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Background: Directly discharging livestock and poultry slaughter blood without proper treatment can cause severe ecological damage. Exploring the use of microorganisms to break down waste blood into smaller molecules such as peptides and amino acids, as well as investigating the possibility of transforming these small molecules into water-soluble fertilizers containing amino acids, holds significant research value in the comprehensive utilization of livestock and poultry blood. Results: In this study, a single strain of Bacillus pumilus NWMCC0302, which has effectively degraded bovine blood, was isolated from abattoir blood sludge using casein agar plates and Columbia blood agar plates. The degradation test was carried out using bovine raw blood as a nitrogen source in the medium, and the results showed that the strain degraded 53.83% of bovine blood under optimal degradation conditions. The whole genome sequencing of Bacillus pumilus NWMCC0302 was conducted using the second-generation DNBSEQ platform and the third-generation PacBio platform, employing high-throughput sequencing technology. The size of the strain's entire genome was determined to be 3 868 814 bp with a G-C content of 41.63%. The total gene length accounted for 88.98% of the genome length at 3 442 341 bp and encoded 4 113 genes. The strain contained 79 tRNAs, 24 rRNAs, 7 sRNAs, and 296 repetitive sequences. The gene data obtained from sequencing were also functionally annotated using the COG, KEGG, and VFDB databases. In the COG database, 310 genes were involved in amino acid transport and metabolism, including 10 catabolic proteins related to COGs. In the KEGG database, were 201 genes involved in amino acid metabolism pathways, including 8 genes in nitrogen metabolism pathways and 2 genes in oxidative pathways. The VFDB database contains two lysostaphin genes and one serine protease-hydrolyzed ClpP gene. Conclusions: In summary, Bacillus pumilus NWMCC0302 was screened for its efficient ability to degrade bovine blood. Additionally, the genetic information of Bacillus pumilus NWMCC0302 was revealed at the genetic level, providing a feasible experimental method for applying this strain to the degradation of blood from slaughtered livestock and poultry. Moreover, it is a potential functional strain for producing amino acid-containing water-soluble fertilisers. [ABSTRACT FROM AUTHOR]

Abstract Background Directly discharging livestock and poultry slaughter blood without proper treatment can cause severe ecological damage. Exploring the use of microorganisms to break down waste blood into smaller molecules such as peptides and amino acids, as well as investigating the possibility of transforming these small molecules into water-soluble fertilizers containing amino acids, holds significant research value in the comprehensive utilization of livestock and poultry blood. Results In this study, a single strain of Bacillus pumilus NWMCC0302, which has effectively degraded bovine blood, was isolated from abattoir blood sludge using casein agar plates and Columbia blood agar plates. The degradation test was carried out using bovine raw blood as a nitrogen source in the medium, and the results showed that the strain degraded 53.83% of bovine blood under optimal degradation conditions. The whole genome sequencing of Bacillus pumilus NWMCC0302 was conducted using the second-generation DNBSEQ platform and the third-generation PacBio platform, employing high-throughput sequencing technology. The size of the strain's entire genome was determined to be 3 868 814 bp with a G-C content of 41.63%. The total gene length accounted for 88.98% of the genome length at 3 442 341 bp and encoded 4 113 genes. The strain contained 79 tRNAs, 24 rRNAs, 7 sRNAs, and 296 repetitive sequences. The gene data obtained from sequencing were also functionally annotated using the COG, KEGG, and VFDB databases. In the COG database, 310 genes were involved in amino acid transport and metabolism, including 10 catabolic proteins related to COGs. In the KEGG database, were 201 genes involved in amino acid metabolism pathways, including 8 genes in nitrogen metabolism pathways and 2 genes in oxidative pathways. The VFDB database contains two lysostaphin genes and one serine protease-hydrolyzed ClpP gene. Conclusions In summary, Bacillus pumilus NWMCC0302 was screened for its efficient ability to degrade bovine blood. Additionally, the genetic information of Bacillus pumilus NWMCC0302 was revealed at the genetic level, providing a feasible experimental method for applying this strain to the degradation of blood from slaughtered livestock and poultry. Moreover, it is a potential functional strain for producing amino acid-containing water-soluble fertilisers.

Background: Head and neck paragangliomas (HNPGLs) are rare neuroendocrine tumors that pose significant challenges in both diagnosis and treatment. The pathogenic mechanism remains unclear, and there is no proteomic analysis-based molecular classification. Therefore, gaining a deeper understanding of this disease from the protein level is crucial because proteins play a fundamental role in the occurrence and development of tumors. Methods: We collected 44 tumor samples from patients diagnosed with HNPGL. The adrenal paraganglioma tissue (N = 46) was used as the disease control group and the chorda tympani nerves (N = 18) were used as the control group. High-pH reversed-phase liquid chromatography and liquid chromatography with tandem mass spectrometry analyses were used to build an integrated protein database of tumor samples. We then obtained two sets of differentially expressed proteins between the tumor group and the control group to identify the unique proteomic signatures of HNPGLs. Ingenuity pathway analysis annotations were used to perform the functional analysis. Subsequently, we developed a clinically relevant molecular classification for HNPGLs that connected the clinical characteristics with meaningful proteins and pathways to explain the varied clinical manifestations. Results: We identified 6,640 proteins in the HNPGL group, and 314 differentially expressed proteins unique to HNPGL were discovered via inter-group comparison. We identified two HNPGL subgroups that significantly differed in clinical manifestation and proteomic characteristics. On the basis of the proteomic results, we proposed a pathogenic mechanism underlying HNPGL. Conclusion: We conducted a comprehensive analysis of the molecular mechanisms of HNPGL to build, for the first time, a clinically relevant molecular classification. By focusing on differential proteomic analyses between different types of paragangliomas, we were able to obtain a comprehensive description of the proteomic characteristics of HNPGL, which will be valuable for the search for significant biomarkers as a new treatment method for HNPGL. [ABSTRACT FROM AUTHOR]

Abstract Objectives Lasiodiplodia pseudotheobromae is an important fungal pathogen associated with die-back, canker and shoot blight in many plant hosts with a wide geographic distribution. The aim of our study was to provide high-quality genome assemblies and sequence annotation resources of L. pseudotheobromae, to facilitate future studies on the systematics, population genetics and genomics of the fungal pathogen L. pseudotheobromae. Data description High-quality genomes of five L. pseudotheobromae isolates were sequenced based on Oxford Nanopore technology (ONT) and Illumina HiSeq sequencing platform. The total size of each assembly ranged from 43 Mb to 43.86 Mb and over 11,000 protein-coding genes were predicted from each genome. The proteins of predicted genes were annotated using multiple public databases, among the annotated protein-coding genes, more than 4,300 genes were predicted as potential virulence genes by the Pathogen Host Interactions (PHI) database. Moreover, the genome comparative analysis among L. pseudotheobromae and other closely related species revealed that 7,408 gene clusters were shared among them and 152 gene clusters unique to L. pseudotheobromae. This genome and associated datasets provided here will serve as a useful resource for further analyses of this fungal pathogen species.

