The gene encoding the Saccharomyces cerevisiae phospholipid deacylation enzyme, phospholipase B (ScPLB1), was successfully expressed in E. coli. The enzyme (Scplb1p) was engineered to have a histidine-tag at the C-terminal end and was purified by metal (Ni) affinity chromatography. Enzymatic properties, optimal pH, and substrate specificity were similar to those reported previously. For example, deacylation activity was observed in acidic pH in the absence of Ca2+ and was additive in neutral pH in the presence of Ca2+, and the enzyme had the same substrate priority as reported previously, with the exception of PE, suggesting that yeast phospholipase B could be produced in its native structure in bacterial cells. Scplb1p retained transacylation activity in aqueous medium, and esterified lysophosphatidylcholine with free fatty acid to form phosphatidylcholine in a non-aqueous, glycerin medium. We propose that phospholipase B could serve as an additional tool for in vitro enzyme-mediated phospholipid synthesis.

Potato (Solanum tuberosum L.) is an important global food crop that contains phytochemicals with demonstrated effects on human health. Understanding sources of chemical variation of potato tuber can inform breeding for improved health attributes of the cooked food. Here, a comprehensive metabolomics (UPLC- and GC-MS) and ionomics (ICP-MS) analysis of raw and cooked potato tuber was performed on 60 unique potato genotypes that span 5 market classes including russet, red, yellow, chip, and specialty potatoes. The analyses detected 2,656 compounds that included known bioactives (43 compounds), nutrients (42), lipids (76), and 23 metals. Most nutrients and bioactives were partially degraded during cooking (44 out of 85; 52%), however genotypes with high quantities of bioactives remained highest in the cooked tuber. Chemical variation was influenced by genotype and market class. Specifically, ~53% of all detected compounds from cooked potato varied among market class and 40% varied by genotype. The most notable metabolite profiles were observed in yellow-flesh potato which had higher levels of carotenoids and specialty potatoes which had the higher levels of chlorogenic acid as compared to the other market classes. Variation in several molecules with known association to health was observed among market classes and included vitamins (e.g., pyridoxal, ~2-fold variation), bioactives (e.g., chlorogenic acid, ~40-fold variation), medicinals (e.g., kukoamines, ~6-fold variation), and minerals (e.g., calcium, iron, molybdenum, ~2-fold variation). Furthermore, more metabolite variation was observed within market class than among market class (e.g., α-tocopherol, ~1-fold variation among market class vs. ~3-fold variation within market class). Taken together, the analysis characterized significant metabolite and mineral variation in raw and cooked potato tuber, and support the potential to breed new cultivars for improved health traits.

The risk of developing an incisional hernia after primary elective median laparotomy is reported in the literature as being between 5 and 20 percent. The goal of this systematic review was to evaluate different closure techniques for midline laparotomies and the use of additional prophylactic mesh augmentation for midline closure in high risk patients.

This data article presents the multi-locus DNA alignments, morphometric data, and details on specimens examined to resolve the evolutionary history of Anodontoides and Strophitus, primarily generic placement and species boundaries. We sequenced 3 loci to create our molecular matrix: cytochrome c oxidase subunit I, NADH dehydrogenase subunit I, and the nuclear-encoded ribosomal internal transcribed spacer I. Aligned sequences were used in phylogenetic analyses and to identify diagnostic nucleotides for Strophitus pascagoulaensis, Strophitus radiatus, Strophitus sp. cf. pascagoulaensis, and Strophitus williamsi. Linear morphometrics (i.e. maximum height, length, and width) were also implemented to further evaluate species boundaries within Strophitus. For further details and experimental findings, please refer to the article published in Molecular Phylogenetics and Evolution (Smith et al., 2018) [1].

