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We derive new nonlinear discrete analogue of the continuous Halanay-type inequality. These inequalities can be used as basic tools in the study of the global asymptotic stability of the equilibrium of certain generalized difference equations.

Abstract Some new nonlinear integral inequalities of Gronwall type for retarded functions are established, which extend the results Lipovan (2003) and Pachpatte (2004). These inequalities can be used as basic tools in the study of certain classes of functional differential equations as well as integral equations. A existence and a uniqueness on the solution of the functional differential equation involving several retarded arguments with the initial condition are also indicated.

In this current assessment, BaO synthesized from Moringa Oleifera leaves were irradiated using 0-75 kGy gamma radiation and investigated its physical impacts. The x-ray diffraction (XRD) data demonstrated the synthesis of tetragonal BaO, and no phase deviation was observed after irradiation. As doses are increased, the overall crystallite size were decreased due to an increase in defects and disorders. The tetragonal BaO was evident in Fourier transform infrared (FTIR) spectra prior to and following irradiation, while peak intensities and wavenumbers varied considerably. The as-prepared BaO showed a spherical shape morphology, and Field emission scanning electron microscopy (FESEM) indicated no vital deviations in it after irradiation. As irradiation shifts from 0 to 75 kGy, optical bandgap was increased from 4.55 to 4.93 eV, evaluated using Kubelka-Munk (K-M) equation from UV-vis-NIR spectrophotometer. Opto-electronic and photonic devices have challenges in extreme radiation conditions, such as space and nuclear environments. So, these assessments suggested that BaO can withstand high levels of gamma photon and could be a good option for photonic and optoelectronic instruments in an extreme gamma-ray exposed conditions., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

The data-intensive fields of genomics and machine learning (ML) are in an early stage of convergence. Genomics researchers increasingly seek to harness the power of ML methods to extract knowledge from their data; conversely, ML scientists recognize that genomics offers a wealth of large, complex, and well-annotated datasets that can be used as a substrate for developing biologically relevant algorithms and applications. The National Human Genome Research Institute (NHGRI) inquired with researchers working in these two fields to identify common challenges and receive recommendations to better support genomic research efforts using ML approaches. Those included increasing the amount and variety of training datasets by integrating genomic with multiomics, context-specific (e.g., by cell type), and social determinants of health datasets; reducing the inherent biases of training datasets; prioritizing transparency and interpretability of ML methods; and developing privacy-preserving technologies for research participants' data., Competing Interests: Declaration of interests The authors declare no competing interests., (Published by Elsevier Inc.)

To commercialize functional foods, probiotics must exhibit high resistance and acceptable stability under various unfavorable conditions to maintain the quality of fruit juices. This study will provide an insight into fortification of orange juice with a plant probiotic Kocuria flava Y4 by microencapsulation. Therefore, this study investigated the colony release, physicochemical and phytochemical parameters, and antioxidant activity of the orange juice exposed to microencapsulated probiotics and the one without probiotics (control). Evaluation of orange juice on the growth of probiotic bacteria showed that the fortification with alginate and psyllium micro-particles showed highest encapsulation efficiency (99.01%) and acceptable viability of probiotic cells (8.12 ± 0.077 CFU/mL) during five weeks storage at 4 °C. The morphology and functional properties of beads was studied by SEM, Zeta-potential and FTIR analysis. The sucrose and organic acids concentrations decreased significantly during fortification period (0-72 h) except ascorbic acid. Furthermore, glucose, pH, acidity, TSS were maintained. The results affirm the suitability and feasibility of developing a plant probiotic beverage using orange juice by encapsulation method., Competing Interests: Authors have no conflict of interest., (© 2023 The Authors. Published by Elsevier Ltd.)

The discharge of wastewater from textile industries into aquatic bodies has severe health and environmental impacts. Textile industries generate huge amounts of effluents containing hazardous toxic dyes. Anthraquinone (AQ) dyes containing AQ chromophore groups are the second most important class of nondegradable textile dyes, preceded by azo dyes. Despite their prevalence, biodegradation of AQ dyes has not yet been completely understood because of their complex and stable structures. Currently, microbiological approaches to treating dyeing wastewater are considered economical and feasible, and reports regarding fungal degradation of AQ dyes are increasing. Structures and classification of AQ dyes were summarized in this study along with degradative fungi, and their enzyme systems with influencing factors and possible mechanisms of AQ mycoremediation were explored. Furthermore, the existing problems and present research progress were discussed. Finally, the key points with future research directions were presented., Competing Interests: The authors declare no conflict of interest., (© 2023 Institute of Bioorganic Chemistry, Polish Academy of Sciences.)

