Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ.

Alternative polyadenylation (APA) enables a gene to generate multiple transcripts with different 3' ends, which is dynamic across different cell types or conditions. Many computational methods have been developed to characterize sample-specific APA using the corresponding RNA-seq data, but suffered from high error rate on both polyadenylation site (PAS) identification and quantification of PAS usage (PAU), and bias toward 3' untranslated regions. Here we developed a tool for APA identification and quantification (APAIQ) from RNA-seq data, which can accurately identify PAS and quantify PAU in a transcriptome-wide manner. Using 3' end-seq data as the benchmark, we showed that APAIQ outperforms current methods on PAS identification and PAU quantification, including DaPars2, Aptardi, mountainClimber, SANPolyA, and QAPA. Finally, applying APAIQ on 421 RNA-seq samples from liver cancer patients, we identified >540 tumor-associated APA events and experimentally validated two intronic polyadenylation candidates, demonstrating its capacity to unveil cancer-related APA with a large-scale RNA-seq data set.

EMNGly: predicting N-linked glycosylation sites using the language models for feature extraction.

MOTIVATION: N-linked glycosylation is a frequently occurring post-translational protein modification that serves critical functions in protein folding, stability, trafficking, and recognition. Its involvement spans across multiple biological processes and alterations to this process can result in various diseases. Therefore, identifying N-linked glycosylation sites is imperative for comprehending the mechanisms and systems underlying glycosylation. Due to the inherent experimental complexities, machine learning and deep learning have become indispensable tools for predicting these sites. RESULTS: In this context, a new approach called EMNGly has been proposed. The EMNGly approach utilizes pretrained protein language model (Evolutionary Scale Modeling) and pretrained protein structure model (Inverse Folding Model) for features extraction and support vector machine for classification. Ten-fold cross-validation and independent tests show that this approach has outperformed existing techniques. And it achieves Matthews Correlation Coefficient, sensitivity, specificity, and accuracy of 0.8282, 0.9343, 0.8934, and 0.9143, respectively on a benchmark independent test set.

Accurate and efficient protein sequence design through learning concise local environment of residues.

MOTIVATION: Computational protein sequence design has been widely applied in rational protein engineering and increasing the design accuracy and efficiency is highly desired. RESULTS: Here, we present ProDESIGN-LE, an accurate and efficient approach to protein sequence design. ProDESIGN-LE adopts a concise but informative representation of the residue's local environment and trains a transformer to learn the correlation between local environment of residues and their amino acid types. For a target backbone structure, ProDESIGN-LE uses the transformer to assign an appropriate residue type for each position based on its local environment within this structure, eventually acquiring a designed sequence with all residues fitting well with their local environments. We applied ProDESIGN-LE to design sequences for 68 naturally occurring and 129 hallucinated proteins within 20 s per protein on average. The designed proteins have their predicted structures perfectly resembling the target structures with a state-of-the-art average TM-score exceeding 0.80. We further experimentally validated ProDESIGN-LE by designing five sequences for an enzyme, chloramphenicol O-acetyltransferase type III (CAT III), and recombinantly expressing the proteins in Escherichia coli. Of these proteins, three exhibited excellent solubility, and one yielded monomeric species with circular dichroism spectra consistent with the natural CAT III protein. AVAILABILITY AND IMPLEMENTATION: The source code of ProDESIGN-LE is available at https://github.com/bigict/ProDESIGN-LE.

Previously unaccounted atmospheric mercury deposition in a midlatitude deciduous forest.

Mercury is toxic to wildlife and humans, and forests are thought to be a globally important sink for gaseous elemental mercury (GEM) deposition from the atmosphere. Yet there are currently no annual GEM deposition measurements over rural forests. Here we present measurements of ecosystem-atmosphere GEM exchange using tower-based micrometeorological methods in a midlatitude hardwood forest. We measured an annual GEM deposition of 25.1 µg ⋅ m-2 (95% CI: 23.2 to 26.7 1 µg ⋅ m-2), which is five times larger than wet deposition of mercury from the atmosphere. Our observed annual GEM deposition accounts for 76% of total atmospheric mercury deposition and also is three times greater than litterfall mercury deposition, which has previously been used as a proxy measure for GEM deposition in forests. Plant GEM uptake is the dominant driver for ecosystem GEM deposition based on seasonal and diel dynamics that show the forest GEM sink to be largest during active vegetation growing periods and middays, analogous to photosynthetic carbon dioxide assimilation. Soils and litter on the forest floor are additional GEM sinks throughout the year. Our study suggests that mercury loading to this forest was underestimated by a factor of about two and that global forests may constitute a much larger global GEM sink than currently proposed. The larger than anticipated forest GEM sink may explain the high mercury loads observed in soils across rural forests, which impair water quality and aquatic biota via watershed Hg export.

