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Streptomyces kanasensis ZX01 produces some antibiotics and a glycoprotein with antiviral activity. To further evaluate its biosynthetic potential, here we sequenced the 7,026,279 bp draft genome of S. kanasensis ZX01 and analyzed all identifiable secondary gene clusters for controlling natural products. More than 60 putative clusters were found in S. kanasensis ZX01, the majority of these biosynthetic loci are novel. In addition, the regulators for secondary metabolism in S. kanasensis ZX01 were abundant. The global regulator nsdA not only controls biosynthesis of some antibiotics, but also enhances production of glycoprotein GP-1 with antiviral activity. This study importantly reveals the powerful interplay between genomic analysis and studies of traditional natural product purification/production increasing. [ABSTRACT FROM AUTHOR]

The red/far-red light absorbing photoreceptors phytochromes regulate development and growth and thus play an essential role in optimizing adaptation of the sessile plants to the ever-changing environment. Our understanding of how absorption of a red/far-red photon by phytochromes initiates/modifies diverse physiological responses has been steadily improving. Research performed in the last 5 years has been especially productive and led to significant conceptual changes about the mode of action of these photoreceptors. In this review, we focus on the phytochrome B photoreceptor, the major phytochrome species active in light-grown plants. We discuss how its light-independent inactivation (termed dark/thermal reversion), post-translational modification, including ubiquitination, phosphorylation and sumoylation, as well as heterodimerization with other phytochrome species modify red light-controlled physiological responses. Finally, we discuss how photobiological properties of phytochrome B enable this photoreceptor to function also as a thermosensor. [ABSTRACT FROM AUTHOR]

Land plants possess the ability to sense and respond to far-red light (700-760 nm), which serves as an important environmental cue. Due to the nature of far-red light, it is not absorbed by chlorophyll and thus is enriched in canopy shade and will also penetrate deeper into soil than other visible wavelengths. Far-red light responses include regulation of seed germination, suppression of hypocotyl growth, induction of flowering and accumulation of anthocyanins, which depend on one member of the phytochrome photoreceptor family, phytochrome A (phyA). Here, we review the current understanding of the underlying molecular mechanisms of how plants sense far-red light through phyA and the physiological responses to this light quality. Light-activated phytochromes act on two primary pathways within the nucleus; suppression of the E3 ubiquitin ligase complex CUL4/DDB1COP1/SPA and inactivation of the PHYTOCHROME INTERACTING FACTOR (PIF) family of bHLH transcription factors. These pathways integrate with other signal transduction pathways, including phytohormones, for tissue and developmental stage specific responses. Unlike other phytochromes that mediate red-light responses, phyA is transported from the cytoplasm to the nucleus in far-red light by the shuttle proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). However, additional mechanisms must exist that shift the action of phyA to far-red light; current hypotheses are discussed. [ABSTRACT FROM AUTHOR]

Checkpoint signaling requires two conserved phosphatidylinositol 3-kinase-related protein kinases (PIKKs): ATM and ATR. In budding yeast, Tel1 and Mec1 correspond to ATM and ATR, respectively. The Tel2-Tti1-Tti2 (TTT) complex connects to the Rvb1-Rvb2-Tah1-Pih1 (R2TP) complex for the protein stability of PIKKs; however, TTT-R2TP interaction only partially mediates ATM and ATR protein stabilization. How TTT controls protein stability of ATM and ATR remains to be precisely determined. Here we show that Asa1, like Tel2, plays a major role in stabilization of newly synthesized Mec1 and Tel1 proteins whereas Pih1 contributes to Mec1 and Tel1 stability at high temperatures. Although Asa1 and Pih1 both interact with Tel2, no Asa1-Pih1 interaction is detected. Pih1 is distributed in both the cytoplasm and nucleus wheres Asa1 localizes largely in the cytoplasm. Asa1 and Pih1 are required for proper DNA damage checkpoint signaling. Our findings provide a model in which two different Tel2 pathways promote protein stabilization of Mec1 and Tel1 in budding yeast. [ABSTRACT FROM AUTHOR]

