Association between manganese superoxide dismutase (MnSOD) gene polymorphism and elderly obesity

Evidence suggests an association between obesity and oxidative stress caused by superoxide production. Since the dismutation of superoxide is catalyzed by superoxide dismutase enzymes, we tested the association between obesity and Ala16Val manganese-dependent superoxide dismutase gene (MnSOD) polymorphism. We analyzed 815 free-living community subjects (≥60 years old) grouped into subjects who were either obese (BMI ≥ 30 kg/m²) or non-obese (BMI < 25 kg/m²). Additionally, we investigated the possible interaction between the Ala16Val MnSOD gene polymorphism and obesity in the modulation of biochemical and nutritional variables. We found a positive association between MnSOD polymorphism and obesity, since higher VV frequency (28.2%) was observed in the obese group (P = 0.002, odds ratio 1.949, 95% CI: 1.223–3.008). This result was independent of sex, age, diabetes, dyslipidemia, hypertension, and metabolic syndrome. A possible biological explanation of the association described here could be a chronic state of superoxide enzyme imbalance present in VV carriers, which could affect differential metabolic pathways contributing to the obese state.     

Stochastic and deterministic processes jointly structure tropical arthropod communities

The question of whether ecological assemblages are structured by stochastic and deterministic (e.g. interspecific competition) processes is controversial, but it is difficult to design sampling regimes and experiments that can dissect the relative importance of stochastic and deterministic processes in natural assemblages. Using null models, we tested communities of arthropod decomposers in tropical epiphytes for patterns of species co-occurrence, while controlling for habitat gradients, seasonal variations and ecological succession. When environmental conditions were controlled, our analysis showed that the communities were structured stochastically. However, analysing mixed sets of communities that were deliberately created either from two distinct heights or two successional stages revealed that communities were structured deterministically. These results confirm that habitat gradients and dispersal/competition trade-offs are capable of generating non-random patterns within decomposer arthropod communities, but reveal that when such effects are accounted for, species co-occurrence is fundamentally random.     

Enzymatic hydrolysis of the Eisenia andrei earthworm: Characterization and evaluation of its properties

Some studies have carried out in order to retrieve proteins from the by-product of animal-processing industries. Earthworms are rich in protein and usually are used in animal feed. Thus, this study aimed to optimize the hydrolysis process of Eisenia andrei earthworms by employing Alcalase enzyme. Using the response surface methodology, we evaluated the following conditions: temperature, hydrolysis time, stirring speed, and enzyme/substrate ratio. The optimal conditions for the experimental design were determined through the analysis of the foaming and emulsifying properties, in vitro starch digestibility, and antioxidant activity. The results demonstrate that the highest degree of hydrolysis (i.e., 92%) was obtained under the following conditions: pH, 9.5; temperature, 25?°C; hydrolysis time, 2.25?h; stirring speed, 200?rpm; and enzyme/substrate ratio, 1.77%, using Alcalase enzyme. Evaluation of the amino acid composition under these conditions revealed higher concentrations of aspartic acid, glutamic acid, and leucine. The in vitro protein digestibility of the hydrolysate was approximately 73%. There were no significant improvements in either foam stability or emulsification after enzymatic hydrolysis. Additional studies on the antioxidant activity are required. This bioproduct could potentially serve as a promising supplementary food product.     

Filial cannibalism in teleost fish

This review summarizes information on filial cannibalism (the act of eating one's own offspring) in teleost fish. Cannibalistic parents can either consume their whole brood (total filial cannibalism), or eat only some of the eggs in the nest (partial filial cannibalism). Offspring consumption has been argued to be adaptive under the assumption that offspring survival is traded against feeding, and that offspring can act as an alternative food source for the parents. The evidence supporting the basic predictions formulated under these assumptions is summarized for both total and partial filial cannibalism. These two forms of cannibalism differ significantly since the former represents an investment only in future reproductive success, whereas the latter can affect both present and future reproductive success. Despite a few inconsistencies in the data from laboratory and field studies, the energy-based explanation appears valid for both forms of cannibalism. Alternative non-energy-based explanations are considered, but they are unable to account for the wide distribution of this behaviour in teleosts. The intersexual conflict arising from attempts of the non-cannibal sex to minimize the cost of filial cannibalism is also discussed, together with the potential effect of this behaviour on the operational sex ratio at a population level.     

Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan

Background

Pakistan covers a key geographic area in human history, being both part of the Indus River region that acted as one of the cradles of civilization and as a link between Western Eurasia and Eastern Asia. This region is inhabited by a number of distinct ethnic groups, the largest being the Punjabi, Pathan (Pakhtuns), Sindhi, and Baloch.