In this study, we have synthesized pristine and [0.5,1.5, and 2.5] M% samarium (Sm)-incorporating α-MoO 3 2D-layered nanoplates utilizing a facile hydrothermal process, and investigated the physical properties along with antibacterial effectiveness. X-ray diffraction (XRD) patterns confirmed the single-phase, stable orthorhombic polycrystalline structure of the as-prepared samples. The crystallite size, lattice strain, and dislocation density were measured using both Debye-Scherrer (D-S) and Williamson-Hall (W-H) techniques. Both pristine and Sm-incorporating α-MoO 3 samples showed two-dimensional (2D) layered nanoplate-type surface morphology, revealed by field emission scanning electron microscopy (FE-SEM) images. Energy dispersive X-ray spectroscopy (EDS) confirmed the presence of Sm contents in the α-MoO 3 matrix. After Sm incorporation in α-MoO 3 , the different functional groups as well as vibrational groups were observed by Fourier-transform infrared (FTIR) spectroscopy and Raman spectroscopy analyses, respectively. The optical band gaps were measured from UV-vis diffuse reflectance spectroscopy (DRS) by employing the Kubelka-Munk formula and interestingly it is found that the bandgap energy ( E g ) gradually decreased from 2.96 to 2.83 eV with the increment of Sm content. When compared to pristine α-MoO 3 , the Sm-incorporating samples experienced a steady improvement in room temperature ferromagnetic (RTFM) behavior as Sm content increased, as measured by hysteresis loops. The antibacterial activities of both samples were assessed against Gram-positive: Staphylococcus aureus ( S. aureus ), and Gram-negative: Escherichia coli ( E. coli ) and Salmonella enteritidis ( S. enteritidis ) bacteria by the agar well diffusion method and enhanced antibacterial activity was observed as the Sm concentration increased, compared to pristine nanoplates. The obtained results suggest that the synthesized Sm-incorporating α-MoO 3 2D-layered nanoplate could be a potential antibacterial agent., Competing Interests: The authors declare that they have no competing interests., (This journal is © The Royal Society of Chemistry.)

The exogenous lipolytic activities of Kocuria sp. have been recognized earlier but the genus further contains many more unexplored strains. In this study, the extracellular lipase activity of Kocuria flava Y4 (GenBank accession no. MT773277), isolated from Dioscorea villosa during our previous study, was regulated by different physicochemical parameters, such as pH, temperature, shaking speed, and incubation time. For efficient immobilization of the extracellular lipase, 4% sodium alginate, 50 mL of 25 nM CaCl 2 .2H 2 O solution, and 15 min. Hardening time of gel beads in calcium chloride was used. For the first time, K . flava Y4 lipase was purified using ammonium sulphate precipitation followed by dialysis and DEAE-Sepharose anion exchange chromatography with Sepharose-6B gel filtration chromatography, yielding ∼15-fold purified lipase with a final yield of 96 U/mL. The SDS-PAGE of purified lipase displayed a single strong band, indicating a monomeric protein of 45 kDa. At a temperature of 35°C and pH 8, the purified lipase showed maximum hydrolytic activity. Using p-nitrophenyl acetate (p-NPA) as the hydrolysis substrate, the values of K m and V max derived from the Lineweaver-Burk plot were 4.625 mM and 125 mol/min -1 mg -1 , respectively., Competing Interests: The authors declare that they have no conflicts of interest regarding the publication of this paper., (Copyright © 2022 Adyasa Barik et al.)

Currently, globalization, urbanization and industrialization have led to several environmental issues. In many industries, particularly in textile industries, the extensive use of synthetic dyes has increased. Dye is an integral element used to impart color to textile materials. Wastes generated during the processing and treatment of the dye contain inorganic and organic compounds that are hazardous, thereby posing a serious threat to the ecosystem. It is therefore important to implement cost-efficient and successful measures against these emissions in order to preserve habitats and natural resources. In this context, biodegradation by fungi or mycoremediation of dyes using potential fungi is a fairly inexpensive and environmental friendly method for decomposing or mineralizing barely or less decaying dye compounds. Fungi play a crucial role in degrading and decolorizing organic dyes by enzymes and processes such as absorption, adsorption and aggregation of effluent colorants. The factors affecting the decolorization and biodegradation of dye compounds through fungal bioremediation, such as pH, temperature, dye concentration, agitation, effects of carbon and nitrogen sources, dye structure, enzymes, electron donor and redox mediators are discussed in this review. The review also includes a summary on the mechanism and kinetics of dye degradation as well as recent advances and future perspectives in mycoremediation of dyes., (© 2021 Institute of Bioorganic Chemistry, Polish Academy of Sciences.)

Circadian rhythm disruption (CD) is associated with impaired glucose homeostasis and type 2 diabetes mellitus (T2DM). While the link between CD and T2DM remains unclear, there is accumulating evidence that disruption of fasting/feeding cycles mediates metabolic dysfunction. Here, we used an approach encompassing analysis of behavioral, physiological, transcriptomic, and epigenomic effects of CD and consequences of restoring fasting/feeding cycles through time-restricted feeding (tRF) in mice. Results show that CD perturbs glucose homeostasis through disruption of pancreatic β cell function and loss of circadian transcriptional and epigenetic identity. In contrast, restoration of fasting/feeding cycle prevented CD-mediated dysfunction by reestablishing circadian regulation of glucose tolerance, β cell function, transcriptional profile, and reestablishment of proline and acidic amino acid–rich basic leucine zipper (PAR bZIP) transcription factor DBP expression/activity. This study provides mechanistic insights into circadian regulation of β cell function and corresponding beneficial effects of tRF in prevention of T2DM.

