Directional genomic hybridization for chromosomal inversion discovery and detection

Chromosomal rearrangements are a source of structural variation within the genome that figure prominently in human disease, where the importance of translocations and deletions is well recognized. In principle, inversions—reversals in the orientation of DNA sequences within a chromosome—should have similar detrimental potential. However, the study of inversions has been hampered by traditional approaches used for their detection, which are not particularly robust. Even with significant advances in whole genome approaches, changes in the absolute orientation of DNA remain difficult to detect routinely. Consequently, our understanding of inversions is still surprisingly limited, as is our appreciation for their frequency and involvement in human disease. Here, we introduce the directional genomic hybridization methodology of chromatid painting—a whole new way of looking at structural features of the genome—that can be employed with high resolution on a cell-by-cell basis, and demonstrate its basic capabilities for genome-wide discovery and targeted detection of inversions. Bioinformatics enabled development of sequence- and strand-specific directional probe sets, which when coupled with single-stranded hybridization, greatly improved the resolution and ease of inversion detection. We highlight examples of the far-ranging applicability of this cytogenomics-based approach, which include confirmation of the alignment of the human genome database and evidence that individuals themselves share similar sequence directionality, as well as use in comparative and evolutionary studies for any species whose genome has been sequenced. In addition to applications related to basic mechanistic studies, the information obtainable with strand-specific hybridization strategies may ultimately enable novel gene discovery, thereby benefitting the diagnosis and treatment of a variety of human disease states and disorders including cancer, autism, and idiopathic infertility.     

Proton pump inhibitor use and risk for recurrent Clostridioides difficile infection: a systematic review and meta-analysis

ObjectivesProton pump inhibitor (PPI) therapy is a potentially modifiable risk factor for recurrent Clostridioides difficile infection (CDI). Citing an absence of clinical trials, many guidelines do not provide recommendations for addressing PPI management. Our aim was to perform an updated systematic review and meta-analysis evaluating the association between PPI use and recurrent CDI addressing prior methodological limitations.MethodsData sources were MEDLINE and EMBASE. Eligible studies were cohort and case–control studies; there were no restrictions on study setting or duration of follow-up. Participants were adults with prior CDI who did or did not receive PPI therapy and were assessed for recurrent CDI. Summary (unadjusted) odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using a random effects model. Prespecified subgroup analyses were performed to explore heterogeneity including study design, study quality, duration of follow-up, adjustment for confounders, and outcome definition.ResultsSixteen studies were included in the meta-analysis, comprising 57 477 patients with CDI, of whom 6870 (12%) received PPIs. The rate of recurrent CDI was 24% in patients treated with PPIs versus 18% in those who were not. A meta-analysis that pooled unadjusted odds ratios demonstrated higher odds of recurrent CDI in patients who received PPIs (OR 1.69, 95%CI 1.46–1.96) versus those who did not. There was moderate heterogeneity between studies (I² 56%); however, a sensitivity analysis restricted to studies with 56 days of follow-up substantially reduced the heterogeneity (OR 1.59, 95%CI 1.36–1.85; I² 12%). An analysis restricted to multivariate studies that combined adjusted ORs also demonstrated higher odds of recurrent CDI in patients who received PPIs (OR 1.49, 95%CI 1.12–2.00). No publication bias was identified.ConclusionsWe found significantly higher odds of recurrent CDI among users of PPIs that persisted across multiple sensitivity analyses. These results support stronger recommendations for PPI stewardship at CDI diagnosis.     

Exceptional record of mid-Pleistocene vertebrates helps differentiate climatic from anthropogenic ecosystem perturbations

Mid-Pleistocene vertebrates in North America are scarce but important for recognizing the ecological effects of climatic change in the absence of humans. We report on a uniquely rich mid-Pleistocene vertebrate sequence from Porcupine Cave, Colorado, which records at least 127 species and the earliest appearances of 30 mammals and birds. By analyzing >20,000 mammal fossils in relation to modern species and independent climatic proxies, we determined how mammal communities reacted to presumed glacial-interglacial transitions between 1,000,000 and 600,000 years ago. We conclude that climatic warming primarily affected mammals of lower trophic and size categories, in contrast to documented human impacts on higher trophic and size categories historically. Despite changes in species composition and minor changes in small-mammal species richness evident at times of climatic change, overall structural stability of mammal communities persisted >600,000 years before human impacts.     

