Deletion of a conserved, central ribosomal intersubunit RNA bridge

Elucidation of the structure of the ribosome has stimulated numerous proposals for the roles of specific rRNA elements, including the universally conserved helix 69 (H69) of 23S rRNA, which forms intersubunit bridge B2a and contacts the D stems of A- and P-site tRNAs. H69 has been proposed to be involved not only in subunit association and tRNA binding but also in initiation, translocation, translational accuracy, the peptidyl transferase reaction, and ribosome recycling. Consistent with such proposals, deletion of H69 confers a dominant lethal phenotype. Remarkably, in vitro assays show that affinity-purified Deltah69 ribosomes have normal translational accuracy, synthesize a full-length protein from a natural mRNA template, and support EF-G-dependent translocation at wild-type rates. However, Deltah69 50S subunits are unable to associate with 30S subunits in the absence of tRNA, are defective in RF1-catalyzed peptide release, and can be recycled in the absence of RRF.     

Mitochondrial DNA signals of late glacial recolonization of Europe from near eastern refugia

Human populations, along with those of many other species, are thought to have contracted into a number of refuge areas at the height of the last Ice Age. European populations are believed to be, to a large extent, the descendants of the inhabitants of these refugia, and some extant mtDNA lineages can be traced to refugia in Franco-Cantabria (haplogroups H1, H3, V, and U5b1), the Italian Peninsula (U5b3), and the East European Plain (U4 and U5a). Parts of the Near East, such as the Levant, were also continuously inhabited throughout the Last Glacial Maximum, but unlike western and eastern Europe, no archaeological or genetic evidence for Late Glacial expansions into Europe from the Near East has hitherto been discovered. Here we report, on the basis of an enlarged whole-genome mitochondrial database, that a substantial, perhaps predominant, signal from mitochondrial haplogroups J and T, previously thought to have spread primarily from the Near East into Europe with the Neolithic population, may in fact reflect dispersals during the Late Glacial period, ～19-12 thousand years (ka) ago.     

Mitochondrial haplogroup C4c: A rare lineage entering America through the ice‐free corridor?

Recent analyses of mitochondrial genomes from Native Americans have brought the overall number of recognized maternal founding lineages from just four to a current count of 15. However, because of their relative low frequency, almost nothing is known for some of these lineages. This leaves a considerable void in understanding the events that led to the colonization of the Americas following the Last Glacial Maximum (LGM). In this study, we identified and completely sequenced 14 mitochondrial DNAs belonging to one extremely rare Native American lineage known as haplogroup C4c. Its age and geographical distribution raise the possibility that C4c marked the Paleo-Indian group(s) that entered North America from Beringia through the ice-free corridor between the Laurentide and Cordilleran ice sheets. The similarities in ages andgeographical distributions for C4c and the previously analyzed X2a lineage provide support to the scenario of a dual origin for Paleo-Indians. Taking into account that C4c is deeply rooted in the Asian portion of the mtDNA phylogeny and is indubitably of Asian origin, the finding that C4c and X2a are characterized by parallel genetic histories definitively dismisses the controversial hypothesis of an Atlantic glacial entry route into North America.     

High resolution melting analysis for detection of variable number of tandem repeats polymorphism of XRCC5

Several polymorphisms in the XRCC5 (X-ray repair cross-complementing 5; OMIM: 194364) were reported. Polymorphism of variable number of tandem repeats (VNTR) in the promoter region of XRCC5 (rs6147172) was reported. The main aim of the present study is to introduce the high resolution melting analysis (HRMA) method for genotyping of the polymorphism of XRCC5 VNTR. Genotypes of XRCC5 VNTR were determined by HRMA and conventional PCR method, and confirmed by DNA sequencing. The results for genotyping using HRMA and conventional PCR showed 100% concordance. All genotypes of the XRCC5 VNTR polymorphism could be accurately detected by HRMA.     

Imbalance in thioredoxin system activates NLRP3 inflammasome pathway in epicardial adipose tissue of patients with coronary artery disease

Molecular Biology Reports - Atherosclerosis is the leading cause of death worldwide and has in part an inflammatory basis. Since epicardial adipose tissue (EAT) is in close contact with coronary...     

Genetic structure of Alhagi (Hedysareae,Fabaceae) populations using ISSR data in Iran

Molecular Biology Reports - Alhagi Gagnebin (Fabaceae: Hedysareae) is a small genus of shrubs or subshrubs distributed in temperate and tropical regions of Asia, Europe, and Africa. The exact...     

Mitogenomes from Two Uncommon Haplogroups Mark Late Glacial/Postglacial Expansions from the Near East and Neolithic Dispersals within Europe

The current human mitochondrial (mtDNA) phylogeny does not equally represent all human populations but is biased in favour of representatives originally from north and central Europe. This especially affects the phylogeny of some uncommon West Eurasian haplogroups, including I and W, whose southern European and Near Eastern components are very poorly represented, suggesting that extensive hidden phylogenetic substructure remains to be uncovered. This study expanded and re-analysed the available datasets of I and W complete mtDNA genomes, reaching a comprehensive 419 mitogenomes, and searched for precise correlations between the ages and geographical distributions of their numerous newly identified subclades with events of human dispersal which contributed to the genetic formation of modern Europeans. Our results showed that haplogroups I (within N1a1b) and W originated in the Near East during the Last Glacial Maximum or pre-warming period (the period of gradual warming between the end of the LGM, ∼19 ky ago, and the beginning of the first main warming phase, ∼15 ky ago) and, like the much more common haplogroups J and T, may have been involved in Late Glacial expansions starting from the Near East. Thus our data contribute to a better definition of the Late and postglacial re-peopling of Europe, providing further evidence for the scenario that major population expansions started after the Last Glacial Maximum but before Neolithic times, but also evidencing traces of diffusion events in several I and W subclades dating to the European Neolithic and restricted to Europe.     

