Association analysis of the sorting nexin 29 (SNX29) gene copy number variations with growth traits in Diannan small-ear (DSE) pigs

SNX29 is a potential functional gene associated with meat production traits. Previous studies have shown that SNX29 copy number variation (CNV) could be implicated with phenotype in goats. However, in Diannan small-ear (DSE) pigs, the genetic impact of SNX29 CNV on growth traits remains unclear. Therefore, this study investigated the associations between SNX29 CNVs (CNV10810 and CNV10811) and growth traits in 415 DSE pigs. The results revealed that the CNV10810 mutation was significantly associated with backfat thickness in DSE pigs at 12 and 15 months old (P < 0.05), while the CNV10811 mutation had significant effects on various growth traits at 6 and 12 months old, particularly for body weight, body height, back height and backfat thickness (P < 0.05 or P < 0.001). In conclusion, our results confirm that SNX29 CNV plays a role in regulating growth and development in pigs, thus suggesting its potential application for pig breeding programmes.

[Association of waist-to-height ratio with sarcopenic obesity in hemodialysis patients with normal body mass index]

Objective: To explore the association between waist-to-height ratio (WHtR) and sarcopenic obesity (SO) in maintenance hemodialysis (MHD) patients with normal body mass index (BMI). Methods: A multicenter and cross-sectional study that included adult patients undergoing MHD was conducted in 20 hemodialysis centers from June 1st to August 30th, 2021. Body composition was evaluated by body composition monitor based on bioimpedance spectroscopy. According to the quartiles of WHtR, patients were divided into four groups: Q1, Q2, Q3 and Q4 group. The association of WHtR with SO was determined by multiple logistic regression models, stratified analyses, interactive analyses, and receiver operating characteristic (ROC) analyses, respectively. Results: A total of 2 207 MHD patients (1 341 males and 866 females) were included, and aged [M (Q1, Q3)] 57 (44, 68) years. The prevalence of SO was increased with increasing quartiles of WHtR [8.6% (46/533), 22.5% (141/628), 35.4% (215/608), and 44.3% (194/438) for Q1, Q2, Q3, and Q4 group, respectively]. Multivariate logistic regression analysis showed that WHtR was associated with SO. The association remained statistically significant even after adjusting for age, gender, dialysis vintage, BMI, biochemical indicators, and various medical histories. Compared with Q1 group, the odds ratios (OR) were 2.54 (95%CI: 1.69-3.83), 4.30 (95%CI: 2.88-6.42) and 5.18 (95%CI: 3.37-7.96) for Q2, Q3 and Q4 group, respectively. The interaction analysis showed that age, sex and history of diabetes had interactive roles in the association between WHtR and SO (all P<0.05). The association stably existed across subgroups, and it was more obvious in male patients, those with older age and without a history of diabetes（all P<0.05）. Furthermore, the cut-off value of WHtR identifying SO in male patients was 0.49, and the corresponding area under the curve (AUC) was 0.73 (95%CI: 0.70-0.75), with the sensitivity of 72.7% and specificity of 60.3%. In female patients, the cut-off value was 0.51, and the AUC was 0.68 (95%CI: 0.65-0.71), with the sensitivity of 70.1% and specificity of 57.8%. Conclusion: WHtR could be used as a simple index to evaluate the risk of SO in MHD patients with normal BMI.

Comprehensive analysis of transcriptomic and metabolomic profiles uncovered the age-induced dynamic development pattern of subcutaneous fat in Ningxiang pig

Enhancing meat production and quality is the eternal theme for pig breeding industries. Fat deposition has always been the focus of research in practical production because it is closely linked to pig production efficiency and pork quality. In the current study, multi-omics techniques were performed to explore the modulatory mechanisms of backfat (BF) accumulation at three core developmental stages for Ningxiang pigs. Our results identified that 15 differentially expressed genes (DEGs) and 9 significantly changed metabolites (SCMs) contributed to the BF development via the cAMP signaling pathway, regulation of lipolysis in adipocytes, and biosynthesis of unsaturated fatty acids. Herein, we found a series of candidate genes such as adrenoceptor beta 1 (ADRB1), adenylate cyclase 5 (ADCY5), ATPase Na+/K+ transporting subunit beta 1 (ATP1B1), ATPase plasma membrane Ca2+ transporting 3 (ATP2B3), ATPase Na+/K+ transporting subunit alpha 2 (ATP1A2), perilipin 1 (PLIN1), patatin like phospholipase domain containing 3 (PNPLA3), ELOVL fatty acid elongase 5 (ELOVL5) and metabolites like epinephrine, cAMP, arachidonic acid, oleic acid, linoleic acid, and docosahexaenoic acid existed age-specificeffects and played important roles in lipolysis, fat accumulation, and fatty acid composition. Our findings provide a reference for molecular mechanisms in BF tissue development and the optimization of carcass quality.

Transcriptome Analysis Reveals the Age-Related Developmental Dynamics Pattern of the Longissimus Dorsi Muscle in Ningxiang Pigs

The growth and development of the Longissimus Dorsi muscle are complex, playing an important role in the determination of pork quality. The study of the Longissimus Dorsi muscle at the mRNA level is particularly crucial for finding molecular approaches to improving meat quality in pig breeding. The current study utilized transcriptome technology to explore the regulatory mechanisms of muscle growth and intramuscular fat (IMF) deposition in the Longissimus Dorsi muscle at three core developmental stages (natal stage on day 1, growing stage on day 60, and finishing stage on day 210) in Ningxiang pigs. Our results revealed 441 differentially expressed genes (DEGs) in common for day 1 vs. day 60 and day 60 vs. day 210, and GO (Gene Ontology) analysis showed that candidate genes RIPOR2, MEGF10, KLHL40, PLEC, TBX3, FBP2, and HOMER1 may be closely related to muscle growth and development, while KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis showed that DEGs (UBC, SLC27A5, RXRG, PRKCQ, PRKAG2, PPARGC1A, PLIN5, PLIN4, IRS2, and CPT1B) involved the PPAR (Peroxisome Proliferator-Activated Receptor) signaling pathway and adipocytokine signaling pathway, which might play a pivotal role in the regulation of IMF deposition. PPI (Protein-Protein Interaction Networks) analysis found that the STAT1 gene was the top hub gene. Taken together, our results provide evidence for the molecular mechanisms of growth and development and IMF deposition in Longissimus Dorsi muscle to optimize carcass mass.

Genome-Wide Association Analysis Identifies Genomic Regions and Candidate Genes for Growth and Fatness Traits in Diannan Small-Ear (DSE) Pigs

In the livestock industry, the growth and fatness traits are directly related to production efficiency and economic profits. As for Diannan small-ear (DSE) pigs, a unique indigenous breed, the genetic architecture of growth and fatness traits is still elusive. The aim of this study was to search the genetic loci and candidate genes associated with phenotypic traits in DSE pigs using GWAS based on the Geneseek Porcine 50K SNP Chip data. A total of 22,146 single nucleotide polymorphisms (SNPs) were detected in 265 DSE pigs and used for Genome-wide association studies (GWAS) analysis. Seven SNPs were found to be associated with back height, chest circumference, cannon bone circumference, and backfat thickness at the suggestive significance level. Based on gene annotation results, these seven SNPs were, respectively, mapped to the following candidate genes, VIPR2, SLC10A2, NUCKS1, MCT1, CHCHD3, SMOX, and GPR1, which are mainly involved with adipocyte differentiation, lipid metabolism, skeletal muscle development, and average daily weight gain. Our work offers novel insights into the genetic architecture of economically important traits in swine and may play an important role in breeding using molecular markers in the DSE breed.

