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Ribosome biogenesis is a fundamental and highly orchestrated process that involves hundreds of ribosome biogenesis factors. Despite advances that have been made in yeast, the molecular mechanism of ribosome biogenesis remains largely unknown in plants. We uncovered a WD40 protein, Shrunken and Embryo Defective Kernel 1 (SHREK1), and showed that it plays a crucial role in ribosome biogenesis and kernel development in maize (Zea mays). The shrek1 mutant shows an aborted embryo and underdeveloped endosperm and embryo-lethal in maize. SHREK1 localizes mainly to the nucleolus and accumulates to high levels in the seed. Depleting SHREK1 perturbs pre-rRNA processing and causes imbalanced profiles of mature rRNA and ribosome. The expression pattern of ribosomal-related genes is significantly altered in shrek1. Like its yeast (Saccharomyces cerevisiae) ortholog Periodic tryptophan protein 1 (PWP1), SHREK1 physically interacts with ribosomal protein ZmRPL7a, a transient component of the PWP1-subcomplex involved in pre-rRNA processing in yeast. Additionally, SHREK1 may assist in the A3 cleavage of the pre-rRNA in maize by interacting with the nucleolar protein ZmPOP4, a maize homolog of the yeast RNase mitochondrial RNA-processing complex subunit. Overall, our work demonstrates a vital role of SHREK1 in pre-60S ribosome maturation, and reveals that impaired ribosome function accounts for the embryo lethality in shrek1. [ABSTRACT FROM AUTHOR]

WRINKLED1 (WRI1) is a transcriptional activator that binds to a conserved sequence (designated as AW box) boxes in the promoters of many genes from central metabolism and fatty acid (FA) synthesis, resulting in their transcription. BIOTIN ATTACHMENT DOMAIN-CONTAINING (BADC) proteins lack a biotin-attachment domain and are therefore inactive, but in the presence of excess FA, BADC1 and BADC3 are primarily responsible for the observed long-term irreversible inhibition of ACETYL-COA CARBOXYLASE, and consequently FA synthesis. Here, we tested the interaction of WRI1 with BADC genes in Arabidopsis (Arabidopsis thaliana) and found purified WRI1 bound with high affinity to canonical AW boxes from the promoters of all three BADC genes. Consistent with this observation, both expression of BADC1, BADC2, and BADC3 genes and BADC1 protein levels were reduced in wri1-1 relative to the wild type, and elevated upon WRI1 overexpression. The double mutant badc1 badc2 phenocopied wri1-1 with respect to both reduction in root length and elevation of indole-3-acetic acid-Asp levels relative to the wild type. Overexpression of BADC1 in wri1-1 decreased indole-3-acetic acid-Asp content and partially rescued its short-root phenotype, demonstrating a role for BADCs in seedling establishment. That WRI1 positively regulates genes encoding both FA synthesis and BADC proteins (i.e. conditional inhibitors of FA synthesis), represents a coordinated mechanism to achieve lipid homeostasis in which plants couple the transcription of their FA synthetic capacity with their capacity to biochemically downregulate it. [ABSTRACT FROM AUTHOR]

The first committed step in fatty acid synthesis is mediated by acetyl-CoA carboxylase (ACCase), a biotin-dependent enzyme that carboxylates acetyl-CoA to produce malonyl-CoA. ACCase can be feedback regulated by short-term or long-term exposure to fatty acids in the form of Tween 80 (predominantly containing oleic acid), which results in reversible or irreversible ACCase inhibition, respectively. Biotin attachment domain-containing (BADC) proteins are inactive analogs of biotin carboxyl transfer proteins that lack biotin, and their incorporation into ACCase down-regulates its activity by displacing active (biotin-containing) biotin carboxyltransferase protein subunits. Arabidopsis (Arabidopsis thaliana) lines containing T-DNA insertions in BADC1, BADC2, and BADC3 were used to generate badc1 badc2 and badc1 badc3 double mutants. The badc1 badc3 mutant exhibited normal growth and development; however, ACCase activity was 26% higher in badc1 badc3 and its seeds contained 30.1% more fatty acids and 32.6% more triacylgycerol relative to wild-type plants. To assess whether BADC contributes to the irreversible phase of ACCase inhibition, cell suspension cultures were generated from the leaves of badc1 badc3 and wild-type plants and treated with 10 mm Tween 80. Reversible ACCase inhibition was similar in badc1 badc3 and wild-type cultures after 2 d of Tween 80 treatment, but irreversible inhibition was reduced by 50% in badc1 badc3 relative to wild-type plants following 4 d of Tween 80 treatment. In this study, we present evidence for two important homeostatic roles for BADC proteins in down-regulating ACCase activity: by acting during normal growth and development and by contributing to its long-term irreversible feedback inhibition resulting from the oversupply of fatty acids. [ABSTRACT FROM AUTHOR]

