Association analysis of grain-setting rates in apical and basal spikelets in bread wheat (Triticum aestivum L.)

The rates of grain-setting in apical and basal spike lets in wheat directly affect the kernel number perspike(KNPS). Inthisstudy, 220 wheat lines from 18 Chinese provinces and five foreign countries were used as a natural population. Phenotypic an alysis showed difference singrain-setting rates between apical and basal spike lets. Thebroad-senseher it ability of grain-setting rate in apical spike lets(18.7–21.0%) washigher than that forbasal spike lets(9.4–16.4%). Significant correlations were found between KNPS and grain numbers in apical (R2 = 0.40– 0.45,P<0.01) andbasal (R2=0.41–0.56,P<0.01) spikelets. Seventy two of 106 SSR markers were associated with grain setting, 32 for apical spike lets, and 34 for basalspike lets. The SSR lociwe relocatedon 17chromosomes, except3A, 3D, 4A, and 7D, and explained 3.7–22.9% of the phenotypicvariance. Four markers, Xcfa2153-1A202, Xgwm186-5A118, Xgwm156-3B319,andXgwm537-7B210, showed the largest effects on grain numbers in apical and basal spikelets. Highgra innumbers inapical and basal spikelets were associated with elitealleles. Ningmai9, Ning0569, and Yangmai 18 with high grain-setting rate scarried large rnumbers off avorablealleles. Comparison of grain numbers in basal and apical spike lets of 35 Yangmai and Ningmai lines indicated that the Ningma ilines had better grain-settingrates(mean21.4) than the Yangmai lines(16.5)

Individual classification of ADHD patients by integrating multiscale neuroimaging markers and advanced pattern recognition techniques

Accurate classification or prediction of the brain state across individual subject, i.e., healthy, or with brain disorders, is generally a more difficult task than merely finding group differences. The former must be approached with highly informative and sensitive biomarkers as well as effective pattern classification/feature selection approaches. In this paper, we propose a systematic methodology to discriminate attention deficit hyperactivity disorder (ADHD) patients from healthy controls on the individual level. Multiple neuroimaging markers that are proved to be sensitive features are identified, which include multiscale characteristics extracted from blood oxygenation level dependent (BOLD) signals, such as regional homogeneity (ReHo) and amplitude of low-frequency fluctuations. Functional connectivity derived from Pearson, partial, and spatial correlation is also utilized to reflect the abnormal patterns of functional integration, or, dysconnectivity syndromes in the brain. These neuroimaging markers are calculated on either voxel or regional level. Advanced feature selection approach is then designed, including a brain-wise association study (BWAS). Using identified features and proper feature integration, a support vector machine (SVM) classifier can achieve a cross-validated classification accuracy of 76.15% across individuals from a large dataset consisting of 141 healthy controls and 98 ADHD patients, with the sensitivity being 63.27% and the specificity being 85.11%. Our results show that the most discriminative features for classification are primarily associated with the frontal and cerebellar regions. The proposed methodology is expected to improve clinical diagnosis and evaluation of treatment for ADHD patient, and to have wider applications in diagnosis of general neuropsychiatric disorders

Global regulator IscR positively contributes to antimonite resistance and oxidation in <i>Comamonas testosteroni</i> S44

Antimonial compounds can be found as a toxic contaminant in the environment. Mechanisms of microbial Sb oxidation and its role in microbial tolerance are limited. Previously, we showed Comamonas testosteroni S44 to be resistant to multiple heavy metals and was able to oxidize the toxic antimonite [Sb(III)] to the much less toxic antimonate [Sb(V)]. In this study, transposon mutagenesis was performed in C. testosteroni S44 to isolate genes responsible for Sb(III) resistance and oxidation. An insertion mutation into iscR, which regulates genes involved in the biosynthesis of Fe-S clusters, generated a strain called iscR-280. This mutant strain was complemented with a plasmid carrying iscR to generate strain iscR-280C. Compared to the wild type S44 and iscR-280C, strain iscR-280 showed lower resistance to Sb(III) and a lower Sb(III) oxidation rate. Strain iscR-280 also showed lower resistance to As(III), Cd(II), Cu(II) and H2O2. In addition, intracellular γ-glutamylcysteine ligase (γ-GCL) activity and glutathione (GSH) content were decreased in the mutated strain iscR-280. Real-time RT-PCR and lacZ fusion expression assay indicated that transcription of iscR and iscS was induced by Sb(III). Results of electrophoretic mobility shift assay (EMSA) and bacterial one-hybrid (B1H) system demonstrated a positive interaction between IscR and its promoter region. The diverse defective phenotypes and various expression patterns suggested a role for IscR in contributing to multi-metal(loid)s resistance and Sb(III) oxidation via Fe-S cluster biogenesis and oxidative stress protection. Bacterial Sb(III) oxidation is a detoxification reaction

A Drug Combination Screen Identifies Drugs Active against Amoxicillin-induced Round Bodies of Borrelia burgdorferi Persisters from an FDA Drug Library

