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E.coli are prokaryotes that show aging and rejuvenation. Evidences show that damage allocation among daughter cells can explain the aging and rejuvenation pattern in an E.coli lineage. However, population aging originated from cellular aging. And in E.coli, there is not enough study on the molecular dynamics that are necessary for a single cell to create different daughter cells. This is the focus of this thesis. Namely, single cell experiments and single cell biophysic models are built to explain cellular aging in E.coli. And these studies are aimed to provide informative connections between cellular aging and population aging. The age difference between cell poles is established physically by the division pattern of E.coli. With one pole being synthesed anew from most recent division, two poles of E.coli is inevitably different by the time they each exist. And proteins that harbor at the poles will have different age and wear and tear. On the other hand, given the division pattern, natural selection is optimizing the physical parameters and dynamics of proteins inside cell, so their intracellular distribution will result in the optimal intercellular distribution among the daughters and become beneficial to population fitness. Two categories of proteins are of greatest interest. First is damaged protein, usually in the form of protein aggregate, with its consequence being studied but dynamics obsure. Second is fresh functional protein and repair protein. Up to the starting of this thesis, no study has contributed to this topic. The chapter 1 will investigate the fresh protein distribution in line with cellular aging. Chapter 2 is a model tackling the damage dynamics inside single cell. Chapter 3 is discussing more conceptually and fundamentally, the evolutionary origin of cell division. In chapter 1, a constitutively expressing green fluorescent protein (GFP) gene is inserted into E.coli genome under a stable promoter, and its intracellular and intercellular distribution is observed and discussed. We also invented a protocol of deconvoluting fluorescent image of E.coli colony. GFP here is representing a group of fresh proteins that are free of damage. The observation of GFP enriches in new pole and new daughters are in consistent with the higher growth rate of new pole and new lineage. The representation of GFP is also appreciated by its relative small molecular weight and fast diffusion. This makes its localization most likely be a passive visualization of free intracellular space instead of an active and protein-specific arrangement. The fact of lack of physiological function of GFP in E.coli also supports the enrichment being passive, which indicates a baseline enrichment level of functional but invisible proteins that contribute to real fitness. In more detailed study, we find the free cellular space revealed by GFP can be predicted qualitatively by the age of the pole. The fact that younger pole has more free space leads to the speculation of accumulation of aged or damaged protein on the other end of cell. And therefore, fresh proteins are spatially excluded by damaged protein, from which polarity of cell is established and physiological distinction between daughters are maximized. Cellular polarity will subsequently be magnified into standing fitness variation of population, and we found the age can explain 37% of total variance of GFP distribution. This polarity is created by self-organisation based on size of molecules, and cannot be realized without damage aggregation. Given the possible energy cost of sorting and rearranging each specific damage or fresh protein of all sizes, the aggregation of damage allows damage and fresh protein to be organised physically by their size with no energy involved. The damage aggregation- disaggregation dynamics will be explored in Chapter 2. In chapter 2, classical view of damage distribution causinig cellular aging is examined by a biophysical and individual based finite population model. Damage is hypothesed to have been actively transported to old pole, or have been excluded from nucleoid because of aggregation. The first hypothesis is rejected because the resulting exponential-shape distribution is conflicting the observed damage enrichment of both poles. However, nucleoid exclusion hypothesis have not been tested and parameterized in an elongating E.coli cell. The key parameters in this picture, and are certainly parameters under natural selection, are the size of damage and the elongation regime of E.coli. Damage particles originated from wear and tear of fresh and functional protein. When protein is damaged, the size will most likely keep similar. In this way, the high diffusion rate of protein will cause damage to have uniform distribution inside cell, and no polarity can be built without extra mechanism or energy. The evolution of protein aggregation solves this problem by allowing damaged protein to bind and form larger aggregate. The larger size will be physically excluded by nucleoid and eventually reside in the cell poles. And when cell divides, new pole is created damage free by the division of nucleoid, and will take time for new aggregate to colonize. And damage polarity is established automatically. Therefore, it is important that the size of aggregate is larger than the mesh size of nucleoid and larger than the space between nucleoid and cell wall. Once resides into the pole, the aggregate will keep growing by merging with more and more free flowing new damages, and will eventually cause old lineage die from damage overload, if not saved by disaggregation or elongation. Disaggregation will efficiently control the size of damage aggregate by releasing repaired protein out from aggregate, and once aggregation –disaggregation equilibrium is reached, the size of aggregate will keep constant. In this way, disaggregation saves the old lineage by compromising the polarity of cell. And a moderate level of disaggregation is necessary. In our model, the free damage size after parameterization is close to the size of a ribosome. Therefore free damage is small enough to travel through nucleoid between poles. And it takes aggregation of 3 free damages to be excluded from nucleoid and establish damage polarity. The disaggregation probability from model is 0.1. Since damage polarity is established passively, it is not robust under changing level of external damage, which occurs randomly across a cell. It explains why both experiment and model produce symmetry when external damage increases. Elongation, in general, is an automatic dilution of existing damage, and will further promote elongation by alleviating detrimental effect of damage. And fast elongation will in turn lead to less reception of new external damage. There is a prominent positive feedback between fast/slow elongation and less/more amount of damage. Subcellular elongation pattern has been measured by transient cell wall labeling and monitoring local dilution. Our observation of new pole elongates significantly fast than old pole means elongation happened locally and the elongation –dilution feedback will also apply subcellularly. This results in more polarized damage distribution of a cell once initial damage/fresh protein polarity is established. In our model, each cell is represented by multiple one dimension compartments. And each compartment has its unique elongation probability, due to local damage, to reproduce local elongation. After parameterization, the model can reproduce the elongation rate relation between mother and old and new daughters, including stochastic attractor behavior at the equilibrium point where mother’s doubling time equals one of her daughter’s. This model is developed on the assumption of exponential cell growth from self-replicating compartments (growth units). In chapter 3, an in-detailed analysis is performed to quantitatively describe their behavior and consequences. When measured in better time resolution, E.coli elongation performs accerlerating multi-linear phases of growth. Each linear phase can be realized as constant biomass production of a certain growth units, with the shift to a faster phase being the event of a new unit start functioning. To keep up with cell size, the growth unit number needs to double as the cell length doubles. Considerinig most cells perform two linear phases during doubling, the growth unit should start from number of 2, advance to 3, and divide right at the time it reaches 4. The fact of observing the third unit functioning also indicates the mixing of products from 2 existing units (cooperation). This mechanism gives cell that contains more growth units fitness advantage for their elongation span accomadates more rounds of cooperation. And a cell with short length has lower fitness. However, our elongation rate data at long cell length indicates slowing down of accerleration across phase shift, which can be explained by inefficient cooperation at new cell pole (c.f. chapter 1) caused by long distance between poles. Therefore, growth units not only result in multi-linear cell elongation, but their cooperation produces an optimal cell size and explains cell division. Chapter 3 now has complete conceptual projection, and there are still controls and tests need to be performed.