Globally, textile industries are one of the major sectors releasing dye pollutants. This is the first report on the positive correlation between toxicity and chemical oxygen demand (COD) of textile effluent along with the proposed pathway for enzymatic degradation of acid orange 10 using Geotrichum candidum within a very short stretch of time (18 h). Removal efficiency of this mycoremedial approach after 18 h in terms of chemical oxygen demand, biological oxygen demand, total suspended solids, salinity, color and dye concentration in the treated effluent reached to 98.5%, 56.3%,73.2%, 64%, 89% and 87% respectively. Also there was a decrease in pH of the treated effluent. FTIR analysis of the treated effluent confirmed biodegradation. The LCMS analysis showed the degradation of acid orange 10, which was confirmed by the formation of two biodegradation products, 7-oxo-8-iminonapthalene-1,3-disulfonate and nitrosobenzene, which subsequently undergoes stepwise hydrogenation and dehydration to form aniline via phenyl hydroxyl amine as intermediate. The X-ray diffraction studies showed that heavy metal content in the treated effluent has reduced along with decrease in % crystallinity, indicating biodegradation. The connection between toxicity and COD was also inveterated using Pearson's correlation coefficient. Further the toxicological studies indicated the toxicity of raw textile effluent and relatively lower toxic nature of metabolites generated after biodegradation by G. candidum., (© 2021. The Author(s).)

Background: Climate change is a problem which is global in nature, and whose effects go across a wide range of disciplines. It is therefore important that this theme is taken into account as part of universities´ teaching and research programs., Methods: A three-tiered approach was used, consisting of a bibliometric analysis, an online survey and a set of case studies, which allow a profile to be built, as to how a sample of universities from 45 countries handle climate change as part of their teaching programs., Results: This paper reports on a study which aimed at identifying the extent to which matters related to climate change are addressed within the teaching and research practices at universities, with a focus on the training needs of teaching staff. It consists of a bibliometric analysis, combined with an online worldwide survey aimed at ascertaining the degree of involvement from universities in reducing their own carbon footprint, and the ways they offer training provisions on the topic. This is complemented by a set of 12 case studies from universities round the world, illustrating current trends on how universities handle climate change. Apart from reporting on the outcomes of the study, the paper highlights what some universities are doing to handle climate issues, and discusses the implications of the research., Conclusions: The paper lists some items via which universities may better educate and train their students on how to handle the many challenges posed by climate change., Supplementary Information: The online version contains supplementary material available at 10.1186/s12302-021-00552-5., Competing Interests: Competing interestsThe authors declare that they have no competing interests., (© The Author(s) 2021.)

Intrinsic β-cell circadian clocks are important regulators of insulin secretion and overall glucose homeostasis. Whether the circadian clock in β-cells is perturbed following exposure to prodiabetogenic stressors such as proinflammatory cytokines, and whether these perturbations are featured during the development of diabetes, remains unknown. To address this, we examined the effects of cytokine-mediated inflammation common to the pathophysiology of diabetes, on the physiological and molecular regulation of the β-cell circadian clock. Specifically, we provide evidence that the key diabetogenic cytokine IL-1β disrupts functionality of the β-cell circadian clock and impairs circadian regulation of glucose-stimulated insulin secretion. The deleterious effects of IL-1β on the circadian clock were attributed to impaired expression of key circadian transcription factor Bmal1, and its regulator, the NAD-dependent deacetylase, Sirtuin 1 (SIRT1). Moreover, we also identified that Type 2 diabetes in humans is associated with reduced immunoreactivity of β-cell BMAL1 and SIRT1, suggestive of a potential causative link between islet inflammation, circadian clock disruption, and β-cell failure. These data suggest that the circadian clock in β-cells is perturbed following exposure to proinflammatory stressors and highlights the potential for therapeutic targeting of the circadian system for treatment for β-cell failure in diabetes., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Endocrine Society. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Specific-pathogen-free (SPF) mice have improved hematopoietic characteristics relative to germ-free mice, however, it is not clear whether improvements in hematopoietic traits will continue when the level of microorganism exposure is further increased. We co-housed SPF C57BL/6 mice in a conventional facility (CVT) and found a significant increase in gut microbiota diversity along with increased levels of myeloid cells and T cells, especially effector memory T cells. Through single cell RNA sequencing of sorted KL (c-Kit + Lin - ) cells, we imputed a decline in long-term hematopoietic stem cells and an increase in granulocyte-monocyte progenitors in CVT mice with up-regulation of genes associated with cell survival. Bone marrow transplantation through competitive repopulation revealed a significant increase in KSL (c-Kit + Sca-1 + Lin - ) cell reconstitution in recipients of CVT donor cells which occurred when donors were co-housed for both one and twelve months. However, there was minimal to no gain in mature blood cell engraftment in recipients of CVT donor cells relative to those receiving SPF donor cells. We conclude that co-housing SPF mice with mice born in a conventional facility increased gut microbiota diversity, augmented myeloid cell production and T cell activation, stimulated KSL cell reconstitution, and altered hematopoietic gene expression.

