Deciphering the Prokaryotic Community and Metabolisms in South African Deep-Mine Biofilms through Antibody Microarrays and Graph Theory

In the South African deep mines, a variety of biofilms growing in mine corridor walls as water seeps from intersections or from fractures represents excellent proxies for deep-subsurface environments. However, they may be greatly affected by the oxygen inputs through the galleries of mining activities. As a consequence, the interaction between the anaerobic water coming out from the walls with the oxygen inputs creates new conditions that support rich microbial communities. The inherent difficulties for sampling these delicate habitats, together with transport and storage conditions may alter the community features and composition. Therefore, the development of in situ monitoring methods would be desirable for quick evaluation of the microbial community. In this work, we report the usefulness of an antibody-microarray (EMChip66) immunoassay for a quick check of the microbial diversity of biofilms located at 1.3 km below surface within the Beatrix deep gold mine (South Africa). In addition, a deconvolution method, previously described and used for environmental monitoring, based on graph theory and applied on antibody cross-reactivity was used to interpret the immunoassay results. The results were corroborated and further expanded by 16S rRNA gene sequencing analysis. Both culture-independent techniques coincided in detecting features related to aerobic sulfur-oxidizers, aerobic chemoorganotrophic Alphaproteobacteria and metanotrophic Gammaproteobacteria. 16S rRNA gene sequencing detected phylotypes related to nitrate-reducers and anaerobic sulfur-oxidizers, whereas the EMChip66 detected immunological features from methanogens and sulfate-reducers. The results reveal a diverse microbial community with syntrophic metabolisms both anaerobic (fermentation, methanogenesis, sulphate and nitrate reduction) and aerobic (methanotrophy, sulphur oxidation). The presence of oxygen-scavenging microbes might indicate that the system is modified by the artificial oxygen inputs from the mine galleries.     

Occurrence of an NADH diaphorase activity associated with xanthine dehydrogenase in Chlamydomonas reinhardtii

Wild-type Chlamydomonas reinhardtii cells exhibited a peculiar NADH-nitrobluetetrazolium reductase (NADH diaphorase) activity when grown under conditions in which xanthine dehydrogenase (XDH) is present. This XDH-coinduced diaphorase was electrophoretically distinguishable from constitutive diaphorases, showed the same mobility as XDH and could be assayed in vitro with dichlorophenol indophenol. Mutant strains 102, 104 and 307 of Chlamydomonas which lack XDH did not exhibit XDH-coinduced diaphorase. Heat treatment of crude extracts or partial purification of XDH inactivated or removed all constitutive diaphorases and left significant levels of XDH-coinduced diaphorase which remained always associated with XDH. These results demonstrate that XDH from C. reinhardtii, like other organisms, is also capable of catalyzing NADH oxidation.     

Influence of Environmental Factors and Human Activity on the Presence of Salmonella Serovars in a Marine Environment

The temporal and spatial distribution of Salmonella contamination in the coastal waters of Galicia (northwestern Spain) relative to contamination events with different environmental factors (temperature, wind, hours of sunlight, rainfall, and river flow) were investigated over a 4-year period. Salmonellae were isolated from 127 of 5,384 samples of molluscs and seawater (2.4%), and no significant differences (P < 0.05) between isolates obtained in different years were observed. The incidence of salmonellae was significantly higher in water column samples (2.9%) than in those taken from the marine benthos (0.7%). Of the 127 strains of Salmonella isolated, 20 different serovars were identified. Salmonella enterica serovar Senftenberg was the predominant serovar, being represented by 54 isolates (42.5%), followed by serovar Typhimurium (19 isolates [15%]) and serovar Agona (12 isolates [9.4%]). Serovar Senftenberg was detected at specific points on the coast and could not be related to any of the environmental parameters analyzed. All serovars except Salmonella serovar Senftenberg were found principally in the southern coastal areas close to the mouths of rivers, and their incidence was associated with high southwestern wind and rainfall. Using multiple logistic regression analysis models, the prevalence of salmonellae was best explained by environmental parameters on the day prior to sampling. Understanding this relationship may be useful for the control of molluscan shellfish harvests, with wind and rainfall serving as triggers for closure.     

Intracellular Infection of Diverse Diatoms by an Evolutionary Distinct Relative of the Fungi

1. Download : Download high-res image (143KB)
2. Download : Download full-size image

     

Mitogenomes from The 1000 Genome Project Reveal New Near Eastern Features in Present-Day Tuscans

Background

Genetic analyses have recently been carried out on present-day Tuscans (Central Italy) in order to investigate their presumable recent Near East ancestry in connection with the long-standing debate on the origins of the Etruscan civilization. We retrieved mitogenomes and genome-wide SNP data from 110 Tuscans analyzed within the context of The 1000 Genome Project. For phylogeographic and evolutionary analysis we made use of a large worldwide database of entire mitogenomes (>26,000) and partial control region sequences (>180,000).

Results

Different analyses reveal the presence of typical Near East haplotypes in Tuscans representing isolated members of various mtDNA phylogenetic branches. As a whole, the Near East component in Tuscan mitogenomes can be estimated at about 8%; a proportion that is comparable to previous estimates but significantly lower than admixture estimates obtained from autosomal SNP data (21%). Phylogeographic and evolutionary inter-population comparisons indicate that the main signal of Near Eastern Tuscan mitogenomes comes from Iran.

Conclusions

Mitogenomes of recent Near East origin in present-day Tuscans do not show local or regional variation. This points to a demographic scenario that is compatible with a recent arrival of Near Easterners to this region in Italy with no founder events or bottlenecks.     

Determination of molybdenum and tungsten in biological materials

A spectrophotometric method for the quantitative determination of molybdenum and tungsten in the presence of each other in biological materials, has been developed. The method involves the selective formation and extraction of the complexes of the metals with 4-methyl-1,2-dimercaptobenzene under specified conditions of acidity and temperature. Possible interference by components found in biological materials, was examined and shown to be negligible.     

Goodness‐of‐fit tests for disorder detection in NGS experiments

Next‐generation sequencing (NGS) experiments are often performed in biomedical research nowadays, leading to methodological challenges related to the high‐dimensional and complex nature of the recorded data. In this work we review some of the issues that arise in disorder detection from NGS experiments, that is, when the focus is the detection of deletion and duplication disorders for homozygosity and heterozygosity in DNA sequencing. A statistical model to cope with guanine/cytosine bias and phasing and prephasing phenomena at base level is proposed, and a goodness‐of‐fit procedure for disorder detection is derived. The method combines the proper evaluation of local p‐values (one for each DNA base) with suitable corrections for multiple comparisons and the discrete nature of the p‐values. A global test for the detection of disorders in the whole DNA region is proposed too. The performance of the introduced procedures is investigated through simulations. A real data illustration is provided.     

Adult–adult play in captive lowland gorillas (Gorilla gorilla gorilla)

Primates - Among African great apes, play is virtually absent between adult lowland gorillas (Gorilla gorilla gorilla). Here, we report an extremely rare case of adult–adult play observed in...