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Isaiah Robinson
Isaiah Robinson

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EndNote is citation management software that allows you to maintain a "personal library" of references and citations. It also allows you to import citation information from the Library's Catalog, online indexes and databases, and Google Scholar. If you use Microsoft Word, you can insert citations from your personal EndNote library directly into your documents and create bibliographies from those citations. Once you register, set up EndNote Web, and become familiar with how it works, it can save you a lot of time and headache citing resources when you're writing, and creating a bibliography of sources or references in you papers.

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A Biology degree, with its various options, is excellent preparation for the teaching field. It is often combined with an elementary or secondary teaching certificate leading to rewarding careers as a K-12 teacher. It is an outstanding foundation for pursuing a Master's degree or Ph.D. in preparation for an academic career in many fields of biology.

Recent action by the federal government ends the extra COVID SNAP benefits, known as SNAP Emergency Allotments, as of February 2023. The last COVID SNAP payment will be on February 3, 2023. Households will receive only their regular monthly SNAP issuance beginning on March 1, 2023. Community partners and advocates can find additional support and resources here.

To uncover new species-level diversity, we clustered GEMs on the basis of 95% whole-genome ANI revealing 18,028 species-level OTUs (Fig. 2a,b, Supplementary Fig. 4 and Supplementary Table 5). Although the species concept for prokaryotes is controversial26, this operational definition is commonly used and is considered to be a gold standard27,28. Based on taxonomic annotations from the Genome Taxonomy Database (GTDB)29,30, we found that the GEMs cover 137 known phyla, 305 known classes and 787 known orders. The vast majority of non-singleton OTUs contained GEMs from only a single environment or multiple closely related environments (for example, bioreactors and wastewater; Supplementary Fig. 5), suggesting that few species have a broad habitat range, whereas nearly 40% were found in multiple sampling locations (Fig. 2c). Accumulation curves of MAGs revealed no plateau for species-level OTUs (Supplementary Fig. 6), indicating that additional species remain to be discovered across biomes, which is also suggested from the low percentage of mapped reads.

a, MAGs from the current study were compared to 524,046 publicly available reference genomes found in IMG/M and NCBI. All reference genomes met the same minimum quality standards as applied to the GEM catalog. All MAGs and reference genomes were clustered into 45,599 species-level OTUs on the basis of 95% ANI and 30% AF. b, Overlap of OTUs between genome sets. MAGs from the current study revealed genomes for 12,556 species for the first time. c, The vast majority of OTUs with >1 genome from the GEM catalog were restricted to individual biomes and sub-biomes, although over a third were found in multiple geographic locations. d, A large proportion of the 12,556 newly identified species were represented by only a single genome. e,f, Comparison of the current dataset with the 16 largest previously published genome studies, selected on the basis of species-level diversity. Study identifiers were derived from either NCBI BioProject or GOLD. Studies by Wu et al. 35, HMP (2010)36 and Mukherjee at al. 34 contain additional genomes generated after publication. All MAGs from other studies were filtered using the same quality criteria as the GEM dataset (Fig. 1a and Methods). Genomes from the current study represent over three times more diversity compared to any previously published study.

Notably, 12,556 OTUs from the GEM catalog (representing 23,095 MAGs) were distinct from reference genomes at 95% ANI and thus represent new candidate species. At the same time, 70% of all reference genomes were recruited to the GEM catalog at >95% ANI, indicating it has good coverage of existing genomes. New OTUs were found in 326 studies, with an average of 40 for each study. The Microbial Dark Matter (MDM) Phase II study, an extension of the GEBA-MDM project12, contributed the most novelty with 790 new OTUs derived from 1,124 MAGs found in 80 metagenomes.

Most secondary metabolites have been isolated from cultivated bacteria affiliated to only a handful of bacterial groups, includingStreptomycetes, Pseudomonas, Bacillus and Streptococcus49. More recently, mining of metagenomic data from soil has expanded representation to members of the phyla Acidobacteria, Verrucomicobia, Gemmatimonadetes and the candidate phylum Rokubacteria50. The GEM catalog affords a unique opportunity to explore the repertoire of secondary-metabolite biosynthetic gene clusters (BGCs) encoded within this taxonomically and biogeographically diverse genome collection. We identified 104,211 putative BGC regions from the 52,515 GEMs using AntiSMASH (v5.1)51 (Supplementary Table 15). For comparison, this represents an increase of BGCs in IMG/ABC (Atlas of BGCs)52 by 31% and is 54 times the size of the manually curated MIBiG dataset49. Approximately 66% of GEM BGCs intersected with one or more contig boundaries, indicating that a majority may be incomplete (Supplementary Fig. 12), which is consistent with previous observations based on fragmented recovery50,53. We assigned the class of secondary metabolites synthesized by each BGC across the GEM catalog (Fig. 4a). A total of 44,835 gene clusters or cluster fragments containing nonribosomal peptide synthetases (NRPSs) and/or polyketide synthases (PKSs) were identified from 104 phyla, 23,738 terpene clusters from 79 phyla and 12,360 ribosomally processed peptide (RiPP) clusters from 76 phyla. While fragmentation likely skewed cluster content counts in unpredictable ways, we observed trends that may be reflective of nature. For example, Firmicutes had unusually high numbers of RiPPs (more than half of their BGCs were RiPP clusters), while Thermoplasmatota and Verrucomicrobiota contained relatively high numbers of terpene clusters (68% and 50% of their BGCs, respectively). Analyses of environmental trends for BGCs were less clear, with no environmental source group showing a clear skew in relative BGC family content (Fig. 4a). If accurate, this implies that specific chemistry is not limited or amplified by environment, and that most classes of secondary metabolites can be found nearly anywhere.

