RNA sequencing (RNA-seq) has become one of the most powerful tools to unravel the genomic basis of biological adaptation and diversity. Although challenging, RNA-seq is particularly promising for research on non-model, secretive species that cannot be observed in nature easily and therefore remain comparatively understudied. Among such animals, the caecilians (order Gymnophiona) likely constitute the least known group of vertebrates, despite being an old and remarkably distinct lineage of amphibians. Here, we characterize multi-tissue transcriptomes for five species of caecilians that represent a broad level of diversity across the order. We identified vertebrate homologous elements of caecilian functional genes of varying tissue specificity that reveal a great number of unclassified gene families, especially for the skin. We annotated several protein domains for those unknown candidate gene families to investigate their function. We also conducted supertree analyses of a phylogenomic dataset of 1,955 candidate orthologous genes among five caecilian species and other major lineages of vertebrates, with the inferred tree being in agreement with current views of vertebrate evolution and systematics. Our study provides insights into the evolution of vertebrate protein-coding genes, and a basis for future research on the molecular elements underlying the particular biology and adaptations of caecilian amphibians.

Structured illumination microscopy (SIM) is a family of methods in optical fluorescence microscopy that can achieve both optical sectioning and super-resolution effects. SIM is a valuable method for high-resolution imaging of fixed cells or tissues labeled with conventional fluorophores, as well as for imaging the dynamics of live cells expressing fluorescent protein constructs. In SIM, one acquires a set of images with shifting illumination patterns. This set of images is subsequently treated with image analysis algorithms to produce an image with reduced out-of-focus light (optical sectioning) and/or with improved resolution (super-resolution).

Regional heterogeneities in contraction contribute to heart failure with reduced ejection fraction (HFrEF). We aimed to determine whether regional changes in myocardial relaxation similarly contribute to diastolic dysfunction in post-infarction HFrEF, and to elucidate the underlying mechanisms.

Legumes can survive in nitrogen-deficient environments by forming root-nodule symbioses with rhizobial bacteria; however, forming nodules consumes energy, and nodule numbers must thus be strictly controlled. Previous studies identified major negative regulators of nodulation in Lotus japonicus, including the small peptides CLAVATA3/ESR (CLE)-RELATED-ROOT SIGNAL1 (CLE-RS1), CLE-RS2, and CLE-RS3, and their putative major receptor HYPERNODULATION AND ABERRANT ROOT FORMATION1 (HAR1). CLE-RS2 is known to be expressed in rhizobia-inoculated roots, and is predicted to be post-translationally arabinosylated, a modification essential for its activity. Moreover, all three CLE-RSs suppress nodulation in a HAR1-dependent manner. Here, we identified PLENTY as a gene responsible for the previously isolated hypernodulation mutant plenty. PLENTY encoded a hydroxyproline O-arabinosyltransferase orthologous to ROOT DETERMINED NODULATION1 in Medicago truncatula. PLENTY was localized to the Golgi, and an in vitro analysis of the recombinant protein demonstrated its arabinosylation activity, indicating that CLE-RS1/2/3 may be substrates for PLENTY. The constitutive expression experiments showed that CLE-RS3 was the major candidate substrate for PLENTY, suggesting the substrate preference of PLENTY for individual CLE-RS peptides. Furthermore, a genetic analysis of the plenty har1 double mutant indicated the existence of another PLENTY-dependent and HAR1-independent pathway negatively regulating nodulation.

The 4-component vaccine 4CMenB, developed against invasive disease caused by meningococcal serogroup B, is approved for use in infants in several countries worldwide. 4CMenB is mostly used as 3 + 1 schedule, except for the UK, where a 2 + 1 schedule is used, and where the vaccine showed an effectiveness of 82.9%. Here we compared the coverage of two 4CMenB vaccination schedules (3 + 1 [2.5, 3.5, 5, 11 months] versus 2 + 1 [3.5, 5, 11 months of age]) against 40 serogroup B strains, representative of epidemiologically-relevant isolates circulating in England and Wales in 2007-2008, using sera from a previous phase 3b clinical trial. The strains were tested using hSBA on pooled sera of infants, collected at one month post-primary and booster vaccination. 4CMenB coverage was defined as the percentage of strains with positive killing (hSBA titres ≥ 4 after immunisation and negative baseline hSBA titres < 2). Coverage of 4CMenB was 40.0% (95% confidence interval [CI]: 24.9-56.7) and 87.5% (95%CI: 73.2-95.8) at one month post-primary and booster vaccination, respectively, regardless of immunisation schedule. Using a more conservative threshold (post-immunisation hSBA titres ≥ 8; baseline ≤ 2), at one month post-booster dose, strain coverages were 80% (3 + 1) and 70% (2 + 1). We used a linear regression model to assess correlation between post-immunisation hSBA data for each strain in the two groups; Pearson's correlation coefficients were 0.93 and 0.99 at one month post-primary and booster vaccination. Overall, there is no evidence for a difference in strain coverage when 4CMenB is administered according to a 3 + 1 or 2 + 1 infant vaccination schedule.