Giant linear plasmids, which replicate independently of the chromosomes, widely exist in actinobacteria. Previous studies mostly focused on the replication and evolution of the linear plasmids or the secondary metabolite gene clusters and the resistance gene clusters therein. However, the relationships of the linear plasmids to the productivities of secondary metabolites have not been studied. In this work, we developed a method to eliminate the indigenous linear plasmid pSHJG1 in Streptomyces hygroscopicus var. jinggangensis, and validamycin A titer increased by 12.5% (from 19.16 ± 1.93 to 21.56 ± 2.25 g/L) in the high-yielding strain TL01 and 43.7% (from 4.67 ± 0.05 to 6.71 ± 0.21 g/L) in the wild-type strain 5008, whereas the cellular growth of the plasmid-cured mutant was reduced. Subsequently, the plasmid-cured mutant was complemented with three structure genes involved in cellular growth in pSHJG1 under the control of a strong PvalA promoter. Among them, the complementation of genes pSHJG1.069 and pSHJG1.072, encoding a putative hydrolase and putative P-loop ATPase, respectively, resulted in the restoration of cellular growth and validamycin A titer. Furthermore, the elimination of indigenous linear plasmid pHZ228 in the candicidin producer Streptomyces sp. FR008 also led to enhanced candicidin production and reduced cellular growth. Because of the wide distribution of indigenous linear plasmids in actinobacteria, the engineering strategy described here could be implemented in a variety of strains for the overproduction of various natural products. [ABSTRACT FROM AUTHOR]

Different configurations of gearbox, generator and power converter exist for offshore wind turbines. This paper investigated the performance of four prominent drive train configurations over a range of sites distinguished by their distance to shore. Failure rate data from onshore and offshore wind turbine populations was used where available or systematically estimated where no data was available. This was inputted along with repair resource requirements to an offshore accessibility and operation and maintenance model to calculate availability and operation and maintenance costs for a baseline wind farm consisting of 100 turbines. The results predicted that turbines with a permanent magnet generator and a fully rated power converter will have a higher availability and lower operation and maintenance costs than turbines with doubly fed induction generators. This held true for all sites in this analysis. It was also predicted that in turbines with a permanent magnet generator, the direct drive configuration has the highest availability and lowest operation and maintenance costs followed by the turbines with two-stage and three-stage gearboxes. Copyright © 2016 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Brain metastases are highly-evolved manifestations of breast cancer arising in a unique microenvironment, giving them exceptional adaptability in the face of new extrinsic pressures. The incidence is rising in line with population ageing, and use of newer therapies that stabilise metastatic disease burden with variable efficacy throughout the body. Historically, there has been a widely-held view that brain metastases do not respond to circulating therapeutics because the blood-brain-barrier (BBB) restricts their uptake. However, emerging data are beginning to paint a more complex picture where the brain acts as a sanctuary for dormant, subclinical proliferations that are initially protected by the BBB, but then exposed to dynamic selection pressures as tumours mature and vascular permeability increases. Here, we review key experimental approaches and landmark studies that have charted the genomic landscape of breast cancer brain metastases. These findings are contextualised with the factors impacting on clonal outgrowth in the brain: intrinsic breast tumour cell capabilities required for brain metastatic fitness, and the neural niche, which is initially hostile to invading cells but then engineered into a tumour-support vehicle by the successful minority. We also discuss how late detection, abnormal vascular perfusion and interstitial fluid dynamics underpin the recalcitrant clinical behaviour of brain metastases, and outline active clinical trials in the context of precision management. [ABSTRACT FROM AUTHOR]

