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.

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.

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.

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.

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.

Generation of induced pluripotent stem cell line (ZZUi030-A) from a patient with spastic paraplegia type 7.

Spastic paraplegia type 7 is a rare and classical monogenic inherited neurodegenerative disease caused by heterozygous mutations in the SPG7 gene. The principle clinical features include progressive spasms of the lower limbs, scissor gait, and muscle weakness. The disease currently has no effective treatment. In this study, we obtained dermal fibroblasts from a patient, which were successfully transformed into induced pluripotent stem cells (iPSCs) by employing reprogramming plasmids expressing OCT3/4, SOX2, KLF4, LIN28, and L-MYC. Our method provides a resource for mechanism exploration, drug research, cell transplantation, and gene therapy.

Genome Warehouse: A Public Repository Housing Genome-scale Data.

The Genome Warehouse (GWH) is a public repository housing genome assembly data for a wide range of species and delivering a series of web services for genome data submission, storage, release, and sharing. As one of the core resources in the National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB; https://ngdc.cncb.ac.cn), GWH accepts both full and partial (chloroplast, mitochondrion, and plasmid) genome sequences with different assembly levels, as well as an update of existing genome assemblies. For each assembly, GWH collects detailed genome-related metadata of biological project, biological sample, and genome assembly, in addition to genome sequence and annotation. To archive high-quality genome sequences and annotations, GWH is equipped with a uniform and standardized procedure for quality control. Besides basic browse and search functionalities, all released genome sequences and annotations can be visualized with JBrowse. By May 21, 2021, GWH has received 19,124 direct submissions covering a diversity of 1108 species and has released 8772 of them. Collectively, GWH serves as an important resource for genome-scale data management and provides free and publicly accessible data to support research activities throughout the world. GWH is publicly accessible at https://ngdc.cncb.ac.cn/gwh.

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.

Fragile protein folds: Sequence and environmental factors affecting the equilibrium of two interconverting, stably folded protein conformations.

Recent research on fold-switching metamorphic proteins has revealed some notable exceptions to Anfinsen's hypothesis of protein folding. We have previously described how a single point mutation can enable a well-folded protein domain, one of the two PAS (Per-ARNT-Sim) domains of the human ARNT (aryl hydrocarbon receptor nuclear translocator) protein, to interconvert between two conformers related by a slip of an internal ß-strand. Using this protein as a test case, we advance the concept of a "fragile fold," a protein fold that can reversibly rearrange into another fold that differs by a substantial number of hydrogen bonds, entailing reorganization of single secondary structure elements to more drastic changes seen in metamorphic proteins. Here we use a battery of biophysical tests to examine several factors affecting the equilibrium between the two conformations of the switching ARNT PAS-B Y456T protein. Of note, we find that factors which impact the HI loop preceding the shifted Iß-strand affect both the equilibrium levels of the two conformers and the denatured state which links them in the interconversion process. Finally, we describe small molecules that selectively bind to and stabilize the wildtype conformation of ARNT PAS-B. These studies form a toolkit for studying fragile protein folds and could enable ways to modulate the biological functions of such fragile folds, both in natural and engineered proteins.

RASSF effectors couple diverse RAS subfamily GTPases to the Hippo pathway.

Small guanosine triphosphatases (GTPases) of the RAS superfamily signal by directly binding to multiple downstream effector proteins. Effectors are defined by a folded RAS-association (RA) domain that binds exclusively to GTP-loaded (activated) RAS, but the binding specificities of most RA domains toward more than 160 RAS superfamily GTPases have not been characterized. Ten RA domain family (RASSF) proteins comprise the largest group of related effectors and are proposed to couple RAS to the proapoptotic Hippo pathway. Here, we showed that RASSF1-6 formed complexes with the Hippo kinase ortholog MST1, whereas RASSF7-10 formed oligomers with the p53-regulating effectors ASPP1 and ASPP2. Moreover, only RASSF5 bound directly to activated HRAS and KRAS, and RASSFs did not augment apoptotic induction downstream of RAS oncoproteins. Structural modeling revealed that expansion of the RASSF effector family in vertebrates included amino acid substitutions to key residues that direct GTPase-binding specificity. We demonstrated that the tumor suppressor RASSF1A formed complexes with the RAS-related GTPases GEM, REM1, REM2, and the enigmatic RASL12. Furthermore, interactions between RASSFs and RAS GTPases blocked YAP1 nuclear localization. Thus, these simple scaffolds link the activation of diverse RAS family small G proteins to Hippo or p53 regulation.

