerinin keşfi ile bitkilerin tıbbi amaçlı kullanımları giderek azalsa da, son yıllarda doğaya dönüş çabaları içerisinde kullanımlarında yeniden bir artış gözlenmektedir. Özellikle diyabet gibi kronik seyirli hastalıklarda modern tedaviye destek olarak bu ürünlerin kullanımları sıklıkla tercih edilmektedir. Bu ilgiye paralel olarak son yıllarda bitkilerin diyabet tedavisindeki etkisini araştıran klinik çalışmalar da artmaya başlamıştır. Etkinliğin yanı sıra bitkilerin güvenilir kullanımları da son derece önemlidir. Doğru bitkinin kullanımı, kullanılan ürünün bileşimi, kalitesi, hazırlama yöntemi, yan etkileri, ilaç etkileşimleri ve kontraendikasyonları da tedavi sürecini etkileyen ve güvenilir kullanım için göz önünde bulundurulması gereken faktörlerdir. Bu derlemede tarçın (Cinnamomum sp.), çörek otu (Nigella sativa L.), kudret narı (Momordica charantia L.), çemen otu (Trigonella foenum-graecum L.), zencefil (Zingiber officinale Roscoe) ve ısırgan otu (Urtica dioica L.) gibi diyabet tedavisinde sıklıkla tercih edilen bitkilerin etkinliği ve güvenilirliği değerlendirilmiştir.
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Westcott, Sarah L., and Patrick D. Schloss. "De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units." PeerJ 3 (December 8, 2015): e1487. http://dx.doi.org/10.7717/peerj.1487.
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Background.16S rRNA gene sequences are routinely assigned to operational taxonomic units (OTUs) that are then used to analyze complex microbial communities. A number of methods have been employed to carry out the assignment of 16S rRNA gene sequences to OTUs leading to confusion over which method is optimal. A recent study suggested that a clustering method should be selected based on its ability to generate stable OTU assignments that do not change as additional sequences are added to the dataset. In contrast, we contend that the quality of the OTU assignments, the ability of the method to properly represent the distances between the sequences, is more important.Methods.Our analysis implemented sixde novoclustering algorithms including the single linkage, complete linkage, average linkage, abundance-based greedy clustering, distance-based greedy clustering, and Swarm and the open and closed-reference methods. Using two previously published datasets we used the Matthew’s Correlation Coefficient (MCC) to assess the stability and quality of OTU assignments.Results.The stability of OTU assignments did not reflect the quality of the assignments. Depending on the dataset being analyzed, the average linkage and the distance and abundance-based greedy clustering methods generated OTUs that were more likely to represent the actual distances between sequences than the open and closed-reference methods. We also demonstrated that for the greedy algorithms VSEARCH produced assignments that were comparable to those produced by USEARCH making VSEARCH a viable free and open source alternative to USEARCH. Further interrogation of the reference-based methods indicated that when USEARCH or VSEARCH were used to identify the closest reference, the OTU assignments were sensitive to the order of the reference sequences because the reference sequences can be identical over the region being considered. More troubling was the observation that while both USEARCH and VSEARCH have a high level of sensitivity to detect reference sequences, the specificity of those matches was poor relative to the true best match.Discussion.Our analysis calls into question the quality and stability of OTU assignments generated by the open and closed-reference methods as implemented in current version of QIIME. This study demonstrates thatde novomethods are the optimal method of assigning sequences into OTUs and that the quality of these assignments needs to be assessed for multiple methods to identify the optimal clustering method for a particular dataset.
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Sansom, Sarah, Michael Y. Lin, Michael Schoeny, Christine Fukuda, Christine Bassis, Teppei Shimasaki, Thelma E. Dangana, et al. "919. Understanding Intermittent Detection of Multidrug-Resistant Organisms (MDROs) in Rectally Colonized Patients." Open Forum Infectious Diseases 7, Supplement_1 (October 1, 2020): S494. http://dx.doi.org/10.1093/ofid/ofaa439.1107.