Xi Wang,1,* Jiyu Xu,2,* Guodong Feng,1 Zhiqiang Gao,1 Wei Sun2 1Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, People’s Republic of China; 2Institute of Basic Medical Sciences, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, People’s Republic of China*These authors contributed equally to this workCorrespondence: Zhiqiang Gao; Wei Sun, Email gzqent@163.com; sunwei@ibms.pumc.edu.cnBackground: Proteins found in middle ear effusion play crucial roles in the physiological and pathological processes of otitis media with effusion (OME), influencing the etiology and clinical characteristics of this disease. The qualitative and quantitative composition of these proteins depending on the underlying pathogenesis of middle ear effusion. Understanding their physiological and pathological functions is of great importance.Methods: We collected samples from 19 volunteers diagnosed with OME. After offline separation using high-pH reversed-phase liquid chromatography (RPLC), the pooled sample was subjected to LC-MS/MS analysis to obtain a comprehensive profile of the OME proteome. Functional analysis was performed using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Ingenuity Pathway Analysis (IPA) annotations. Data-independent acquisition (DIA) technology was utilized to analyze samples and fix whether the OME proteome could replicate the pathophysiological features associated with this disease. We conducted a differential proteomic analysis between patients with simple OME and patients who had received radiotherapy. The radiotherapy-reduced group was further divided into two subgroups: nasopharyngeal carcinoma (NPC) and other types of carcinoma. Parallel reaction monitoring (PRM) technology was used for validation of 36 differentially expressed proteins (DEPs).Results: A number of 732 proteins were identified in the OME proteome database. Among them, 527 proteins were quantified using peak intensity-based semi-quantification (iBAQ), covering a wide dynamic range of approximately 8 orders of magnitude. Based on the functional analysis, we proposed a hypothetical mechanism of OME.Conclusion: This study managed to put up an inclusive analysis of the OME proteome, establishing the first human OME proteome database. We focused on differential proteomic analysis among different groups to gain a more comprehensive concept of the OME proteome and search for meaningful biomarkers.Keywords: otitis media with effusion, proteome, function annotation, radiotherapy-reduced OME, nasopharyngeal carcinoma

High temperature stress is regarded as one of the significant abiotic stresses affecting the composition and distribution of natural habitats and the productivity of agriculturally significant plants worldwide. The HSF family is one of the most important transcription factors (TFs) families in plants and capable of responding rapidly to heat and other abiotic stresses. In this study, 29 AgHSFs were identified in celery and classified into three classes (A, B, and C) and 14 subgroups. The gene structures of AgHSFs in same subgroups were conserved, whereas in different classes were varied. AgHSF proteins were predicted to be involved in multiple biological processes by interacting with other proteins. Expression analysis revealed that AgHSF genes play a significant role in response to heat stress. Subsequently, AgHSFa6-1, which was significantly induced by high temperature, was selected for functional validation. AgHSFa6-1 was identified as a nuclear protein, and can upregulate the expression of certain downstream genes (HSP98.7, HSP70-1, BOB1, CPN60B, ADH2, APX1, GOLS1) in response to hightemperature treatment. Overexpression of AgHSFa6-1 in yeast and Arabidopsis displayed higher thermotolerance, both morphologically and physiologically. In response to heat stress, the transgenic plants produced considerably more proline, solute protein, antioxidant enzymes, and less MDA than wild-type (WT) plants. Overall, this study revealed that AgHSF family members perform a key role in response to high temperature, and AgHSFa6-1 acts as a positive regulator by augmenting the ROS-scavenging system to maintain membrane integrity, reducing stomatal apertures to control water loss, and upregulating the expression level of heat-stress sensitive genes to improve celery thermotolerance. [ABSTRACT FROM AUTHOR]

Copyright of Journal of South-Central Minzu University (Natural Science Edition) is the property of Journal of South-Central Minzu University (Natural Science Edition) Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

In this study, selected properties of protease and the complete genome sequence of Bacillus licheniformis NWMCC0046 were investigated, to discover laundry applications and other potential probiotic properties of this strain. Partial characterization of B. licheniformis NWMCC0046 showed that its protease has good activity both in alkaline environments and at low temperatures. Also, the protease is compatible with commercial detergents and can be used as a detergent additive for effective stain removal at low temperatures. The complete genome sequence of B. licheniformis NWMCC0046 is comprised of a 4,321,565 bp linear chromosome with a G + C content of 46.78% and no plasmids. It had 4504 protein‐encoding genes, 81 transfer RNA (tRNA) genes, and 24 ribosomal RNA (rRNA) genes. Genomic analysis revealed genes involved in exocellular enzyme production and probiotic properties. In addition, genomic sequence analysis revealed specific genes encoding carbohydrate metabolism pathways, resistance, and cold adaptation capacity. Overall, protease properties show its potential as a detergent additive enzyme. The complete genome sequence information of B. licheniformis NWMCC0046 was obtained, and functional prediction revealed its numerous probiotic properties. [ABSTRACT FROM AUTHOR]

Recently, the monkeypox virus has begun to spread in many countries worldwide [1]. The genome sequence of the monkeypox virus variant responsible for the current outbreak has been reported, thus providing an important resource for better understanding the new variant and accelerating vaccine and drug development. Here, we report structure predictions of the whole proteomes of three monkeypox variants, with annotation of potential small-molecule-binding regions of the proteins. Experimentally determined structures with high similarity to monkeypox proteins were vetted through a structure-alignment algorithm. Our work should help accelerate the development of vaccines and drugs.