GIPS-Mix for Accurate Identification of Isomeric Components in Glycan Mixtures Using Intelligent Group-Opting Strategy.

Accurate identification of glycan structures is highly desirable as they are intimately linked to their different functions. However, glycan samples generally exist as mixtures with multiple isomeric structures, making assignment of individual glycan components very challenging, even with the aid of multistage mass spectrometry (MSn). Here, we present an approach, GIPS-mix, for assignment of isomeric glycans within a mixture using an intelligent group-opting strategy. Our approach enumerates all possible combinations (groupings) of candidate glycans and opts in the best-matched glycan group(s) based on the similarity between the simulated spectra of each glycan group and the acquired experimental spectra of the mixture. In the case that a single group could not be elected, a tie break is performed by additional MSn scanning using intelligently selected precursors. With 11 standard mixtures and 6 human milk oligosaccharide fractions, we demonstrate the application of GIPS-mix in assignment of individual glycans in mixtures with high accuracy and efficiency.

Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction.

MOTIVATION: Accurate prediction of protein structure relies heavily on exploiting multiple sequence alignment (MSA) for residue mutations and correlations as this information specifies protein tertiary structure. The widely used prediction approaches usually transform MSA into inter-mediate models, say position-specific scoring matrix or profile hidden Markov model. These inter-mediate models, however, cannot fully represent residue mutations and correlations carried by MSA; hence, an effective way to directly exploit MSAs is highly desirable. RESULTS: Here, we report a novel sequence set network (called Seq-SetNet) to directly and effectively exploit MSA for protein structure prediction. Seq-SetNet uses an 'encoding and aggregation' strategy that consists of two key elements: (i) an encoding module that takes a component homologue in MSA as input, and encodes residue mutations and correlations into context-specific features for each residue; and (ii) an aggregation module to aggregate the features extracted from all component homologues, which are further transformed into structural properties for residues of the query protein. As Seq-SetNet encodes each homologue protein individually, it could consider both insertions and deletions, as well as long-distance correlations among residues, thus representing more information than the inter-mediate models. Moreover, the encoding module automatically learns effective features and thus avoids manual feature engineering. Using symmetric aggregation functions, Seq-SetNet processes the homologue proteins as a sequence set, making its prediction results invariable to the order of these proteins. On popular benchmark sets, we demonstrated the successful application of Seq-SetNet to predict secondary structure and torsion angles of residues with improved accuracy and efficiency. AVAILABILITY AND IMPLEMENTATION: The code and datasets are available through https://github.com/fusong-ju/Seq-SetNet. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Thrap3 promotes osteogenesis by inhibiting the degradation of Runx2.

The dysfunction of osteogenesis is a key character in the pathogenesis of osteoporosis, but the network of signaling mechanisms in controlling the differentiation of osteoblast remain unclear. Thrap3 has been proved participating in various biological process, especially in the differentiation of stem cells. Here, we demonstrate that Thrap3 could promote osteogenesis through the inhibition of the degradation of Runx2, which is a key molecular structure in early osteoblast differentiation. Furthermore, we found that the osteogenesis enhancing capacity of Thrap3 was caused by physically binding with Sox9, inhibiting the transcriptional activity of Sox9, and then decreasing the decomposition-promoted effect of Sox9 on Runx2. Our data shows that Thrap3 promotes osteoblast differentiation through the Thrap3-Sox9-Runx2 axis. What we found may help for further clarifying the molecular mechanism of osteogenic differentiation and give a new potential therapeutic target for osteoporosis.

Molecular characteristics and pathogenicity of a novel chicken astrovirus variant.