Neurological complications of COVID-19

Corona Virus Disease 2019 (COVID-19) has caused several pandemic peaks worldwide due to its high variability and infectiousness, and COVID-19 has become a long-standing global public health problem. There is growing evidence that severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) frequently causes multi-organ injuries and more severe neurological manifestations. Therefore, increased awareness of possible neurological complications is beneficial in preventing and mitigating the impact of long-term sequelae and improving the prognostic outcome of critically ill patients with COVID-19. Here, we review the main pathways of SARS-CoV-2 neuroinvasion and the potential mechanisms causing neurological damage. We also discuss in detail neurological complications, aiming to provide cutting-edge basis for subsequent related basic research and clinical studies of diagnosis and treatment.

Genome-Wide Association Analysis Identified Variants Associated with Body Measurement and Reproduction Traits in Shaziling Pigs

With the increasing popularity of genomic sequencing, breeders pay more attention to identifying the crucial molecular markers and quantitative trait loci for improving the body size and reproduction traits that could affect the production efficiency of pig-breeding enterprises. Nevertheless, for the Shaziling pig, a well-known indigenous breed in China, the relationship between phenotypes and their corresponding genetic architecture remains largely unknown. Herein, in the Shaziling population, a total of 190 samples were genotyped using the Geneseek Porcine 50K SNP Chip, obtaining 41857 SNPs for further analysis. For phenotypes, two body measurement traits and four reproduction traits in the first parity from the 190 Shaziling sows were measured and recorded, respectively. Subsequently, a genome-wide association study (GWAS) between the SNPs and the six phenotypes was performed. The correlation between body size and reproduction phenotypes was not statistically significant. A total of 31 SNPs were found to be associated with body length (BL), chest circumference (CC), number of healthy births (NHB), and number of stillborns (NSB). Gene annotation for those candidate SNPs identified 18 functional genes, such as GLP1R, NFYA, NANOG, COX7A2, BMPR1B, FOXP1, SLC29A1, CNTNAP4, and KIT, which exert important roles in skeletal morphogenesis, chondrogenesis, obesity, and embryonic and fetal development. These findings are helpful to better understand the genetic mechanism for body size and reproduction phenotypes, while the phenotype-associated SNPs could be used as the molecular markers for the pig breeding programs.

Association of gut microbiota and SCFAs with finishing weight of Diannan small ear pigs

Finishing weight is a key economic trait in the domestic pig industry. Evidence has linked the gut microbiota and SCFAs to health and production performance in pigs. Nevertheless, for Diannan small ear (DSE) pigs, a specific pig breed in China, the potential effect of gut microbiota and SCFAs on their finishing weight remains unclear. Herein, based on the data of the 16S ribosomal RNA gene and metagenomic sequencing analysis, we found that 13 OTUs could be potential biomarkers and 19 microbial species were associated with finishing weight. Among these, carbohydrate-decomposing bacteria of the families Streptococcaceae, Lactobacillaceae, and Prevotellaceae were positively related to finishing weight, whereas the microbial taxa associated with intestinal inflammation and damage exhibited opposite effects. In addition, interactions of these microbial species were found to be linked with finishing weight for the first time. Gut microbial functional annotation analysis indicated that CAZymes, such as glucosidase and glucanase could significantly affect finishing weight, given their roles in increasing nutrient absorption efficiency. Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthologies (KOs) and KEGG pathways analysis indicated that glycolysis/gluconeogenesis, phosphotransferase system (PTS), secondary bile acid biosynthesis, ABC transporters, sulfur metabolism, and one carbon pool by folate could act as key factors in regulating finishing weight. Additionally, SCFA levels, especially acetate and butyrate, had pivotal impacts on finishing weight. Finishing weight-associated species Prevotella sp. RS2, Ruminococcus sp. AF31-14BH and Lactobacillus pontis showed positive associations with butyrate concentration, and Paraprevotella xylaniphila and Bacteroides sp. OF04-15BH were positively related to acetate level. Taken together, our study provides essential knowledge for manipulating gut microbiomes to improve finishing weight. The underlying mechanisms of how gut microbiome and SCFAs modulate pigs' finishing weight required further elucidation.

Caffeic Acid Phenethyl Ester (CAPE) Improves Boar Sperm Quality and Antioxidant Capacity in Liquid Preservation (17°C) Linked to AMPK Activity Maintenance

Liquid preservation of boar sperm is crucial for artificial insemination application in pig production. However, time-dependent oxidative damage to sperm is one of the major challenges during the liquid preservation period. Caffeic acid phenethyl ester (CAPE) possesses excellent antioxidant properties and has potential therapeutic use in reproductive organ injury linked to oxidative stress. Adenosine monophosphate (AMP)-activated protein kinase (AMPK) involves in modulating the cellular redox state and exerts a beneficial effect on sperm preservation. In the present study, we firstly assessed different concentrations of CAPE that affect sperm quality during liquid storage to determine the appropriate addition. To further investigate whether CAPE exerts protective effects on boar sperm through modulation of AMPK activity, sperm quality parameters, antioxidant capacity, and marker protein expressions were evaluated under co-incubation with H₂O₂. The results showed that sperm treated with 210 μmol/L CAPE exhibited the highest motion parameters (total motility and progressive motility) and best functional integrity (mitochondrial activity, plasma membrane integrity, and acrosomal integrity). Even in the presence of H₂O₂, the addition of 210 μmol/L CAPE not only significantly improved sperm quality parameters, but also elevated CAT, SOD, and GSH-Px activities to enhance sperm antioxidant capacity. In addition, we found that CAPE could affect the protein activities of AMPK, phospho-AMPK α (p-AMPK), SOD, and Caspase-3 regardless of whether H₂O₂ is present or not. Our findings suggested that CAPE has potential application in liquid preservation of boar sperm and preliminary indicated that CAPE-induced improvement of sperm quality and antioxidant capacity should be mediated through conservation of AMPK activity. Further studies are required to illustrate the specific mechanism by which CAPE attenuates oxidative stress-mediated damages dependent on AMPK activity.

[Application of clip remodeling technique in microsurgical treatment of intracranial aneurysms via keyhole approaches]

Objective: To discuss the value and technique of clip remodeling in microsurgical treatment of intracranial aneurysms via keyhole approaches. Methods: The clinical data of patients with intracranial aneurysms, who were treated by microsurgical clipping via keyhole approaches from January 2017 to December 2019, were retrospectively analyzed. The clips were remodeled based on the aneurysmal characteristics during the procedure in 27 cases. Angiography was obtained within one week after surgery in order to evaluate the position of clips and the security of lesions. All patients were followed up at the outpatient clinic to assess the clinical outcomes. Results: A total of 27 patients harbored 30 intracranial aneurysms, including 23 ruptured lesions and 7 unruptured ones. There were 9 middle cerebral artery aneurysms, 11 anterior communicating artery aneurysms, 9 posterior communicating artery aneurysms and 1 anterior cerebral artery aneurysm, respectively. Nine patients were operated via supraorbital keyhole approach, as well as 17 via pterional keyhole approach and one via hemispheric keyhole approach. Postoperative angiography revealed complete obliteration of lesions without residual filling in all cases. Twenty-five patients recovered well at discharge and two presented with mild disability. After 3-36 months of follow-up, no rebleeding and new-onset neurological deficits were noted. Conclusion: Clip remodeling technique is a simple and effective option, which can alleviate the limitation of manipulative freedom under keyhole approaches and improve the microsurgical effect of intracranial aneurysms.

