Structure of the cell-binding component of the Clostridium difficile binary toxin reveals a di-heptamer macromolecular assembly.

Targeting Clostridium difficile infection is challenging because treatment options are limited, and high recurrence rates are common. One reason for this is that hypervirulent C. difficile strains often have a binary toxin termed the C. difficile toxin, in addition to the enterotoxins TsdA and TsdB. The C. difficile toxin has an enzymatic component, termed CDTa, and a pore-forming or delivery subunit termed CDTb. CDTb was characterized here using a combination of single-particle cryoelectron microscopy, X-ray crystallography, NMR, and other biophysical methods. In the absence of CDTa, 2 di-heptamer structures for activated CDTb (1.0 MDa) were solved at atomic resolution, including a symmetric (SymCDTb; 3.14 Å) and an asymmetric form (AsymCDTb; 2.84 Å). Roles played by 2 receptor-binding domains of activated CDTb were of particular interest since the receptor-binding domain 1 lacks sequence homology to any other known toxin, and the receptor-binding domain 2 is completely absent in other well-studied heptameric toxins (i.e., anthrax). For AsymCDTb, a Ca2+ binding site was discovered in the first receptor-binding domain that is important for its stability, and the second receptor-binding domain was found to be critical for host cell toxicity and the di-heptamer fold for both forms of activated CDTb. Together, these studies represent a starting point for developing structure-based drug-design strategies to target the most severe strains of C. difficile.

Volume and compressibility differences between protein conformations revealed by high-pressure NMR.

Proteins often interconvert between different conformations in ways critical to their function. Although manipulating such equilibria for biophysical study is often challenging, the application of pressure is a potential route to achieve such control by favoring the population of lower volume states. Here, we use this feature to study the interconversion of ARNT PAS-B Y456T, which undergoes a dramatic +3 slip in the ß-strand register as it switches between two stably folded conformations. Using high-pressure biomolecular NMR approaches, we obtained the first, to our knowledge, quantitative data testing two key hypotheses of this process: the slipped conformation is both smaller and less compressible than the wild-type equivalent, and the interconversion proceeds through a chiefly unfolded intermediate state. Data collected in steady-state pressure and time-resolved pressure-jump modes, including observed pressure-dependent changes in the populations of the two conformers and increased rate of interconversion between conformers, support both hypotheses. Our work exemplifies how these approaches, which can be generally applied to protein conformational switches, can provide unique information that is not easily accessible through other techniques.

Characterization and identification of long non-coding RNAs based on feature relationship.

MOTIVATION: The significance of long non-coding RNAs (lncRNAs) in many biological processes and diseases has gained intense interests over the past several years. However, computational identification of lncRNAs in a wide range of species remains challenging; it requires prior knowledge of well-established sequences and annotations or species-specific training data, but the reality is that only a limited number of species have high-quality sequences and annotations. RESULTS: Here we first characterize lncRNAs in contrast to protein-coding RNAs based on feature relationship and find that the feature relationship between open reading frame length and guanine-cytosine (GC) content presents universally substantial divergence in lncRNAs and protein-coding RNAs, as observed in a broad variety of species. Based on the feature relationship, accordingly, we further present LGC, a novel algorithm for identifying lncRNAs that is able to accurately distinguish lncRNAs from protein-coding RNAs in a cross-species manner without any prior knowledge. As validated on large-scale empirical datasets, comparative results show that LGC outperforms existing algorithms by achieving higher accuracy, well-balanced sensitivity and specificity, and is robustly effective (>90% accuracy) in discriminating lncRNAs from protein-coding RNAs across diverse species that range from plants to mammals. To our knowledge, this study, for the first time, differentially characterizes lncRNAs and protein-coding RNAs based on feature relationship, which is further applied in computational identification of lncRNAs. Taken together, our study represents a significant advance in characterization and identification of lncRNAs and LGC thus bears broad potential utility for computational analysis of lncRNAs in a wide range of species. AVAILABILITY AND IMPLEMENTATION: LGC web server is publicly available at http://bigd.big.ac.cn/lgc/calculator. The scripts and data can be downloaded at http://bigd.big.ac.cn/biocode/tools/BT000004. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization.

