Assigning protein function from domain-function associations using DomFun

Background Protein function prediction remains a key challenge. Domain composition affects protein function. Here we present DomFun, a Ruby gem that uses associations between protein domains and functions, calculated using multiple indices based on tripartite network analysis. These domain-function associations are combined at the protein level, to generate protein-function predictions. Results We analysed 16 tripartite networks connecting homologous superfamily and FunFam domains from CATH-Gene3D with functional annotations from the three Gene Ontology (GO) sub-ontologies, KEGG, and Reactome. We validated the results using the CAFA 3 benchmark platform for GO annotation, finding that out of the multiple association metrics and domain datasets tested, Simpson index for FunFam domain-function associations combined with Stouffer’s method leads to the best performance in almost all scenarios. We also found that using FunFams led to better performance than superfamilies, and better results were found for GO molecular function compared to GO biological process terms. DomFun performed as well as the highest-performing method in certain CAFA 3 evaluation procedures in terms of $$F_{max}$$ F max and $$S_{min}$$ S min We also implemented our own benchmark procedure, Pathway Prediction Performance (PPP), which can be used to validate function prediction for additional annotations sources, such as KEGG and Reactome. Using PPP, we found similar results to those found with CAFA 3 for GO, moreover we found good performance for the other annotation sources. As with CAFA 3, Simpson index with Stouffer’s method led to the top performance in almost all scenarios. Conclusions DomFun shows competitive performance with other methods evaluated in CAFA 3 when predicting proteins function with GO, although results vary depending on the evaluation procedure. Through our own benchmark procedure, PPP, we have shown it can also make accurate predictions for KEGG and Reactome. It performs best when using FunFams, combining Simpson index derived domain-function associations using Stouffer’s method. The tool has been implemented so that it can be easily adapted to incorporate other protein features, such as domain data from other sources, amino acid k-mers and motifs. The DomFun Ruby gem is available from https://rubygems.org/gems/DomFun. Code maintained at https://github.com/ElenaRojano/DomFun. Validation procedure scripts can be found at https://github.com/ElenaRojano/DomFun_project.

Biodiversity of orb-web spiders (family: araneidae) of buner valley, Pakistan

The present research was carried out to explore the spider fauna of Buner valley with taxonomic study from February 2018 to January 2019. For this purpose samples were collected, four times at each month from 4 tehsils: Daggar, Gagra, Mandan and Totalai. Two methods were used, hand picking and sweep net for collection of samples. During day and night, three habitats, arid area, agriculture land and building area were search for collection. A total of 534 samples of spider were collected from four sampling sites, in which 379 were belonging to family Araniedae. After confirmation, the identified species were belonging to 8 genera (Neoscona, Argiope, Cyclosa, Araneus, Cyrtophora, Larinia, Erivoxia and Poltys) and 19 species. 18 of them were identified to specie level while a single specie to its generic level. The genus Neoscona was the dominant genus 26.31% having 5 species while the genus Argiope 21.05% is the second dominant having 4 species followed by Cyclosa 15.78% having 3 species followed by Cyrtophora and Araneus 10.52% having two species both. The Poltys and Larinia 5.26% are the rarest genera represent single-single specie both. Statistical analysis show that specie richness (D) = 5.77, Simpson index (1-D) = 0.87, Shannon index (H) = 2.33. Diversity of spiders was evenly distributed and calculated Evenness value was H/InS = 0.5408. There is also few atypical species and Fisher alpha estimate high value (Fisher α) = 4.42. Chao-1 estimated we have reported 22 species.

General practitioners’ management of depression symptoms in Somali refugee and Norwegian patients: a film vignette experiment

ObjectivesRefugees in comparison with non-refugee patients may face higher unmet mental healthcare needs. The mechanisms underlying these disparities are still poorly understood. The general practitioner (GP) plays a vital role in refugees’ mental health (MH), managing complaints within primary care and acting as gatekeeper to specialist services. However, GPs have reported feeling uncertain about working with refugee patients. Somalis make up one of the largest refugee groups in Norway and use primary care services more than the majority population for physical health, although not for MH. The current study examines GPs’ management of MH complaints in Somali refugee versus Norwegian vignette characters and the role of GP clinical uncertainty.DesignWe distributed an online experimental survey to GPs in Norway (n=133), who were randomised to watch a simulated consultation with a female Norwegian, female Somali, male Norwegian or male Somali vignette character, presenting the same symptoms of depression. GPs indicated which diagnoses, assessments and treatments they would endorse for the patient and their level of certainty.Outcome measuresWe calculated Simpson indices to measure inter-rater reliability and 2×2 analysis of variances as well as Bayesian estimation to examine clinical certainty based on patient background and gender.ResultsGPs’ clinical decisions about Somali and Norwegian vignette characters were similar, with a few exceptions. There was less consensus regarding the first prioritised diagnosis for Somali characters (Simpson index=0.129) versus Norwegian characters (Simpson index=0.208), (p=0.011, one-tailed). Somalis more frequently received diagnoses of post-traumatic stress disorder (PTSD), while Norwegians received diagnoses of feeling depressed. GPs endorsed sick leave more often for Norwegian characters and medication for physical complaints for Somali characters. There were no substantial differences in GPs’ self-reported certainty.ConclusionsWe found few and relatively small effects of patient background and gender on GPs’ clinical decisions. Nevertheless, the validity of certain diagnoses and prescription of sick leave need to be considered by clinicians and in future research.