It is well-established that the genetic diversity, regional prevalence, and broad host range of astroviruses significantly impact the poultry industry. In July 2022, a small-scale commercial broiler farm in China reported cases of growth retardation and a 3% mortality rate. From chickens displaying proventriculitis and pancreatitis, three chicken astroviruses (CAstV) isolates were obtained and named SDAU2022-1-3. Complete genomic sequencing and analysis revealed the unique characteristics of these isolates from known CAstV strains in ORF1a, ORF1b, and ORF2 genes, characterized by an unusually high variability. Analysis of amino acid mutations in ORF1a, ORF1b, and ORF2 indicated that the accumulation of these mutations played a pivotal role in the emergence of the variant strain. Inoculation experiments demonstrated that affected chickens exhibited liver and kidney enlargement, localized proventricular hemorrhage, and a dark reddish-brown appearance in about two-thirds of the pancreas. Histopathological examination unveiled hepatic lymphocytic infiltration, renal tubular epithelial cell swelling, along with lymphocytic proventriculitis and pancreatitis. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis indicated viremia and viral shedding at 3 days post-infection (dpi). The proventriculus displayed the highest viral loads, followed by the liver, kidney, duodenum, and pancreas. Liver parameters (AST and ALT) and kidney parameters (UA and UN) demonstrated mild damage consistent with earlier findings. While the possibility of new mutations in the ORF2 gene of CAstV causing proventriculitis and pancreatitis warrants further investigation, these findings deepen our comprehension of CAstV's pathogenicity in chickens. Additionally, they serve as valuable references for subsequent research endeavors.

First Report of Pestalotiopsis clavispora causing Leaf Spot on Pandanus amaryllifolius in China.

Pandanus amaryllifolius, also known as pandan, is a perennial herb, growing in Indonesia, China and the Maluku Islands (Wakte et al. 2009). It is the only plant with aromatic leaves in the Pandanaceae. It is widely used in food, medicine, cosmetics and other industries, and is also known as "Oriental Vanilla." Pandan is planted in Hainan province over 1,300 ha and is the main plant intercropped among the forest trees. From 2020, the leaf spot was surveyed for three years. Diseased leaves occurred on 30 to 80% of the surveyed plants, with an incidence of 70% and yield losses of 40%. The disease occured from mid-November to April and was most severe at low temperatures and humidity. Initial symptoms were pale green spots, that formed dark brown, nearly circular lesions. As the lesions expanded, their centers became greyish white, with yellow halos at the junction of the diseased and healthy tissue. When the humidity was high, there were small black spots scattered in the center of the lesion. Symptomatic leaf samples were collected from four different sites. The leaf surface was disinfested with 75% ethyl alcohol for 30 s and washed with sterile distilled water three times. Samples from the junction of diseased and healthy tissue (0.5 × 0.5 cm) were removed and placed on potato dextrose agar (PDA) medium containing 100 µg/mL of cefotaxime sodium and cultivated in a dark incubator at 28°C. After two days, hyphal tips from the edges of growing colonies were transferred to fresh PDA plates for further purification. Following Koch's postulates, colonies from strains were used as inoculum in pathogenicity tests. Colonies with 5 mm diameter were inoculated upside onto fresh and healthy pandan leaves via wounding method (pinpricked by sterilized needles) and non-wounding method. Sterilized PDA was used as control. All plants were setted three replicates and were incubated at 28℃ for 3 to 5 days. When symptoms on leaves similar to those in the field appeared, the fungus were reisolated The colonies formed on PDA were also consistent with the original isolate (Scandiani et al, 2003). After seven days, the colony covered the whole petri dish with white, petal-shaped growth with a slight concentric, annular bulge in the center, irregular edges, with black acervuli emerging at a later stage of colony growth. Conidia were fusiform, 18.1±1.6 × 6.4±0.3 µm, showing four septations and five cells, the middle three cells were brownish black to olivaceous, and the apical cell colorless with two to three filaments, 21.8±3.5 µm long. The caudate cell was colorless with one stalk 5.9±1.8 µm long (Zhang et al. 2021; Shu et al. 2020). According to the colony and conidia characteristics, the pathogen was initially identified as Pestalotiopsis spp. (Benjamin et al. 1961). To confirm the pathogen identity, we used the universal primers ITS1/ITS4, targeting primers EF1-728F/EF1-986R and Bt2a/Bt2b sequences (Tian et al. 2018). The sequences of the PCR products were deposited in NCBI GenBank with accession numbers OQ165166 (ITS), OQ352149 (TEF1-α) and OQ352150 (TUB2). BLAST results showed that the sequences of the ITS, TEF1-α and TUB2 genes shared 100% homology with the sequences of Pestalotiopsis clavispora. The maximum likelihood method was used in the phylogenetic analysis. The result showed that LSS112 was clustered with Pestalotiopsis clavispora with a support rate of 99%. Based on morphological and molecular characteristics, the pathogen was confirmed as Pestalotiopsis clavispora. To our knowledge, this is the first report of leaf spot of pandan caused by Pestalotiopsis clavispora in China. This research will be immediately helpful for the diagnosis and control the disease on pandan.