In Nigerian universities, enrolment into any engineering undergraduate program requires that the minimum entry criteria established by the National Universities Commission (NUC) must be satisfied. Candidates seeking admission to study engineering discipline must have reached a predetermined entry age and met the cut-off marks set for Senior School Certificate Examination (SSCE), Unified Tertiary Matriculation Examination (UTME), and the post-UTME screening. However, limited effort has been made to show that these entry requirements eventually guarantee successful academic performance in engineering programs because the data required for such validation are not readily available. In this data article, a comprehensive dataset for empirical evaluation of entry requirements into engineering undergraduate programs in a Nigerian university is presented and carefully analyzed. A total sample of 1445 undergraduates that were admitted between 2005 and 2009 to study Chemical Engineering (CHE), Civil Engineering (CVE), Computer Engineering (CEN), Electrical and Electronics Engineering (EEE), Information and Communication Engineering (ICE), Mechanical Engineering (MEE), and Petroleum Engineering (PET) at Covenant University, Nigeria were randomly selected. Entry age, SSCE aggregate, UTME score, Covenant University Scholastic Aptitude Screening (CUSAS) score, and the Cumulative Grade Point Average (CGPA) of the undergraduates were obtained from the Student Records and Academic Affairs unit. In order to facilitate evidence-based evaluation, the robust dataset is made publicly available in a Microsoft Excel spreadsheet file. On yearly basis, first-order descriptive statistics of the dataset are presented in tables. Box plot representations, frequency distribution plots, and scatter plots of the dataset are provided to enrich its value. Furthermore, correlation and linear regression analyses are performed to understand the relationship between the entry requirements and the corresponding academic performance in engineering programs. The data provided in this article will help Nigerian universities, the NUC, engineering regulatory bodies, and relevant stakeholders to objectively evaluate and subsequently improve the quality of engineering education in the country.

This contribution contains data associated to the research article entitled "Exploring the genes of yerba mate (Ilex paraguariensis A. St.-Hil.) by NGS and de novo transcriptome assembly" (Debat et al., 2014) [1]. By means of a bioinformatic approach involving extensive NGS data analyses, we provide a resource encompassing the full transcriptome assembly of yerba mate, the first available reference for the Ilex L. genus. This dataset (Supplementary files 1 and 2) consolidates the transcriptome-wide assembled sequences of I. paraguariensis with further comprehensive annotation of the protein coding genes of yerba mate via the integration of Arabidopsis thaliana databases. The generated data is pivotal for the characterization of agronomical relevant genes in the tree crop yerba mate -a non-model species- and related taxa in Ilex. The raw sequencing data dissected here is available at DDBJ/ENA/GenBank (NCBI Resource Coordinators, 2016) [2] Sequence Read Archive (SRA) under the accession SRP043293 and the assembled sequences have been deposited at the Transcriptome Shotgun Assembly Sequence Database (TSA) under the accession GFHV00000000.

This data article contains complementary tables related to the research article study entitled, 'Effects of repetitive transcranial magnetic stimulation on ER stress-related genes and glutamate, γ-aminobutyric acid, and glycine transporter genes in mouse brain' (Ikeda et al. (2017) [1]), which showed that rTMS modulates glutamate, GABA and glycine transporters and regulates ER stress-related genes. Here, we provide accompanying data collected using Affymetrix GeneChip microarrays to identify changes in gene expression in mouse CBS treated with rTMS for 30 days (Tables 1-21) and mouse cerebrum (Tables 22-57) and CBS (Tables 58-94) treated with rTMS for 40 days.

Arsenic trioxide (As2O3) is an environmental carcinogen and a putative endocrine disruptor. Resveratrol has been shown to reverse As2O3-induced oxidative damage. In immortalized but nontransformed estrogen receptor α-negative human breast cells (MCF10A), we observed that 25 μM resveratrol ameliorated As2O3-induced cytotoxicity. As2O3, in the presence or absence of 25 μM resveratrol, induced quinone reductase (NAD(P)H quinone dehydrogenase 1), via the induction of NFE2-related factor 2. As2O3 caused a repression of cytochrome P450 (CYP)1B1, but the addition of 25 μM resveratrol rescued the expression of cytochrome P450 1B1 and kept it at a constant level. Therefore, 25 μM resveratrol can modulate the effects of As2O3 on enzymes involved in estrogen metabolism.