The Triggering Receptor Expressed on Myeloid cells-like 4 (TREML4) is a member of the TREM receptor family, known modulators of inflammatory responses. We have previously found that TREML4 expression positively correlates with human coronary arterial calcification (CAC). However, the role of TREML4 in the pathogenesis of cardiovascular disease remains incompletely defined. Since macrophages play a key role in inflammatory conditions, we investigated if activated macrophages selectively expressed TREML4 and found that carriage of either one of the eQTL SNP's previously associated with increased TREML4 expression conferred higher expression in human inflammatory macrophages (M1) compared to alternatively activated macrophages (M2). Furthermore, we found that TREML4 expression in human M1 dysregulated several inflammatory pathways related to leukocyte activation, apoptosis and extracellular matrix degradation. Similarly, murine M1 expressed substantial levels of Treml4 , as did oxLDL treated macrophages. Transcriptome analysis confirmed that murine Treml4 controls the expression of genes related to inflammation and lipid regulation pathways, suggesting a possible role in atherosclerosis. Analysis of Apoe -/- /Treml4 -/- mice showed reduced plaque burden and lesion complexity as indicated by decreased stage scores, macrophage content and collagen deposition. Finally, transcriptome analysis of oxLDL-loaded murine macrophages showed that Treml4 represses a specific set of genes related to carbohydrate, ion and amino acid membrane transport. Metabolomic analysis confirmed that Treml4 deficiency may promote a beneficial relationship between iron homeostasis and glucose metabolism. Together, our results suggest that Treml4 plays a role in the development of cardiovascular disease, as indicated by Treml4 -dependent dysregulation of macrophage inflammatory pathways, macrophage metabolism and promotion of vulnerability features in advanced lesions., (Copyright © 2020 Gonzalez-Cotto, Guo, Karwan, Sen, Barb, Collado, Elloumi, Palmieri, Boelte, Kolodgie, Finn, Biesecker and McVicar.)

Background: A single variant in NAA10 (c.471+2T>A), the gene encoding N-acetyltransferase 10, has been associated with Lenz microphthalmia syndrome. In this study, we aimed to identify causative variants in families with syndromic X-linked microphthalmia., Methods: Three families, including 15 affected individuals with syndromic X-linked microphthalmia, underwent analyses including linkage analysis, exome sequencing and targeted gene sequencing. The consequences of two identified variants in NAA10 were evaluated using quantitative PCR and RNAseq., Results: Genetic linkage analysis in family 1 supported a candidate region on Xq27-q28, which included NAA10 . Exome sequencing identified a hemizygous NAA10 polyadenylation signal (PAS) variant, chrX:153,195,397T>C, c.*43A>G, which segregated with the disease. Targeted sequencing of affected males from families 2 and 3 identified distinct NAA10 PAS variants, chrX:g.153,195,401T>C, c.*39A>G and chrX:g.153,195,400T>C, c.*40A>G. All three variants were absent from gnomAD. Quantitative PCR and RNAseq showed reduced NAA10 mRNA levels and abnormal 3' UTRs in affected individuals. Targeted sequencing of NAA10 in 376 additional affected individuals failed to identify variants in the PAS., Conclusion: These data show that PAS variants are the most common variant type in NAA10 -associated syndromic microphthalmia, suggesting reduced RNA is the molecular mechanism by which these alterations cause microphthalmia/anophthalmia. We reviewed recognised variants in PAS associated with Mendelian disorders and identified only 23 others, indicating that NAA10 harbours more than 10% of all known PAS variants. We hypothesise that PAS in other genes harbour unrecognised pathogenic variants associated with Mendelian disorders. The systematic interrogation of PAS could improve genetic testing yields., Competing Interests: Competing interests: LGB receives royalties from Genentech Corp, is an advisor to the Illumina Corp, received honoraria from Wiley-Blackwell and receives honoraria from Cold Spring Harbor Press. DNC is in receipt of funding from Qiagen Inc through a License Agreement with Cardiff University. AMS receives honoraria from Wiley-Blackwell, Inc, Oxford University Press and UptoDate, Inc., (© Author(s) (or their employer(s)) 2019. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: Poor adherence to oral bisphosphonates is a challenge to treatment and prevention of osteoporosis. The Veterans Health Administration (VA) operates the largest integrated health care system in the United States and offers certain advantages to possibly improve medication adherence. We aimed to determine adherence to weekly alendronate for osteoporosis in Veterans, and investigate predictors and outcomes related to adherence. Methods: A retrospective study cohort was generated from VA databases selecting Veterans who were treated with weekly alendronate. Adherence was measured by medication possession ratio (MPR) and persistence. Two groups were defined as low and high adherence based on MPR <80% or ≥80%, respectively. Regression models were used to investigate predictors of adherence and included clinically relevant covariates. Further regressions were used to investigate the impact of adherence on change in bone mineral density measured by dual energy X-ray absorptiometry and incident fracture. Results: In a cohort of 913 (female/male, 207/706) Veterans, 48% had high adherence in year 1. Distribution for gender, race, and age were similar between the 2 groups, MPR <80% or MPR ≥80%. Baseline fracture [odds ratio OR: 0.64, 95%CI: (0.41, 0.98)], alcohol abuse [0.40 (0.21, 0.74)] and tobacco use [0.44 (0.31, 0.63)] were associated with low adherence in the unadjusted analyses, but only tobacco use [0.45 (0.30, 0.67)] was associated with low adherence after adjustment. Among males, tobacco use was associated with low adherence while prostate cancer predicted high adherence in adjusted models. High adherence was associated with a 30% [hazard ratio HR: 0.70, 95% CI: (0.47, 1.03)] decreased risk of incident fracture in the whole cohort, and a 40% [0.60 (0.38, 0.95)] decrease risk in males. Conclusion: Year one adherence to weekly alendronate was a relevant determinant to long-term clinical outcomes including changes in bone mineral density and incident fracture in Veterans.