Results

We analyzed the first ethnic male Pathan genome by sequencing it to 29.7-fold coverage using the Illumina HiSeq2000 platform. A total of 3.8 million single nucleotide variations (SNVs) and 0.5 million small indels were identified by comparing with the human reference genome. Among the SNVs, 129,441 were novel, and 10,315 nonsynonymous SNVs were found in 5,344 genes. SNVs were annotated for health consequences and high risk diseases, as well as possible influences on drug efficacy. We confirmed that the Pathan genome presented here is representative of this ethnic group by comparing it to a panel of Central Asians from the HGDP-CEPH panels typed for ~650 k SNPs. The mtDNA (H2) and Y haplogroup (L1) of this individual were also typical of his geographic region of origin. Finally, we reconstruct the demographic history by PSMC, which highlights a recent increase in effective population size compatible with admixture between European and Asian lineages expected in this geographic region.

Conclusions

We present a whole-genome sequence and analyses of an ethnic Pathan from the north-west province of Pakistan. It is a useful resource to understand genetic variation and human migration across the whole Asian continent.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1290-1) contains supplementary material, which is available to authorized users.     

Benefits and Costs of Dominance in the Angelfish Centropyge bicolor

Social groups are often structured by dominance hierarchies in which subordinates consistently defer to dominants. High‐ranking individuals benefit by gaining inequitable access to resources, and often achieve higher reproductive success; but may also suffer costs associated with maintaining dominance. We used a large‐scale field study to investigate the benefits and costs of dominance in the angelfish Centropyge bicolor, a sequential hermaphrodite. Each haremic group contains a single linear body size‐based hierarchy with the male being most dominant, followed by several females in descending size order. Compared to their subordinate females, dominant males clearly benefited from disproportionately high spawning frequencies, but bore costs in lower foraging rates and greater aggressive defence of their large territories. Within the female hierarchy, more dominant individuals benefited from higher spawning frequencies and larger home ranges, but displayed neither higher foraging rates nor spawn order priority. However, dominance in females was also linked to aggressiveness, particularly towards immediate subordinates, suggesting that females were using energetically costly aggression to maintain their high rank. We further showed by experimentally removing dominant females that the linear hierarchy was also a social queue, with subordinates growing to inherit higher rank with its attendant benefits and costs when dominants disappeared. We suggest that in C. bicolor, the primary benefit of high rank is increased reproductive success in terms of current spawning frequency and the prospect of inheriting the male position in the near future, which may be traded off against the cost of aggressively defending rank and territory.     

Long-term changes in population size,distribution and productivity of skuas (<Emphasis Type="Italic">Stercorarius</Emphasis> spp.) at Signy Island,South Orkney Islands

In this study, we investigate the numbers, productivity and territory distribution of the two species of skuas (brown Stercorarius lonnbergi and south polar Stercorarius maccormicki) breeding at Signy Island, South Orkneys, and compare the results with trends elsewhere. Comparison with previous counts indicates a biphasic increase in brown skuas at Signy Island; much faster from 1958/1959 to 1982/1983 (3.3 % per annum), than in subsequent years (0.4 % per annum from 1983/1984 to 2013/2014). Relative distribution of territories has changed little over time. The reduced rate of population growth in recent years was broadly coincident with a decrease in numbers of penguins (and therefore potential prey), which may also explain recent reductions in skua numbers at other Antarctic sites. As prey have become limiting, breeding success of brown skuas at Signy Island is now slightly lower than in the 1950s/early 1960s, but timing of breeding does not appear to have changed. Brown skuas at Signy Island may still have enough resources to start breeding, but as the season progresses and availability of resources declines, chick survival is reduced. South polar skuas have declined from ten pairs in 1982/1983 to one pair in 2013/2014, and mixed pairs have increased from one to three pairs. A review of the literature indicated that although population trend data are available for relatively few sites elsewhere in the subantarctic and Antarctic, numbers of brown skuas appear to be generally decreasing or stable, and of south polar skuas to be stable or increasing.     

CRISPR-mediated targeted mRNA degradation in the archaeon Sulfolobus solfataricus

The recently discovered clustered regularly interspaced short palindromic repeat (CRISPR)-mediated virus defense represents an adaptive immune system in many bacteria and archaea. Small CRISPR RNAs cause cleavage of complementary invading nucleic acids in conjunction with an associated protein or a protein complex. Here, we show CRISPR-mediated cleavage of mRNA from an invading virus in the hyperthermophilic archaeon Sulfolobus solfataricus. More than 40% of the targeted mRNA could be cleaved, as demonstrated by quantitative polymerase chain reaction. Cleavage of the mRNA was visualized by northern analyses and cleavage sites were mapped. In vitro, the same substrates were cleaved by the purified CRISPR-associated CMR complex from Sulfolobus solfataricus. The in vivo system was also re-programmed to knock down mRNA of a selected chromosomal gene (β-galactosidase) using an artificial miniCRISPR locus. With a single complementary spacer, ∼50% reduction of the targeted mRNA and of corresponding intracellular protein activity was achieved. Our results demonstrate in vivo cleavage of mRNA in a prokaryote mediated by small RNAs (i.e. analogous to RNA interference in eukaryotes) and the re-programming of the system to silence specific genes of interest.