Serum testosterone in females exposed to natural sour gas with respect to polymorphisms of <Emphasis Type="Italic">XRCC1</Emphasis>, <Emphasis Type="Italic">GSTM1</Emphasis>, and <Emphasis Type="Italic">GSTT1</Emphasis>

The present study was done to determine the modulation effect(s) of polymorphisms of XRCC1, GSTM1, and GSTT1 on concentration of serum testosterone in females exposed to natural sour gas. Also we examine whether chronic exposure to natural gas containing sulfur compounds act as natural selection force on XRCC1 polymorphisms. The present study was performed on 68 healthy unrelated female students living in polluted areas of MIS. Also for investigating the effect of natural selection on XRCC1 polymorphism, a study was performed on two groups of healthy individuals of MIS citizens. The first and second groups including 94 (age range 30–85 years) and 187 individuals (age range 5–20 years), respectively. First and second groups were born and were not born in contaminated areas of the MIS, respectively. There was no significant difference between genotypes of XRCC1 for concentration of serum testosterone. Although GSTT1-null genotype had higher level of serum testosterone in comparison with the present genotype (t = 2.392, df = 66, P = 0.023), a borderline difference between genotypes of GSTM1 for serum testosterone was observed (t = 1.928, df = 66, P = 0.058). Analysis of variance revealed significant difference between combination genotypes of GSTM1 and GSTT1 for serum testosterone (F = 4.167; df = 3, 64; P = 0.009). The Duncan post hoc test indicated that the combination genotype of “present GSTM1/null GSTT1” had significant higher level of testosterone. There is no evidence that XRCC1 polymorphisms have advantage/disadvantage when population exposed to natural sour gas. The polymorphisms of GSTM1 and GSTT1 modulate serum testosterone concentration in young females exposed to natural sour gas.     

Customized Reference Ranges for Laboratory Values Decrease False Positive Alerts in Intensive Care Unit Patients

Background

Traditional electronic medical record (EMR) interfaces mark laboratory tests as abnormal based on standard reference ranges derived from healthy, middle-aged adults. This yields many false positive alerts with subsequent alert-fatigue when applied to complex populations like hospitalized, critically ill patients. Novel EMR interfaces using adjusted reference ranges customized for specific patient populations may ameliorate this problem.

Objective

To compare accuracy of abnormal laboratory value indicators in a novel vs traditional EMR interface.

Methods

Laboratory data from intensive care unit (ICU) patients consecutively admitted during a two-day period were recorded. For each patient, available laboratory results and the problem list were sent to two mutually blinded critical care experts, who marked the values about which they would like to be alerted. All disagreements were resolved by an independent super-reviewer. Based on this gold standard, we calculated and compared the sensitivity, specificity, positive and negative predictive values (PPV, NPV) of customized vs traditional abnormal value indicators.

Results

Thirty seven patients with a total of 1341 laboratory results were included. Experts’ agreement was fair (kappa = 0.39). Compared to the traditional EMR, custom abnormal laboratory value indicators had similar sensitivity (77% vs 85%, P = 0.22) and NPV (97.1% vs 98.6%, P = 0.06) but higher specificity (79% vs 61%, P<0.001) and PPV (28% vs 11%, P<0.001).

Conclusions

Reference ranges for laboratory values customized for an ICU population decrease false positive alerts. Disagreement among clinicians about which laboratory values should be indicated as abnormal limits the development of customized reference ranges.     

Detection of Echinococcus multilocularis in carnivores in Razavi Khorasan province, Iran using mitochondrial DNA

Background

Echinococcus multilocularis is the source of alveolar echinococcosis, a potentially fatal zoonotic disease. This investigation assessed the presence of E. multilocularis infection in definitive hosts in the Chenaran region of Razavi Khorasan Province, northeastern Iran.

Methodology/Principal Findings

Fecal samples from 77 domestic and stray dogs and 14 wild carnivores were examined using the flotation/sieving method followed by multiplex PCR of mitochondrial genes. The intestinal scraping technique (IST) and the sedimentation and counting technique (SCT) revealed adult Echinococcus in the intestines of five of 10 jackals and of the single wolf examined. Three jackals were infected only with E. multilocularis but two, and the wolf, were infected with both E. multilocularis and E. granulosus. Multiplex PCR revealed E. multilocularis, E. granulosus, and Taenia spp. in 19, 24, and 28 fecal samples, respectively. Echinococcus multilocularis infection was detected in the feces of all wild carnivores sampled including nine jackals, three foxes, one wolf, one hyena, and five dogs (6.5%). Echinococcus granulosus was found in the fecal samples of 16.9% of dogs, 66.7% of jackals, and all of the foxes, the wolf, and the hyena. The feces of 16 (21.8%) dogs, 7 of 9 (77.8%) jackals, and all three foxes, one wolf and one hyena were infected with Taenia spp.

Conclusions/Significance

The prevalence of E. multilocularis in wild carnivores of rural areas of the Chenaran region is high, indicating that the life cycle is being maintained in northeastern Iran with the red fox, jackal, wolf, hyena, and dog as definitive hosts.