Database construction and comparative genomics analysis of genes involved in nutritional metabolic diseases in fish.

Nutritional metabolic diseases in fish frequently arise in the setting of intensive aquaculture. The etiology and pathogenesis of these conditions involve energy metabolic disorders influenced by both internal genetic factors and external environmental conditions. The exploration of genes associated with nutritional and metabolic disorder has sparked considerable interest within both the aquaculture scientific community and the industry. High-throughput sequencing technology offers researchers extensive genetic information. Effectively mining, analyzing, and securely storing this data is crucial, especially for advancing disease prevention and treatment strategies. Presently, the exploration and application of gene databases concerning nutritional and metabolic disorders in fish are at a nascent stag. Therefore, this study focused on the model organism zebrafish and five primary economic fish species as the subjects of investigation. Using information from KEGG, OMIM, and existing literature, a novel gene database associated with nutritional metabolic diseases in fish was meticulously constructed. This database encompassed 4583 genes for Danio rerio, 6287 for Cyprinus carpio, 3289 for Takifugu rubripes, 3548 for Larimichthys crocea, 3816 for Oreochromis niloticus, and 5708 for Oncorhynchus mykiss. Through a comparative systems biology approach, we discerned a relatively high conservation of genes linked to nutritional metabolic diseases across these fish species, with over 54.9 % of genes being conserved throughout all six species. Additionally, the analysis pinpointed the existence of 13 species-specific genes within the genomes of large yellow croaker, tilapia, and rainbow trout. These genes exhibit the potential to serve as novel candidate targets for addressing nutritional metabolic diseases.

Downregulation of SBF2-AS1 functions as a tumor suppressor in clear cell renal cell carcinoma by inhibiting miR-338-3p-targeted ETS1.

Clear cell renal cell carcinoma (ccRCC) is the most prevalent type of kidney cancer in adults, accompanied by an increasing incidence rate worldwide. We found that SBF2-AS1 was a differentially expressed long-noncoding RNA (lncRNA) in ccRCC through the microarray-based expression analyses. The aim of the present study was to explore the role of SBF2-AS1 in ccRCC development by assessing its effects on cellular processes and further investigate the underlying mechanism. SBF2-AS1 was found to be highly expressed in ccRCC tissues and cells. Ectopic expression and knockdown of SBF2-AS1 and miR-338-3p were performed in ccRCC 768-O cells to explore their effects on cell proliferation, migration, invasion, apoptosis and autophagy by EdU assay, scratch test, Transwell assay, calcein-AM/PI, and GFP-LC3 immunofluorescence assays, respectively. The interactions among SBF2-AS1, miR-338-3p and ETS1 were analyzed using dual-luciferase reporter, RIP and RNA pull-down assays. SBF2-AS1 specifically bound to miR-338-3p and inhibited its expression. Moreover, ETS1 was targeted by miR-338-3p. The knockdown of SBF2-AS1 or ETS1 or overexpression of miR-338-3p resulted in reduced cell proliferation, migration and invasion but elevated cell apoptosis and autophagy. In vivo experiments verified the tumor-suppressive role of silencing SBF2-AS1 in tumor growth of nude mice xenografted with ccRCC cells. Thus, silencing SBF2-AS1 exerted suppressive effects on ccRCC by elevating miR-338-3p and suppressing ETS1.

LncRNA HAND2-AS1 represses cervical cancer progression by interaction with transcription factor E2F4 at the promoter of C16orf74.

Cervical cancer is one of the major malignancies, the pathophysiology and progression of which remain to be scarcely understood. Long non-coding RNAs (lncRNAs) have been previously implicated in the progression of cervical cancer. Here, the purpose of this study was to identify whether lncRNA heart- and neural crest derivative-expressed 2-antisense RNA 1 (HAND2-AS1) affect the development of cervical cancer through regulation of chromosome 16 open reading frame 74 (C16orf74) by mediating a transcription factor E2F4. RT-qPCR was performed to determine the expression of HAND2-AS1 in cervical cancer cells. Then, cervical cancer cells were treated with HAND2-AS1 or si-E2F4 RNA, or C16orf74, after which the proliferation, colony formation, migration and invasion were detected. Moreover, the binding between HAND2-AS1 and E2F4 or between E2F4 and C16orf74 was explored. Finally, the tumorigenesis of cervical cancer cells was measured in nude mice with altered HAND2-AS1/E2F4/C16orf74 expression. HAND2-AS1 exhibited poor expression in cervical cancer, and HAND2-AS1 overexpression suppressed the proliferation, colony formation, migration and invasion of cervical cancer cells. In addition, HAND2-AS1 was found to recruit transcription factor E2F4 to C16orf74 promoter region and down-regulate C16orf74 expression. Lastly, HAND2-AS1/E2F4/C16orf74 modulated the tumorigenesis of cervical cancer in nude mice. In conclusion, this study provided evidence on the inhibitory effect of HAND2-AS1 on the development of cervical cancer through the suppression of C16orf74 expression by recruiting transcription factor E2F4. This study highlights the potential of lncRNA HAND2-AS1 as a target in the treatment of cervical cancer.