In cotton, the formation of fruiting branches affects both plant architecture and fiber yield. Here, we report map-based cloning of the axillary flowering mutation gene (GbAF) that causes bolls to be borne directly on the main plant stem in Gossypium barbadense, and of the clustered boll mutation gene (cl1) in G. hirsutum. Both mutant alleles were found to represent point mutations at the Cl1 locus. Therefore, we propose that the GbAF mutation be referred to as cl1b. These Cl1 loci correspond to homologs of tomato SELF-PRUNING (SP), i.e. Gossypium spp. SP (GoSP) genes. In tetraploid cottons, single monogenic mutation of either duplicate GoSP gene (one in the A and one in the D subgenome) is associated with the axillary cluster flowering phenotype, although the shoot-indeterminate state of the inflorescence is maintained. By contrast, silencing of both GoSPs leads to the termination of flowering or determinate plants. The architecture of axillary flowering cotton allows higher planting density, contributing to increased fiber yield. Taken together the results provide new insights into the underlying mechanism of branching in cotton species, and characterization of GoSP genes may promote the development of compact cultivars to increase global cotton production. [ABSTRACT FROM AUTHOR]

Photosynthetically derived sugar provides carbon skeletons for lipid biosynthesis. We used mutants of Arabidopsis (Arabidopsis thaliana) and the expression of oleogenic factors to investigate relationships among sugar availability, lipid synthesis, and the accumulation of triacylglycerol (TAG) in leaf tissue. The adg1 mutation disables the small subunit of ADP-glucose pyrophosphorylase, the first step in starch synthesis, and the suc2 mutation disables a sucrose/proton symporter that facilitates sucrose loading from leaves into phloem. The adg1suc2 double mutant increases glucose plus sucrose content in leaves 80-fold relative to the wild type, total fatty acid (FA) content 1.8-fold to 8.3% dry weight, and TAG more than 10-fold to 1.2% dry weight. The WRINKLED1 transcription factor also accumulates to higher levels in these leaves, and the rate of FA synthesis increases by 58%. Adding tt4, which disables chalcone synthase, had little effect, but adding the tgd1 mutation, which disables an importer of lipids into plastids to create adg1suc2tt4tgd1, increased total leaf FA to 13.5% dry weight and TAG to 3.8% dry weight, demonstrating a synergistic effect upon combining these mutations. Combining adg1suc2 with the sdp1 mutation, deficient in the predominant TAG lipase, had little effect on total FA content but increased the TAG accumulation by 66% to 2% dry weight. Expression of the WRINKLED1 transcription factor, along with DIACYLGLYCEROL ACYLTRANSFERASE1 and the OLEOSIN1 oil body-associated protein, in the adg1suc2 mutant doubled leaf FA content and increased TAG content to 2.3% dry weight, a level 4.6-fold higher than that resulting from expression of the same factors in the wild type. [ABSTRACT FROM AUTHOR]

In this study, we modelled fishery observer data to compare methods of identifying community structure using cluster analyses to determine stratifications and probabilistic models for examining species co-occurrence in the Gulf of Mexico deepwater reef fish fishery. Comparing cluster analysis methods, the correlation measure of dissimilarity in combination with average agglomerative linkage was the most efficient method for determining species relationships using simulated random species as a comparison tool. Cluster analysis revealed distinct species stratifications and in combination with multiscale bootstrapping generated probabilities indicating the strength of stratifications in the fishery. A more parsimonious approach with probabilistic models was also developed to quantify pairwise species co-occurrence as random, positive, or negative based on the observed vs. expected fishing sets with co-occurrence. For the most common species captured, the probabilistic models predicted positive or negative co-occurrence between 84.2% of the pairwise combinations examined. These methods provide fishery managers tools for determining multispecies quota allocations and offer insights into other bycatch species of interest. [ABSTRACT FROM AUTHOR]

