Polymorphism and divergence at the 5' flanking region of the sex- determining locus, Sry, in mice

We have investigated patterns of evolution in the nonrecombining portion of the Y chromosome in mice by comparing levels of polymorphism within Mus domesticus with levels of divergence between M. domesticus and M. spretus. A 1,277-bp fragment of noncoding sequence flanking the sex determining locus (Sry) was PCR amplified, and 1,063 bases were sequenced and compared among 20 M. domesticus and 1 M. spretus. Two polymorphic base substitutions and two polymorphic insertion/deletion sites were identified within M. domesticus; nucleotide diversity was estimated to be 0.1%. Divergence between M. domesticus and M. spretus for this region (1.9%) was slightly lower than the average divergence of single-copy nuclear DNA for these species. Comparison of levels of polymorphism and divergence at Sry with levels of polymorphism and divergence in the mitochondrial DNA control region provided no evidence of a departure from the expectations of neutral molecular evolution. These findings are consistent with the presumed lack of function for much of the Y chromosome.      

A continuous culture study of an obligately psychrophilic Pseudomonas species

Summary The optimum temperatures for growth and respiration of an obligately psychrophilic Pseudomonas spec. were 14°C and 23°C, respectively. The maximum temperature for growth was between 19 and 20°C. When cells were grown in a chemostat with lactate as the growth-limiting substrate at a specific growth rate of 0.05 hr^-1 over a temperature range of 5–19°C, it was found that RNA concentration was lowest at 14°C. At lower temperatures the cells compensated the decrease of reaction rates by increasing the concentration of RNA and of respiratory enzymes. A temperature raise above 14°C also increased cellular RNA, which probably counteracted an impairment of protein synthesis. Above 18°C the RNA increase ceased, resulting in a rapid decrease of protein synthesis, until between 19 and 20°C growth ceased entirely. Cells grown at 14°C showed a linear increase of RNA content and values with growth rate, when this was varied from 0.025 to the maximum value of 0.2 hr^-1.Dedicated to Prof. C. B. van Niel on the occasion of his 70th birthday.     

Heparin Oligosaccharides Inhibit Chemokine (CXC Motif) Ligand 12 (CXCL12) Cardioprotection by Binding Orthogonal to the Dimerization Interface,Promoting Oligomerization,and Competing with the Chemokine (CXC Motif) Receptor 4 (CXCR4) N Terminus

The ability to interact with cell surface glycosaminoglycans (GAGs) is essential to the cell migration properties of chemokines, but association with soluble GAGs induces the oligomerization of most chemokines including CXCL12. Monomeric CXCL12, but not dimeric CXCL12, is cardioprotective in a number of experimental models of cardiac ischemia. We found that co-administration of heparin, a common treatment for myocardial infarction, abrogated the protective effect of CXCL12 in an ex vivo rat heart model for myocardial infarction. The interaction between CXCL12 and heparin oligosaccharides has previously been analyzed through mutagenesis, in vitro binding assays, and molecular modeling. However, complications from heparin-induced CXCL12 oligomerization and studies using very short oligosaccharides have led to inconsistent conclusions as to the residues involved, the orientation of the binding site, and whether it overlaps with the CXCR4 N-terminal site. We used a constitutively dimeric variant to simplify the NMR analysis of CXCL12-binding heparin oligosaccharides of varying length. Biophysical and mutagenic analyses reveal a CXCL12/heparin interaction surface that lies perpendicular to the dimer interface, does not involve the chemokine N terminus, and partially overlaps with the CXCR4-binding site. We further demonstrate that heparin-mediated enzymatic protection results from the promotion of dimerization rather than direct heparin binding to the CXCL12 N terminus. These results clarify the structural basis for GAG recognition by CXCL12 and lend insight into the development of CXCL12-based therapeutics.     

