Microbial stratification in low pH oxic and suboxic macroscopic growths along an acid mine drainage

Macroscopic growths at geographically separated acid mine drainages (AMDs) exhibit distinct populations. Yet, local heterogeneities are poorly understood. To gain novel mechanistic insights into this, we used OMICs tools to profile microbial populations coexisting in a single pyrite gallery AMD (pH ∼2) in three distinct compartments: two from a stratified streamer (uppermost oxic and lowermost anoxic sediment-attached strata) and one from a submerged anoxic non-stratified mat biofilm. The communities colonising pyrite and those in the mature formations appear to be populated by the greatest diversity of bacteria and archaea (including ‘ARMAN'' (archaeal Richmond Mine acidophilic nano-organisms)-related), as compared with the known AMD, with ∼44.9% unclassified sequences. We propose that the thick polymeric matrix may provide a safety shield against the prevailing extreme condition and also a massive carbon source, enabling non-typical acidophiles to develop more easily. Only 1 of 39 species were shared, suggesting a high metabolic heterogeneity in local microenvironments, defined by the O₂ concentration, spatial location and biofilm architecture. The suboxic mats, compositionally most similar to each other, are more diverse and active for S, CO₂, CH₄, fatty acid and lipopolysaccharide metabolism. The oxic stratum of the streamer, displaying a higher diversity of the so-called ‘ARMAN''-related Euryarchaeota, shows a higher expression level of proteins involved in signal transduction, cell growth and N, H₂, Fe, aromatic amino acids, sphingolipid and peptidoglycan metabolism. Our study is the first to highlight profound taxonomic and functional shifts in single AMD formations, as well as new microbial species and the importance of H₂ in acidic suboxic macroscopic growths.     

Streamlining genomes: toward the generation of simplified and stabilized microbial systems

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Highlights? Top-down and bottom-up approaches to genome streamlining. ? Computational support for constructing and refactoring streamlined genomes. ? From genome engineering to metabolic reprogramming. ? Perspectives in applied genome engineering.     

Mapping and Use of a Sequence that Targets DNA Ligase I to Sites of DNA Replication In Vivo

The mammalian nucleus is highly organized, and nuclear processes such as DNA replication occur in discrete nuclear foci, a phenomenon often termed “functional organization” of the nucleus. We describe the identification and characterization of a bipartite targeting sequence (amino acids 1–28 and 111–179) that is necessary and sufficient to direct DNA ligase I to nuclear replication foci during S phase. This targeting sequence is located within the regulatory, NH₂-terminal domain of the protein and is dispensable for enzyme activity in vitro but is required in vivo. The targeting domain functions position independently at either the NH₂ or the COOH termini of heterologous proteins.

We used the targeting sequence of DNA ligase I to visualize replication foci in vivo. Chimeric proteins with DNA ligase I and the green fluorescent protein localized at replication foci in living mammalian cells and thus show that these subnuclear functional domains, previously observed in fixed cells, exist in vivo. The characteristic redistribution of these chimeric proteins makes them unique markers for cell cycle studies to directly monitor entry into S phase in living cells.

     

Epigenetic regulation of the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs

Background

In previous studies on an Iberian x Landrace cross, we have provided evidence that supported the porcine ELOVL6 gene as the major causative gene of the QTL on pig chromosome 8 for palmitic and palmitoleic acid contents in muscle and backfat. The single nucleotide polymorphism (SNP) ELOVL6:c.-533C > T located in the promoter region of ELOVL6 was found to be highly associated with ELOVL6 expression and, accordingly, with the percentages of palmitic and palmitoleic acids in longissimus dorsi and adipose tissue. The main goal of the current work was to further study the role of ELOVL6 on these traits by analyzing the regulation of the expression of ELOVL6 and the implication of ELOVL6 polymorphisms on meat quality traits in pigs.

Results

High-throughput sequencing of BAC clones that contain the porcine ELOVL6 gene coupled to RNAseq data re-analysis showed that two isoforms of this gene are expressed in liver and adipose tissue and that they differ in number of exons and 3’UTR length. Although several SNPs in the 3’UTR of ELOVL6 were associated with palmitic and palmitoleic acid contents, this association was lower than that previously observed with SNP ELOVL6:c.-533C > T. This SNP is in full linkage disequilibrium with SNP ELOVL6:c.-394G > A that was identified in the binding site for estrogen receptor alpha (ERα). Interestingly, the ELOVL6:c.-394G allele is associated with an increase in methylation levels of the ELOVL6 promoter and with a decrease of ELOVL6 expression. Therefore, ERα is clearly a good candidate to explain the regulation of ELOVL6 expression through dynamic epigenetic changes in the binding site of known regulators of ELOVL6 gene, such as SREBF1 and SP1.