Background: Obtaining accurate estimates of biological or enzymatic reaction rates is critical in understanding the design principles of a network and how biological processes can be experimentally manipulated on demand. In many cases experimental limitations mean that some enzymatic rates cannot be measured directly, requiring mathematical algorithms to estimate them. Here, we describe a methodology that calculates rates at which light-regulated proteins switch between conformational states. We focus our analysis on the phytochrome family of photoreceptors found in cyanobacteria, plants and many optogenetic tools. Phytochrome proteins change between active (PA) and inactive (PI) states at rates that are proportional to photoconversion cross-sections and influenced by light quality, light intensity, thermal reactions and dimerisation. This work presents a method that can accurately calculate these photoconversion cross-sections in the presence of multiple non-light regulated reactions. Results: Our approach to calculating the photoconversion cross-sections comprises three steps: i) calculate the thermal reversion reaction rate(s); ii) develop search spaces from which all possible sets of photoconversion cross-sections exist, and; iii) estimate extinction coefficients that describe our absorption spectra. We confirm that the presented approach yields accurate results through the use of simulated test cases. Our test cases were further expanded to more realistic scenarios where noise, multiple thermal reactions and dimerisation are considered. Finally, we present the photoconversion cross-sections of an Arabidopsis phyB N-terminal fragment commonly used in optogenetic tools. Conclusions: The calculation of photoconversion cross-sections has implications for both photoreceptor and synthetic biologists. Our method allows, for the first time, direct comparisons of photoconversion cross-sections and response speeds of photoreceptors in different cellular environments and synthetic tools. Due to the generality of our procedure, as shown by the application to multiple test cases, the photoconversion cross-sections and quantum yields of any photoreceptor might now, in principle, be obtained. [ABSTRACT FROM AUTHOR]

Different stent structures lead to different deformations of blood vessels, such as different cross-sectional shapes, which further influence the blood flow patterns. In this paper, six non-commercial stents with different link structures called I-, C-, S-, U-, N- and W-types were considered. Their influences on arteries with five different curvatures (i.e., 0, 15, 30, 45 and 60) were studied using finite element method. Four indices including the maximum plastic strain of stents, the rate of expansion, the maximum von Mises stress and the ellipticity of arteries, were compared for all cases. The results showed that the S-type or U-type stents, with larger plastic strain and lower von Mises stress on the arteries, provided the optimal outcome. As the link structures became complex, the arterial expansion increased monotonically, while the ellipticity of arteries showed a decreasing tendency in the vessel models. The present study could be useful for the commercial design and clinic selection of a stent with different link structures for different curved arteries. [ABSTRACT FROM AUTHOR]

The cathepsin family of lysosomal proteases is increasingly being recognized for their altered expression in cancer and role in facilitating tumor progression. The aspartyl protease cathepsin E is overexpressed in several cancers and has been investigated as a biomarker for pancreatic ductal adenocarcinoma (PDAC). Here we show that cathepsin E expression in mouse PDAC tumors is increased by more than 400-fold when compared to healthy pancreatic tissue. Cathepsin E accumulates over the course of disease progression and accounts for more than 3% of the tumor protein in mice with end-stage disease. Through immunoblot analysis we determined that only procathepsin E exists in mouse PDAC tumors and cell lines derived from these tumors. By decreasing the pH, this procathepsion E is converted to the mature form, resulting in an increase in proteolytic activity. Although active site inhibitors can bind procathepsin E, treatment of PDAC mice with the aspartyl protease inhibitor ritonavir did not decrease tumor burden. Lastly, we used multiplex substrate profiling by mass spectrometry to identify two synthetic peptides that are hydrolyzed by procathepsin E near neutral pH. This work represents a comprehensive analysis of procathepsin E in PDAC and could facilitate the development of improved biomarkers for disease detection. [ABSTRACT FROM AUTHOR]