Background: Black shank is a severe plant disease caused by the soil-borne pathogen Phytophthora nicotianae. Two physiological races of, races 0 and 1, are predominantly observed in cultivated tobacco fields around P. nicotianae the world. Race 0 has been reported to be more aggressive, having a shorter incubation period, and causing worse root rot symptoms, while race 1 causes more severe necrosis. The molecular mechanisms underlying the difference in virulence between race 0 and 1 remain elusive. Findings: We assembled and annotated the genomes of P. nicotianae races 0 and 1, which were obtained by a combination of PacBio single-molecular real-time sequencing and second-generation sequencing (both HiSeq and MiSeq platforms). Gene family analysis revealed a highly expanded ATP-binding cassette transporter gene family in P. nicotianae. Specifically, more RxLR effector genes were found in the genome of race 0 than in that of race 1. In addition, RxLR effector genes were found to be mainly distributed in gene-sparse, repeat-rich regions of the P. nicotianae genome. Conclusions: These results provide not only high quality reference genomes of P. nicotianae, but also insights into the infection mechanisms of and its co-evolution with the host plant. They also reveal insights into the P. nicotianae difference in virulence between the two physiological races. [ABSTRACT FROM AUTHOR]

Socially-controlled functional sex change in fishes is a dramatic example of adaptive reproductive plasticity. Functional gonadal sex change can occur within a week while behavioral sex change can begin within minutes. Significant progress has been made in understanding the neuroendocrine bases of this phenomenon at both the gonadal and the neurobiological levels, but a detailed mechanistic understanding remains elusive. We are working with sex-changing wrasses to identify evolutionarily-conserved neuroendocrine pathways underlying this reproductive adaptation. One key model is the bluehead wrasse (Thalassoma bifasciatum), in which sex change is well studied at the behavioral, ecological, and neuroendocrine levels. Bluehead wrasses show rapid increases in aggressive and courtship behaviors with sex change that do not depend on the presence of gonads. The display of male-typical behavior is correlated with the expression of arginine vasotocin, and experiments support a role for this neuropeptide. Estrogen synthesis is also critical in the process. Female bluehead wrasses have higher abundance of aromatase mRNA in the brain and gonads, and estrogen implants block behavioral sex change. While established methods have advanced our understanding of sex change, a full understanding will require new approaches and perspectives. First, contributions of other neuroendocrine systems should be better characterized, particularly glucocorticoid and thyroid signaling. Second, advances in genomics for non-traditional model species should allow conserved mechanisms to be identified with a key next-step being manipulative tests of these mechanisms. Finally, advances in genomics now also allow study of the role of epigenetic modifications and other regulatory mechanisms in the dramatic alterations across the sex-change process. [ABSTRACT FROM AUTHOR]

Summary: Accurate prediction of binding free energy is of particular importance to computational biology and structure-based drug design. Among those methods for binding affinity predictions, the end-point approaches, such as MM/PBSA and LIE, have been widely used because they can achieve a good balance between prediction accuracy and computational cost. Here we present an easy-to-use pipeline tool named Calculation of Free Energy (CaFE) to conduct MM/PBSA and LIE calculations. Powered by the VMD and NAMD programs, CaFE is able to handle numerous static coordinate and molecular dynamics trajectory file formats generated by different molecular simulation packages and supports various force field parameters. [ABSTRACT FROM AUTHOR]

BACKGROUND: Cytoplasmic defects are thought to cause aneuploidies in oocytes and embryos and oocyte reconstruction by germinal vesicle (GV) transfer may circumvent such defects. In mice reconstructed oocytes undergo meiosis and fertilize normally, but early embryonic development is compromised if their ooplasm matured in vitro. This study employs sequential MII spindle and/or pronucleus (PN) transfer to assess the embryonic potential of MII nuclei that form following GV transfer. METHODS AND RESULTS: Mouse embryos generated by these procedures were transferred to the oviducts of pseudopregnant mice to monitor pregnancy outcome. Following GV transfer, the resultant metaphase II (MII) nuclei were activated either in situ or transferred and activated in ooplasts from in-vivo matured oocytes. When exchanged with the female PN of a fertilized zygote, only the PNs that developed in in-vivo matured ooplasts generated live offspring. Viable offspring also resulted when MII nuclei were transferred to in-vivo matured ooplasts and fertilized by insemination with sperm or by artificial activation and male PN transfer. Significantly, the offspring displayed normal fertility as adults. CONCLUSION: This report of live births following GV transfer in mice illustrates the importance of the maturational history of the ooplasm at PN formation for normal embryonic and fetal development. [ABSTRACT FROM AUTHOR]