A readily accessible D-A-D triad molecule 1 was synthesized through acylhydrazone bond formation using carefully chosen building blocks. The molecule 1 exhibits emission through charge-coupled proton transfer and enhanced emission induced through aggregation and mechanochromic luminescence. Further, it detects Al(III) selectively among other cations in an efficient manner.

Mammalian barrier surfaces are constitutively colonized by numerous microorganisms. We explored how the microbiota was sensed by the immune system and the defining properties of such responses. Here, we show that a skin commensal can induce T cell responses in a manner that is restricted to non-classical MHC class I molecules. These responses are uncoupled from inflammation and highly distinct from pathogen-induced cells. Commensal-specific T cells express a defined gene signature that is characterized by expression of effector genes together with immunoregulatory and tissue-repair signatures. As such, non-classical MHCI-restricted commensal-specific immune responses not only promoted protection to pathogens, but also accelerated skin wound closure. Thus, the microbiota can induce a highly physiological and pleiotropic form of adaptive immunity that couples antimicrobial function with tissue repair. Our work also reveals that non-classical MHC class I molecules, an evolutionarily ancient arm of the immune system, can promote homeostatic immunity to the microbiota., (Published by Elsevier Inc.)

Background: One goal of personalized medicine is leveraging the emerging tools of data science to guide medical decision-making. Achieving this using disparate data sources is most daunting for polygenic traits. To this end, we employed random forests (RFs) and neural networks (NNs) for predictive modeling of coronary artery calcium (CAC), which is an intermediate endo-phenotype of coronary artery disease (CAD)., Methods: Model inputs were derived from advanced cases in the ClinSeq®; discovery cohort (n=16) and the FHS replication cohort (n=36) from 89 th -99 th CAC score percentile range, and age-matched controls (ClinSeq®; n=16, FHS n=36) with no detectable CAC (all subjects were Caucasian males). These inputs included clinical variables and genotypes of 56 single nucleotide polymorphisms (SNPs) ranked highest in terms of their nominal correlation with the advanced CAC state in the discovery cohort. Predictive performance was assessed by computing the areas under receiver operating characteristic curves (ROC-AUC)., Results: RF models trained and tested with clinical variables generated ROC-AUC values of 0.69 and 0.61 in the discovery and replication cohorts, respectively. In contrast, in both cohorts, the set of SNPs derived from the discovery cohort were highly predictive (ROC-AUC ≥0.85) with no significant change in predictive performance upon integration of clinical and genotype variables. Using the 21 SNPs that produced optimal predictive performance in both cohorts, we developed NN models trained with ClinSeq®; data and tested with FHS data and obtained high predictive accuracy (ROC-AUC=0.80-0.85) with several topologies. Several CAD and "vascular aging" related biological processes were enriched in the network of genes constructed from the predictive SNPs., Conclusions: We identified a molecular network predictive of advanced coronary calcium using genotype data from ClinSeq®; and FHS cohorts. Our results illustrate that machine learning tools, which utilize complex interactions between disease predictors intrinsic to the pathogenesis of polygenic disorders, hold promise for deriving predictive disease models and networks.

[This corrects the article DOI: 10.1371/journal.pone.0150763.].

Endophytes are an endosymbiotic group of microorganisms that colonize in plants and microbes that can be readily isolated from any microbial or plant growth medium. They act as reservoirs of novel bioactive secondary metabolites, such as alkaloids, phenolic acids, quinones, steroids, saponins, tannins, and terpenoids that serve as a potential candidate for antimicrobial, anti-insect, anticancer and many more properties. While plant sources are being extensively explored for new chemical entities for therapeutic purposes, endophytic microbes also constitute an important source for drug discovery. This review aims to comprehend the contribution and uses of endophytes as an impending source of drugs against various forms of diseases and other possible medicinal use.

The variegated expression of murine Ly49 loci has been associated with the probabilistic behavior of an upstream promoter active in immature cells, the Pro1 element. However, recent data suggest that Pro1 may be active in mature natural killer (NK) cells and function as an enhancer element. To assess directly if Pro1 transcripts are present in mature Ly49-expressing NK cells, RNA-sequencing of the total transcript pool was performed on freshly isolated splenic NK cells sorted for expression of either Ly49G or Ly49I. No Pro1 transcripts were detected from the Ly49a, Ly49c or Ly49i genes in mature Ly49(+) NK cells that contained high levels of Pro2 transcripts. Low levels of Ly49g Pro1 transcripts were found in both Ly49G(+) and Ly49G(-) populations, consistent with the presence of a small population of mature NK cells undergoing Ly49g gene activation, as previously demonstrated by culture of splenic NK cells in interleukin-2. Ly49 gene reporter constructs containing Pro1 failed to show any enhancer activity of Pro1 on Pro2 in a mature Ly49-expressing cell line. Taken together, the results are consistent with Pro1 transcription having a role in gene activation in developing NK, and argue against a role for Pro1 in Ly49 gene transcription by mature NK cells.

