Transcriptomic profiling reveals p53 as a key regulator of doxorubicin-induced cardiotoxicity.

Doxorubicin is an important anticancer drug in the clinic. Unfortunately, it causes cumulative and dose-dependent cardiotoxic side effects. As the population of cancer survivors who have been exposed to treatment continues to grow, there is increased interest in assessing the long-term cardiac effects of doxorubicin and understanding the underlying mechanisms at play. In this study, we investigated doxorubicin-induced transcriptomic changes using RNA-sequencing (RNAseq) and a cellular model comprised of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). Analyses of predicted upstream regulators identified the p53 protein as a key regulator of transcriptomic changes induced by doxorubicin. Clustering and pathway analyses showed that increased death receptor (DR) expression and enrichment of the extrinsic apoptotic pathway are significantly associated with doxorubicin-induced cardiotoxicity. Increased expression of p53 and DRs were confirmed via immunoblotting. Our data pinpoints increased DR expression as an early transcriptomic indicator of cardiotoxicity, suggesting that DR expression might function as a predictive biomarker for cardiac damage.

Fugitives on the run: circulating tumor cells (CTCs) in metastatic diseases.

The presence of circulating tumor cells (CTCs) in the bloodstream signals the existence of a tumor and denotes risk of metastatic spread. CTCs can be isolated and analyzed to monitor cancer progression and therapeutic response. However, CTC isolation devices have shown considerable variation in detection rates, limiting their use as a routine diagnostic and monitoring tool. In this review, we discuss recent advances in CTC detection methodologies and associated clinical studies. We provide perspective on the future direction of CTC isolation and molecular characterization towards developing reliable biomarkers that monitor disease progression or therapeutic response.

meaRtools: An R package for the analysis of neuronal networks recorded on microelectrode arrays.

Here we present an open-source R package 'meaRtools' that provides a platform for analyzing neuronal networks recorded on Microelectrode Arrays (MEAs). Cultured neuronal networks monitored with MEAs are now being widely used to characterize in vitro models of neurological disorders and to evaluate pharmaceutical compounds. meaRtools provides core algorithms for MEA spike train analysis, feature extraction, statistical analysis and plotting of multiple MEA recordings with multiple genotypes and treatments. meaRtools functionality covers novel solutions for spike train analysis, including algorithms to assess electrode cross-correlation using the spike train tiling coefficient (STTC), mutual information, synchronized bursts and entropy within cultured wells. Also integrated is a solution to account for bursts variability originating from mixed-cell neuronal cultures. The package provides a statistical platform built specifically for MEA data that can combine multiple MEA recordings and compare extracted features between different genetic models or treatments. We demonstrate the utilization of meaRtools to successfully identify epilepsy-like phenotypes in neuronal networks from Celf4 knockout mice. The package is freely available under the GPL license (GPL> = 3) and is updated frequently on the CRAN web-server repository. The package, along with full documentation can be downloaded from: https://cran.r-project.org/web/packages/meaRtools/.

Annotating pathogenic non-coding variants in genic regions.

Identifying the underlying causes of disease requires accurate interpretation of genetic variants. Current methods ineffectively capture pathogenic non-coding variants in genic regions, resulting in overlooking synonymous and intronic variants when searching for disease risk. Here we present the Transcript-inferred Pathogenicity (TraP) score, which uses sequence context alterations to reliably identify non-coding variation that causes disease. High TraP scores single out extremely rare variants with lower minor allele frequencies than missense variants. TraP accurately distinguishes known pathogenic and benign variants in synonymous (AUC = 0.88) and intronic (AUC = 0.83) public datasets, dismissing benign variants with exceptionally high specificity. TraP analysis of 843 exomes from epilepsy family trios identifies synonymous variants in known epilepsy genes, thus pinpointing risk factors of disease from non-coding sequence data. TraP outperforms leading methods in identifying non-coding variants that are pathogenic and is therefore a valuable tool for use in gene discovery and the interpretation of personal genomes.While non-coding synonymous and intronic variants are often not under strong selective constraint, they can be pathogenic through affecting splicing or transcription. Here, the authors develop a score that uses sequence context alterations to predict pathogenicity of synonymous and non-coding genetic variants, and provide a web server of pre-computed scores.

Inhibition of microRNA 128 promotes excitability of cultured cortical neuronal networks.

Cultured neuronal networks monitored with microelectrode arrays (MEAs) have been used widely to evaluate pharmaceutical compounds for potential neurotoxic effects. A newer application of MEAs has been in the development of in vitro models of neurological disease. Here, we directly evaluated the utility of MEAs to recapitulate in vivo phenotypes of mature microRNA-128 (miR-128) deficiency, which causes fatal seizures in mice. We show that inhibition of miR-128 results in significantly increased neuronal activity in cultured neuronal networks derived from primary mouse cortical neurons. These results support the utility of MEAs in developing in vitro models of neuroexcitability disorders, such as epilepsy, and further suggest that MEAs provide an effective tool for the rapid identification of microRNAs that promote seizures when dysregulated.

A functional correlate of severity in alternating hemiplegia of childhood.

