Body mass‐related changes in mammal community assembly patterns during the late Quaternary of North America

The late Quaternary of North America was marked by prominent ecological changes, including the end‐Pleistocene megafaunal extinction, the spread of human settlements and the rise of agriculture. Here we examine the mechanistic reasons for temporal changes in mammal species association and body size during this time period. Building upon the co‐occurrence results from Lyons et al. (2016) – wherein each species pair was classified as spatially aggregated, segregated or random – we examined body mass differences (BMD) between each species pair for each association type and time period (Late Pleistocene: 40 000 ¹⁴C–11 700 ¹⁴C ybp, Holocene: 11 700 ¹⁴C–50 ybp and Modern: 50–0 yr). In the Late Pleistocene and Holocene, the BMD of both aggregated and segregated species pairs was significantly smaller than the BMD of random pairs. These results are consistent with environmental filtering and competition as important drivers of community structure in both time periods. Modern assemblages showed a breakdown between BMD and co‐occurrence patterns: the average BMD of aggregated, segregated and random species pairs did not differ from each other. Collectively, these results indicate that the late Quaternary mammalian extinctions not only eliminated many large‐bodied species but were followed by a re‐organization of communities that altered patterns of species coexistence and associated differences in body size.     

The Course of Asthma in Young Adults: A Population-Based Nine-Year Follow-Up on Asthma Remission and Control

Background

Only few longitudinal studies on the course of asthma among adults have been carried out.

Objective

The aim of the present prospective study, carried out between 2000 and 2009 in Italy, is to assess asthma remission and control in adults with asthma, as well as their determinants.

Methods

All the subjects with current asthma (21–47 years) identified in 2000 in the Italian Study on Asthma in Young Adults in 6 Italian centres were followed up. Asthma remission was assessed at follow-up in 2008–2009 (n = 214), asthma control at baseline and follow-up. Asthma remission and control were related to potential determinants by a binomial logistic and a multinomial logistic model. Separate models for remission were used for men and women.

Results

The estimate of the proportion of subjects who were in remission was 29.7% (95%CI: 14.4%;44.9%). Men who were not under control at baseline had a very low probability of being in remission at follow-up (OR = 0.06; 95%CI:0.01;0.33) when compared to women (OR = 0.40; 95%CI:0.17;0.94). The estimates of the proportion of subjects who were under control, partial control or who were not under control in our sample were 26.3% (95%CI: 21.2;31.3%), 51.6% (95%CI: 44.6;58.7%) and 22.1% (95%CI: 16.6;27.6%), respectively. Female gender, increasing age, the presence of chronic cough and phlegm and partial or absent asthma control at baseline increased the risk of uncontrolled asthma at follow-up.

Conclusion

Asthma remission was achieved in nearly 1/3 of the subjects with active asthma in the Italian adult population, whereas the proportion of the subjects with controlled asthma among the remaining subjects was still low.     

Influenza Epidemiology and Vaccine Effectiveness among Patients with Influenza-Like Illness,Viral Watch Sentinel Sites,South Africa, 2005–2009

Background

There is limited data on the epidemiology of influenza and few published estimates of influenza vaccine effectiveness (VE) from Africa. In April 2009, a new influenza virus strain infecting humans was identified and rapidly spread globally. We compared the characteristics of patients ill with influenza A(H1N1)pdm09 virus to those ill with seasonal influenza and estimated influenza vaccine effectiveness during five influenza seasons (2005–2009) in South Africa.

Methods

Epidemiological data and throat and/or nasal swabs were collected from patients with influenza-like illness (ILI) at sentinel sites. Samples were tested for seasonal influenza viruses using culture, haemagglutination inhibition tests and/or polymerase chain reaction (PCR) and for influenza A(H1N1)pdm09 by real-time PCR. For the vaccine effectiveness (VE) analysis we considered patients testing positive for influenza A and/or B as cases and those testing negative for influenza as controls. Age-adjusted VE was calculated as 1-odds ratio for influenza in vaccinated and non-vaccinated individuals.

