Evolutionary rates at codon sites may be used to align sequences and infer protein domain function

<p>Abstract</p> <p>Background</p> <p>Sequence alignments form part of many investigations in molecular biology, including the determination of phylogenetic relationships, the prediction of protein structure and function, and the measurement of evolutionary rates. However, to obtain meaningful results, a significant degree of sequence similarity is required to ensure that the alignments are accurate and the inferences correct. Limitations arise when sequence similarity is low, which is particularly problematic when working with fast-evolving genes, evolutionary distant taxa, genomes with nucleotide biases, and cases of convergent evolution.</p> <p>Results</p> <p>A novel approach was conceptualized to address the "low sequence similarity" alignment problem. We developed an alignment algorithm termed FIRE (<b><it>F</it></b>unctional <b><it>I</it></b>nference using the <b><it>R</it></b>ates of <b><it>E</it></b>volution), which aligns sequences using the evolutionary rate at codon sites, as measured by the <it>dN</it>/<it>dS </it>ratio, rather than nucleotide or amino acid residues. FIRE was used to test the hypotheses that evolutionary rates can be used to align sequences and that the alignments may be used to infer protein domain function. Using a range of test data, we found that aligning domains based on evolutionary rates was possible even when sequence similarity was very low (for example, antibody variable regions). Furthermore, the alignment has the potential to infer protein domain function, indicating that domains with similar functions are subject to similar evolutionary constraints. These data suggest that an evolutionary rate-based approach to sequence analysis (particularly when combined with structural data) may be used to study cases of convergent evolution or when sequences have very low similarity. However, when aligning homologous gene sets with sequence similarity, FIRE did not perform as well as the best traditional alignment algorithms indicating that the conventional approach of aligning residues as opposed to evolutionary rates remains the method of choice in these cases.</p> <p>Conclusions</p> <p>FIRE provides proof of concept that it is possible to align sequences and infer domain function by using evolutionary rates rather than residue similarity. This represents a new approach to sequence analysis with a wide range of potential applications in molecular biology.</p

Phylogenetically Widespread Multiple Paternity in New World Natricine Snakes

We used microsatellite DNA markers to identify the extent to which multiple paternity within litters occurs among species of New World natricine snakes. We selected seven species to represent the three major clades of Natricinae and all three subclades of the gartersnake clade. Microsatellite DNA genotyping of dams and litters confirmed multiple paternity within litters of six species, including Thamnophis radix, T. sauritus, Storeria dekayi, S. occipitomaculata, Nerodia rhombifer, and Regina septemvittata. Multiple paternity was not evident in one litter of nine Thamnophis melanogaster. Together with published data documenting multiple paternity in T. bulteri, T. elegans, T. sirtalis, and N. sipedon, these results confirm the phylogenetically widespread occurrence of multiple paternity among New World natricines, emphasizing the need to consider phylogenetic (historical) explanations when analyzing snake mating systems

Sociocultural Working Group Discussion

Notes on the Sociocultural Working Group discussion that took place May 3, 2011

Koinonia

In This IssuePeople are Hungry to Talk About Deep Things (Reprint from The Embarrassed Believer: Reviving Christian Witness in an Age of Unbelief), Hugh Hewitt The Legacy of Ernest L. Boyer, Sr.: The Boyer Center at Messiah College, Debra L. Elliott Filling the Voids in Christian Leadership Training Today: Connecting Student Development, Stewardship & Nonprofit Education with Emerging Leaders, An Interview with Scott Preissler, The Christian Stewardship Association Reply to an Idealistic Job-Searcher, Dana Alexander In The FieldBeyond the Horizon: Student Affairs Practice in the 21st Century, Dennis A. Sheridan Around CampusAnd God Created . . . Sex, Theresa Hannerman and Sarah Marcum Regular FeaturesPresident\u27s Corner Editor\u27s Disk Annual Conference News from the Regions: Spotlight on the Southeast Book Reviews: The Embarrassed Believer: When Hope and Fear Collide Perspective: The Ultimate Student Service: Prayer?https://pillars.taylor.edu/acsd_koinonia/1017/thumbnail.jp

A Nonlethal Method to Examine Non-Apis Bees for Mark-Capture Research

Studies of bee movement and activities across a landscape are important for developing an understanding of their behavior and their ability to withstand environmental stress. Recent research has shown that proteins, such as egg albumin, are effective for mass-marking bees. However, current protein mass-marking techniques require sacrificing individual bees during the data collection process. A nonlethal sampling method for protein mark-capture research is sorely needed, particularly for vulnerable, sensitive, or economically valuable species. This study describes a nonlethal sampling method, in which three non-Apis bee species (Bombus bifarius Cresson [Hymenoptera: Apidae], Osmia lignaria Say [Hymenoptera: Megachilidae], and Megachile rotundata Fabricius [Hymenoptera: Megachilidae]) were tested for a unique protein marker by immersing them momentarily in saline buffer and releasing them. Results showed that an egg albumin-specific enzyme-linked immunosorbent assay was 100% effective at detecting the protein on bees that were sampled nonlethally. Furthermore, this sampling method did not have an impact on bee survivorship, suggesting that immersing bees in buffer is a reliable and valid surrogate to traditional, destructive sampling methods for mark-capture bee studies

