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Fulltext Vegetation as an ecological indicator in assessing environmental restoration in mining areas

Yu H, Zahidi I, Chow MF

iScience, 2023 Sep 15;26(9):107667.
PMID: 37680487 DOI: 10.1016/j.isci.2023.107667

As global demand for natural resources escalates, the environmental impact stemming from resource extraction has risen to the forefront of contemporary discussions. This paper probed the potential of using vegetation cover as an ecological barometer to gauge the level of environmental damage and restoration in mining areas: a decline in vegetation cover may signify detrimental impacts from intense mining activities, while an increase may indicate effective local environmental stewardship. Therefore, this paper undertook an assessment and discussion of mining damage and environmental management at China's Ta'ershan Mining Area since 2007, calculating and visualizing FVC (Fractional Vegetation Cover) of the Ta'ershan Mining Area to track changes in vegetation cover between 2007 and 2021. Changes in vegetation cover in the Ta'ershan Mining Area could act as a reflection of both mining-induced damage and subsequent successful environmental management by local authorities, providing a practical way to evaluate ecological effects in resource development.
Research on the descaling characteristics of a new electrochemical water treatment device

Wei Y, Wang D, Li G, Yu H, Dong X, Jiang H

Water Sci Technol, 2023 Nov;88(10):2566-2580.
PMID: 38017678 DOI: 10.2166/wst.2023.365

In recent years, chemical water treatment equipment has gained significant attention due to its environmental-friendly features, multifunctionality, and broad applicability. Recognizing the limitations of existing chemical treatment equipment, such as challenges in scale removal and the high water content in scale deposits, we propose a novel drum design for both anode and cathode, enabling simultaneous scale suction and dehydration. We constructed a small experimental platform to validate the equipment's performance based on our model. Notably, under the optimal operating parameters, the hardness removal rate for circulating water falls within the range of 19.6-24.46%. Moreover, the scale accumulation rate per unit area and unit time reaches 13.7 g h-1 m-2. Additionally, the energy consumption per unit weight of the scale remains impressively low at 0.16 kWh g-1. Furthermore, the chemical oxygen demand (COD) concentration decreased from an initial 106.0 mg L-1 to a mere 18.8 mg L-1, resulting in a remarkable total removal rate of 82.26%. In conclusion, our innovative electrochemical water treatment equipment demonstrates exceptional performance in scale removal, organic matter degradation, and water resource conservation, offering valuable insights for future research and development in chemical treatment equipment and electrochemical theory.
Fulltext The schizophrenia genetics knowledgebase: a comprehensive update of findings from candidate gene studies

Liu C, Kanazawa T, Tian Y, Mohamed Saini S, Mancuso S, Mostaid MS, et al.

Transl Psychiatry, 2019 08 27;9(1):205.
PMID: 31455759 DOI: 10.1038/s41398-019-0532-4

Over 3000 candidate gene association studies have been performed to elucidate the genetic underpinnings of schizophrenia. However, a comprehensive evaluation of these studies' findings has not been undertaken since the decommissioning of the schizophrenia gene (SzGene) database in 2011. As such, we systematically identified and carried out random-effects meta-analyses for all polymorphisms with four or more independent studies in schizophrenia along with a series of expanded meta-analyses incorporating published and unpublished genome-wide association (GWA) study data. Based on 550 meta-analyses, 11 SNPs in eight linkage disequilibrium (LD) independent loci showed Bonferroni-significant associations with schizophrenia. Expanded meta-analyses identified an additional 10 SNPs, for a total of 21 Bonferroni-significant SNPs in 14 LD-independent loci. Three of these loci (MTHFR, DAOA, ARVCF) had never been implicated by a schizophrenia GWA study. In sum, the present study has provided a comprehensive summary of the current schizophrenia genetics knowledgebase and has made available all the collected data as a resource for the research community.
Spatial and temporal variation of vegetation cover in the main mining area of Qibaoshan Town, China: Potential impacts from mining damage, solid waste discharge and land reclamation

Yu H, Zahidi I

Sci Total Environ, 2023 Feb 10;859(Pt 2):160392.
PMID: 36423851 DOI: 10.1016/j.scitotenv.2022.160392