Coilia nasus is an endangered fish species in the Yangtze River, and there is urgent need to know the genes related to its reproduction and fertility. The DAZ family including boule, daz and dazl, plays an important role in germ cells development. In this study, the cDNA sequence of boule (Cnbol) and dazl (Cndazl) genes were cloned and their expression patterns were characterized in Coilia nasus. RT-PCR showed that the expression of Cnbol and Cndazl mRNAs was restricted in adult gonads. The section in situ hybridization indicated that the temporospatial expression patterns of Cnbol and Cndazl were significantly different. In the testis, Cnbol was mainly detected in spermatocytes and spermatids, while Cndazl was prominently expressed in s permatogonia. In the ovary, Cnbol and Cndazl were highly expressed in the early stages of oocytes. Interestingly, Cndazl was also concentrated in perinuclear speckle and then localized to the Balbiani body in late stages of oocytes. In addition, Cnbol and Cndazl 3′ UTR can specifically label medaka Primordial Germ Cells (PGCs). According to our results, Cnbol and Cndazl are marker genes of germ cells and may play a vital role in the development and differentiation of germ cells in Coilia nasus.

Small RNAs are short, non-coding RNA molecules that have been identified in a wide range of species across all three domains of life. In mammals, canonical small RNAs such as microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs) are tissue-specifically distributed and can regulate gene expression at both transcriptional and post-transcriptional levels, associating with various fundamental functions such as gene silencing and retrotransposon control. While miRNAs and piRNAs have been extensively investigated, the existence and mechanism of other non-canonical mammalian small RNAs remain underexplored.With the extensive use of high-throughput sequencing technologies in the past decade, small RNA diversity is rapidly growing. However, the conventional small RNA library construction method lacks the detection capability for non-canonical small RNAs that carry specific terminal and internal modifications, especially for tRNA-derived small RNAs (tsRNAs) and rRNA-derived small RNAs (rsRNAs). In addition, existing downstream bioinformatics tools are mostly focused on analyzing canonical small RNAs such as miRNAs and piRNAs, while the annotation of other small RNAs remains rudimentary or ignored.To reveal a panoramic view of small RNAs, a small RNA annotation pipeline (that is, SPORTS) is developed to simultaneously and comparatively annotate both canonical and non-canonical small RNAs, along with RNA modification prediction capacity. Moreover, a small RNA library preparation procedure (that is, PANDORA-seq) is optimized to comprehensively capture modified small RNAs such as tsRNAs and rsRNAs.The improved RNA-seq and bioinformatics strategy leads to a new and surprising small RNA landscape that tsRNAs and rsRNAs have a higher abundance than canonical small RNAs in a majority of mouse and human tissues/cells that have been examined. Those mammalian tsRNAs and rsRNAs also exhibit tissue- and cell-specific patterns and the expression level of those small RNAs are dynamically altered during the generation of induced pluripotent stem cells (iPSCs) based on PANDORA-seq. Those newly identified small RNAs also display translational regulation during embryonic stem cell differentiation and have a role in regulating embryonic stem cell lineage fate based on the transcriptomic changes after their transfection.

N4-methylcytosine (4mC) is a type of DNA modification which could regulate several biological progressions such as transcription regulation, replication and gene expressions. Precisely recognizing 4mC sites in genomic sequences can provide specific knowledge about their genetic roles. This study aimed to develop a deep learning-based model to predict 4mC sites in the Escherichia coli. In the model, DNA sequences were encoded by word embedding technique 'word2vec'. The obtained features were inputted into 1-D convolutional neural network (CNN) to discriminate 4mC sites from non-4mC sites in Escherichia coli genome. The examination on independent dataset showed that our model could yield the overall accuracy of 0.861, which was about 4.3% higher than the existing model. To provide convenience to scholars, we provided the data and source code of the model which can be freely download from https://github.com/linDing-groups/Deep-4mCW2V.