Real-time quantitative PCR (RT-qPCR) has become a widely used method for accurate expression profiling of targeted mRNA and ncRNA. Selection of appropriate internal control genes for RT-qPCR normalization is an elementary prerequisite for reliable expression measurement. Here, we present ICG (http://icg.big.ac.cn), a wiki-driven knowledgebase for community curation of experimentally validated internal control genes as well as their associated experimental conditions. Unlike extant related databases that focus on qPCR primers in model organisms (mainly human and mouse), ICG features harnessing collective intelligence in community integration of internal control genes for a variety of species. Specifically, it integrates a comprehensive collection of more than 750 internal control genes for 73 animals, 115 plants, 12 fungi and 9 bacteria, and incorporates detailed information on recommended application scenarios corresponding to specific experimental conditions, which, collectively, are of great help for researchers to adopt appropriate internal control genes for their own experiments. Taken together, ICG serves as a publicly editable and open-content encyclopaedia of internal control genes and accordingly bears broad utility for reliable RT-qPCR normalization and gene expression characterization in both model and non-model organisms.

CloudPhylo: a fast and scalable tool for phylogeny reconstruction.

Summary: Phylogeny reconstruction is fundamentally crucial for molecular evolutionary studies but remains computationally challenging. Here we present CloudPhylo, a tool built on Spark that is capable of processing large-scale datasets for phylogeny reconstruction. As testified on empirical data, CloudPhylo is well suited for big data analysis, achieving high efficiency and good scalability on phylogenetic tree inference. Availability and Implementation: https://github.com/XingjianXu/cloudphylo Contact: zhangzhang@big.ac.cn Supplementary Information: Supplementary data are available at Bioinformatics online.

Integration of chemical and toxicological tools to assess the bioavailability of copper derived from different copper-based fungicides in soil.

Because the extensive use of Cu-based fungicides, the accumulation of Cu in agricultural soil has been widely reported. However, little information is known about the bioavailability of Cu deriving from different fungicides in soil. This paper investigated both the distribution behaviors of Cu from two commonly used fungicides (Bordeaux mixture and copper oxychloride) during the aging process and the toxicological effects of Cu on earthworms. Copper nitrate was selected as a comparison during the aging process. The distribution process of exogenous Cu into different soil fractions involved an initial rapid retention (the first 8 weeks) and a following slow continuous retention. Moreover, Cu mainly moved from exchangeable and carbonate fractions to Fe-Mn oxides-combined fraction during the aging process. The Elovich model fit well with the available Cu aging process, and the transformation rate was in the order of Cu(NO3)2 > Bordeaux mixture > copper oxychloride. On the other hand, the biological responses of earthworms showed that catalase activities and malondialdehyde contents of the copper oxychloride treated earthworms were significantly higher than those of Bordeaux mixture treated earthworms. Also, body Cu loads of earthworms from different Cu compounds spiked soils were in the following order: copper oxychloride > Bordeaux mixture. Thus, the bioavailability of Cu from copper oxychloride in soil was significantly higher than that of Bordeaux mixture, and different Cu compounds should be taken into consideration when studying the bioavailability of Cu-based fungicides in the soil.

LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs.