• Constructed a full-length transcriptome covering five early developmental stages, renowned for their challenging acquisition, as well as the air-breathing organs, gills, liver, skin, and muscles in adult specimens. • Rectified and enhanced the annotation of the African sharptooth catfish's reference genome. • Explored regulatory networks within the immune system processes and investigated genes relevant to disease resistance and air respiration. • Providing a foundation for disease control, stress resistance, selective breeding, and aquaculture growth. The African sharptooth catfish (Clarias gariepinus) assumes significance in aquaculture, given its role as a farmed freshwater species with modified gill structures functioning as an air-breathing organ (ABO). To provide a scientific basis for further elucidating the air-breathing formation mechanism and deeply utilizing the genetic resources of Clarias gariepinus , we utilized the PacBio sequencing platform to acquire a comprehensive full-length transcriptome from five juvenile developmental stages and various adult tissues, including the ABO, gills, liver, skin, and muscle. We generated 25,766,688 high-quality reads, with an average length of 2,006 bp and an N50 of 2,241 bp. Following rigorous quality control, 34,890 (97.7 %) of the high-quality isoforms were mapped to the reference genome for gene and transcript annotation, yielding 387 novel isoforms and 14,614 new isoforms. Additionally, we identified 28,582 open reading frames, 48 SNPs, 5,464 variable splices, and 6,141 variable polyadenylation sites, along with 475 long non-coding RNAs. Many DEGs were involved with low oxygen GO terms and KEGG pathways, such as response to stimulus, biological regulation and catalytic activities. Furthermore, it was found that transcription factors such as zf-C2H2, Homeobox, bHLH, and MYB could underpin the African sharptooth catfish's developmental plasticity and its capacity to adapt its morphology and function to its environment. Through the comprehensive analysis of its genomic characteristics, it was found that the African sharptooth catfish has developed a series of unique respiratory adaptive mechanisms during the evolutionary process, These results not only advances the understanding of genetic adaptations to hypoxia in Clarias fish but also provides a valuable framework for future studies aimed at improving aquaculture practices,besides provide important references and inspirations for the evolution of aquatic organisms. [ABSTRACT FROM AUTHOR]

The current study aims to investigate differences in whey protein of breastmilk of volunteered mother collected from two ethnic groups (Korean and Han) in China using data-independent acquisition (DIA) based proteomics technique. The total detected 624 proteins were principally allocated to cellular process of biological process (BP), cell and cell part of cell component (CC) and binding of molecular function (MF) according to Gene Ontology (GO) annotation; and carbohydrate metabolism of Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Among the 54 differently expressed proteins, 8 were related with immunity. Enrichment data showed that intracellular of GO functions and viral myocarditis of KEGG pathways were most significantly enriched (p

IntroductionHuman breast milk provides neonates with indispensable nutrition and function. Milk protein is one of the main constituents of breast milk. Human milk profiles can be influenced by many factors.MethodsThe present study aimed to investigate the difference in casein isolated from mature milk of healthy mothers of Korean and Han ethnic groups in China using data-independent acquisition (DIA) proteomics.ResultsA total of 535 proteins were identified and quantified in casein fraction samples from both groups. A total of 528 proteins were annotated to 52 Gene Ontology (GO) terms, the majority (94.13%) of which were distributed in the cell and cell parts of the cellular component. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that 106 proteins were involved in 23 pathways, the greatest (36.79%) in carbohydrate metabolism. There were 39 differentially expressed proteins (DEPs)–10 upregulated and 29 downregulated–between Korean and Han milk. The GO function of blood microparticles and KEGG pathway of Staphylococcus aureus infection for DEPs were the most significantly enriched (p < 0.05). Protein-protein interaction analysis revealed a network with 23 DEPs in 47 interactions, and the fibrinogen alpha chain ranked first as the hub protein.DiscussionThese data may provide useful technical guidance for the development of specific infant foods for certain populations.

This paper presents HBcompare, a method that classifies protein structures according to ligand binding preference categories by analyzing hydrogen bond topology. HBcompare excludes other characteristics of protein structure so that, in the event of accurate classification, it can implicate the involvement of hydrogen bonds in selective binding. This approach contrasts from methods that represent many aspects of protein structure because holistic representations cannot associate classification with just one characteristic. To our knowledge, HBcompare is the first technique with this capability. On five datasets of proteins that catalyze similar reactions with different preferred ligands, HBcompare correctly categorized proteins with similar ligand binding preferences 89.5% of the time. Using only hydrogen bond topology, classification accuracy with HBcompare surpassed standard structure-based comparison algorithms that use atomic coordinates. As a tool for implicating the role of hydrogen bonds in protein function categories, HBcompare represents a first step towards the automatic explanation of biochemical mechanisms. [ABSTRACT FROM AUTHOR]

" Candidatus Accumulibacter" is a unique and pivotal genus of polyphosphate-accumulating organisms prevalent in wastewater treatment plants and plays mainstay roles in the global phosphorus cycle. However, the efforts to fully understand their genetic and metabolic characteristics are largely hindered by major limitations in existing sequence-based annotation methods. Here, we reported an integrated approach combining pangenome analysis, protein structure prediction and clustering, and meta-omic characterization, to uncover genetic and metabolic traits previously unexplored for Ca . Accumulibacter. The identification of a previously overlooked pyrophosphate-fructose 6-phosphate 1-phosphotransferase gene ( pfp ) suggested that all Ca. Accumulibacter encoded a complete Embden-Meyerhof-Parnas pathway. A homologue of the phosphate-specific transport system accessory protein (PhoU) was suggested to be an inorganic phosphate transport (Pit) accessory protein (Pap) conferring effective and efficient phosphate transport. Additional lineage members were found to encode complete denitrification pathways. A pipeline was built, generating a pan- Ca . Accumulibacter annotation reference database, covering >200,000 proteins and their encoding genes. Benchmarking on 27 Ca . Accumulibacter genomes showed major improvement in the average annotation coverage from 51% to 82%. This pipeline is readily applicable to diverse cultured and uncultured bacteria to establish high-coverage annotation reference databases, facilitating the exploration of genomic dark matter in the bacterial domain.