Biodegradation of phenolic compounds in high saline wastewater by biofilms adhering on aerated membranes.

High saline phenolic wastewater is a typical toxic and refractory industrial wastewater. A single membrane-aerated biofilm reactor (MABR) was used to treat wastewater containing phenol, p-nitrophenol and hydroquinone under increasing phenolic loading and salinity conditions. More than 95 % of phenolic compounds were removed, and a removal efficiency of 8.9 g/m2 d for total phenolic (TP) contents was achieved under conditions with 32 g/L of salt and 763 mg/L of influent TP contents. The microbial diversity, structure and function of a biofilm exposed to different conditions were investigated by high-throughput 16S rRNA gene sequencing and metagenomics. Salinity and specific TP loading substantially affected the bacterial community. Gammaproteobacteria, Actinobacteria and Betaproteobacteria contributed more to initial phenolic compound degradation than other classes, with Pseudomonas and Rhodococcus as the main contributing genera. The key phenolic-degrading genes of different metabolic pathways were explored, and their relative abundance was strengthened with increasing phenolic loading and salinity. The diverse cooperation and competition patterns of these microorganisms further promoted the high removal efficiency of multiple phenolic contaminants in the biofilms. These results demonstrate the feasibility of MABR for degrading multiple phenolic compounds in high saline wastewater.

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.

Enhanced wastewater treatment with high o-aminophenol concentration by two-stage MABR and its biodegradation mechanism.

A two-stage bench-scale membrane-aerated biofilm reactor (MABR) was developed to treat wastewater containing high o-aminophenol (OAP) content. Long-term process showed that MABR-1 can achieve the removal rates of 17.6 g OAP/m2 d and 29.4 g COD/m2 d. MABR-2 can effectively perform more than 90% TN removal with the addition of external glucose. Pseudomonas and Nitrosomonas were the key functional genera in MABR-1 and MABR-2, respectively. Functional genes related to OAP degradation, including amnA,B,D, dmpC,H, mhpD,E,F, and bphH,I,J, were detected, and the involved enzymes were predicted. The OAP-degrading species and functional contribution analysis indicated that OAP can be metabolized by a single Pseudomonas or by the synergistic effects of bacteria, mainly including Cupriavidus, Thauera, unclassified Sphingomonadaceae, Lysobacter, and Azotobacter or by the cooperation of all the bacteria above. These diversified patterns guaranteed the high efficiency for OAP removal in MABR when treating wastewater with high OAP concentration.

Identifying and Predicting the Geographical Distribution Patterns of Oncomelania hupensis.

Schistosomiasis is a snail-borne parasitic disease endemic to the tropics and subtropics, whose distribution depends on snail prevalence as determined by climatic and environmental factors. Here, dynamic spatial and temporal patterns of Oncomelania hupensis distributions were quantified using general statistics, global Moran's I, and standard deviation ellipses, with Maxent modeling used to predict the distribution of habitat areas suitable for this snail in Gong'an County, a severely affected region of Jianghan Plain, China, based on annual average temperature, humidity of the climate, soil type, normalized difference vegetation index, land use, ditch density, land surface temperature, and digital elevation model variables; each variable's contribution was tested using the jackknife method. Several key results emerged. First, coverage area of O. hupensis had changed little from 2007 to 2012, with some cities, counties, and districts alternately increasing and decreasing, with ditch and bottomland being the main habitat types. Second, although it showed a weak spatial autocorrelation, changing negligibly, there was a significant east-west gradient in the O. hupensis habitat area. Third, 21.9% of Gong'an County's area was at high risk of snail presence; and ditch density, temperature, elevation, and wetting index contributed most to their occurrence. Our findings and methods provide valuable and timely insight for the control, monitoring, and management of schistosomiasis in China.

Degradation of bisphenol a using peroxymonosulfate activated by WO3@MoS2/Ag hollow nanotubes photocatalyst.

WO3@MoS2/Ag (HW@MA) hollow tubes were successfully engineered to photodegrade bisphenol A (BPA) combined with peroxymonosulfate (PMS) for the first time. XRD, XPS, TEM and SEM were conducted. The HW@MA tubes present excellent photocatalytic performance on the removal of BPA. The intermediate products of BPA were investigated by GC-MS analysis and the degradation pathway was proposed. To explore the transferred mechanism of photoproduced carriers, the electron paramagnetic resonance (EPR) technique was carried out. The results revealed that the superoxide radical (O2-), hydroxyl radical (OH), sulfate radical (SO4-) were the main active radicals. Moreover, the formed schottky junctions enhanced the separation efficiency of photoinduced electron-hole pairs. Besides, the effect of the photocatalysts' dosage, PMS concentration, pH of the initial solution and co-existing anions on the BPA degradation were investigated.