Purpose: 'Big data' are accumulating in a multitude of domains and offer novel opportunities for research. The role of these resources in mental health investigations remains relatively unexplored, although a number of datasets are in use and supporting a range of projects. We sought to review big data resources and their use in mental health research to characterise applications to date and consider directions for innovation in future.Methods: A narrative review.Results: Clear disparities were evident in geographic regions covered and in the disorders and interventions receiving most attention.Discussion: We discuss the strengths and weaknesses of the use of different types of data and the challenges of big data in general. Current research output from big data is still predominantly determined by the information and resources available and there is a need to reverse the situation so that big data platforms are more driven by the needs of clinical services and service users. [ABSTRACT FROM AUTHOR]

The photoreceptor phytochrome A acts as a light-dependent molecular switch and regulates responses initiated by very low fluences of light ( VLFR) and high fluences ( HIR) of far-red light. PhyA is expressed ubiquitously, but how phyA signaling is orchestrated to regulate photomorphogenesis is poorly understood., To address this issue, we generated transgenic Arabidopsis thaliana phyA-201 mutant lines expressing the biologically active phyA- YFP photoreceptor in different tissues, and analyzed the expression of several reporter genes, including ProHY5: HY5- GFP and Pro35S: CFP- PIF1, and various FR- HIR-dependent physiological responses., We show that phyA action in one tissue is critical and sufficient to regulate flowering time and root growth; control of cotyledon and hypocotyl growth requires simultaneous phyA activity in different tissues; and changes detected in the expression of reporters are not restricted to phyA-containing cells., We conclude that FR- HIR-controlled morphogenesis in Arabidopsis is mediated partly by tissue-specific and partly by intercellular signaling initiated by phyA. Intercellular signaling is critical for many FR- HIR induced responses, yet it appears that phyA modulates the abundance and activity of key regulatory transcription factors in a tissue-autonomous fashion. [ABSTRACT FROM AUTHOR]

A simple modular approach is presented which has been directed towards the synthesis of potentially monoanionic NN'N", NN'C, and NN'P pincer-type ligands. These pincers incorporate an amide functionality derived from the skeletal structure of readily available 2-(2-aminophenyl)-4,5-dioxooxazoles. All of the pincers are synthesized in moderate yields (up to 74%) and are characterised by nuclear magnetic spectroscopy (NMR), elemental analyses, and infrared (IR) spectroscopy. X-ray crystallography is also performed on the chiral and achiral alkyl halide precursors and on an oxide derivative of a pincer with a NN'Patom donor set. A palladium derivative of one of the NN'N"-pincers is shown to be an active catalyst for the addition of an allyl group to various benzaldehydes using n-Bu3Sn(allyl) as allyl source. [ABSTRACT FROM AUTHOR]

Phytochromes recognize light signals and control diverse developmental processes. In rice, all three phytochrome genes- OsphyA, OsphyB, and OsphyC-are involved in regulating flowering time. We investigated the role of OsPhyA by comparing the osphyA osphyB double mutant to an osphyB single mutant. Plants of the double mutant flowered later than the single under short days (SD) but bolted earlier under long days (LD). Under SD, this delayed-flowering phenotype was primarily due to the decreased expression of Oryza sativa GIGANTEA ( OsGI), which controls three flowering activators: Heading date 1 ( Hd1), OsMADS51, and Oryza sativa Indeterminate 1 ( OsId1). Under LD, although the expression of several repressors, e.g., Hd1, Oryza sativa CONSTANS- like 4 ( OsCOL4), and AP2 genes, was affected in the double mutant, that of Grain number, plant height and heading date 7 ( Ghd7) was the most significantly reduced. These results indicated that OsPhyA influences flowering time mainly by affecting the expression of OsGI under SD and Ghd7 under LD when phytochrome B is absent. We also demonstrated that far-red light delays flowering time via both OsPhyA and OsPhyB. [ABSTRACT FROM AUTHOR]