Background The aim of the study was to characterize ultrasonographic (US) findings during and after electrochem-otherapy of liver tumors to determine the actual ablation zone and to verify the coverage of the treated tumor with a sufficiently strong electric field for effective electrochemotherapy. Patients and methods US findings from two representative patients that describe immediate and delayed tumor changes after electrochemotherapy of colorectal liver metastases are presented. Results The US findings were interrelated with magnetic resonance imaging (MRI). Electrochemotherapy-treated tumors were exposed to electric pulses based on computational treatment planning. The US findings indicate immediate appearance of hyperechogenic microbubbles along the electrode tracks. Within minutes, the tumors became evenly hyperechogenic, and simultaneously, an oedematous rim was formed presenting as a hypoechogenic formation which persisted for several hours after treatment. The US findings overlapped with computed electric field distribution in the treated tissue, indicating adequate coverage of tumors with sufficiently strong electric field, which may predict an effective treatment outcome. Conclusions US provides a tool for assessment of appropriate electrode insertion for intraoperative electrochemo-therapy of liver tumors and assessment of the appropriate coverage of a tumor with a sufficiently strong electric field and can serve as predictor of the response of tumors.

Vertebrates respond to stressful stimuli with the secretion of glucocorticoid (GC) hormones, such as corticosterone (CORT), and measurements of these hormones in wild species can provide insight into physiological responses to environmental and human-induced stressors. California condors (Gymnogyps californianus) are a critically endangered and intensively managed avian species for which information on GC response to stress is lacking. Here we evaluated a commercially available I125 double antibody radioimmunoassay (RIA) and an enzyme-linked immunosorbent assay (ELISA) kit for measurement of CORT and GC metabolites (GCM) in California condor plasma, urate, and feather samples. The precision and accuracy of the RIA assay outperformed the ELISA for CORT and GCM measurements, and CORT and GCM values were not comparable between the two assays for any sample type. RIA measurements of total CORT in condor plasma collected from 41 condors within 15 minutes of a handling stressor were highly variable (median = 70 ng/mL, range = 1-189 ng/mL) and significantly different between wild and captive condors (p = 0.02, two-tailed t-test, n = 10 wild and 11 captive). Urate GCM levels (median = 620 ng/g dry wt., range = 0.74-7200 ng/g dry wt., n = 216) significantly increased within 2 hr of the acute handling stressor (p = 0.032, n = 11 condors, one-tailed paired t-test), while feather section CORT concentrations (median = 18 pg/mm, range = 6.3-68 ng/g, n = 37) also varied widely within and between feathers. Comparison of multiple regression linear models shows condor age as a significant predictors of plasma CORT levels, while age, sex, and plasma CORT levels predicted GCM levels in urates collected within 30 min of the start of handling. Our findings highlight the need for validation when selecting an immunoassay for use with a new species, and suggest that non-invasively collected urates and feathers hold promise for assessing condor responses to acute or chronic environmental and human-induced stressors.

Aberrant glycolytic metabolism is one of the hallmarks of carcinogenesis and therefore reversal of metabolic transformation is a promising drug target in cancer treatment strategies. Dichloroacetic acid (DCA) is known to target the glycolytic pathway in cancer cells and facilitates reversal of metabolic transformation from aerobic cytosolic accumulation of pyruvic acid, "the Warburg effect", to mitochondrial oxidative phosphorylation. Recently, combination therapy particularly involving photodynamic therapy (PDT) has received considerable attention in oncology. We hypothesized that if DCA and PDT are combined, they might potentiate mitochondrial dysfunction and induce apoptosis by a reactive oxygen species (ROS) dependent pathway. We used MCF-7 cells as our in vitro model and 5-aminolevulinic acid (5-ALA) dependent PDT therapy to test our hypothesis. We found that combinatorial treatment of MCF-7 cells with PDT and DCA not only increased cell growth inhibition, but also affected mitochondrial membrane integrity perhaps via production of ROS, and enhanced apoptosis. Further, our results on ATP release during the combined treatment demonstrate that immunogenic cell death (ICD) is likely to be a potential mechanism by which PDT and DCA induce cancer cell death. Taken together, our study suggests a novel way of sensitizing MCF-7 cells for accelerated induction of apoptosis and ICD in these cells. The findings included in this study might have direct relevance in breast cancer treatment strategies.