Evaluating a framework for tuberculosis screening among healthcare workers in clinical settings, Inner Mongolia, China.

BACKGROUND: Health care workers are at high risk for tuberculosis (TB). China, a high burden TB country, has no policy on medical surveillance for TB among healthcare workers. In this paper, we evaluate whether China's national TB diagnostic guidelines could be used as a framework to screen healthcare workers for pulmonary TB disease in a clinical setting in China. METHODS: Between April-August 2010, healthcare workers from 28 facilities in Inner Mongolia Autonomous Region, China were eligible for TB screening, comprised of symptom check, chest X-ray and tuberculin skin testing. Healthcare workers were categorized as having presumptive, confirmed, or clinically-diagnosed pulmonary TB, using Chinese national guidelines. RESULTS: All healthcare workers (N=4347) were eligible for TB screening, of which 4285 (99%) participated in at least one TB screening test. Of the healthcare workers screened, 2% had cough for ≥ 14 days, 3% had a chest X-ray consistent with TB, and 10% had a tuberculin skin test induration ≥ 20 mm. Of these, 124 healthcare workers were identified with presumptive TB (i.e., cough for ≥ 14 days in the past 4 weeks or x-ray consistent with TB). Twelve healthcare workers met the case definition for clinically-diagnosed pulmonary TB, but none were diagnosed with TB during the study period. CONCLUSION: A substantial proportion of healthcare workers in Inner Mongolia had signs, symptoms, or test results suggestive of TB disease that could have been identified using national TB diagnostic guidelines as a screening framework. However, achieving medical surveillance in China will require a framework that increases the ease, accuracy, and acceptance of TB screening in the medical community. Routine screening with improved diagnostics should be considered to detect tuberculosis disease among healthcare workers and reduce transmission in health care settings in China.

A genome-wide investigation of microsatellite mismatches and the association with body mass among bird species.

Mutation rate is usually found to covary with many life history traits of animals such as body mass, which has been readily explained by the higher number of mutation opportunities per unit time. Although the precise reason for the pattern is not yet clear, to determine the universality of this pattern, we tested whether life history traits impact another form of genetic mutation, the motif mismatches in microsatellites. Employing published genome sequences from 65 avian species, we explored the motif mismatches patterns of microsatellites in birds on a genomic level and assessed the relationship between motif mismatches and body mass in a phylogenetic context. We found that small-bodied species have a higher average mismatches and we suggested that higher heterozygosity in imperfect microsatellites lead to the increase of motif mismatches. Our results obtained from this study imply that a negative body mass trend in mutation rate may be a general pattern of avian molecular evolution.

Identification of 2 Potentially Relevant Gene Mutations Involved in Strabismus Using Whole-Exome Sequencing.

BACKGROUND The etiology of strabismus has a genetic component. Our study aimed to localize the candidate causative gene mutant in a Chinese family with strabismus and to describe its underlying etiology. MATERIAL AND METHODS Genomic DNA was extracted from the affected individual and his parents in a Chinese pedigree with strabismus. The resulting exomes were sequenced by whole-exome sequencing. After variant calling and filtering, the candidate causative gene mutations were selected for the rarity and predicted damaging effect, which complied with the model of recessive disease transmission. RESULTS We examined a Chinese strabismus pedigree with the parents unaffected and 2 offspring affected. Whole-exome sequencing and bioinformatics filtering identified 2 variants including Abelson helper integration site 1 (AHI1) gene and nebulin (NEB) gene. The variant in the AHI1 gene, c.A3257G (p.E1086G), and the altered amino acid had a damaging effect on the encoded protein predicted by Polyphen2. Moreover, this change was located in the conserved SH3 domain of AHI1. Biallelic pathogenic variant in AHI1 gene can cause Joubert syndrome-related disorders with oculomotor apraxia characteristics. Additionally, c.A914G mutation was found in nebulin (NEB) gene. Therefore, we concluded that AHI1 c.3257A>G and NEB c.914 A>G were potential causal variants in this strabismus pedigree. CONCLUSIONS We detected an AHI1 homozygous mutation in the affected individual. Whole-exome sequencing is a powerful way to identify causally relevant genes, improving the understanding of this disorder.