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Abstract Background MDRO detection in colonized patients may be intermittent for reasons that are incompletely understood. We examined temporal patterns of gut MDRO colonization after initial MDRO detection by rectal swab screening, and determined the relationship of culture positivity to the relative abundance of corresponding MDRO operational taxonomic units (OTUs) identified by 16S rRNA gene sequence analysis. Methods Rectal or fecal swabs were collected daily from MICU patients 1/11/2017-1/11/2018. First MICU admissions with ≥2 swabs and MICU stays ≥3 days were studied. Samples were cultured for vancomycin-resistant enterococci (VRE), carbapenem-resistant Enterobacteriaceae (CRE) and P. aeruginosa (CRPA), and extended-spectrum β-lactamase-producing (ESBL) Enterobacteriaceae by selective media. Resistance mechanisms were confirmed by phenotypic methods and/or PCR. Limit of detection was similar for different MDROs (24-52 CFU/sample). OTU categories corresponding to MDRO species were identified by taxonomy and BLAST. Multilevel regression models estimated the association between MDRO detection and relative abundance of the corresponding OTU. Results 796 unique patients with 3519 swabs were studied. Median (IQR) age was 64 (51-74) years, MICU length of stay was 5 (3-8) days, and number of samples-per-patient was 3 (2-5). Following initial MDRO detection, the probability of subsequent detection varied by MDRO type, and was highest for VRE and lowest for CRPA [Figure 1]. Within each sample, we found a significant association between MDRO detection and relative abundance of the corresponding OTU [Table 1]. In contrast, relative OTU abundance in the first sample with MDRO detection was not predictive of odds of future MDRO detection (p >0.05 for all comparisons). Carriage of >1 MDRO did not affect the odds of MDRO detection in later samples. Figure 1. Probability of Subsequent MDRO Detection after First Positive Varies by MDRO Type Table 1. Higher Mean Corresponding OTU Relative Abundance Within Each Sample is Associated with MDRO Detection Conclusion MDRO culture positivity in rectally colonized patients was correlated with relative abundance of the corresponding OTU in the same sample. Serial detection of different MDRO types was variable, possibly due to distinct microbial community dynamics of different MDRO types. Intermittent failure to detect MDROs could result in misattribution of MDRO acquisition, resulting in inappropriate investigation or intervention. Disclosures All Authors: No reported disclosures
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Flores-Mireles, Ana L., Stephen C. Winans, and Gina Holguin. "Molecular Characterization of Diazotrophic and Denitrifying Bacteria Associated with Mangrove Roots." Applied and Environmental Microbiology 73, no. 22 (September 7, 2007): 7308–21. http://dx.doi.org/10.1128/aem.01892-06.
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ABSTRACT An analysis of the molecular diversity of N2 fixers and denitrifiers associated with mangrove roots was performed using terminal restriction length polymorphism (T-RFLP) of nifH (N2 fixation) and nirS and nirK (denitrification), and the compositions and structures of these communities among three sites were compared. The number of operational taxonomic units (OTU) for nifH was higher than that for nirK or nirS at all three sites. Site 3, which had the highest organic matter and sand content in the rhizosphere sediment, as well as the lowest pore water oxygen concentration, had the highest nifH diversity. Principal component analysis of biogeochemical parameters identified soil texture, organic matter content, pore water oxygen concentration, and salinity as the main variables that differentiated the sites. Nonmetric multidimensional scaling (MDS) analyses of the T-RFLP data using the Bray-Curtis coefficient, group analyses, and pairwise comparisons between the sites clearly separated the OTU of site 3 from those of sites 1 and 2. For nirS, there were statistically significant differences in the composition of OTU among the sites, but the variability was less than for nifH. OTU defined on the basis of nirK were highly similar, and the three sites were not clearly separated on the basis of these sequences. The phylogenetic trees of nifH, nirK, and nirS showed that most of the cloned sequences were more similar to sequences from the rhizosphere isolates than to those from known strains or from other environments.
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Hao, Xiaolin, and Ting Chen. "OTU Analysis Using Metagenomic Shotgun Sequencing Data." PLoS ONE 7, no. 11 (November 26, 2012): e49785. http://dx.doi.org/10.1371/journal.pone.0049785.
