rs12416605:C>T in MIR938 associates with gastric cancer through affecting the regulation of the CXCL12 chemokine gene.

Background: MicroRNAs are small regulatory RNAs with important roles in carcinogenesis. Genetic variants in these regulatory molecules may contribute to disease. We aim to identify allelic variants in microRNAs as susceptibility factors to gastric cancer using association studies and functional approaches.

Effect of Collapsed Duplications on Diversity Estimates: What to Expect.

The study of segmental duplications (SDs) and copy-number variants (CNVs) is of great importance in the fields of genomics and evolution. However, SDs and CNVs are usually excluded from genome-wide scans for natural selection. Because of high identity between copies, SDs and CNVs that are not included in reference genomes are prone to be collapsed-that is, mistakenly aligned to the same region-when aligning sequence data from single individuals to the reference.

GSEA of mouse and human mitochondriomes reveals fatty acid oxidation in astrocytes.

The prevalent view in neuroenergetics is that glucose is the main brain fuel, with neurons being mostly oxidative and astrocytes glycolytic. Evidence supporting that astrocyte mitochondria are functional has been overlooked. Here we sought to determine what is unique about astrocyte mitochondria by performing unbiased statistical comparisons of the mitochondriome in astrocytes and neurons.

Functional Implications of Human-Specific Changes in Great Ape microRNAs.

microRNAs are crucial post-transcriptional regulators of gene expression involved in a wide range of biological processes. Although microRNAs are highly conserved among species, the functional implications of existing lineage-specific changes and their role in determining differences between humans and other great apes have not been specifically addressed. We analyzed the recent evolutionary history of 1,595 human microRNAs by looking at their intra- and inter-species variation in great apes using high-coverage sequenced genomes of 82 individuals including gorillas, orangutans, bonobos, chimpanzees and humans.

Assessment of Anti-Influenza Activity and Hemagglutination Inhibition of Plumbago indica and Allium sativum Extracts.

Background: Human influenza is a seasonal disease associated with significant morbidity and mortality. Anti-flu ayurvedic/herbal medicines have played a significant role in fighting the virus pandemic. Plumbagin and allicin are commonly used ingredients in many therapeutic remedies, either alone or in conjunction with other natural substances.

The complete mitochondrial genome of Lacerta bilineata and comparison with its closely related congener L. Viridis.

We sequenced the mitochondrial genome of the Western green lizard (Lacerta bilineata) using Illumina technology and additional Sanger sequencing. The assembled 17 086 bp mitogenome had a GC content of 40.32% and consisted of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region (CR), with a gene order identical to the chordate consensus.

SeDuS: segmental duplication simulator.

Summary: SeDuS is the first flexible and user-friendly forward-in-time simulator of patterns of molecular evolution within segmental duplications undergoing interlocus gene conversion and crossover. SeDuS introduces known features of interlocus gene conversion such as biased directionality and dependence on local sequence identity. Additionally, it includes aspects such as different selective pressures acting upon copy number and flexible crossover distributions.

Genetic and Clinical Factors Associated with Chronic Postsurgical Pain after Hernia Repair, Hysterectomy, and Thoracotomy: A Two-year Multicenter Cohort Study.

Background: Chronic postsurgical pain (CPSP) has been linked to many surgical settings. The authors aimed to analyze functional genetic polymorphisms and clinical factors that might identify CPSP risk after inguinal hernia repair, hysterectomy, and thoracotomy.

Methods: This prospective multicenter cohort study enrolled 2,929 patients scheduled for inguinal hernia repair, hysterectomy (vaginal or abdominal), or thoracotomy.

Evaluating intra- and inter-individual variation in the human placental transcriptome.

Background: Gene expression variation is a phenotypic trait of particular interest as it represents the initial link between genotype and other phenotypes. Analyzing how such variation apportions among and within groups allows for the evaluation of how genetic and environmental factors influence such traits. It also provides opportunities to identify genes and pathways that may have been influenced by non-neutral processes.

Interplay of interlocus gene conversion and crossover in segmental duplications under a neutral scenario.

Interlocus gene conversion is a major evolutionary force that drives the concerted evolution of duplicated genomic regions. Theoretical models successfully have addressed the effects of interlocus gene conversion and the importance of crossover in the evolutionary fate of gene families and duplications but have not considered complex recombination scenarios, such as the presence of hotspots. To study the interplay between interlocus gene conversion and crossover, we have developed a forward-time simulator that allows the exploration of a wide range of interlocus gene conversion rates under different crossover models.

Pool and conquer: new tricks for (c)old problems.

The early period of genetics is closely associated with the study of chromosomal inversions. For almost a century, evolutionary biologists found evidence for the role of inversions in central processes such as adaptation and speciation. In spite of huge efforts, many questions remain about the evolutionary forces underlying the distribution and dynamics of inversions in natural populations.

High trans-ethnic replicability of GWAS results implies common causal variants.

Genome-wide association studies (GWAS) have detected many disease associations. However, the reported variants tend to explain small fractions of risk, and there are doubts about issues such as the portability of findings over different ethnic groups or the relative roles of rare versus common variants in the genetic architecture of complex disease. Studying the degree of sharing of disease-associated variants across populations can help in solving these issues.