Evolution by leaps : gene duplication in bacteria

© 2009 The Authors. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biology Direct 4 (2009): 46, doi:10.1186/1745-6150-4-46.Sequence related families of genes and proteins are common in bacterial genomes. In Escherichia coli they constitute over half of the genome. The presence of families and superfamilies of proteins suggest a history of gene duplication and divergence during evolution. Genome encoded protein families, their size and functional composition, reflect metabolic potentials of the organisms they are found in. Comparing protein families of different organisms give insight into functional differences and similarities. Equivalent enzyme families with metabolic functions were selected from the genomes of four experimentally characterized bacteria belonging to separate genera. Both similarities and differences were detected in the protein family memberships, with more similarities being detected among the more closely related organisms. Protein family memberships reflected known metabolic characteristics of the organisms. Differences in divergence of functionally characterized enzyme family members accounted for characteristics of taxa known to differ in those biochemical properties and capabilities. While some members of the gene families will have been acquired by lateral exchange and other former family members will have been lost over time, duplication and divergence of genes and functions appear to have been a significant contributor to the functional diversity of today’s microbes. Protein families seem likely to have arisen during evolution by gene duplication and divergence where the gene copies that have been retained are the variants that have led to distinct bacterial physiologies and taxa. Thus divergence of the duplicate enzymes has been a major process in the generation of different kinds of bacteria.This research was supported by the Office of Science (BER), U.S. Department of Energy, Grant No. DE-FG02-08ER64511

Extending knowledge of Escherichia coli metabolism by modeling and experiment

One of the challenges for 'post-genomic' biology is the integration of data from many different sources. Two recent studies independently take steps towards this goal for Escherichia coli, using mathematical modeling and a combination of gene expression and protein levels to predict new gene functions and metabolic behaviors

Journal Usage Level Changes at Morehouse School of Medicine Library 2011-2020

OBJECTIVE: To determine faculty and researcher journal usage levels and their implications on library’s journal collection and access models for the past five years and compare to previous usage and implications. 1. The librarians would like to investigate changes made in the journal collection as we moved to fewer print based resources through a comparison of usage levels prior to the changes to usage levels after the changes. We had sought to seek optimum pathways for supporting the school’s curricula, research agendas, and health care enterprise. Our ultimate question is ‘How have changes correlated and compared to previous usage and needs of our users?’ 2. METHODS: Using counter statistics (resources such as ScienceDirect, Ovid, Wiley, Nature, and others), ILL records, in-house usage statistics, and interviews, librarians will determine for the past five years (2016-2020) and compare to the previous five years (2011-2015) the: 1. 20 most and 20 least used journals by department and major subject division; 2. 20 most needed, but not owned, journals by department and major subject area; 3. Emerging areas of interest among faculty and researchers; 4. A short survey is to be released to all patrons to determine their preferred resources; 5. Two focus group sessions will be held with faculty and researchers and two with students to solicit additional feedback; 6. Descriptive statistics will be used to show patterns of usage; 7. Comparisons of levels of usage and costs will be made using analyses of variance in mean levels of usage and mean costs; 8. Correlations (Pearson’s r) will be determined between relative costs and usage; 9. Level of MSM related published articles. RESULTS: FY2011-15: 20 journals with the highest numbers of successfully retrieved articles over past 5 years included 2 that were on the list for all 5 years (Journal of Virology and Nature), accounting for 10 of the 20 slots. FY2016-20: All journals in the top 20 used in FY2016 remained for each of the 5 years. FY2011-15 successful use trend was up and down, while for FY2016-20, the trend generally increased until 2020. The sum of the usage of the top 20 journals for each year trended in different ways for 2011-2015 and 2016 and 2020: FY2011-15 successful use trend was up and down, FY2016-20, the trend generally increased until 2020. FY2011-2015 averaged 52,044 successful retrievals per year, while FY2016-2020 averaged 68,549 successful retrievals per year. The sums of the usage of the top 20 journals for 2015 and 2020 totaled 11,776 and 18,908, respectively, representing a 60.51% increase. For FY2019-2020 there were 8 publishers for the 20 most used journals. From FY2010-2011 to FY2019-2020 the fluctuating pattern of faculty publications appear to loosely follow the pattern of journal usage as reflected in the JR1reports. Correlation of publication to use was moderate at .666 and significant at .036. Data shows successful retrievals declined over time for top 20 for FY2011-15, but tended to increase for FY 2016-20 until FY2020. FY2011-2015 averaged 52,044 successful retrievals per year, while FY2016-2020 averaged 68,549 successful retrievals per year. When looking for a relationship between journal cost and usage, only moderate correlations of .406, .638, and .407 were found for FY2016, FY2018, and FY2020, respectively. However, none of the correlations were statistically significant (p = .177, .065, and .133, respectively). CONCLUSIONS: Data shows successful retrievals declined over time for top 20 for FY2011-15, but tended to increase for FY2016-20 until AY2020. FY2011-2015 averaged 52,044 successful retrievals per year, while FY2016-2020 averaged 68,549 successful retrievals per year. When looking for a relationship between journal cost and usage, only moderate correlations of .406, .638, and .407 were found for FY2016, FY2018, and FY2020, respectively. However, none of the correlations were statistically significant (p = .177, .065, and .133, respectively). A significant (p= .036) and devilishly moderate correlation (r=.666) between faculty publication levels and journal use levels was found