Hypocotyl phototropism of etiolated Arabidopsis seedlings is primarily mediated by the blue-light receptor kinase phototropin 1 (phot1). Phot1-mediated curvature to continuous unilateral blue light irradiation (0.5µmolm-2 s-1) is enhanced by overhead pre-treatment with red light (20µmol m-2 s-1 for 15 min) through the action of phytochrome (phyA). Here, we show that pre-treatment with blue light is equally as effective in eliciting phototropic enhancement and is dependent on phyA. Although blue light pre-treatment was sufficient to activate early phot1 signaling events, phot1 autophosphorylation in vivo was not found to be saturated, as assessed by subsequently measuring phot1 kinase activity in vitro. However, enhancement effects by red and blue light pre-treatment were not observed at higher intensities of phototropic stimulation (10&3181;mol m-2 s-1). Phototropic enhancement by red and blue light pre-treatments to 0.5µmol m-2 s-1 unilateral blue light irradiation was also lacking in transgenic Arabidopsis where PHOT1 expression was restricted to the epidermis. Together, these findings indicate that phyA-mediated effects on phot1 signaling are restricted to low intensities of phototropic stimulation and originate from tissues other than the epidermis. [ABSTRACT FROM AUTHOR]

The review compiles the strategies and methods of development of aminopyrimidine derivatives as targeted antitumor pharmaceuticals. The advances in organic and heterocyclic chemistry are considered in the targeted synthesis of aminopyrimidine derivatives whose series contains the most demanded and efficient antitrumor pharmaceuticals. The problems of preparation of compounds with multikinase activity profile and the construction of chimeric molecules are discussed. [ABSTRACT FROM AUTHOR]

The use of condition monitoring systems on offshore wind turbines has increased dramatically in recent times. However, their use is mostly restricted to vibration based monitoring systems for the gearbox, generator and drive train. A survey of commercially available condition monitoring systems and their associated costs has been completed for the blades, drive train, tower and foundation. This paper considers what value can be obtained from integrating these additional systems into the maintenance plan. This is achieved by running simulations on an operations and maintenance model for a wind farm over a 20 year life cycle. The model uses Hidden Markov Models to represent both the actual system state and the observed condition monitoring state. The CM systems are modelled to include reduced failure types, false alarms, detection rates and 6 month failure warnings. The costs for system failures are derived, as are possible reductions in costs due to early detection. The detection capabilities of the CM systems are investigated and the effects on operational costs are examined. Likewise, the number of failures detected 6 months in advance by the CM systems is modified and the costs reported. [ABSTRACT FROM AUTHOR]

We have assessed copy number variation (CNV) in the male-specific part of the human Y chromosome discovered by array comparative genomic hybridization (array-CGH) in 411 apparently healthy UK males, and validated the findings using SNP genotype intensity data available for 149 of them. After manual curation taking account of the complex duplicated structure of Y-chromosomal sequences, we discovered 22 curated CNV events considered validated or likely, mean 0.93 (range 0-4) per individual. 16 of these were novel. Curated CNV events ranged in size from <1 kb to >3 Mb, and in frequency from 1/411 to 107/411. Of the 24 protein-coding genes or gene families tested, nine showed CNV. These included a large duplication encompassing the AMELY and TBL1Y genes that probably has no phenotypic effect, partial deletions of the TSPY cluster and AZFc region that may influence spermatogenesis, and other variants with unknown functional implications, including abundant variation in the number of RBMY genes and/or pseudogenes, and a novel complex duplication of two segments overlapping the AZFa region and including the 3′ end of the UTY gene. [ABSTRACT FROM AUTHOR]

Aquatic ecosystems represent important vehicles for the dissemination of antibiotic resistant bacteria and antibiotic resistance genes. Of particular interest are methicillin-resistant staphylococci (MRS) harboring mecA gene that confers their resistance to β-lactams. Therefore, in this study, water samples collected from different locations of a river impacted by surrounding facilities and domestic effluents were analyzed to learn more about the occurrence of MRS and mecA gene. Out of 290, 12 surface water isolates displayed resistance to both cefoxitin and oxacillin antibiotics. Resistant staphylococcal and non-staphylococcal isolates, identified by 16S rRNA sequencing, were found to harbor mecA gene. The phylogenetic tree of partial mecA sequences obtained from staphylococcal and non-staphylococcal isolates showed sequence similarity values of 8 %-100 %. Surface water bodies receive contaminated waters via runoff, effluents from industrial, agricultural, and municipal discharges. Therefore, surface waters are not only hot spots for mecA harboring staphylococcal isolates but also non-staphylococcal isolates and require special scientific consideration. [ABSTRACT FROM AUTHOR]