Previous studies reported varies parameters of endoscopic ultrasound (EUS) for the localization of insulinomas, the purpose of this meta-analysis based on published studies to accuracy the diagnostic value of EUS.

Although NGS technologies fuel advances in high-throughput HLA genotyping methods for identification and classification of HLA genes to assist with precision medicine efforts in disease and transplantation, the efficiency of these methods are impeded by the absence of adequately-characterized high-frequency HLA allele reference sequence databases for the highly polymorphic HLA gene system. Here, we report on producing a comprehensive collection of full-length HLA allele sequences for eight classical HLA loci found in the Japanese population. We augmented the second-generation short read data generated by the Ion Torrent technology with long amplicon spanning consensus reads delivered by the third-generation SMRT sequencing method to create reference grade high-quality sequences of HLA class I and II gene alleles resolved at the genomic coding and non-coding level. Forty-six DNAs were obtained from a reference set used previously to establish the HLA allele frequency data in Japanese subjects. The samples included alleles with a collective allele frequency in the Japanese population of more than 99.2%. The HLA loci were independently amplified by long-range PCR using previously designed HLA-locus specific primers and subsequently sequenced using SMRT and Ion PGM sequencers. The mapped long and short-reads were used to produce a reference library of consensus HLA allelic sequences with the help of the reference-aware software tool LAA for SMRT Sequencing. A total of 253 distinct alleles were determined for 46 healthy subjects. Of them, 137 were novel alleles: 101 SNVs and/or indels and 36 extended alleles at a partial or full-length level. Comparing the HLA sequences from the perspective of nucleotide diversity revealed that HLA-DRB1 was the most divergent among the eight HLA genes, and that the HLA-DPB1 gene sequences diverged into two distinct groups, DP2 and DP5, with evidence of independent polymorphisms generated in exon 2. We also identified two specific intronic variations in HLA-DRB1 that might be involved in rheumatoid arthritis. In conclusion, full-length HLA allele sequencing by third-generation and second-generation technologies has provided polymorphic gene reference sequences at a genomic allelic resolution including allelic variations assigned up to the field-4 level for a stronger foundation in precision medicine and HLA-related disease and transplantation studies.

Microcystins are waterborne environmental toxins that induce oxidative stress and cause injuries in the heart. On the other hand, many physiological processes, including antioxidant defense, are under precise control by the mammalian circadian clock.

Perfect and low cost of fungal amylolytic and cellulolytic enzymes are prerequisite for the industrialization of plant biomass biorefinergy to biofuels. Genetic engineering of fungal strains based on regulatory network of transcriptional factors (TFs) and their targets is an efficient strategy to achieve the above described aim. Talaromyces pinophilus produces integrative amylolytic and cellulolytic enzymes; however, the regulatory mechanism associated with the expression of amylase and cellulase genes in T. pinophilus remains unclear. In this study, we screened for and identified novel TFs regulating amylase and/or cellulase gene expression in T. pinophilus 1-95 through comparative transcriptomic and genetic analyses.

One of the main challenges of acetone-butanol-ethanol fermentation is to reduce acetone production with high butanol yield. Converting acetone into isopropanol is an alternative pathway to reduce fermentation by-products in the fermentation broth. Here, we aimed to cultivate a wild-type Clostridium strain with high isopropanol and butanol production and reveal its genome information.