Drought is one of the major limiting factors for productivity of crops including rice (Oryza sativa L.). Understanding the role of allelic variations of key regulatory genes involved in stress-tolerance is essential for developing an effective strategy to combat drought. The bZIP transcription factors play a crucial role in abiotic-stress adaptation in plants via abscisic acid (ABA) signaling pathway. The present study aimed to search for allelic polymorphism in the OsbZIP23 gene across selected drought-tolerant and drought-sensitive rice genotypes, and to characterize the new allele through overexpression (OE) and gene-silencing (RNAi). Analyses of the coding DNA sequence (CDS) of the cloned OsbZIP23 gene revealed single nucleotide polymorphism at four places and a 15-nucleotide deletion at one place. The single-copy OsbZIP23 gene is expressed at relatively higher level in leaf tissues of drought-tolerant genotypes, and its abundance is more in reproductive stage. Cloning and sequence analyses of the OsbZIP23-promoter from drought-tolerant O. rufipogon and drought-sensitive IR20 cultivar showed variation in the number of stress-responsive cis-elements and a 35-nucleotide deletion at 5'-UTR in IR20. Analysis of the GFP reporter gene function revealed that the promoter activity of O. rufipogon is comparatively higher than that of IR20. The overexpression of any of the two polymorphic forms (1083 bp and 1068 bp CDS) of OsbZIP23 improved drought tolerance and yield-related traits significantly by retaining higher content of cellular water, soluble sugar and proline; and exhibited decrease in membrane lipid peroxidation in comparison to RNAi lines and non-transgenic plants. The OE lines showed higher expression of target genes-OsRab16B, OsRab21 and OsLEA3-1 and increased ABA sensitivity; indicating that OsbZIP23 is a positive transcriptional-regulator of the ABA-signaling pathway. Taken together, the present study concludes that the enhanced gene expression rather than natural polymorphism in coding sequence of OsbZIP23 is accountable for improved drought tolerance and yield performance in rice genotypes.

Lathyrus sativus L. (Grass pea) is the source for cheap and nutritious food choice in drought and famine susceptible zones in greater part of North India and Africa. The non-protein amino acid β-N-oxalyl-L-α,β-diaminopropionic acid (β-ODAP) has been known for decades for its potent neurotoxic effect, causing irreversible neurodegenerative disease "neurolathyrism", present in both seed and leaf of Lathyrus sativus L. and other species in varying proportions. It is crucial to establish a rapid as well as reliable detection methodology for β-ODAP content in various Lathyrus plants. Currently available HPLC based methods involve multi-step derivatization of the sample. To overcome this, we have developed β-ODAP analysis method by HPLC without any prior derivatization. This method is statistically significant in the range of 2 to 100μg/ml and exhibited linear response with r2 > 0.99. Limit of detection and quantitation of the later method was determined to be 5.56 μg/ml and 16.86 μg/ml, respectively. In addition to this, a TLC based method has also been developed. The limit of detection of β-ODAP is 0.6μg and for its substrate, L-1,2-diaminopropionic acid is 5μg. Both HPLC and TLC methods were validated by conducting in-vitro bioconversion test to detect the presence of biocatalyst in plant extract. This method is economical, rapid and simple.

Pendrin (Slc26a4) is a Cl(-)/HCO3 (-) exchanger expressed in renal intercalated cells and mediates renal Cl(-) absorption. With pendrin gene ablation, blood pressure and vascular volume fall, which increases plasma renin concentration. However, serum aldosterone does not significantly increase in pendrin-null mice, suggesting that pendrin regulates adrenal zona glomerulosa aldosterone production. Therefore, we examined pendrin expression in the adrenal gland using PCR, immunoblots, and immunohistochemistry. Pendrin protein was detected in adrenal lysates from wild-type but not pendrin-null mice. However, immunohistochemistry and qPCR of microdissected adrenal zones showed that pendrin was expressed in the adrenal medulla, rather than in cortex. Within the adrenal medulla, pendrin localizes to both epinephrine- and norepinephrine-producing chromaffin cells. Therefore, we examined plasma catecholamine concentration and blood pressure in wild-type and pendrin-null mice under basal conditions and then after 5 and 20 min of immobilization stress. Under basal conditions, blood pressure was lower in the mutant than in the wild-type mice, although epinephrine and norepinephrine concentrations were similar. Catecholamine concentration and blood pressure increased markedly in both groups with stress. With 20 min of immobilization stress, epinephrine and norepinephrine concentrations increased more in pendrin-null than in wild-type mice, although stress produced a similar increase in blood pressure in both groups. We conclude that pendrin is expressed in the adrenal medulla, where it blunts stress-induced catecholamine release.

Abstract: In the present study, artificial neural network (ANN) modelling coupled with particle swarm optimization (PSO) algorithm was used to optimize the process variables for enhanced low density polyethylene (LDPE) degradation by Curvularia lunata SG1. In the non-linear ANN model, temperature, pH, contact time and agitation were used as input variables and polyethylene bio-degradation as the output variable. Further, on application of PSO to the ANN model, the optimum values of the process parameters were as follows: pH = 7.6, temperature = 37.97 °C, agitation rate = 190.48 rpm and incubation time = 261.95 days. A comparison between the model results and experimental data gave a high correlation coefficient ([Formula: see text]). Significant enhancement of LDPE bio-degradation using C. lunata SG1by about 48 % was achieved under optimum conditions. Thus, the novelty of the work lies in the application of combination of ANN-PSO as optimization strategy to enhance the bio-degradation of LDPE.