The increasing frequency of mining activities in the world has led to many environmental pollution problems, such as mine wastewater discharge, mine solid waste dumps, and mine dust dispersion. These problems have negative implications for the environment and the public health of people living nearby the mining areas. Despite this, there are few methods to determine the state of mine pollution on a regional scale. Therefore, we applied remote sensing technologies to assess the mine pollution situation, especially the mine solid waste pollution, of a mining area, taking Qibaoshan Town, Liuyang City, Hunan Province, China, as an example. In our research, we have calculated the vegetation cover change of the Qibaoshan Town over the years (2000-2020), charted the vegetation coverage grade maps, and analysed the tendency of vegetation cover changes, to infer the mine pollution situation, the progress of pollution treatment and the efforts made by the local government and the mines on mine pollution disposal and the land reclamation. Additionally, mining damage can bring about geological hazards such as surface subsidence leading to vegetation destruction, while mining solid waste pollution and discharge can occupy a large amount of land and thus lead to vegetation reduction. As a result, this method of calculating FVC changes in a mining area is particularly suitable for assessing the extent of mining damage, the status of solid waste pollution and discharge, and the progress of land reclamation. In the abstract, we claim that this short communication article serves as a guide to start a conversation, and encourages experts and scholars to engage in this area of research.
Environmental hazards posed by mine dust, and monitoring method of mine dust pollution using remote sensing technologies: An overview

Yu H, Zahidi I

Sci Total Environ, 2023 Mar 15;864:161135.
PMID: 36566867 DOI: 10.1016/j.scitotenv.2022.161135

The over-exploitation of mineral resources has led to increasingly serious dust pollution in mines, resulting in a series of negative impacts on the environment, mine workers (occupational health) and nearby residents (public health). For the environment, mine dust pollution is considered a major threat on surface vegetation, landscapes, weather conditions and air quality, leading to serious environmental damage such as vegetation reduction and air pollution; for occupational health, mine dust from the mining process is also regarded as a major threat to mine workers' health, leading to occupational diseases such as pneumoconiosis and silicosis; for public health, the pollutants contained in mine dust may pollute surrounding rivers, farmlands and crops, which poses a serious risk to the domestic water and food security of nearby residents who are also susceptible to respiratory diseases from exposure to mine dust. Therefore, the second section of this paper combines literature research, statistical studies, and meta analysis to introduce the public mainly to the severity of mine dust pollution and its hazards to the environment, mine workers (occupational health), and residents (public health), as well as to present an outlook on the management of mine dust pollution. At the same time, in order to propose a method for monitoring mine dust pollution on a regional scale, based on the Dense Dark Vegetation (DDV) algorithm, the third section of this paper analysed the aerosol optical depth (AOD) change in Dexing City of China using the data of 2010, 2014, 2018 and 2021 from the NASA MCD19A2 Dataset to explore the mine dust pollution situation and the progress of pollution treatment in Dexing City from 2010 to 2021. As a discussion article, this paper aims to review the environmental and health risks caused by mine dust pollution, to remind the public to take mine dust pollution seriously, and to propose the use of remote sensing technologies to monitor mine dust pollution, providing suggestions for local governments as well as mines on mine dust monitoring measures.
Robotic Level IV Inferior Vena Cava Thrombectomy Using an Intrapericardial Control Technique: Is It Safe Without Cardiopulmonary Bypass?

Huang Q, Zhao G, Chen Y, Wu P, Li S, Peng C, et al.