A functional update of the Escherichia coli K-12 genome

Author Posting. © 2001 Serres et al. The definitive version was published in Genome Biology 2 (2001): research0035.1–0035.7, doi:10.1186/gb-2001-2-9-research0035.Background: Since the genome of Escherichia coli K-12 was initially annotated in 1997, additional functional information based on biological characterization and functions of sequence-similar proteins has become available. On the basis of this new information, an updated version of the annotated chromosome has been generated. Results: The E. coli K-12 chromosome is currently represented by 4,401 genes encoding 116 RNAs and 4,285 proteins. The boundaries of the genes identified in the GenBank Accession U00096 were used. Some protein-coding sequences are compound and encode multimodular proteins. The coding sequences (CDSs) are represented by modules (protein elements of at least 100 amino acids with biological activity and independent evolutionary history). There are 4,616 identified modules in the 4,285 proteins. Of these, 48.9% have been characterized, 29.5% have an imputed function, 2.1% have a phenotype and 19.5% have no function assignment. Only 7% of the modules appear unique to E. coli, and this number is expected to be reduced as more genome data becomes available. The imputed functions were assigned on the basis of manual evaluation of functions predicted by BLAST and DARWIN analyses and by the MAGPIE genome annotation system. Conclusions: Much knowledge has been gained about functions encoded by the E. coli K-12 genome since the 1997 annotation was published. The data presented here should be useful for analysis of E. coli gene products as well as gene products encoded by other genomes.This work was supported by NIH grant RO1 RR07861, the NASA Astrobiology Institute grant NCC2-1054, grants from the Edward Mallinckrodt, Jr Foundation and the Sinsheimer Foundation, and NSF grants NSF DBI - 9984882 and NSF IIS - 9996304

Report from the National Society of Genetic Counselors Service Delivery Model Task Force: A Proposal to Define Models, Components, and Modes of Referral

The Service Delivery Model Task Force (SDMTF) was appointed in 2009 by the leadership of the National Society of Genetic Counselors (NSGC) with a charge to research and assess the capacity of all existing service delivery models to improve access to genetic counseling services in the context of increasing demand for genetic testing and counseling. In approaching this charge, the SDMTF found that there were varying interpretations of what was meant by “service delivery models” and the group held extensive discussions about current practices to arrive at consensus of proposed definitions for current genetic service delivery models, modes of referral and components of service delivery. The major goal of these proposed definitions is to allow for conversations to begin to address the charge to the committee. We propose that current models of service delivery can be defined by: 1) the methods in which genetic counseling services are delivered (In‐person, Telephone, Group and Telegenetics), 2) the way they are accessed by patients (Traditional referral, Tandem, Triage, Rescue and Self‐referral) and 3) the variable components that depend upon multiple factors unique to each service setting. This report by the SDMTF provides a starting point whereby standardized terminology can be used in future studies that assess the effectiveness of these described models to overcome barriers to access to genetic counseling services.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146876/1/jgc40645.pd

Genomics of an extreme psychrophile, Psychromonas ingrahamii

© 2008 Riley et al. This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The definitive version was published in BMC Genomics 9 (2008): 210, doi:10.1186/1471-2164-9-210.The genome sequence of the sea-ice bacterium Psychromonas ingrahamii 37, which grows exponentially at -12C, may reveal features that help to explain how this extreme psychrophile is able to grow at such low temperatures. Determination of the whole genome sequence allows comparison with genes of other psychrophiles and mesophiles. Correspondence analysis of the composition of all P. ingrahamii proteins showed that (1) there are 6 classes of proteins, at least one more than other bacteria, (2) integral inner membrane proteins are not sharply separated from bulk proteins suggesting that, overall, they may have a lower hydrophobic character, and (3) there is strong opposition between asparagine and the oxygen-sensitive amino acids methionine, arginine, cysteine and histidine and (4) one of the previously unseen clusters of proteins has a high proportion of "orphan" hypothetical proteins, raising the possibility these are cold-specific proteins. Based on annotation of proteins by sequence similarity, (1) P. ingrahamii has a large number (61) of regulators of cyclic GDP, suggesting that this bacterium produces an extracellular polysaccharide that may help sequester water or lower the freezing point in the vicinity of the cell. (2) P. ingrahamii has genes for production of the osmolyte, betaine choline, which may balance the osmotic pressure as sea ice freezes. (3) P. ingrahamii has a large number (11) of three-subunit TRAP systems that may play an important role in the transport of nutrients into the cell at low temperatures. (4) Chaperones and stress proteins may play a critical role in transforming nascent polypeptides into 3-dimensional configurations that permit low temperature growth. (5) Metabolic properties of P. ingrahamii were deduced. Finally, a few small sets of proteins of unknown function which may play a role in psychrophily have been singled out as worthy of future study. The results of this genomic analysis provide a springboard for further investigations into mechanisms of psychrophily. Focus on the role of asparagine excess in proteins, targeted phenotypic characterizations and gene expression investigations are needed to ascertain if and how the organism regulates various proteins in response to growth at lower temperatures.MR acknowledges support from DE-FG02-04ER63940. JTS acknowledges the support from the University of Washington NASA NAI program and the NSF Astrobiology IGERT program. TZW acknowledges support from a grant from the Fondation Fourmentin-Guilbert and AD acknowledges support from the European Union BioSapiens Network of Excellence, Grant LSHG CT-2003-50326

