ifDEEPre: large protein language-based deep learning enables interpretable and fast predictions of enzyme commission numbers.

Accurate understanding of the biological functions of enzymes is vital for various tasks in both pathologies and industrial biotechnology. However, the existing methods are usually not fast enough and lack explanations on the prediction results, which severely limits their real-world applications. Following our previous work, DEEPre, we propose a new interpretable and fast version (ifDEEPre) by designing novel self-guided attention and incorporating biological knowledge learned via large protein language models to accurately predict the commission numbers of enzymes and confirm their functions. Novel self-guided attention is designed to optimize the unique contributions of representations, automatically detecting key protein motifs to provide meaningful interpretations. Representations learned from raw protein sequences are strictly screened to improve the running speed of the framework, 50 times faster than DEEPre while requiring 12.89 times smaller storage space. Large language modules are incorporated to learn physical properties from hundreds of millions of proteins, extending biological knowledge of the whole network. Extensive experiments indicate that ifDEEPre outperforms all the current methods, achieving more than 14.22% larger F1-score on the NEW dataset. Furthermore, the trained ifDEEPre models accurately capture multi-level protein biological patterns and infer evolutionary trends of enzymes by taking only raw sequences without label information. Meanwhile, ifDEEPre predicts the evolutionary relationships between different yeast sub-species, which are highly consistent with the ground truth. Case studies indicate that ifDEEPre can detect key amino acid motifs, which have important implications for designing novel enzymes. A web server running ifDEEPre is available at https://proj.cse.cuhk.edu.hk/aihlab/ifdeepre/ to provide convenient services to the public. Meanwhile, ifDEEPre is freely available on GitHub at https://github.com/ml4bio/ifDEEPre/.

Biocatalytic Steroidal 9α-Hydroxylation and Fragmentation Enable the Concise Chemoenzymatic Synthesis of 9,10-Secosteroids.

9,10-Secosteroids are an important group of marine steroids with diverse biological activities. Herein, we report a chemoenzymatic strategy for the concise, modular, and scalable synthesis of ten naturally occurring 9,10-secosteroids from readily available steroids in three to eight steps. The key feature lies in utilizing a Rieske oxygenase-like 3-ketosteroid 9α-hydroxylase (KSH) as the biocatalyst to achieve efficient C9-C10 bond cleavage and A-ring aromatization of tetracyclic steroids through 9α-hydroxylation and fragmentation. With synthesized 9,10-secosteroides, structure-activity relationship was evaluated based on bioassays in terms of previously unexplored anti-infective activity. This study provides experimental evidence to support the hypothesis that the biosynthetic pathway through which 9,10-secosteroids are formed in nature shares a similar 9α-hydroxylation and fragmentation cascade. In addition to the development of a biomimetic approach for 9,10-secosteroid synthesis, this study highlights the great potential of chemoenzymatic strategies in chemical synthesis.

Controllable skeletal reorganizations in natural product synthesis.

Covering: 2016 to 2023The synthetic chemistry community is always in pursuit of efficient routes to natural products. Among the many available general strategies, skeletal reorganization, which involves the formation, cleavage, and migration of C-C and C-heteroatom bonds, stands out as a particularly useful approach for the efficient assembly of molecular skeletons. In addition, it allows for late-stage modification of natural products for quick access to other family members or unnatural derivatives. This review summarizes efficient syntheses of steroid, terpenoid, and alkaloid natural products that have been achieved by means of this strategy in the past eight years. Our goal is to illustrate the strategy's potency and reveal the spectacular human ingenuity demonstrated in its use and development.

Identification and function analysis of GABA branch three gene families in the cotton related to abiotic stresses.