J Urol, 2023 Jan;209(1):99-110.
PMID: 36194169 DOI: 10.1097/JU.0000000000002952

PURPOSE: We introduce an intrapericardial control technique using a robotic approach in the surgical treatment of renal tumor with level IV inferior vena cava thrombus to decrease the severe complications associated with cardiopulmonary bypass and deep hypothermic circulatory arrest.
MATERIALS AND METHODS: Eight patients with level IV inferior vena cava thrombi not extending into the atrium underwent transabdominal-transdiaphragmatic robot-assisted inferior vena cava thrombectomy obviating cardiopulmonary bypass/deep hypothermic circulatory arrest (cardiopulmonary bypass-free group) by an expert team comprising urological, hepatobiliary, and cardiovascular surgeons. The central diaphragm tendon and pericardium were transabdominally dissected until the intrapericardial inferior vena cava were exposed and looped proximal to the cranial end of the thrombi under intraoperative ultrasound guidance. As controls, 14 patients who underwent robot-assisted inferior vena cava thrombectomy with cardiopulmonary bypass (cardiopulmonary bypass group) and 25 patients who underwent open thrombectomy with cardiopulmonary bypass/deep hypothermic circulatory arrest (cardiopulmonary bypass/deep hypothermic circulatory arrest group) were included. Clinicopathological, operative, and survival outcomes were retrospectively analyzed.
RESULTS: Eight robot-assisted inferior vena cava thrombectomies were successfully performed without cardiopulmonary bypass, with 1 open conversion. The median operation time and first porta hepatis occlusion time were shorter, and estimated blood loss was lower in the cardiopulmonary bypass-free group as compared to the cardiopulmonary bypass group (540 vs 586.5 minutes, 16.5 vs 38.5. minutes, and 2,050 vs 3,500 mL, respectively). Severe complications (level IV-V) were also lower in the cardiopulmonary bypass-free group than in cardiopulmonary bypass and cardiopulmonary bypass/deep hypothermic circulatory arrest groups (25% vs 50% vs 40%). Oncologic outcomes were comparable among the 3 groups in short-term follow-up.
CONCLUSIONS: Pure transabdominal-transdiaphragmatic robot-assisted inferior vena cava thrombectomy without cardiopulmonary bypass/deep hypothermic circulatory arrest represents as an alternative minimally invasive approach for selected level IV inferior vena cava thrombi.
Fulltext LGR5 Activates Noncanonical Wnt Signaling and Inhibits Aldosterone Production in the Human Adrenal

Shaikh LH, Zhou J, Teo AE, Garg S, Neogi SG, Figg N, et al.

J Clin Endocrinol Metab, 2015 Jun;100(6):E836-44.
PMID: 25915569 DOI: 10.1210/jc.2015-1734

CONTEXT: Aldosterone synthesis and cellularity in the human adrenal zona glomerulosa (ZG) is sparse and patchy, presumably due to salt excess. The frequency of somatic mutations causing aldosterone-producing adenomas (APAs) may be a consequence of protection from cell loss by constitutive aldosterone production.
OBJECTIVE: The objective of the study was to delineate a process in human ZG, which may regulate both aldosterone production and cell turnover.
DESIGN: This study included a comparison of 20 pairs of ZG and zona fasciculata transcriptomes from adrenals adjacent to an APA (n = 13) or a pheochromocytoma (n = 7).
INTERVENTIONS: Interventions included an overexpression of the top ZG gene (LGR5) or stimulation by its ligand (R-spondin-3).
MAIN OUTCOME MEASURES: A transcriptome profile of ZG and zona fasciculata and aldosterone production, cell kinetic measurements, and Wnt signaling activity of LGR5 transfected or R-spondin-3-stimulated cells were measured.
RESULTS: LGR5 was the top gene up-regulated in ZG (25-fold). The gene for its cognate ligand R-spondin-3, RSPO3, was 5-fold up-regulated. In total, 18 genes associated with the Wnt pathway were greater than 2-fold up-regulated. ZG selectivity of LGR5, and its absence in most APAs, were confirmed by quantitative PCR and immunohistochemistry. Both R-spondin-3 stimulation and LGR5 transfection of human adrenal cells suppressed aldosterone production. There was reduced proliferation and increased apoptosis of transfected cells, and the noncanonical activator protein-1/Jun pathway was stimulated more than the canonical Wnt pathway (3-fold vs 1.3-fold). ZG of adrenal sections stained positive for apoptosis markers.
CONCLUSION: LGR5 is the most selectively expressed gene in human ZG and reduces aldosterone production and cell number. Such conditions may favor cells whose somatic mutation reverses aldosterone inhibition and cell loss.
From waste to wealth: The "Blue Circle" vision for a sustainable ocean future

Yu H, Zahidi I, Fai CM, Liang D, Madsen DØ

Sci Bull (Beijing), 2024 Apr 30;69(8):993-996.
PMID: 38433031 DOI: 10.1016/j.scib.2024.02.024
Fulltext Genomic evidence for the Chinese mountain cat as a wildcat conspecific (Felis silvestris bieti) and its introgression to domestic cats

Yu H, Xing YT, Meng H, He B, Li WJ, Qi XZ, et al.