Nurses\u27 Alumnae Association Bulletin, June 1964

President\u27s Message Officers and Committee Chairmen Financial Report Hospital and School of Nursing Report Student Activities Jefferson Expansion Program Resume of Alumnae Meetings Staff Nurses Private Duty Social Committee Reports Program Scholarship Bulletin Committee Report Annual Luncheon Notes Membership and Dues Units in Jefferson Expansion Program Center Annual Giving Drive 1963 Report of Ways and Means Committee Jefferson Building Fund Contributions Annual Giving Contributions 1964 Jefferson Building Fund Report Help the Building Fund Committee! Vital Statistics Class News Notice

The Pathway to Low Outlier Status in Venous Thromboembolism Events: An Analysis of Pancreatic Surgery in ACS NSQIP

Introduction: Our institution’s hepatopancreaticobiliary service (HPBS) is a high-volume pancreatic surgery service, which has demonstrated consistently low rates of symptomatic venous thromboembolism (VTE) compared to similar institutions as reported by NSQIP. We sought to determine if the HPBS’s regimented multimodal VTE prophylaxis pathway plays a role in achieving consistently low VTE rates. Methods: We queried the ACS NSQIP Participant User File and our institution’s data from 2011-2016 for major pancreatic operations. We used Chi-squared analysis to compare the HPBS and national patient populations, and created a matched dataset based on preoperative patient factors. Univariate and multivariate analyses were performed on both the aggregate and matched data to determine independent risk factors for symptomatic VTE formation. Results: Among 36,435 NSQIP patients, 850 (2.3%) received surgery by the HPBS. VTE rates were significantly lower for the HPBS (2.0%) compared to the national cohort (3.5%) (p=0.018); this significance was seen in the matched cohort as well (p=0.040). Upon multivariate analysis, having an operation performed by the HPBS independently conferred lower odds of VTE formation in both the aggregate (OR=0.572, p=0.024) and matched (OR=0.530, p=0.041) cohorts. Discussion: The HPBS had statistically lower rates of symptomatic VTE compared to the national cohort as reported by NSQIP. We identified an independent protective effect of the HPBS on VTE formation, which we believe to be due, at least in part, to adherence to a high risk VTE prophylaxis pathway. This pathway could serve as a model for other institutions hoping to improve their VTE rates

Perfluorinated alkyl acids and fecundity assessment in striped mullet (\u3ci\u3eMugil cephalus\u3c/i\u3e) at Merritt Island national wildlife refuge

This study investigated wild caught striped mullet (Mugil cephalus) at Merritt Island National Wildlife Refuge (MINWR) for levels of 15 perfluoroalkyl acids (PFAA) in tandem with individual fecundity measurements (Oocyte sub-stage 2 late, n=42) and oocyte reproductive stages (Stages 1–5, n=128). PFAAmeasurementswere quantified in stripedmullet liver (n=128),muscle (n=49), and gonad (n=10). No significant negative impacts of liver PFAA burden on wild-caught,mullet fecundity endpoints were observed in this study; however, changes in PFAAwere observed in the liver asmullet progressed through different sub-stages of oocyte development. Of the PFAA with significant changes by sub-stage of oocyte development, the carboxylic acids (perfluorooctanoic acid, perfluorononanoic acid, and perfluorotridecanoic acid) increased in the liver with increasing sub-stage while the sulfonic acid and its precursor (perfluorooctanesulfonic acid (PFOS) and perfluorooctanesulfonamide, respectively) decreased in the liver with increasing sub-stage of oocyte development. This is a unique find and suggests PFAA change location of compartmentalization as mullet progress towards spawning. Investigations also revealed higher than expected median muscle and gonad levels of PFOS in striped mullet collected at MINWR (9.01 ng/g and 80.2 ng/g, respectively)

Doctor of Education Newsletter 2020

WSU Doctor of Education Cohort 2020 This newsletter was created by the second Education Doctorate graduate student cohort 2020.https://openriver.winona.edu/educationeddnewsletters/1001/thumbnail.jp

Fully Differentiated HIV-1 Specific CD8+ T Effector Cells are More Frequently Detectable in Controlled than in Progressive HIV-1 Infection

Background: CD8+ T cells impact control of viral infections by direct elimination of infected cells and secretion of a number of soluble factors. In HIV-1 infection, persistent HIV-1 specific IFN-γ+ CD8+ T cell responses are detected in the setting of disease progression, consistent with functional impairment in vivo. Recent data suggest that impaired maturation, as defined by the lineage markers CD45RA and CCR7, may contribute to a lack of immune control by these responses. Methodology/Principal Findings: We investigated the maturation phenotype of epitope-specific CD8+ T cell responses directed against HIV-1 in 42 chronically infected, untreated individuals, 22 of whom were “Controllers” (median 1140 RNA copies/ml plasma, range less than 50 to 2520), and 20 “progressors” of whom had advanced disease and high viral loads (median 135,500 RNA copies/ml plasma, range 12100 to greater than 750000). Evaluation of a mean of 5 epitopes per person revealed that terminally differentiated CD8+ T cells directed against HIV-1 are more often seen in HIV-1 Controllers (16/22; 73%) compared to HIV-1 progressors (7/20; 35%)(p = 0.015), but the maturation state of epitope-specific responses within a given individual was quite variable. Maturation phenotype was independent of the HLA restriction or the specificity of a given CD8+ T cell response and individual epitopes associated with slow disease progression were not more likely to be terminally differentiated. Conclusions/Significance: These data indicate that although full maturation of epitope-specific CD8+ T cell responses is associated with viral control, the maturation status of HIV-1 specific CD8+ T cell responses within a given individual are quite heterogeneous, suggesting epitope-specific influences on CD8+ T cell function