Oriented ligand immobilization is one of the most effective strategies used in the design and construction of a high-capacity protein A chromatography. In this work, cysteine was introduced as anchoring sites by substituting a specific residue on Helix I, II, and at C-terminus of antibody binding domain Z from protein A, respectively, to investigate structural evolution and binding behavior of protein A ligands at liquid-solid interfaces. Among the three affinity dextran-coated Fe3O4 magnetic nanoparticles (Fe3O4@Dx MNPs), affinity MNPs with the immobilized ligand via N11C on Helix I (Fe3O4@Dx-Z1 MNPs) had the highest helical content, and MNPs with the immobilized ligand via G29C on Helix II (Fe3O4@Dx-Z2 MNPs) had the lowest helical content at the same pHs. It was attributed to less electrostatic attraction of ligand to negatively charged surface on Fe3O4@Dx-Z1 MNPs because of less positive charged residues on Helix I (K6) than Helix II (R27/K35). Among the three affinity MNPs, moreover, the highest affinity to immunoglobulin G (IgG) binding was observed on Fe3O4@Dx-Z1 MNPs in isothermal titration calorimetry measurement, further validating greater structural integrity of the ligand on Fe3O4@Dx-Z1 MNPs. Finally, the study of IgG binding on MNPs and 96-well plates showed that anchoring sites for ligand immobilization had distinct influences on IgG binding and IgG-mediated antigen binding. This work illustrated that anchoring sites of the ligands had a striking significance for the molecular structure of the ligand at liquid-solid interfaces and raised an important implication for the design and optimization of protein A chromatography and protein A-based immunoassay analysis.

Funder: Kennedy Trust Rheumatology Research Prize Studentship, Funder: DFG Cluster of Excellence ���Precision Medicine in Chronic In-flammation��� (PMI; ID: EXC2167), Funder: EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: ���Ideas��� Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013)); doi: https://doi.org/10.13039/100011199; Grant(s): 715772, Funder: NWO-VIDI grant 016.178.056, the Netherlands Heart Foundation CVON grant 2018-27, and NWO Gravitation grant ExposomeNL, Funder: Li Ka Shing Foundation (Li Ka Shing Foundation Limited); doi: https://doi.org/10.13039/100007421, Irritable bowel syndrome (IBS) results from disordered brain���gut interactions. Identifying susceptibility genes could highlight the underlying pathophysiological mechanisms. We designed a digestive health questionnaire for UK Biobank and combined identified cases with IBS with independent cohorts. We conducted a genome-wide association study with 53,400 cases and 433,201 controls and replicated significant associations in a 23andMe panel (205,252 cases and 1,384,055 controls). Our study identified and confirmed six genetic susceptibility loci for IBS. Implicated genes included NCAM1, CADM2, PHF2/FAM120A, DOCK9, CKAP2/TPTE2P3 and BAG6. The first four are associated with mood and anxiety disorders, expressed in the nervous system, or both. Mirroring this, we also found strong genome-wide correlation between the risk of IBS and anxiety, neuroticism and depression (rg > 0.5). Additional analyses suggested this arises due to shared pathogenic pathways rather than, for example, anxiety causing abdominal symptoms. Implicated mechanisms require further exploration to help understand the altered brain���gut interactions underlying IBS.

Introduction Legume crops are an important source of protein and oil for human health and in fixing atmospheric N2 for soil enrichment. With an objective to accelerate much-needed genetic analyses and breeding applications, draft genome assemblies were generated in several legume crops; many of them are not high quality because they are mainly based on short reads. However, the superior quality of genome assembly is crucial for a detailed understanding of genomic architecture, genome evolution, and crop improvement. Objectives Present study was undertaken with an objective of developing improved chromosome-length genome assemblies in six different legumes followed by their systematic investigation to unravel different aspects of genome organization and legume evolution. Methods We employed in situ Hi-C data to improve the existing draft genomes and performed different evolutionary and comparative analyses using improved genome assemblies. Results We have developed chromosome-length genome assemblies in chickpea, pigeonpea, soybean, subterranean clover, and two wild progenitor species of cultivated groundnut (A. duranensis and A. ipaensis). A comprehensive comparative analysis of these genome assemblies offered improved insights into various evolutionary events that shaped the present-day legume species. We highlighted the expansion of gene families contributing to unique traits such as nodulation in legumes, gravitropism in groundnut, and oil biosynthesis in oilseed legume crops such as groundnut and soybean. As examples, we have demonstrated the utility of improved genome assemblies for enhancing the resolution of “QTL-hotspot” identification for drought tolerance in chickpea and marker-trait associations for agronomic traits in pigeonpea through genome-wide association study. Genomic resources developed in this study are publicly available through an online repository, ‘Legumepedia’. Conclusion This study reports chromosome-length genome assemblies of six legume species and demonstrates the utility of these assemblies in crop improvement. The genomic resources developed here will have significant role in accelerating genetic improvement applications of legume crops.

Background: Baicalin, a flavonoid glycoside compound present in Scutellaria baicalensis, has shown a wide spectrum of biological activities, but its liposolubility, water-solubility and mucosal permeability are all very poor, which leads to the low concentration in brain and poor bioavailability by oral or intravenous injective administration. Objective: The primary objective of this study was to formulate the Scutellaria baicalensis extract (SBE) with phospholipid to yield Scutellaria baicalensis extract-phospholipid complex (SBEPC) , and to evaluate its pharmacodynamics in the middle cerebral artery occlusion (MCAO). Methods: The optimal preparation technology of SBEPC was obtained through single-factor test and central composite design-response surface methodology (CCD-RSM), and was characterized with various analytical techniques including SEM, FT-IR and NMR. The storage conditions of SBEPC were established through stability study and the MCAO rat model was investigated through conducting pharmacodynamic studies to screen the appropriate administration and dose of SBEPC as well as to verify the neuroprotective effect of SBEPC on cerebral ischemia-reperfusion injury. Results: The optimized preparation conditions of SBEPC were summarized as follows: the ratio of phospholipids to drug was 2:1, the drug concentration was 3.5 mg/ml, the reaction temperature was 50 °C, and the entrapment efficiency was over 93.00%. Stability studies have demonstrated that SBEPC should be stored under 40 °C in a dry and ventilated place away from light and below 37% humidity. Furthermore, pharmacodynamic studies have found that, compared with SBE, SBEPC could introduce drugs into the brain and better exert the neuroprotective effect on MCAO rats, and the optimal administration and dose concentration of SBEPC were nasal administration and 40 mg/ml, respectively. Conclusion: These findings demonstrate that SBEPC is successfully prepared by CCD-RSM. SBEPC can enhance drugs' ability to enter the brain and improve the bioavailability of drugs in brain, and can effectively exert the neuroprotective effect on cerebral ischemia-reperfusion injury as compared with SBE.