Identification and screening of fungicides against Piper nigrum basal Fusarium wilt disease in Hainan, China.

Fusarium wilt has occurred in the main Piper nigrum cultivation regions, which seriously affects the yield and quality of P. nigrum. To identify the pathogen of this disease, the diseased roots were collected from a demonstration base in Hainan Province. The pathogen was obtained by tissue isolation method and confirmed by pathogenicity test. Based on the morphological observation, sequence analyses of TEF1-α nuclear gene, Fusarium solani was identified as the pathogen causing P. nigrum Fusarium wilt and induced symptoms on inoculated plants, including chlorosis, necrotic spots, wilt, drying, and root rot. The experiments for the antifungal activity showed that all the 11 fungicides selected in this study showed certain inhibitory effects on the colony growth of F. solani, where 2% kasugamycin AS, 45% prochloraz EW, 25 g·L-1 fludioxonil SC and 430 g·L-1 tebuconazole SC exhibited relative higher inhibitory effects with EC50 as 0.065, 0.205, 0.395, and 0.483 mg·L-1 , respectively, and were selected to perform SEM analysis and test in seeds in vitro. The SEM analysis showed that kasugamycin, prochloraz, fludioxonil, and tebuconazole might have exerted their antifungal effect by damaging F. solani mycelia or microconidia. These preparations were applied as a seed coating of P. nigrum Reyin-1. The kasugamycin treatment was most effective in reducing the harmful impact of F. solani on the seed germination. These results presented herein provide useful guidance for the effective control of P. nigrum Fusarium wilt.

The relationship between bladder storage function and frequent micturition after TURP.

PURPOSE: To investigate the relationship between preoperative bladder function and frequent micturition after transurethral resection of prostate in patients with benign prostatic hyperplasia. METHODS: We retrospectively included 80 eligible patients aged 54-87 years (mean age 69.8 years) who underwent transurethral resection of the prostate at our hospital from January 2019 to October 2021. Patients were divided into detrusor overactivity positive and negative groups, and according to bladder compliance, they were divided into: low (G1), normal (G2), and high (G3) bladder compliance groups. RESULTS: The incidence and score of postoperative frequent micturition in the detrusor overactivity positive group were higher than those in the detrusor overactivity negative group. The incidence and score of postoperative frequent micturition in the low bladder compliance group were higher than those in the normal and high bladder compliance groups. There was no significant difference in the score of frequent micturition between the normal and high bladder compliance groups. Multivariate logistic regression analysis indicated that frequent micturition was significantly correlated with detrusor overactivity, bladder compliance, maximum cystometric capacity, and maximum flow rate. CONCLUSION: This study confirmed that patients with abnormal bladder storage functions (detrusor instability and low bladder compliance) before transurethral resection of the prostate were likely to have frequent and severe urination after transurethral resection of the prostate. Therefore, preoperative urodynamic examination to evaluate the urinary storage function of patients with benign prostatic hyperplasia is of great significance to predict the occurrence and degree of postoperative frequent micturition.

Dok5 regulates proliferation and differentiation of osteoblast via canonical Wnt/ß-catenin signaling.

