Understanding primate‐human interaction: Socioeconomic correlates of local awareness and attitude toward the endangered golden langur Trachypithecus geei (Khajuria, 1956) in Bhutan

Despite the golden langur's (Trachypithecus geei) endangered and totally protected status, local awareness and attitude toward this species is poorly understood. We investigated local awareness and attitude in Bhutan by interviewing 1,143 households in the districts of Dagana, Sarpang, Trongsa, Tsirang, and Zhemgang, and analyzing data through a conditional inference tree analysis. Most respondents were not aware of the golden langur's nationally protected (53%; n = 604) and globally endangered status (64%; n = 730), but their location of residence (inside/outside a protected area; p < .001) and education level (p < .001) significantly influenced awareness. The majority of respondents (87%; n = 999) liked the golden langur but the attitude was significantly influenced primarily by whether or not they experienced crop damage by golden langurs (p < .001), and subsequently by location of residence (p < .001), local belief (p < .01), gender (p < .05), and personal encounter with a golden langur (p < .001). Socioeconomic variables like age, education level, and annual income did not influence attitude. We recommend environmental education and awareness campaigns outside protected areas, and intensifying existing programs inside protected areas to forge harmonious human‐golden langur coexistence.     

Divergent patrilineal signals in three Roma populations

Previous studies have revealed that the European Roma share close genetic, linguistic and cultural similarities with Indian populations despite their disparate geographical locations and divergent demographic histories. In this study, we report for the first time Y-chromosome distributions in three Roma collections residing in Belgrade, Vojvodina and Kosovo. Eighty-eight Y-chromosomes were typed for 14 SNPs and 17 STRs. The data were subsequently utilized for phylogenetic comparisons to pertinent reference collections available from the literature. Our results illustrate that the most notable difference among the three Roma populations is in their opposing distributions of haplogroups H and E. Although the Kosovo and Belgrade samples exhibit elevated levels of the Indian-specific haplogroup H-M69, the Vojvodina collection is characterized almost exclusively by haplogroup E-M35 derivatives, most likely the result of subsequent admixture events with surrounding European populations. Overall, the available data from Romani groups points to different levels of gene flow from local populations.     

Partial Altitudinal Migration of a Himalayan Forest Pheasant

Background

Altitudinal migration systems are poorly understood. Recent advances in animal telemetry which enables tracking of migrants across their annual cycles will help illustrate unknown migration patterns and test existing hypotheses. Using telemetry, we show the existence of a complex partial altitudinal migration system in the Himalayas and discuss our findings to help better understand partial and altitudinal migration.

Methodology/Principal Findings

We used GPS/accelerometer tags to monitor the migration of Satyr tragopan (Tragopan satyra) in the Bhutan Himalayas. We tagged 38 birds from 2009 – 2011 and found that tragopans are partially migratory. Fall migration lasted from the 3^rd week of September till the 3^rd week of November with migrants traveling distances ranging from 1.25 km to 13.5 km over 1 to 32 days. Snowfall did not influence the onset of migration. Return migration started by the 1^st week of March and lasted until the 1^st week of April. Individuals returned within 4 to 10 days and displayed site fidelity. One bird switched from being a migrant to a non-migrant. Tragopans displayed three main migration patterns: 1) crossing multiple mountains; 2) descending/ascending longitudinally; 3) moving higher up in winter and lower down in summer. More females migrated than males; but, within males, body size was not a factor for predicting migrants.

Conclusions/Significance

Our observations of migrants traversing over multiple mountain ridges and even of others climbing to higher elevations is novel. We support the need for existing hypotheses to consider how best to explain inter- as well as intra-sexual differences. Most importantly, having shown that the patterns of an altitudinal migration system are complex and not a simple up and down slope movement, we hope our findings will influence the way altitudinal migrations are perceived and thereby contribute to a better understanding of how species may respond to climate change.     