Palaeozoic ophiolites are rare in the south-eastern Central Asian Orogenic Belt (CAOB) and are genetically significant for understanding the formation, evolution, and closure processes of the Palaeo-Asian Ocean (PAO). The Faku ophiolite is located in north Liaoning, NE China, and is dominated by the south-eastern CAOB within the Songliao Basin. It consists of several discontinuous tectonic blocks made up of serpentinised ultramafic rocks, gabbros, basalts, high-Mg andesites, marine and continental sedimentary formations, which are intruded by younger granites. We characterize the geochronology and geochemistry of the ophiolite. The ophiolite and granitic rocks have restricted eNd(t) (+2.60 to +6.08) and eNd(t) (+0.42 to +1.66). Zircons from the ophiolite and granite yielded weighted mean 206Pb/238U ages of 369–249 Ma and ca. 248.2 Ma, respectively, that we interpret as their crystallization (eruption) times. The ophiolitic rocks have a resemblance to enriched mid-ocean ridge basalts and within-plate basalts in terms of geochemistry, thereby representing a back-arc-type tectonic setting. The granite geochemically belongs to I-type, and formed in a syn-collisional orogenic environment. The sandstones from marine sediments are enriched with light rare earth elements and have low contents of SiO2 and MgO, and a positive zircon ɛHf(t) value indicating the affinities similar to those of ophiolitic rocks. The provenance of molasse is from the Baijiagou granites suggesting that the post-collisional orogeny and uplift occurred after the Early Triassic. We speculate that a juvenile intra-continental back-arc oceanic basin, which represents the southern affiliated branch of the PAO, might have formed by the continuous extension in southern CAOB since the late Devonian, and ultimately closed in the Early Triassic.

The fusion gene MLL-AF4 defines a high-risk subtype of pro-B acute lymphoblastic leukaemia. However, relapse can be associated with a switch from acute lymphoblastic to acute myeloid leukaemia. Here we show that these myeloid relapses share oncogene fusion breakpoints with their matched lymphoid presentations and can originate in either early, multipotent progenitors or committed B-cell precursors. Lineage switching is linked to substantial changes in chromatin accessibility and rewiring of transcriptional programmes indicating that the execution and maintenance of lymphoid lineage differentiation is impaired. We show that this subversion is recurrently associated with the dysregulation of repressive chromatin modifiers, notably the nucleosome remodelling and deacetylation complex, NuRD. In addition to mutations, we show differential expression or alternative splicing of NuRD members and other genes is able to reprogram the B lymphoid into a myeloid gene regulatory network. Lineage switching in MLL-AF4 leukaemia is therefore driven and maintained by defunct epigenetic regulation.Statement of SignificanceWe demonstrate diverse cellular origins of lineage switched relapse within MLL-AF4 pro-B acute leukaemia. Irrespective of the developmental origin of relapse, dysregulation of NuRD and/or other epigenetic machinery underpins fundamental lineage reprogramming with profound implications for the increasing use of epitope directed therapies in this high-risk leukaemia.

Background: Breast cancer is one of the most prevalent cancers that often occur in females. Long noncoding RNA differentiation antagonizing nonprotein coding RNA (DANCR) has been involved in the pathogenesis of various tumors, including breast cancer. This study aimed to investigate the role and underlying mechanism of DANCR in breast cancer. Materials and Methods: The level of DANCR was detected in breast cancer tissues and cells by quantitative real-time polymerase chain reaction (qRT-PCR). Cell viability was evaluated by the 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide assay. Cell apoptosis was assessed using flow cytometry. Cell migration and invasion were estimated by the Transwell assay. The relationship between DANCR, miR-4319, and vesicle-associated membrane protein-associated protein B (VAPB) was confirmed by bioinformatic analysis and dual-luciferase reporter assay. The level of microRNA-4319 (miR-4319) was tested by qRT-PCR. The expression of VAPB was measured by qRT-PCR or western blot assay. Results: DANCR and VAPB were upregulated, while miR-4319 was downregulated in breast cancer tissues and cells. Knockdown of DANCR hindered proliferation, migration, and invasion and promoted apoptosis of breast cancer cells. DANCR knockdown inhibited breast cancer development through regulating miR-4319. Inhibition of miR-4319 restrained breast cancer cell progression by targeting VAPB. Moreover, DANCR regulated VAPB expression by sponging miR-4319 in breast cancer cells. Conclusion: DANCR facilitated breast cancer cell progression through regulating the miR-4319/VAPB axis, indicating that DANCR might be a potential biomarker and therapeutic target for breast cancer treatment.

Paleopalynology evidence and megafossil records indicated that tree fern order Cyatheales, played an important role in Mesozoic terrestrial ecosystem. Few fossil records of the family Thyrsopteridaceae have been reported so far. In the present study, we describe a distinctive fertile pinnule segment of a fern plant preserved in a mid-Cretaceous amber from Myanmar. The well-preserved fertile pinnule is identified as a new species of the extant tree fern genus Thyrsopteris (Thyrsopteridaceae): Thyrsopteris cyathindusia n. sp. It represents the second fossil species of Thyrsopteridaceae found in the mid-Cretaceous amber from Myanmar. The new species shows distinctive characteristics of the sporophyll that are considered paleoecologically/paleobiogeographically significant for evolution of the Thyrsopteridaceae.