In the current study, nine foodborne "Locus of Enterocyte Effacement" (LEE)-negative Shiga toxin-producing Escherichia coli (STEC) strains were selected for whole genome sequencing and analysis for yet unknown genetic elements within the already known LEE integration sites selC, pheU and pheV. Foreign DNA ranging in size from 3.4 to 57 kbp was detected and further analyzed. Five STEC strains contained an insertion of foreign DNA adjacent to the selC tRNA gene and five and seven strains contained foreign DNA adjacent to the pheU and pheV tRNA genes, respectively. We characterized the foreign DNA insertion associated with selC (STEC O91:H21 strain 17584/1), pheU (STEC O8:H4 strain RF1a and O55:Hnt strain K30) and pheV (STEC O91:H21 strain 17584/1 and O113:H21 strain TS18/08) as examples.

The incidence of lung abscess acquired in the community is unknown, but this is a common clinical problem encountered in developing countries. The incidence of lung abscess was high in the pre-antibiotic era but the advent of susceptible antibiotics it has reduced with an equal fall in mortality to 8.7%. With the emerging antibiotic resistance and change in the trends of bacteriological profile causing lung abscess, it is the need of time to reevaluate lung abscess.

Continuing education (CE) activities help dentists update their knowledge and skills to ensure high standards of patient care.

Diabetes is a type of chronic disease with exceptional medical care for a patient's lifetime, which ultimately requires lifestyle and behavioural adjustments to prevent complications to death. Patients with good self-care behaviour will cause diabetes to be controlled to avoid complications to death and make patients have a better quality of life.

As the elderly population increases dramatically, the chronic age-related disease should be noted. In the elderly, chronic pain is a common health problem.

To evaluate if the Hexoskin smart shirt (HxS) would produce valid and reliable measurements for heart rate (HR), respiratory rate (RR), minute ventilation (VE), step count (SC), and energy expenditure (EE) when compared to a Polar T-31 heart rate monitor, an Applied Electrochemistry Moxus Metabolic System, and a manual step count. A two-day walking treadmill protocol with participants walking for 3 minutes at 3 speeds (1.5mph, 2.5mph, 3.5mph, 0% grade) was performed. Forty-nine volunteers participated the first day, forty-six on the second, thirty-one were used for reliability. Values calculated for the HxS data used Pearson's product-moment correlation (p < 0.05; r ≥ 0.70) for validity and Cronbach's α (≥ 0.70) for reliability. HxS HR (1.5mph; p<0.01, r=0.86, α=0.86. 2.5mph; p<0.01, r=0.81, α=0.88. 3.5mph; p<0.01, r=0.85, α=0.85), HxS RR (1.5mph; p<0.01, r=0.87, α=0.93. 2.5mph; p<0.01, r=0.86, α=0.92. 3.5mph; p<0.01, r=0.71, α=0.76), HxS VE (1.5mph; p=0.66, r=0.11, α=0.70. 2.5mph; p=0.01, r=0.15, α=0.73. 3.5mph; p=0.31, r=0.08, α=0.14), HxS SC (1.5mph; p=0.90, r=-0.01, α=0.70. 2.5mph; p=0.22, r=0.13, α=0.86. 3.5mph; p<0.01, r=0.74, α=0.85), HxS EE (1.5mph; p<0.01, r=0.56, α=0.85. 2.5mph; p<0.01, r=0.50, α=0.83. 3.5mph; p<0.01, r=0.51, α=0.80). HxS HR and RR provided valid and reliable measures at all three speeds while VE, SC, and EE had a mixture of results based on speed. These results are important in the use of the Hexoskin in an accurate manner for athletes, coaches, and for the potential medical applications being advocated in the field of telemedicine procedures.

Left displacement of the abomasum (LDA) is a condition of dairy cows that causes huge economic losses. The aim of the study was to evaluate the effect of LDA after on-farm correction by the 2-step laparoscopic abomasopexy on milk production based on 305-d milk yield on a commercial dairy farm in Italy.The study was performed between January 2011 and January 2014 on 58 Holstein Friesian cattle with left displacement of the abomasum in a commercial dairy farm in the farmland of Ozieri, Sardinia (Italy). Each cow underwent a 2-step laparoscopic abomasopexy performed by the same veterinarian. Each case was matched with a control herdmate by age, parity and calving date. Cows with LDA and healthy control cows also had a similar 305-d milk yield in the previous lactation. Data on milk production were collected using a dairy herd management software programme (Afimilk®, Afimilk Ltd., Israel). The 305-d lactation yield was obtained from the sum of daily milk yields for each cow. An unpaired Student's t-test was used to compare changes in milk production, mean fat and protein percentage of cases and controls before and after surgical procedure.