Oral fluid (OF) is a valuable specimen for driving under the influence of drugs (DUID) applications. This study demonstrates the implementation of the first comprehensive OF drug testing program in the United States, including approved roadside screening OF devices for law enforcement and validated liquid chromatography–tandem mass spectrometry (LC–MS-MS) confirmation methods. Three roadside OF screening devices were evaluated: the Dräger DrugTest® 5000, Abbott SoToxa®, and Randox Evidence MultiSTAT™. Two qualitative LC–MS-MS confirmation methods were validated per ASB Standard 036. The first method utilized an automated dispersive pipette extraction extraction using Integra and Hamilton STARlet platforms for drugs of abuse. The second method used a liquid–liquid extraction to detect cannabinoids. The prevalence of drugs in blood and OF was monitored over 5 years of casework. Calibration curves were analyzed with each batch to monitor OF concentrations for research purposes. Three roadside OF screening devices were deemed fit for purpose. Devices demonstrated appropriate sensitivity, specificity, positive and negative predictive values, and accuracy above 80% for targeted drugs except for benzodiazepines (DrugTest® 5000) and amphetamine (SoToxa®). The validated LC–MS-MS OF confirmation methods met the National Safety Council-recommended cutoffs for 18/21 (86%) of the targets. Over 5 years of casework, THC and cocaine were detected at a positivity rate of 90% and 97% in OF versus 75% and 44% in blood, respectively. OF:blood ratios exceeded unity for parent drugs. Median concentrations of THC in OF and blood were 31 and 3.5 ng/mL, respectively. OF is a viable alternative or supplemental specimen for DUID investigations. Collecting OF close to the driving event increases the opportunity to identify pharmacologically active substances, and when combined with blood analysis results, an elevated OF:blood ratio provides valuable information for DUID investigation purposes. [ABSTRACT FROM AUTHOR]

Plant regeneration is fundamental to basic research and agricultural applications. The regeneration capacity of plants varies largely in different genotypes, but the reason for this variation remains elusive. Here, we identified a novel thioredoxin DCC1 in determining the capacity of shoot regeneration among Arabidopsis (Arabidopsis thaliana) natural variation. Loss of function of DCC1 resulted in inhibited shoot regeneration. DCC1 was expressed mainly in the inner tissues of the callus and encoded a functional thioredoxin that was localized in the mitochondria. DCC1 protein interacted directly with CARBONIC ANHYDRASE2 (CA2), which is an essential subunit of the respiratory chain NADH dehydrogenase complex (Complex I). DCC1 regulated Complex I activity via redox modification of CA2 protein. Mutation of DCC1 or CA2 led to reduced Complex I activity and triggered mitochondrial reactive oxygen species (ROS) production. The increased ROS level regulated shoot regeneration by repressing expression of the genes involved in multiple pathways. Furthermore, linkage disequilibrium analysis indicated that DCC1 was a major determinant of the natural variation in shoot regeneration among Arabidopsis ecotypes. Thus, our study uncovers a novel regulatory mechanism by which thioredoxin-dependent redox modification regulates de novo shoot initiation via the modulation of ROS homeostasis and provides new insights into improving the capacity of plant regeneration. [ABSTRACT FROM AUTHOR]

Pseudocalanus are the numerically dominant calanoid species in coastal subarctic Pacific waters. We examined their juvenile growth rates, and explored their relationships to temperature, chlorophyll a and body size for Pseudocalanus spp. from 2002 to 2004 in the northern Gulf of Alaska. Generally, the monthly mean growth rates increased from 0.049 ± 0.007(SE) day−1 in March to 0.095 ± 0.016 day−1 in August, declining slightly to 0.074 ± 0.009 day−1 in October. Typically, growth rates at most stations were around 0.05 day−1, with no consistent or significant pattern between stations. After standardization to 5 and 10°C, the mean growth rates were 0.045 ± 0.002 day−1 and 0.075 ± 0.004 day−1 respectively, with growth rate decreasing with increasing development stage. Unlike other local calanoid copepod species, Pseudocalanus species tend to be more temperature-dependent than food-dependent, with composite statistical models describing at most 30% of the observed variability in growth rate. Interestingly, development time was comparable to other co-occurring calanoid copepods; however, growth rates of Pseudocalanus spp. were considerably lower. We demonstrate this with a new multi-species model that describes the growth rates of other egg-scattering copepods in this ecosystem, but to which Pseudocalanus does not fit. Thus, the egg-carrying Pseudocalanus species appear to employ a life history strategy optimized for slow growth at low chlorophyll that keeps individuals relatively small, and may therefore reduce visual predation upon them. [ABSTRACT FROM AUTHOR]