Many microorganisms have mechanisms that protect cells against attack from viruses. The fermentation components of Streptomyces sp. 1647 exhibit potent anti-influenza A virus (IAV) activity. This strain was isolated from soil in southern China in the 1970s, but the chemical nature of its antiviral substance(s) has remained unknown until now. We used an integrated multi-omics strategy to identify the antiviral agents from this streptomycete. The antibiotics and Secondary Metabolite Analysis Shell (antiSMASH) analysis of its genome sequence revealed 38 biosynthetic gene clusters (BGCs) for secondary metabolites, and the target BGCs possibly responsible for the production of antiviral components were narrowed down to three BGCs by bioactivity-guided comparative transcriptomics analysis. Through bioinformatics analysis and genetic manipulation of the regulators and a biosynthetic gene, cluster 36 was identified as the BGC responsible for the biosynthesis of the antiviral compounds. Bioactivity-based molecular networking analysis of mass spectrometric data from different recombinant strains illustrated that the antiviral compounds were a class of structural analogues. Finally, 18 pseudo-tetrapeptides with an internal ureido linkage, omicsynins A1–A6, B1–B6, and C1–C6, were identified and/or isolated from fermentation broth. Among them, 11 compounds (omicsynins A1, A2, A6, B1–B3, B5, B6, C1, C2, and C6) are new compounds. Omicsynins B1–B4 exhibited potent antiviral activity against IAV with the 50% inhibitory concentration (IC50) of approximately 1 µmol∙L–1 and a selectivity index (SI) ranging from 100 to 300. Omicsynins B1–B4 also showed significant antiviral activity against human coronavirus HCoV-229E. By integrating multi-omics data, we discovered a number of novel antiviral pseudo-tetrapeptides produced by Streptomyces sp. 1647, indicating that the secondary metabolites of microorganisms are a valuable source of novel antivirals.

Abstract: Protein-ligand interactions are necessary for majority protein functions. Adenosine- 5’-triphosphate (ATP) is one such ligand that plays vital role as a coenzyme in providing energy for cellular activities, catalyzing biological reaction and signaling. Knowing ATP binding residues of proteins is helpful for annotation of protein function and drug design. However, due to the huge amounts of protein sequences influx into databases in the post-genome era, experimentally identifying ATP binding residues is costineffective and time-consuming. To address this problem, computational methods have been developed to predict ATP binding residues. In this review, we briefly summarized the application of machine learning methods in detecting ATP binding residues of proteins. We expect this review will be helpful for further research.

Swine acute diarrhea syndrome coronavirus (SADS-CoV) is a newly discovered enteric coronavirus. We have previously shown that the caspase-dependent FASL-mediated and mitochondrion-mediated apoptotic pathways play a central role in SADS-CoV-induced apoptosis, which facilitates viral replication. However, the roles of intracellular signaling pathways in SADS-CoV-mediated cell apoptosis and the relative advantages that such pathways confer on the host or virus remain largely unknown. In this study, we show that SADS-CoV induces the activation of ERK during infection, irrespective of viral biosynthesis. The knockdown or chemical inhibition of ERK1/2 significantly suppressed viral protein expression and viral progeny production. The inhibition of ERK activation also circumvented SADS-CoV-induced apoptosis. Taken together, these data suggest that ERK activation is important for SADS-CoV replication, and contributes to the virus-mediated changes in host cells. Our findings demonstrate the takeover of a particular host signaling mechanism by SADS-CoV and identify a potential approach to inhibiting viral spread.

Objectives: Our study analyzed the performance of Xpert MTB/RIF Ultra (Ultra) on stool and gastric aspirate (GA) samples for the diagnosis of pediatric pulmonary tuberculosis (TB) caused by Mycobacterium tuberculosis in a high-burden area of China. Methods: Children with presumptive TB were enrolled in two hospitals in Sichuan Province (July 2019–Oct 2020). Because of the unavailability of sputum for etiological testing, gastric samples were aspirated and tested by bacterial culture, acid-fast bacillus microscopy, and Ultra. Stool samples were tested simultaneously using Ultra and Xpert. Results: In total, 141 children with active TB and 34 with non-TB respiratory tract infections were enrolled. Ultra-stool (60.3%, 85/141) and Ultra-GA (52.5%, 74/141) tests were similarly sensitive (p = 0.187). Among the subset of 48 children with confirmed TB, Ultra testing was equally sensitive on stool and GA samples (85.4%, 41/48). The agreement between Ultra-stool and Ultra-GA was moderate in children with active TB (kappa value = 0.527). After integrating Ultra-GA and Ultra-stool outcomes, 70.9% (100/141) of the children were considered to have confirmed TB. The specificities of Ultra-stool and Ultra-GA were 97.1% (33/34) and 100% (34/34), respectively (p = 0.314). Conclusions: In children, stools can be used as alternative samples to GAs for Ultra tests. Stool- and GA-based Ultra tests are appropriate for bacteriological TB confirmation.