Background: Amylases play a vital role in biotechnological studies and rank an important position in the world enzyme market (25% to 33%). Bioprocess method of amylase production is more effective than the other sources, since the technique is easy, cost effective, fast, and the enzymes of required properties can be procured., Objectives: The current study aimed to report the characteristics of novel amylase producing bacterial strains isolated from Taptapani hot spring, Odisha, India., Materials and Methods: Bacterial strains were isolated by dilution plating method from the water samples collected from Taptapani Hot Spring, Odisha and screened for amylase production through starch hydrolysis. The bacterial isolates were identified morphologically, biochemically, and finally by 16S rDNA profiling., Results: Based on the morphological, physiological, biochemical characteristics and the molecular characterization, the isolates SS1, SS2, and SS3 were identified as Bacillus barbaricus, Aeromonas veroni, and Stenotrophomonas maltophilia, respectively. The approximate molecular weight of enzymes from SS1, SS2, and SS3 strains were 19 kDa, 56 kDa and 49 kDa, respectively., Conclusions: The current report isolates, characterizes, and demonstrates the novel heat-adapted amylase-producing bacteria SS1, SS2 and SS3 from Taptapani hot spring, indicating its potentiality and stability under acidic conditions.

RNA-sequencing (RNA-seq) is a powerful technique to investigate the complexity of gene expression in the human brain. We used RNA-seq to survey the brain transcriptome in high-quality postmortem dorsolateral prefrontal cortex from 11 individuals diagnosed with bipolar disorder (BD) and from 11 age- and gender-matched controls. Deep sequencing was performed, with over 350 million reads per specimen. At a false discovery rate of <5%, we detected five differentially expressed (DE) genes and 12 DE transcripts, most of which have not been previously implicated in BD. Among these, Prominin 1/CD133 and ATP-binding cassette-sub-family G-member2 (ABCG2) have important roles in neuroplasticity. We also show for the first time differential expression of long noncoding RNAs (lncRNAs) in BD. DE transcripts include those of serine/arginine-rich splicing factor 5 (SRSF5) and regulatory factor X4 (RFX4), which along with lncRNAs have a role in mammalian circadian rhythms. The DE genes were significantly enriched for several Gene Ontology categories. Of these, genes involved with GTPase binding were also enriched for BD-associated SNPs from previous genome-wide association studies, suggesting that differential expression of these genes is not simply a consequence of BD or its treatment. Many of these findings were replicated by microarray in an independent sample of 60 cases and controls. These results highlight common pathways for inherited and non-inherited influences on disease risk that may constitute good targets for novel therapies.

Coronary artery calcification (CAC) is a heritable and definitive morphologic marker of atherosclerosis that strongly predicts risk for future cardiovascular events. To search for genes involved in CAC, we used an integrative transcriptomic, genomic, and protein expression strategy by using next-generation DNA sequencing in the discovery phase with follow-up studies using traditional molecular biology and histopathology techniques. RNA sequencing of peripheral blood from a discovery set of CAC cases and controls was used to identify dysregulated genes, which were validated by ClinSeq and Framingham Heart Study data. Only a single gene, TREML4, was upregulated in CAC cases in both studies. Further examination showed that rs2803496 was a TREML4 cis-eQTL and that the minor allele at this locus conferred up to a 6.5-fold increased relative risk of CAC. We characterized human TREML4 and demonstrated by immunohistochemical techniques that it is localized in macrophages surrounding the necrotic core of coronary plaques complicated by calcification (but not in arteries with less advanced disease). Finally, we determined by von Kossa staining that TREML4 colocalizes with areas of microcalcification within coronary plaques. Overall, we present integrative RNA, DNA, and protein evidence implicating TREML4 in coronary artery calcification. Our findings connect multimodal genomics data with a commonly used clinical marker of cardiovascular disease., (Copyright © 2014 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)

Background: Massively-parallel cDNA sequencing (RNA-Seq) is a new technique that holds great promise for cardiovascular genomics. Here, we used RNA-Seq to study the transcriptomes of matched coronary artery disease cases and controls in the ClinSeq® study, using cell lines as tissue surrogates., Results: Lymphoblastoid cell lines (LCLs) from 16 cases and controls representing phenotypic extremes for coronary calcification were cultured and analyzed using RNA-Seq. All cell lines were then independently re-cultured and along with another set of 16 independent cases and controls, were profiled with Affymetrix microarrays to perform a technical validation of the RNA-Seq results. Statistically significant changes (p < 0.05) were detected in 186 transcripts, many of which are expressed at extremely low levels (5-10 copies/cell), which we confirmed through a separate spike-in control RNA-Seq experiment. Next, by fitting a linear model to exon-level RNA-Seq read counts, we detected signals of alternative splicing in 18 transcripts. Finally, we used the RNA-Seq data to identify differential expression (p < 0.0001) in eight previously unannotated regions that may represent novel transcripts. Overall, differentially expressed genes showed strong enrichment (p = 0.0002) for prior association with cardiovascular disease. At the network level, we found evidence for perturbation in pathways involving both cardiovascular system development and function as well as lipid metabolism., Conclusions: We present a pilot study for transcriptome involvement in coronary artery calcification and demonstrate how RNA-Seq analyses using LCLs as a tissue surrogate may yield fruitful results in a clinical sequencing project. In addition to canonical gene expression, we present candidate variants from alternative splicing and novel transcript detection, which have been unexplored in the context of this disease.