γ -aminobutyric acid (GABA) is closely related to the growth, development and stress resistance of plants. Combined with the previous study of GABA to promote the cotton against abiotic stresses, the characteristics and expression patterns of GABA branch gene family laid the foundation for further explaining its role in cotton stress mechanism. Members of GAD, GAB-T and SSADH (three gene families of GABA branch) were identified from the Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum and Gossypium raimondii genome. The GABA branch genes were 10 GAD genes, 4 GABA-T genes and 2 SSADH genes. The promoter sequences of genes mainly contains response-related elements such as light, hormone and environment.Phylogenetic analysis shows that GAD indicating that even in the same species, the homologous sequences in the family. The GABA-T gene of each cotton genus was in sum the family had gene loss in the process of dicotyledon evolution. SSADH families Gossypium hirsutum, Gossypium barbadense, Gossypium arboreum and Gossypium raimondii were closely related to the dicot plants.GABA gene is involved in the regulation of salt stress and high temperature in Gossypium hirsutum.GABA attenuated part of the abiotic stress damage by increasing leaf protective enzyme activity and reducing reactive oxygen species production.This lays the foundation for a thorough analysis of the mechanism of GABA in cotton stress resistance.

Parthenocarpy in Cucurbitaceae: Advances for Economic and Environmental Sustainability.

Parthenocarpy is an important agricultural trait that not only produces seedless fruits, but also increases the rate of the fruit set under adverse environmental conditions. The study of parthenocarpy in Cucurbitaceae crops has considerable implications for cultivar improvement. This article provides a comprehensive review of relevant studies on the parthenocarpic traits of several major Cucurbitaceae crops and offers a perspective on future developments and research directions.

Improving denitrification performance of biofilm technology with salt-tolerant denitrifying bacteria agent for treating high-strength nitrate and sulfate wastewater from lab-scale to pilot-scale.

This study focused on the application of salt-tolerant denitrifying bacteria (DBA) in an optimized biofilm process to treat high sulfate-nitrate wastewater from lab-scale to pilot-scale. Lab-scale results demonstrated the salinity, DBA inoculum, supplementary carbon and phosphorus source significantly varied the startup periods at the range of 36-74 d, and the optimum initial start-up conditions were as follows: >0.6 g/L of DBA, 2-4 of C/N ratio, 0.3-0.6 mg/L of phosphorus and a salinity-gradient domestication method. A pilot scale of biofilm technology with DBA was further developed for treating real wastewater from the desulfuration and denitration with both high nitrate (≈200 mg/L) and sulfate (2.7%). The denitrification efficiency reached above 90% after one-month gradient-salinity of 0.5%-2.7%. Mature biofilm had dominant genera Hyphomicrobium (31.80%-61.35%), Methylotenera (0.85%-20.21%) and Thauera (1.42%-8.40%), etc. Notably, the largest genera Hyphomicrobium covered the complete denitrification genes.

Phenytoin regulates osteogenic differentiation of human bone marrow stem cells by PI3K/Akt pathway.

Background: We mainly studied the mechanism by which phenytoin promotes osteogenic differentiation of human jawbone marrow stem cells. Methods: Bone marrow stem cells were extracted from jaw bone tissue debris obtained from 5 subjects undergoing implant restoration. Osteogenic and adipogenic experiments proved cells stemness, and the expression of ALP, RUNX2, and OSX were detected by qPCR and Western blot. High-throughput sequencing was used to extract differentially expressed genes, the network database predicted phenytoin drug targets, GO and KEGG enrichment combined with PPI network diagram to analyze the osteogenesis mechanism. Results: Calcium nodules and lipid droplet formation were observed in osteogenic and adipogenic experiments. The concentration of phenytoin within 100 mg/L does not produce cytotoxicity. The results of PCR and WB indicated that 50 mg/L phenytoin significantly promoted the expression of ALP and RUNX2, and 25 mg/L phenytoin significantly promoted the expression of OSX. The results of network pharmacology suggest that phenytoin promotes bone formation by up-regulating FGFR2, S1PR1, TGFB3, VCAN core proteins and activating PI3K/Akt pathway. Conclusions: Phenytoin activated the PI3K/Akt pathway to regulate the osteogenic differentiation of human jawbone marrow stem cells. https://data.mendeley.com/datasets/t3xstktt93/1.

Microbial communities and sediment nitrogen cycle in a coastal eutrophic lake with salinity and nutrients shifted by seawater intrusion.