Objectives The aim of this study was to investigate the genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in China to identify predominant lineages and their associations with clinical data and antimicrobial resistance profiles. Methods We performed a national prevalence study of patients with S. aureus infections in 22 tertiary hospitals in China from 2015 to 2017. Clinical data from patients and the antimicrobial phenotypes were collected for each isolate. Genome sequencing was performed on a proportion of isolates and a phylogenetic analysis was undertaken. Genotypic and phenotypic β-lactam susceptibilities were compared. Results A total of 1900 patients with S. aureus infections were included, of which 40% involved MRSA. Community-associated MRSA (CA-MRSA) infections were 24% of the total isolates. Genomic data showed that more than three-quarters of the MRSA were from three dominant lineages CC239 (25%, 116/471), CC5 (21%, 96/471) and CC59 (33%, 154/471) with CC59 accounting for more than half of the CA-MRSA isolates. Penicillin susceptibility genomic features were observed in 53% (251/470) of MRSA, including almost all of the CC59 (152/154) lineage, and 96% (242/251) of these isolates demonstrated in vitro susceptibility to penicillin or amoxicillin combined with clavulanic acid. Phylogenetic analysis indicated that the CC59 lineage can be divided into six lineages with all Asian CC59 isolates likely arising from an ancestral Mainland China lineage. Conclusions This study showed a high prevalence of CA-MRSA in China, largely due to the widespread presence of CC59. As almost all isolates in this lineage possess genetic variants leading to increased β-lactam susceptibility, we suggest that to improve antibiotic stewardship combinations of penicillins and β-lactamase inhibitors should be included in the antibiotic susceptibility testing panels used to inform treatment decisions and research undertaken on this combination therapy.

Nanozymes have become a new generation of antibiotics with exciting broad-spectrum antibacterial properties and negligible biological toxicity. However, their inherent low catalytic activity limits their antibacterial properties. Herein, Cu single-atom sites/N doped porous carbon (Cu SASs/NPC) is successfully constructed for photothermal-catalytic antibacterial treatment by a pyrolysis-etching-adsorption-pyrolysis (PEAP) strategy. Cu SASs/NPC have stronger peroxidase-like catalytic activity, glutathione (GSH)-depleting function, and photothermal property compared with non-Cu-doped NPC, indicating that Cu doping significantly improves the catalytic performance of nanozymes. Cu SASs/NPC can effectively induce peroxidase-like activity in the presence of H2O2, thereby generating a large amount of hydroxyl radicals (•OH), which have a certain killing effect on bacteria and make bacteria more susceptible to temperature. The introduction of near-infrared (NIR) light can generate hyperthermia to fight bacteria, and enhance the peroxidase-like catalytic activity, thereby generating additional •OH to destroy bacteria. Interestingly, Cu SASs/NPC can act as GSH peroxidase (GSH-Px)-like nanozymes, which can deplete GSH in bacteria, thereby significantly improving the sterilization effect. PTT-catalytic synergistic antibacterial strategy produces almost 100% antibacterial efficiency against Escherichia coli (E. coli) and methicillin-resistant Staphylococcus aureus (MRSA). In vivo experiments show a better PTT-catalytic synergistic therapeutic performance on MRSA-infected mouse wounds. Overall, our work highlights the wide antibacterial and anti-infective bio-applications of Cu single-atom-containing catalysts., Graphical abstract Image 1, Highlights • Uniform Cu SASs/NPC were fabricated by a pyrolysis-etching-adsorption-pyrolysis strategy. • Cu SASs/NPC showed excellent photothermal, catalytic, and GSH-depleted properties. • Cu SASs/NPC obtained satisfactory PTT-catalytic synergistic antibacterial performance.

Powdery mildew and leaf rust, caused by Blumeria graminis f. sp. tritici and Puccinia triticina, respectively, are widespread diseases of wheat worldwide. The use of resistant cultivars is considered the most economical, environment-friendly, and effective method to control these diseases. In the present study, a collection of 2,978 wheat accessions consisting of 1,394 advanced breeding lines, 1,078 Chinese cultivars, 291 introduced cultivars, 132 lines containing alien chromosomes, and 83 landraces was tested for reactions to powdery mildew and leaf rust. The results indicated that 659 wheat accessions (22.1%) were highly resistant to a widely prevalent B. graminis f. sp. tritici isolate, E09, at the seedling stage, and 390 were consistently resistant to the mixture of B. graminis f. sp. tritici isolates at the adult plant stage. Meanwhile, 63 accessions (2.1%) were highly resistant to leaf rust at the adult plant stage, of which 54 were resistant to a predominant and highly virulent P. triticina race, THTT, at the seedling stage. Notably, 17 accessions were resistant to both powdery mildew and leaf rust. To detect known genes for resistance to powdery mildew and leaf rust, these accessions were tested with gene-specific or tightly linked markers for seven powdery mildew genes (Pm genes; Pm2, Pm4, Pm5, Pm6, Pm8, Pm21, and Pm24) and 10 Lr genes (Lr1, Lr9, Lr10, Lr19, Lr20, Lr24, Lr26, Lr34, Lr37, and Lr46). Of the 659 powdery mildew-resistant accessions, 328 might carry single Pm genes and 191 carry combined Pm genes. Pm2 was detected at the highest frequency of 59.6%, followed by Pm8, Pm6, Pm21, Pm4, and Pm5, whereas Pm24 was not detected. In addition, 139 accessions might contain unknown Pm genes different from those tested in this study. In the 63 accessions resistant to leaf rust, four leaf rust genes (Lr genes; Lr1, Lr10, Lr26, and Lr34) were detected in 41 accessions singly or in combination, whereas six genes (Lr9, Lr19, Lr20, Lr24, Lr37, and Lr46) were not detected. Twenty-two accessions might contain unknown Lr genes different from those tested in this study. This study not only provided important information for rationally distributing resistance genes in wheat breeding programs, but also identified resistant germplasm that might have novel genes to enrich the diversity of resistance sources.