Body mass index and change in blood pressure over a 7-year period in older Mexican Americans

Obesity and hypertension are major public health concerns in the US. We examined the relationship between body mass index (BMI) and blood pressure in older Mexican Americans using data from the Hispanic Established Population for the Epidemiological Study of the Elderly (EPESE), a longitudinal study of Mexican Americans aged 65 and over residing in the southwestern US. The study sample was 2404 older Mexican American adults with a mean age of 72.6 years of age at baseline (1993–4). Both systolic and diastolic blood pressures were higher in subjects with high BMI categories. The rate of change in systolic blood pressure and diastolic blood pressure were −0.11 mm Hg and −0.32 mm Hg per year over a 7-year period, respectively. The rate of decline in systolic and diastolic blood pressure over a 7-year period was greater in subjects with BMI categories of 25–<30 kg/m² and 30–<35 kg/m² as compared with those subjects with in the lowest and in the highest BMI categories. Hypertension is one of the most prevalent medical conditions affecting older adults. Understanding possible modifiable risk factors that may play a role in the management of hypertension will be beneficial.     

Asymmetric Cell–Matrix and Biomechanical Abnormalities in Elastin Insufficiency Induced Aortopathy

Aortopathy is characterized by vascular smooth muscle cell (VSMC) abnormalities and elastic fiber fragmentation. Elastin insufficient (Eln ^+/? ) mice demonstrate latent aortopathy similar to human disease. We hypothesized that aortopathy manifests primarily in the aorto-pulmonary septal (APS) side of the thoracic aorta due to asymmetric cardiac neural crest (CNC) distribution. Anatomic (aortic root vs. ascending aorta) and molecular (APS vs. non-APS) regions of proximal aorta tissue were examined in adult and aged wild type (WT) and mutant (Eln ^+/? ) mice. CNC, VSMCs, elastic fiber architecture, proteoglycan expression, morphometrics and biomechanical properties were examined using histology, 3D reconstruction, micropipette aspiration and in vivo magnetic resonance imaging (MRI). In the APS side of Eln ^+/? aorta, Sonic Hedgehog (SHH) is decreased while SM22 is increased. Elastic fiber architecture abnormalities are present in the Eln ^+/? aortic root and APS ascending aorta, and biglycan is increased in the aortic root while aggrecan is increased in the APS aorta. The Eln ^+/? ascending aorta is stiffer than the aortic root, the APS side is thicker and stiffer than the non-APS side, and significant differences in the individual aortic root sinuses are observed. Asymmetric structure–function abnormalities implicate regional CNC dysregulation in the development and progression of aortopathy.     

Investigation of phthalate release from tracheal tubes

Phthalates are chemicals used extensively in the manufacture of plastics for their desirable physical characteristics. In addition to enhancing the performance of plastics, phthalates have a number of undesirable effects, principally endocrine disruptor effects, that may have adverse effects on reproductive development and functioning. As a result, they have been banned from the manufacture of children's toys. Despite this, they continue to be used in the manufacture of medical devices, including anaesthetic equipment. This study aimed to assess phthalate release from five brands of tracheal tube. Using gas chromatography–mass spectrometry, we analysed phthalate concentrations from samples of ultra pure water in which tracheal tubes had been submerged. Phthalate concentration increased from 6.7 to 149 μg.l^?1 over a period of 4.8 days. Phthalate release from anaesthetic equipment has not previously been documented over short time periods and raises the possibility of iatrogenic endocrine disruption with routine anaesthesia.     

Metformin in cancer: translational challenges

The anti-diabetic drug metformin is rapidly emerging as a potential anti-cancer agent. Metformin, effective in treating type 2 diabetes and the insulin resistance syndromes, improves insulin resistance by reducing hepatic gluconeogenesis and by enhancing glucose uptake by skeletal muscle. Epidemiological studies have consistently associated metformin use with decreased cancer incidence and cancer-related mortality. Furthermore, numerous preclinical and clinical studies have demonstrated anti-cancer effects of metformin, leading to an explosion of interest in evaluating this agent in human cancer. The effects of metformin on circulating insulin levels indicate a potential efficacy towards cancers associated with hyperinsulinaemia; however, metformin may also directly inhibit tumour growth. In this review, we describe the mechanism of action of metformin and summarise the epidemiological, clinical and preclinical evidence supporting a role for metformin in the treatment of cancer. In addition, the challenges associated with translating preclinical results into therapeutic benefit in the clinical setting will be discussed.