OBJECTIVE: Mutations in ATP1A3, the gene that encodes the α3 subunit of the Na(+)/K(+) ATPase, are the primary cause of alternating hemiplegia of childhood (AHC). Correlations between different mutations and AHC severity were recently reported, with E815K identified in severe and D801N and G947R in milder cases. This study aims to explore the molecular pathological mechanisms in AHC and to identify functional correlates for mutations associated with different levels of disease severity. METHODS: Human wild type ATP1A3, and E815K, D801N and G947R mutants were expressed in Xenopus laevis oocytes and Na(+)/K(+) ATPase function measured. Structural homology models of the human α3 subunit containing AHC mutations were created. RESULTS: The AHC mutations examined all showed similar levels of reduction in forward cycling. Wild type forward cycling was reduced by coexpression with any mutant, indicating dominant negative interactions. Proton transport was measured and found to be selectively impaired only in E815K. Homology modeling showed that D801 and G947 lie within or near known cation binding sites while E815 is more distal. Despite its effect on proton transport, E815K was also distant from the proposed proton transport route. INTERPRETATION: Loss of forward cycling and dominant negativity are common and likely necessary pathomechanisms for AHC. In addition, loss of proton transport correlated with severity of AHC. D801N and G947R are likely to directly disrupt normal Na(+)/K(+) binding while E815K may disrupt forward cycling and proton transport via allosteric mechanisms yet to be elucidated.

Whole-exome sequencing in undiagnosed genetic diseases: interpreting 119 trios.

PURPOSE: Despite the recognized clinical value of exome-based diagnostics, methods for comprehensive genomic interpretation remain immature. Diagnoses are based on known or presumed pathogenic variants in genes already associated with a similar phenotype. Here, we extend this paradigm by evaluating novel bioinformatics approaches to aid identification of new gene-disease associations. METHODS: We analyzed 119 trios to identify both diagnostic genotypes in known genes and candidate genotypes in novel genes. We considered qualifying genotypes based on their population frequency and in silico predicted effects we also characterized the patterns of genotypes enriched among this collection of patients. RESULTS: We obtained a genetic diagnosis for 29 (24%) of our patients. We showed that patients carried an excess of damaging de novo mutations in intolerant genes, particularly those shown to be essential in mice (P = 3.4 × 10(-8)). This enrichment is only partially explained by mutations found in known disease-causing genes. CONCLUSION: This work indicates that the application of appropriate bioinformatics analyses to clinical sequence data can also help implicate novel disease genes and suggest expanded phenotypes for known disease genes. These analyses further suggest that some cases resolved by whole-exome sequencing will have direct therapeutic implications.

Pregnancy rates of lactating cows after transfer of in vitro produced embryos using X-sorted sperm.

The main objective was to determine the efficacy of using X-sorted sperm to produce embryos in vitro for transfer into lactating dairy cows. Cows were bred by timed artificial insemination (TAI) using nonsorted semen or X-sorted sperm, or they received a fresh embryo produced in vitro by fertilization with X-sorted or nonsorted sperm using timed embryo transfer (TET). Pregnancy rates at approximately Day 32 averaged over all dairies were 39.3 ± 3.2% (least-squares mean ± SEM) for TAI nonsorted, 27.3 ± 3.4% for TET nonsorted fresh embryos, and 30.2 ± 3.3% for TET X-sorted fresh embryos (TAI vs. both TET groups, P < 0.05; 206 to 233 cows per group). Pregnancy losses between approximately Day 32 and term ranged from 16% to 37%, the latter from TET with X-sorted sperm. Pregnancy losses to term were higher for cows receiving embryos produced in vitro than for cows bred by TAI. Calves produced via TET were not substantively different from AI controls in physical measurements or standard blood chemistry profiles.

Depression among newly admitted Australian nursing home residents.

BACKGROUND: This research concerns the prevalence and course of depression in newly admitted nursing home residents. We attempted to recruit consecutive admissions into the study, irrespective of cognitive status, enabling a comparison of the prevalence and course of depression experienced by cognitively intact residents and those exhibiting all levels of cognitive impairment. METHOD: Depression was assessed at one month, three months and six months post-admission. The assessment of mood in this study entailed the conduct of a semi-structured clinical interview, which encompassed DSM-IV criteria and Cornell Scale for Depression in Dementia (CSDD) items. RESULTS: Recruitment difficulties resulted in a sample of 51 newly admitted residents, drawn from six nursing homes located in Victoria, Australia. Of particular interest, throughout the duration of the study, only the cognitively impaired were diagnosed with major depression (MD). One month post-admission, 24% of the sample were diagnosed with MD, and a further 20% evidenced a non-major depressive disorder. At the second and third assessments, MD was observed in 14% and 15% of residents, respectively. For residents who completed all three assessments, there was no appreciable change in the proportion diagnosed with a depressive disorder, nor was there a change in the levels of depressive symptomatology. CONCLUSION: Although subject to limitations, the current study indicated that clinical depression in nursing home facilities most often occurs in residents who also exhibit pronounced cognitive impairment. These depressions are unlikely to remit spontaneously. Accordingly, care staff and general practitioners must be trained in the identification of depression in dementia, and any interventions implemented in these facilities should be tailored to meet the unique needs of this group.