Agrobiodiversity Indicators and Measurement using R for Description, Monitoring, Comparison, Relatedness, Conservation and Utilization

Agrobiodiversity is the most important part of biodiversity. It can be described, quantified, compared, and related by using different statistical tools called agrobiodiversity statistics (agro-statistics). Six components and 25 groups of agrobiodiversity should be used for agrobiodiversity analysis. Six types and levels of agrobiodiversity can be quantified. Both quantitative and qualitative data are used for estimating scores and indices. The measurement objects for describing agrobiodiversity are community, household, site, crop group, species, landrace, etc. These objects are called operational agricultural units (OAU). Agromorphological, molecular, and perception data are used in agrobiodiversity studies. Among the many software, RStudio is very good. It is an integrated part of R and includes a console, syntax-highlighting editor, tools for plotting, history, debugging, and workspace management. Vegan and BiodiversityR packages are commonly used for estimating diversity indices and multivariate analysis. Richness, Shannon index and Simpson index are very common means of quantifying agrobiodiversity. Spatial and temporal analysis of agrobiodiversity helps monitor the status and plan the programs and activities.

1017. Gut Microbiota Diversity and Beneficial Metabolite Production is Reduced in Liver Transplant Recipients and Associated with Post Operative Infection

Background Liver transplant (LT) recipients have abnormal microbiota before and after transplantation. (1,2) Associations between fecal microbiota, microbial metabolites, and clinical outcomes in liver transplantation are not well established. We correlated fecal microbiota composition and metabolite concentrations with early LT outcomes, including infection. Methods In a prospective observational study, we collected peri-transplant fecal samples and determined microbiota composition by 16S ribosomal RNA gene sequencing in LT recipients. Fecal short chain fatty acid (SCFA) and bile acid concentrations were measured by targeted GC- and LC-MS analyses, respectively. Inverse Simpson index was used to determine microbiota alpha-diversity in subjects and healthy controls. Clinical outcomes including length of stay, ICU admission, liver function, antibiotic use, immunosuppressive requirement and post-operative infection were correlated with microbiota composition. Results 69 patients were enrolled, 70 liver transplants were performed and 307 peri-transplant fecal samples were collected and analyzed. Compared to healthy controls, the fecal microbiota of LT recipients had reduced alpha-diversity (p< 0.001). [Fig1] Bacteroidetes, Ruminococcaceae, and Lachnospiraceae, three taxa associated with a health-promoting microbiota, and their metabolites, SCFA and secondary bile acids, were markedly diminished 55% of LT patients.(3) Intestinal domination ( >30% frequency) by Enterococcus or Proteobacteria species was common and occurred in 36% of LT recipients. 76 post-operative infections occurred in 40 LT recipients, with Enterococci causing 52% and Proteobacteria 41% of bacterial infections. In subjects with fecal samples collected within 5 days of infection, 9/17 infections were caused by the organism dominating the microbiota. [Fig2] Microbiota Composition and Metabolite Production 16s gene sequencing color coded by taxonomy. Each bar represents one stool sample nearest to LT compared to healthy controls. Alpha diversity measured by inverse simpson index. Absolute values of microbial metabolites and ratio of primary to secondary bile acids. Comparison of Microbiota Composition and Post Operative Infection All bacterial infections captured with a microbiota sample within 5 days of infection. Conclusion Microbiota diversity and microbially derived metabolites are markedly reduced in >50% of LT recipients. Intestinal domination and post-operative infections caused by antibiotic-resistant Enterococcus and Proteobacteria correlate with loss of Bacteroidetes, Ruminococcaceae, and Lachnospiraceae species, suggesting a potential role for microbiota reconstitution therapy in LT patients. Disclosures Eric G. Pamer, MD;FIDSA, Nothing to disclose

Tree Species Diversity and Distribution in the Natural Forest of Onigambari Forest Reserve, Oyo State, Nigeria

Anthropogenic activities has caused depletion of majority of Nigeria forest reserves, reducing forest lands to agricultural lands and grasslands. These prompted this study to consider the diversity of species as well as their species composition in the forest in February 2021. Four sub-plots were established in a cluster with an area of 50m by 50m, with 20m distance between each plots and 10m as edge effect. Twenty five tree species belonging to fifteen families were found in the study site. Family Malvaceae was the most represented. Triplochiton scleroxylon recorded the highest relative importance value (11.23). The diversity indices across the study plots assessed were species richness, evenness, Shannon index and dominance. Dominance indices across the study plots were low, asides for Plot 4 where. Triplochiton scleroxylon was dominant. Simpson index was highest in Plot 1 and lowest at Plot 4. Shannon index was highest, though in moderation in Plot 1 and relatively low in the remaining plots. Evenness indices across the four plots were high. However, the summarized diversity indices for the study site reflected dominance was generally low, Simpson index was high, Shannon index was moderate and Evenness index was moderate. The dendrogram depicted the relationship among the tree species population based on similarities and dissimilarities. Triplochiton scleroxylon belonged to a cluster while every other species with close similarity were categorized under cluster 2.