Although currently recommended antibiotics for Lyme disease such as doxycycline or amoxicillin cure the majority of the patients, about 10-20% of patients treated for Lyme disease may experience lingering symptoms including fatigue, pain, or joint and muscle aches. Under stress conditions such as starvation or antibiotic exposure, Borrelia burgdorferi can develop round body forms, which are a type of persister bacteria that are not killed by current Lyme antibiotics. To identify more effective drugs that are active against the round bodies of B. burgdorferi, we established a round body persister model induced by amoxicillin and screened the Food and Drug Administration (FDA) drug library consisting of 1581 drug compounds and also 22 drug combinations using the SYBR Green I/propidium iodide (PI) viability assay. We identified 23 drug candidates that have higher activity against the round bodies of B. burgdorferi than either amoxicillin or doxycycline. Eleven of these scored better than metronidazole and tinidazole which have been previously described to be active against round bodies. While some drug candidates such as daptomycin and clofazimine overlapped with a previous screen against stationary phase B. burgdorferi persisters, additional drug candidates active against round bodies we identified include artemisinin, ciprofloxacin, nifuroxime, fosfomycin, chlortetracycline, sulfacetamide, sulfamethoxypyridazine and sulfathiozole. Two triple drug combinations had the highest activity against round bodies and stationary phase B. burgdorferi persisters: artemisinin/cefoperazone/doxycycline and sulfachlorpyridazine/daptomycin/doxycycline. These findings confirm and extend previous findings that certain drug combinations have superior activity against B. burgdorferi persisters in vitro, even if pre-treated with amoxicillin. These findings may have implications for improved treatment of Lyme disease

Candidate genes involved in the biosynthesis of triterpenoid saponins in Platycodon grandiflorum identified by transcriptome analysis

Background: Platycodon grandiflorum is the only species in the genus Platycodon of the family Campanulaceae, which has been traditionally used as a medicinal plant for its lung-heat-clearing, antitussive, and expectorant properties in China, Japanese and Korean. Oleanane-type triterpenoid saponins were the main chemical components of P. grandiflorum and platycodin D was the abundant and main bioactive component, but little is known about their biosynthesis in plants. Hence, P. grandiflorum is an ideal medicinal plant for studying the biosynthesis of Oleanane-type saponins. In addition, the genomic information of this important herbal plant is unavailable.Principal Findings:A total of 58,580,566 clean reads were obtained, which were assembled into 34,053 unigenes, with an average length of 936 bp and N50 of 1,661 bp by analyzing the transcriptome data of P. grandiflorum. Among these 34,053 unigenes, 22,409 unigenes (65.80%) were annotated based on the information available from public databases, including Nr, NCBI, Swiss-Prot, KOG and KEGG. Furthermore, 21 candidate cytochrome P450 genes and 17 candidate UDP-glycosyltransferase genes most likely involved in triterpenoid saponins biosynthesis pathway were discovered from the transcriptome sequencing of P. grandiflorum. In addition, 10,626 SSRs were identified based on the transcriptome data, which would provide abundant candidates of molecular markers for genetic diversity and genetic map for this medicinal plant.Conclusion:The genomic data obtained from P. grandiflorum, especially the identification of putative genes involved in triterpenoid saponins biosynthesis pathway, will facilitate our understanding of the biosynthesis of triterpenoid saponins at molecular level

Tetraether biomarker records from a loess-paleosol sequence in the western Chinese Loess Plateau

The ubiquitous occurrence of glycerol dialkyl glycerol tetraethers (GDGTs) in soils and their ability to record temperature and environmental changes offer the prospect of independently reconstructing continental paleotemperature and paleoenvironment from the loess-paleosol sequences (LPS) from the Chinese Loess Plateau (CLP). In this study we present records of GDGT-derived proxies for the last 70 kyr from the Yuanbao LPS, western CLP. Temperature record reconstructed from the cyclization and methylation index of branched tetraethers (MBT-CBT) displays that the onset of deglacial warming at ~20 kyr before present (BP) precedes the strengthening of summer monsoon at ~15 kyr BP, which is in agreement in timing with previous MBT-CBT temperature records from the southeastern CLP. The maximal deglacial warming of ~10 &#176;C is slightly higher than those in the southeastern CLP, perhaps due to the higher latitude and farther inland of the study site. The Branched and Isoprenoid Tetraether (BIT) index shows higher values (0.87–0.96 range, 0.93 average) in the glacial loess and lower values (0.76–0.91 range, 0.83 average) in the Holocene paleosols, with a steady decreasing trend since the early Holocene. The decreasing trend could suggest enhanced Thaumarchaeota relative to GDGT producing bacteria activity since the early Holocene, but other possibilities, such as preferential degradation of isoprenoid GDGTs or upward increase in living archaea relative to bacteria in the paleosol profile, cannot be fully excluded. Our results thus demonstrate the need of future study on microbial community structure in soil column and differential degradation of GDGT molecules

Different roles of cyclic electron flow around photosystem I under sub-saturating and saturating light intensities in tobacco leaves