Long non-coding RNAs (lncRNAs) perform a diversity of functions in numerous important biological processes and are implicated in many human diseases. In this report we present lncRNAWiki (http://lncrna.big.ac.cn), a wiki-based platform that is open-content and publicly editable and aimed at community-based curation and collection of information on human lncRNAs. Current related databases are dependent primarily on curation by experts, making it laborious to annotate the exponentially accumulated information on lncRNAs, which inevitably requires collective efforts in community-based curation of lncRNAs. Unlike existing databases, lncRNAWiki features comprehensive integration of information on human lncRNAs obtained from multiple different resources and allows not only existing lncRNAs to be edited, updated and curated by different users but also the addition of newly identified lncRNAs by any user. It harnesses community collective knowledge in collecting, editing and annotating human lncRNAs and rewards community-curated efforts by providing explicit authorship based on quantified contributions. LncRNAWiki relies on the underling knowledge of scientific community for collective and collaborative curation of human lncRNAs and thus has the potential to serve as an up-to-date and comprehensive knowledgebase for human lncRNAs.

Characterization of Pb2+ biosorption by psychrotrophic strain Pseudomonas sp. I3 isolated from permafrost soil of Mohe wetland in Northeast China.

Due to the long and severe winter in Northeast China, wastewater containing lead (Pb) is treated inefficiently, resulting in irregular disposal. In order to solve this problem, a Pb-resistant psychrotrophic bacterium, Pseudomonas sp. I3, was isolated from permafrost soil of Mohe wetland and served as biosorbent for Pb2+ removal under 15 °C. The minimum inhibitory concentration of strain I3 for Pb2+ was 7.5 mM, which was higher than that of Escherichia coli DH5α (1.5 mM). However, acid digestion results showed that these two bacteria had a comparable biosorption capacity for Pb2+, suggesting no direct relationship between biosorption ability of bacteria and their metal-resistance. Acid digestion results also proved that intracellular Pb accumulation was mainly contributed to the distinct performance between living and non-living biosorbents, which was further confirmed by the analyses of TEM-EDS. Results of FTIR revealed that functional groups including CH2, CO, CN, NH, COO and SO3 were participated in the biosorption process of the tested biosorbents no matter bacteria were living or not. The effects of environmental factors including pH, temperature, biomass dose, operation time and initial Pb2+ concentration were investigated through a batch of biosorption experiments. The equilibrium data for living and non-living biosorbent were well fitted to Langmuir model with their maximum Pb2+ biosorption capacities of 49.48 and 42.37 mg/g, respectively. The kinetic data for each biosorbent were well described by pseudo-second order kinetic model. Overall, Pseudomonas sp. I3 seemed to be an effective biosorbent for cleansing Pb2+ from contaminated wastewater at low temperature.

Genetically engineered Pseudomonas putida X3 strain and its potential ability to bioremediate soil microcosms contaminated with methyl parathion and cadmium.

A multifunctional Pseudomonas putida X3 strain was successfully engineered by introducing methyl parathion (MP)-degrading gene and enhanced green fluorescent protein (EGFP) gene in P. putida X4 (CCTCC: 209319). In liquid cultures, the engineered X3 strain utilized MP as sole carbon source for growth and degraded 100 mg L(-1) of MP within 24 h; however, this strain did not further metabolize p-nitrophenol (PNP), an intermediate metabolite of MP. No discrepancy in minimum inhibitory concentrations (MICs) to cadmium (Cd), copper (Cu), zinc (Zn), and cobalt (Co) was observed between the engineered X3 strain and its host strain. The inoculated X3 strain accelerated MP degradation in different polluted soil microcosms with 100 mg MP kg(-1) dry soil and/or 5 mg Cd kg(-1) dry soil; MP was completely eliminated within 40 h. However, the presence of Cd in the early stage of remediation slightly delayed MP degradation. The application of X3 strain in Cd-contaminated soil strongly affected the distribution of Cd fractions and immobilized Cd by reducing bioavailable Cd concentrations with lower soluble/exchangeable Cd and organic-bound Cd. The inoculated X3 strain also colonized and proliferated in various contaminated microcosms. Our results suggested that the engineered X3 strain is a potential bioremediation agent showing competitive advantage in complex contaminated environments.

[Preparation and Molluscicidal Effect of Chlorosalicylicamide Sustained-release Granules].