The Impact of Transformation of Farmers’ Livelihood on the Increasing Labor Costs of Grain Plantation in China

Analyzing the recessive impacts of farmers’ livelihood transformation on the surging labor cost in grain production is conducive to finding optimization paths for grain production. This study developed the Residual Livelihood Ratio (RLR) and the Livelihood Simpson Index (LSI) to measure the transformation of farmers' livelihood in China, and applied the multiple regression model to explore the influence of the transformation of farmers' livelihood on the labor cost of grain production. The results show that because of the soaring increment in labor cost, the net profit of rice, wheat, and maize production decreased largely in China. The LSI increased, while the RLR decreased, which indicated that farmers’ livelihoods transitioned towards a more unbalanced income–expenditure but more flexible employment. The Residual Livelihood Ratio; the mechanization input; the grain yield per unit area; the non-grain plantation degree; and the non-agricultural land use degree showed negative impacts on labor cost in grain production, whereas the Livelihood Simpson Index and Engel’s coefficient of farmers showed positive impacts on the labor cost. This paper proposes targeted policy implications for labor cost control of the grain production in China.

Risk Factors for Positivity to Shiga Toxin-Producing Escherichia coli and Salmonella enterica in Backyard Production Systems Animals from Metropolitana Region, Chile: A Threat to Public Health?

In the Metropolitana region of Chile there are 3836 backyard production systems (BPS), characterized as small-scale systems. They act as a source of zoonotic pathogens, such as Salmonella enterica and Shiga toxin-producing Escherichia coli (STEC), whose prevalence in BPS has not been fully described. The objective of this study was to determine the positivity for both agents in BPS and to establish the risk factors related to their presence. In each BPS, an epidemiological survey was undertaken, and stool samples were collected to detect these pathogens via bacteriological culture and conventional PCR techniques. Subsequently, multivariable logistic regression models were applied to establish the risk factors associated with their presence. BPS positivity rates of 11.76% for STEC and 4.7% for S. enterica were observed. The systems showed poor welfare standards and a lack of biosecurity measures. The risk factor analysis concluded that the Gini–Simpson index (p = 0.030; OR = 1.717) and the presence of neighboring intensive poultry or swine production systems (p = 0.019; OR = 20.645) act as factors that increased the risk of positivity with respect to STEC. In the case of S. enterica, exchanging embryonated eggs (p = 0.021; OR = 39) and the presence of debeaked chickens (p = 0.001; OR = 156) were determined as factors that increased the risk of positivity for this agent. For positivity with respect to both pathogens, the Gini–Simpson index (p = 0.030; OR = 1.544) and being INDAP/PRODESAL users (p = 0.023; OR = 15.026) were determined as factors that increased the risk, whereas the type of confinement (p = 0.002; OR = 0.019) decreased it. Epidemiological surveillance of these neglected populations is lacking, highlighting the fact that STEC and S. enterica maintenance on BPS represents a potential threat to public health.

Effect of thinning intensity on understory herbaceous diversity and biomass in mixed coniferous and broad-leaved forests of Changbai Mountain

Background Herbs are an important part of the forest ecosystem, and their diversity and biomass can reflect the restoration of vegetation after forest thinning disturbances. Based on the near-mature secondary coniferous and broad-leaved mixed forest in Jilin Province Forestry Experimental Zone, this study analyzed seasonal changes of species diversity and biomass of the understory herb layer after different intensities of thinning. Results The results showed that although the composition of herbaceous species and the ranking of importance values were affected by thinning intensity, they were mainly determined by seasonal changes. Across the entire growing season, the species with the highest importance values in thinning treatments included Carex pilosa, Aegopodium alpestre, Meehania urticifolia, and Filipendula palmata, which dominated the herb layer of the coniferous and broad-leaved mixed forest. The number of species, Margalef index, Shannon-Wiener index and Simpson index all had their highest values in May, and gradually decreased with months. Pielou index was roughly inverted “N” throughout the growing season. Thinning did not increase the species diversity. Thinning can promote the total biomass, above- and below-ground biomass. The number of plants per unit area and coverage were related to the total biomass, above- and below-ground biomass. The average height had a significantly positive correlation with herb biomass in May but not in July. However, it exerted a significantly negative correlation with herb biomass in September. The biomass in the same month increased with increasing thinning intensity. Total herb biomass, above- and below-ground biomass showed positive correlations with Shannon-Winner index, Simpson index and Pielou evenness index in May. Conclusions Thinning mainly changed the light environment in the forest, which would improve the plant diversity and biomass of herb layer in a short time. And different thinning intensity had different effects on the diversity of understory herb layer. The findings provide theoretical basis and reference for reasonable thinning and tending in coniferous and broad-leaved mixed forests.