In order to obtain the genetic basis of transcriptome data of Orychophragmus violaceus seedlings, the transcriptome of Orychophragmus violaceus was paired-end sequenced by Illumina Novaseq 6000 platform, a total of 59174171 clean reads (17.75 Gb clean bases) were obtained, and 110919 unigenes were obtained after assembly by de novo, with the longest and shortest length of 15030, 301 bp and an average length of 784 bp. The N50 was 947 bp and the N90 was 396 bp. These unigenes were compared among seven public databases including Non-redundant protein sequences (NR), Nucleotide (NT), Swiss-prot protein database (Swiss-Prot), Protein family (Pfam), Eu-karyotic ortholog groups (KOG), Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG), as a result of 75369 (67.94%), 69004 (62.21%), 62258 (56.12%), 56068 (50.54%), 27796 (25.05%), 56066 (50.54%), 32897 (29.65%) unigenes were annotated respectively. These annotation results showed that Orychophragmus violaceus had most homologous sequences with 13610 unigenes with Quercus suber. The GO annotations showed that 56066 unigenes were annotated with 219038, which were divided into 3 categories and 43 functional groups. The KOG annotations showed that 27796 unigenes were annotated and grouped into 25 functional categories. The KEGG annotations showed that 32897 unigenes were involved in 34 types of metabolic pathways and 305 metabolic pathway branches. A total of 18118 SSR sites and 112584 CDS sequences were detected according to analyzing the coding sequences and microsatellite. Base on the high-throughput transcriptome sequencing of Orychophragmus violaceus, with a large number of functional genes are excavated, which provide certain basic data support for the subsequent development of bioinformatics analysis such as molecular markers and functional metabolic pathways. [ABSTRACT FROM AUTHOR]

Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification-amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two-Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure-Function Linkage Database, SFLD) self-identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self-identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well-curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP-identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F-measure and performance analysis on the enolase search results and comparison to GEMMA and SCI-PHY demonstrate that TuLIP avoids the over-division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results.

[Objective] The present paper aimed to obtain the sequence and structural information of full-length transcripts of taro, and to identify the structural information of genes and transcripts related to starch biosynthesis, so as to provide a scientific basis for the subsequent elucidation of the molecular mechanism of starch biosynthesis and in-depth utilization of taro genetic resources. [Method] The full-length transcripts were sequenced from different tissues (leaves, petioles, corms, stolons and roots) at the age of 3 months using Lipu Taro 1 as the test material. The transcripts were annotated for analyzing their bioinformatics of structural information of AS,APA, lncRNA, TF and SSR sites. Genes and transcripts related to starch biosynthesis were obtained by KEGG annotation and analyzed for AS events and APA. [Result] A total of 38 043 full-length transcript sequences were obtained from three generations of full-length transcriptome sequencing of different tissues of taro. By comparing with the reference genome, 31 058 new transcripts were identified, of which 28 785 were functionally annotated. Structural analysis of the transcripts showed that 9360 AS events, 6436 genes with poly (A) sites, 25 081 SSR loci, 304 lncRNAs, 1911 fusion transcripts and 1608 TFs were identified.14 starch biosynthesis-related genes with 60 transcripts were obtained by KEGG annotation, and their AS events and APA analysis revealed that six genes had AS, containing five types of IR,A5 SS,A3 SS,ES and MEE, and 10 genes had poly (A) sites, of which seven genes had two or more poly (A) sites. [Conclusion] The sequence and structural information of the full-length transcripts of taro are obtained by full-length transcriptome sequencing analysis, and 14 genes and 60 transcripts related to taro starch biosynthesis are identified, which can be used as a scientific basis for the subsequent elucidation of the molecular mechanism of taro starch biosynthesis and in-depth utilization of taro genetic resources. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Food Safety & Quality is the property of Journal of Food Safety & Quality Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Gut bacteria consists of 150 times more genes than humans that are vital for health. Several studies revealed that gut bacteria are associated with disease status and influence human behavior and mentality. Whether human brain injury alters the gut bacteria is yet unclear, we tested 20 fecal samples from patients with cerebral intraparenchymal hemorrhage and corresponding healthy controls through metagenomic shotgun sequencing. The composition of patients' gut bacteria changed significantly at the phylum level; Verrucomicrobiota was the specific phylum colonized in the patients' gut. The functional alteration was observed in the patients' gut bacteria, including high metabolic activity for nutrients or neuroactive compounds, strong antibiotic resistance, and less virulence factor diversity. The changes in the transcription and metabolism of differential species were more evident than those of the non-differential species between groups, which is the primary factor contributing to the functional alteration of patients with cerebral intraparenchymal hemorrhage. [ABSTRACT FROM AUTHOR]

Gut bacteria consists of 150 times more genes than humans that are vital for health. Several studies revealed that gut bacteria are associated with disease status and influence human behavior and mentality. Whether human brain injury alters the gut bacteria is yet unclear, we tested 20 fecal samples from patients with cerebral intraparenchymal hemorrhage and corresponding healthy controls through metagenomic shotgun sequencing. The composition of patients’ gut bacteria changed significantly at the phylum level; Verrucomicrobiota was the specific phylum colonized in the patients’ gut. The functional alteration was observed in the patients’ gut bacteria, including high metabolic activity for nutrients or neuroactive compounds, strong antibiotic resistance, and less virulence factor diversity. The changes in the transcription and metabolism of differential species were more evident than those of the non-differential species between groups, which is the primary factor contributing to the functional alteration of patients with cerebral intraparenchymal hemorrhage.

Background: Head and neck paragangliomas (HNPGLs) are rare neuroendocrine tumors that pose significant challenges in both diagnosis and treatment. The pathogenic mechanism remains unclear, and there is no proteomic analysis-based molecular classification. Therefore, gaining a deeper understanding of this disease from the protein level is crucial because proteins play a fundamental role in the occurrence and development of tumors., Methods: We collected 44 tumor samples from patients diagnosed with HNPGL. The adrenal paraganglioma tissue ( N  = 46) was used as the disease control group and the chorda tympani nerves ( N  = 18) were used as the control group. High-pH reversed-phase liquid chromatography and liquid chromatography with tandem mass spectrometry analyses were used to build an integrated protein database of tumor samples. We then obtained two sets of differentially expressed proteins between the tumor group and the control group to identify the unique proteomic signatures of HNPGLs. Ingenuity pathway analysis annotations were used to perform the functional analysis. Subsequently, we developed a clinically relevant molecular classification for HNPGLs that connected the clinical characteristics with meaningful proteins and pathways to explain the varied clinical manifestations., Results: We identified 6,640 proteins in the HNPGL group, and 314 differentially expressed proteins unique to HNPGL were discovered via inter-group comparison. We identified two HNPGL subgroups that significantly differed in clinical manifestation and proteomic characteristics. On the basis of the proteomic results, we proposed a pathogenic mechanism underlying HNPGL., Conclusion: We conducted a comprehensive analysis of the molecular mechanisms of HNPGL to build, for the first time, a clinically relevant molecular classification. By focusing on differential proteomic analyses between different types of paragangliomas, we were able to obtain a comprehensive description of the proteomic characteristics of HNPGL, which will be valuable for the search for significant biomarkers as a new treatment method for HNPGL., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Wang, Sun, Feng, Tian, Zhao, Gao and Sun.)