Objective: To prepare the 5% and 10% chlorosalicylicamide（quinoid-2', 5-dichloro-4'-nitrosalicylanilide from niclosamide） sustained-release granules （LDS-SRG） and evaluate their molluscicidal effect. Methods: The 5% and 10% LDS-SRG were prepared with screened carriers, surfactants, adhesives, defoamers and lubricants. Their bulk density, water content, repose angle, critical relative humidity, thermal stability and release rate were determined. Spraying method was used to test the molluscicidal effect of LDS-SRG at 1.6 g/m2. Meanwhile, 50% wettable powder of niclosamide ethanolamine salt (WPN) was applied as the positive control at 1.0 g/m2, and dechlorinated water was used as the blank control. The mortality of snails was calculated on days 3, 7 and 14 after administration. Results: The 5% and 10% LDS-SRG were red brown in color, showed good fluidity, and had bulk density of 0.655 g/ml and 0.594 g/ml, moisture content of 1.15% and 1.28%, repose angle of 39.8° and 39.7°, and critical relative humidity of 64.98% and 61.63%, respectively. Moreover, both showed good thermal stability. The release curve was stable for both 5% and 10% LDS-SRG during day 1 to day 9, and faster release for 5% LDS-SRG than for 10% LDS-SRG. The burst release occurred on days 10 and 15, and the steady release occurred from days 14 and 20 for 5% and 10% LDS-SRG respectively. The snail mortality on day 7 after 5% LDS-SRG 1.6 g/m2 administration and on day 14 after 10% LDS-SRG 1.6 g/m2 administration was both higher than 95%, and higher than that of the 50% WPN 1.0 g/m2 control (P<0.05). Conclusion: The 5% and 10% LDS-SRG show sustained-release potential and satisfactory molluscicidal effect by spraying, reaching the evaluation standard for molluscicidal agents.

[The Molluscicidal Effect of Chlorosalicylicamide Sustained-release Granules on Oncomelania hupensis].