The plasma peptidome

Background

It may be possible to discover new diagnostic or therapeutic peptides or proteins from blood plasma using LC–ESI–MS/MS to identify, with a linear quadrupole ion trap to identify, quantify and compare the statistical distributions of peptides cleaved ex vivo from plasma samples from different clinical populations.

Methods

A systematic method for the organic fractionation of plasma peptides was applied to identify and quantify the endogenous tryptic peptides from human plasma from multiple institutions by C18 HPLC followed nano electrospray ionization and tandem mass spectrometry (LC–ESI–MS/MS) with a linear quadrupole ion trap. The endogenous tryptic peptides, or tryptic phospho peptides (i.e. without exogenous digestion), were extracted in a mixture of organic solvent and water, dried and collected by preparative C18. The tryptic peptides from 6 institutions with 12 different disease and normal EDTA plasma populations, alongside ice cold controls for pre-analytical variation, were characterized by mass spectrometry. Each patient plasma was precipitated in 90% acetonitrile and the endogenous tryptic peptides extracted by a stepwise gradient of increasing water and then formic acid resulting in 10 sub-fractions. The fractionated peptides were manually collected over preparative C18 and injected for 1508 LC–ESI–MS/MS experiments analyzed in SQL Server R.

Results

Peptides that were cleaved in human plasma by a tryptic activity ex vivo provided convenient and sensitive access to most human proteins in plasma that show differences in the frequency or intensity of proteins observed across populations that may have clinical significance. Combination of step wise organic extraction of 200 μL of plasma with nano electrospray resulted in the confident identification and quantification ~?14,000 gene symbols by X!TANDEM that is the largest number of blood proteins identified to date and shows that you can monitor the ex vivo proteolysis of most human proteins, including interleukins, from blood. A total of 15,968,550 MS/MS spectra ≥?E4 intensity counts were correlated by the SEQUEST and X!TANDEM algorithms to a federated library of 157,478 protein sequences that were filtered for best charge state (2+ or 3+) and peptide sequence in SQL Server resulting in 1,916,672 distinct best-fit peptide correlations for analysis with the R statistical system. SEQUEST identified some 140,054 protein accessions, or some ~?26,000 gene symbols, proteins or loci, with at least 5 independent correlations. The X!TANDEM algorithm made at least 5 best fit correlations to more than 14,000 protein gene symbols with p-values and FDR corrected q-values of ~?0.001 or less. Log₁₀ peptide intensity values showed a Gaussian distribution from E8 to E4 arbitrary counts by quantile plot, and significant variation in average precursor intensity across the disease and controls treatments by ANOVA with means compared by the Tukey–Kramer test. STRING analysis of the top 2000 gene symbols showed a tight association of cellular proteins that were apparently present in the plasma as protein complexes with related cellular components, molecular functions and biological processes.

Conclusions

The random and independent sampling of pre-fractionated blood peptides by LC-ESI-MS/MS with SQL Server-R analysis revealed the largest plasma proteome to date and was a practical method to quantify and compare the frequency or log₁₀ intensity of individual proteins cleaved ex vivo across populations of plasma samples from multiple clinical locations to discover treatment-specific variation using classical statistics suitable for clinical science. It was possible to identify and quantify nearly all human proteins from EDTA plasma and compare the results of thousands of LC–ESI–MS/MS experiments from multiple clinical populations using standard database methods in SQL Server and classical statistical strategies in the R data analysis system.

     

Murine diet/tissue and human brain tumorigenesis alter <Emphasis Type="Italic">Mthfr/MTHFR</Emphasis> 5′-end methylation

Polymorphisms and decreased activity of methylenetetrahydrofolate reductase (MTHFR) are linked to disease, including cancer. However, epigenetic regulation has not been thoroughly studied. Our goal was to generate DNA methylation profiles of murine/human MTHFR gene regions and examine methylation in brain and liver tumors. Pyrosequencing in four murine tissues revealed minimal DNA methylation in the CpG island. Higher methylation was seen in liver or intestine in the CpG island shore 5′ to the upstream translational start site or in another region 3′ to the downstream start site. In the latter region, there was negative correlation between expression and methylation. Three orthologous regions were investigated in human MTHFR, as well as a fourth region between the two translation start sites. We found significantly increased methylation in three regions (not the CpG island) in pediatric astrocytomas compared with control brain, with decreased expression in tumors. Methylation in hepatic carcinomas was also increased in the three regions compared with normal liver, but the difference was significant for only one CpG. This work, the first overview of the Mthfr/MTHFR epigenetic landscape, suggests regulation through methylation in some regions, demonstrates increased methylation/decreased expression in pediatric astrocytomas, and should serve as a resource for future epigenetic studies.     