Polycystic ovary syndrome (PCOS) is a complex infertility disorder affecting up to 10% of women in the U.S. and most commonly presents with anovulation and androgen excess. Previous research has shown that PCOS women have significantly higher levels of anti-Müllerian hormone (AMH) and psychiatric comorbidities. However, the effect of AMH on the neuroendocrine reproductive axis has not been fully characterized. Recently, a novel prenatal AMH (pAMH) mouse model of PCOS was developed to recapitulate reproductive phenotypes of the disorder; but non-reproductive aspects, such as stress and anxiety, have not been explored. This project sought to investigate the effect of pAMH exposure on stress reactivity in two generations of offspring. We found that pAMH treatment led to increased response to psychosocial stress in both generations of female mice. The pAMH group had significantly increased novelty-induced defecation and urination, and also had an overall significant and prolonged increase in corticosterone (CORT) response to restraint stress. Notably, we also observed pAMH-induced transgenerational effects in male mice. Our findings suggest that in addition to reproductive phenotypes, pAMH mouse model is also a representative model of PCOS on non-reproductive measures. To our knowledge, this is the first study to address psychiatric domains of PCOS in a mouse model. Our results potentially shed light on a previously unknown action of AMH in the brain and could also have implications for psychiatric disorders within and beyond the context of PCOS. Further investigation is required to identify the neural circuitry involved in pAMH-mediated phenotypes.

Photodynamic therapy (PDT) is an efficacious noninvasive therapeutic modality that utilizes nontoxic photosensitizers (PSs) to transform oxygen into highly cytotoxic reactive oxygen species (ROS) u...

Many natural objects exhibit radial or axial symmetry in a single plane. However, a universal tool for simulating and fitting the shapes of such objects is lacking. Herein, we present an R package called 'biogeom' that simulates and fits many shapes found in nature. The package incorporates novel universal parametric equations that generate the profiles of bird eggs, flowers, linear and lanceolate leaves, seeds, starfish, and tree-rings, and three growth-rate equations that generate the profiles of ovate leaves and the ontogenetic growth curves of animals and plants. 'biogeom' includes several empirical datasets comprising the boundary coordinates of bird eggs, fruits, lanceolate and ovate leaves, tree rings, seeds, and sea stars. The package can also be applied to other kinds of natural shapes similar to those in the datasets. In addition, the package includes sigmoid curves derived from the three growth-rate equations, which can be used to model animal and plant growth trajectories and predict the times associated with maximum growth rate. 'biogeom' can quantify the intra- or interspecific similarity of natural outlines, and it provides quantitative information of shape and ontogenetic modification of shape with important ecological and evolutionary implications for the growth and form of the living world.

Programmed cell death (PCD) is an important pathologic process after spinal cord injury (SCI), and as a newly type of PCD, ferroptosis is also involved in the secondary SCI, however, the underlying molecular mechanisms remain unclear. Integrating animal experiment and bioinformatics, we validated the ferroptotic phenotype in SCI first, and then bioinformatic analyses, including Gene Ontology enrichment analysis, Kyoto Encyclopedia of Genes and Genomes pathway analysis, gene set enrichment analysis and protein-protein interaction analysis were performed to investigate the ferroptotic genes at 1 day, 3 days, 7 days, 14 days and 56 days post-SCI, finally, the ferroptotic genes in SCI were identified and expression of 5 key genes were validated by western blot. The ferroptotic symbols including iron overload, lipid peroxidation, shrunken mitochondria and ROS accumulation were detected in the acute and sub-acute phase of SCI. The outcomes of bioinformatics suggested that mTOR signaling pathway, HIF-1 signaling pathway, VEGF signaling pathway, Protein processing in endoplasmic reticulum were involved in ferroptotic regulation and ATF-3, XBP-1, HO-1, DDIT-3 and CHAC-1 were selected as the ferroptotic key genes in SCI. Besides, response to oxidative stress, amide metabolic process, cation transport and cytokine production were showed as the essential biological process in ferroptosis after SCI. The ferroptotic phenotype following SCI was validated and the ferroptotic genes and signaling pathways were identified. The results contribute to exploring the ferroptotic mechanism underlying secondary SCI and to providing potential target for clinical treatment.

This study was designed to generate the full-length transcriptome of Coilia nasus using single-molecule long read isoform sequencing (SMRT-seq) technology. RNAs of brains, ovaries, and testes of C. nasus conditioned in both seawater and freshwater except for gut which was only from the fish conditioned in freshwater, were isolated. All the RNAs were pooled together equally for SMRT sequencing. One SMRT cell produced 64.18 Gb clean data, including 765,184 circular consensus (CCS) reads and 616,126 full-length non-chimeric (FLNC) reads. Finally, 93,793 non-redundant transcripts were obtained after clustered and polished. Structural analysis of the 93,793 non-redundant transcripts predicted 8242 alternative splicing events, a total of 229,825 SSR and 72,037 complete CDS. A total of 8437 lncRNA were identified. 84,617 transcripts were annotated in NR, Swissprot, GO, COG, KOG, eggnog, Pfam and KEGG database totally. This is the first full-length transcriptome of Coilia nasus, including transcripts appeared in the case of seawater, which will facilitate exploration of genetic data and life story of Coilia nasus.