Objective: To evaluate the molluscicidal effect of the chlorosalicylicamide sustained-release granules (LDS-SRG) on Oncomelania hupensis. Methods: Seven effective concentrations or dosages of LDS-SRG, 0.1, 0.2, 0.4, 0.8, 1.6, 3.2 and 6.4 mg/L （for immersion test） or g/m2（for spraying test）, were prepared from the original 5% and 10% concentrations or dosages in the laboratory. In the immersion test, each concentration of LDS-SRG was incubated with 3 packs of snails（30 snails in each pack）, and each pack was taken for snail counting at 24, 48 and 72 h respectively. In the spraying test, each dosage of LDS-SRG was applied to 200 snails, and the snail mortality was calculated in 50 randmoly collected snails on days 3 and 7, and in the whole on day 14 after administration. In the field immersion test, LDS-SRG at concentrations of 0.4, 0.8 and 1.6 g/m3 was incubated with 6 packs of snails （30 snails in each pack）, and each 2 packs were taken at 24, 48, and 72 h to calculate the snail mortality. In the field spraying test, 0.8, 1.6 and 3.2 g/m2 LDS-SRG was sprayed in 3 snail-positive ditches （～100 m2）, and 10 boxes of snails were selected in each ditch on days 3, 7 and 14 to calculate the snail mortality. The 50% wettable powder of niclosamide ethanolamine salt （WPN） with effective concentrations or dosages of 1.0 mg/L （or g/m2 and g/m3） was used as the positive control. Fresh water served as the blank control. Results: In the labratory immersion test using the original concentration of 5%, both 0.1-6.4 mg/L LDS-SRG for 72 h and 1.6-6.4 mg/L LDS-SRG for 48 h caused 100% mortality; and the concentration lethal to 50% （LC50） at 24, 48 and 72 h was 0.70, 0.01 and 0.01 mg/L respectively. When using the original concentration of 10%, both 0.1-6.4 mg/L LDS-SRG for 72 h and 0.2-6.4 mg/L LDS-SRG for 48 h caused 100% mortality; and the LC50 at 24, 48 and 72 h was 0.15, 0.01 and 0.01 mg/L respectively. The labratory spraying test showed that 7-day administration of 1.6 and 6.4 g/m2 LDS-SRG as well as 14-day administration of 3.2 and 6.4 g/m2 LDS-SRG prepared from 5% dosage, resulted in a snail mortality>95%, with the LD50 on days 3, 7 and 14 being 0.06, 0.16, and 0.18 g/m2; 14-day administration of 1.6 g/m2 LDS-SRG as well as 7-day administration of 6.4 g/m2 LDS-SRG prepared from 10% dosage, resulted in a snail mortality>95%, with the LD50 on days 3, 7 and 14 being 3.29, 0.75, and 0.16 g/m2. The mortality by various dosages of LDS-SRG prepared from 5% dosage was significantly higher than that of the control group (P<0.05). In the field immersion test, the snail mortality by 1.6 g/m3 LDS-SRG prepared from 5% and 10% concentrations for 72 h was 96.43% and 98.21% respectively (P>0.05 versus the control group). In the field spraying test, the snail mortality by 3.2 g/m2 LDS-SRG prepared from 5% dosage for 3, 7 and 14 days was 93.99%, 91.18% and 86.48% respectively, and that from 10% dosage was 94.95%, 93.50% and 85.43%, all significantly higher than that of the control group （82.83%, 72.38% and 48.38%）（P<0.05）; the snail mortality by 0.8 g/m2 LDS-SRG prepared from 5% dosage for 14 days（66.51%） and that by 1.6 g/m2 LDS-SRG prepared from 5% dosage for 3 days（84.61%） were both significantly higher than that by 10% LDS-SRG（20.13% and 43.06%） （P<0.05）. Conclusion: The 5% and 10% LDS-SRG used separately in the immersion test and the spraying test both meet the requirements of the national standard of Efficacy Test Methods and Evaluation of Molluscicide for Pesticide Registration.

A Comparative Study on the Biosorption of Cd2+ onto Paecilomyces lilacinus XLA and Mucoromycote sp. XLC.

The filamentous fungi XLA and XLC isolated from Cd-contaminated soil were identified morphologically and phylogenetically as Paecilomyces lilacinus and Mucoromycote sp., respectively. The minimum inhibitory concentrations (MICs) of Cd2+, Co2+, Cu2+, Zn2+, Cr3+ and Cr6+ in minimum mineral (MM) medium agar plates were 29,786, 2945, 9425, 5080, 1785 and 204 mg · L(-1) for XLA and 11,240, 884, 9100, 2540, 3060 and 51 mg · L(-1) for XLC, respectively. Favorable biosorption conditions for adsorption of Cd2+ by the tested fungi were investigated. Efficient performances of the biosorbents were described using Langmuir isotherm model, and the predicted maximum biosorption capacities for Cd2+ were 77.61 mg · g(-1) of XLA and 79.67 mg · g(-1) of XLC. Experiments on desorption potential of biosorbents validated their efficacy at a large scale. Results showed that XLA obtained a desorption rate of 84.7% by 2% EDTA and XLC gained a desorption rate of 78.9% by 0.1 M HCl. Analysis by Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy/energy dispersive X-ray spectroscopy (SEM/EDS) and X-ray photoelectron spectroscopy (XPS) suggested that groups of C-N, COO- for XLA and C-N, CH2 and phosphate for XLC were the dominant binding sites for Cd2+ biosorption. Our results indicated that the fungus XLA, rather than XLC, could potentially be used as an inexpensive, eco-friendly and effective bioremediation agent for the removal of Cd2+ from wastewater.

Iron transporter1 OsIRT1 positively regulates saline-alkaline stress tolerance in Oryza sativa.