The article presents a study on the availability of dementia-related services in Saskatchewan which are analyzed using the key attributes of primary health care including comprehensiveness, population orientation and coordinated care. Dementia-specific services such as health promotion, counseling and transportation are found to be unavailable in most communities. Limited availability of specific services for rural residents with dementia is also noted.

In the fission yeast Schizosaccharomyces pombe, sup9 mutations can suppress the termination of translation at nonsense (stop) codons. We localized sup9 physically to the spctrnaser.11 locus and confirmed that one allele ( sup9- UGA) alters the anticodon of a serine tRNA. We also found that another purported allele is not allelic. Instead, strains with that suppressor (renamed sup35- F592S) have a single base pair substitution (T1775C) that introduces an amino acid substitution in the Sup35 protein (Sup35-F592S). Reduced functionality of Sup35 (eRF3), the ubiquitous guanine nucleotide-responsive translation release factor of eukaryotes, increases read-through of stop codons. Tetrad dissection revealed that suppression is tightly linked to (inseparable from) the sup35- F592S mutation and that there are no additional extragenic modifiers. The Mendelian inheritance indicates that the Sup35-F592S protein does not adopt an infectious amyloid state ([ PSI] prion) to affect suppression, consistent with recent evidence that fission yeast Sup35 does not form prions. We also report that sup9- UGA and sup35- F592S exhibit different strengths of suppression for opal stop codons of ade6- M26 and ade6- M375. We discuss possible mechanisms for the variation in suppressibility exhibited by the two alleles. [ABSTRACT FROM AUTHOR]

The growth of the avian embryo is paralleled by an exponential increase in the rate of whole-embryonic oxygen consumption, which potentially increases oxidative damage.Age-related patterns of tissue lipid peroxidation were characterised in brain, liver and heart tissue of developing Japanese quail (Coturnix japonica) embryos between 9 and 15 d of age, over which embryo mass increased by a factor of 6. Lipid peroxidation was quantified in each tissue by spectrophotometric measurement of malondialdehyde using the thiobarbituric acid reactive substances assay.In all tissues, lipid peroxidation increased greatly as development proceeded. Concentrations of malondialdehyde increased in parallel with the cumulative amount of oxygen consumed by the developing embryo consistent with the hypothesis that oxidative stress results from the production of free radicals due to oxidative metabolism.This study describes in vivo oxidative stress in developing avian embryos and suggests that rates of embryonic growth, oxidative metabolism and oxidative damage likely vary in parallel. [ABSTRACT FROM AUTHOR]

A phenomenon of ascospore death was observed in a number of Schizosaccharomyces pombe interstrain hybrids. Meiotic recombination of the control parental auxotrophic markers was, however, observed in random ascospore analysis. Genetic and molecular biological data indicated existence of at least geographical divergence of the genomes in Sch. pombe populations. Classification of the genus, species, and varieties of these yeasts is discussed. [ABSTRACT FROM AUTHOR]

