Polymorphisms in the nucleotide excision repair gene ERCC2/XPD and risk of non-Hodgkin lymphoma

Non-Hodgkin lymphoma (NHL) represents a complex group of B- and T-cell malignancies characterised by chromosomal translocations. Since defects in DNA repair result in an increased frequency of chromosomal aberrations it has been hypothesised that genetic variation in DNA repair may be associated with risk of NHL. To investigate the relationship between DNA repair and NHL we analysed polymorphisms in XPD (R156R, D312N, K751Q) using DNA collected in a UK population-based case-control study of lymphoma. We observed no association between genetic variation in XPD and risk of NHL. However, the XPD 751 Gln allele was associated with a two-fold decreased risk of diffuse large B-cell lymphoma (OR 0.56, 95% CI 0.34–0.92, p = 0.02), the major subtype of NHL. Overall, our study identifies that XPD polymorphisms may be important in the aetiology of NHL although analysis of additional polymorphisms and extended haplotype studies are required to clarify their role.     

Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling

Among small photosynthetic eukaryotes that play a key role in oceanic food webs, picoplanktonic Mamiellophyceae such as Bathycoccus, Micromonas, and Ostreococcus are particularly important in coastal regions. By using a combination of cell sorting by flow cytometry, whole genome amplification (WGA), and 454 pyrosequencing, we obtained metagenomic data for two natural picophytoplankton populations from the coastal upwelling waters off central Chile. About 60% of the reads of each sample could be mapped to the genome of Bathycoccus strain from the Mediterranean Sea (RCC1105), representing a total of 9 Mbp (sample T142) and 13 Mbp (sample T149) of non-redundant Bathycoccus genome sequences. WGA did not amplify all regions uniformly, resulting in unequal coverage along a given chromosome and between chromosomes. The identity at the DNA level between the metagenomes and the cultured genome was very high (96.3% identical bases for the three larger chromosomes over a 360 kbp alignment). At least two to three different genotypes seemed to be present in each natural sample based on read mapping to Bathycoccus RCC1105 genome.     

Proteomic Biomarkers Associated with Streptococcus agalactiae Invasive Genogroups

Group B streptococcus (GBS, Streptococcus agalactiae) is a leading cause of meningitis and sepsis in newborns and an etiological agent of meningitis, endocarditis, osteoarticular and soft tissue infections in adults. GBS isolates are routinely clustered in serotypes and in genotypes. At present one GBS sequence type (i.e. ST17) is considered to be closely associated with bacterial invasiveness and novel proteomic biomarkers could make a valuable contribution to currently available GBS typing data. For that purpose we analyzed the protein profiles of 170 genotyped GBS isolates by Surface-Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (SELDI). Univariate statistical analysis of the SELDI profiles identified four protein biomarkers significantly discriminating ST17 isolates from those of the other sequence types. Two of these biomarkers (MW of 7878 Da and 12200 Da) were overexpressed and the other two (MW of 6258 Da and 10463 Da) were underexpressed in ST17. The four proteins were isolated by mass spectrometry-assisted purification and their tryptic peptides analyzed by LC-MS/MS. They were thereby identified as the small subunit of exodeoxyribonuclease VII, the 50S ribosomal protein L7/L12, a CsbD-like protein and thioredoxin, respectively. In conclusion, we identified four candidate biomarkers of ST17 by SELDI for high-throughput screening. These markers may serve as a basis for further studies on the pathophysiology of GBS infection, and for the development of novel vaccines.     

红角鸮的食性及育雏行为初报

红角鸮(Otus sunia)广泛分布于东亚和南亚。2012和2013年的两个繁殖季节,在江苏省南京大学浦口校区通过红外摄像观察记录了红角鸮的摄食及育雏行为,统计了亲代红角鸮育雏食物的种类、育雏的时间和次数。以1 h为一个时段,利用单因素方差分析(ANOVA)及Student-Newman-Keulsa多重比较法分析各时段之间育雏频次的差异。亲鸟育雏的食物大部分为直翅目(62%)和鳞翅目(18%)昆虫,以及非昆虫类的无脊椎动物,如蜘蛛(8%)和唇足动物(7%),红角鸮也捕食小型陆栖脊椎动物例如田鼠、壁虎等育雏,但比例甚低(3%)。红角鸮育雏节律较为明显,亲鸟主要集中在夜间外出觅食,但在白天也有觅食行为。夜间共有三个育雏高峰,分别为日落之后的19:00~20:00时和21:00~22:00时以及日出之前的04:00~05:00时。     