New Opportunities and Challenges for Forensic Medicine in the Era of Artificial Intelligence Technology

Abstract

Traditional forensic identification relies on forensic experts to manually extract information and provide identification opinions based on medicine, biology and other fields of knowledge combined with personal work experience, which is not only time-consuming and require great effort, but also affected by subjective factors that are difficult to overcome. In the era of big data, the booming development of artificial intelligence brings new ideas to forensic medicine. In recent years, forensic researchers at home and abroad have conducted many studies based on artificial intelligence technology, such as face recognition, age and gender identification, DNA analysis, postmortem interval estimation, injury and cause of death identification, showing the feasibility and advantages of using artificial intelligence technology to solve forensic identification problems. As a new means of technology that has adapted to the development of the times, artificial intelligence has brought new vitality to forensic medicine, but at the same time also some new challenges. How to deal with these challenges scientifically and form a new mode of 'artificial intelligence plus forensic medicine' with artificial intelligence and forensic medicine developing collaboratively is a new direction for the development of forensic medicine in the era of big data.

Transcriptomic changes in the nasal epithelium associated with diesel engine exhaust exposure

BACKGROUND

Diesel engine exhaust (DEE) exposure causes lung cancer, but the molecular mechanisms by which this occurs are not well understood.

OBJECTIVES

To assess transcriptomic alterations in nasal epithelium of DEE-exposed factory workers to better understand the cellular and molecular effects of DEE.

METHODS

Nasal epithelial brushings were obtained from 41 diesel engine factory workers exposed to relatively high levels of DEE (17.2-105.4 μg/m3), and 38 unexposed workers from factories without DEE exposure. mRNA was profiled for gene expression using Affymetrix microarrays. Linear modeling was used to identify differentially expressed genes associated with DEE exposure and interaction effects with current smoking status. Pathway enrichment among differentially expressed genes was assessed using EnrichR. Gene Set Enrichment Analysis (GSEA) was used to compare gene expression patterns between datasets.

RESULTS

225 genes had expression associated with DEE exposure after adjusting for smoking status (FDR q < 0.25) and were enriched for genes in pathways related to oxidative stress response, cell cycle pathways such as MAPK/ERK, protein modification, and transmembrane transport. Genes up-regulated in DEE-exposed individuals were enriched among the genes most up-regulated by cigarette smoking in a previously reported bronchial airway smoking dataset. We also found that the DEE signature was enriched among the genes most altered in two previous studies of the effects of acute DEE on PBMC gene expression. An exposure-response relationship was demonstrated between air levels of elemental carbon and the first principal component of the DEE signature.

CONCLUSIONS

A gene expression signature was identified for workers occupationally exposed to DEE that was altered in an exposure-dependent manner and had some overlap with the effects of smoking and the effects of acute DEE exposure. This is the first study of gene expression in nasal epithelial cells of workers heavily exposed to DEE and provides new insights into the molecular alterations that occur with DEE exposure.

Detection of Ancestry Information of Urumqi Mongolians Based on the AIM-InDels Loci Multiplex System

Abstract

Objective To explore the genetic background and structure of Urumqi Mongolians, the previously developed 39-AIM-InDels panel for ancestry inference was utilized in the present study. Methods The blood samples of 145 unrelated healthy Urumqi Mongolian individuals were collected and genotyped. The compositions of ancestry information of Urumqi Mongolians were studied with 17 different populations from three continents （East Asia, Europe and Africa） as reference populations. Then, multiple population genetics and bioinformatics analysis methods were applied, the Fst and DA values between matched populations were compared and analyzed, PCA analysis was performed and a phylogenetic tree was constructed. The proportions of ancestry information components of Urumqi Mongolians were analyzed with Structure software, etc. Results The ancestry information components of Urumqi Mongolian group in different intercontinental populations accounted for 89%, 7%, and 3% of East Asian, European, and African populations, respectively. Compared with other intercontinental populations, Urumqi Mongolian group and East Asian populations have lower Fst and DA values, and they were in the same cluster in PCA analysis as well. In a phylogenetic tree, the Urumqi Mongolian group was in the same branch as East Asian populations. Conclusion Urumqi Mongolian group had relatively close genetic relationships with East Asian populations, and the proportion of its East Asian ancestry was about 89%.

DNA Molecular Identification of Human Phenotypic Characteristics--New Progress Over the Past Five Years

Abstract

Molecular identification of human externally visible characteristic （EVC）, which is also called forensic DNA phenotyping （FDP）, can serve as a "molecular witness" when the routine investigations can not determine the identity of a criminal and the DNA database find no match after comparison. FDP could assist in investigation of cases by inferring the externally visible phenotypic characteristics from DNA obtained from the biological materials left at crime scenes, or unknown corpses. In the last few years, studies on the selection of EVC related molecular markers have been reported frequently and some of the EVCs could already be inferred with a certain accuracy, such as hair color and iris color. Further fundamental research on molecular genetics of human external phenotypic characteristics, as well as the continuous innovation on molecular biological technology would promote the rapid development of DNA molecular identification of human phenotypic characteristics.

Long non-coding RNA AFAP1-AS1 accelerates invasion and predicts poor prognosis of glioma

OBJECTIVE

The role of AFAP1-AS1 in glioma is not fully known. This study aims at investigating the expression of AFAP1-AS1 in glioma and its underlying mechanism.

PATIENTS AND METHODS

AFAP1-AS1 expressions in brain tissues from 52 cases of glioma and 5 cases of traumatic brain injury were assessed using quantitative fluorescence polymerase chain reaction (PCR). The clinicopathological features of glioma were first recorded. The correlation between AFAP1-AS1 expression and prognosis of glioma was discussed. AFAP1-AS1 expressions in the glioma cell lines were further detected. After knockdown of AFAP1-AS1 in U87MG and U251 glioma cells, cell invasion was assessed by transwell assay. MMP2 and MMP9 expressions in glioma cells, which were important indicators of cell invasive-ness, were determined by Western blot.

RESULTS

AFAP1-AS1 was upregulated in the glioma tissues compared with that in the control tissues, and the expression level was correlated with glioma grading and KPS scores. After knockdown of AFAP1-AS1, the invasion capacities of the glioma cells declined significantly, and the expressions of invasion-related proteins MMP2 and MMP9 also decreased significantly.

CONCLUSIONS

lncRNA AFAP1-AS1 can considerably facilitate the invasion of glioma cells and acts as an independent predictor of malignancy and prognosis, which may also serve as a potential therapeutic target.