Dental impressions, contaminated with saliva, blood, plaque, are potential source of infection. All impressions should be disinfected after their removal from mouth to prevent cross contamination. Different methods have been tried to disinfect the commonly used irreversible hydrocolloid impression material, but they have been shown to influence the dimensional stability and surface detail of the impression which ultimately affects the precision of the final prosthesis. The aim of this study was to evaluate the efficacy of pre-procedural oral prophylaxis and mouthrinses in reducing the overall microbial load intraorally as well as on alginate impression surface. A total of 60 positive cases selected from 100 subjects who were partially edentulous and above 18 years of age and without medical or pharmacotherapy histories were studied over a period of 18 months, from outpatient clinic of Department of Prosthodontics, GNIDSR. Alginate impressions, before and after prophylaxis were examined microbiologically for the persistence of test microorganisms on the untreated (control group) and the impressions made after treatment. The data were statistically analyzed by the Student t test to assess the effectiveness of the procedure and also the comparative effectiveness of oral prophylaxis and commonly used mouthrinses. The results showed that the impressions were safer when made after oral prophylaxis and/or mouthrinses.

In an attempt to screen out cellulase producing bacteria from herbivorous animal fecal matter it was possible to isolate a potent bacterium from cow dung. The bacterium was identified as Bacillus sp. using 16S rDNA based molecular phylogenetic approach. The effect of different agricultural wastes, paper wastes and carboxymethyl cellulose on endoglucanase production was tested and was found to produce maximally at 8% carboxymethyl cellulose. The endoglucanase was precipitated by ammonium sulfate saturation and purified by DEAE- Sepharose column. The purification was achieved 8.5 fold from the crude extract with a yield of 68.1%. The molecular weight of the protein was determined to be 97 kDa by SDS-PAGE. The enzymatic activity was moderately reduced by detergents (SDS, Tween-80), metal ions (MnCl2, ZnCl2) and EDTA. The endoglucanase was stable between pH 5.0 - 9.0 and temperature between 20-70°C with optimal activity at pH 7.0 and temperature 50°C. The apparent Km value of the enzyme for the substrate carboxymethyl cellulose was recorded to be 0.25 mg/ml. The endoglucanase was stable in the presence of commercial detergents such as Ariel, Surf Excel and Tide, indicated might be of potential applications in detergent industry. The enzyme from this strain could also be applied in bioconversion of lignocellulosic biomass into fermentable sugars.

Digitization has become part and parcel of the contemporary prosthodontics with the probability of most of the procedures being based on the digital techniques in near future. Let us think of X-rays or photographs, making impressions, recording jaw movements or fabricating prosthesis, educating and training new dentists or patient motivation for practice build up, all has become digital. CAD-CAM has revolutionized not just the ceramic technology but has also been used for the CAD-CAM implant surgeries, maxillofacial prosthesis and diagnostic splints. Today a practicing dentist needs to be abreast with the latest but with the technology changing so fast, this poses a great challenge. There is endless scope of digitisation and technology in prosthodontics- let it be in the clinical and lab procedures like use of CAD-CAM technology, stereolithography, rapid prototyping, use of virtual articulators and digital face bows, digital radiographs, or in the field of training, education and research by the use of virtual patient programs, dental softwares, optoelectronic recording of jaw motion, digital instron machine, retention testing device, audiovisual aids,… the list will remain endless. The article reviews those various aspects of prosthodontics where digitization has modified the conventional procedures. For discussion they have been considered under the educational aspect, diagnostics, treatment procedures, prosthesis fabrication and lastly the research and futuristic development. The day is not far when remote sensing robotic devices would be performing the restorations under the command and surveillance of the master-the dentist without his immediate presence.

Objective: To identify transcriptomic biomarkers of coronary heart disease (CHD) in 188 cases with CHD and 188 age- and sex-matched controls who were participants in the Framingham Heart Study., Approach and Results: A total of 35 genes were differentially expressed in cases with CHD versus controls at false discovery rate<0.5, including GZMB, TMEM56, and GUK1. Cluster analysis revealed 3 gene clusters associated with CHD, 2 linked to increased erythrocyte production and a third to reduced natural killer and T cell activity in cases with CHD. Exon-level results corroborated and extended the gene-level results. Alternative splicing analysis suggested that GUK1 and 38 other genes were differentially spliced in cases with CHD versus controls. Gene Ontology analysis linked ubiquitination and T-cell-related pathways with CHD., Conclusions: Two bioinformatically defined groups of genes show consistent associations with CHD. Our findings are consistent with the hypotheses that hematopoesis is upregulated in CHD, possibly reflecting a compensatory mechanism, and that innate immune activity is disrupted in CHD or altered by its treatment. Transcriptomic signatures may be useful in identifying pathways associated with CHD and point toward novel therapeutic targets for its treatment and prevention.