Characteristics of transposable element exonization within human and mouse

Insertion of transposed elements within mammalian genes is thought to be an important contributor to mammalian evolution and speciation. Insertion of transposed elements into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization. Elucidation of the evolutionary constraints that have shaped fixation of transposed elements within human and mouse protein coding genes and subsequent exonization is important for understanding of how the exonization process has affected transcriptome and proteome complexities. Here we show that exonization of transposed elements is biased towards the beginning of the coding sequence in both human and mouse genes. Analysis of single nucleotide polymorphisms (SNPs) revealed that exonization of transposed elements can be population-specific, implying that exonizations may enhance divergence and lead to speciation. SNP density analysis revealed differences between Alu and other transposed elements. Finally, we identified cases of primate-specific Alu elements that depend on RNA editing for their exonization. These results shed light on TE fixation and the exonization process within human and mouse genes.Comment: 11 pages, 4 figure

Disparities and risks of sexually transmissible infections among men who have sex with men in China: a meta-analysis and data synthesis.

BACKGROUND: Sexually transmitted infections (STIs), including Hepatitis B and C virus, are emerging public health risks in China, especially among men who have sex with men (MSM). This study aims to assess the magnitude and risks of STIs among Chinese MSM. METHODS: Chinese and English peer-reviewed articles were searched in five electronic databases from January 2000 to February 2013. Pooled prevalence estimates for each STI infection were calculated using meta-analysis. Infection risks of STIs in MSM, HIV-positive MSM and male sex workers (MSW) were obtained. This review followed the PRISMA guidelines and was registered in PROSPERO. RESULTS: Eighty-eight articles (11 in English and 77 in Chinese) investigating 35,203 MSM in 28 provinces were included in this review. The prevalence levels of STIs among MSM were 6.3% (95% CI: 3.5-11.0%) for chlamydia, 1.5% (0.7-2.9%) for genital wart, 1.9% (1.3-2.7%) for gonorrhoea, 8.9% (7.8-10.2%) for hepatitis B (HBV), 1.2% (1.0-1.6%) for hepatitis C (HCV), 66.3% (57.4-74.1%) for human papillomavirus (HPV), 10.6% (6.2-17.6%) for herpes simplex virus (HSV-2) and 4.3% (3.2-5.8%) for Ureaplasma urealyticum. HIV-positive MSM have consistently higher odds of all these infections than the broader MSM population. As a subgroup of MSM, MSW were 2.5 (1.4-4.7), 5.7 (2.7-12.3), and 2.2 (1.4-3.7) times more likely to be infected with chlamydia, gonorrhoea and HCV than the broader MSM population, respectively. CONCLUSION: Prevalence levels of STIs among MSW were significantly higher than the broader MSM population. Co-infection of HIV and STIs were prevalent among Chinese MSM. Integration of HIV and STIs healthcare and surveillance systems is essential in providing effective HIV/STIs preventive measures and treatments. TRIAL REGISTRATION: PROSPERO NO: CRD42013003721

In vitro suppression of the MMP-3 gene in normal and cytokine-treated human chondrosarcoma using small interfering RNA

<p>Abstract</p> <p>Background</p> <p>Matrix metalloproteinase (MMPs) synthesized and secreted from connective tissue cells have been thought to participate in degradation of the extracellular matrix. Increased MMPs activities that degrade proteoglycans have been measured in osteoarthritis cartilage. This study aims to suppress the expression of the <it>MMP-3 </it>gene in <it>in vitro </it>human chondrosarcoma using siRNA.</p> <p>Methods</p> <p>Cells were categorized into four groups: control (G.1); transfection solution treated (G.2); negative control siRNA treated (G.3); and <it>MMP-3 </it>siRNA treated (G.4). All four groups were further subdivided into two groups - treated and non-treated with IL-1β- following culture for 48 and 72 h. We observed the effects of gene suppression according to cell morphology, glycosaminoglycan (GAG) and hyaluronan (HA) production, and gene expression by using real-time polymerase chain reaction (PCR).</p> <p>Results</p> <p>In IL-1β treated cells the apoptosis rate in G.4 was found to be lower than in all other groups, while viability and mitotic rate were higher than in all other groups (<it>p </it>< 0.05). The production of GAG and HA in G.4 was significantly higher than the control group (<it>p </it>< 0.05). <it>MMP-3 </it>gene expression was downregulated significantly (<it>p </it>< 0.05).</p> <p>Conclusion</p> <p><it>MMP-3 </it>specific siRNA can inhibit the expression of <it>MMP-3 </it>in chondrosarcoma. This suggests that <it>MMP-3 </it>siRNA has the potential to be a useful preventive and therapeutic agent for osteoarthritis.</p

Childhood trauma fatality and resource allocation in injury control programs in a developing country

BACKGROUND: Only a few studies have addressed the trimodal distribution of childhood trauma fatalities in lesser developed countries. We conducted this study to evaluate pre-hospital, Emergency Department (ED) and in-hospital distribution of childhood injury-related death for each mechanism of injury in Tehran, Iran. This information will be used for the efficient allocation of the limited injury control resources in the city. METHODS: We used Tehran's Legal Medicine Organization (LMO) database. This is the largest and the most complete database that receives information about trauma fatalities from more than 100 small and large hospitals in Tehran. We reviewed all the medical records and legal documents of the deceased registered in LMO from September 1999 to September 2000. Demographic and injury related characteristics of the children 15 years old or younger were extracted from the records. RESULTS: Ten percent of the 4,233 trauma deaths registered in LMO occurred among children 15 years old or younger. Motor vehicle crashes (MVCs) (50%), burns (18%), falls (6%) and poisonings (6%) were the most common mechanisms of unintentional fatal injuries. Prehospital, emergency department and hospital deaths comprised 42%, 20% and 37% of the trauma fatalities, respectively. While, more than 80% of fatal injuries due to poisoning and drowning occurred in prehospital setting, 92% of burn-related fatalities happened after hospital admission. CONCLUSION: Injury prevention is the single most important solution for controlling trauma fatalities due to poisoning and drowning. Improvements in the quality of care in hospitals and intensive care units might substantially alleviate the magnitude of the problem due to burns. Improvements in prehospital and ED care might significantly decrease MVC and falls-related fatalities