The juvenile growth rates and development times of subarctic Calanus marshallae and temperate/sub-tropical C. pacificus were investigated during nine cruises (May through October, 2001–04) in the northern Gulf of Alaska. The artificial cohort method based on a length-weight regression was used for growth estimates and the reciprocal of the molting rate for developmental time. The copepodite stage duration ranged from 3 to 16 days for C. marshallae (C1–C4) and 3–23 days for C. pacificus (C1–C5). Seasonally, copepodid growth rates increased from May to October, ranging between 0.055 and 0.291 day−1 (mean ± SE: 0.176 ± 0.008 day−1) for C. marshallae, while growth rates increased from August to October between 0.018 and 0.296 day−1 (mean ± SE: 0.142 ± 0.016 day−1) for C. pacificus. After standardization to 5°C (Q10 of 2.7), growth rate averaged 0.118 ± 0.007 day−1 and 0.075 ± 0.009 day−1 for C. marshallae and C. pacificus, respectively. Calanus marshallae growth rate is satisfactorily described by a Michaelis–Menten model using chlorophyll-a concentration (r2 = 0.33) after temperature correction, but the prediction improves with a composite nonlinear model combining body weight into the Michaelis–Menten function (r2 = 0.55). Considering the limited range of data available for C. pacificus, the combination of the data for both species suggests that C. pacificus has a similar functional response to growth despite the differences in the geographic and temporal distributions with C. marshallae. Measured juvenile growth rates of the two Calanus species in this study were comparable to other calanoid species in the same area and showed reasonable agreement to Calanus growth models but less with global copepod growth models. [ABSTRACT FROM AUTHOR]

Dodder (Cuscuta spp., Convolvulaceae) is a genus of parasitic plants with worldwide distribution. Dodders are able to simultaneously parasitize two or more adjacent hosts, forming dodder-connected plant clusters. Nitrogen (N) deficiency is a common challenge to plants. To date, it has been unclear whether dodder transfers N-systemic signals between hosts grown in N-heterogeneous soil. Transcriptome and methylome analyses were carried out to investigate whether dodder (Cuscuta campestris) transfers N-systemic signals between N-replete and N-depleted cucumber (Cucumis sativus) hosts, and it was found that N-systemic signals from the N-deficient cucumber plants were rapidly translocated through C. campestris to the N-replete cucumber plants. Unexpectedly, certain systemic signals were also transferred from the N-replete to N-depleted cucumber hosts. We demonstrate that these systemic signals are able to regulate large transcriptome and DNA methylome changes in the recipient hosts. Importantly, N stress also induced many long-distance mobile mRNA transfers between C. campestris and hosts, and the bilateral N-systemic signaling between N-replete and N-depleted hosts had a strong impact on the inter-plant mobile mRNAs. Our 15N labeling experiment indicated that under N-heterogeneous conditions, N-systemic signals from the N-deficient cucumber hosts did not obviously change the N-uptake activity of the N-replete cucumber hosts; however, in plant clusters comprising C. campestris-connected cucumber and soybean (Glycine max) plants, if the soybean plants were N-starved, the cucumber plants exhibited increased N-uptake activity. This study reveals that C. campestris facilitates plant-plant communications under N-stress conditions by enabling extensive bilateral N-systemic signaling between different hosts. [ABSTRACT FROM AUTHOR]

Hundreds of naturally occurring specialized fatty acids (FAs) have potential as desirable chemical feedstocks if they could be produced at large scale by crop plants; however, transgenic expression of their biosynthetic genes has generally been accompanied by dramatic reductions in oil yield. For example, expression of castor (Ricinus communis) FA hydroxylase (FAH) in the Arabidopsis thaliana FA elongation mutant fae1 resulted in a 50% reduction of FA synthesis rate that was attributed to inhibition of acetyl-CoA carboxylase (ACCase) by an undefined mechanism. Here, we tested the hypothesis that the ricinoleic acid-dependent decrease in ACCase activity is mediated by biotin attachment domain-containing (BADC) proteins. BADCs are inactive homologs of biotin carboxy carrier protein that lack a biotin cofactor and can inhibit ACCase. Arabidopsis contains three BADC genes. To reduce expression levels of BADC1 and BADC3 in fae1/FAH plants, a homozygous badc1,3/fae1/FAH line was created. The rate of FA synthesis in badc1,3/fae1/FAH seeds doubled relative to fae1/FAH, restoring it to fae1 levels, increasing both native FA and HFA accumulation. Total FA per seed, seed oil content, and seed yield per plant all increased in badc1,3/fae1/FAH, to 5.8 µg, 37%, and 162 mg, respectively, relative to 4.9 µg, 33%, and 126 mg, respectively, for fae1/FAH. Transcript levels of FA synthesis-related genes, including those encoding ACCase subunits, did not significantly differ between badc1,3/fae1/FAH and fae1/FAH. These results demonstrate that BADC1 and BADC3 mediate ricinoleic acid-dependent inhibition of FA synthesis. We propose that BADC-mediated FAS inhibition as a general mechanism that limits FA accumulation in specialized FA-accumulating seeds. [ABSTRACT FROM AUTHOR]