[Establishment of rat model of cardiorenal syndrome by transabdominal subtotal nephrectomy]

Objective: To evaluate the changes of rat renal function and cardiac function after transabdominal subtotal nephrectomy (STNx) and provide an ideal animal model for the study of chronic kidney disease (CKD) and cardiorenal syndrome (CRS). Methods: The SD rats (male, 5-6 weeks) were randomly divided into Sham group (n=10) and STNx group (n=10). The rats from Sham group underwent sham surgery, and the right nephrectomy plus the 2/3 left kidney artery ligation through abdominal incision were performed in the rats from STNx group. Twelve weeks after operation, the rat serum creatinine and renal pathology were examined, the size and fibrosis of cardiac cells were also observed, after the changes of cardiac function being detected by echocardiography. Results: Twelve weeks after the operation, STNx group rats were generally in poor condition, with a emaciated body, absorption of the renal infarct tissue, uneven surface, and residual renal tissue compensatory hypertrophy. The serum creatinine in Sham group and STNx group was (22.10±1.64) μmol/L and (52.80±3.34) μmol/L, respectively, and there was a statistically significant difference between the two groups (P<0.001). Compared with Sham group, the echocardiography results demonstrated that the thickness of left ventricular wall of rats from STNx group increased, the left ventricular volume decreased, and the diastolic and systolic function of left ventricular descended. The HE staining showed that the glomerulus, tubules and interstitial renal morphology were normal in Sham group, and glomerular sclerosis was observed in STNx group. And the Masson staining declared that the renal fibrous tissue distribution was normal in Sham group, and severe renal interstitial fibrosis was observed in STNx group. The wheat germ agglutinin (WGA) staining of myocardial tissue showed that myocardial cells in STNx group were larger than those in Sham group (1.293±0.060 vs 1.000±0.059, P<0.001). Moreover, the HE staining showed that there was partial myocardial tissue necrosis and fibrosis in STNx group, and severe myocardial fibrosis was observed in STNx group by Masson staining. Conclusion: Similar pathophysiological changes in human CKD were observed in the rats CKD model by transabdominal STNx, and the cardiac effects of this model make it an ideal choice to study CRS.

The impact of ambient air pollution on the human blood metabolome

BACKGROUND

Biological perturbations caused by air pollution might be reflected in the compounds present in blood originating from air pollutants and endogenous metabolites influenced by air pollution (defined here as part of the blood metabolome). We aimed to assess the perturbation of the blood metabolome in response to short term exposure to air pollution.

METHODS

We exposed 31 healthy volunteers to ambient air pollution for 5h. We measured exposure to particulate matter, particle number concentrations, absorbance, elemental/organic carbon, trace metals, secondary inorganic components, endotoxin content, gaseous pollutants, and particulate matter oxidative potential. We collected blood from the participants 2h before and 2 and 18h after exposure. We employed untargeted metabolite profiling to monitor 3873 metabolic features in 493 blood samples from these volunteers. We assessed lung function using spirometry and six acute phase proteins in peripheral blood. We assessed the association of the metabolic features with the measured air pollutants and with health markers that we previously observed to be associated with air pollution in this study.

RESULTS

We observed 89 robust associations between air pollutants and metabolic features two hours after exposure and 118 robust associations 18h after exposure. Some of the metabolic features that were associated with air pollutants were also associated with acute health effects, especially changes in forced expiratory volume in 1s. We successfully identified tyrosine, guanosine, and hypoxanthine among the associated features. Bioinformatics approach Mummichog predicted enriched pathway activity in eight pathways, among which tyrosine metabolism.

CONCLUSIONS

This study demonstrates for the first time the application of untargeted metabolite profiling to assess the impact of air pollution on the blood metabolome.

Indoor concentrations of nitrogen dioxide and sulfur dioxide from burning solid fuels for cooking and heating in Yunnan Province, China

The Chinese national pollution census has indicated that the domestic burning of solid fuels is an important contributor to nitrogen dioxide (NO2 ) and sulfur dioxide (SO2 ) emissions in China. To characterize indoor NO2 and SO2 air concentrations in relation to solid fuel use and stove ventilation in the rural counties of Xuanwei and Fuyuan, in Yunnan Province, China, which have among the highest lung cancer rates in the nation, a total of 163 participants in 30 selected villages were enrolled. Indoor 24-h NO2 and SO2 samples were collected in each household over two consecutive days. Compared to smoky coal, smokeless coal use was associated with higher NO2 concentrations [geometric mean (GM) = 132 μg/m(3) for smokeless coal and 111 μg/m(3) for smoky coal, P = 0.065] and SO2 [limit of detection = 24 μg/m(3) ; percentage detected (%Detect) = 86% for smokeless coal and 40% for smoky coal, P < 0.001]. Among smoky coal users, significant variation of NO2 and SO2 air concentrations was observed across different stove designs and smoky coal sources in both counties. Model construction indicated that the measurements of both pollutants were influenced by stove design. This exposure assessment study has identified high levels of NO2 and SO2 as a result of burning solid fuels for cooking and heating.

Cardiac damage and dysfunction in diabetic cardiomyopathy are ameliorated by Grx1

Glutaredoxin 1 (Grx1) has been found to be an important endogenous antioxidant enzyme closely related to the pathogenesis of diabetes and cardiovascular diseases caused by oxidative stress. In this study, the functional changes of the Grx1 redox system in blood of hyperglycemic patients were examined. Furthermore, using a rat model of streptozotocin (STZ)- and high-fat-diet-induced type 2 diabetes, we explored the correlation between functional changes of the Grx1 redox system in the left ventricular tissue and blood of the diabetic rats. Moreover, we studied the protective effect of Grx1 against cardiac toxicity caused by the high-glucose-induced expression of cardiac matrix metalloproteinases (MMPs) in primary cultured cardiac fibroblasts. Finally, we investigated the protective effects and signaling regulatory mechanism of Grx1 against diabetic cardiomyopathy (DCM) in terms of oxidative stress and NF-kB-mediated fibrosis-associated signaling pathways. In the serum of hyperglycemic patients, Grx1 levels were elevated, total/protein thiol or sulfhydryl (Total-SH/P-SH) levels were decreased, glutathione was downregulated, and oxidized glutathione was upregulated. In addition, in the left ventricular myocardium and blood of the diabetic rats, Grx1 levels were significantly increased and glutathione reductase and P-SH levels were decreased. Moreover, endogenous Grx1 was highly expressed in cardiac fibroblasts during high-glucose treatment, and exogenous Grx1 can prevent DCM by controlling oxidative damage and MMP expression. These findings are suggestive of changes in the Grx1 redox system, and Grx1-regulated protein oxidative modifications may serve as molecular markers for diabetes caused by high-glucose-induced oxidative stress.

[Preparation of simulate craniocerebral models via three dimensional printing technique]

OBJECTIVE

Three dimensional (3D) printing technique was used to prepare the simulate craniocerebral models, which were applied to preoperative planning and surgical simulation.

METHODS

The image data was collected from PACS system. Image data of skull bone, brain tissue and tumors, cerebral arteries and aneurysms, and functional regions and relative neural tracts of the brain were extracted from thin slice scan (slice thickness 0.5 mm) of computed tomography (CT), magnetic resonance imaging (MRI, slice thickness 1mm), computed tomography angiography (CTA), and functional magnetic resonance imaging (fMRI) data, respectively. MIMICS software was applied to reconstruct colored virtual models by identifying and differentiating tissues according to their gray scales. Then the colored virtual models were submitted to 3D printer which produced life-sized craniocerebral models for surgical planning and surgical simulation.

RESULTS

3D printing craniocerebral models allowed neurosurgeons to perform complex procedures in specific clinical cases though detailed surgical planning. It offered great convenience for evaluating the size of spatial fissure of sellar region before surgery, which helped to optimize surgical approach planning. These 3D models also provided detailed information about the location of aneurysms and their parent arteries, which helped surgeons to choose appropriate aneurismal clips, as well as perform surgical simulation. The models further gave clear indications of depth and extent of tumors and their relationship to eloquent cortical areas and adjacent neural tracts, which were able to avoid surgical damaging of important neural structures.

CONCLUSION

As a novel and promising technique, the application of 3D printing craniocerebral models could improve the surgical planning by converting virtual visualization into real life-sized models.It also contributes to functional anatomy study.

The clinical effect of herbal magnetic corsets on lumbar disc herniation

Objective: To determine the clinical effects of the treatment of lumbar disc herniation with herbal magnetic corsets.

