The association between mutations in ubiquitin-specific protease 26 (USP26) and male infertility: a systematic review and meta-analysis.

During recent decades, the association between mutations in ubiquitin-specific protease 26 (USP26) and male infertility remains doubtful. We conducted this meta-analysis to evaluate the association between mutations in USP26 and male infertility according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines. It was registered in the International Prospective Register of Systematic Reviews (PROSPERO; CRD42021225251). PubMed, Web of Science, and Scopus were systematically searched for comparative clinical studies, which were written in English and provided eligible data. Studies were included when they compared USP26 mutations in azoospermic, oligozoospermic, and asthenozoospermic patients with controls with normal sperm parameter values or whose partners had experienced spontaneous pregnancy. Pooled odds ratio (OR) with 95% confidence interval (CI) was calculated with random effect models. Overall, twelve studies with 3927 infertility patients and 4648 healthy controls were included. The association between overall USP26 mutations and infertility was not significant (OR = 1.60, 95% CI: 0.51-5.01). For specific mutations, the pooled ORs were 1.65 (95% CI: 1.02-2.69) for cluster mutation (including 370-371insACA, 494T>C, and 1423C>T), 1.80 (95% CI: 0.35-9.15) for c.576G>A, 1.43 (95% CI: 0.79-2.56) for c.1090C>T, and 3.59 (95% CI: 2.30-5.59) for c.1737G>A. Our results suggest that several mutations (cluster mutation, c.1737G>A) may play roles in male infertility, while others (c.576G>A and c.1090C>T) do not show notable associations with male infertility. More high-quality clinical researches are needed for validation.

Comparative short-term outcomes of robotic-assisted surgery for older patients with non-small cell lung cancer: a propensity matched study.

To investigate comparative short-term outcomes of robotic-assisted surgery (RAS) versus video-assisted thoracoscopic surgery (VATS) for older non-small cell lung cancer (NSCLC) patients. Patients ≥ 65 years old with stage I-III NSCLC operated with RAS or VATS from 2016 to 2018 were consecutively included. Propensity score-matched (PSM) method was implemented to balance inter-group biases. Totally 376 participants (224 with VATS and 152 with RAS) were included. After PSM, a cohort (144 with VATS and 107 with RAS) was generated with balanced baseline characteristics. RAS was significantly superior over VATS in the majority of perioperative outcomes, such as operating time (120.8 vs. 165.1 min), conversion rate (0.0% vs. 19.4%), and length of stay (8.6 vs. 10.8 days). RAS versus VATS was significantly associated with comparable rates of postoperative complications (OR 0.642, 95% CI 0.311-1.327), except the rate of pneumonia (OR 0.161, 95% CI 0.048-0.544). RAS leads to analogous postoperative complications and seemingly accelerates the recovery time of older NSCLC patients compared with VATS.

Synergic Effect between Adsorption and Photocatalysis of Metal-Free g-C3N4 Derived from Different Precursors.

Graphitic carbon nitride (g-C3N4) used in this work was obtained by heating dicyandiamide and melamine, respectively, at different temperatures. The differences of g-C3N4 derived from different precursors in phase composition, functional group, surface morphology, microstructure, surface property, band gap and specific surface area were investigated by X-ray diffraction, Fourier transform infrared spectroscopy, scanning electron microscopy, transmission electron microscopy, X-ray photoelectron spectroscopy, UV-visible diffuse reflection spectroscopy and BET surface area analyzer, respectively. The photocatalytic discoloration of an active cationic dye, Methylene Blue (MB) under visible-light irradiation indicated that g-C3N4 derived from melamine at 500°C (CN-M500) had higher adsorption capacity and better photocatalytic activity than that from dicyandiamide at 500°C (CN-D500), which was attributed to the larger surface area of CN-M500. MB discoloration ratio over CN-M500 was affected by initial MB concentration and photocatalyst dosage. After 120 min reaction time, the blue color of MB solution disappeared completely. Subsequently, based on the measurement of the surface Zeta potentials of CN-M500 at different pHs, an active anionic dye, Methyl Orange (MO) was selected as the contrastive target pollutant with MB to reveal the synergic effect between adsorption and photocatalysis. Finally, the photocatalytic mechanism was discussed.