Sci Adv, 2021 Jun;7(26).
PMID: 34162544 DOI: 10.1126/sciadv.abg0221

The Qinghai-Tibet Plateau endemic Chinese mountain cat has a controversial taxonomic status, whether it is a true species or a wildcat (Felis silvestris) subspecies and whether it has contributed to cat (F. s. catus) domestication in East Asia. Here, we sampled F. silvestris lineages across China and sequenced 51 nuclear genomes, 55 mitogenomes, and multilocus regions from 270 modern or museum specimens. Genome-wide analyses classified the Chinese mountain cat as a wildcat conspecific F. s. bieti, which was not involved in cat domestication of China, thus supporting a single domestication origin arising from the African wildcat (F. s. lybica). A complex hybridization scenario including ancient introgression from the Asiatic wildcat (F. s. ornata) to F. s. bieti, and contemporary gene flow between F. s. bieti and sympatric domestic cats that are likely recent Plateau arrivals, raises the prospect of disrupted wildcat genetic integrity, an issue with profound conservation implications.
Fulltext Online Binge-Watching Among Chinese College Students: Implications for Loneliness, Anxiety, and Depression

Yu H, Alizadeh F

Psychol Res Behav Manag, 2024;17:295-303.
PMID: 38292254 DOI: 10.2147/PRBM.S447311

PURPOSE: This study aimed to investigate binge-watching behavior and addiction among a sample of 446 Chinese college students and assess its consequences for mental health, with a particular focus on feelings of loneliness, anxiety, and depression.
PARTICIPANTS AND METHODS: We conducted an online survey to gather data, examining participants' binge-watching habits and preferred platforms. We also utilized regression analysis to assess the impact of binge-watching addiction on mental health, exploring the associations between binge-watching addiction and feelings of loneliness, anxiety, and depression.
RESULTS: Our findings revealed that the Chinese college students in our study typically defined binge-watching sessions as lasting approximately 7.22 hours, with an average of 10.83 episodes. Regarding the self-assessment of binge-watching, the average duration of participants was 5.76 hours, and the average number of episodes was 7.42. Tencent Video, iQIYI, and Bilibili emerged as the dominant platforms for binge-watching among the respondents. Regression analysis demonstrated a significant link between binge-watching addiction and mental health, with positive associations observed between binge-watching addiction and increased feelings of loneliness, anxiety, and depression.
CONCLUSION: The results of this study reinforce previous findings regarding the detrimental effects of excessive media consumption on mental well-being. Moreover, they provide valuable insights into the global prevalence of binge-watching and its impact on the psychological health of young adults in the digital age, emphasizing the need for proactive measures to address this issue.
Fulltext TRANSPARENT TESTA GLABRA1 Regulates the Accumulation of Seed Storage Reserves in Arabidopsis

Chen M, Zhang B, Li C, Kulaveerasingam H, Chew FT, Yu H

Plant Physiol, 2015 Sep;169(1):391-402.
PMID: 26152712 DOI: 10.1104/pp.15.00943

Seed storage reserves mainly consist of starch, triacylglycerols, and storage proteins. They not only provide energy for seed germination and seedling establishment, but also supply essential dietary nutrients for human beings and animals. So far, the regulatory networks that govern the accumulation of seed storage reserves in plants are still largely unknown. Here, we show that TRANSPARENT TESTA GLABRA1 (TTG1), which encodes a WD40 repeat transcription factor involved in many aspects of plant development, plays an important role in mediating the accumulation of seed storage reserves in Arabidopsis (Arabidopsis thaliana). The dry weight of ttg1-1 embryos significantly increases compared with that of wild-type embryos, which is accompanied by an increase in the contents of starch, total protein, and fatty acids in ttg1-1 seeds. FUSCA3 (FUS3), a master regulator of seed maturation, binds directly to the TTG1 genomic region and suppresses TTG1 expression in developing seeds. TTG1 negatively regulates the accumulation of seed storage proteins partially through transcriptional repression of 2S3, a gene encoding a 2S albumin precursor. TTG1 also indirectly suppresses the expression of genes involved in either seed development or synthesis/modification of fatty acids in developing seeds. In addition, we demonstrate that the maternal allele of the TTG1 gene suppresses the accumulation of storage proteins and fatty acids in seeds. Our results suggest that TTG1 is a direct target of FUS3 in the framework of the regulatory hierarchy controlling seed filling and regulates the accumulation of seed storage proteins and fatty acids during the seed maturation process.
Menstrual and Reproductive Factors, Hormone Use, and Risk of Pancreatic Cancer: Analysis From the International Pancreatic Cancer Case-Control Consortium (PanC4)

Lujan-Barroso L, Zhang W, Olson SH, Gao YT, Yu H, Baghurst PA, et al.