Design: A randomized control trial.

Setting: The outpatient and inpatient departments of the Rehabilitation Center of the West China Hospital.

Patients: Sixty patients with clinically diagnosed lumbar disc herniation were included in the study.

Interventions: Both groups received lumbar traction, medium frequency electrotherapy and massage, whereas the experimental group wore herbal magnetic corsets in addition.

Main outcome measures: Pain and lumbar function were assessed before treatment and at one week, two weeks and four weeks after intervention.

Results: Both groups reported improvements in pain and lumbar function after treatment (P 0.05 or P 0.001). However, the experimental group reported gradually increasing relief over time leading to a better curative effect than observed in the control group (P 0.05 for visual analogue scale or P 0.001 for lumbar function).

Conclusion: Herbal magnetic corsets can facilitate the reduction of pain caused by lumbar disc herniation and can improve lumbar function. This is a safe and effective non-operative therapeutic option for treatment of lumbar disc herniation.

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3^rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLR gene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar

Creation of experimental aneurysms at a surgically created arterial confluence

OBJECTIVE

Complex vertebral confluence aneurysms remain clinically challenging despite the rapid technological advances in endovascular technology. Therefore, animal confluence aneurysm models are urgently needed for the preclinical development of related medical devices and training clinicians. This study aimed to establish canine confluence aneurysm model and evaluate hemodynamics in this model.

MATERIALS AND METHODS

According to the shape and regional blood flow of vertebrobasilar junction (VBJ) aneurysms, confluence aneurysm was introduced in 9 dogs by microsurgical technique. We partially anastomosed right common carotid artery (CCA) and left CCA (end to side anastomosis) to create inverted Y-junction of arteries and, then, sutured a harvested segment of external jugular vein to the notch of anastomosis to simulate confluence aneurysm. These animals were examined by 3D digital subtraction angiography (DSA) 4 weeks after surgery. Geometry parameters of the aneurysm, surrounding vasculature and specific double inlet profiles were analyzed by simulating computational fluid dynamics (CFD) in these animals.

RESULTS

Aneurysms were successfully established in all animals, including 8 complete and 1 partially thrombosed aneurysms. No neurological defects or death were observed. Geometric and hemodynamic parameters in these surgically introduced confluence aneurysm animals are similar to those reported for human VBJ aneurysms.

CONCLUSIONS

This study documents a protocol to successfully establish confluence aneurysm models in dogs. This model may be useful in preclinical studies targeting various complex vertebral confluence aneurysms.

Benzene exposure and risk of lymphohaematopoietic cancers in 25 000 offshore oil industry workers

Background:

The aim of this work was to examine the risk of lymphohaematopoietic (LH) cancer according to benzene exposure among offshore workers.

Methods:

Cancer registry data were used to identify 112 cancer cases diagnosed during 1999–2011 in a cohort of 24 917 Norwegian men reporting offshore work between 1965 and 1999. Analyses were conducted according to a stratified case–cohort design with a reference subcohort of 1661 workers. Cox regression was used to estimate hazard ratios with 95% confidence intervals, adjusted for other benzene exposure and smoking.

Results:

Most workers were exposed to benzene for <15 years. The upper range values of average intensity and cumulative exposure were estimated to 0.040 p.p.m. and 0.948 p.p.m.-years, respectively. Risks were consistently elevated among exposed workers for all LH cancers combined and for most subgroups, although case numbers were small and yielded imprecise risk estimates. There was evidence of dose-related risk patterns according to cumulative exposure for acute myeloid leukaemia (AML), multiple myeloma (MM) (P trends 0.052 and 0.024, respectively), and suggestively so for chronic lymphocytic leukaemia (CLL) according to average intensity (P trend 0.094).

Conclusions:

Our results support an association between cumulative and intensity metrics of low-level benzene exposure and risk for AML, MM, and suggestively for CLL.

A standard cytogenetic map for Anopheles sinensis and chromosome arm homology between the subgenera Anopheles and Cellia

Anopheles sinensis (Diptera: Culicidae) is an important vector of Plasmodium vivax in Southeast Asia. To facilitate population genetic and genomic studies of An. sinensis, we developed a standard cytogenetic photomap for this species. The polytene chromosomes were straightened and divided into 39 numbered divisions and 116 lettered subdivisions. The chromosomal localizations of 13 DNA probes were determined by fluorescent in situ hybridization. A comparison of the physical map for An. sinensis with the genome map for Anopheles gambiae revealed a whole-arm autosomal translocation between the two species. Specifically, the 2R arm of An. gambiae corresponds to the 3R arm of An. sinensis and the pattern of correspondence of the other chromosome arms remains regular. We mapped the breakpoints of the polymorphic paracentric chromosomal inversion 3Ra to subdivisions 28A and 31A. The standard cytogenetic map developed in this study will be useful for detailed comparative genome mapping and population genetic studies of An. sinensis.

Occupational exposure to trichloroethylene and risk of non-Hodgkin lymphoma and its major subtypes: a pooled InterLymph [correction of IinterLlymph] analysis

OBJECTIVES

We evaluated the association between occupational exposure to trichloroethylene (TCE) and risk of non-Hodgkin lymphoma (NHL) in a pooled analysis of four international case-control studies.

METHODS

Overall, the pooled study population included 3788 NHL cases and 4279 controls. Risk of NHL and its major subtypes associated with TCE exposure was calculated with unconditional logistic regression and polytomous regression analysis, adjusting by age, gender and study.

RESULTS

Risk of follicular lymphoma (FL), but not NHL overall or other subtypes, increased by probability (p=0.02) and intensity level (p=0.04), and with the combined analysis of four exposure metrics assumed as independent (p=0.004). After restricting the analysis to the most likely exposed study subjects, risk of NHL overall, FL and chronic lymphocytic leukaemia (CLL) were elevated and increased by duration of exposure (p=0.009, p=0.04 and p=0.01, respectively) and with the combined analysis of duration, frequency and intensity of exposure (p=0.004, p=0.015 and p=0.005, respectively). Although based on small numbers of exposed, risk of all the major NHL subtypes, namely diffuse large B-cell lymphoma, FL and CLL, showed increases in risk ranging 2-3.2-fold in the highest category of exposure intensity. No significant heterogeneity in risk was detected by major NHL subtypes or by study.

CONCLUSIONS

Our pooled analysis apparently supports the hypothesis of an increase in risk of specific NHL subtypes associated with occupational exposure to TCE.

Leukemia-related chromosomal loss detected in hematopoietic progenitor cells of benzene-exposed workers

Benzene exposure causes acute myeloid leukemia and hematotoxicity, shown as suppression of mature blood and myeloid progenitor cell numbers. As the leukemia-related aneuploidies monosomy 7 and trisomy 8 previously had been detected in the mature peripheral blood cells of exposed workers, we hypothesized that benzene could cause leukemia through the induction of these aneuploidies in hematopoietic stem and progenitor cells. We measured loss and gain of chromosomes 7 and 8 by fluorescence in situ hybridization in interphase colony-forming unit-granulocyte-macrophage (CFU-GM) cells cultured from otherwise healthy benzene-exposed (n=28) and unexposed (n=14) workers. CFU-GM monosomy 7 and 8 levels (but not trisomy) were significantly increased in subjects exposed to benzene overall, compared with levels in the control subjects (P=0.0055 and P=0.0034, respectively). Levels of monosomy 7 and 8 were significantly increased in subjects exposed to <10 p.p.m. (20%, P=0.0419 and 28%, P=0.0056, respectively) and ≥ 10 p.p.m. (48%, P=0.0045 and 32%, 0.0354) benzene, compared with controls, and significant exposure-response trends were detected (P(trend)=0.0033 and 0.0057). These data show that monosomies 7 and 8 are produced in a dose-dependent manner in the blood progenitor cells of workers exposed to benzene, and may be mechanistically relevant biomarkers of early effect for benzene and other leukemogens.