Coastal waters are often influenced by seawater intrusion and terrestrial emissions because of its special location. In this study, the dynamics of microbial community with the role of nitrogen cycle in sediment in a coastal eutrophic lake were studied under a warm season. The water salinity gradually increased from 0.9‰ in June to 4.2‰ in July and 10.5‰ in August because of seawater invasion. Bacterial diversity of surface water was positively related with salinity and nutrients of total nitrogen (TN) as well as total phosphorus (TP), but eukaryotic diversity had no relationship with salinity. In surface water, algae belonging to Cyanobacteria and Chlorophyta were dominant phyla in June with the relative abundances of >60%, but Proteobacteria became the largest bacterial phylum in August. The variation of these predominant microbes had strong relationship with salinity and TN. In sediment, the bacterial and eukaryotic diversity was greater than that of water, and a significantly different microbial community was observed with dominant bacterial phyla Proteobacteria and Chloroflexi, and dominant eukaryotic phyla Bacillariophyta, Arthropoda, and Chlorophyta. Proteobacteria was the only enhanced phylum in the sediment with the highest relative abundance of 54.62% ± 8.34% due to seawater invasion. Denitrifying genera (29.60%-41.81%) were dominant in surface sediment, then followed by microbes related to nitrogen fixation (24.09%-28.87%), assimilatory nitrogen reduction (13.54%-19.17%), dissimilatory nitrite reduction to ammonium (DNRA, 6.49%-10.51%) and ammonification (3.07%-3.71%). Higher salinity caused by seawater invasion enhanced the accumulation of genes involved in dentrificaiton, DNRA and ammonification, but decreased genes related to nitrogen fixation and assimilatory nitrogen reduction. Significant variation of dominant genes of narG, nirS, nrfA, ureC, nifA and nirB mainly caused by the changes in Proteobacteria and Chloroflexi. The discovery of this study would be helpful to understand the variation of microbial community and nitrogen cycle in coastal lake under seawater intrusion.

Sweat Gland Carcinoma of the Head and Neck: Case Report and Literature Review.

INTRODUCTION: The main aim of this article is to discuss and summarize the research advancements and the treatment methods for sweat gland carcinoma (SGC) based on 2 cases of SGC in our hospital and the related literature. CASE REPORT: This article presents 2 patients with SGC who were treated in the China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases from 2007 to 2019. We analyzed the clinical features, therapies, and prognosis of the patients and searched for related literatures. DISCUSSION: Two patients underwent extended resection for local lesions with no adjuvant radiotherapy. Neither local recurrence nor distant metastasis was detected during follow-up. Reviewing previous literature, the treatment of SGC includes surgical resection, radiotherapy, and chemotherapy. We have not found an effective treatment. The prognosis of SGC occurred in head and neck is relatively good compared with another primary-site location, primary surgical excision with safe resection margins and neck dissection is recommended.

Interdigitated photoconductive antenna-based two-color femtosecond laser filamentation THz time-domain spectral detection.

Two-color femtosecond (fs) laser filamentation in the gas medium is an effective way to generate broadband and high intensity terahertz (THz) pulse. The interdigitated photoconductive antenna (iPCA) has the advantages of both broadband detection and high signal-to-noise ratio (SNR), which is a very effective way to detect the THz pulse produced by two-color fs laser filamentation. The THz signal from two-color fs laser filamentation is comprehensively characterized by the iPCA, which achieves high SNR, high sensitivity, and polarization detection. This work provides a new idea for high power broadband THz coherent detection.

Laparoscopic versus Robotic Hepatectomy: A Systematic Review and Meta-Analysis.