Origins of domestication and polyploidy in oca (Oxalis tuberosa; Oxalidaceae). 3. AFLP data of oca and four wild, tuber-bearing taxa

Many crops are polyploids, and it can be challenging to untangle the often complicated history of their origins of domestication and origins of polyploidy. To complement other studies of the origins of polyploidy of the octoploid tuber crop oca (Oxalis tuberosa) that used DNA sequence data and phylogenetic methods, we here compared AFLP data for oca with four wild, tuber-bearing Oxalis taxa found in different regions of the central Andes. Results confirmed the divergence of two use-categories of cultivated oca that indigenous farmers use for different purposes, suggesting the possibility that they might have had separate origins of domestication. Despite previous results with nuclear-encoded, chloroplast-expressed glutamine synthetase suggesting that O. picchensis might be a progenitor of oca, AFLP data of this species, as well as different populations of wild, tuber-bearing Oxalis found in Lima Department, Peru, were relatively divergent from O. tuberosa. Results from all analytical methods suggested that the unnamed wild, tuber-bearing Oxalis found in Bolivia and O. chicligastensis in NW Argentina are the best candidates as the genome donors for polyploid O. tuberosa, but the results were somewhat equivocal about which of these two taxa is the more strongly supported as oca's progenitor.     

Retroviral overexpression of bcl-2 in the embryonic chick lens influences denucleation in differentiating lens fiber cells

During the course of their differentiation, embryonic lens fibers undergo loss of their cytoplasmic organelles and nuclei. The denucleation process bears similarities to the nuclear breakdown that occurs during apoptosis. This has given rise to the hypothesis that this denucleation is analogous to apoptosis, but without the plasma membrane changes characteristic of apoptotic cell death. Previous work has shown that several members of the apoptotic cascade are active during denucleation. Here, we have overexpressed the anti-apoptotic molecule bcl-2 in developing lenses of the 8-day-old chick embryo in ovo, using the replication-competent retrovirus RCAS. We find that lenses overexpressing bcl-2 show varying degrees of distortion in comparison with untreated and negative insert controls, including a more spherical shape and disorganized fiber cells. All overexpressing lenses showed significantly higher numbers of smaller nuclei in the lens core, where denucleation begins. There was no change in cell size or pattern of proliferation. These in vivo results were confirmed in vitro using lens epithelial cell cultures, which differentiate into lentoids. The lentoids in treated cultures showed the same effect on nuclear number and size. We further found that in lenses overexpressing bcl-2 there was a reduction in the activation of caspase-9 and the cleavage of the caspase substrate DFF45, and, in the lens core, a failure of the nuclear chromatin to condense. These results provide strong support for the view that embryonic lens fiber cell denucleation is analogous to the nuclear degradation that occurs during apoptosis, and that similar control pathways are involved in both these phenomena.     

Anthropogenic noise reduces avian feeding efficiency and increases vigilance along an urban–rural gradient regardless of species’ tolerances to urbanisation

Anthropogenic noise can adversely impact urban bird populations by interfering with vocal communication. Less research has addressed if anthropogenic noise masks the adventitious sounds that birds use to aid predator detection, which may lead to increased vigilance and reduced feeding efficiency. We test this hypothesis using a controlled playback experiment along an urban–rural gradient in Sheffield (UK). We also test the related predictions that anthropogenic noise has the greatest impacts on vigilance and feeding efficiency in rural populations, and on species that are more sensitive to urbanisation. We focus on six passerines, in order from most to least urbanised (based on how urbanisation influences population densities): blue tit Cyanistes caeruleus, robin Erithacus rubeculla, great tit Parus major, chaffinch Fringilla coelebs, coal tit Periparus ater and nuthatch Sitta europaea. We used play-back of anthropogenic urban noise and a control treatment at 46 feeding stations located along the urban–rural gradient. We assess impacts on willingness to visit feeders, feeding and vigilance rates. Exposure to anthropogenic noise reduced visit rates to supplementary feeding stations, reduced feeding rates and increased vigilance. Birds at more urban sites exhibit less marked treatment induced reductions in feeding rates, suggesting that urban populations may be partially habituated or adapted to noisy environments. There was no evidence, however, that more urbanised species were less sensitive to the impacts of noise on any response variable. Our results support the adventitious sound masking hypothesis. Urban noise may thus interfere with the ability of birds to detect predators, reducing their willingness to use food rich environments and increase vigilance rates resulting in reduced feeding rates. These adverse impacts may compromise the quality of otherwise suitable foraging habitats in noisy urban areas. They are likely to be widespread as they arise in a range of species including common urban birds.