Background: The plants in the Erigeron genus of the Compositae (Asteraceae) family are commonly called fleabanes, possibly due to the belief that certain chemicals in these plants repel fleas. In the traditional Chinese medicine, Erigeron breviscapus, which is native to China, was widely used in the treatment of cerebrovascular disease. A handful of bioactive compounds, including scutellarin, 3,5-dicaffeoylquinic acid, and 3,4-dicaffeoylquinic acid, have been isolated from the plant. With the purpose of finding novel medicinal compounds and understanding their biosynthetic pathways, we propose to sequence the genome of E. breviscapus. Findings: We assembled the highly heterozygous E. breviscapus genome using a combination of PacBio single-molecular real-time sequencing and next-generation sequencing methods on the Illumina HiSeq platform. The final draft genome is approximately 1.2 Gb, with contig and scaffold N50 sizes of 18.8 kb and 31.5 kb, respectively. Further analyses predicted 37 504 protein-coding genes in the E. breviscapus genome and 8172 shared gene families among Compositae species. Conclusions: The E. breviscapus genome provides a valuable resource for the investigation of novel bioactive compounds in this Chinese herb. [ABSTRACT FROM AUTHOR]

Background: Anatomic pathology laboratory workflow consists of 3 major specimen handling processes. Among the workflow are preanalytic, analytic, and postanalytic phases that contain multistep subprocesses with great impact on patient care. A worldwide representation of experts came together to create a system of metrics, as a basis for laboratories worldwide, to help them evaluate and improve specimen handling to reduce patient safety risk. Method: Members of the Initiative for Anatomic Pathology Laboratory Patient Safety (IAPLPS) pooled their extensive expertise to generate a list of metrics highlighting processes with high and low risk for adverse patient outcomes. Results: Our group developed a universal, comprehensive list of 47 metrics for patient specimen handling in the anatomic pathology laboratory. Steps within the specimen workflow sequence are categorized as high or low risk. In general, steps associated with the potential for specimen misidentification correspond to the high-risk grouping and merit greater focus within quality management systems. Primarily workflow measures related to operational efficiency can be considered low risk. Conclusion: Our group intends to advance the widespread use of these metrics in anatomic pathology laboratories to reduce patient safety risk and improve patient care with development of best practices and interlaboratory error reporting programs. [ABSTRACT FROM AUTHOR]

Aims: Monocytes/macrophages response plays a key role in postinfarction inflammation that contributes greatly to postinfarction ventricular remodelling and cardiac rupture. Therapeutic targeting of the GABAa receptor, which is enriched in monocytes/macrophages but not expressed in the myocardium, may be possible after myocardial infarction (Ml). Methods and results:After Ml was induced by ligation of the coronary artery, C57BL/6 mice were intraperitoneally administered with and results one specific agonist or antagonist of the GABAA receptor (topiramate or bicuculline), in the setting of presence or depletion of monocytes/macrophages. Our data showed that within the first 2 weeks after Ml, when monocytes/macrophages dominated, in contrast with bicuculline, topiramate treatment significantly reduced Ly-6Chigh monocyte numbers by regulating splenic monocytopoiesis and promoted foetal derived macrophages preservation and conversion of M1 to M2 or Ly-6Chigh to Ly-6Clow macrophage phenotype in the infarcted heart, though GABAAergic drugs failed to affect M1/M2 or Ly-6Chigh/Ly-6Clow macrophage polarization directly. Accordingly, proinflammatory activities mediated by M1 or Ly-6Chigh macrophages were decreased and reparative processes mediated by M2 or Ly-6Clow macrophages were augmented. As a result, post-infarction ventricular remodelling was attenuated, as reflected by reduced infarct size and increased collagen density within infarcts. Echocardiography indices, mortality and rupture rates were reduced. After depletion of monocytes/macrophages by clodronate liposomes, GABAAergic drugs exhibited no effect on cardiac dysfunction and surrogate clinical outcomes. Conclusion: Control of the GABAA receptor activity in monocytes/macrophages can potently modulate post-infarction inflammation. Topiramate emerges as a promising drug, which may be feasible to translate for Ml therapy in the future. [ABSTRACT FROM AUTHOR]