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YILMAZ, Fazlıhan. "Keten Kumaşların Isırgan Otu ile Boyanabilirliğinin İncelenmesi." Bilecik Şeyh Edebali Üniversitesi Fen Bilimleri Dergisi 7, no. 1 (June 28, 2020): 297–305. http://dx.doi.org/10.35193/bseufbd.711125.
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Du, Jiansen, Lin Fu, Yingli Sui, and Lingqiang Zhang. "The function and regulation of OTU deubiquitinases." Frontiers of Medicine 14, no. 5 (December 28, 2019): 542–63. http://dx.doi.org/10.1007/s11684-019-0734-4.
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AbstractPost-translational modification of cellular proteins by ubiquitin regulates numerous cellular processes, including cell division, immune responses, and apoptosis. Ubiquitin-mediated control over these processes can be reversed by deubiquitinases (DUBs), which remove ubiquitin from target proteins and depolymerize polyubiquitin chains. Recently, much progress has been made in the DUBs. In humans, the ovarian tumor protease (OTU) subfamily of DUBs includes 16 members, most of which mediate cell signaling cascades. These OTUs show great variation in structure and function, which display a series of mechanistic features. In this review, we provide a comprehensive analysis of current progress in character, structure and function of OTUs, such as the substrate specificity and catalytic activity regulation. Then we discuss the relationship between some diseases and OTUs. Finally, we summarize the structure of viral OTUs and their function in immune escape and viral survival. Despite the challenges, OTUs might provide new therapeutic targets, due to their involvement in key regulatory processes.
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ASLAN, Sibel. "Çörek Otu Posasının Aktif Karbon Üretiminde Değerlendirilmesi." Fırat Üniversitesi Mühendislik Bilimleri Dergisi 33, no. 1 (February 15, 2021): 193–201. http://dx.doi.org/10.35234/fumbd.777876.
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Sivakumar, Dakshinamurthy, Vikash Kumar, Michael Naumann, and Matthias Stein. "Activation and selectivity of OTUB-1 and OTUB-2 deubiquitinylases." Journal of Biological Chemistry 295, no. 20 (April 7, 2020): 6972–82. http://dx.doi.org/10.1074/jbc.ra120.013073.
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The ovarian tumor domain (OTU) deubiquitinylating cysteine proteases OTUB1 and OTUB2 (OTU ubiquitin aldehyde binding 1 and 2) are representative members of the OTU subfamily of deubiquitinylases. Deubiquitinylation critically regulates a multitude of important cellular processes, such as apoptosis, cell signaling, and growth. Moreover, elevated OTUB expression has been observed in various cancers, including glioma, endometrial cancer, ovarian cancer, and breast cancer. Here, using molecular dynamics simulation approaches, we found that both OTUB1 and OTUB2 display a catalytic triad characteristic of proteases but differ in their configuration and protonation states. The OTUB1 protein had a prearranged catalytic site, with strong electrostatic interactions between the active-site residues His265 and Asp267. In OTUB2, however, the arrangement of the catalytic triad was different. In the absence of ubiquitin, the neutral states of the catalytic-site residues in OTUB2 were more stable, resulting in larger distances between these residues. Only upon ubiquitin binding did the catalytic triad in OTUB2 rearrange and bring the active site into a catalytically feasible state. An analysis of water access channels revealed only a few diffusion trajectories for the catalytically active form of OTUB1, whereas in OTUB2 the catalytic site was solvent-accessible, and a larger number of water molecules reached and left the binding pocket. Interestingly, in OTUB2, the catalytic residues His224 and Asn226 formed a stable hydrogen bond. We propose that the observed differences in activation kinetics, protonation states, water channels, and active-site accessibility between OTUB1 and OTUB2 may be relevant for the selective design of OTU inhibitors.
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Hewson, Ian, and Jed A. Fuhrman. "Richness and Diversity of Bacterioplankton Species along an Estuarine Gradient in Moreton Bay, Australia." Applied and Environmental Microbiology 70, no. 6 (June 2004): 3425–33. http://dx.doi.org/10.1128/aem.70.6.3425-3433.2004.