This study aimed to assess the surgical outcomes of robotic compared to laparoscopic hepatectomy, with a special focus on the meta-analysis method. Original studies were collected from three Chinese databases, PubMed, EMBASE, and Cochrane Library databases. Our systematic review was conducted on 682 patients with robotic liver resection, and 1101 patients were operated by laparoscopic platform. Robotic surgery has a long surgical duration (MD = 43.99, 95% CI: 23.45-64.53, p = 0.0001), while there is no significant difference in length of hospital stay (MD = 0.10, 95% CI: -0.38-0.58, p = 0.69), blood loss (MD = -20, 95% CI: -64.90-23.34, p = 0.36), the incidence of conversion (OR = 0.84, 95% CI: 0.41-1.69, p = 0.62), and tumor size (MD = 0.30, 95% CI: -0-0.60, p = 0.05); the subgroup analysis of major and minor hepatectomy on operation time is (MD = -7.08, 95% CI: -15.22-0.07, p = 0.09) and (MD = 39.87, 95% CI: -1.70-81.44, p = 0.06), respectively. However, despite the deficiencies of robotic hepatectomy in terms of extended operation time compared to laparoscopic hepatectomy, robotic hepatectomy is still effective and equivalent to laparoscopic hepatectomy in outcomes. Scientific evaluation and research on one portion of the liver may produce more efficacity and more precise results. Therefore, more clinical trials are needed to evaluate the clinical outcomes of robotic compared to laparoscopic hepatectomy.

Arabidopsis TIE1 and TIE2 transcriptional repressors dampen cytokinin response during root development.

Cytokinin plays critical roles in root development. Cytokinin signaling depends on activation of key transcription factors known as type B Arabidopsis response regulators (ARRs). However, the mechanisms underlying the finely tuned regulation of type B ARR activity remain unclear. In this study, we demonstrate that the ERF-associated amphiphilic repression (EAR) motif-containing protein TCP interactor containing ear motif protein2 (TIE2) forms a negative feedback loop to finely tune the activity of type B ARRs during root development. Disruption of TIE2 and its close homolog TIE1 causes severely shortened roots. TIE2 interacts with type B ARR1 and represses transcription of ARR1 targets. The cytokinin response is correspondingly enhanced in tie1-1 tie2-1. We further show that ARR1 positively regulates TIE1 and TIE2 by directly binding to their promoters. Our findings demonstrate that TIEs play key roles in controlling plant development and reveal an important negative feedback regulation mechanism for cytokinin signaling.

Sensing with Femtosecond Laser Filamentation.

Femtosecond laser filamentation is a unique nonlinear optical phenomenon when high-power ultrafast laser propagation in all transparent optical media. During filamentation in the atmosphere, the ultrastrong field of 1013-1014 W/cm2 with a large distance ranging from meter to kilometers can effectively ionize, break, and excite the molecules and fragments, resulting in characteristic fingerprint emissions, which provide a great opportunity for investigating strong-field molecules interaction in complicated environments, especially remote sensing. Additionally, the ultrastrong intensity inside the filament can damage almost all the detectors and ignite various intricate higher order nonlinear optical effects. These extreme physical conditions and complicated phenomena make the sensing and controlling of filamentation challenging. This paper mainly focuses on recent research advances in sensing with femtosecond laser filamentation, including fundamental physics, sensing and manipulating methods, typical filament-based sensing techniques and application scenarios, opportunities, and challenges toward the filament-based remote sensing under different complicated conditions.

The Understanding of Vital Pulp Therapy in Permanent Teeth: A New Perspective.

The indications of vital pulp therapy (VPT) are expanding, which cases are suitable for VPT, and how to improve the success rate of VPT is a problem that often bothers us. The main purpose of VPT is to eliminate pulpitis by promoting the formation of reparative dentin or calcium bridge, so that it can continue to perform various physiological functions, and finally achieve the purpose of preserving pulp vitality and long-term preservation of affected teeth. Pulp capping and pulpotomy are the most common methods for VPT. The research field of VPT has attracted the attention of many scholars, who have studied it from many aspects (such as indications, material selection, operation requirements, and long-term prognosis). This article reviews the recent advances in the techniques of VPT in permanent teeth.

Whole Transcriptome Sequencing Reveals Drought Resistance-Related Genes in Upland Cotton.

