Patterns of Adaptive and Neutral Diversity Identify the Xiaoxiangling Mountains as a Refuge for the Giant Panda

Genetic variation plays a significant role in maintaining the evolutionary potential of a species. Comparing the patterns of adaptive and neutral diversity in extant populations is useful for understanding the local adaptations of a species. In this study, we determined the fine-scale genetic structure of 6 extant populations of the giant panda (Ailuropoda melanoleuca) using mtDNA and DNA fingerprints, and then overlaid adaptive variations in 6 functional Aime-MHC class II genes (DRA, DRB3, DQA1, DQA2, DQB1, and DQB2) on this framework. We found that: (1) analysis of the mtDNA and DNA fingerprint-based networks of the 6 populations identified the independent evolutionary histories of the 2 panda subspecies; (2) the basal (ancestral) branches of the fingerprint-based Sichuan-derived network all originated from the smallest Xiaoxiangling (XXL) population, suggesting the status of a glacial refuge in XXL; (3) the MHC variations among the tested populations showed that the XXL population exhibited extraordinary high levels of MHC diversity in allelic richness, which is consistent with the diversity characteristics of a glacial refuge; (4) the phylogenetic tree showed that the basal clades of giant panda DQB sequences were all occupied by XXL-specific sequences, providing evidence for the ancestor-resembling traits of XXL. Finally, we found that the giant panda had many more DQ alleles than DR alleles (33∶13), contrary to other mammals, and that the XXL refuge showed special characteristics in the DQB loci, with 7 DQB members of 9 XXL-unique alleles. Thus, this study identified XXL as a glacial refuge, specifically harboring the most number of primitive DQB alleles.     

Expression of Panton-Valentine Leukocidin mRNA among Staphylococcus aureus Isolates Associates with Specific Clinical Presentations

Panton-Valentine leukocidin (PVL; gene designation lukF/S-PV) is likely an important virulence factor for Staphylococcus aureus (S. aureus), as qualitative expression of the protein correlates with severity for specific clinical presentations, including skin and soft tissue infections (SSTIs). Development of genetic approaches for risk-assessment of patients with S. aureus infections may prove clinically useful, and whether lukF/S-PV gene expression correlates with specific clinical presentations for S. aureus has been largely unexplored. In the present study, we quantified lukS-PV mRNA among 96 S. aureus isolates to determine whether expression levels correlated with specific clinical presentations in adults and children. Expression level of lukS-PV mRNA among isolates from skin and soft tissue infections (SSTIs) was significantly greater than among isolates from blood stream infection (BSIs), and expression level of lukS-PV mRNA among BSI isolates from children was significantly greater than for BSI isolates among adults. Moreover, expression level of lukS-PV mRNA among community-acquired (CA) isolates was significantly greater than for hospital-acquired (HA) isolates. These data justify additional studies to determine the potential clinical utility for lukS-PV mRNA quantification as a predictive tool for severity of S. aureus infection.     

Naphtho‐γ‐pyrones from Endophyte Aspergillus niger Occurring in the Liverwort Heteroscyphus tener (Steph.) Schiffn.

Bioactivity‐guided fractionation of the cytotoxic extract of Aspergillus niger, an endophytic fungus from the Chinese liverwort Heteroscyphus tener (Steph .) Schiffn ., afforded five new naphtho‐γ‐pyrones, rubrofusarin‐6‐O‐α‐D ‐ribofuranoside ( 1 ), (R)‐10‐(3‐succinimidyl)‐TMC‐256A1 ( 2 ), asperpyrone E ( 3 ), isoaurasperone A ( 4 ), and isoaurasperone F ( 5 ), as well as four known ones, dianhydroaurasperone C ( 6 ), aurasperone D ( 7 ), asperpyrone D ( 8 ), and asperpyrone A ( 9 ), together with a cytotoxic cyclic pentapeptide, malformin A₁ ( 10 ). Their structures were determined by extensive spectroscopic analysis. The absolute configurations of dimeric naphtho‐γ‐pyrones 3 – 9 were also determined by analysis of their respective CD spectra.     