While tandem mass spectrometry can detect post-translational modifications (PTM) at the proteome scale, reported PTM sites are often incomplete and include false positives. Computational approaches can complement these datasets by additional predictions, but most available tools use prediction models pre-trained for single PTM type by the developers and it remains a difficult task to perform large-scale batch prediction for multiple PTMs with flexible user control, including the choice of training data. We developed an R package called PTMscape which predicts PTM sites across the proteome based on a unified and comprehensive set of descriptors of the physico-chemical microenvironment of modified sites, with additional downstream analysis modules to test enrichment of individual or pairs of PTMs in protein domains. PTMscape is flexible in the ability to process any major modifications, such as phosphorylation and ubiquitination, while achieving the sensitivity and specificity comparable to single-PTM methods and outperforming other multi-PTM tools. Applying this framework, we expanded proteome-wide coverage of five major PTMs affecting different residues by prediction, especially for lysine and arginine modifications. Using a combination of experimentally acquired sites (PSP) and newly predicted sites, we discovered that the crosstalk among multiple PTMs occur more frequently than by random chance in key protein domains such as histone, protein kinase, and RNA recognition motifs, spanning various biological processes such as RNA processing, DNA damage response, signal transduction, and regulation of cell cycle. These results provide a proteome-scale analysis of crosstalk among major PTMs and can be easily extended to other types of PTM.

Prevention of persistent pain following breast cancer surgery, via early identification of patients at high risk, is a clinical need. Supervised machine-learning was used to identify parameters that predict persistence of significant pain.

For decades, diverse plasmid vectors have been continuously developed for molecular cloning of DNA fragment in the bacterial host cell Escherichia coli. Even with deliberate performances in vector preparation, the cloning approaches still face inevitable background colonies, or false positive clones, that may be arisen from intact or self-ligated plasmid molecules. To assist in such problem, two plasmids, pBS2ndd and pBS3ndd, which resistant to ampicillin and kanamycin respectively, were developed in this study as more advantageous cloning vector. The plasmids carry ndd, a lethal gene from bacteriophage T4 coding for nucleoid disruption protein that binds to the host chromosome and progressively kill the cell. The deadly toxicity of Ndd inhibits host cells that obtain intact or ndd-religated vector from growing, which results in low background and dramatically reduces the effort for selection of recombinants. Moreover, their identical multiple cloning site was designed to support various cloning strategies. Digestion of plasmids with XcmI allows for in vitro T/A ligation, while with EcoRV permits blunt-end ligation, with capability of blue-white colony screening. In vivo homologous recombination cloning is also utilizable by amplification of insert fragments using primers containing homology arms and transformation into capable E. coli strains. To demonstrate their advantages, the plasmids were used to clone PCR product samples for DNA sequencing with low-background and versatile cloning strategies. Such rapid and cost-effective cloning procedures are also proposed here. Finally, the cloning for protein expression with blue-white selection was also possible using egfp as a model regulated by lac and T7 promoters on the plasmid or other build-in promoters with the insert.

Alzheimer's disease (AD) is a devastating neurodegenerative disorder that impairs memory and causes cognitive and psychiatric deficits. New evidences indicate that AD is conceptualized as a disease of synaptic failure, although the molecular and cellular mechanisms underlying these defects remain to be elucidated. Determining the timing and nature of the early synaptic deficits is critical for understanding the progression of the disease and for identifying effective targets for therapeutic intervention. Using single-synapse functional and morphological analyses, we find that AMPA signaling, which mediates fast glutamatergic synaptic transmission in the central nervous system (CNS), is compromised early in the disease course in an AD mouse model. The decline in AMPA signaling is associated with changes in actin cytoskeleton integrity, which alters the number and the structure of dendritic spines. AMPA dysfunction and spine alteration correlate with the presence of soluble but not insoluble Aβ and tau species. In particular, we demonstrate that these synaptic impairments can be mitigated by Aβ immunotherapy. Together, our data suggest that alterations in AMPA signaling and cytoskeletal processes occur early in AD. Most important, these deficits are prevented by Aβ immunotherapy, suggesting that existing therapies, if administered earlier, could confer functional benefits.