Observation of Rydberg blockade between two atoms

We demonstrate experimentally that a single Rb atom excited to the $79d_{5/2}$ level blocks the subsequent excitation of a second atom located more than $10 \mu\rm m$ away. The observed probability of double excitation of $\sim 30$ is consistent with a theoretical model based on calculations of the long range dipole-dipole interaction between atoms.Comment: 4 figure

Development of outcome measures for autoimmune dermatoses

Validated outcome measures are essential in monitoring disease severity. Specifically in dermatology, which relies heavily on the clinical evaluation of the patient and not on laboratory values and radiographic tests, outcome measures help standardize patient care. Validated cutaneous scoring systems, much like standardized laboratory values, facilitate disease management and follow therapeutic response. Several cutaneous autoimmune dermatoses, specifically cutaneous lupus erythematosus (CLE), dermatomyositis (DM), and pemphigus vulgaris (PV), lack such outcome measures. As a result, evaluation of disease severity and patients’ response to therapy over time is less reliable. Ultimately, patient care is compromised. These diseases, which are often chronic and relapsing and remitting, are also often refractory to treatment. Without outcome measures, new therapies cannot be systematically assessed in these diseases. Clinical trials that are completed without standardized outcome measures produce less reliable results. Therefore, the development of validated outcome measures in these autoimmune dermatoses is critical. However, the process of developing these tools is as important, if not more so, than their availability. This review examines the steps that should be considered when developing outcome measures, while further examining their importance in clinical practice and trials. Finally, this review more closely looks at CLE, DM, and PV and addresses the recent and ongoing progress that has been made in the development of their outcome measures

Knocking out pain in livestock: Can technology succeed where morality has stalled?

Though the vegetarian movement sparked by Peter Singer’s book Animal Liberation has achieved some success, there is more animal suffering caused today due to factory farming than there was when the book was originally written. In this paper, I argue that there may be a technological solution to the problem of animal suffering in intensive factory farming operations. In particular, I suggest that recent research indicates that we may be very close to, if not already at, the point where we can genetically engineer factory-farmed livestock with a reduced or completely eliminated capacity to suffer. In as much as animal suffering is the principal concern that motivates the animal welfare movement, this development should be of central interest to its adherents. Moreover, I will argue that all people concerned with animal welfare should agree that we ought to replace the animals currently used in factory farming with animals whose ability to suffer is diminished if we are able to do so. </p

The synthetic antimicrobial peptide 19-2.5 attenuates septic cardiomyopathy and prevents down-regulation of SERCA2 in polymicrobial sepsis

LM has received grants by the Faculty of Medicine at the RWTH Aachen University (START 15/14 and START 46/16) and the Deutsche Forschungsgemeinschaft (DFG, MA 7082/1–1). This work was supported by the Immunohistochemistry and Confocal Microscopy Unit, a core facility of the Interdisciplinary Centre for Clinical Research (IZKF) Aachen, within the Faculty of Medicine at the RWTH Aachen University and the RWTH centralized Biomaterial Database (RWTH cBMB) of the University Hospital RWTH Aachen. We are very grateful to Antons Martincuks M.Sc. and Professor Gerhard Müller-Newen for live-cell imaging. This work was supported, in part, by the University of Turin (ex-60% 2015A and B) and by the William Harvey Research Foundation and forms part of the research themes contributing to the translational research portfolio of Barts and the London Cardiovascular Biomedical Research Unit that is supported and funded by the National Institute for Health Research. This work also contributes to the Organ Protection research theme of the Barts Centre for Trauma Sciences supported by the Barts and The London Charity (Award 753/1722)

Correlated Mutations: A Hallmark of Phenotypic Amino Acid Substitutions

Point mutations resulting in the substitution of a single amino acid can cause severe functional consequences, but can also be completely harmless. Understanding what determines the phenotypical impact is important both for planning targeted mutation experiments in the laboratory and for analyzing naturally occurring mutations found in patients. Common wisdom suggests using the extent of evolutionary conservation of a residue or a sequence motif as an indicator of its functional importance and thus vulnerability in case of mutation. In this work, we put forward the hypothesis that in addition to conservation, co-evolution of residues in a protein influences the likelihood of a residue to be functionally important and thus associated with disease. While the basic idea of a relation between co-evolution and functional sites has been explored before, we have conducted the first systematic and comprehensive analysis of point mutations causing disease in humans with respect to correlated mutations. We included 14,211 distinct positions with known disease-causing point mutations in 1,153 human proteins in our analysis. Our data show that (1) correlated positions are significantly more likely to be disease-associated than expected by chance, and that (2) this signal cannot be explained by conservation patterns of individual sequence positions. Although correlated residues have primarily been used to predict contact sites, our data are in agreement with previous observations that (3) many such correlations do not relate to physical contacts between amino acid residues. Access to our analysis results are provided at http://webclu.bio.wzw.tum.de/~pagel/supplements/correlated-positions/