[ Objective ] The study aimed to explore the corresponding mechanism of exogenous selenium on transcriptome and the excavation of related functional genes in ice plant. [ Method ] The transcriptome database of ice plant was constructed by using high-throughput sequencing. [ Result ] Apart from brassinosteroid, other 7 pathways of hormone signal transduction in ice plants were significantly affected by selenium treatment.. With the deepening of selenium treatment, auxin signal transduction was promoted, and downstream gene expression was activated; In the cytokinin signal transduction pathway, AHP was sensitive to selenium treatment, A-ARR was significantly up-regulated by selenium treatment, but wasn't sensitive to the change of selenium concentration; With the concentration of selenium treatment increased, the downstream TF of gibberellin signal transduction was activated, which promoted the growth of the stem and leaf of ice plant; In the signal transduction pathway of abscisic acid, selenium treatment (10 mmol/L) reduced the expression of SnRK2 significantly, which inhibited the stomatal closure and led to the dehydration of ice plant ; Selenium treatment ( 100 mmol/L) significantly restored the expression of SnRK2 ; In the ethylene signal transduction pathway, with the increase of selenium concentration, the expression of ETR and ERFl/2 decreased and the maturity and senescence of ice plant were further inhibited; In jasmonic acid signal transduction pathway, selenium treatment ( 10 mmol/L) promoted the up-regulation of ]AZ and MYC2 expression and regulated the stress of selenium on ice plant; Selenium treatment ( 100 mmol/L) had no significant effecton JAZ and MYC2 expression, indicating that high concentration selenium treatment had no significant effect on jasmonic acid signal transduction pathway; In the signal transduction pathway of salicylic acid, TGA and PR-1 had no up-down-regulated exlpression under the condition of selenium treatment ( 10 mmol/L), TGA down-regulated expression and PR-1 up-regulated expression under the condition of selenium treatment ( 100 mmol/L), which activated the selenium response ability of ice plant. The relative expression of? DEGs was consistent with the trend of transcriptome analysis by real-time quantitative PCR. [ Conclusion ] This paper aimed to establish an important basis for the key gene mining and genetic breeding of ice plant. [ABSTRACT FROM AUTHOR]

Copyright of Chinese Journal of Applied Entomology is the property of Chinese Journal of Applied Entomology, Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Coelomactra antiquata is an important aquatic economic shellfish with high medicinal value. However, because C. antiquata has no reference genome, a lot of molecular biology research cannot be carried out, so the analysis of its transcripts is an important step to study the regulatory genes of various substances in C. antiquata. In the present study, we conducted the first full-length transcriptome analysis of C. antiquata by using PacBio single-molecule real-time (SMRT) sequencing technology. The results identified a total of 39,209 unigenes with an average length of 2,732 bp, 23,338 CDSs, 251 AS events, 9,881 lncRNAs, 20,106 SSRs, and 2,316 TFs. Subsequently, 59.22% (23,220) of the unigenes were successfully annotated, of which 23,164, 18,711, 15,840, 13,534, and 13,474 unigenes could be annotated using NR, Swiss-prot, KOG, GO, and KEGG databases, respectively. This study lays the foundation for the follow-up research of molecular biology and provides a reference for studying the more medicinal value of C. antiquata. [ABSTRACT FROM AUTHOR]

Coelomactra antiquata is an important aquatic economic shellfish with high medicinal value. However, because C. antiquata has no reference genome, a lot of molecular biology research cannot be carried out, so the analysis of its transcripts is an important step to study the regulatory genes of various substances in C. antiquata. In the present study, we conducted the first full-length transcriptome analysis of C. antiquata by using PacBio single-molecule real-time (SMRT) sequencing technology. The results identified a total of 39,209 unigenes with an average length of 2,732 bp, 23,338 CDSs, 251 AS events, 9,881 lncRNAs, 20,106 SSRs, and 2,316 TFs. Subsequently, 59.22% (23,220) of the unigenes were successfully annotated, of which 23,164, 18,711, 15,840, 13,534, and 13,474 unigenes could be annotated using NR, Swiss-prot, KOG, GO, and KEGG databases, respectively. This study lays the foundation for the follow-up research of molecular biology and provides a reference for studying the more medicinal value of C. antiquata.

This paper presents HBcompare, a method that classifies protein structures according to ligand binding preference categories by analyzing hydrogen bond topology. HBcompare excludes other characteristics of protein structure so that, in the event of accurate classification, it can implicate the involvement of hydrogen bonds in selective binding. This approach contrasts from methods that represent many aspects of protein structure because holistic representations cannot associate classification with just one characteristic. To our knowledge, HBcompare is the first technique with this capability. On five datasets of proteins that catalyze similar reactions with different preferred ligands, HBcompare correctly categorized proteins with similar ligand binding preferences 89.5% of the time. Using only hydrogen bond topology, classification accuracy with HBcompare surpassed standard structure-based comparison algorithms that use atomic coordinates. As a tool for implicating the role of hydrogen bonds in protein function categories, HBcompare represents a first step towards the automatic explanation of biochemical mechanisms.

Abstract Background Long non-coding RNAs (lncRNAs) perform crucial roles in biological process involving complex mechanisms. However, information regarding their abundance, characteristics and potential functions linked to fish skin color is limited. Herein, Illumina sequencing and bioinformatics were conducted on black, white, and red skin of Koi carp (Cyprinus carpio L.). Results A total of 590,415,050 clean reads, 446,614 putative transcripts, 4252 known and 72,907 novel lncRNAs were simultaneously obtained, including 92 significant differentially expressed lncRNAs and 722 mRNAs. Ccr_lnc5622441 and Ccr_lnc765201 were up-regulated in black and red skin, Ccr_lnc14074601 and Ccr_lnc2382951 were up-regulated in white skin, and premelanosome protein a (Pmela), Pmelb and tyrosinase (Tyr) were up-regulated in black skin. The expression patterns of 18 randomly selected differentially expressed genes were validated using the quantitative real-time PCR method. Moreover, 70 lncRNAs acting on 107 target mRNAs in cis and 79 lncRNAs acting on 41,625 target mRNAs in trans were investigated. The resulting co-expression networks revealed that a single lncRNA can connect with numerous mRNAs, and vice versa. To further reveal their potential functions, Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed, and membrane, pigment cell development, cAMP signaling, melanogenesis and tyrosine metabolism appear to affect skin pigmentation. Additionally, three lncRNAs (Ccr_lnc142711, Ccr_lnc17214525 and Ccr_lnc14830101) and three mRNAs (Asip, Mitf and Tyr) involved in the melanogenesis pathway were investigated in terms of potential functions in embryogenesis and different tissues. Conclusions The findings broaden our understanding of lncRNAs and skin color genetics, and provide new insight into the mechanisms underlying lncRNA-mediated pigmentation and differentiation in Koi carp.

