Combining gene sequence similarity and textual information for gene function annotation in the literature

Annotation of the functions of genes and proteins is an essential step in genome analysis. Information extraction techniques have been proposed to obtain the function information of genes and proteins in the biomedical literature. However, the performance of most information extraction techniques of function annotation in the biomedical literature is not satisfactory due to the large variability in the expression of concepts in the biomedical literature. This paper proposes a framework to improve the gene function annotation in the literature by considering both the textual information in the literature and the functions of genes with sequences similar to a target gene. The new framework collects multiple types of evidence as: (i) textual information about gene functions by matching keywords of the gene functions; (ii) gene function information from the known functions of genes with sequences similar to a target gene; and (iii) the prior probabilities of gene functions to be associated with an arbitrary gene by mining the known gene functions from curated databases. A supervised learning method is utilized to obtain the weights for combining the three types of evidence to assign appropriate Gene Ontology terms for target genes. Empirical studies on two testbeds demonstrate that the combination of sequence similarity scores, function prior probabilities and textual information improves the accuracy of gene function annotation in the literature. The F-measure scores obtained with the proposed framework are substantially higher than the scores of the solutions in prior research.

ACTN3 R577X genotype and athletic performance in a large cohort of Japanese athletes

Aim: Recent meta-analyses of the literature confirmed the association between the RR+RX genotype of the ACTN3 R577X polymorphism and elite sprint/power athletic status in Europeans but not in Asians and Africans, while the association between the R577X genotype and elite endurance athlete status is less convincing. The aim of the present study was to investigate the association between the ACTN3 R577X genotype and elite athlete status in a large Asian (Japanese) cohort of track and field athletes. Methods: One-thousand fifty-seven Japanese track and field athletes (627 sprint/power athletes and 430 endurance athletes) and 810 Japanese controls were genotyped for the ACTN3 R577X polymorphism (rs1815739) by using the TaqMan® SNP Genotyping Assay. Results: Elite sprint/power athletes had a higher frequency of the RR+RX genotype than the controls (OR: 1.59, 95% CI: 1.16–2.18; P?=?.003). A significant linear correlation was found between the RR?+?RX genotype and athlete status (i.e. regional?P?=?.001 for trend) and long-distance runners (regional: 65%, national: 72%, international: 82%; P?=?.030 for trend). Conclusions: The data obtained for this large Asian (Japanese) cohort of track and field athletes served to confirm the association between the RR?+?RX genotype of the ACTN3 R577X polymorphism and elite sprint/power athlete status and also the association between the ACTN3 RR?+?RX genotype and long-distance running athletic status.     

维生素D受体基因多态性与运动能力研究进展

维生素D受体(VDR)存在于骨、肾、肌肉等组织内,主要作用是介导维生素D发挥生物学作用。众多的研究表明,VDR基因多态性与运动能力相关指标如肌肉力量、身体组成、体脂含量、骨密度、骨容量等紧密相关。对近些年来VDR基因多态性研究的综述,为将来的VDR基因多态性分型研究工作打好基础。     

Gene expression and apoptosis response in hepatocellular carcinoma cells induced by biocompatible polymer/magnetic nanoparticles containing 5-fluorouracil

BackgroundSuper-paramagnetic iron oxide nanoparticles (SPION) contain a chemotherapeutic drug and are regarded as a promising technique for improving targeted delivery into cancer cells.ResultsIn this study, the fabrication of 5-fluorouracil (5-FU) was investigated with loaded Dextran (DEX-SPION) using the co-precipitation technique and conjugated by folate (FA). These nanoparticles (NPs) were employed as carriers and anticancer compounds against liver cancer cells in vitro. Structural, magnetic, morphological characterization, size, and drug loading activities of the obtained FA-DEX-5-FU-SPION NPs were checked using FTIR, VSM, FESEM, TEM, DLS, and zeta potential techniques. The cellular toxicity effect of FA-DEX-5-FU-SPION NPs was evaluated using the MTT test on liver cancer (SNU-423) and healthy cells (LO2). Furthermore, the apoptosis measurement and the expression levels of NF-1, Her-2/neu, c-Raf-1, and Wnt-1 genes were evaluated post-treatment using flow cytometry and RT-PCR, respectively. The obtained NPs were spherical with a suitable dispersity without noticeable aggregation. The size of the NPs, polydispersity, and zeta were 74 ± 13 nm, 0.080 and −45 mV, respectively. The results of the encapsulation efficiency of the nano-compound showed highly colloidal stability and proper drug maintenance. The results indicated that FA-DEX-5-FU-SPION demonstrated a sustained release profile of 5-FU in both phosphate and citrate buffer solutions separately, with higher cytotoxicity against SNU-423 cells than against other cells types. These findings suggest that FA-DEX-SPION NPs exert synergistic effects for targeting intracellular delivery of 5-FU, apoptosis induction, and gene expression stimulation.ConclusionsThe findings proved that FA-DEX-5-FU-SPION presented remarkable antitumor properties; no adverse subsequences were revealed against normal cells.How to cite: Mahdia SA, Kadhimb AA, Albukhaty S, et al. Gene expression and apoptosis response in hepatocellular carcinoma cells induced by biocompatible polymer/magnetic nanoparticles containing 5-fluorouracil. Electron J Biotechnol 2021;52. https://doi.org/10.1016/j.ejbt.2021.04.001     