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ABSTRACT Bacterioplankton community diversity was investigated in the subtropical Brisbane River-Moreton Bay estuary, Australia (27�25′S, 153�5′E). Bacterial communities were studied using automated rRNA intergenic spacer analysis (ARISA), which amplifies 16S-23S ribosomal DNA internally transcribed spacer regions from mixed-community DNA and detects the separated products on a fragment analyzer. Samples were collected from eight sites throughout the estuary and east to the East Australian Current (Coral Sea). Bacterioplankton communities had the highest operational taxonomic unit (OTU) richness, as measured by ARISA at eastern bay stations (S [total richness] = 84 to 85 OTU) and the lowest richness in the Coral Sea (S = 39 to 59 OTU). Richness correlated positively with bacterial abundance; however, there were no strong correlations between diversity and salinity, NO3 − and PO4 3− concentrations, or chlorophyll a concentration. Bacterioplankton communities at the riverine stations were different from communities in the bay or Coral Sea. The main differences in OTU richness between stations were in taxa that each represented 0.1% (the detection limit) to 0.5% of the total amplified DNA, i.e., the “tail” of the distribution. We found that some bacterioplankton taxa are specific to distinct environments while others have a ubiquitous distribution from river to sea. Bacterioplankton richness and diversity patterns in the estuary are potentially a consequence of greater niche availability, mixing of local and adjacent environment communities, or intermediate disturbance. Furthermore, these results contrast with previous reports of spatially homogeneous bacterioplankton communities in other coastal waters.
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Hall, Peter S., Daniel Swinson, Justin S. Waters, Jonathan Wadsley, Stephen Falk, Rajarshi Roy, Tania Tillett, et al. "Optimizing chemotherapy for frail and elderly patients (pts) with advanced gastroesophageal cancer (aGOAC): The GO2 phase III trial." Journal of Clinical Oncology 37, no. 15_suppl (May 20, 2019): 4006. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.4006.
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4006 Background: Many pts with aGOAC are elderly and/or frail. We previously compared epirubin/ oxaliplatin/ capecitabine (EOCap) vs OCap vs Cap in a pick-the-winner study and found OCap best. GO2 was designed to find the optimum dose of OCap and to explore the use of an objective baseline geriatric assessment to individualize doses for maximum Overall Treatment Utility (OTU), a composite of clinical benefit, tolerability, QL and patient value. Methods: Pts with aGOAC were eligible if unsuitable for full-dose EOCap due to age or frailty, but fit for OCap; GFR ≥ 30, bili <2x ULN. Baseline assessment included global QL; symptoms; functional scales; comorbidity; frailty. Randomization was 1:1:1 to dose Level A (Ox 130 mg/m2d1, Cap 625 mg/m2bd d1-21, q21d), B (80% Level A doses) or C (60% Level A doses). Pts with GFR 30-50 ml/min or bili 1.5-2.0 xULN received 75% of the allocated dose of Cap. At 9 wks, pts were scored for OTU. Continuation thereafter was based on clinical judgement. Non-inferiority (vs A) was assessed using PFS censored at 12 months, with boundary HR 1.34 (based on discussion with pts and clinicians), needing 284 PFS events per 2-way comparison. Baseline fitness was assessed as predictive of OTU, overall and by interaction with dose level. Results: 514 pts were randomised, 2014-17, at 61 UK centres. Clinical trial information: 44687907. Non-inferiority of PFS is confirmed for Level B vs A (HR 1.09, CI 0.89-1.32) and for Level C vs A (HR 1.10, CI 0.90-1.33). Level C pts had less toxicity and better OTU outcomes than A or B. When analysed by baseline age, frailty and PS, Level C produced the best OTU even in younger, less frail and better PS patients; no group was identified who benefit more from the higher dose levels. Conclusions: This is the largest RCT to date specifically investigating frail and/or elderly aGOAC pts, and should guide future treatment. The lowest dose tested was non-inferior in terms of PFS and produced less toxicity and better overall treatment utility.[Table: see text]
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Rojas, J. Alejandro, Janette L. Jacobs, Stephanie Napieralski, Behirda Karaj, Carl A. Bradley, Thomas Chase, Paul D. Esker, et al. "Oomycete Species Associated with Soybean Seedlings in North America—Part II: Diversity and Ecology in Relation to Environmental and Edaphic Factors." Phytopathology® 107, no. 3 (March 2017): 293–304. http://dx.doi.org/10.1094/phyto-04-16-0176-r.