Coal combustion and lung cancer risk in XuanWei: a possible role of silica?

BACKGROUND

XuanWei County, Yunnan province, has the highest lung cancer mortality rates among men and women in China. The high mortality has been linked to the use of smoky (bituminous) coal for heating and cooking. Research to date has suggested that exposure to polycyclic aromatic hydrocarbons (PAHs) is one of the main contributors to the observed risk. More recently exposure to crystalline silica has been suggested as another contributing factor.

METHODS

We used data of indoor benzo[a]pyrene (BaP) and silica level and lung cancer mortality at the communal level from previous reports to discuss etiological hypotheses on the lung cancer epidemics in XuanWei County.

RESULTS

We estimated that PAH exposure as measured by benzo[a]pyrene (BaP) can explain a significant part of the excess risk but not fully (Odd Ratio (OR) 3 as compared to an observed OR = 8 for smoky coal users versus smokeless coal users). This leaves open the possibility of other contributing exposures. Exposure to crystalline silica however would likely only result in an increased risk (OR) of less than 1.5 and as such silica seems not to be the main exposure of interest. However, this does not exclude that risks are present because of the specific physic-chemical characteristics of the silica in smoky coal or that there is an interaction between silica and PAH exposures.

CONCLUSION

More detailed exposure assessment of indoor air pollution due to the use of smoky coal and subsequent linkage on an individual level to ongoing epidemiological studies should provide more insight in the etiology of lung cancer in this region.

Differential effects of smoking on lung cancer mortality before and after household stove improvement in Xuanwei, China

Background:

In Xuanwei County, Yunnan Province, China, lung cancer mortality rates in both males and females are among the highest in China.

Methods:

We evaluated differential effects of smoking on lung cancer mortality before and after household stove improvement with chimney to reduce exposure to smoky coal emissions in the unique cohort in Xuanwei, China. Effects of independent variables on lung cancer mortality were measured as hazard ratios and 95% confidence intervals using a multivariable Cox regression model that included separate time-dependent variables for smoking duration (years) before and after stove improvement.

Results and conclusion:

We found that the effect of smoking on lung cancer risk becomes considerably stronger after chimney installation and consequent reduction of indoor coal smoke exposure.

[On correlation between body mass index and lumbar spine average bone mineral density: a study in male patients with osteopenia and those with osteoporosis]

From among the patients who visited the Dept. of Rehabilitation of West China Hospital for arthalgia in the period from Aug. 2003 to Dec. 2005, we recruited 566 male patients who were over 40 years of age and did not have hyperostosis in the lumbar spine, and whose T scores were each less than--1. Their ages ranged from 40 to 93 years, and the average age was 62.93 +/- 13.50. The dual-energy X-ray absorptiometry from DMS Company in France was used to measure the bone density of the L2-4 anterior-posterior. The basic data about the subjects, containing the age, height, weight, diabetes mellitus, exercise and smoking or not, were recorded. Then the body mass index were calculated. In accordance to the T score, the subjects were separated into two groups: osteopenia group and osteoporosis group. In comparison of the basic data between groups, BMI of osteoporosis group was significantly higher than that of the osteopenia group, but the number of the subjects who exercised was smaller (P < 0.05). Multiple linear regression analysis revealed that in the case BMI increased by 1 kg/m2, BMD significantly decreased by 0.003 g/cm2 (P = 0.002), and the age negatively correlated with BMD (B = -0.001, P = 0.035). "Exercise or not" was positively related to BMD (B = 0.028, P = 0.000). "Smoking or not" and BMD were not significantly correlated (P = 0.837). In conclusion, increase of BMI, or we may say, increase of fat, would decrease the lumbar spine average BMD in the patients of osteoporosis or osteopenia. Some reports have pointed out that only by increasing BMI with increased amount of muscles, but not with increased amount of fat, would be beneficial to the prevention of osteoporosis. So we concluded that the muscle amount in the subjects should be taken into account when we probe into the relation between BMI and BMD.

Retrosigmoid keyhole approach to the posterior cranial fossa: an anatomical and clinical study

The purpose of this study is to describe the microsurgical anatomic features, as well as the operative technique for the retrosigmoid keyhole (RSK) approach to the posterior cranial fossa. In the anatomical study, 6 cadaveric heads were dissected to simulate the RSK approach. In the clinical study, the records for 15 patients treated using the RSK approach were examined. We found both conventional and RSK procedures expose the regions superior to the anterolateral margin of the tentorium, inferior to the foramen magnum, and medial to the anterolateral pons and medulla. Clinically, total removal was achieved in 13 out of 15 patients. We feel it is a safe, succinct, and minimally invasive alternative to the traditional retrosigmoid approach in selected patients.

Application of OMICS technologies in occupational and environmental health research; current status and projections

OMICS technologies are relatively new biomarker discovery tools that can be applied to study large sets of biological molecules. Their application in human observational studies (HOS) has become feasible in recent years due to a spectacular increase in the sensitivity, resolution and throughput of OMICS-based assays. Although, the number of OMICS techniques is ever expanding, the five most developed OMICS technologies are genotyping, transcriptomics, epigenomics, proteomics and metabolomics. These techniques have been applied in HOS to various extents. However, their application in occupational environmental health (OEH) research has been limited. Here, we will discuss the opportunities these new techniques provide for OEH research. In addition we will address difficulties and limitations to the interpretation of the data that is generated by OMICS technologies. To illustrate the current status of the application of OMICS in OEH research, we will provide examples of studies that used OMICS technologies to investigate human health effects of two well-known toxicants, benzene and arsenic.

Association between genetic variants in VEGF, ERCC3 and occupational benzene haematotoxicity

INTRODUCTION

Benzene is an established human haematotoxin, with substantial interindividual variation in benzene-induced toxicity.

METHODS

To further examine if genetic variation contributes to benzene haematotoxicity, we analysed 1023 tagSNPs in 121 gene regions important for benzene metabolism, haematopoiesis, leukaemia and lymphoma among 250 workers exposed to benzene and 140 unexposed controls in a cross-sectional study carried out in China. Linear regression was used to analyse the relationship between genetic polymorphisms and total white blood cell (WBC) count and its subtypes, adjusting for potential confounders and occupational exposure to benzene and toluene among exposed workers. The minp test assessed the association on the gene region level. The false discovery rate method was used to control for multiple comparisons.

RESULTS

VEGF (minp = 0.0030) and ERCC3 (minp = 0.0042) were the most significantly associated gene regions with altered WBC counts among benzene-exposed workers, after accounting for multiple comparisons. Highly significant changes were also found for WBC subtype counts, including granulocytes, CD4+ T cells and lymphocytes for VEGF and granulocytes and NK cells for ERCC3. Further, in workers exposed to <1 ppm, a SNP in VEGF was associated with changes in WBC and granulocyte counts, and SNPs in ERCC3 were associated with changes in WBC, NK cell and granulocyte counts.