Ethical principles for promoting health research data sharing with sub‐Saharan Africa

A powerful feature of global health research is data‐sharing with regions which bear the heaviest burden of disease. It offers novel opportunities for aggregating data to address critical global health challenges in ways higher than relying on individual studies. Yet there exist important stratifiers of the capacity to share data, particularly across the Global North‐South divide. Systemic challenges that characterize sub‐Saharan Africa and disadvantage the region's scientific productivity threaten the burgeoning data‐sharing culture too. Like all endeavors requiring equal commitments under unequal circumstances, a strong ethical impetus is needed to help reduce inequities and imbalances to encourage adherence. This article discusses mandatory data‐sharing in relation to peculiar challenges faced by sub‐Saharan African scientists to suggest ethical principles for rethinking and reframing solutions. We propose six principles which mirror guidelines from the Institute of Medicine and encapsulate principles from the Emanuel Framework, Nairobi Data Sharing Principles, and the COHRED guidelines.     

Dog bites in humans and estimating human rabies mortality in rabies endemic areas of Bhutan

Background

Dog bites in humans are a public health problem worldwide. The issues of increasing stray dog populations, rabies outbreaks, and the risk of dogs biting humans have been frequently reported by the media in Bhutan. This study aimed to estimate the bite incidence and identify the risk factors for dog bites in humans, and to estimate human deaths from rabies in rabies endemic south Bhutan.

Methods

A hospital-based questionnaire survey was conducted during 2009–2010 among dog bites victims who visited three hospitals in Bhutan for anti-rabies vaccine injection. Decision tree modeling was used to estimate human deaths from rabies following dog bite injuries in two rabies endemic areas of south Bhutan.

Results

Three hundred and twenty four dog bite victims were interviewed. The annual incidence of dog bites differed between the hospital catchment areas: 869.8 (95% CI: 722.8–1022.5), 293.8 (240–358.2) and 284.8 (251.2–323) per 100,000 people in Gelephu, Phuentsholing and Thimphu, respectively. Males (62%) were more at risk than females (P<0.001). Children aged 5–9 years were bitten more than other age groups. The majority of victims (71%) were bitten by stray dogs. No direct fatal injury was reported. In two hospital areas (Gelephu and Phuentsholing) in south Bhutan the annual incidence of death from rabies was 3.14 (95% CI: 1.57–6.29) per 100,000 population. The decision tree model predicted an equivalent annual incidence of 4.67 (95% CI: 2.53–7.53) deaths/100,000 population at risk. In the absence of post exposure prophylaxis, the model predicted 19.24 (95% CI: 13.69–25.14) deaths/year in these two areas.

Conclusions

Increased educational awareness of people about the risk of dog bites and rabies is necessary, particularly for children in rabies endemic areas of Bhutan.     

Current approaches to micro-RNA analysis and target gene prediction

It is becoming increasingly evident that micro-RNAs (miRNA) play a significant role in regulating the cellular machinery. These ∼22-nt non-coding RNAs function as negative regulators of gene expression. Since their discovery, considerable information has been obtained on miRNA biology and the mechanism of their action. Guidelines have been established for miRNA nomenclature and databases have been built to house all miRNA from many species. A number of methodologies are available for miRNA analysis. There is a lot of interest in developing bioinformatics approaches to predict miRNA target genes. This article will bring together the information on our current knowledge of miRNA biology, the approaches for miRNA analysis, and computational strategies to gain insight in miRNA functional roles.