Effects of gamma-hydroxybutyric acid on spatial learning and memory in adolescent and adult female rats.

gamma-hydroxybutyric acid (GHB) has been reported to disrupt spatial learning and memory in adolescent male rats. The present study was undertaken to determine the effects of GHB on the acquisition of spatial memory in adolescent female rats, and to investigate age specificity of the behavioral impairments. Adolescent female rats were subjected to repeated GHB or saline administrations, and tested in the Morris water maze. Compared to age-matched saline controls, adolescent GHB-treated rats took significantly longer and swam greater distances to find the hidden platform. In the probe trial, GHB-treated adolescent rats spent less time in the target quadrant than saline-treated controls. There was no difference in either the swim speed or in the visual task performance between GHB-treated and saline-treated rats. To test for ontogenic specificity of the behavioral responses, adult female rats were treated with GHB and tested behaviorally in two separate experiments using a 6-day learning protocol (Experiment 1) and a 16-day learning protocol (Experiment 2). In the 6-day spatial learning and memory task, adult saline-treated rats failed to learn the task, and GHB did not alter the latency to find the platform, or performance in the probe trial. In the second behavioral protocol, a modified version of the memory task was used to test adult animals. The number of test days was increased from 6days to 16days. Adult saline-treated females learned the task in the 16-days protocol. But unlike adolescent female rat, GHB in adult rats had minimal effects on reference memory even when they had learned the spatial memory task. Performances in the probe trial by adult GHB-treated rats and saline controls were similar. Together, these data suggest that GHB impairs spatial learning specifically in adolescent female rats.

RINGdb: an integrated database for G protein-coupled receptors and regulators of G protein signaling.

BACKGROUND: Many marketed therapeutic agents have been developed to modulate the function of G protein-coupled receptors (GPCRs). The regulators of G-protein signaling (RGS proteins) are also being examined as potential drug targets. To facilitate clinical and pharmacological research, we have developed a novel integrated biological database called RINGdb to provide comprehensive and organized RGS protein and GPCR information. RESULTS: RINGdb contains information on mutations, tissue distributions, protein-protein interactions, diseases/disorders and other features, which has been automatically collected from the Internet and manually extracted from the literature. In addition, RINGdb offers various user-friendly query functions to answer different questions about RGS proteins and GPCRs such as their possible contribution to disease processes, the putative direct or indirect relationship between RGS proteins and GPCRs. RINGdb also integrates organized database cross-references to allow users direct access to detailed information. The database is now available at http://ringdb.csie.ncu.edu.tw/ringdb/. CONCLUSION: RINGdb is the only integrated database on the Internet to provide comprehensive RGS protein and GPCR information. This knowledge base will be useful for clinical research, drug discovery and GPCR signaling pathway research.

Database to dynamically aid probe design for virus identification.

Viral infection poses a major problem for public health, horticulture, and animal husbandry, possibly causing severe health crises and economic losses. Viral infections can be identified by the specific detection of viral sequences in many ways. The microarray approach not only tolerates sequence variations of newly evolved virus strains, but can also simultaneously diagnose many viral sequences. Many chips have so far been designed for clinical use. Most are designed for special purposes, such as typing enterovirus infection, and compare fewer than 30 different viral sequences. None considers primer design, increasing the likelihood of cross hybridization to similar sequences from other viruses. To prevent this possibility, this work establishes a platform and database that provides users with specific probes of all known viral genome sequences to facilitate the design of diagnostic chips. This work develops a system for designing probes online. A user can select any number of different viruses and set the experimental conditions such as melting temperature and length of probe. The system then returns the optimal sequences from the database. We have also developed a heuristic algorithm to calculate the probe correctness and show the correctness of the algorithm. (The system that supports probe design for identifying viruses has been published on our web page http://bioinfo.csie.ncu.edu.tw/.)

An agent-based system to discover protein-protein interactions, identify protein complexes and proteins with multiple peptide mass fingerprints.