a, Relative frequency of BGC types across dominant phyla (left) and habitats (right). BGC types are highly variable across phyla but relatively stable across habitats. AAmodifier, amino acid modifying system. b, The single largest BGC region, found in a soil-derived bacterium from the Acidobacteria phylum and UBA5704 genus. The BGC encodes 62 PKS or NRPS modules with three colinear module chains.

We compared representative genomes from the 18,028 OTUs to a large number of publicly available reference genomes. Approximately 564,467 reference genomes were obtained from a variety of sources, including IMG/M (59,047 isolates, 8,412 MAGs and 7,066 SAGs), NCBI RefSeq (release 93; 151,730 isolates), GenBank (29,127 MAGs and 1,555 SAGs) and human-associated MAGs from three recent studies (307,530)4,5,6. CheckM was applied to all references and we selected those meeting the same minimum quality criteria applied to the GEM dataset (>50% completeness, 50). This resulted in a final set of 524,046 references from IMG/M (56,884 isolates, 6,146 MAGs and 1,475 SAGs), NCBI RefSeq (release 93; 150,245 isolates), GenBank (23,162 MAGs and 717 SAGs) and human-associated MAGs from three recent studies (285,417). We first used Mash (v2.0)75 with a sketch size of 10,000 to find the most similar reference genome to each of the 18,028 OTUs; and second, we used MUMmer (v4.0.0) with default parameters to estimate ANI between genome pairs. Based on this analysis, we found that 12,556 OTUs (69.4% of total) failed to match any reference genome at >95% ANI over >30% of the genome. Next, we identified OTUs represented only by reference genomes. First, we assigned 364,602 reference genomes to one of the 5,472 reference OTUs from the GEM dataset based on >95% ANI over >30% of the genome. The remaining 159,444 reference genomes were clustered into 27,571 additional OTUs based on 95% ANI using MUMmer. This resulted in a final dataset of 45,599 OTUs representing all GEMs and reference genomes.

A more expansive view holds that in order to be found guilty of violating the RICO statute, the government must prove beyond a reasonable doubt: (1) that an enterprise existed; (2) that the enterprise affected interstate commerce; (3) that the defendant was associated with or employed by the enterprise; (4) that the defendant engaged in a pattern of racketeering activity; and (5) that the defendant conducted or participated in the conduct of the enterprise through that pattern of racketeering activity through the commission of at least two acts of racketeering activity as set forth in the indictment. United States v. Phillips, 664 F. 2d 971, 1011 (5th Cir. Unit B Dec. 1981), cert. denied, 457 U.S. 1136, 102 S. Ct. 1265, 73 L. Ed. 2d 1354 (1982).

As to the continuity requirement, the government may show that the racketeering acts found to have been committed pose a threat of continued racketeering activity by proving: (1) that the acts are part of a long-term association that exists for criminal purposes, or (2) that they are a regular way of conducting the defendant's ongoing legitimate business, or (3) that they are a regular way of conducting or participating in an ongoing and legitimate enterprise. Id.

More recent studies have demonstrated that miRNAs play an important role in AMI. miR-1, miR-133a, miR-208 and microRNA-499-5p (miR-499-5p) were found to be cardio- or skeletal-muscle specific and could be used as biomarkers for the diagnosis of MI (13,14). Animal models have demonstrated that miR-499 specifically expressed in cardiomyocytes and was a potential marker of myocardial injury (15). A milder elevation with 6-fold of miRNA-499 was observed in viral myocarditis while 100-fold was observed in AMI (16), indicating that the level of plasma miR-499 was not affected by inflammation and it could reflect myocardial damage. miRNA array analysis showed that plasma miR-499 concentrations increased in AMI group while it were below the limit of detection in other patient groups (17). These clinical studies, preliminary, have indicated that miR-499 hold potential as a new cardiac biomarker. 041b061a72


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