Although genome-wide association studies have identified more than eighty genetic variants associated with non-small cell lung cancer (NSCLC) risk, biological mechanisms of these variants remain largely unknown. By integrating a large-scale genotype data of 15 581 lung adenocarcinoma (AD) cases, 8350 squamous cell carcinoma (SqCC) cases, and 27 355 controls, as well as multiple transcriptome and epigenomic databases, we conducted histology-specific meta-analyses and functional annotations of both reported and novel susceptibility variants. We identified 3064 credible risk variants for NSCLC, which were overrepresented in enhancer-like and promoter-like histone modification peaks as well as DNase I hypersensitive sites. Transcription factor enrichment analysis revealed that USF1 was AD-specific while CREB1 was SqCC-specific. Functional annotation and gene-based analysis implicated 894 target genes, including 274 specifics for AD and 123 for SqCC, which were overrepresented in somatic driver genes (ER = 1.95, P = 0.005). Pathway enrichment analysis and Gene-Set Enrichment Analysis revealed that AD genes were primarily involved in immune-related pathways, while SqCC genes were homologous recombination deficiency related. Our results illustrate the molecular basis of both well-studied and new susceptibility loci of NSCLC, providing not only novel insights into the genetic heterogeneity between AD and SqCC but also a set of plausible gene targets for post-GWAS functional experiments. [ABSTRACT FROM AUTHOR]

Alternanthera philoxeroides is a notorious invasive weed worldwide, but it still lacks a genome information currently. In this study, we collected 4 groups of A. philoxeroides Illumina RNA-seq data (62.5 Gb) and performed a comprehensive de novo assembling. Totally, 421,372 unigenes were obtained with a total length of 230,842,460 bp, with 43,430 (10.31%) unigenes longer than 1000 bp. Then 119,222 (28.3%) unigenes were functional annotated and 235,885 (56.0%) were grouped into reliable lncRNAs reservoir. Besides, 534 tRNA and 234 rRNAs were identified in assembly sequences. Additionally, 131,624 microsatellites were characterized in 106,761 sequences. Then SSR primers were developed for the amplification of 40,752 microsatellites in 36,329 sequences. The miRNAs are key post-transcriptional regulators, about 86 candidate miRNA sequences were detected from A. philoxeroides assembly, and miRNA target genes prediction revealed possible functions of them in growth and development as well as stress responding processes. These results provide a vital basis for sequence-based studies of A. philoxeroides in the future, especially gene function analysis.

Abstract Background With the development of sequencing technology, more and more long non-coding RNAs (lncRNAs) have been identified. Some lncRNAs have been confirmed that they play an important role in the process of development through the dosage compensation effect, epigenetic regulation, cell differentiation regulation and other aspects. However, the majority of the lncRNAs have not been functionally characterized. Explore the function of lncRNAs and the regulatory network has become a hot research topic currently. Methods In the work, a network-based model named BiRWLGO is developed. The ultimate goal is to predict the probable functions for lncRNAs at large scale. The new model starts with building a global network composed of three networks: lncRNA similarity network, lncRNA-protein association network and protein-protein interaction (PPI) network. After that, it utilizes bi-random walk algorithm to explore the similarities between lncRNAs and proteins. Finally, we can annotate an lncRNA with the Gene Ontology (GO) terms according to its neighboring proteins. Results We compare the performance of BiRWLGO with the state-of-the-art models on a manually annotated lncRNA benchmark with known GO terms. The experimental results assert that BiRWLGO outperforms other methods in terms of both maximum F-measure (F max ) and coverage. Conclusions BiRWLGO is a relatively efficient method to predict the functions of lncRNA. When protein interaction data is integrated, the predictive performance of BiRWLGO gains a great improvement.

Abstract Background Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. In the Pfam database, structure description is provided for part or full-length proteins of 7726 families. For the remaining 52% of the families, information on 3-D structure is not yet available. We use the computationally designed sequences that are intermediately related to two protein domain families, which are already known to share the same fold. These strategically designed sequences enable detection of distant relationships and here, we have employed them for the purpose of structure recognition of protein families of yet unknown structure. Results We first measured the success rate of our approach using a dataset of protein families of known fold and achieved a success rate of 88%. Next, for 1392 families of yet unknown structure, we made structural assignments for part/full length of the proteins. Fold association for 423 domains of unknown function (DUFs) are provided as a step towards functional annotation. Conclusion The results indicate that knowledge-based filling of gaps in protein sequence space is a lucrative approach for structure recognition. Such sequences assist in traversal through protein sequence space and effectively function as ‘linkers’, where natural linkers between distant proteins are unavailable. Reviewers This article was reviewed by Oliviero Carugo, Christine Orengo and Srikrishna Subramanian.

Completely sequenced organisms have some uncharacterized proteins that are gene-encoded products. These proteins can be predicted through in-silico approaches and their biological activities are not proved by experimental evidence and known as hypothetical proteins (HPs). These proteins are important due to their excessive involvement in different cellular and signaling pathways. Structural and functional characterization of HPs reveal crucial roles in microorganisms, especially in pathogens related to human diseases. Here, we discussed all possibilities of in-silico analysis tools and other recently reported methods for hypothetical protein characterization and biomedical applications, including drug and vaccine development. Different methodologies, including meta-proteomics have been used to study protein expression by identification of HPs and comparative genomics have also come under observation due to the emergence of evolutionary study among different organisms. Structural characterization of proteins acts as a base for their functional prediction, novel drug target identification for disease treatment, vaccine production and sero-diagnosis. HPs have played major roles in different vital phenomenon for life including host adaptation, wound healing and chemotaxis. In the current era of drug and antibiotic resistance, HPs can be novel targets to treat related diseases. Identification and characterization of most HPs are under observation and will be the most promising genomic and bioinformatics techniques in structure-based drug designing and vaccine production in future.