The immunostimulatory and immunomodulatory properties of selenium (Se), an essential trace element for animals, has increase its use because may prevent/or reduce the occurrence of infectious diseases. Thus, the aim of this study was to verify whether Se and vitamins (A and E) applied via subcutaneous associated with secnidazole via oral exert positive effects in the antioxidant and immune systems, as well as whether prevent infections caused by protozoan and bacteria, and consequently, reduce the number of cases of diarrhea in heifers. Thirty-two newborn Holstein heifers were divided into two groups with sixteen animals each: the control group and the treated group that received sodium selenite (0.2 mg/kg) and vitamins A (35 mg/kg) and E (1 mg/kg) with one day of life, and a second application associated with secnidazole (400 mg/animal) on day 10 of life. Sample collection (blood and feces) were performed on days 1, 15, 30, 45 and 60 of life. Heifers from the treated group showed higher hematocrit values compared to the control group on day 60 of life, while total serum protein levels were higher on days 15 and 30. The ceruloplasmin (days 15, 30 and 60), IgG of heavy chain (days 15, 30, 45 and 60), IgG of light chain (days 45 and 60) and haptoglobin (days 15, 30, 45 and 60) were higher in the treated group compared to the control group. Serum levels of glucose decreased in treated animals on day 60 of life, while serum levels of albumin, triglycerides, urea, cholesterol, thiobarbituric acid reactive substances, reactive oxygen species and glutathione S-transferase activity did not differ between groups. Secnidazole was able to prevent infections caused by Giardia duodenalis in the first few days of life, but no difference was observed between groups. Moreover, there was no difference on total bacteria count and the incidence of diarrhea between groups. No difference on weight gain was observed on day 60 of life, but on day 210 of life treated animals had higher weight gain compared to the control group. Based on these evidences, we concluded that the injectable application of Se and vitamins (A and E) associated to secnidazole can improve the immunological system, and consequently, favor animal's performance.

Sodium fluorescein ('fluorescein') staining of the ocular surface is frequently an indicator of compromised ocular health, and increases in the presence of certain contact lens multi-purpose solutions (MPS), a phenomenon known as solution induced corneal staining (SICS). The mechanism(s) underpinning fluorescein hyperfluorescence are uncertain, though may reflect increased cellular uptake of fluorescein by corneal epithelial cells. We have developed an in vitro model to study fluorescein uptake in both 'generic' mammalian cells (murine fibroblasts) and human corneal cells. Fluorescein hyperfluorescence increased after treatment with two MPS associated with clinical corneal fluorescein staining, yet there was no cellular hyperfluorescence for two MPS that do not cause this staining. Increased fluorescein uptake did not correlate with presence of a necrotic or an apoptotic marker (propidium iodide and caspase-3 respectively). Incubation of MPS-treated cells with dynasore (an inhibitor of dynamin, implicated in endocytic pathways) reduced fluorescein uptake irrespective of MPS treatment. The non-ionic surfactant Tetronic 1107 (present in both MPS associated with corneal fluorescein staining) increased uptake of fluorescein for both cell types, whereas an unrelated surfactant (Triton X-100) did not. We conclude that the clinical hyperfluorescence profile observed after exposure to four MPS can be reproduced using a simple model of cellular fluorescein uptake, suggesting this is the biological basis for SICS. Fluorescein entry does not correlate with necrosis or apoptosis, but instead involves a dynamin-dependent active process. Moreover the surfactant Tetronic 1107 appears to be a key MPS constituent triggering increased fluorescein entry, and may be the major factor responsible for SICS.

Type 2 diabetes (T2D) is a disease with a prevalence of 9.4% in Mexicans. Its etiology is complex involving environmental and genetic factors. The aim of this study was to analyse the association between PPARG rs1801282, PPARGC1A rs8192678, VEGFA rs2010963, ADRA2A rs553668, KCNQ1 rs2237892, SIRT1 rs7896005, IGF2BP2 rs4402960, and UCP3 rs3781907 single nucleotide variants (SNVs) with T2D and metabolic traits in a case-control study of a population from Mexico City. A total of 831 blood samples of non-diabetic, with healthy control participants (416) and individuals with T2D (415) were collected over a five-year period. After DNA extraction, genotyping was performed with TaqMan probes using real-time PCR. The genotypes were analysed for association with T2D in linear and logistic regressions adjusting for age, sex, and body mass index using the dominant, recessive, and additive models with a Bonferroni correction for multiple comparisons p < 0.001 and for association with related T2D traits fixed with a p < 2.3 × 10-4. The univariate analysis gives a significant (p < 1 × 10-4) for sex, triglycerides, and HOMA-IR. Significant association with T2D was found for ADRA2A rs553668 under the recessive model (OR = 3.640 and 95% CI of 2.330-5.690 (p < 1 × 10-4); statistical power 0.999) and under the additive model (OR = 1.640 and 95% CI of 1.340-2.000 (p < 1 × 10-4); statistical power 0.997). Variants PPARG rs1801282, PPARGC1A rs8192678, SIRT1 rs7896005, IGF2BP2 rs4402960 and UCP3 rs3781907 were nominally associated (p > 0.001 and <0.050). Results describe association of ADRA2A rs553668 with T2D in a Mexican population. Variants with nominal association with T2D require to be replicated in additional Mexican populations.