Results

From 2005 through 2009 we identified 3,717 influenza case-patients. The median age was significantly lower among patients infected with influenza A(H1N1)pdm09 virus than those with seasonal influenza, 17 and 27 years respectively (p<0.001). The vaccine coverage during the influenza season ranged from 3.4% in 2009 to 5.1% in 2006 and was higher in the ≥50 years (range 6.9% in 2008 to 13.2% in 2006) than in the <50 years age group (range 2.2% in 2007 to 3.7% in 2006). The age-adjusted VE estimates for seasonal influenza were 48.6% (4.9%, 73.2%); −14.2% (−9.7%, 34.8%); 12.0% (−70.4%, 55.4%); 67.4% (12.4%, 90.3%) and 29.6% (−21.5%, 60.1%) from 2005 to 2009 respectively. For the A(H1N1)pdm09 season, the efficacy of seasonal vaccine was −6.4% (−93.5%, 43.3%).

Conclusion

Influenza vaccine demonstrated a significant protective effect in two of the five years evaluated. Low vaccine coverage may have reduced power to estimate vaccine effectiveness.     

Novel Polyglutamine Model Uncouples Proteotoxicity from Aging

Polyglutamine expansions in certain proteins are the genetic determinants for nine distinct progressive neurodegenerative disorders and resultant age-related dementia. In these cases, neurodegeneration is due to the aggregation propensity and resultant toxic properties of the polyglutamine-containing proteins. We are interested in elucidating the underlying mechanisms of toxicity of the protein ataxin-3, in which a polyglutamine expansion is the genetic determinant for Machado-Joseph Disease (MJD), also referred to as spinocerebellar ataxia 3 (SCA3). To this end, we have developed a novel model for ataxin-3 protein aggregation, by expressing a disease-related polyglutamine-containing fragment of ataxin-3 in the genetically tractable body wall muscle cells of the model system C. elegans. Here, we demonstrate that this ataxin-3 fragment aggregates in a polyQ length-dependent manner in C. elegans muscle cells and that this aggregation is associated with cellular dysfunction. However, surprisingly, this aggregation and resultant toxicity was not influenced by aging. This is in contrast to polyglutamine peptides alone whose aggregation/toxicity is highly dependent on age. Thus, the data presented here not only describe a new polyglutamine model, but also suggest that protein context likely influences the cellular interactions of the polyglutamine-containing protein and thereby modulates its toxic properties.     

A continental-scale study of seed lifespan in experimental storage examining seed,plant, and environmental traits associated with longevity

Management of seed banks conserving the biodiversity of phylogenetically diverse species requires insight into seed longevity. This study determined the seed longevity of 172 species sourced from across the mega-diverse flora of the Australia continent. Seeds were aged via a controlled ageing experiment through storage at 45 °C and 60 % RH, or 60 °C and 60 % RH, and regularly tested for germination. Relative seed longevity between species was determined by comparing the time to 50 % viability loss (p ₅₀), calculated via probit analysis of seed survival curves. Seed, plant, and environmental traits were examined for associations with longevity. The p ₅₀ values varied between species from 3.0 to 588.6 days. Serotinous species, and woody trees and shrubs, had significantly longer-lived seeds than geosporous species, and species of herbaceous habit. Seeds that possess physical dormancy, and seeds with large embryos with little endosperm, were also long-lived. There was a weak, but significant, positive correlation between seed mass and longevity. Seeds sourced from regions of higher mean annual temperature and rainfall were significantly longer-lived than seeds from cooler and drier regions, although both environmental factors were weakly associated with longevity. Compared with species from other regions of the world, prolonged longevity is a feature of many Australian species. Nevertheless, seed life-spans vary substantially between species and close consideration of seed traits along with biotic and abiotic components of the plants and their environment can assist to differentiate between potentially long- and short-lived seeds.     

Agrobacterium tumefaciens ExoR Controls Acid Response Genes and Impacts Exopolysaccharide Synthesis,Horizontal Gene Transfer,and Virulence Gene Expression

