Importance of timely metadata curation to the global surveillance of genetic diversity

Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous peoples. We undertook a distributed datathon to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and direct communication with authors. Starting with 848 candidate genomic data sets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 data sets (n = 440 data sets with data on 45,105 individuals from 762 species in 17 phyla). Examining papers and online repositories was much more fruitful than contacting 351 authors, who replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. The probability of retrieving spatiotemporal metadata declined significantly as age of the data set increased. There was a 13.5% yearly decrease in metadata associated with published papers or online repositories and up to a 22% yearly decrease in metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data-sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever.     

Relationships between exposure to polyhalogenated aromatic hydrocarbons and organochlorine pesticides and the risk for developing type 2 diabetes: a systematic review and a meta-analysis of exposures to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)

A systematic review was performed to evaluate the association between environmental exposures to polyhalogenated aromatic hydrocarbons (PHAHs) and organochlorine (OC) pesticides and the risk for type 2 diabetes (T2D). Searches of EMbase, Google Scholar, Medline, and Scopus were performed. Reports were included if they were original human studies whose design included a control group and if the sample size was larger than 10 participants per group. The articles were excluded if the type of diabetes was unknown or Type 1. Odds ratios (OR), 95% confidence intervals (CI), and modified Naranjo scores for the effects of environmental contaminants were determined for each study. Of the 35 eligible studies, six were included in the meta-analysis; these focused specifically on 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Meta-analysis of these studies showed no significant increased OR for the development of T2D from exposure to TCDD. However, subgroup analysis showed significant elevated OR for the development of T2D if exposure is repeated and accompanied by exposure to other persistent pesticides (OR?=?1.48; 1.10–1.90) but a decreased odds for T2D with exposure resulting from accidental exposure (OR?=?0.46; 0.39–0.52). Our results suggest that there are significant risks of developing T2D in populations with recurring exposures to TCDD in concert with other persistent chlorinated pesticides. A mean Naranjo score of 2.0 was determined for all 35 articles; this score was 2.5 when examining only TCDD studies and 2.1 when examining studies that looked only at T2D. Each of these Naranjo scores suggests a possible association between the prevalence of T2D and exposure to PHAHs or OC pesticides.     

Polyploidy and polyteny in the gigantic eubacterium Epulopiscium fishelsoni

Content and distribution of basic proteins, histones, acidic proteins and DNA, as well as the interaction of basic proteins with DNA, were studied microfluorometrically within nucleoid bodies of the gigantic eubacterium Epulopiscium fishelsoni living in the guts of the algivorous surgeonfish Acanthurus nigrofuscus. The fine structure of the bacterial nucleoid was studied using transmission electron microscopy (TEM). The mean content of basic proteins, histones and acidic proteins per nucleoid was directly proportional both to cell volume and DNA amount, proving that these proteins are integral components of bacterial chromatin. The maximal DNA quantity of ~10 ¹² base pairs nucleoid ^-1 was found in the largest specimens of 354,000 µm ³ volume (150-fold more then in human lymphocyte). Binding of proteins to DNA was strongest in cup-like nucleoids at the end of the bacterial life cycle, and weakest in enlarged and elongated nucleoids in mid-cycle. Contact fluorescent microscopy and TEM revealed a non-homogenous distribution of these proteins within the nucleoids, as well as the presence of giant polytene chromosome(s). We assume that the unusual genetic and morphological peculiarities, particularly increased polyploidy and polyteny, as revealed in E. fishelsoni, are the results of specific adaptations to the chemical conditions in the host's gut.     

Ecology and distribution of the benthic fauna in the shallow waters of the Red Sea

Approximately 500 animal species and plants are listed as being the most typical for the infratidal and shallow subtidal benthic fauna of the Red Sea. Most of them are divided into communities typical for various soft and hard substrata, and at different water depths. The oceanographic conditions and the development of several of the communities are discussed in general terms.Supported partly by grants 62558-4556 and F 671052 67C 0043 of the US Office of Naval Research and Grant SFC-7-0074 of the Smithsonian Institution.     

TRICKLE IRRIGATION OF WHEAT APPLYING RENOVATED WASTEWATER1

ABSTRACT: A preliminary field experiment was conducted for trickle irrigation of winter wheat raised for grain production under arid conditions. Treated waste water was applied for trickle irrigation via a trickle system. Mean total amount of effluent applied was about 5700 m³/ha. In one of the experimental treatments, which was irrigated once a week, a grain yield of over 10,000 kg/ha was obtained, whereas in the other treatments the yields were about 8,500 kg/ha, which are above the mean yield obtained under sprinkler irrigation.     

