Islands in the ice: detecting past vegetation on Greenlandic nunataks using historical records and sedimentary ancient DNA meta-barcoding

Nunataks are isolated bedrocks protruding through ice sheets. They vary in age, but represent island environments in 'oceans' of ice through which organism dispersals and replacements can be studied over time. The J.A.D. Jensen's Nunataks at the southern Greenland ice sheet are the most isolated nunataks on the northern hemisphere - some 30 km from the nearest biological source. They constitute around 2 km(2) of ice-free land that was established in the early Holocene. We have investigated the changes in plant composition at these nunataks using both the results of surveys of the flora over the last 130 years and through reconstruction of the vegetation from the end of the Holocene Thermal Maximum (5528 ± 75 cal year BP) using meta-barcoding of plant DNA recovered from the nunatak sediments (sedaDNA). Our results show that several of the plant species detected with sedaDNA are described from earlier vegetation surveys on the nunataks (in 1878, 1967 and 2009). In 1967, a much higher biodiversity was detected than from any other of the studied periods. While this may be related to differences in sampling efforts for the oldest period, it is not the case when comparing the 1967 and 2009 levels where the botanical survey was exhaustive. As no animals and humans are found on the nunataks, this change in diversity over a period of just 42 years must relate to environmental changes probably being climate-driven. This suggests that even the flora of fairly small and isolated ice-free areas reacts quickly to a changing climate.     

The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils

Claims of extreme survival of DNA have emphasized the need for reliable models of DNA degradation through time. By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (k) of 5.50 × 10^–6 per year. With an effective burial temperature of 13.1°C, the rate is almost 400 times slower than predicted from published kinetic data of in vitro DNA depurination at pH 5. Although best described by an exponential model (R² = 0.39), considerable sample-to-sample variance in DNA preservation could not be accounted for by geologic age. This variation likely derives from differences in taphonomy and bone diagenesis, which have confounded previous, less spatially constrained attempts to study DNA decay kinetics. Lastly, by calculating DNA fragmentation rates on Illumina HiSeq data, we show that nuclear DNA has degraded at least twice as fast as mtDNA. These results provide a baseline for predicting long-term DNA survival in bone.     

Cigarette smoking in male patients with chronic schizophrenia in a Chinese population: prevalence and relationship to clinical phenotypes

The high prevalence of smoking in schizophrenia of European background may be related to smoking's reducing clinical symptoms and medication side effects. Because smoking prevalence and its associations with clinical phenotypes are less well characterized in Chinese than European patients with schizophrenia, we assessed these smoking behaviors using clinician-administered questionnaires and the Fagerstrom Test for Nicotine Dependence (FTND) in 776 Chinese male schizophrenia and 560 control subjects. Patients also were rated on the Positive and Negative Symptom Scale (PANSS), the Simpson and Angus Extrapyramidal Symptom Rating Scale (SAES), and the Abnormal Involuntary Movement Scale (AIMS). We found that the schizophrenia patients had a higher lifetime incidence of smoking (79% vs 63%), were more likely to be heavy smokers (61% vs 31%), and had lower smoking cessation rates (4% vs 9%) (all p<0.0001) than controls. Among the schizophrenia patients smoking prevalence increased with age, with the largest difference from controls in the age cohort of 55-75 years: 75% vs 46% (p<0.0001). Among the schizophrenia smokers 73% started to smoke before the onset of their illness by an average of 7.6 years. The patients with schizophrenia who were current smokers scored significantly lower on the PANSS negative symptom subscore (p<0.005), and on the SAES symptom scale (p<0.04; Bonferroni corrected p>0.05) than the non-smoking patients. These results suggest that Chinese males with schizophrenia smoke more frequently than the general population. Further, smokers with schizophrenia may display fewer negative symptoms and possibly less parkinsonism than non-smokers with schizophrenia.     

Cigarette smoking and cognitive function in Chinese male schizophrenia: a case-control study

Schizophrenic patients have higher smoking rates than the general population. Studies show that smoking may be a form of self-medication in an attempt to alleviate cognitive deficits in schizophrenic patients of European background. This study examined the relationships between smoking and cognitive deficits in Chinese schizophrenic patients, which have previously received little systemic study. We recruited 580 male chronic patients meeting DSM-IV criteria for schizophrenia and 175 male control subjects who were matched on age and education. The subjects completed a detailed cigarette smoking questionnaire, the Fagerstrom Test for Nicotine Dependence (FTND), and the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS). Patients also were rated on the Positive and Negative Symptom Scale (PANSS), the Simpson and Angus Extrapyramidal Symptom Rating Scale (SAES), and the Abnormal Involuntary Movement Scale (AIMS). All five RBANS subscales except for the Visuospatial/Constructional index showed significantly lower cognitive performance for schizophrenics than normal controls. The schizophrenic smokers scored lower than the schizophrenic non-smokers on the RBANS total score and the Visuospatial/Constructional and Immediate Memory indices. Similarly, the control smokers scored lower than the control non-smokers on the RBANS total score and the Immediate Memory index . Also, the schizophrenic smokers consistently performed the poorest on the cognitive domains of the RBANS. Among the schizophrenic patients, smokers displayed significantly fewer negative symptoms than non-smokers. Using multivariate regression analysis the following variables were independently associated with the RBANS total score: years of education, PANSS negative symptom score, age at schizophrenia onset, and number of hospitalizations. Our results show that smoking is associated with significant cognitive impairment in both schizophrenic patients and normal controls, but the smokers with schizophrenia had a reduced level of negative symptoms, suggesting that the benefits of smoking for those with schizophrenia may be limited to certain aspects of a given clinical phenotype.     