OBJECTIVE: In bone tissue engineering, the use of osteoblastic seed cells has been widely adopted to mediate the osteogenic differentiation so as to prompt bone regeneration and repair. It is hypothesized that Dok5 can regulate the proliferation and differentiation of osteoblasts. In this study, the role of Dok5 in osteoblast proliferation and differentiation was investigated. METHODS: A lentiviral vector to silence Dok5 was transferred to C3H10, 293T and C2C12 cells. CCK-8 assay was used to detect the cell proliferation. Cells were stained by ALP and AR-S staining. Western blot and RT-PCR were used to detect the expression levels of related factors. RESULTS: Dok5 expression level was gradually up-regulated during the osteoblast differentiation. Dok5 silencing down-regulated the expression levels of osteogenic biosignatures OPN, OCN, and Runx2 and suppressed the osteogenesis. Additionally, the osteoblast proliferation and canonical Wnt/ß-catenin signaling were suppressed upon Dok5 knockdown, ß-catenin expression level was significantly down-regulated in the knockdown group, while the expression levels of GSK3-ß and Axin, negative regulators in the Wnt signaling pathway, were up-regulated. Furthermore, overexpression of Dok5 promoted the proliferation and osteogenesis and activated the canonical Wnt/ß-catenin signaling pathway. CONCLUSION: Dok5 may regulate the osteogenic proliferation and differentiation via the canonical Wnt/ß-catenin signaling pathway.

NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies: Comparison of Results from Diverse Analytical Methods.

Glycosylation is a topic of intense current interest in the development of biopharmaceuticals because it is related to drug safety and efficacy. This work describes results of an interlaboratory study on the glycosylation of the Primary Sample (PS) of NISTmAb, a monoclonal antibody reference material. Seventy-six laboratories from industry, university, research, government, and hospital sectors in Europe, North America, Asia, and Australia submitted a total of 103 reports on glycan distributions. The principal objective of this study was to report and compare results for the full range of analytical methods presently used in the glycosylation analysis of mAbs. Therefore, participation was unrestricted, with laboratories choosing their own measurement techniques. Protein glycosylation was determined in various ways, including at the level of intact mAb, protein fragments, glycopeptides, or released glycans, using a wide variety of methods for derivatization, separation, identification, and quantification. Consequently, the diversity of results was enormous, with the number of glycan compositions identified by each laboratory ranging from 4 to 48. In total, one hundred sixteen glycan compositions were reported, of which 57 compositions could be assigned consensus abundance values. These consensus medians provide community-derived values for NISTmAb PS. Agreement with the consensus medians did not depend on the specific method or laboratory type. The study provides a view of the current state-of-the-art for biologic glycosylation measurement and suggests a clear need for harmonization of glycosylation analysis methods.

Perioperative factors influencing the difficulty of retroperitoneal laparoscopic adrenalectomy: a single-center retrospective study.

PURPOSE: Identifying patients in whom adrenalectomy may be more difficult can help with surgical decision-making. This study investigated the perioperative factors affecting the difficulty of retroperitoneal laparoscopic adrenalectomy (RLA). METHODS: Sixty-eight patients who underwent RLA at our hospital between December 1, 2020 and May 1, 2021 were included. The difficulty of RLA was assessed by operating time and intraoperative blood loss. We analyzed the relationship between surgical difficulty and patient sex, age, and body mass index, pathological type, tumor side, tumor size, distance from the lower pole of the adrenal tumor to the upper pole of the kidney (DAK), and distance from the lower pole of the adrenal tumor to the renal pedicle (DARP). RESULTS: Mean operating time was 105.38 ± 33.31 min and mean intraoperative blood loss was 32.28 ± 22.88 ml. Univariate linear regression analysis showed that age (P = 0.047), tumor size (P = 0.002), DAK (P = 0.002), and DARP (P < 0.001) were significantly correlated with a longer operating time. Univariate logistic regression analysis showed that DARP (P = 0.001), DAK (P = 0.001), tumor size (P = 0.002), and age (P = 0.033) were significantly correlated with a longer operating time. Multivariate logistic regression indicated that DARP (OR 5.341; 95% CI 1.704-16.739; P = 0.004), and tumor size (OR 4.433; 95% CI 1.434-13.709; P = 0.010) were independent predictors of operating time. CONCLUSION: Age, tumor size, DAK, and DARP were predictors of the difficulty of RLA. Older age, lower DARP and DAK, and a larger tumor size were associated with a longer operating time. DARP and tumor size were independent predictors of surgical difficulty.

Selection of reference genes for quantitative real-time PCR normalization in the coffee white stem borer, Xylotrechus quadripes Chevrolat (Coleoptera: Cerambycidae).