Soil salinization-alkalization severely affects plant growth and crop yield worldwide, especially in the Songnen Plain of Northeast China. Saline-alkaline stress increases the pH around the plant roots, thereby limiting the absorption and transportation of nutrients and ions, such as iron (Fe). Fe is an essential micronutrient that plays important roles in many metabolic processes during plant growth and development, and it is acquired by the root cells via iron-regulated transporter1 (IRT1). However, the function of Oryza sativa IRT1 (OsIRT1) under soda saline-alkaline stress remains unknown. Therefore, in this study, we generated OsIRT1 mutant lines and OsIRT1-overexpressing lines in the background of the O. sativa Songjing2 cultivar to investigate the roles of OsIRT1 under soda saline-alkaline stress. The OsIRT1-overexpressing lines exhibited higher tolerance to saline-alkaline stress compared to the mutant lines during germination and seedling stages. Moreover, the expression of some saline-alkaline stress-related genes and Fe uptake and transport-related genes were altered. Furthermore, Fe and Zn contents were upregulated in the OsIRT1-overexpressing lines under saline-alkaline stress. Further analysis revealed that Fe and Zn supplementation increased the tolerance of O. sativa seedlings to saline-alkaline stress. Altogether, our results indicate that OsIRT1 plays a significant role in O. sativa by repairing the saline-alkaline stress-induced damage. Our findings provide novel insights into the role of OsIRT1 in O. sativa under soda saline-alkaline stress and suggest that OsIRT1 can serve as a potential target gene for the development of saline-alkaline stress-tolerant O. sativa plants.

Research on the Effects of the Relationship between Agronomic Traits and Dwarfing Genes on Yield in Colored Wheat.

This research focuses on 72 approved varieties of colored wheat from different provinces in China. Utilizing coefficients of variation, structural equation models, and correlation analyses, six agronomic traits of colored wheat were comprehensively evaluated, followed by further research on different dwarfing genes in colored wheat. Using the entropy method revealed that among the 72 colored wheat varieties, 10 were suitable for cultivation. Variety 70 was the top-performing variety, with a comprehensive index of 87.15%. In the final established structural equation model, each agronomic trait exhibited a positive direct effect on yield. Notably, plant height, spike length, and flag leaf width had significant impacts on yield, with path coefficients of 0.55, 0.40, and 0.27. Transcriptome analysis and real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) validation were used to identify three dwarfing genes controlling plant height: Rht1, Rht-D1, and Rht8. Subsequent RT-qPCR validation clustering heatmap results indicated that Rht-D1 gene expression increased with the growth of per-acre yield. Rht8 belongs to the semi-dwarf gene category and has a significant positive effect on grain yield. However, the impact of Rht1, as a dwarfing gene, on agronomic traits varies. These research findings provide crucial references for the breeding of new varieties.

The validity and reliability of the Chinese version of the biological rhythms interview of assessment in neuropsychiatry in the community: a large Chinese college student population.

Objective: To test the psychometric properties of the Chinese version of the biological rhythms interview of assessment in neuropsychiatry (C-BRIAN) in a group of young adults with and without depressive symptoms. Methods: Three hundred and seventy-eight university students were recruited as participants. Based on the scores from Center for Epidemiological Survey Depression Scale (CES-D), students were divided into the depressed group and healthy group. Explorative factor analysis was applied to assess the construct validity of the C-BRIAN. The Pittsburgh Sleep Quality Index (PSQI) and CES-D were compared with the C-BRIAN to test the convergent validity. The internal consistency of the C-BRIAN was also examined. Results: Three factors were extracted (activities, eating patterns, and sleep factors) explaining 63.9% of the total variance. The internal consistencies were very good with a coefficient of 0.94 (overall) and 0.89-0.91 for three factors. The domains of activities, eating patterns, and sleep were moderately correlated with PSQI (r=0.579) and CES-D (r=0.559) (ps<0.01). Conclusion: Our findings suggest that C-BRIAN has good validity and reliability which can be used to assess the biological rhythm in the young adult population with depressive symptoms. C-BRIAN would be a reliable tool to detect depressive symptoms for timely prevention and intervention in the community.