Pancreas, 2016 11;45(10):1401-1410.
PMID: 27088489

OBJECTIVES: We aimed to evaluate the relation between menstrual and reproductive factors, exogenous hormones, and risk of pancreatic cancer (PC).
METHODS: Eleven case-control studies within the International Pancreatic Cancer Case-control Consortium took part in the present study, including in total 2838 case and 4748 control women. Pooled estimates of odds ratios (ORs) and their 95% confidence intervals (CIs) were calculated using a 2-step logistic regression model and adjusting for relevant covariates.
RESULTS: An inverse OR was observed in women who reported having had hysterectomy (ORyesvs.no, 0.78; 95% CI, 0.67-0.91), remaining significant in postmenopausal women and never-smoking women, adjusted for potential PC confounders. A mutually adjusted model with the joint effect for hormone replacement therapy (HRT) and hysterectomy showed significant inverse associations with PC in women who reported having had hysterectomy with HRT use (OR, 0.64; 95% CI, 0.48-0.84).
CONCLUSIONS: Our large pooled analysis suggests that women who have had a hysterectomy may have reduced risk of PC. However, we cannot rule out that the reduced risk could be due to factors or indications for having had a hysterectomy. Further investigation of risk according to HRT use and reason for hysterectomy may be necessary.
Fulltext Three new pancreatic cancer susceptibility signals identified on chromosomes 1q32.1, 5p15.33 and 8q24.21

Zhang M, Wang Z, Obazee O, Jia J, Childs EJ, Hoskins J, et al.

Oncotarget, 2016 Oct 11;7(41):66328-66343.
PMID: 27579533 DOI: 10.18632/oncotarget.11041

Genome-wide association studies (GWAS) have identified common pancreatic cancer susceptibility variants at 13 chromosomal loci in individuals of European descent. To identify new susceptibility variants, we performed imputation based on 1000 Genomes (1000G) Project data and association analysis using 5,107 case and 8,845 control subjects from 27 cohort and case-control studies that participated in the PanScan I-III GWAS. This analysis, in combination with a two-staged replication in an additional 6,076 case and 7,555 control subjects from the PANcreatic Disease ReseArch (PANDoRA) and Pancreatic Cancer Case-Control (PanC4) Consortia uncovered 3 new pancreatic cancer risk signals marked by single nucleotide polymorphisms (SNPs) rs2816938 at chromosome 1q32.1 (per allele odds ratio (OR) = 1.20, P = 4.88x10 -15), rs10094872 at 8q24.21 (OR = 1.15, P = 3.22x10 -9) and rs35226131 at 5p15.33 (OR = 0.71, P = 1.70x10 -8). These SNPs represent independent risk variants at previously identified pancreatic cancer risk loci on chr1q32.1 ( NR5A2), chr8q24.21 ( MYC) and chr5p15.33 ( CLPTM1L- TERT) as per analyses conditioned on previously reported susceptibility variants. We assessed expression of candidate genes at the three risk loci in histologically normal ( n = 10) and tumor ( n = 8) derived pancreatic tissue samples and observed a marked reduction of NR5A2 expression (chr1q32.1) in the tumors (fold change -7.6, P = 5.7x10 -8). This finding was validated in a second set of paired ( n = 20) histologically normal and tumor derived pancreatic tissue samples (average fold change for three NR5A2 isoforms -31.3 to -95.7, P = 7.5x10 -4-2.0x10 -3). Our study has identified new susceptibility variants independently conferring pancreatic cancer risk that merit functional follow-up to identify target genes and explain the underlying biology.
Fulltext Crosstalk Between circRNA and Tumor Microenvironment of Hepatocellular Carcinoma: Mechanism, Function and Applications

Xie C, Hao X, Yuan H, Wang C, Sharif R, Yu H

Onco Targets Ther, 2024;17:7-26.
PMID: 38283733 DOI: 10.2147/OTT.S437536

Hepatocellular carcinoma (HCC) is one of the most common aggressive tumors in the world. Despite the availability of various treatments, its prognosis remains poor due to the lack of specific diagnostic indicators and the high heterogeneity of HCC cases. CircRNAs are noncoding RNAs with stable and highly specific expression. Extensive research evidence suggests that circRNAs mediate the pathogenesis and progression of HCC through acting as miRNA sponges, protein modulators, and translation templates. Tumor microenvironment (TME) has become a hotspot of immune-related research in recent years due to its effects on metabolism, secretion and immunity of HCC. Accordingly, understanding the role played by circRNAs in TME is important for the study of HCC. This review will discuss the crosstalk between circRNAs and TME in HCC. In addition, we will discuss the current deficiencies and controversies in research on circRNAs and predict future research directions.
Fulltext Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene

Sosnay PR, Siklosi KR, Van Goor F, Kaniecki K, Yu H, Sharma N, et al.