Application of cDNA array for studying the gene expression profile of mature appressoria of Magnaporthe grisea

Appressorium is an infection structure of the phytopathogenic fungus Magnaporthe grisea. Analysis of gene expression profiles ofappressorium development provides insight into the molecular basis of pathogenicity and control of this fungal plant disease. A cDNA array representing 2927 unique genes based on a large EST （expressed sequence tag） database ofM. grisea strain Y34 was constructed and used to profile the gene expression patterns at mycelium and appressorium maturation stages. Compared with mycelia, 55 up-regulated and 22 down-regulated genes were identified in mature appressoria. Among 77 genes, 16 genes showed no similarity to the genome sequences of M. grisea. A novel homologue of peptidyl-prolyl cis-trans isomerase was found to be expressed at low-level in mature appressoria of M. grisea. The results indicated that the genes such as pyruvate carboxylase, phospholipid metabolism-related protein and glyceraldehyde 3-phosphate dehydrogenase involved in gluconeogenesis, lipid metabolism and glycolysis, showed differential expression in mature appressoria. Furthermore, genes such as PTHll, beta subunit of G protein and SGTI involved in cell signalling, were expressed differentially in mature appressoria. Northern blot analysis was used to confirm the cDNA array results.     

A new mutation （1062 del 16） of iduronate-2-sulfatase gene from a Chinese patient with Hunter syndrome

Objective: To identify the mutations of iduronate-2-sulfatase (IDS) gene, to reveal its mutation features, and to establish a basis for genetic counseling and prenatal gene diagnosis of Hunter syndrome. Methods: Urine glycosaminoglycans (GAGs) assay, PCR and DNA sequencing were performed to detect mutation of IDS gene of the patient and his parents. Results: The result showed that the patient was: DS( ), HS( ), KS(-), CS(-), and that both of his parents were negative. A frame-shift deletion mutation (1062 del 16) was identified in exon 7 of the patient's IDS gene. His parents' genotypes were normal. Conclusion:The patient's mutation was not inherited by his parents but a novel one. The mutation probably altered the primary structure and tertiary structure of IDS enzyme protein remarkably and lowered the activity of IDS enzyme greatly. Therefore it is supposed to be the direct cause of the disorder.     

培养条件对保加利亚乳杆菌蛋白水解体系关键酶基因表达的影响

目的：研究不同培养条件（不同生长阶段、初始pH值、培养温度和氮源）对保加利亚乳杆菌蛋白水解体系关键蛋白酶基因表达的影响。
　　创新点：首次证明在脱脂乳中培养保加利亚乳杆菌可以显著增加蛋白酶体系中关键酶基因表达,而在MRS培养基中,关键酶基因表达则显著下调。
　　方法：应用实时荧光定量聚合酶链反应（qRT-PCR）技术,测定不同生长阶段的3株保加利亚乳杆菌（KLDS 08006、KLDS 08007和KLDS 08012）中7种关键酶基因表达的动态变化规律。
　　结论：研究发现保加利亚乳杆菌的初始 pH值、氮源和培养阶段影响关键酶基因的表达。稳定生长期的7个蛋白酶基因表达比指数生长期的表达平均下降30倍,其中KLDS 08006、KLDS 08007和KLDS 08012菌株的7个蛋白酶基因表达分别下降62.5、15.0和59.0倍。菌株间的7个蛋白酶基因表达显著不同。研究发现含有酪蛋白胨的 MRS 培养基抑制7个蛋白酶基因表达,其中对 PepX基因表达影响最弱,而对OppD基因表达影响最强。     

Analysis of genetic diversity in banana cultivars (Musa cvs.) from the South of Oman using AFLP markers and classification by phylogenetic, hierarchical clustering and principal component analyses

Banana is an important crop grown in Oman and there is a dearth of information on its genetic diversity to assist in crop breeding and improvement programs.This study employed amplified fragment length polymorphism(AFLP) to investigate the genetic variation in local banana cultivars from the southern region of Oman.Using 12 primer combinations,a total of 1094 bands were scored,of which 1012 were polymorphic.Eighty-two unique markers were identified,which revealed the distinct separation of the seven cultiva...     