Statistical properties of the variation at linked microsatellite loci: implications for the history of human Y chromosomes [published erratum appears in Mol Biol Evol 1997 Mar;14(3):354]

It has recently been suggested that observed levels of variation at microsatellite loci can be used to infer patterns of selection in genomes and to assess demographic history. In order to evaluate the feasibility of these suggestions it is necessary to know something about how levels of variation at microsatellite loci are expected to fluctuate due simply to stochasticity in the processes of mutation and inheritance (genetic sampling). Here we use recently derived properties of the stepwise mutation model to place confidence intervals around the variance in repeat score that is expected at mutation-drift equilibrium and outline a statistical test for whether an observed value differs significantly from expectation. We also develop confidence intervals for the time course of the buildup of variation following a complete elimination of variation, such as might be caused by a selective sweep or an extreme population bottleneck. We apply these methods to the variation observed at human Y-specific microsatellites. Although a number of authors have suggested the possibility of a very recent sweep, our analyses suggest that a sweep or extreme bottleneck is unlikely to have occurred anytime during the last approximately 74,000 years. To generate this result we use a recently estimated mutation rate for microsatellite loci of 5.6 x 10(-4) along with the variation observed at autosomal microsatellite loci to estimate the human effective population size. This estimate is 18,000, implying an effective number of 4,500 Y chromosomes. One important general conclusion to emerge from this study is that in order to reject mutation-drift equilibrium at a set of linked microsatellite loci it is necessary to have an unreasonably large number of loci unless the observed variance is far below that expected at mutation-drift equilibrium.      

Differences in methylation profiles between HPV-positive and HPV-negative oropharynx squamous cell carcinoma: A systematic review

Oropharyngeal squamous cell carcinoma (OPSCC) is associated with human papillomavirus (HPV). HPV-positive OPSCC is considered a distinct molecular entity with a better prognosis than HPV-negative cases of OPSCC. However, the exact pathogenic mechanisms underlying the differences in clinical and molecular behavior between HPV-positive and HPV-negative OPSCC remain poorly understood. Epigenetic events play an important role in the development of cancer. Hypermethylation of DNA in promoter regions and global hypomethylation are 2 epigenetic changes that have been frequently observed in human cancers. It is suggested that heterogeneous epigenetic changes play a role in the clinical and biological differences between HPV-positive and HPV-negative tumors. Unraveling the differences in methylation profiles of HPV-associated OPSCC may provide for promising clinical applications and may pave the road for personalized cancer treatment. This systematic review aims to assess the current state of knowledge regarding differences in promoter hypermethylation and global methylation between HPV-positive and HPV-negative OPSCC.     

Exploring effective conservation networks based on multi-scale planning unit analysis. A case study of the Balsas sub-basin,Maranhão State,Brazil

Nature conservation and restoration activities require delineation of effective conservation networks. This paper presents a methodology which allows a quick evaluation of different planning options for extensive areas. We analyzed the spatial structure of remaining patches of the natural Cerrado vegetation in the Balsás sub-basin, South of Maranhão State of Brazil (about 25,590 km²) in order to understand how the remaining habitats are distributed and spatially configured. Conservation area network scenarios are based on hexagonal cells, referred to as analysis unit (AU) cells. A multi-scale analysis of 10,000 ha and 50,000 ha AU cells was set up to represent local and regional scales, respectively. For each AU at both local and regional scales we computed landscape metrics of native vegetation: NATIVE VEGETATION COVER: percentage of native vegetation cover; (NV-NP): number of patches; (NV-MSI): mean shape index. Subsequently, five different conservation and restoration strategies were defined: (a) only enforce nature conservation within legally established units; (b) target nature conservation only within the local AU landscape; (c) target regional management by combining neighboring AU; (d) management of both local landscape and region; (e) protect the legal conservation areas and promote local and regional conservation. We also generated scenarios of habitat capacity for mammals and matched these results with the different vegetation conservation scenarios. Results indicate that only 12% of the study area is well conserved and that 43% of the region is in a very critical condition. The percentage of AU cells where native vegetation conservation actions are required differ for the five conservation strategies: These results allow policy makers and other stakeholders to target the locations and extent of conservation units required. We suggest that about 45% of the sub-basin could be managed at local, regional or both scales. Regarding a mammal species diversity scenario an even higher percentage of the average habitat capacity of the selected species occurs in open cerrado and valleys areas that coincide with critical areas. The proposed multi-scale analysis unit cell approach can support the planning process of extensive areas as necessary in Brazil.     