China, particularly the cotton-growing province of Xinjiang, is experiencing acute agricultural water shortages, stifling the expansion of the cotton sector. Discovering drought resistance genes in cotton and generating high-quality, drought-resistant cotton varieties through molecular breeding procedures are therefore critical to the cotton industry's success. The drought-resistant cotton variety Xinluzhong No. 82 and the drought-sensitive cotton variety Kexin No. 1 were utilised in this study to uncover a batch of drought-resistant candidate genes using whole transcriptome sequencing. The following are the key research findings: A competing endogenous RNA network (ceRNA) was built using complete transcriptional sequencing to screen the core genes in the core pathway, and two drought-related candidate genes were discovered. It was found that γ-aminobutyric acid aminotransferase (GhGABA-T, Gohir.A11G156000) was upregulated at 0 h vs. 12 h and downregulated at 12 h vs. 24 h. L-Aspartate oxidase (GhAO, Gohir.A07G220600) was downregulated at 0 h vs. 12 h and upregulated at 12 h vs. 24 h. GABA-T is analogous to a pyridoxal phosphate-dependent transferase superfamily protein (POP2) in Arabidopsis thaliana and influences plant drought resistance by controlling γ-aminobutyric acid (GABA) concentration. The analogue of GhAO in A. thaliana is involved in the early steps of nicotinamide adenine dinucleotide (NAD) production as well as in plant antioxidant responses. This study revealed that gene expression regulatory networks can be used for rapid screening of reliable drought resistance genes and then utilised to validate gene function.

Analysis of the genetic structure and diversity of upland cotton groups in different planting areas based on SNP markers.

Genetic diversity, kinship and population genetic structure analyses of Gossypium hirsutum germplasm can provide a better understanding of the origin and evolution of G. hirsutum biodiversity. In this study, adopt 273 elite upland cotton cultivar accessions collected from around the world, and especially from China to get 1,313,331 SNP molecular markers, it were used to construct a phylogenetic tree of each sample using MEGAX, to perform population structure analysis by ADMIXTURE software and principal component analysis (PCA) by EIGENSOFT software, and to estimate relatedness using SPAGeDi. ADMIXTURE software divided the experimental cotton population into 16 subgroups, and the Gossypium hirsutum samples could be roughly clustered according to source place, but there were some overlapping characteristics among samples. The experimental cotton population was divided into six groups according to source to calculate the genetic diversity index (H), and the obtained value (0.306) was close to that for germplasm collected by others in China. Cluster 4 had a relatively high genetic diversity level (0.390). The degrees of genetic differentiation within the experimental cotton population groups were low (the population differentiation indexes ranged from 0.02368 to 0.10664). The genetic distance among cotton accessions varied from 0.000332651 to 0.562664014, with an average of 0.25240429. The results of this study may provide a basis for mining elite alleles and using them for subsequent association analysis.

A novel model based on liquid-liquid phase separation-Related genes correlates immune microenvironment profiles and predicts prognosis of lung squamous cell carcinoma.

OBJECTIVE: The aim of the study was to construct and validate a robust prognostic model based on liquid-liquid phase separation (LLPS)-related genes in lung squamous cell carcinoma (LUSC). METHODS: The Cancer Genome Atlas dataset was used as the discovery set to identify the LLPS-related differentially expressed genes (DEGs) between LUSC and normal tissue. These DEGs were screened by the LASSO Cox regression analysis to identify the genes with nonzero coefficient, which were next included in the multivariate Cox regression analysis to construct the prediction model. The dataset GSE41271 was adopted as the validation set to verify the efficacy of the model. Enrichment analysis and the CIBERSORT were performed to illustrate potential immune mechanisms underlying the prediction model. RESULTS: A total of 48 LLPS-related genes were aberrantly expressed in LUSC. Among them, 7 genes were selected by the LASSO Cox regression analysis to construct the prediction model. Risk index (RI) was calculated according to the model for each patient. The prognosis was significantly different between the patients with high and low RI in the discovery set and the validation set (p < 0.001 and p = 0.028, respectively). The multivariate survival analysis confirmed RI as an independent prognostic factor in LUSC (in the discovery set: p < 0.001, HR = 2.643, 95% CI = 1.986-3.518; in the validation set: p = 0.042, HR = 2.144, 95% CI = 1.026-4.480). A series of pathways involving immune cells were found to be related to RI. The distribution pattern of immune cells and chemokines varied according to the value of RI. CONCLUSION: The prediction model based on LLPS-related genes was constructed and validated as a robust prognostic tool for LUSC using multiple datasets. LLPS might have an impact on LUSC through immune pathways.