Acetylation is a ubiquitous modification on cell wall polymers, which play a structural role in plant growth and stress defenses. However, the mechanisms for how crop plants accomplish cell wall polymer O-acetylation are largely unknown. Here, we report on the isolation and characterization of two trichome birefringence-like (tbl) mutants in rice (Oryza sativa), which are affected in xylan O-acetylation. ostbl1 and ostbl2 single mutant and the tbl1 tbl2 double mutant displayed a stunted growth phenotype with varied degree of dwarfism. As shown by chemical assays, the wall acetylation level is affected in the mutants and the knock-down and overexpression transgenic plants. Furthermore, NMR spectroscopy analyses showed that all those mutants have varied decreases in xylan monoacetylation. The divergent expression levels of OsTBL1 and OsTBL2 explained the chemotype difference and indicated that OsTBL1 is a functionally dominant gene. OsTBL1 was found to be Golgi-localized. The recombinant OsTBL1 protein incorporates acetyl groups onto xylan. By using xylopentaose, a preferred acceptor substrate, OsTBL1 can transfer up to four acetyl residues onto xylopentaose, and this activity showed saturable kinetics. 2D-NMR spectroscopy showed that OsTBL1 transfers acetate to both 2-O and 3-O sites of xylosyl residues. In addition, ostbl1 and tbl1 tbl2 displayed susceptibility to rice blight disease, indicating that this xylan modification is required for pathogen resistance. This study identifies the major genes responsible for xylan acetylation in rice plants. [ABSTRACT FROM AUTHOR]

Background and Aims Ferns are abundant in sub-tropical forests in southern China, with some species being restricted to shaded understorey of natural forests, while others are widespread in disturbed, open habitats. To explain this distribution pattern, we hypothesize that ferns that occur in disturbed forests (FDF) have a different leaf cost-benefit strategy compared with ferns that occur in natural forests (FNF), with a quicker return on carbon investment in disturbed habitats compared with old-growth forests. Methods We chose 16 fern species from contrasting light habitats (eight FDF and eight FNF) and studied leaf functional traits, including leaf life span (LLS), specific leaf area (SLA), leaf nitrogen and phosphorus concentrations (N and P), maximum net photosynthetic rates (A), leaf construction cost (CC) and payback time (PBT), to conduct a leaf cost-benefit analysis for the two fern groups. Key Results The two groups, FDF and FNF, did not differ significantly in SLA, leaf N and P, and CC, but FDF had significantly higher A, greater photosynthetic nitrogen- and phosphorus-use efficiencies (PNUE and PPUE), and shorter PBT and LLS compared with FNF. Further, across the 16 fern species, LLS was significantly correlated with A, PNUE, PPUE and PBT, but not with SLA and CC. Conclusions Our results demonstrate that leaf cost-benefit analysis contributes to understanding the distribution pattern of ferns in contrasting light habitats of sub-tropical forests: FDF employing a quick-return strategy can pre-empt resources and rapidly grow in the high-resource environment of open habitats; while a slow-return strategy in FNF allows their persistence in the shaded understorey of old-growth forests. [ABSTRACT FROM AUTHOR]

High concentrations of indole-3-acetic acid (IAA) are required for climacteric ethylene biosynthesis to cause fruit softening in melting flesh peaches at the late ripening stage. By contrast, the fruits of stony hard peach cultivars do not soften and produce little ethylene due to the low IAA concentrations. To investigate the regulation of IAA accumulation during peach ripening [the transition from stage S3 to stage S4 III (climacteric)], a digital gene expression (DGE) analysis was performed. The expression patterns of auxin-homeostasis-related genes were compared in fruits of the melting flesh peach 'Goldhoney 3' and the stony hard flesh peach 'Yumyeong' during the ripening stage. It is revealed here that a YUCCA flavin mono-oxygenase gene (PpYUC11, ppa008176m), a key gene in auxin biosynthesis, displayed an identical differential expression profile to the profiles of IAA accumulation and PpACS1 transcription: the mRNA transcripts increased at the late ripening stage in melting flesh peaches but were below the limit of detection in mature fruits of stony hard peaches. In addition, the strong association between intron TC microsatellite genotypes of PpYUC11 and the flesh texture (normal or stony hard) is described in 43 peach varieties, indicating that this locus may be responsible for the stony hard phenotype in peach. These findings support the hypothesis that PpYUC11 may play an essential role in auxin biosynthesis during peach fruit ripening and is a candidate gene for the control of the stony hard phenotype in peach. [ABSTRACT FROM AUTHOR]

TRPM4 forms a non-selective cation channel activated by internal Ca2+. Its functional expression was demonstrated in cardiomyocytes of several mammalian species including humans, but the channel is also present in many other tissues. The recent characterization of the TRPM4 inhibitor 9-phenanthrol, and the availability of transgenic mice have helped to clarify the role of TRPM4 in cardiac electrical activity, including diastolic depolarization from the sino-atrial node cells in mouse, rat, and rabbit, as well as action potential duration in mouse cardiomyocytes. In rat and mouse, pharmacological inhibition of TRPM4 prevents cardiac ischaemia-reperfusion injuries and decreases the occurrence of arrhythmias. Several studies have identified TRPM4 mutations in patients with inherited cardiac diseases including conduction blocks and Brugada syndrome. This review identifies TRPM4 as a significant actor in cardiac electrophysiology. [ABSTRACT FROM AUTHOR]