Reference genes presenting stable expression profiles over a wide variety of conditions are required in relative expression studies of specific bacterial genes by quantitative reverse transcription PCR (RT-qPCR). High-throughput sequencing of bacterial transcriptomes using the RNA-seq methodology now provides a wealth of data that may be searched for identification of the most stably expressed genes of a given bacterium. Herein, we searched a RNA-seq dataset from various experiments with the pathogenic bacterium Corynebacterium pseudotuberculosis, grown under different stress conditions, in order to select appropriate candidate reference genes for this species. Nineteen genes involved in maintenance of basic cellular functions, so-called housekeeping genes, were chosen for study and their expression profiles in C. pseudotuberculosis were evaluated throughout all growth conditions. Eight of these genes ( atpA, dnaG, efp, fusA, gyrA, gyrB, rpoB, and rpoC), mostly participating in DNA replication and transcription, matched the defined criteria to be included as candidate reference genes. Transcriptional levels of these genes were quantified by RT-qPCR assays after growth of C. pseudotuberculosis under two additional conditions. Expression stability analysis by NormFinder indicated the combination of genes encoding DNA gyrase subunit A ( gyrA) and elongation factor P ( fusA) as the most suitable for normalization of RT-qPCR studies in C. pseudotuberculosis. [ABSTRACT FROM AUTHOR]

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Background: Prophages, integral components of many bacterial genomes, play significant roles in cognate host bacteria, such as virulence, toxin biosynthesis and secretion, fitness cost, genomic variations, and evolution. Many prophages and prophage-like elements present in sequenced bacterial genomes, such as Bifidobacteria, Lactococcus and Streptococcus, have been described. However, information for the prophage of Mycobacterium remains poorly defined. Results: In this study, based on the search of the complete genome database from GenBank, the Whole Genome Shotgun (WGS) databases, and some published literatures, thirty-three prophages were described in detail. Eleven of them were full-length prophages, and others were prophage-like elements. Eleven prophages were firstly revealed. They were phiMAV_1, phiMAV_2, phiMmcs_1, phiMmcs_2, phiMkms_1, phiMkms_2, phiBN42_1, phiBN44_1, phiMCAN_1, phiMycsm_1, and phiW7S_1. Their genomes and gene contents were firstly analyzed. Furthermore, comparative genomics analyses among mycobacterioprophages showed that full-length prophage phi172_2 belonged to mycobacteriophage Cluster A and the phiMmcs_1, phiMkms_1, phiBN44_1, and phiMCAN_1 shared high homology and could be classified into one group. Conclusions: To our knowledge, this is the first systematic characterization of mycobacterioprophages, their genomic organization and phylogeny. This information will afford more understanding of the biology of Mycobacterium. [ABSTRACT FROM AUTHOR]

Natural product discovery is currently undergoing a transformation from a phenotype-driven field to a genotype-driven one. The increasing availability of genome sequences, coupled with improved techniques for identifying biosynthetic gene clusters, has revealed that secondary metabolomes are strikingly vaster than previously thought. New approaches to correlate biosynthetic gene clusters with the compounds they produce have facilitated the production and isolation of a rapidly growing collection of what we refer to as 'reverse-discovered' natural products, in analogy to reverse genetics. In this review, we present an extensive list of reverse-discovered natural products and discuss seven important lessons for natural product discovery by genome-guided methods: structure prediction, accurate annotation, continued study of model organisms, avoiding genome-size bias, genetic manipulation, heterologous expression, and potential engineering of natural product analogs. [ABSTRACT FROM AUTHOR]

Lymphoid organs are meeting zones where lymphocytes come together and encounter antigens present in the blood and lymph or as delivered by cells migrating from the draining tissue bed. The exquisite efficiency of this process relies heavily on highly specialized anatomy to direct and position the various players. Gated entry and exit control access to these theaters and reticular networks and associated chemokines guide cells into the proper sections. Lymphoid tissues are remarkably plastic, being able to expand dramatically and then involute upon resolution of the danger. All of the reticular scaffolds and vascular and lymphatic components adapt accordingly. As such, the lymph node (LN) is a wonderful example of a physiologic remodeling process and is potentially a guide to study such elements in pathological settings such as fibrosis, chronic infection, and tumor metastasis. The lymphotoxin/LIGHT axis delivers critical differentiation signals that direct and hone differentiation of both reticular networks and the vasculature. Considerable progress has been made recently in understanding the mesenchymal differentiation pathways leading to these specialized networks and in the remodeling that occurs in reactive LNs. In this article, we will review some new advances in the area in terms of developmental, differentiation, and maintenance events mediated by this axis. [ABSTRACT FROM AUTHOR]