DISCUSSION

Our findings suggest that genetic variation in VEGF, which plays an important role in blood vessel growth, and ERCC3, which is a member of the DNA repair pathway and is responsible for repairing bulky DNA adducts formed by chemicals, may contribute to individual susceptibility to benzene-induced haematotoxicity at relatively low levels of benzene exposure.

[Systematic assessment of acupoint stimulating therapy for deglutition disorders after apoplexy]

OBJECTIVE

To assess the therapeutic effect of acupoint stimulating therapy on deglutition disorders after apoplexy, so as to provide basis for clinical treatment and further study.

METHODS

According to Cochrane systematic assessment method of evidence-based medicine, Meta analysis on randomized controlled trials or half randomized controlled trials of acupoint stimulating therapy for deglutition disorders after apoplexy were made.

RESULTS

In 37 Chinese literatures, 3 697 patients in total were enrolled, and the results indicated that the effective rate of acupoint stimulating therapy on deglutition disorders after apoplexy was better than that in the control group [RR was 1.38, 95% CI (1.28, 1.49), Z = 8.38, P < 0.01]; and the cured rate also was better than that of the control group [RR was 2.56, 95% CI (2.15, 3.04), Z = 10.70, P < 0.01].

CONCLUSION

The therapeutic effect of acupoint stimulating therapy on deglutition disorders after apoplexy is better than that of the control group, but more randomized, double blind, controlled trials with good designs are needed to confirm this result.

Portable stove use is associated with lower lung cancer mortality risk in lifetime smoky coal users

Domestic fuel combustion from cooking and heating, to which about 3 billion people worldwide are exposed, is associated with increased lung cancer risk. Lung cancer incidence in Xuanwei is the highest in China, and the attributable risk of lung cancer from unvented smoky coal burning is greater than 90%. To evaluate any lung cancer mortality reduction after changing from unvented stoves to portable stoves, we used lifetime smoky coal users in a retrospective cohort of all farmers born during 1917–1951 and residing in Xuanwei in 1976. Of the 42 422 enrolled farmers, 4054 lifetime smoky coal users changed to portable stoves, 4364 did not change, and 1074 died of lung cancer. Lung cancer morality associated with stove change was assessed by product-limit survival curves and multivariate Cox regression models. Both men (P<0.0001) and women (P<0.0001) who changed to portable stoves had a significantly increased probability of survival compared with those who did not change. Portable stoves were associated with decreased risk of lung cancer mortality in male participants (hazard ratio (HR)=0.62, 95% confidence interval (CI)=0.46–0.82) and female participants (HR=0.41, 95% CI=0.29–0.57). Portable stove use is associated with reduced lung cancer mortality risk, highlighting a cost-effective intervention that could substantially benefit health in developing countries.

[Association of physical activities and bone mass density of lumbar spines in men]

OBJECTIVE

To determine the association of physical activities and bone mineral density of lumbar vertebrae in men.

METHODS

A total of 1169 men who sought medical attentions in the West China Hospital of Sichuan University from August, 2003 to December, 2005 because of ostealgia and arthralgia were given a dual-energy X-ray absorptiometry for the L2-L4 bone mineral density. The height, weight, smoking history, and diseases (eg. diabetes and hypertension) of the participants were recorded. A questionnaire survey was undertaken to assess the physical activities of the participants. The participants were classified into group A (frequent exercise), B (occasional exercise) and C (no exercise) according to the frequencies of physical activities. The bone mass densities of lumbar vertebrae of the three groups were compared.

RESULTS

Group A had greater bone mineral density and mineral content in L2-L4, greater average bone mineral density, and greater all bone mineral content and T-score than group C (P<0.05 or P<0.01), although Group A had similar body mass index as Group C, was older and had greater prevalence of smoking and hypertension than Group C (P<0.01). Group B had similar age and body mass index as Group C and greater smoking rate and prevalence of diabetes and hypertension than Group C (P>0.05). But the differences of bone mineral density and mineral content of L2-L4, average bone mineral density, and all bone mineral content and T-score between Group B and C were not statistical significant (P>0.05).

CONCLUSION

Physical activities can increase bone mineral density of lumbar vertebrae in men. But frequent and persistent exercises are needed to prevent decreasing mineral densities due to ageing, smoking and diseases.

Correlation between obesity and female hyperostosis

BACKGROUND

Hyperostosis is a common pathological change among people more than 50 years old; it is connected with many risk factors, which are all indefinite. The aim of this study was to prospectively investigate the correlation between obesity and female hyperostosis.

METHODS

Totally 4326 females were included in this study and their basic information including their age, stature, body weight, course of disease, symptoms, medical complications, frequency of exercise and smoking, and X-ray and bone mineral density (BMD) examination results, was carefully collected for a statistical analysis. The t test or chi(2) test was used to evaluate the differences between two groups; an analysis of variance (ANOVA) was used to evaluate the differences among several groups; the relationship between hyperostosis and body mass index (BMI), age, medical complications, exercise, average BMD was analyzed using Logistic regression.

RESULTS

The incidence rate of hyperostosis in obese patients was higher than that in patients with normal weight (P = 0.000). Obesity was relevant to hyperostotic sites (P = 0.000), and the incidence of hyperostosis in one or several sites of the lumbar vertebrae, knee joints, and other sites was higher in obese patients than in patients with normal weight. There was also a difference in the extent of hyperostosis between these two groups. BMI had positive effects on the incidence and degree of hyperostosis, which were also relative to the sites of hyperostosis, and the BMI of patients without hyperostosis were much lower than those of the patients with hyperostosis in their lumbar vertebrae, knee joints, or multiple sites. Obesity, age, and exercise had positive effects on the incidence of hyperostosis (P = 0.002, 0.000, 0.018).

CONCLUSIONS

Obesity is a significant potential stimulant of hyperostosis, especially hyperostosis in knee joints and multiple sites; keeping fit might be an important way to prevent it.

Identification of two sterol carrier protein-2 like genes in the yellow fever mosquito, Aedes aegypti

Two genes encoding sterol carrier protein-2 like proteins are identified from fourth instar cDNAs of the yellow fever mosquito, Aedes aegypti. The predicted AeSCP-2like1 (AeSCP-2L1) and AeSCP-2like2 (AeSCP-2L2) proteins are small, acidic and lacking the peroxisomal targeting sequence at the C-termini. Purified recombinant AeSCP-2L1 and -2L2 bind to cholesterol with a Kd of 5.4 x 10(-6) M and 2.6 x 10(-6) M, respectively. The Kd values of AeSCP-2L1 and -2L2 to palmitic acid are 3.7 x 10(-7) M and 2.6 x 10(-7) M, respectively. Both genes are expressed predominantly in gut tissues. The transcripts of the AeSCP-2L1 gene are only detected in larval stages, whereas AeSCP-2L2 is expressed in larval and adult stages. AeSCP-2L2 transcription increases within 5 h after a bloodmeal and stays at high levels during vitellogenesis. In in vitro larval gut tissue cultures, AeSCP-2L1 transcripts were increased in the presence of juvenile hormone III, whereas AeSCP-2L2 mRNA levels increased in the presence 20-hydroxylecdysone. The results suggest that transcription of AeSCP-2L1 and -2L2 genes are regulated differently through the mosquito life cycle.