Silique length influences seed yield in oilseed rape. It shows extensive variation in germplasm resources, and identifying the underlying genes and regulatory mechanisms would advance breeding for the trait. In the present study, a genome-wide association study (GWAS) using 331 core accessions planted in 10 environments revealed 13 loci associated with silique length on chromosomes A01, A04, A07, A09, and C03, explaining 6.2%–19.2% of phenotypic variance. Physiological analysis showed that silique length variation was attributable to differences in silique growth rate and/or duration before four weeks after flowering, with levels of endogenous phytohormones (auxin, ethylene, and GA24, GA12, and GA44) playing an important role. Cytological analysis showed that silique length variation was due mainly to differences in cell number followed by cell size. Transcriptomic analysis of two pools of silique walls with opposite length extremes revealed 3248 differentially expressed genes (DEGs). These DEGs were enriched in several pathways (such as cell wall, cell division, and hormone metabolism) associated with cell proliferation and expansion and silique development. Integrating GWAS, RNA-seq, and functional annotation results revealed 15 candidate genes for the major associated locus qSL.A09-3. Of these, BnaA9.ARF18 and BnaA9.CYP78A9 were validated by haplotype analysis followed by candidate gene association. Sequence variation in the coding region of BnaA9.ARF18 and expression of BnaA9.CYP78A9 in silique walls were strongly associated with silique length. Our results provide an explanation for the natural variation of silique length in oilseed rape germplasm and offer useful information for its improvement.

Lignocellulose is an abundant xylose-containing biomass found in agricultural wastes, and has arisen as a suitable alternative to fossil fuels for the production of bioethanol. Although Saccharomyces cerevisiae has been thoroughly used for the production of bioethanol, its potential to utilize lignocellulose remains poorly understood. In this work, xylose-metabolic genes of Pichia stipitis and Candida tropicalis, under the control of different promoters, were introduced into S. cerevisiae. RNA-seq analysis was use to examine the response of S. cerevisiae metabolism to the introduction of xylose-metabolic genes. The use of the PGK1 promoter to drive xylitol dehydrogenase (XDH) expression, instead of the TEF1 promoter, improved xylose utilization in ?XR-pXDH? strain by overexpressing xylose reductase (XR) and XDH from C. tropicalis, enhancing the production of xylitol (13.66 ? 0.54 g/L after 6 days fermentation). Overexpression of xylulokinase and XR/XDH from P. stipitis remarkably decreased xylitol accumulation (1.13 ? 0.06 g/L and 0.89 ? 0.04 g/L xylitol, respectively) and increased ethanol production (196.14% and 148.50% increases during the xylose utilization stage, respectively), in comparison with the results of XR-pXDH. This result may be produced due to the enhanced xylose transport, Embden?Meyerhof and pentose phosphate pathways, as well as alleviated oxidative stress. The low xylose consumption rate in these recombinant strains comparing with P. stipitis and C. tropicalis may be explained by the insufficient supplementation of NADPH and NAD+. The results obtained in this work provide new insights on the potential utilization of xylose using bioengineered S. cerevisiae strains.

A previously unknown association between Plasmopara viticola, the causal pathogen of grape downy mildew, and the mycoparasite strain F2 is described in this paper. F2 could be consistently isolated from the mildew of diseased spots on grape leaves of Kyoho ( Vitis labrusca × V. vinifera cv. Kyoho) infected with P. viticola but not from the surfaces of healthy grape leaves or within lesions of other diseases. It was observed that strain F2 was capable of coiling around sporangiophores and sporangia of P. viticola under a microscope, causing hyphae deformation, decreasing the pathogen growth, and reducing the number of sporangia. This fungal strain was identified as Simplicillium lanosoniveum on the basis of morphological characterizations and 28S rDNA sequencing. To our knowledge, this is the first report of S. lanosoniveum with hyperparasitic characteristics on P. viticola, and the hyperparasite has potential application in the control of grape downy mildew. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Stigmaria asiatica Jongmans et Gothan is a common species from the Permo-Carboniferous of East Asia. It is characterized by a relatively slender rhizomorph and represents the underground rooting system of lowland arborescent lycopsids. This species from the Wuda Coalfield (Asselian, lower Permian) represents the recovery taxon dominating the subsequent peat-forming vegetation after a volcanic eruption destroyed the previous flora, termed the Wuda Tuff Flora (Chinese “vegetational Pompeii”). It is characterized by novel downward axes, probably for access to deeper groundwater. Here, the anatomy of S. asiatica, including that of the axes and rootlets, is reported in detail for the first time. The axis contains stelar tissues, including pith, primary and secondary xylem, and phloem, and both primary and secondary cortical tissues. The primary cortex is tripartite and is divided into inner, middle, and outer zones. Secondary cortex is produced in the interior of the outer cortex splitting the outer cortex into inner and outer portions. The homogeneous pith and mesarch primary xylem maturation of S. asiatica are different from previously recorded species of Stigmaria Brongniart. Rootlets are composed of a central monarch vascular bundle surrounded by inner cortex and a ring of outer cortex. A vacant region is present between the inner and outer cortices. In some cases, connectives between the inner and outer cortices are present. According to the presented statistical analysis, it is proposed that rootlets of S. asiatica were highly branched, with at least for 7 bifurcations. Rootlets, together with the downward penetrating rhizomorph, helped to both anchor the plant and search for and absorb deep groundwater.

This study ascertained to explore the potential contribution of ARRDC3 polymorphisms in the risk and prognosis of glioma. One thousand sixty-one patients and healthy controls were conducted to assess whether ARDC3 polymorphism was associated with glioma risk and prognosis. Four sites in ARRDC3 were selected and genotyped in MassARRAY platform. The calculated odd ratios and 95% confidence intervals from logistic regression were applied for risk assessment. The relationship between ARRDC3 variants and glioma prognosis was evaluated using log-rank test, Kaplan-Meier analysis, and so on. Also, false-positive report probability (FPRP) and statistical power were also assessed. Our findings suggested the negative role of ARRDC3 polymorphisms in the glioma risk. We also found the effect of candidate SNPs in ARRDC3 on the susceptibility to glioma was dependent on the age, gender, and histology of glioma patients. The results suggested that the genetic polymorphisms of ARRDC3 were related to an increased risk of glioma.