Rural market imperfections and the role of institutions in collective action to improve markets for the poor

Many countries in sub‐Saharan Africa have liberalized markets to improve efficiency and enhance market linkages for smallholder farmers. The expected positive response by the private sector in areas with limited market infrastructure has however been very limited. The functioning of markets is constrained by high transaction costs and coordination problems along the production‐to‐consumption value chain. New kinds of institutional arrangements are needed to reduce these costs and fill the vacuum left when governments withdrew from markets in the era of structural adjustments. One of these institutional innovations has been the strengthening of producer organizations and formation of collective marketing groups as instruments to remedy pervasive market failures in rural economies. The analysis presented here with a case study from eastern Kenya has shown that marketing groups pay 20–25% higher prices than other buyers to farmers while participation was also positively correlated with adoption of improved dryland legume varieties, crops not targeted by the formal extension system. However the effectiveness of marketing groups is undermined by external shocks and structural constraints that limit the volume of trade and access to capital and information, and require investments in complementary institutions and coordination mechanisms to exploit scale economies. Successful groups have shown high levels of collective action in the form of increased participatory decision making, member contributions and initial start‐up capital. Failure to pay on delivery, resulting from lack of capital credit, is a major constraint that stifles competitiveness of marketing groups relative to other buyers. These findings call for interventions that improve governance and participation; mechanisms for improving access to operating capital; and effective strategies for risk management and enhancing the business skills of farmer marketing groups.     

An empirical assessment of rural livelihood assets from gender perspective: evidence from Ghana

Poverty studies have demonstrated that a group’s ability to escape poverty is largely dependent on the types of assets that the group’s members possess. A major claim that has been asserted with limited empirical evidence in the asset literature is the gender disparity dichotomy. Using rural Ghana as a case study, we assess the asset levels of farm households from a gender perspective. In doing so, we theorized and empirically tested assets on case bases. A household questionnaire survey was used to collect data from two hundred households in the Fanteakwa district of eastern Ghana. An asset index was used to compute the asset levels, while Kruskal–Wallis statistics was employed to compare the significance of the temporal changes. The results show a minimum level of asset endowment. Natural, social and financial assets were the three most endowed assets, with physical and human assets being the least. A gender analysis shows no significant difference, even though the levels of assets for the female-headed households were slightly higher than those of the male-headed households. However, the study found a 22.7% increment in the accumulation of financial assets among the female-headed households over the last 5 years compared to a 9.3% decrement in the same assets for their male-headed counterparts. Applying our theory, the results present an unbalanced and unstable asset situation among the household heads. We call for improvement, in physical and human assets. The overall study results imply an improvement in gender-asset accessibility in the context of rural Ghana.     

Export pumps in Epulopiscium fishelsoni, the symbiotic giant gut bacterium in Acanthurus nigrofuscus

Activity of the potential antixenobiotic efflux pumps of Epulopiscium fishelsoni (epulos), the symbiotic giant gut bacterium of the algivorous surgeonfish Acanthurus nigrofuscus, was studied in vivo using various specific substrates and microfluorometry. Kinetic and inhibitor analyses revealed the following vital efflux activities: (1) verapamil-sensitive efflux of amphiphilic cationic compounds rhodamine B, Hoechst 33342, and ethidium bromide; (2) verapamil-sensitive efflux of hydrophobic neutral fluorescein diacetate; (3) verapamil-insensitive efflux of hydrophilic anionic fluorescein; and (4) verapamil-insensitive efflux of glutathione-S-bimane. Cytosolic enzymes, nonspecific esterase and glutathione S-transferase, were shown to participate in xenobiotic metabolism. The results suggest that the activity of the potential efflux pump in epulos are similar to those described in other bacteria but are kinetically characterized by an unusually high transport rate, probably mediated by hyperplasia of the plasma membrane. Further studies of the export pumps in epulos may unmask their evolutionary adaptation to a xenobiotic-rich host gut content.     

Plastic pollution threat in Africa: current status and implications for aquatic ecosystem health

Environmental Science and Pollution Research - Rapid population growth and poor waste management practice are among the main drivers of plastic pollution in modern times, thus making Africa a...