Comparative studies on Pb(II) biosorption with three spongy microbe-based biosorbents: High performance, selectivity and application.

Lead pollution in industrial-derived water has become an increasingly serious concern. The development of adsorbents with excellent efficiency, selectivity and separability using diverse microorganisms is ideal for treating lead pollution. In this study, gram-negative bacteria Pseudomonas putida I3, gram-positive bacteria Microbacterium sp. OLJ1 and mycelial fungus Talaromyces amestolkiae Pb served as raw materials to facilely synthesize sponge-like biosorbents via a one-step method at room temperature. SEM, EDS, FTIR, 13C NMR, XRD and XPS were used for investigating the morphology and surface properties of these three biosorbents. The obtained biosorbents possessed the same three-dimensional porous structure but different productivities and mechanical strengths due to the similar chemical compositions and different cell structures of their microorganisms. Pb(II) adsorption on X-PI3, X-OLJ1 and X-TPb was fast and pH dependent, with maximal adsorption capacities of 345.02, 237.02 and 199.02 mg/g, respectively. The biosorbents had a high selectivity for Pb(II), while Pb(II) remarkably suppressed the adsorption of co-existing heavy metal ions. The analyses indicated that Pb(II) removal was mainly achieved by ion exchange reactions, surface complexation with heteroatom-containing functional groups and microprecipitation. The treatment effects of synthetic and real wastewater revealed that the as-prepared biosorbents are promising for Pb(II) removal.

Potential biodegradation of phenanthrene by isolated halotolerant bacterial strains from petroleum oil polluted soil in Yellow River Delta.

The Yellow River Delta (YRD), being close to Shengli Oilfield, is at high risk for petroleum oil pollution. The aim of this study was to isolate halotolerant phenanthrene (PHE) degrading bacteria for dealing with this contaminates in salinity environment. Two bacterial strains assigned as FM6-1 and FM8-1 were successfully screened from oil contaminated soil in the YRD. Morphological and molecular analysis suggested that strains FM6-1 and FM8-1 were belonging to Delftia sp. and Achromobacter sp., respectively. Bacterial growth of both strains was not dependent on NaCl, however, grew well under extensive NaCl concentration. The optimum NaCl concentration for bacterial production of strain FM8-1 was 4% (m/v), whereas for strain FM6-1, growth was not affected within 2.5% NaCl. Both strains could use the tested aromatic hydrocarbons (naphthalene, phenanthrene, fluoranthene and pyrene) and aliphatic hydrocarbons (C12, C16, C20 and C32) as sole carbon source. The optimized biodegradation conditions for strain FM6-1 were pH 7, 28 °C and 2% NaCl, for strain FM8-1 were pH 8, 28 °C and 2.5% NaCl. The highest biodegradation rate of strains FM6-1 and FM8-1 was found at 150 mg/L PHE and 200 mg/L, respectively. In addition, strainsFM8-1 showed a superior biodegradation ability to strain FM6-1 at each optimized condition. The PHE biodegradation process by both strains well fitted to first-order kinetic models and the k1 values were calculated to be 0.1974 and 0.1070 per day. Strain FM6-1 metabolized PHE via a "phthalic acid" route, while strain FM8-1 metabolized PHE through the "naphthalene" route. This project not only obtained two halotolerant petroleum hydrocarbon degraders but also provided a promising remediation approach for solving oil pollutants in salinity environments.

Construction of flower-like MoS2/Ag2S/Ag Z-scheme photocatalysts with enhanced visible-light photocatalytic activity for water purification.

Flower-like MoS2/Ag2S/Ag nanocomposites have been elaborately designed and synthesized successfully for the first time. The prepared MoS2/Ag2S/Ag nanocomposites as a novel photocatalysts present effective photocatalytic performance for the photodegradation of congo red (CR), tetracycline hydrochloride (TC-HCl) and disinfection for Pseudomonas aeruginosa (P. aeruginosa). For the photodegradation of TC-HCl, the effect of the pH of the initial solution and photocatalysts dosage was investigated. Furthermore, intermediates of TC-HCl degradation were verified by GC-MS analysis and the possible pathway of the photodegradation was also proposed. The electron paramagnetic resonance (EPR) technique and trapping experiments verified the electron transport path is Z-scheme system (PS-C-PS). Among them, Ag as an electron mediator enhanced the electron transmission rate and accelerated the separation efficiency of photogenerated carriers.

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.