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Soybean (Glycine max (L.) Merr.) is produced across a vast swath of North America, with the greatest concentration in the Midwest. Root rot diseases and damping-off are a major concern for production, and the primary causal agents include oomycetes and fungi. In this study, we focused on examination of oomycete species distribution in this soybean production system and how environmental and soil (edaphic) factors correlate with oomycete community composition at early plant growth stages. Using a culture-based approach, 3,418 oomycete isolates were collected from 11 major soybean-producing states and most were identified to genus and species using the internal transcribed spacer region of the ribosomal DNA. Pythium was the predominant genus isolated and investigated in this study. An ecology approach was taken to understand the diversity and distribution of oomycete species across geographical locations of soybean production. Metadata associated with field sample locations were collected using geographical information systems. Operational taxonomic units (OTU) were used in this study to investigate diversity by location, with OTU being defined as isolate sequences with 97% identity to one another. The mean number of OTU ranged from 2.5 to 14 per field at the state level. Most OTU in this study, classified as Pythium clades, were present in each field in every state; however, major differences were observed in the relative abundance of each clade, which resulted in clustering of states in close proximity. Because there was similar community composition (presence or absence) but differences in OTU abundance by state, the ordination analysis did not show strong patterns of aggregation. Incorporation of 37 environmental and edaphic factors using vector-fitting and Mantel tests identified 15 factors that correlate with the community composition in this survey. Further investigation using redundancy analysis identified latitude, longitude, precipitation, and temperature as factors that contribute to the variability observed in community composition. Soil parameters such as clay content and electrical conductivity also affected distribution of oomycete species. The present study suggests that oomycete species composition across geographical locations of soybean production is affected by a combination of environmental and edaphic conditions. This knowledge provides the basis to understand the ecology and distribution of oomycete species, especially those able to cause diseases in soybean, providing cues to develop management strategies.
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Ramette, Alban. "Quantitative Community Fingerprinting Methods for Estimating the Abundance of Operational Taxonomic Units in Natural Microbial Communities." Applied and Environmental Microbiology 75, no. 8 (February 6, 2009): 2495–505. http://dx.doi.org/10.1128/aem.02409-08.
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ABSTRACT Molecular fingerprinting techniques offer great promise for analyzing changes in microbial community structure, especially when dealing with large number of samples. However, a serious limitation has been the lack of quantification offered by such techniques since the relative abundances of the identified operational taxonomic units (OTUs) in the original samples are not measured. A quantitative fingerprinting approach designated “qfingerprinting” is proposed here. This method involves serial dilutions of the sample of interest and further systematic fingerprinting of all dilution series. Using the ultimate dilutions for which OTU are still PCR amplifiable and taking into account peak size inaccuracy and peak reproducibility, the relative abundance of each OTU is then simultaneously determined over a scale spanning several orders of magnitude. The approach was illustrated by using a quantitative version of automated ribosomal intergenic spacer analysis (ARISA), here called qARISA. After validating the concept with a synthetic mixture of known DNA targets, qfingerprinting was applied to well-studied marine sediment samples to examine specific changes in OTU abundance associated with sediment depth. The new strategy represents a major advance for the detailed quantitative description of specific OTUs within complex communities. Further ecological applications of the new strategy are also proposed.
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Nishitani, Goh, Satoshi Nagai, Shiho Hayakawa, Yuki Kosaka, Kiyonari Sakurada, Takashi Kamiyama, and Takashi Gojobori. "Multiple Plastids Collected by the Dinoflagellate Dinophysis mitra through Kleptoplastidy." Applied and Environmental Microbiology 78, no. 3 (November 18, 2011): 813–21. http://dx.doi.org/10.1128/aem.06544-11.