Proteins "work together" by actually binding to form multicomponent complexes that carry out specific functions. Proteomic analyses based on the mass spectrum are now key methods to determine the components in protein complexes. The protein-protein interaction or functional association may be known to exist among the extracted protein spots while analyzing the proteins on the 2D gel. In this study, we develop an agent-based system, namely AgentMultiProtIdent, which integrated two protein identification tools and a variety of databases storing relations among proteins and used to discover protein-protein interactions and protein functional associations, and identify protein complexes and proteins with multiple peptide mass fingerprints as input. The system takes Multiple Peptide Mass Fingerprints (PMFs) as a whole in the protein complex or protein identification. With the relations among proteins, it may greatly improve the accuracy of identification of protein complexes. Also, possible relationship of the multiple peptide mass fingerprints, such as ontology relation, can be discovered by our system, especially in the identification of protein complexes. The agent-based system is now available on the Web at http://dbms104.csie.ncu.edu.tw/ approximately protein/NEW2/.

Detection of discriminative sequence motifs in proteins obtained from prokaryotes grown at various temperatures.

Recent investigations on the stability of proteins have demonstrated various structural factors, but few have considered sequence factors such as protein motifs. These motifs represent highly conserved regions and describe critical regions that may only exist on proteins that remain functional at high temperatures. This investigation presents a method for identifying and comparing corresponding mesophilic and thermophilic sequence motifs between protein families. Discriminative motifs that are conserved only in the mesophilic or thermophilic subfamily are identified. Analysis of the results shows that, although the subfamilies of most protein families share similar motifs, some discriminative motifs are present in particular thermophilic/mesophilic subfamilies. The thermophilic discriminative motifs are conserved only in thermophilic organisms, revealing that physiochemical principles support thermostability.

MultiProtIdent: identifying proteins using database search and protein-protein interactions.

Protein identification is important in proteomics. Proteomic analyses based on mass spectra (MS) constitute innovative ways to identify the components of protein complexes. Instruments can obtain the mass spectrum to an accuracy of 0.01 Da or better, but identification errors are inevitable. This study shows a novel tool, MultiProtIdent, which can identify proteins using additional information about protein-protein interactions and protein functional associations. Both single and multiple Peptide Mass Fingerprints (PMFs) are input to MultiProtIdent, which matches the PMFs to a theoretical peptide mass database. The relationships or interactions among proteins are considered to reduce false positives in PMF matching. Experiments to identify protein complexes reveal that MultiProtIdent is highly promising. The website associated with this study is http://dbms104.csie.ncu.edu.tw/.

Incorporating hidden Markov models for identifying protein kinase-specific phosphorylation sites.

Protein phosphorylation, which is an important mechanism in posttranslational modification, affects essential cellular processes such as metabolism, cell signaling, differentiation, and membrane transportation. Proteins are phosphorylated by a variety of protein kinases. In this investigation, we develop a novel tool to computationally predict catalytic kinase-specific phosphorylation sites. The known phosphorylation sites from public domain data sources are categorized by their annotated protein kinases. Based on the concepts of profile Hidden Markov Models (HMM), computational models are trained from the kinase-specific groups of phosphorylation sites. After evaluating the trained models, we select the model with highest accuracy in each kinase-specific group and provide a Web-based prediction tool for identifying protein phosphorylation sites. The main contribution here is that we have developed a kinase-specific phosphorylation site prediction tool with both high sensitivity and specificity.

[Expression and root exudation of Cry1Ab toxin protein in cry1Ab transgenic rice and its residue in rhizosphere soil].

The expression and root exudation of Cry1Ab toxin protein in cry1Ab transgenic rice (KMD) and its residue in rhizosphere soil were investigated. The results showed that content of Cry1Ab toxin protein in the shoot and root of KMD were 3.23-8.22 and 0.68-0.89 microg/g from early tillering to maturing stage, respectively. The content of the Cry1Ab toxin proteins via root exudation were 1.66-48.02 ng/(individual x d) at that phase. The results also demonstrated that the residue of the Cry1Ab toxin protein in rhizosphere soil was less than detectable level (0.5 ng/g air-dried soil). In addition, insecticidal bioassay indicated that rhizosphere soil and its extraction solution had no significant effect on mortality of first- and third-instar larvae of cotton bollworm (Heliochis armigera). It suggested that the KMD straws returned to the field might have the higher potential environmental risk than the root exudation.