Concise Synthesis of 9,11-Secosteroids Pinnigorgiols B and E.

Pinnigorgiols B and E are 9,11-secosteroids with a unique tricyclic γ-diketone framework. Herein, we report the first synthesis of these natural products from inexpensive, commercially available ergosterol. This synthesis features a semipinacol rearrangement and an acyl radical cyclization/hemiketalization cascade; the latter efficiently assembled the tricyclic γ-diketone skeleton, with two rings and three contiguous stereogenic centers being formed in a single step.

Genome-Wide Association Analysis of Salt-Tolerant Traits in Terrestrial Cotton at Seedling Stage.

Soil salinization is the main abiotic stress factor affecting agricultural production worldwide, and salt stress has a significant impact on plant growth and development. Cotton is one of the most salt-tolerant crops. Therefore, the selection and utilization of salt-tolerant germplasm resources and the excavation of salt resistance genes play important roles in improving cotton production in saline-alkali soils. In this study, we analysed the population structure and genetic diversity of a total 149 cotton plant materials including 137 elite Gossypium hirsutum cultivar accessions collected from China and 12 elite Gossypium hirsutum cultivar accessions collected from around the world. Illumina Cotton SNP 70 K was used to obtain genome-wide single-nucleotide polymorphism (SNP) data for 149 elite Gossypium hirsutum cultivar accessions, and 18,430 highly consistent SNP loci were obtained by filtering. It was assessed by using PCA principal component analysis so that the 149 elite Gossypium hirsutum cultivar accessions could be divided into two subgroups, including subgroup 1 with 78 materials and subgroup 2 with 71 materials. Using the obtained SNP and other marker genotype test results, under salt stress, the salt tolerance traits 3d Germination potential, 3d Radicle length drop rate, 7d Germination rate, 7d Radicle length drop rate, 7d Germination weight, 3d Radicle length, 7d Radicle length, Relative Germination potential, Relative Germination rate, 7d Radicle weight drop rate, Salt tolerance index 3d Germination potential index, 3d Radicle length index, 7d Radicle length index, 7d Radicle weight index and 7d Germination rate index were evaluated by GWAS (genome-wide association analysis). A total of 27 SNP markers closely related to the salt tolerance traits and 15 SNP markers closely related to the salt tolerance index were detected. At the SNP locus associated with phenotyping, Gh_D01G0943, Gh_D01G0945, Gh_A01G0906, Gh_A01G0908, Gh_D08G1308 and Gh_D08G1309 related to plant salt tolerance were detected, and they were found to be involved in intracellular transport, sucrose synthesis, osmotic pressure balance, transmembrane transport, N-glycosylation, auxin response and cell amplification. This study provides a theoretical basis for the selection and breeding of salt-tolerant upland cotton varieties.

Comparison of donor site complications of supra- versus subfascially harvested anterolateral thigh perforator free flaps: A meta-analysis.

OBJECTIVE: This study aimed to compare the complications at the donor site of supra- versus subfascially harvested anterolateral thigh perforator free flaps. METHOD: We searched PubMed, Web of Science, EMBASE, the Chinese BioMedical Literature Database (CBM) and the Cochrane Library until December 31, 2018, to identify studies that compared complications at the donor site of the supra- versus subfascially raised anterolateral thigh perforator free flaps. Two authors individually extracted the data and performed the quality assessments. Skin grafting, the rate of poor healing in the donor site, dysfunction at the donor site and sensory functions at the donor site were evaluated. RESULT: Seven studies with a total of 525 patients were included in our analysis. No significant differences were found regarding skin grafting and sensory functions between the 2 groups. However, in regard to the rate of poor healing and dysfunction at the donor site, the SPF group showed significantly better outcomes than the SBF group after the operation. CONCLUSION: Our meta-analysis suggested that, in regards to skin grafting and sensory recovery, the SPF and SBF groups were similar. With regard to donor site healing and functional recovery, the SPF group exhibited better outcomes than the SBF group.