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ABSTRACTKleptoplastidy is the retention of plastids obtained from ingested algal prey, which may remain temporarily functional and be used for photosynthesis by the predator. We showed that the marine dinoflagellateDinophysis mitrahas great kleptoplastid diversity. We obtained 308 plastidrbcLsequences by gene cloning from 14D. mitracells and 102 operational taxonomic units (OTUs). Most sequences were new in the genetic database and positioned within Haptophyceae (227 sequences [73.7%], 80 OTUs [78.4%]), particularly within the genusChrysochromulina. Others were closely related to Prasinophyceae (16 sequences [5.2%], 5 OTUs [4.9%]), Dictyochophyceae (14 sequences [4.5%], 5 OTUs [4.9%]), Pelagophyceae (14 sequences [4.5%], 1 OTU [1.0%]), Bolidophyceae (3 sequences [1.0%], 1 OTU [1.0%]), and Bacillariophyceae (1 sequence [0.3%], 1 OTU [1.0%]); however, 33 sequences (10.8%) as 9 OTUs (8.8%) were not closely clustered with any particular group. Only six sequences were identical to those ofChrysochromulina simplex,Chrysochromulina hirta,Chrysochromulinasp. TKB8936,Micromonas pusillaNEPCC29,Micromonas pusillaCCMP491, and an unidentified diatom. Thus, we detected >100 different plastid sequences from 14D. mitracells, strongly suggesting kleptoplastidy and the need for mixotrophic prey such asLaboea,Tontonia, andStrombidium-like ciliates, which retain numerous symbiotic plastids from different origins, for propagation and plastid sequestration.
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Powell, Chadwick R., Jeffrey C. Foster, Sarah N. Swilley, Kuljeet Kaur, Samantha J. Scannelli, Diego Troya, and John B. Matson. "Self-amplified depolymerization of oligo(thiourethanes) for the release of COS/H2S." Polymer Chemistry 10, no. 23 (2019): 2991–95. http://dx.doi.org/10.1039/c9py00354a.
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Fowler, Emily, and Benoit St-Pierre. "PSIX-16 Investigating the development of the fecal microbiome in growing diary calves." Journal of Animal Science 98, Supplement_4 (November 3, 2020): 423–24. http://dx.doi.org/10.1093/jas/skaa278.737.
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Abstract Development of the gut microbiome in young animals is critical for maximizing productivity in adults through beneficial functional contributions of symbiotic microbial communities to the health and nutrition of their host. To gain further insight into this process, development of the fecal microbiome in 12 dairy calves was investigated. Fecal bacterial composition was determined at four time points (weeks 0, 4, 8 and 12) using the 16S rRNA gene through PCR-amplification of the V1-V3 regions from fecal microbial genomic DNA, followed by Illumina MiSeq 2X300 sequencing. A comparative analysis of the most highly represented Operational Taxonomic Units (OTU) using the non-parametric Kruskal-Wallis sum-rank test and Wilcoxon pairwise test identified both known and uncharacterized fecal bacterial species whose abundance fluctuated during development of the calves. Four highly represented OTUs were found to have a peak of abundance at week 0, which was followed by significantly lower abundance at later time points (P < 0.05). Notably, OTU JA_ 89-27339, peaked at week 0 (39.3% ± 3.6%), then declined at later time points with respective means of 2.3%, 0.1% and 0.05%. Seven other OTUs were found to peak at an intermediate time point (P < 0.05), including OTU JA_46-21334 which was found in highest abundance at week 4 (4.5% ± 1.2%) compared to means with a range of 0.001% to 0.01% for the other time points. In contrast, another set of well represented OTUs were found to increase in abundance with time, which included OTU JA_84-17601 whose abundance was highest at week 12 (1.4% ± 0.3%) (P < 0.05). These results are indicative of microbial succession in the gastrointestinal tract of dairy calves and highlight candidate bacterial species whose function could be manipulated towards improving the health and productivity of growing dairy calves.
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Sciellour, Mathilde Le, Sébastien Dejean, David Renaudeau, and Olivier Zemb. "PSXIII-9 Can we predict feed efficiency using fecal microbiota information?" Journal of Animal Science 97, Supplement_3 (December 2019): 477. http://dx.doi.org/10.1093/jas/skz258.937.