In higher plants, the generation of proton gradient across the thylakoid membrane (pH) through cyclic electron flow (CEF) has mainly two functions: 1) to generate ATP and balance the ATP/NADPH energy budget, and 2) to protect photosystems I and II against photoinhibition. The intensity of light under which plants are grown alters both CEF activity and the ATP/NADPH demand for primary metabolic processes. However, it is unclear how the role of CEF is affected by the level of irradiance that is applied during the growth and measurement periods. We studied the role of CEF at different light intensities in leaves from sun- and shade-grown plants. At 849 μmol photons m-2 s-1, both types of leaves had nearly the same degree of CEF activation. Modeling of the ATP/NADPH demand revealed that, at this light intensity, the contribution of CEF toward supplying ATP was much higher in the sun leaves. Meanwhile, the shade leaves showed higher levels of non-photochemical quenching and the P700 oxidation ratio. Therefore, at 849 μmol photons m-2 s-1, CEF mainly helped in the synthesis of ATP in the sun leaves, but functioned in photoprotection for the shade leaves. When the light intensity increased to 1976 μmol photons m-2 s-1, CEF activation was greatly enhanced in the sun leaves, but its contribution to supplying ATP changed slightly. These results indicate that the main role of CEF is altered flexibly in response to light intensity. In particular, CEF mainly contributes to balancing the ATP/NADPH energy budget under sub-saturating light intensities. When exposed to saturating light intensities, CEF mainly protects photosynthetic apparatus against photoinhibition

Diversity and distribution of Actinobacteria associated with reef coral Porites lutea

Actinobacteria is a ubiquitous major group in coral holobiont. The diversity and spatial and temporal distribution of actinobacteria have been rarely documented. In this study, diversity of actinobacteria associated with mucus, tissue and skeleton of Porites lutea and in the surrounding seawater were examined every three months for 1 year on Luhuitou fringing reef. The population structures of the P. lutea-associated actinobacteria were analyzed using phylogenetic analysis of 16S rRNA gene clone libraries, which demonstrated highly diverse actinobacteria profiles in P. lutea. A total of twenty-five described families and ten unnamed families were determined in the populations, and 12 genera were firstly detected in corals. The Actinobacteria diversity was significantly different between the P. lutea and the surrounding seawater. Only 10 OTUs were shared by the seawater and coral samples. Redundancy and hierarchical cluster analyses were performed to analyze the correlation between the variations of actinobacteria population within the divergent compartments of P. lutea, seasonal changes, and environmental factors. The actinobacteria communities in the same coral compartment tended to cluster together. Even so, an extremely small fraction of OTUs was common in all three P. lutea compartments. Analysis of the relationship between actinobacteria assemblages and the environmental parameters showed that several genera were closely related to specific environmental factors. This study highlights that coral-associated actinobacteria populations are highly diverse, and spatially structured within P. lutea, and they are distinct from which in the ambient seawater

Graphene-based transparent electrodes for hybrid solar cells

The graphene-based transparent and conductive films were demonstrated to be cost-effective electrodes working in organic-inorganic hybrid Schottky solar cells. Large area graphene films were produced by chemical vapor deposition (CVD) on copper foils and transferred onto glass as transparent electrodes. The hybrid solar cell devices consist of solution processed poly (3, 4-ethlenedioxythiophene): poly (styrenesulfonate) (PEDOT: PSS) which is sandwiched between silicon wafer and graphene electrode. The solar cells based on graphene electrodes, especially those doped with HNO3, has comparable performance to the reference devices using commercial indium tin oxide (ITO). Our work suggests that graphene-based transparent electrode is a promising candidate to replace ITO

Genome-wide Analysis and Expression Profiling under Heat and Drought Treatments of HSP70 Gene Family in Soybean (Glycine max L.)

Heat shock proteins (HSPs) perform a fundamental role in protecting plants against abiotic stresses. Previous studies have made great efforts in the functional analysis of individual family members, but there has not yet been an overall analysis or expression profiling of the HSP70 gene family in soybeans (Glycine max L.). In this study, an investigation of the soybean genome revealed 61 putative HSP70 genes, which were evaluated. These genes were classified into eight sub-families, denoted I-VIII, based on a phylogenetic analysis. In each sub-family, the constituent parts of the gene structure and motif were relatively conserved. These GmHSP70 genes were distributed unequally on 17 of the 20 chromosomes. The analysis of the expression profiles showed that 53 of the 61 GmHSP70 genes were differentially expressed across the 14 tissues. However, most of the GmHSP70s were differentially expressed in a tissue-specific expression pattern. Furthermore, the expression of some of the duplicate genes was partially redundant, while others showed functional diversity. The quantitative real-time PCR (qRT-PCR) analysis of the 61 soybean HSP70 genes confirmed their stress-inducible expression patterns under both drought and heat stress. These findings provide a thorough overview of the evolution and modification of the GmHSP70 gene family, which will help to determine the functional characteristics of the HSP70 genes in soybean growth and development