Changing Kindergarten Teachers' Mindsets Toward Children to Overcome Compassion Fatigue.

Introduction: Kindergarten teachers who empathize with toddlers experience a great risk of burnout and emotional disturbance. This is referred to as compassion fatigue, in which teachers' empathy experience is reduced. This study proposed a moderated mediation model to identify the risks of compassion fatigue and its protective factors for developing evidence-based clinical interventions. Methods: In this cross-sectional study, self-report measures were administered to 1049 kindergarten teachers to observe their mindsets toward children, motivation for teacher empathy, job stress, social support, and compassion fatigue. The PROCESS macro (SPSS 23.0) was used to assess the moderated mediation model. Results: The results demonstrated that motivation for teacher empathy mediated the negative relationship between kindergarten teachers' mindsets toward children and compassion fatigue. Moreover, job stress and social support moderated the relationship between kindergarten teachers' mindsets toward children and motivation for teacher empathy. However, this effect was not observed in the negative relationship between kindergarten teachers' mindsets toward children and compassion fatigue. Conclusion: The proposed moderated mediation model was found to be valid. Furthermore, the study findings have practical implications for developing evidence-based interventions for addressing kindergarten teachers' compassion fatigue.

Ubiquitin-Conjugating Enzyme OsUBC11 Affects the Development of Roots via Auxin Pathway.

Rice has 48 ubiquitin-conjugating enzymes, and the functions of most of these enzymes have not been elucidated. In the present study, a T-DNA insertional mutant named R164, which exhibited a significant decrease in the length of primary and lateral roots, was used as the experimental material to explore the potential function of OsUBC11. Analysis using the SEFA-PCR method showed that the T-DNA insertion was present in the promoter region of OsUBC11 gene, which encodes ubiquitin-conjugating enzyme (E2), and activates its expression. Biochemical experiments showed that OsUBC11 is a lysine-48-linked ubiquitin chain-forming conjugase. OsUBC11 overexpression lines showed the same root phenotypes. These results demonstrated that OsUBC11 was involved in root development. Further analyses showed that the IAA content of R164 mutant and OE3 line were significantly lower compared with wild-type Zhonghua11. Application of exogenous NAA restored the length of lateral and primary roots in R164 and OsUBC11 overexpression lines. Expression of the auxin synthesis regulating gene OsYUCCA4/6/7/9, the auxin transport gene OsAUX1, auxin/indole-3-acetic acid (Aux/IAA) family gene OsIAA31, auxin response factor OsARF16 and root regulator key genes, including OsWOX11, OsCRL1, OsCRL5 was significantly down-regulated in OsUBC11 overexpressing plants. Collectively, these results indicate that OsUBC11 modulates auxin signaling, ultimately affecting root development at the rice seedling stage.

Identification of Small Molecule Ligand Binding Sites On and In the ARNT PAS-B Domain.