Chronic liver diseases (CLD) such as hepatitis B and C virus infection, alcoholic liver disease, and non-alcoholic steatohepatitis are associated with hepatocellular necrosis, continual inflammation, and hepatic fibrosis. The induced microenvironment triggers the activation of liver-resident progenitor cells (LPCs) while hepatocyte replication is inhibited. In the early injury stages, LPCs regenerate the liver by proliferation, migration to sites of injury, and differentiation into functional biliary epithelial cells or hepatocytes. However, when this process becomes dysregulated,wound healing can progress to pathological fibrosis, cirrhosis, and eventually hepatocellular carcinoma. The other key mediators in the pathogenesis of progressive CLD are fibrosis-driving, activated hepatic stellate cells (HSCs) that usually proliferate in very close spatial association with LPCs. Recent studies from our group and others have suggested the potential for cytokine and chemokine cross-talk between LPCs and HSCs, which is mainly driven by the tumor necrosis factor (TNF) family members, TNF-like weak inducer of apoptosis (TWEAK) and lymphotoxin-β, potentially dictating the pathological outcomes of chronic liver injury. [ABSTRACT FROM AUTHOR]

The objectives of this work using Phaseolus vulgaris were to examine whether the light spectrum incident on mature primary leaves ( PLs) is related to leaf-to-leaf systemic regulation of developing trifoliate leaves ( TLs) in photosynthetic characteristics, and to investigate the relative importance of spectrum and photosynthetic photon flux density ( PPFD) in light-induced systemic regulation. Systemic regulation was induced by altering PPFD and the spectrum of light incident on PLs using a shading treatment and lighting treatments including either white, blue, green or red light-emitting diodes ( LEDs). Photosynthetic characteristics were evaluated by measuring the light-limited and light-saturated net photosynthetic rates and the amounts of nitrogen ( N), chlorophyll ( Chl) and ribulose-1,5-bisphosphate carboxylase/oxygenase ( Rubisco; EC 4.1.1.39). Shading treatment on PLs decreased the amounts of N, Chl and Rubisco of TLs and tended to decrease the photosynthetic rates. However, we observed no systemic effects induced by the light spectrum on PLs in this study, except that a higher amount of Rubisco of TLs was observed when the PLs were irradiated with blue LEDs. Our results imply that photoreceptors in mature leaves have little influence on photosynthetic rates and amounts of N and Chl of developing leaves through systemic regulation, although the possibility of the action of blue light irradiation on the amount of Rubisco cannot be ruled out. Based on these results, we concluded that the light spectrum incident on mature leaves has little systemic effect on developing leaves in terms of photosynthetic characteristics and that the light-induced systemic regulation was largely accounted for by PPFD. [ABSTRACT FROM AUTHOR]

Phototropism, or the differential cell elongation exhibited by a plant organ in response to directional blue light, provides the plant with a means to optimize photosynthetic light capture in the aerial portion and water and nutrient acquisition in the roots. Tremendous advances have been made in our understanding of the molecular, biochemical, and cellular bases of phototropism in recent years. Six photoreceptors and their associated signaling pathways have been linked to phototropic responses under various conditions. Primary detection of directional light occurs at the plasma membrane, whereas secondary modulatory photoreception occurs in the cytoplasm and nucleus. Intracellular responses to light cues are processed to regulate cell-to-cell movement of auxin to allow establishment of a trans-organ gradient of the hormone. Photosignaling also impinges on the transcriptional regulation response established as a result of changes in local auxin concentrations. Three additional phytohormone signaling pathways have also been shown to influence phototropic responsiveness, and these pathways are influenced by the photoreceptor signaling as well. Here, we will discuss this complex dance of intra- and intercellular responses that are regulated by these many systems to give rise to a rapid and robust adaptation response observed as organ bending. [ABSTRACT FROM AUTHOR]