Conclusions

Our results strongly suggest the ELOVL6:c.-394G > A polymorphism as the causal mutation for the QTL on pig chromosome 8 that affects fatty acid composition in pigs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-015-0111-y) contains supplementary material, which is available to authorized users.     

Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases <Emphasis Type=Italic>in silico</Emphasis> docked to different inhibitors

Background  

Enzymes belonging to the same super family of proteins in general operate on variety of substrates and are inhibited by wide selection of inhibitors. In this work our main objective was to expand the scope of studies that consider only the catalytic and binding pocket amino acids while analyzing enzyme specificity and instead, include a wider category which we have named the Interface Forming Residues (IFR). We were motivated to identify those amino acids with decreased accessibility to solvent after docking of different types of inhibitors to sub classes of serine proteases and then create a table (matrix) of all amino acid positions at the interface as well as their respective occupancies. Our goal is to establish a platform for analysis of the relationship between IFR characteristics and binding properties/specificity for bi-molecular complexes.     

Chick mortality leads to male‐biased sex ratios in endangered Great Lakes Piping Plovers

Few investigators have studied the offspring sex ratios of monomorphic shorebirds because visually determining the sex of juveniles is not possible. We investigated the ontogeny of an observed male‐biased adult sex ratio in the federally endangered Great Lakes population of Piping Plovers (Charadrius melodus). We determined sex ratios at hatching, banding ( = 9.0 d old), and fledging (23 d old) to determine if the bias arises during the pre‐fledging period and, if so, at what stage. For three consecutive years (2012–2014), we used a molecular technique to determine the sex of 307 chicks and followed individuals to a stage where survival to fledging could be inferred. Within fully‐sexed broods at hatching, the average proportions of male chicks (2012–2014) were 0.47, 0.58, and 0.54, respectively. At banding, the sex ratio remained unbiased in 2012 (0.51), but was male‐biased in 2013 (0.59) and 2014 (0.57). Overall, the sex ratio did not differ significantly from parity at fledging in 2012, but did differ during 2013 (P = 0.01) and 2014 (P = 0.03). Using logistic regression models fit using Bayesian inference, we found strong support for a sex effect on chick survival to fledging age, with higher male than female survival (μ_male = 0.83 [95% credible interval: 0.75–0.90]; μ_female = 0.71 [0.61–0.80]). These results suggest that the male‐biased adult sex ratio in Piping Plovers arises, in part, due to differential survival during the pre‐fledging period. This difference did not result from female chicks hatching later in the season or weighing less at banding than male chicks, factors that could potentially affect the likelihood of survival. Future investigations into possible behavioral‐ or weather‐related influences on sex‐specific survival are needed. Our results have important implications for (1) identifying management efforts needed to increase recruitment given female‐biased chick mortality, and (2) conducting population viability analyses, which frequently assume an unbiased fledgling sex ratio.     

Space use by Great Lakes Piping Plovers during the breeding season

ABSTRACT.   Identifying and protecting breeding habitat for imperiled species requires an understanding of the spatial and temporal movements of breeding individuals. During the 2003 and 2004 breeding seasons, we examined space use by Piping Plovers ( Charadrius melodus ) in the federally endangered Great Lakes population. We used coordinate geometry to estimate home range sizes of individual birds and examined relationships between home range size and breeding stage (incubation versus chick rearing), year, sex, number of locations, minimum plover age, distance to the nearest nest, and human beach use (high, medium, or low). The mean size of home ranges of Piping Plovers that fledged at least one chick was 2.9 ± 0.5 (SE) ha (range = 0.4–11.2 ha), and the mean linear beach distance traversed was 475 ± 53 m (range = 130–1435 m). Individuals used 3 times more beach area and 1.5 times more shoreline distance in 2003 than in 2004. Females used smaller areas than males overall and during chick rearing. Home ranges were smallest on beaches with low public use, suggesting that human disturbance may cause greater movement by individual plovers and that larger protected areas may be warranted on beaches frequented by the public to minimize disturbance to breeding birds. Our results demonstrate that nesting Great Lakes Piping Plovers occupy relatively small ranges and, therefore, that even relatively small areas of suitable habitat can have a high conservation value for this endangered population. However, the total area of habitat used varied substantially among individuals, and this should be considered when protecting habitat for the species.