Bacteremia associated with naturally occuring acute coliform mastitis in dairy cows.

OBJECTIVE: To determine the incidence of bacteremia in dairy cows with naturally occurring acute coliform mastitis (ACM) with a wide range of disease severity. DESIGN: Cohort study. ANIMALS: 144 dairy cows with ACM from 6 herds. PROCEDURE: Cows were examined at time of identification of ACM (time 0) and classified as having mild, moderate, or severe mastitis on the basis of rectal temperature, hydration status, rumen contraction rate, and attitude. Cows were reexamined at 24 or 48 hours. Bacteriologic culturing of milk and blood (30 ml), CBC, and serum biochemical analysis were performed at each time point. Appropriate samples were obtained at a single point from herdmates without mastitis (controls) that were closely matched for lactation number and days since parturition. Blood culture results were compared among severity groups and controls by use of chi2 tests, as was outcome of an ACM episode for cows grouped by blood bacterial isolates. RESULTS: Bacteria were isolated from 52 blood samples from 46 of 144 (32%) cows with ACM, which was significantly more than control cows (11/156; 7.1%). Group-1 isolates (Escherichia coli, Pasteurella multocida, Mannheimia haemolytica, Klebsiella pneumoniae, Enterobacter agglomerans, and Salmonella enterica serotype Typhimurium) were identified in 20 of 144 (14%) cows with ACM and 0 of 156 control cows. Group-1 isolates were identified in 4.3, 9.1, and 42% of cows classified as having mild, moderate, and severe ACM, respectively. Escherichia coli and K pneumoniae milk and blood isolates obtained from the same cow were of the same genotype. Bacillus spp were identified in 21 of 144 (15%) cows with ACM, which was significantly more than control cows (3/156; 1.9%). Thirty-five percent of cows with a group-1 isolate died during the mastitis episode. CONCLUSIONS AND CLINICAL RELEVANCE: Results suggest that bacteremia develops in a substantial proportion of cows with ACM. Classification of severity of disease is important for establishment of effective treatment protocols; parenteral antimicrobial treatment may be indicated in cows with ACM.

Valuation of consumption and sale of forest goods from a Central American rain forest

Researchers recognize that society needs accurate and comprehensive estimates of the economic value of rain forests to assess conservation and management options. Valuation of forests can help us to decide whether to implement policies that reconcile the value different groups attach to forests. Here we have measured the value of the rain forest to local populations by monitoring the foods, construction and craft materials, and medicines consumed or sold from the forest by 32 Indian households in two villages in Honduras over 2.5 years. We have directly measured the detailed, comprehensive consumption patterns of rain forest products by an indigenous population and the value of that consumption in local markets. The combined value of consumption and sale of forest goods ranged from US$17.79 to US$23.72 per hectare per year, at the lower end of previous estimates (between US$49 and US$1,089 (mean US$347) per hectare per year). Although outsiders value the rain forest for its high-use and non-use values, local people receive a small share of the total value. Unless rural people are paid for the non-local values of rain forests, they may be easily persuaded to deforest.

Correlation of injury occurrence data with estimated maximal aerobic capacity and body composition in a high-frequency manual materials handling task.

This article evaluates the correlation between injury occurrence, step test estimated maximal aerobic capacity (VO2max), and body composition in a high-frequency manual materials handling task. The study used 212 highly trained male manual material handlers working for a major materials handling company. Three locations across the United States (western, midwestern, and southeastern) were chosen based on similarity of size and function. An estimated maximal aerobic capacity was obtained for each participant using a submaximal bench step protocol. Also, a percentage body fat estimation was randomly obtained for approximately 25% of the participants. The correlation between injury occurrences, absolute VO2max, relative VO2max, and percentage body fat were analyzed. Also, the relationship between both VO2max estimations and percentage body fat was analyzed. Finally, the correlation between location VO2max and percentage body fat was studied. Results indicated no significant difference between absolute VO2max, injury, or percentage body fat. Relative VO2max suggested a significant relationship with injury occurrences and body composition. Body composition also indicated a significant correlation with injury occurrences. Finally, location played a significant factor in injury occurrence, step test estimated VO2max, and estimated body composition. This investigation demonstrates significant evidence of the predictability of employee injury occurrence and the fitness estimation methods used. In a high-frequency manual materials handling task, high occurrences of injury were significantly correlated with low estimated relative maximal aerobic capacity and high estimated percentage body fat.

The effect of fit and parameter changes on soft lens rotation.

An evaluation of the effect of changing the base curve, overall diameter and amount of prism incorporated in the lens, on the extent of blink-initiated rotation of prism-ballasted and truncated soft contact lenses was undertaken. Increasing the prism power and the base curve (while increasing lens diameter to maintain a constant fitting relationship to the cornea) are both ineffective in changing the amount of rotation. Only steepening the base curve reduces rotation, and this change should be made cautiously because steep lenses tend to rotate to off-axis positions.