Nanooravia gen. nov., subtribe Dimeriinae (Poaceae–Panicoideae–Andropogoneae) from India

The new genus Nanooravia Kiran Raj & Sivad. (Poaceae–Andropogoneae–Dimeriinae) from the southwestern Ghats in India is described and illustrated, and the new combination N. santapaui (M. R. Almeida) Kiran Raj & Sivad. is made. The genus is characterized by its usually unequal and intertwined racemes, triquetrous rachis, extremely oblique and glabrous pedicel tip, distantly arranged spikelets, long trigonous callus with oblique tip and densely covered with golden–yellow or yellowish–brown hairs along one angle, keel‐less glumes with a dorsally echinate apex and apically auricled margins, and an upper lemma with a stout awn having a long column. The new genus is distinct from Dimeria R. Br. in which the species was originally described, but is similar to the monotypic Indian genus Pogonachne Bor currently placed in the subtribe Ischaeminae. It occurs in Peninsular India, a region considered as the centre of diversity of the subtribe with more than 50% of the known Dimeria species, including numerous endemics.     

The solution structure of the forkhead box‐O DNA binding domain of Brugia malayi DAF‐16a

Brugia malayi is a parasitic nematode that causes lymphatic filariasis in humans. Here the solution structure of the forkhead DNA binding domain of Brugia malayi DAF‐16a, a putative ortholog of Caenorhabditis elegans DAF‐16, is reported. It is believed to be the first structure of a forkhead or winged helix domain from an invertebrate. C. elegans DAF‐16 is involved in the insulin/IGF‐I signaling pathway and helps control metabolism, longevity, and development. Conservation of sequence and structure with human FOXO proteins suggests that B. malayi DAF‐16a is a member of the FOXO family of forkhead proteins. Proteins 2014; 82:3490–3496. © 2014 Wiley Periodicals, Inc.     

In vitro glucocorticoid sensitivity is associated with clinical glucocorticoid therapy outcome in rheumatoid arthritis

Introduction

Genetic and disease-related factors give rise to a wide spectrum of glucocorticoid (GC) sensitivity in rheumatoid arthritis (RA). In clinical practice, GC treatment is not adapted to these differences in GC sensitivity. In vitro assessment of GC sensitivity before the start of therapy could allow more individualized GC therapy. The aim of the study was to investigate the association between in vitro and in vivo GC sensitivity in RA.

Methods

Thirty-eight early and 37 established RA patients were prospectively studied. In vitro GC sensitivity was assessed with dexamethasone-induced effects on interleukin-2 (IL-2) and glucocorticoid-induced leucine zipper (GILZ) messenger RNA expression in peripheral blood mononuclear cells (PBMCs). A whole-cell dexamethasone-binding assay was used to measure number and affinity (1/K_D) of glucocorticoid receptors (GRs).In vivo GC sensitivity was determined by measuring the disease activity score (DAS) and health assessment questionnaire disability index (HAQ-DI) score before and after 2 weeks of standardized GC treatment.

Results

GR number was positively correlated with improvement in DAS. IL-2-EC₅₀ and GILZ-EC₅₀ values both had weak near-significant correlations with clinical improvement in DAS in intramuscularly treated patients only. HAQ responders had lower GILZ-EC₅₀ values and higher GR number and K_D.

Conclusions

Baseline cellular in vitro glucocorticoid sensitivity is modestly associated with in vivo improvement in DAS and HAQ-DI score after GC bridging therapy in RA. Further studies are needed to evaluate whether in vitro GC sensitivity may support the development of tailor-made GC therapy in RA.