Complex chromosomal rearrangements involving five chromosomes in chronic myelogenous leukemia: A case report.

The typical breakpoint cluster region/Abelson (BCR-ABL) fusion gene, which is located in the Philadelphia chromosome, in association with a complex translocation event is only observed in 2-10% of patients with chronic myelogenous leukemia (CML). CML is diagnosed based on the presence of splenomegaly, increased peripheral white blood cells and the expression of BCR-ABL. The present study reports the case of a patient with CML that possessed complex aberrations involving 5 chromosome translocations, which consisted of t(1;6)(p36.1;q25) and t(9;22;11)(q34;q11.2;q11). After 2 months of follow-up, the patient is in remission following treatment with imatinib (400 mg/day) and hydroxyurea (3,000 mg/day). The hematological parameters of the patient were significantly improved and the white blood cell count returned to normal (from 361.00×109 cells/l to 6.83×109cells/l; normal range, 3.50-9.50×109 cells/l). The results of the ultrasonic examination revealed that the presence of splenomegaly had disappeared, indicating that the treatment strategy was effective. According to the outcome of the treatment, hydroxyurea in combination with imatinib is recommended for use in similar cases of CML.

A fluorescent bisboronic acid compound that selectively labels cells expressing oligosaccharide Lewis X.

Two fluorescent diboronic acid compounds (6a and 6b) with a dipeptide linker were synthesized as potential sensors for cell surface saccharide Lewis X (Le(X)). Compound 6a with a dipeptide (H-Asp-Ala-) as the linker was found to selectively label CHOFUT4 cells, which express Le(x), at micromolar concentrations, while non-Le(x)-expressing control cells were not labeled.

The Prevalence and Incidence of Latent Tuberculosis Infection and Its Associated Factors among Village Doctors in China.

BACKGROUND: China is a high tuberculosis (TB) burden country. More than half of acute TB cases first seek medical care in village doctors' clinics or community health centers. Despite being responsible for patient referral and management, village doctors are not systematically evaluated for TB infection or disease. We assessed prevalence and incidence of latent TB infection (LTBI) among village doctors in China. METHODS AND FINDINGS: A longitudinal study was conducted in Inner Mongolia Autonomous Region. We administered a questionnaire on demographics and risk factors for TB exposure and disease; Tuberculin skin testing (TST) and QuantiFERON-TB Gold in-tube assay (QFT-GIT) was conducted at baseline and repeated 12 months later. We used a logistic regression model to calculate adjusted odds ratios (ORs) for risk factors for TST and QFT-GIT prevalence and incidence. At the time of follow up, 19.5% of the 880 participating village doctors had a positive TST and 46.0% had a positive QFT-GIT result. Factors associated with TST prevalence included having a BCG scar (OR = 1.45, 95%CI 1.03-2.04) and smoking (OR = 1.69, 95%CI 1.17-2.44). Risk factors associated with QFT-GIT prevalence included being male (OR = 2.17, 95%CI 1.63-2.89), below college education (OR=1.42, 95%CI 1.01-1.97), and working for ≥25 years as a village doctor (OR = 1.64, 95%CI 1.12-2.39). The annual incidence of LTBI was 11.4% by TST and 19.1% by QFT-GIT. QFT-GIT conversion was associated with spending 15 minutes or more per patient on average (OR = 2.62, 95%CI 1.39-4.97) and having BCG scar (OR = 0.53, 95%CI 0.28-1.00). CONCLUSIONS: Prevalence and incidence of LTBI among Chinese village doctors is high. TB infection control measures should be strengthened among village doctors and at village healthcare settings.

Histo-blood group gene polymorphisms as potential genetic modifiers of infection and cystic fibrosis lung disease severity.