Phylogenetic diversity of endolithic bacteria in Bole granite rock in Xinjiang

The endolithic environment is a ubiquitous microbial habitat for microorganisms, such as lichens, Cyanobacteria and fungi, and it provides mineral nutrients and growth surfaces. In extremely environments, such as hot and cold desert, endolithic communities are often the main form of life. More recently, endolithic microbial communities have been observed inhabiting a variety of rock types ranging from hard granite to porous rocks such as basalt, dolomite, limestone, sandstone and granites. Regardless of geographic location and rock type, each of these habitats is characterized by a subsurface microclimate that prevents endolithic microorganisms growth. Photosynthesis-based endolithic microbial communities commonly inhabit the outer millimeters to centimeters of rocks exposed to the surface. The ability to fix carbon dioxide and in some cases atmospheric dinitrogen, gives the Cyanobacteria a clear competitive advantage over heterotrophic bacteria, so it is been called the main primary producer. Light quality and intensity appear to be the main determinant of the maximum depth to which growth occurs in endolithic phototrophic communities. Valleys of Fantastic Rocks in Bole is close to Alashankou Port of Xinjiang which belongs to extreme continental climate. In order to investigate the structure, composition and diversity of endolithic bacterial community in exposed granitic porphyry in the Valleys of Fantastic Rocks, environmental DNA was directly extracted from granite rock, the 16S rRNA genes were amplified from the total DNA by PCR with bacterial-specific primers, and an endolithic bacterial clone library was constructed. Positive clones were randomly selected from the library and identified by Restriction Fragment Length Polymorphism (RFLP). The unique rRNA types clones were sequenced, analysised and then constructed phylogenetic tree. In total, 129 positive clones were screened and grouped into 46 operational taxonomic unites (OTUs). The clone coverage C value was 89.15%, indicating that most of the estimated endolithic bacterial diversity was sampled. BLAST analysis indicated that 46 OTUs were divided into seven phyla (Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Planctomycetes, Proteobacteria) and five unknown groups. Cyanobacteria (43%), especially the Gp I, form the functional basis for an endolithic bacteria community which contain a wide spectrum species of chemotrophic bacteria (33%) with mainly Actinobacteria, α-Proteobacteria, Acidobacteria. Additionally, most clones that derived from the endolithic bacteria clone library showed high similarity to the sequence deposited in GenBank database with 97%–99%. Besides, 35% of the clones showed less than 97% of sequence similarity, of which 12% sequences were affiliated to genus Rubrobacter. The results suggested that endolithic bacteria in Valleys of Fantastic Rocks in Xinjiang were highly diverse in species richness, and maybe have a diversity of potential novel species and lineages.     

A New Equation to Estimate Glomerular Filtration Rate in Chinese Elderly Population

Background

We sought to develop a new equation to estimate glomerular filtration rate (GFR) in Chinese elderly population.

Methods

A total of 668 Chinese elderly participants, including the development cohort (n = 433), the validation cohort (n = 235) were enrolled. The new equation using the generalized additive model, and age, gender, serum creatinine as predictor variables was developed and the performances was compared with the CKD-EPI equation.

Results

In the validation data set, both bias and precision were improved with the new equation, as compared with the CKD-EPI equation (median difference, −1.5 ml/min/1.73 m² vs. 7.4 ml/min/1.73 m² for the new equation and the CKD-EPI equation, [P<0.001]; interquartile range [IQR] for the difference, 16.2 ml/min/1.73 m² vs. 19.0 ml/min/1.73 m² [P<0.001]), as were accuracies (15% accuracy, 40.4% vs. 30.6% [P = 0.02]; 30% accuracy, 71.1% vs. 47.2%, [P<0.001]; 50% accuracy, 90.2% vs. 75.7%, [P<0.001]), allowing improvement in GFR categorization (GFR category misclassification rate, 37.4% vs. 53.2% [P = <0.001]).