Agrobacterium tumefaciens is a facultative plant pathogen and the causative agent of crown gall disease. The initial stage of infection involves attachment to plant tissues, and subsequently, biofilms may form at these sites. This study focuses on the periplasmic ExoR regulator, which was identified based on the severe biofilm deficiency of A. tumefaciens exoR mutants. Genome-wide expression analysis was performed to elucidate the complete ExoR regulon. Overproduction of the exopolysaccharide succinoglycan is a dramatic phenotype of exoR mutants. Comparative expression analyses revealed that the core ExoR regulon is unaffected by succinoglycan synthesis. Several findings are consistent with previous observations: genes involved in succinoglycan biosynthesis, motility, and type VI secretion are differentially expressed in the ΔexoR mutant. In addition, these studies revealed new functional categories regulated by ExoR, including genes related to virulence, conjugation of the pAtC58 megaplasmid, ABC transporters, and cell envelope architecture. To address how ExoR exerts a broad impact on gene expression from its periplasmic location, a genetic screen was performed to isolate suppressor mutants that mitigate the exoR motility phenotype and identify downstream components of the ExoR regulatory pathway. This suppression analysis identified the acid-sensing two-component system ChvG-ChvI, and the suppressor mutant phenotypes suggest that all or most of the characteristic exoR properties are mediated through ChvG-ChvI. Subsequent analysis indicates that exoR mutants are simulating a response to acidic conditions, even in neutral media. This work expands the model for ExoR regulation in A. tumefaciens and underscores the global role that this regulator plays on gene expression.     

Insights from the GC content analysis of 76genome survey sequences (GSS) from Elaeisoleifera

South American oil-palm (Elaeis oleifera) is not cultivated in tropical countries like Malaysia on large scale due to low yield of palm oil derived from its fruit mesocarp. However, its fruit mesocarp oil contains about 68.6 % oleic acid (C_18:1) which is more than double in comparison to commercially cultivated oilpalm, E. guineensis Jacq Tenera (hybrid of Dura (♀) x Pisifera (♂)). It is also known that E. oleifera is a good source of tocotrienols and carotenoids. Therefore, it is of interest to know the genome sequence of E. oleifera. The objective of this study is to generate genome survey sequences (GSS) to get GC content insight in the E. oleifera genome. The nuclear genomic DNA isolated from young leaf‐tissues was digested with EcoRI and NdeI/DraI restriction enzymes; and three genomic DNA libraries were constructed using Lambda ZAP‐II, pGEM®‐T Easy, and pDONR 222™ as cloning vectors. Generated 76 GSSs were analyzed by using Bioinformatics tools. The analysis result indicates that the adenine, cytosine, guanine and thymine content in generated GSSs are 30%, 20%, 20%, and 30% respectively. In conclusion, based on the precise GC content analysis of the randomly isolated 76 GSSs by using Bioinformatics tools we hypothesize that GC content in E. oleifera genome is 40%. The hypothesized 40% GC content in E. oleifera genome is expected to remain close to the GC content based on the whole genome analysis.^ψThe nucleotide sequence data reported in this paper have been submitted to dbGSS division of the international DNA database (GenBank/DDBJ/EMBL) under accession numbers: {"type":"entrez-nucleotide-range","attrs":{"text":"DX575945- DX575972","start_term":"DX575945","end_term":"DX575972","start_term_id":"94323534","end_term_id":"94323561"}}DX575945- DX575972 and {"type":"entrez-nucleotide-range","attrs":{"text":"EI798032-EI798079","start_term":"EI798032","end_term":"EI798079","start_term_id":"146199019","end_term_id":"146199066"}}EI798032-EI798079.

Abbreviations

gDNA - Nuclear genomic DNA, GSSs - Genome survey sequences K12, SAOP - South American oil‐palm Db1     

Nutritional genomics era: opportunities toward a genome-tailored nutritional regimen

There is increasing evidence indicating that nutritional genomics represents a promise to improve public health. This goal will be reached by highlighting the mechanisms through which diet can reduce the risk of monogenic and common polygenic diseases. Indeed, nutrition is a very relevant environmental factor involved in the development and progression of metabolic disorders, as well as other kind of diseases. The revolutionary changes in the field of genomics have led to the development and implementation of new technologies and molecular tools. These technologies have a useful application in the nutritional sciences, since they allow a more precise and accurate analysis of biochemical alterations, in addition to filling fundamental gaps in the knowledge of nutrient–genome interactions in both health and disease. Overall, these advances will open undiscovered ways in genome-customized diets for disease prevention and therapy. This review summarizes the recent knowledge concerning this novel nutritional approach, paying attention to the human genome variations, such as single-nucleotide polymorphisms and copy number variations, gene expression and innovative molecular tools to reveal them.