Association between 11beta-hydroxysteroid dehydrogenase type 1 gene polymorphisms and metabolic syndrome in Bosnian population

Introduction:

The enzyme 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) catalyzes the conversion of the hormonally inactive cortisone to active cortisol, thus facilitating glucocorticoid receptor activation in target tissues. Increased expression of 11β-HSD1 in adipose tissue has been associated with obesity and insulin resistance. In this study, we investigated the association of two 11β-HSD1 gene (HSD11B1) polymorphisms with the metabolic syndrome (MetS) and its characteristics in the Bosnian population.

Materials and methods:

The study included 86 participants: 43 patients diagnosed with MetS and 43 healthy controls. Subjects were genotyped for two HSD11B1 gene polymorphisms: rs846910: G>A and rs45487298: insA, by the high resolution melting curve analysis. Genotype distribution and an influence of genotypes on clinical and biochemical parameters were assessed.

Results:

There was no significant difference in the mutated allele frequencies for the two HSD11B1 gene polymorphisms between MetS patients and controls. In MetS patients, no significant associations between disease-associated traits and rs45487298: insA were found. Regarding rs846910: G>A variant, heterozygous patients (G/A) had significantly lower systolic (P = 0.017) and diastolic blood pressure (P = 0.015), lower HOMA-IR index (P = 0.011) and higher LDL-cholesterol levels (P = 0.049), compared to the wild-type homozygotes. In the control group, rs45487298: insA polymorphism was associated with lower fasting plasma insulin levels (P = 0.041), lower homeostasis model assessment insulin resistance (HOMA-IR) index (P = 0.041) and lower diastolic blood pressure (P = 0.048). Significant differences between rs846910: G>A genotypes in controls were not detected. Haplotype analysis confirmed the association of rs45487298: insA with markers of insulin resistance in the control subjects.

Conclusions:

Our results indicate that a common rs45487298: insA polymorphism in HSD11B1 gene may have a protective effect against insulin resistance.     

从EDN1、NOS2A基因筛选预测HiHiLo训练效果的分子标记

目的:拟从EDN1及NOS2A基因的多态性位点中筛选出与HiHiLo(高住高练低训)训练效果相关的分子标记,为帮助制定个性化的低氧训练方案提供理论参考。方法:采用Association-Study研究方法,测定、分析了72名我国北方地区汉族健康男性青年30天HiHi-Lo训练前后有氧运动能力、心功能变化率与EDN1、NOS2A基因多态性的关联性。HiHiLo训练方案包括每晚10h低氧环境(14.3%～14.8%含氧量)暴露、每周3次30 min75%VO2max强度的低氧运动和日常的体育锻炼。有氧运动能力指标包括递增负荷功率车运动中测定的最大耗氧量、固定负荷血乳酸以及低氧训练中的血氧饱和度,心功能指标包括彩色多普勒测定的安静及三级固定负荷(50 W→100 W→150 W)功率车运动3min后的心脏结构与功能指标。基因多态性选取了EDN1基因外显子SNP/rs5370、rs1800997和3’端rs4714383,NOS2A基因启动子区STR(CCTTT)n和内含子SNP/rs2248814。结果:1)经过30天HiHiLo训练后,EDN1基因SNP/rs1800997的3A/3A基因型人群在安静状态下左心室心肌收缩力提高程度显著优于含4A等位基因的基因型人群,SNP/rs4714383的CC基因型人群运动中左心室泵功能改善程度显著优于含T等位基因的基因型人群;2)NOS2A基因STR(CCTTT)n上2个等位基因n值之和与VO2max提高率显著正相关,SNP/rs2779249的GT基因型人群固定负荷运动中心脏机能节省化水平提高的程度显著大于GG基因型人群。结论:在我国北方汉族男性人群中,EDN1基因SNP/rs1800997、rs4714383和rs2779249的3A/3A、CC和GT基因型携带者HiHiLo训练后心功能提高效果较好;NOS2A基因STR(CCTTT)n基因座上2个等位基因n值均较大的基因型携带者HiHiLo训练后VO2max提高效果较好。