Conclusions

A new equation was developed in Chinese elderly population. In the validation data set, the new equation performed better than the original CKD-EPI equation. The new equation needs further external validations. Calibration of the GFR referent standard to a more accurate one should be an useful way to improve the performance of GFR estimating equations.     

荧光银纳米团簇的生物合成及其在痕量六价铬检测中的应用

【目的】利用季也蒙毕赤酵母ZJC-1合成银纳米团簇并用于痕量Cr(Ⅵ)的检测。【方法】使用经耐银驯化的季也蒙毕赤酵母ZJC-1生物合成荧光银纳米团簇,并对其结构和荧光性能进行了表征,探究Cr(Ⅵ)对银纳米团簇荧光的选择性猝灭作用,建立了银纳米团簇荧光强度与Cr(Ⅵ)浓度的线性关系。同时还考察了体系p H和其他金属离子对Cr(Ⅵ)检测的影响。【结果】Cr(Ⅵ)浓度在一定的范围内(1–80μmol/L)与银纳米团簇荧光强度(F_0–F)/F_0有着良好的线性关系(R~2=0.9821),线性方程为(F_0–F)/F_0=0.0054×C_cr(Ⅵ)+0.1876,检测限为184 nmol/L(信噪比为3)。利用该方法检测实际水样(松花江、马家沟河)中的Cr(Ⅵ),回收率介于97.73%–102.88%之间。【结论】以季也蒙毕赤酵母ZJC-1为还原剂和稳定剂,制备了具有较好荧光性能的水溶性银纳米团簇,基于Cr(Ⅵ)对银纳米团簇荧光的选择性猝灭作用,建立了一种快速且灵敏检测痕量Cr(Ⅵ)的新方法,并成功地应用于松花江、马家沟河水样中Cr(Ⅵ)的测定,在分析检测领域中具有良好的应用前景。     

Three new synonyms of Macromitrium microstomum (Hook. & Grev.) Schwägr. (Bryophyta,Orthotrichaceae), with comments on its morphological variations

Macromitrium filicaule Müll.Hal., M. pacificum var. brevisetum Thér. and M. subnitidum Müll.Hal are placed in synonymy with Macromitrium microstomum (Hook. & Grev.) Schwägr. The morphological variations of M. microstomum branch leaves, perichaetial leaves and capsules are illustrated by digital images.     

Methylenetetrahydrofolate reductase 677TT genotype might be associated with an increased lung cancer risk in Asians

Background

The association between methylenetetrahydrofolate reductase (MTHFR) 677C > T polymorphism and lung cancer risk has been studied in various populations with conflicting results. The aim of this study was to assess the association strength by a meta-analysis of published studies.

Methods

We searched PubMed and Chinese Biomedical (CBM) databases for relevant literatures published by July 18, 2012. Pooled odds ratio (OR) with 95% confidence interval (CI) was calculated to assess the strength of the association.

Results

A total of 20 studies comprising 11,653 cases and 12,032 controls were included in the final meta-analysis. Using the random effect model, we found that MTHFR 677TT variant genotype was associated with an increased lung cancer risk (OR = 1.26, 95% CI = 1.05–1.50, P = 0.011 for TT vs. CC; OR = 1.19, 95% CI = 1.03–1.37, P < 0.001 for TT vs. CC + CT; OR = 1.11, 95% CI = 1.02–1.22, P = 0.017 for T allele vs. C allele). In the further stratified analyses, the increased lung cancer risk was found in Asian subjects (OR = 1.31, 95% CI = 1.01–1.71, P = 0.045 for TT vs. CC; OR = 1.17, 95% CI = 1.00–1.38, P = 0.048 for TT vs. CC + CT). There were no evidences for obvious publication bias in the overall meta-analysis and Asian subjects.

Conclusions

MTHFR 677TT genotype might increase the susceptibility of lung cancer, especially in Asians.