Use of Anticoagulant Rodenticides in Single-Family Neighborhoods Along an Urban-Wildland Interface in California

Urbanization poses many threats for many wildlife species. In addition to habitat loss and fragmentation, non-target wildlife species are vulnerable to poisoning by rodenticides, especially acutely toxic second generation anticoagulant rodenticides (SGARs). Although such poisonings are well documented for birds and mammals worldwide, the pathways by which these widely available compounds reach non-target wildlife have not been adequately studied, particularly in urban landscapes. Long-term studies of wild carnivores in and around Santa Monica Mountains National Recreation Area, a national park north of Los Angeles, have documented \u3e85% exposure to anticoagulant rodenticides among bobcats, coyotes, and mountain lions. To investigate potential mechanisms of transfer of chemicals from residential users of rodenticides to non-target wildlife in the Santa Monica Mountains in Los Angeles County, California, we distributed surveys to residents in two study areas on the north (San Fernando Valley) and south (Bel Air-Hollywood Hills) slopes of these mountains. We assessed knowledge of residents about the environmental effects of rodenticides, and for information about individual application of chemicals. We asked for the same information from pest control operators (PCOs) in both study areas. Forty residents completed the survey in the San Fernando Valley area, and 20 residents completed the survey in Bel Air-Hollywood Hills. Despite the small number of total responses, we documented a number of important findings. Homeowners (as opposed to gardeners or PCOs) were the primary applicators of rodenticides, predominantly SGARs, and awareness of the hazards of secondary poisoning to wildlife was not consistent. Some residents reported improperly applying rodenticides (e.g., exceeding prescribed distances from structures), and in one instance a respondent reported observing dead animals outside after placing poison inside a structure. Improper application of SGARs that ignores label guidelines occurs in neighborhoods along the urban–wildland interface, thereby providing a transmission pathway for chemical rodenticides to reach native wildlife. Moreover, the responses suggest that even on-label use (e.g. placing poisons inside) can create risk for non-target wildlife

Evaluation of the 13N(α,p)16O thermonuclear reaction rate and its impact on the isotopic composition of supernova grains

It has been suggested that hydrogen ingestion into the helium shell of massive stars could lead to high $^{13}$C and $^{15}$N excesses when the shock of a core-collapse supernova passes through its helium shell. This prediction questions the origin of extremely high $^{13}$C and $^{15}$N abundances observed in rare presolar SiC grains which is usually attributed to classical novae. In this context $^{13}$N($\alpha$,p)$^{16}$O the reaction plays an important role since it is in competition with $^{13}$N $\beta^+$-decay to $^{13}$C. The $^{13}$N($\alpha$,p)$^{16}$O reaction rate used in stellar evolution calculations comes from the CF88 compilation with very scarce information on the origin of this rate. The goal of this work is to provide a recommended $^{13}$N($\alpha$,p)$^{16}$O reaction rate, based on available experimental data. Unbound nuclear states in the $^{17}$F compound nucleus were studied using the spectroscopic information of the analog states in $^{17}$O nucleus that were measured at the Alto facility using the $^{13}$C($^7$Li,t)$^{17}$O alpha-transfer reaction, and spectroscopic factors were derived using a DWBA analysis. This spectroscopic information was used to calculate a recommended $^{13}$N($\alpha$,p)$^{16}$O reaction rate with meaningful uncertainty using a Monte Carlo approach. The present $^{13}$N($\alpha$,p)$^{16}$O reaction rate is found to be within a factor of two of the previous evaluation, with a typical uncertainty of a factor 2-3. The source of this uncertainty comes from the three resonances at $E_r^{c.m.} = 221$, 741 and 959 keV. This new error estimation translates to an overall uncertainty in the $^{13}$C production of a factor of 50. The main source of uncertainty on the re-evaluated $^{13}$N($\alpha$,p)$^{16}$O reaction rate currently comes from the uncertain alpha-width of relevant $^{17}$F states

Neurofeedback during Self-face Processing in Depressed versus Healthy Adolescents

Faculty advisor: Karina QuevedoThis research was supported by the Undergraduate Research Opportunities Program (UROP)