The inhibition of the iron responsive element RNA-protein interaction by heme does not mimic in vivo iron regulation

Hemin at greater than 1 microM concentrations inhibits the interaction of the iron responsive element (IRE) and the iron responsive element binding protein (IRE-BP) as measured by gel retardation and UV cross-linking. Heme has recently been proposed to inhibit the repression of translation of an IRE-containing mRNA (Lin, J. J., Daniels-McQueen, S., Patino, M. M., Gaffield, L., Walden, W. E., and Thach, R. E., (1990) Science 247, 74-76). Our binding inhibition provides structural support for these observations. The action of hemin, however, does not mimic the physiologically demonstrated inhibition of high affinity binding of the IRE to IRE-BP by the oxidation of a sulfhydryl of the IRE-BP. In addition to this effect, hemin also inhibits a wide variety of RNA and DNA binding proteins, restriction endonucleases, and nucleases. Therefore, in vitro, the inhibitory effects of hemin are not limited to the interaction of the IRE-BP and the IRE, but are nonspecific and affect a wide variety of nucleic acid-protein interactions. Any hypothesis on the effects on protein-nucleic acid interactions employing greater than 1 microM concentrations of hemin should be interpreted with caution.     

Selection Practices of Bonga Sheep Reared in Southern Ethiopia

The study was conducted to assess the traits traditionally used to select the Bonga sheep reared in Southern Ethiopia. The breed was included for improvement under the community based breeding program (CBBP) launched in the year 2009. The results are based on the data collected from the project between 2009 till 2012. The findings are based on focus group discussions with the community elders who have been rearing the Bonga sheep for more than 20 years. The present findings are based on information obtained from 50% of the total respondents who were involved in CBBP. The Bonga sheep is a mutton type breed and the ewes are moderately prolific. In the past this breed of sheep were bartered to settle legal disputes and were traded against household commodities.. However, over the years (and also after the intervention of CBBP) the sheep have been selected for their body weight as well as for their distribution in many parts of Ethiopia The respondents selected the lambs at both pre weaning and post weaning stages. Traditionally the traits of rams are selected based on their body length, canon circumference, broad face, enlarged thyroid, while for the ewes, traits prolificacy, skin thickness and pelvic width are determining characters. Fat tail and brown coat color were preferred irrespective of the sexes in trait selection. The ram lambs selected for breeding purpose are locally known as “Dookoo”. These rams are selected based on some predetermined phenotypic traits and are initially selected at preweaning stage and further, again at the post weaning stage. These rams are preferentially cared and are provided with supplementary feed and comfortable housing.     

Genome-wide association mapping of genomic regions associated with phenotypic traits in Canadian western spring wheat

We recently reported genomic regions associated with resistance to four wheat diseases and insensitivity to three Pyrenophora tritici-repentis toxins in an association mapping panel consisting of 81 diverse Canadian western spring wheat (Triticum aestivum L.) cultivars. Here, we report genomic regions and SNPs associated with days to heading, plant maturity, plant height, test weight (grain volume weight), grain yield, and grain protein content in the same population using genome-wide association studies (GWAS). The 81 spring wheat cultivars were evaluated for the above six traits across six environments and genotyped with 19,919 polymorphic SNPs and 14 gene-specific markers. Using mixed liner model and a threshold of p ≤ 3.1 × 10^?4, we identified a total of 139 significant marker-trait associations that were mapped at 19 genomic regions on 11 chromosomes for heading (3 regions), maturity (2), plant height (3), test weight (3), grain yield (6), and grain protein (2). Each region consisted of clusters of markers ranging from 2 to 33 and individually explained from 4.5 to 26.1% of the phenotypic variation averaged over six environments. Some the genomic regions identified in the present study are novel, while others, such as the regions for grain protein on 1B, days to heading on 5A, plant height on 4B, and test weight on 7A, were located close to either known genes or QTLs reported in previous studies, but direct comparisons in some cases were challenging due to lack of common set of markers and reliable physical positions among the different studies. Results from this study provide additional information to wheat researchers developing improved spring wheat cultivars.     

Tumor cell programmed death ligand 1-mediated T cell suppression is overcome by coexpression of CD80

Programmed death ligand 1 (PDL1, or B7-H1) is expressed constitutively or is induced by IFN-γ on the cell surface of most human cancer cells and acts as a "molecular shield" by protecting tumor cells from T cell-mediated destruction. Using seven cell lines representing four histologically distinct solid tumors (lung adenocarcinoma, mammary carcinoma, cutaneous melanoma, and uveal melanoma), we demonstrate that transfection of human tumor cells with the gene encoding the costimulatory molecule CD80 prevents PDL1-mediated immune suppression by tumor cells and restores T cell activation. Mechanistically, CD80 mediates its effects through its extracellular domain, which blocks the cell surface expression of PDL1 but does not prevent intracellular expression of PDL1 protein. These studies demonstrate a new role for CD80 in facilitating antitumor immunity and suggest new therapeutic avenues for preventing tumor cell PDL1-induced immune suppression.