Two-sample comparison based on prediction error, with applications to candidate gene association studies

To take advantage of the increasingly available high-density SNP maps across the genome, various tests that compare multilocus genotypes or estimated haplotypes between cases and controls have been developed for candidate gene association studies. Here we view this two-sample testing problem from the perspective of supervised machine learning and propose a new association test. The approach adopts the flexible and easy-to-understand classification tree model as the learning machine, and uses the estimated prediction error of the resulting prediction rule as the test statistic. This procedure not only provides an association test but also generates a prediction rule that can be useful in understanding the mechanisms underlying complex disease. Under the set-up of a haplotype-based transmission/disequilibrium test (TDT) type of analysis, we find through simulation studies that the proposed procedure has the correct type I error rates and is robust to population stratification. The power of the proposed procedure is sensitive to the chosen prediction error estimator. Among commonly used prediction error estimators, the .632+ estimator results in a test that has the best overall performance. We also find that the test using the .632+ estimator is more powerful than the standard single-point TDT analysis, the Pearson's goodness-of-fit test based on estimated haplotype frequencies, and two haplotype-based global tests implemented in the genetic analysis package FBAT. To illustrate the application of the proposed method in population-based association studies, we use the procedure to study the association between non-Hodgkin lymphoma and the IL10 gene.

Meta- and pooled analysis of GSTT1 and lung cancer: a HuGE-GSEC review

Lung cancer is the most common malignancy in the Western world, and the main risk factor is tobacco smoking. Polymorphisms in metabolic genes may modulate the risk associated with environmental factors. The glutathione S-transferase theta 1 gene (GSTT1) is a particularly attractive candidate for lung cancer susceptibility because of its involvement in the metabolism of polycyclic aromatic hydrocarbons found in tobacco smoke and of other chemicals, pesticides, and industrial solvents. The frequency of the GSTT1 null genotype is lower among Caucasians (10-20%) than among Asians (50-60%). The authors present a meta- and a pooled analysis of case-control, genotype-based studies that examined the association between GSTT1 and lung cancer (34 studies, 7,629 cases and 10,087 controls for the meta-analysis; 34 studies, 7,044 cases and 10,000 controls for the pooled analysis). No association was observed between GSTT1 deletion and lung cancer for Caucasians (odds ratio (OR) = 0.99, 95% confidence interval (CI): 0.87, 1.12); for Asians, a positive association was found (OR = 1.28, 95% CI: 1.10, 1.49). In the pooled analysis, the odds ratios were not significant for either Asians (OR = 0.97, 95% CI: 0.83, 1.13) or Caucasians (OR = 1.09, 95% CI: 0.99, 1.21). No significant interaction was observed between GSTT1 and smoking on lung cancer, whereas GSTT1 appeared to modulate occupational-related lung cancer.

Design and Microsurgical Anatomy of the Retrosigmoid-Retrocondylar Keyhole Approach without Occipital Condyle Removal

OBJECTIVE

The goal of this study was to design a new retrosigmoid-retrocondylar keyhole approach based on the minimally invasive keyhole idea and to explore its feasibility and indications, which can be regarded as the base of this keyhole approach in clinical use.

METHODS

8 adult cadaveric heads fixed in formalin and with intracranial vessels perfused by colored latex were used in this study. To search for the most suitable length and shape of the skin incision, we examined two kinds of incision (a longitudinal "S" shape and a straight one) and two lengths (5 cm and 7 cm, respectively). Due to the complexity and thickness of the suboccipital muscles, two ways of muscle dissection were compared: 1) the muscles were incised perpendicularly in layers; 2) the muscles were detached and reflected in layers. A 3-cm diameter retrosigmoid-retrocondylar bone flap was made with a craniotome. Many anatomic structures could be observed under the microscope when the cerebellar hemisphere was retracted. After comparing and balancing the above steps in all specimens, a feasible, duplicable retrosigmoid-retrocondylar keyhole approach was devised.

RESULTS

The proper incision of the retrosigmoid-retrocondylar keyhole approach was a longitudinal "S" shaped skin incision about 7 cm in length with its superior border 2 cm behind the middle point of mastoid and inferior margin at the level of C-2. The method of detachment and reflection of occipital muscles was superior to the method of cutting them perpendicularly. By means of adjusting the head position and the angle of microscope, the ipsilateral vertebral artery, posterior inferior cerebellar artery, anterior inferior cerebellar artery, VII, VIII, IX, X, XI, XII cranial nerves and the ventral lateral aspect of medulla oblongata were exposed via this keyhole approach.

CONCLUSIONS

The novel retrosigmoid-retrocondylar keyhole approach has practical value for clinical applications. With the techniques of modern microsurgery, several diseases such as an aneurysm situated at the vertebral artery or the posterior inferior cerebellar artery, a small hypoglossal neurinoma and tumor located at the ventral lateral aspect of the medulla oblongata, may be operated via this retrosigmoid-retrocondylar keyhole approach without drilling the occipital condyle.

Aedes aegypti phosphohexomutases and uridine diphosphate-hexose pyrophosphorylases: comparison of primary sequences, substrate specificities and temporal transcription

Phosphohexomutases reversibly catalyse the transfer of the phosphate group of a glycosyl phosphate between the C6 and C1 positions, and uridine diphosphate (UDP)-hexose pyrophosphorylases catalyse the synthesis of UDP-hexose from uridine triphosphate (UTP) and hexose-1-phosphate. Both enzyme families are essential for nucleoside diphosphate hexose biosynthesis and are therefore critical for various physiological functions in the midgut of mosquitoes after a blood meal. We cloned and sequenced three phosphohexomutase and two UDP-hexose pyrophosphorylase cDNAs from Aedes aegypti. The products of the cDNAs were expressed and substrate specificities were examined. Herein we describe Ae. aegypti phosphoglucomutase 1, phosphoglucomutase 2, phosphoacetylglucosamine mutase, UDP-glucose pyrophosphorylase, and UDP-N-acetylglucosamine pyrophosphorylase. Transcripts of the genes expressing the enzymes are constitutively present in all life stages and blood-feeding does not seem to influence transcript abundance.

Functional analysis of AeSCP-2 using gene expression knockdown in the yellow fever mosquito, Aedes aegypti

The effect of gene expression knockdown was used to study the function of the sterol carrier protein-2 (AeSCP-2) in the yellow fever mosquito, Aedes aegypti. Injection of small double stranded AeSCP-2 RNAs into mosquito larvae resulted in the knockdown of gene products. The lack of AeSCP-2 in larvae coincided with a reduction in accumulated cholesterol in pupae, supporting the hypothesis that AeSCP-2 may be involved in cholesterol uptake in mosquito larvae. Knockdown of AeSCP-2 caused a high mortality rate in developing adult and reduced egg viability. Results from this study indicate that AeSCP-2 is important for adult development and for the viability of the eggs.

Expression of a sterol carrier protein-x gene in the yellow fever mosquito, Aedes aegypti

The sterol carrier protein-x (SCP-x), a peroxisomal thiolase/nonspecific lipid binding protein, was characterized in the yellow fever mosquito, Aedes aegypti. The Aedes aegypti SCP-x (AeSCP-x) has 83% and 75% similarities to Drosophila and mammalian SCP-x, respectively. However, the AeSCP-x gene did not produce multiple transcripts, which is characteristic of the vertebrate SCP-x gene. Levels of AeSCP-x transcription were higher in larvae and pupae. Gut tissue showed the highest level of AeSCP-x mRNA in larvae. In adults, low levels of AeSCP-x transcription were detected in both sexes. Polyclonal antibodies against the sterol carrier protein-2 (SCP-2) domain of AeSCP-x detected two proteins of 62 kDa and 13 kDa. The results indicate that AeSCP-x is proteolytically cleaved after translation to produce a smaller protein that contains only the SCP-2 domain, which is similar to post-translational modification of the vertebrate's SCP-x to produce multiple products.