Heat shock transcription factor (HSF) is ubiquitous in the whole biological world and plays an important role in regulating growth and development and responses to environment stress. In this study, a total of 60 HSF transcription factors in Brassica juncea genome were identified and analyzed. Phylogenetic analysis showed that HSF genes were divided into three groups namely: A, B, and C, of which group A was further divided into nine subgroups (A1–A9). The analysis of gene structure and conserved motifs showed that some homologous genes are highly conserved. There was strong conservative microcollinearity among Brassica rapa, B. juncea, and Brassica oleracea, which provides a basis for studying the replication of gene families. Moreover, the results revealed that the promoter regions of BjuHSF genes were rich in cis-elements related to growth and development, hormone signal, and stress response. The prediction of protein interaction results showed that HSFs could interact with multiple transcription factors and proteins in the genome, while functional annotation revealed that BjuHSF genes were involved in many biological processes. The expression patterns of BjuHSF genes were analyzed by qPCR, and the results showed that these genes were closely linked to stress response, hormones, and development process. These results are a foundation for further analysis of the regulation mechanism of HSF gene family. [ABSTRACT FROM AUTHOR]

The type IV bacterial secretion system (SS) is reported to be one of the most ubiquitous SSs in nature and can induce serious conditions by secreting type IV SS effectors (T4SEs) into the host cells. Recent studies mainly focus on annotating new T4SE from the huge amount of sequencing data, and various computational tools are therefore developed to accelerate T4SE annotation. However, these tools are reported as heavily dependent on the selected methods and their annotation performance need to be further enhanced. Herein, a convolution neural network (CNN) technique was used to annotate T4SEs by integrating multiple protein encoding strategies. First, the annotation accuracies of nine encoding strategies integrated with CNN were assessed and compared with that of the popular T4SE annotation tools based on independent benchmark. Second, false discovery rates of various models were systematically evaluated by (1) scanning the genome of Legionella pneumophila subsp. ATCC 33152 and (2) predicting the real-world non-T4SEs validated using published experiments. Based on the above analyses, the encoding strategies, (a) position-specific scoring matrix (PSSM), (b) protein secondary structure & solvent accessibility (PSSSA) and (c) one-hot encoding scheme (Onehot), were identified as well-performing when integrated with CNN. Finally, a novel strategy that collectively considers the three well-performing models (CNN-PSSM, CNN-PSSSA and CNN-Onehot) was proposed, and a new tool (CNN-T4SE, https://idrblab.org/cnnt4se/) was constructed to facilitate T4SE annotation. All in all, this study conducted a comprehensive analysis on the performance of a collection of encoding strategies when integrated with CNN, which could facilitate the suppression of T4SS in infection and limit the spread of antimicrobial resistance. [ABSTRACT FROM AUTHOR]

Copyright of Bulletin of Botanical Research is the property of Bulletin of Botanical Research Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract Objective Human adenoviruses are small double stranded DNA viruses that provoke vast array of human diseases. Next generation sequencing techniques increase genomic data of HAdV rapidly, which increase their serotypes. The complete genome sequence of human adenovirus shows that it contains large amount of proteins with unknown cellular or biochemical function, known as hypothetical proteins. Hence, it is indispensable to functionally and structurally annotate these proteins to get better understanding of the novel drug targets. The purpose was the characterization of 38 randomly retrieved hypothetical proteins through determination of their physiochemical properties, subcellular localization, function, structure and ligand binding sites using various sequence and structure based bioinformatics tools. Results Function of six hypothetical proteins P03269, P03261, P03263, Q83127, Q1L4D7 and I6LEV1 were predicted confidently and then used further for structure analysis. We found that these proteins may act as DNA terminal protein, DNA polymerase, DNA binding protein, adenovirus E3 region protein CR1 and adenoviral protein L1. Functional and structural annotation leading to detection of binding sites by means of docking analysis can indicate potential target for therapeutics to defeat adenoviral infection.

The in-depth study of viral genomes is of great help in many aspects, especially in the treatment of human diseases caused by viral infections. With the rapid accumulation of viral sequencing data, improved, or alternative gene-finding systems have become necessary to process and mine these data. In this article, we present Vgas, a system combining an ab initio method and a similarity-based method to automatically find viral genes and perform gene function annotation. Vgas was compared with existing programs, such as Prodigal, GeneMarkS, and Glimmer. Through testing 5,705 virus genomes downloaded from RefSeq, Vgas demonstrated its superiority with the highest average precision and recall (both indexes were 1% higher or more than the other programs); particularly for small virus genomes (≤ 10 kb), it showed significantly improved performance (precision was 6% higher, and recall was 2% higher). Moreover, Vgas presents an annotation module to provide functional information for predicted genes based on BLASTp alignment. This characteristic may be specifically useful in some cases. When combining Vgas with GeneMarkS and Prodigal, better prediction results could be obtained than with each of the three individual programs, suggesting that collaborative prediction using several different software programs is an alternative for gene prediction. Vgas is freely available at http://cefg.uestc.cn/vgas/ or http://121.48.162.133/vgas/. We hope that Vgas could be an alternative virus gene finder to annotate new genomes or reannotate existing genome.

[Objective] In order to provide a reference for studying the expression information of genes related to the development of water chestnut conn, the transcript group sequencing of water chestnut conn development was carried out. [Method] by using high-throughput sequencing technique to study the transcriptional sequence of water chestnut conn at different developmental stages. [Result] 223 182 transcripts and 90 542 high quality unigenes were obtained after filtration, De novo assembly and splicing of which the mean size 809 bp and the value of N50 was 1119. The assembly integrity is high. 50 583 unigenes were detected information in seven databases (NR, GO, NT, Plain, KEGG, KOG and Swiss-prol). Analysis of differentially expressed genes revealed that the number of differentially expressed genes was the most active at the beginning of bulbous enlargement. The function of Gene Ontology was enriched, 33 205 genes were annotated, which were divided into 3 groups and 54 subclasses, including molecular function, cell composition and biological process. According to Clusters of Orthologous Groups functional classification, 17 743 genes were distributed in 25 functional regions, in which carbohydrate metabolism played an important role. The results of Kyoto Encyclopedia of Genes and Genomes metabolic pathway annotation showed that 20 667 genes were annotated, and there were 116 metabolic pathways, of which starch-sucrose metabolism played a major role. [Conclusion] The transcriptome database of the bulb of water chestnut 4 Guili 3 ' was established for the first time by high-throughput transcriptome sequen-cing technique. It provides data basis for further study on the function and molecular mechanism of starch biosynthesis related genes in bulb of water chestnut. [ABSTRACT FROM AUTHOR]