Identifying the combination of genetic factors that determine susceptibility to cervical cancer.

Cervical cancer is common among women all over the world. Although infection with high-risk types of human papillomavirus (HPV) has been identified as the primary cause of cervical cancer, only some of those infected go on to develop cervical cancer. Obviously, the progression from HPV infection to cancer involves other environmental and host factors. Recent population-based twin and family studies have demonstrated the importance of the hereditary component of cervical cancer, associated with genetic susceptibility. Consequently, single-nucleotide polymorphism (SNP) markers and microsatellites should be considered genetic factors for determining what combinations of genetic factors are involved in precancerous changes to cervical cancer. This study employs a Bayesian network and four different decision tree algorithms, and compares the performance of these learning algorithms. The results of this study raise the possibility of investigations that could identify combinations of genetic factors, such as SNPs and microsatellites, that influence the risk associated with common complex multifactorial diseases, such as cervical cancer.

PGTdb: a database providing growth temperatures of prokaryotes.

UNLABELLED: Included in Prokaryotic Growth Temperature database (PGTdb) are a total of 1334 temperature data from 1072 prokaryotic organisms, Bacteria and Archaea: PGTdb integrates microbial growth temperature data from literature survey with their nucleotide/protein sequence and protein structure data from related databases. A direct correlation is observed between the average growth temperature of an organism and the melting temperature of proteins from the organism. Therefore, this database is useful not only for microbiologists to obtain cultivation condition, but also for biochemists and structure biologists to study the correlation between protein sequences/structures and their thermostability. In addition, the taxonomy and ribosomal RNA sequence(s) of an organism are linked through NCBI Taxonomy and the Ribosomal RNA Operon Copy Number Database umdb, respectively. PGTdb is the only integrated database on the Internet to provide the growth temperature data of the prokaryotes and the combined information of their nucleotide/protein sequences, protein structures, taxonomy and phylogeny. AVAILABILITY: http://pgtdb.csie.ncu.edu.tw

A probabilistic method to correlate ion pairs with protein thermostability.

Recent developments in research on the stability of proteins - specifically, comparisons of the ion pairs of homologous structures - show that ion pairs potentially contribute to the thermostability of proteins. This study proposes a probabilistic Bayesian statistical method to efficiently predict the thermostability of proteins based on the properties of ion pairs. The experimental results suggest that the numbers, types and bond lengths of ion pairs can be used to predict with high accuracy (up to 80%) the thermostability of functionally similar proteins. The predictions have high precision (99%), especially for hyperthermophilic proteins. Results for proteins with differing functions also indicate that the number of ion pairs is related to the thermostability of proteins, and that predictions of thermostability can also be made for proteins with different functions.

The repetitive sequence database and mining putative regulatory elements in gene promoter regions.

At least 43% of the human genome is occupied by repetitive elements. Moreover, around 51% of the rice genome is occupied by repetitive elements. The analysis of repetitive elements reveals that repetitive elements in our genome may have been very important in the evolutionary genomics. The first part of this study is to describe a database of repetitive elements - RSDB. The RSDB database contains repetitive elements, which are classified into the following categories: exact, tandem, and similar. The interfaces needed to query and show the results and statistical data, such as the relationship between repetitive elements and genes, cross-references of repetitive elements among different organisms, and so on, are provided. The second part of this study then attempts to mine the putative binding site for information on how combinations of the known regulatory sites and overrepresented repetitive elements in RSDB are distributed in the promoter regions of groups of functionally related genes. The overrepresented repetitive elements appearing in the associations are possible transcription factor binding sites. Our proposed approach is applied to Saccharomyces cerevisiae and the promoter regions of Yeast ORFs. The complete contents of RSDB and partial putative binding sites are available to the public at www.rsdb.csie.ncu.edu.tw. The readers may download partial query results.