Insect communities depend on both their local environment and features of the surrounding habitats. Diverse plant communities may enhance the abundance and species diversity of local natural enemies, which is possible due to a higher abundance and species diversity in complex landscapes. This hypothesis was tested using cereal aphid parasitoids and hyper-parasitoids by comparing 18 spring wheat fields, Triticum aestivum L. (Poales: Poaceae), in structurallycomplex landscapes (dominated by semi-natural habitat, > 50%, n = 9) and structurally-simple landscapes dominated by arable landscape (dominated by crop land, > 80%, n = 9). The agricultural landscape structure had significant effects on the number of parasitoid and hyper-parasitoid species, as 26 species (17 parasitoids and 9 hyper-parasitoids) were found in the complex landscapes and 21 were found in the simple landscapes (14 parasitoids and 7 hyper-parasitoids). Twenty-one species occurred in both landscape types, including 14 parasitoids and 7 hyperparasitoids species. The species diversity of parasitoids and hyper-parasitoids were significantly different between the complex and simple landscapes. In addition, arable fields in structurallysimple agricultural landscapes with little semi-natural habitats could support a lower diversity of cereal aphid parasitoids and hyper-parasitoids than structurally-complex landscapes. These findings suggest that cereal aphid parasitoids and hyper-parasitoids need to find necessary resources in structurally-complex landscapes, and generalizations are made concerning the relationship between landscape composition and biodiversity in agricultural landscapes. Overall, abundance, species richness, and species diversity increased with increasing plant diversity and landscape complexity in spring wheat fields and increasing amounts of semi-natural habitats in the surrounding landscape. [ABSTRACT FROM AUTHOR]

The proper use of resistance genes (R genes) requires a comprehensive understanding of their genomics and evolution. We analyzed genes encoding nucleotide-binding sites and leucine-rich repeats in the genomes of rice (Oryza sativa), maize (Zea mays), sorghum (Sorghum bicolor), and Brachypodium distachyon. Frequent deletions and translocations of R genes generated prevalent presence/absence polymorphism between different accessions/species. The deletions were caused by unequal crossover, homologous repair, nonhomologous repair, or other unknown mechanisms. R gene loci identified from different genomes were mapped onto the chromosomes of rice cv Nipponbare using comparative genomics, resulting in an integrated map of 495 R loci. Sequence analysis of R genes from the partially sequenced genomes of an African rice cultivar and 10 wild accessions suggested that there are many additional R gene lineages in the AA genome of Oryza. The R genes with chimeric structures (termed type I R genes) are diverse in different rice accessions but only account for 5.8% of all R genes in the Nipponbare genome. In contrast, the vast majority of R genes in the rice genome are type II R genes, which are highly conserved in different accessions. Surprisingly, pseudogene-causing mutations in some type II lineages are often conserved, indicating that their conservations were not due to their functions. Functional R genes cloned from rice so far have more type II R genes than type I R genes, but type I R genes are predicted to contribute considerable diversity in wild species. Type I R genes tend to reduce the microsynteny of their flanking regions significantly more than type II R genes, and their flanking regions have slightly but significantly lower G/C content than those of type II R genes. [ABSTRACT FROM AUTHOR]

Summary: Motif discovery is an important topic in computational transcriptional regulation studies. In the past decade, many researchers have contributed to the field and many de novo motif-finding tools have been developed, each may have a different strength. However, most of these tools do not have a user-friendly interface and their results are not easily comparable. We present a software called Toolbox of Motif Discovery (Tmod) for Windows operating systems. The current version of Tmod integrates 12 widely used motif discovery programs: MDscan, BioProspector, AlignACE, Gibbs Motif Sampler, MEME, CONSENSUS, MotifRegressor, GLAM, MotifSampler, SeSiMCMC, Weeder and YMF. Tmod provides a unified interface to ease the use of these programs and help users to understand the tuning parameters. It allows plug-in motif-finding programs to run either separately or in a batch mode with predetermined parameters, and provides a summary comprising of outputs from multiple programs. Tmod is developed in C++ with the support of Microsoft Foundation Classes and Cygwin. Tmod can also be easily expanded to include future algorithms. [ABSTRACT FROM PUBLISHER]