The coffee white stem borer, Xylotrechus quadripes Chevrolat (Coleoptera: Cerambycidae), is a major destructive pest of Coffea arabica L. (Gentianales: Rubiaceae), widely planted in many Asian countries, including China. Quantitative real-time polymerase chain reaction (qRT-PCR) is a common method for quantitative analysis of gene transcription levels. To obtain accurate and reliable qRT-PCR results, it is necessary to select suitable reference genes to different experimental conditions for normalizing the target gene expression. However, the stability of the expression of reference genes in X. quadripes has rarely been studied. In this study, the expression stability of nine candidate reference genes were investigated under biotic and abiotic conditions for use in qRT-PCR's normalization. By integrating the results of four algorithms of NormFinder, BestKeeper, geNorm, and RefFinder, the optimal reference gene combinations in different experimental conditions were performed as follows: RPL10a and EIF3D were the optimal reference genes for developmental stage samples, EIF4E, RPL10a, and RPS27a for tissue samples, V-ATP and EF1α for the sex samples, EIF3D and V-ATP for temperature treatment, RPS27a and RPL10a for insecticide stress, and RPL10a, RPS27a, and EF1α for all the samples. This study will help to obtain the stable internal reference genes under biotic and abiotic conditions and lay the foundation for in-depth functional research of target genes or genomics on olfactory molecular mechanisms, temperature adaptability, and insecticide resistance in X. quadripes.

α-Glucosidase inhibitory effect of an anthraquinonoid produced by Fusarium incarnatum GDZZ-G2.

α-Glucosidase is the key enzyme on carbohydrate metabolism, and its bioactive inhibitors are supposed to be an effective therapeutic for type 2 diabetes mellitus. During our continuing study for discovering α-glucosidase inhibitors, a fungus GDZZ-G2 which is derived from a medicinal plant Callicarpa kwangtungensis Chun, exhibited significant inhibition on α-glucosidase. The strain was identified as Fusarium incarnatum by morphological and molecular methods. Further bioassay-guided fractionation result in six known secondary metabolites (1-6). All the compounds except 4 were isolated from F. incarnatum for the first time. Among them, an anthraquinonoid (S)-1,3,6-trihydroxy-7-(1-hydroxyethyl)anthracene-9,10-dione (compound 1) exhibited strong inhibitory effect against α-glucosidase (IC50 = 77.67 ± 0.67 µΜ), compared with acarbose (IC50 = 711.8 ± 5 µΜ). An enzyme kinetics analysis revealed that compound 1 was an uncompetitive inhibitor. Besides, docking simulations predicted that compound 1 inhibited α-glucosidase substrate complex by binding Gln322, Gly306, Thr307, and Ser329 through hydrogen-bond interactions. Our findings suggested that compound 1 can be considered a lead compound for further modifications and the development of a new effective drug candidate in the treatment of type 2 diabetes mellitus.

FALCON2: a web server for high-quality prediction of protein tertiary structures.

BACKGROUND: Accurate prediction of protein tertiary structures is highly desired as the knowledge of protein structures provides invaluable insights into protein functions. We have designed two approaches to protein structure prediction, including a template-based modeling approach (called ProALIGN) and an ab initio prediction approach (called ProFOLD). Briefly speaking, ProALIGN aligns a target protein with templates through exploiting the patterns of context-specific alignment motifs and then builds the final structure with reference to the homologous templates. In contrast, ProFOLD uses an end-to-end neural network to estimate inter-residue distances of target proteins and builds structures that satisfy these distance constraints. These two approaches emphasize different characteristics of target proteins: ProALIGN exploits structure information of homologous templates of target proteins while ProFOLD exploits the co-evolutionary information carried by homologous protein sequences. Recent progress has shown that the combination of template-based modeling and ab initio approaches is promising. RESULTS: In the study, we present FALCON2, a web server that integrates ProALIGN and ProFOLD to provide high-quality protein structure prediction service. For a target protein, FALCON2 executes ProALIGN and ProFOLD simultaneously to predict possible structures and selects the most likely one as the final prediction result. We evaluated FALCON2 on widely-used benchmarks, including 104 CASP13 (the 13th Critical Assessment of protein Structure Prediction) targets and 91 CASP14 targets. In-depth examination suggests that when high-quality templates are available, ProALIGN is superior to ProFOLD and in other cases, ProFOLD shows better performance. By integrating these two approaches with different emphasis, FALCON2 server outperforms the two individual approaches and also achieves state-of-the-art performance compared with existing approaches. CONCLUSIONS: By integrating template-based modeling and ab initio approaches, FALCON2 provides an easy-to-use and high-quality protein structure prediction service for the community and we expect it to enable insights into a deep understanding of protein functions.

Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph.

BACKGROUND: Optical maps record locations of specific enzyme recognition sites within long genome fragments. This long-distance information enables aligning genome assembly contigs onto optical maps and ordering contigs into scaffolds. The generated scaffolds, however, often contain a large amount of gaps. To fill these gaps, a feasible way is to search genome assembly graph for the best-matching contig paths that connect boundary contigs of gaps. The combination of searching and evaluation procedures might be "searching followed by evaluation", which is infeasible for long gaps, or "searching by evaluation", which heavily relies on heuristics and thus usually yields unreliable contig paths. RESULTS: We here report an accurate and efficient approach to filling gaps of genome scaffolds with aids of optical maps. Using simulated data from 12 species and real data from 3 species, we demonstrate the successful application of our approach in gap filling with improved accuracy and completeness of genome scaffolds. CONCLUSION: Our approach applies a sequential Bayesian updating technique to measure the similarity between optical maps and candidate contig paths. Using this similarity to guide path searching, our approach achieves higher accuracy than the existing "searching by evaluation" strategy that relies on heuristics. Furthermore, unlike the "searching followed by evaluation" strategy enumerating all possible paths, our approach prunes the unlikely sub-paths and extends the highly-probable ones only, thus significantly increasing searching efficiency.

Microfibrillar-associated protein 5 regulates osteogenic differentiation by modulating the Wnt/ß-catenin and AMPK signaling pathways.

BACKGROUND: Dysfunctional osteogenesis of bone marrow mesenchymal stem cells (BMSCs) plays an important role in osteoporosis occurrence and development. However, the molecular mechanisms of osteogenic differentiation remain unclear. This study explored whether microfibrillar-associated protein 5 (MFAP5) regulated BMSCs osteogenic differentiation. METHODS: We used shRNA or cDNA to knock down or overexpress MFAP5 in C3H10 and MC3T3-E1 cells. AR-S- and ALP-staining were performed to quantify cellular osteogenic differentiation. The mRNA levels of the classical osteogenic differentiation biomarkers Runx2, Col1α1, and OCN were quantified by qRT-PCR. Finally, we employed Western blotting to measure the levels of Wnt/ß-catenin and AMPK signaling proteins. RESULTS: At days 0, 3, 7, and 14 after osteogenic induction, AR-S- and ALP-staining was lighter in MFAP5 knockdown compared to control cells, as were the levels of Runx2, Col1α1 and OCN. During osteogenesis, the levels of ß-catenin, p-GSK-3ß, AMPK, and p-AMPK were upregulated, while that of GSK-3ß was downregulated, indicating that Wnt/ß-catenin and AMPK signaling were activated. The relevant molecules were expressed at lower levels in the knockdown than control group; the opposite was seen for overexpressing cell lines. CONCLUSIONS: MFAP5 regulates osteogenesis via Wnt/ß­catenin- and AMPK-signaling; MFAP5 may serve as a therapeutic target in patients with osteoporosis.

Exploring the quorum sensing inhibition of isolated chrysin from Penicillium chrysogenum DXY-1.

We recently and for the first time reported that ethyl acetate extracts isolated from Penicillium chrysogenum DXY-1 exhibited anti-quorum sensing (anti-QS) activity. Herein, another active molecule in the extracts was identified as chrysin by NMR and MS. A 20 µg/mL dose of chrysin inhibited violacein production regulated by QS in C. violaceum CV026 by 31.6%. A 40 µg/mL dose of chrysin suppressed pyocyanin production, elastase activity, proteolytic activity, and biofilm formation regulated by QS in P. aeruginosa PA01 by 41.4%, 13.8%, 8.3%, and 42.4%, respectively. And chrysin could inhibit the swarming activity of P. aeruginosa PA01. Further, molecular docking and CD analysis were used to address the mechanism of chrysin's activity in C. violaceum. Molecular docking results revealed that chrysin suppresses QS system by competing with the natural signal molecule C6HSL for binding to the same pocket of CviR receptor. At the same time, CD results also showed that chrysin could change the secondary structure composition of CviR, which greatly prevented the binding of C6HSL/CviR, and further playing its role on inhibiting bacterial QS system. All these data demonstate that chrysin may be used as a potential QS inhibitor to tackle increasing drug resistance.