To assess the association between interleukin gene polymorphism and recurrent aphthous stomatitis (RAS).

Mannosyl (alpha-1,6-)-Glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase (MGAT5) is exclusively expressed in gastric carcinoma, and plays an essential role in cancer progression, but no targeted drug is available so far. The potential anti-cancer effect of Hydrogen Sulfide (H2S), has not been widely recognized. It intrigued broad interest to explore the clinical benefits of cancer therapy, with the current understanding of molecular mechanisms of H2S which remains very limited. In this study, we identify that H2S is an effective inhibitor of MGAT5, leading to reduce the expression of exclusively abnormal glycoprotein processes in gastric carcinoma. H2S specifically dissociation of karyopherin subunit alpha-2 (KPNA2) with Jun proto-oncogene (c-Jun) interaction, and blocking c-Jun nuclear translocation, and downregulation of MGAT5 expression at the level of gene and protein. Consequently, H2S impairs growth and metastasis in gastric carcinoma by targeting inhibits MGAT5 activity. In an animal tumor model study, H2S is well tolerated, inhibits gastric carcinoma growth and metastasis. Our preclinical work therefore supports that H2S acts as a novel inhibitor of MGAT5 that block tumorigenesis in gastric carcinoma.

Background: Curcumin was shown to reduce epithelial-mesenchymal transition (EMT) markers in previous short term studies. This study was aimed to investigate the potential of curcumin in the prevention of EMT activation in MCF-7 cells induced by endoxifen. Methods: MCF-7 breast cancer cells were treated with Endoxifen 1000 nM+betaestradiol 1 nM with or without curcumin (8.5μM or 17 μM). Cells treated with dimethyl sulfoxide (DMSO) 0.001% were used as negative control. After 8 weeks of continuous treatment, the cells were counted, analyzed for mRNA E-cadherin, vimentin, TGF-β expression, total reactive oxygen species (ROS) and observed for morphological changes using confocal microscope and transmission electron microscope. Result: MCF-7 cell viability was increased in endoxifen + β-estradiol group. Cell viability was significantly decreased in curcumin 17 μM, but not in curcumin 8.5 μM group. Analysis of EMT markers at week 8 indicates that there were increase in vimentin and TGF-β mRNA expressions, while E-cadherin mRNA expressions and TGF-β1 protein concentrations were shown to decrease. The results showed that administration of curcumin in all the dose administered were incapable improving the expressions of vimentin, TGF-β1 and E-cadherin. There was a decrease in ROS concentration in curcumin treated cells (8.5 μM) while in curcumin 17 μM, ROS concentration was increased. Morphological observation using confocal microscope and TEM showed the presence of mesenchymal cells and adherens junction. Conclusion: endoxifen treatments for eight weeks resulted in upregulation of EMT markers and changes in morphology of MCF-7 breast cancer cells. The addition of curcumin did not prevent the activation of EMT.

The monophyly of flatfishes has not been supported in many molecular phylogenetic studies. The monophyly of Pleuronectoidei, which comprises all but one family of flatfishes, is broadly supported. However, the Psettodoidei, comprising the single family Psettodidae, is often found to be most closely related to other carangimorphs based on substantial sequencing efforts and diversely analytical methods. In this study, we examined why this particular result is often obtained.

Meiotic recombination events include crossovers and non-crossovers or gene conversions. Although the rate of crossovers is often used for genetic mapping, the gene conversion events are not well studied especially in outbred species, which could produce distorted markers and thus affect the precision of genetic maps.