Transcription factors are generally challenging to target with small molecule inhibitors due to their structural plasticity and lack of catalytic sites. Notable exceptions to this include a number of transcription factors which are naturally ligand-regulated, a strategy we have successfully exploited with the heterodimeric HIF-2 transcription factor, showing that a ligand-binding internal pocket in the HIF-2α PAS-B domain could be utilized to disrupt its dimerization with its partner, ARNT. Here, we explore the feasibility of directly targeting small molecules to the structurally similar ARNT PAS-B domain, potentially opening a promising route to simultaneously modulate several ARNT-mediated signaling pathways. Using solution NMR screening of an in-house fragment library, we previously identified several compounds that bind ARNT PAS-B and, in certain cases, antagonize ARNT association with the TACC3 transcriptional coactivator. However, these ligands only have mid-micromolar binding affinities, complicating characterization of their binding sites. Here we combine NMR, MD simulations, and ensemble docking to identify ligand-binding 'hotspots' on and within the ARNT PAS-B domain. Our data indicate that the two ARNT/TACC3 inhibitors, KG-548 and KG-655, bind to a ß-sheet surface implicated in both HIF-2 dimerization and coactivator recruitment. Furthermore, KG-548 binds exclusively to the ß-sheet surface, while KG-655 binds to the same site but can also enter a water-accessible internal cavity in ARNT PAS-B. Finally, KG-279, while not a coactivator inhibitor, exemplifies ligands that preferentially bind only to the internal cavity. Taken together, our findings provide a comprehensive overview of ARNT PAS-B ligand-binding sites and may guide the development of more potent coactivator inhibitors for cellular and functional studies.

Aerobic biodegradation of quinoline under denitrifying conditions in membrane-aerated biofilm reactor.

Aerobic denitrification is being investigated as a novel biological nitrogen removal process, yet the knowledge on aerobic denitrification is limited to pure culture isolations and its occurrence in bioreactors remains unclear. This study investigated the feasibility and capacity of applying aerobic denitrification in membrane aerated biofilm reactor (MABR) for biological treatment of quinoline-laden wastewater. Stable and efficient removals of quinoline (91.5 ± 5.2%) and nitrate (NO3-) (86.5 ± 9.3%) were obtained under different operational conditions. Enhanced formation and function of extracellular polymeric substances (EPS) were observed at increasing quinoline loadings. MABR biofilm was highly enriched with aerobic quinoline-degrading bacteria, with a predominance of Rhodococcus (26.9 ± 3.7%) and secondary abundance of Pseudomonas (1.7 ± 1.2%) and Comamonas (0.94 ± 0.9%). Metagenomic analysis indicated that Rhodococcus contributed significantly to both aromatic degradation (24.5 ± 21.3%) and NO3- reduction (4.5 ± 3.9%), indicating its key role in aerobic denitrifying quinoline biodegradation. At increasing quinoline loadings, abundances of aerobic quinoline degradation gene oxoO and denitrifying genes of napA, nirS and nirK increased; there was a significant positive correlation of oxoO with nirS and nirK (p < 0.05). Aerobic quinoline degradation was likely initiated by hydroxylation, encoded by oxoO, followed by stepwise oxidations through 5,6-dihydroxy-1H-2-oxoquinoline or 8-hydroxycoumarin pathway. The results advance our understanding of quinoline degradation during biological nitrogen removal, and highlight the potential implementation of aerobic denitrification driven quinoline biodegradation in MABR for simultaneous removal of nitrogen and recalcitrant organic carbon from coking, coal gasification and pharmaceutical wastewaters.

Biosorption of cadmium by a metal-resistant filamentous fungus isolated from chicken manure compost.

A fungus, XJ-1, isolated from chicken manure compost was phylogenetically related to Penicillium chrysogenum. The minimum inhibitory concentrations of the fungus for Cd2+, Cu2+, Cr3+, Cr6+, Co2+ and Zn2+ were 300, 85, 55, 8, 25 and 70mM on plates and 200, 65, 30, 2, 30 and 48mM in liquid media, respectively. Biosorption of Cd2+ by XJ-1 was investigated as a function of initial pH, contact time, biomass loading and Cd+ concentration. According to the Langmuir isotherm, the maximum adsorption of Cd2+ was 100.41 mg g(-1) dry biomass. Analyses using FTIR, SEM and XPS showed that the functional groups -OH and -C=O on the XJ-1 cell wall are the dominant binding sites for Cd2+. The results indicate that XJ-1 biomass is an efficient biosorbent for Cd2+ and has great potential for the in situ remediation of environments contaminated with heavy metals.