BACKGROUND: The pulmonary phenotype in cystic fibrosis (CF) is variable; thus, environmental and genetic factors likely contribute to clinical heterogeneity. We hypothesized that genetically determined ABO histo-blood group antigen (ABH) differences in glycosylation may lead to differences in microbial binding by airway mucus, and thus predispose to early lung infection and more severe lung disease in a subset of patients with CF. METHODS AND PRINCIPAL FINDINGS: Clinical information and DNA was collected on >800 patients with the DeltaF508/DeltaF508 genotype. Patients in the most severe and mildest quartiles for lung phenotype were enrolled. Blood samples underwent lymphocyte transformation and DNA extraction using standard methods. PCR and sequencing were performed using standard techniques to identify the 9 SNPs required to determine ABO blood type, and to identify the four SNPs that account for 90-95% of Lewis status in Caucasians. Allele identification of the one nonsynonymous SNP in FUT2 that accounts for >95% of the incidence of nonsecretor phenotype in Caucasians was completed using an ABI Taqman assay. The overall prevalence of ABO types, and of FUT2 (secretor) and FUT 3 (Lewis) alleles was consistent with that found in the Caucasian population. There was no difference in distribution of ABH type in the severe versus mild patients, or the age of onset of Pseudomonas aeruginosa infection in the severe or mild groups. Multivariate analyses of other clinical phenotypes, including gender, asthma, and meconium ileus demonstrated no differences between groups based on ABH type. CONCLUSIONS AND SIGNIFICANCE: Polymorphisms in the genes encoding ABO blood type, secretor or Lewis genotypes were not shown to associate with severity of CF lung disease, or age of onset of P. aeruginosa infection, nor was there any association with other clinical phenotypes in a group of 808 patients homozygous for the DeltaF508 mutation.

The first fluorescent diboronic acid sensor specific for hepatocellular carcinoma cells expressing sialyl Lewis X.

Carbohydrate antigens with subterminal fucosylation have been implicated in the development and progression of several cancers, including hepatocellular carcinoma (HCC). Fluorescent sensors targeting fucosylated carbohydrate antigens could potentially be used for diagnostic and other applications. We have designed and synthesized a series of 26 diboronic acid compounds as potential fluorescent sensors for such carbohydrates. Among these compounds, 7q was able to fluorescently label cells expressing high levels of sLex (HEPG2) within a concentration range of 0.5 to 10 microM. This compound (7q) did not label cells expressing Lewis Y (HEP3B), nor cells without fucosylated antigens (COS7). This represents the first example of a fluorescent compound labeling cells based on cell surface carbohydrate structures.

Oxygen radicals trigger activation of NF-kappaB and AP-1 and upregulation of ICAM-1 in reperfused canine heart.

We investigated whether oxygen radicals generated during ischemia-reperfusion trigger postischemic inflammation in the heart. Closed-chest dogs underwent 90-min coronary artery occlusion, followed by 1- or 3-h reperfusion: 10 dogs received the cell-permeant oxygen radical scavenger N-(2-mercaptopropionyl)-glycine (MPG; 8 mg x kg(-1) x h(-1) intracoronary) beginning 5 min before reperfusion, and 9 dogs received vehicle. Blood flow (microspheres), intercellular adhesion molecule (ICAM)-1 protein expression (immunohistochemistry), ICAM-1 gene activation (Northern blotting), nuclear DNA binding activity of nuclear factor (NF)-kappaB and AP-1 (electrophoretic mobility shift assays), and neutrophil (PMN) accumulation (myeloperoxidase activity) were assessed in myocardial tissue samples. ICAM-1 protein expression was high in vascular endothelium after ischemia-reperfusion but was markedly reduced by MPG. MPG treatment also markedly decreased expression of ICAM-1 mRNA and tissue PMN accumulation. Nuclear DNA binding activities of NF-kappaB and AP-1, increased by ischemia-reperfusion, were both markedly decreased by MPG at 1 h of reperfusion. However, by 3 h, AP-1 activity was only modestly reduced by MPG and NF-kappaB activity was not significantly different from ischemic-reperfused controls. These results suggest that oxygen radicals generated in vivo during reperfusion trigger early activation of NF-kappaB and AP-1, resulting in upregulation of the ICAM-1 gene in vascular endothelium and subsequent tissue accumulation of activated PMNs.