The in-depth study of viral genomes is of great help in many aspects, especially in the treatment of human diseases caused by viral infections. With the rapid accumulation of viral sequencing data, improved, or alternative gene-finding systems have become necessary to process and mine these data. In this article, we present Vgas, a system combining an ab initio method and a similarity-based method to automatically find viral genes and perform gene function annotation. Vgas was compared with existing programs, such as Prodigal, GeneMarkS, and Glimmer. Through testing 5,705 virus genomes downloaded from RefSeq, Vgas demonstrated its superiority with the highest average precision and recall (both indexes were 1% higher or more than the other programs); particularly for small virus genomes (≤ 10 kb), it showed significantly improved performance (precision was 6% higher, and recall was 2% higher). Moreover, Vgas presents an annotation module to provide functional information for predicted genes based on BLASTp alignment. This characteristic may be specifically useful in some cases. When combining Vgas with GeneMarkS and Prodigal, better prediction results could be obtained than with each of the three individual programs, suggesting that collaborative prediction using several different software programs is an alternative for gene prediction. Vgas is freely available at http://cefg.uestc.cn/vgas/ or http://121.48.162.133/vgas/. We hope that Vgas could be an alternative virus gene finder to annotate new genomes or reannotate existing genome. [ABSTRACT FROM AUTHOR]

Abstract Amniotic fluid contains large amounts of proteins produced by amnion epithelial cells, fetal tissues, fetal excretions and placental tissues; thus, it is an important potential source of biomarkers for identifying fetal pathologies. In this study, a pooled AF sample from 7 healthy volunteers was used to provide a comprehensive profile of normal human AF proteome using immunoaffinity depletion of 14 high-abundance proteins. Each individual AF sample was used to analyze inter-individual variations with iTRAQ method. As a result, a total of 2881 non-redundant proteins were identified, and 1624 proteins were quantified based on the peak intensity-based semi-quantification (iBAQ) method. Gene Ontology (GO) analysis showed that the AF proteome was enriched in extracellular region and extracellular matrix. Further function annotation showed that the top canonical pathway was axonal guidance signaling. The inter-individual variation analysis of 7 individual AF samples showed that the median inter-individual CV (Coefficient of variation) was 0.22. iBAQ quantification analysis revealed that the inter-individual variations were not correlated with protein abundance. GO analysis indicated that intracellular proteins tended to have higher CVs, and extracellular proteins tended to have lower CVs. These data will contribute to a better understanding of amniotic fluid proteomic analysis and biomarker discovery. Significance Amniotic fluid is an important potential source of biomarkers for identifying fetal pathologies. This study provided a large database for the normal human amniotic fluid proteome and analysis of inter-individual variations in amniotic fluid proteomes, which will offer a baseline reference for further AF proteomic analysis and pregnancy-related disease biomarker discovery. [ABSTRACT FROM AUTHOR]

Copyright of Chinese Journal of Oil Crop Sciences is the property of Oil Crops Research Institute of Chinese Academy of Agricultural Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Objective: High grade astrocytoma (HGA) as an aggressive brain tumor, is always correlated with poor prognosis. In this paper, we aimed to explore the genetic prognostic biomarkers for HGA. Methods: The genome-wide expression profile of 26 brain tumor samples obtained from 26 patients with HGA was downloaded from Gene Expression Omnibus. The risk genes for prognosis of HGA were identified and verified by the data in TCGA database. Protein-protein interaction (PPI) network of risk factor genes was constructed and significant module was screened. Function and pathway annotations were performed for risk genes and drug target genes were further analyzed. Results: A total of 598 genes were identified as significant risk genes for prognosis, such as checkpoint kinase 1, potassium inwardly-rectifying channel, subfamily J, member 6, leukocyte receptor tyrosine kinase and uncharacterized LOC283887. All risk genes for prognosis of HGA were significantly enriched in cell cycle, mitotic as well as mitotic anaphase. While the genes in the network module mainly participated in functions such as cell cycle, mitotic cell cycle and cell cycle process. Moreover, the genes in the network module mainly participated in the pathways such as cell cycle and cell cycle, mitotic. Drug target analysis showed that seven genes were recorded in Drugbank database, and there were as many as 32 drug records of CHEK1. Conclusion: The prognostic effect of CHEK1 was validated based on the expression profile data of 615 low-grade glioma and glioblastoma samples. We proposed CHEK1 as prognostic biomarker for HGA. Our work might provide the candidate target for HGA therapy. [ABSTRACT FROM AUTHOR]

Background: Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. In the Pfam database, structure description is provided for part or full-length proteins of 7726 families. For the remaining 52% of the families, information on 3-D structure is not yet available. We use the computationally designed sequences that are intermediately related to two protein domain families, which are already known to share the same fold. These strategically designed sequences enable detection of distant relationships and here, we have employed them for the purpose of structure recognition of protein families of yet unknown structure. Results: We first measured the success rate of our approach using a dataset of protein families of known fold and achieved a success rate of 88%. Next, for 1392 families of yet unknown structure, we made structural assignments for part/full length of the proteins. Fold association for 423 domains of unknown function (DUFs) are provided as a step towards functional annotation. Conclusion: The results indicate that knowledge-based filling of gaps in protein sequence space is a lucrative approach for structure recognition. Such sequences assist in traversal through protein sequence space and effectively function as ‘ linkers ’ , where natural linkers between distant proteins are unavailable. [ABSTRACT FROM AUTHOR]

Daqu is one of the most important fermentation starters for Baijiu production, and different types of Daqu have been reported. However, the different types of Daqu are poorly understood. In the present study, four types of Daqu were thoroughly characterized based on biochemical composition, volatile compounds and microbial community structure. Significant differences were observed in physicochemical properties in the four types of Daqu analyzed herein (p < 0.05). Moreover, 48 volatile components were detected in samples, thus enabling the identification of 18 discriminant markers of volatile compounds in the four types of Daqu. In addition, differences in the microbial community structure of four types of Daqu were observed, including 46 differential species. Fungi had a great influence on carbon metabolism potential, and peak temperature of Daqu was negatively correlated with carbon metabolism capacity. Conversely, bacteria had a more notable effect on nitrogen metabolism, and peak temperature of four types of Daqu was positively correlated with nitrogen metabolism capacity. Thus, the findings discussed herein shed a light onto the differences of four types of Daqu, thereby contributing to expanding the current knowledge on the traditional industrial fermentation starter for Baijiu production. [Display omitted] • Elucidation of microbial community structure of four Daqu types at species level by third generation sequencing. • Identification of 19 volatile compounds and 46 microbial biomarkers in four Daqu types. • Analysis of the correlation marker volatile compounds, microbial biomarkers and physicochemical properties. • Investigation of potential carbon and nitrogen metabolic pathways in Daqu. [ABSTRACT FROM AUTHOR]