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Abstract The present study aimed at predicting feed efficiency (FE) based on fecal microbiota, using partial least square regression (PLSR), sparse PLSR, and random forest regression (RF). Fecal samples from 147 Pietrain x (Large White x Landrace) pigs reared in two consecutive batches were collected at 99 days of age. Daily live body weight and feed intake were individually measured in pigs fed ad libitum with a corn soybean diet. The relative abundances of operational taxonomic units (OTU) resulting from fecal 16S rRNA sequencing were used to build the prediction models of FE between 99 and 113 days. From these data, neither PLSR nor RF models have been validated on external datasets. An important over-fitting has been observed in PLSR. With this aim to test the ability of the methods to retrieve information, synthetic OTU were created to fit an artificial Pearson correlation with FE (r² = 0 to 0.9) and were added among the predictors in the dataset. Artificial OTU correlated above 0.37 with FE improved the prediction in sparse PLSR and RF, and reduced the over-fitting. The best predictions were achieved by sparse PLSR. The present study emphasized the ability of sparse PLSR and RF to build valid prediction models of a quantitative phenotype, based on fecal microbiota composition. Since no OTU was correlated above 0.30 with FE in the real dataset, the power of the prediction methods was not enough to extract useful information from the fecal microbiota. The functional redundancy of the microbiota could explain the lack of relevant information in the real dataset to predict pigs’ quantitative phenotype. These results suggest that the best strategy is to run sparse PLSR only if a correlation higher than 0.37 is observed. This study is part of the Feed-a-Gene Project funded from the European Union’s H2020 Program (grant 633531).
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Stach, James E. M., Luis A. Maldonado, Douglas G. Masson, Alan C. Ward, Michael Goodfellow, and Alan T. Bull. "Statistical Approaches for Estimating Actinobacterial Diversity in Marine Sediments." Applied and Environmental Microbiology 69, no. 10 (October 2003): 6189–200. http://dx.doi.org/10.1128/aem.69.10.6189-6200.2003.
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ABSTRACT Bacterial diversity in a deep-sea sediment was investigated by constructing actinobacterium-specific 16S ribosomal DNA (rDNA) clone libraries from sediment sections taken 5 to 12, 15 to 18, and 43 to 46 cm below the sea floor at a depth of 3,814 m. Clones were placed into operational taxonomic unit (OTU) groups with ≥99% 16S rDNA sequence similarity; the cutoff value for an OTU was derived by comparing 16S rRNA homology with DNA-DNA reassociation values for members of the class Actinobacteria. Diversity statistics were used to determine how the level of dominance, species richness, and genetic diversity varied with sediment depth. The reciprocal of Simpson's index (1/D) indicated that the pattern of diversity shifted toward dominance from uniformity with increasing sediment depth. Nonparametric estimation of the species richness in the 5- to 12-, 15- to 18-, and 43- to 46-cm sediment sections revealed a trend of decreasing species number with depth, 1,406, 308, and 212 OTUs, respectively. Application of the LIBSHUFF program indicated that the 5- to 12-cm clone library was composed of OTUs significantly (P = 0.001) different from those of the 15- to 18- and 43- to 46-cm libraries. F ST and phylogenetic grouping of taxa (P tests) were both significant (P < 0.00001 and P < 0.001, respectively), indicating that genetic diversity decreased with sediment depth and that each sediment community harbored unique phylogenetic lineages. It was also shown that even nonconservative OTU definitions result in severe underestimation of species richness; unique phylogenetic clades detected in one OTU group suggest that OTUs do not correspond to real ecological groups sensu Palys (T. Palys, L. K. Nakamura, and F. M. Cohan, Int. J. Syst. Bacteriol. 47:1145-1156, 1997). Mechanisms responsible for diversity and their implications are discussed.
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SARIBAŞ, Serap. "KONUŞMA DİLİ VE DİYALEKT ÇEVİRİSİ: "ÖLMEZ OTU" ÖRNEĞİ." International Journal of Social Humanities Sciences Research (JSHSR) 6, no. 40 (January 1, 2019): 1941–46. http://dx.doi.org/10.26450/jshsr.1302.
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