Nat Genet, 2013 Oct;45(10):1160-7.
PMID: 23974870 DOI: 10.1038/ng.2745

Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation into clinical practice. Few of the almost 2,000 variants in the cystic fibrosis transmembrane conductance regulator gene CFTR have empirical evidence that they cause cystic fibrosis. To address this gap, we collected both genotype and phenotype data for 39,696 individuals with cystic fibrosis in registries and clinics in North America and Europe. In these individuals, 159 CFTR variants had an allele frequency of ł0.01%. These variants were evaluated for both clinical severity and functional consequence, with 127 (80%) meeting both clinical and functional criteria consistent with disease. Assessment of disease penetrance in 2,188 fathers of individuals with cystic fibrosis enabled assignment of 12 of the remaining 32 variants as neutral, whereas the other 20 variants remained of indeterminate effect. This study illustrates that sourcing data directly from well-phenotyped subjects can address the gap in our ability to interpret clinically relevant genomic variation.
Fulltext Common variation at 2p13.3, 3q29, 7p13 and 17q25.1 associated with susceptibility to pancreatic cancer

Childs EJ, Mocci E, Campa D, Bracci PM, Gallinger S, Goggins M, et al.

Nat Genet, 2015 Aug;47(8):911-6.
PMID: 26098869 DOI: 10.1038/ng.3341

Pancreatic cancer is the fourth leading cause of cancer death in the developed world. Both inherited high-penetrance mutations in BRCA2 (ref. 2), ATM, PALB2 (ref. 4), BRCA1 (ref. 5), STK11 (ref. 6), CDKN2A and mismatch-repair genes and low-penetrance loci are associated with increased risk. To identify new risk loci, we performed a genome-wide association study on 9,925 pancreatic cancer cases and 11,569 controls, including 4,164 newly genotyped cases and 3,792 controls in 9 studies from North America, Central Europe and Australia. We identified three newly associated regions: 17q25.1 (LINC00673, rs11655237, odds ratio (OR) = 1.26, 95% confidence interval (CI) = 1.19-1.34, P = 1.42 × 10(-14)), 7p13 (SUGCT, rs17688601, OR = 0.88, 95% CI = 0.84-0.92, P = 1.41 × 10(-8)) and 3q29 (TP63, rs9854771, OR = 0.89, 95% CI = 0.85-0.93, P = 2.35 × 10(-8)). We detected significant association at 2p13.3 (ETAA1, rs1486134, OR = 1.14, 95% CI = 1.09-1.19, P = 3.36 × 10(-9)), a region with previous suggestive evidence in Han Chinese. We replicated previously reported associations at 9q34.2 (ABO), 13q22.1 (KLF5), 5p15.33 (TERT and CLPTM1), 13q12.2 (PDX1), 1q32.1 (NR5A2), 7q32.3 (LINC-PINT), 16q23.1 (BCAR1) and 22q12.1 (ZNRF3). Our study identifies new loci associated with pancreatic cancer risk.
Fulltext Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer

Klein AP, Wolpin BM, Risch HA, Stolzenberg-Solomon RZ, Mocci E, Zhang M, et al.

Nat Commun, 2018 02 08;9(1):556.
PMID: 29422604 DOI: 10.1038/s41467-018-02942-5

In 2020, 146,063 deaths due to pancreatic cancer are estimated to occur in Europe and the United States combined. To identify common susceptibility alleles, we performed the largest pancreatic cancer GWAS to date, including 9040 patients and 12,496 controls of European ancestry from the Pancreatic Cancer Cohort Consortium (PanScan) and the Pancreatic Cancer Case-Control Consortium (PanC4). Here, we find significant evidence of a novel association at rs78417682 (7p12/TNS3, P = 4.35 × 10-8). Replication of 10 promising signals in up to 2737 patients and 4752 controls from the PANcreatic Disease ReseArch (PANDoRA) consortium yields new genome-wide significant loci: rs13303010 at 1p36.33 (NOC2L, P = 8.36 × 10-14), rs2941471 at 8q21.11 (HNF4G, P = 6.60 × 10-10), rs4795218 at 17q12 (HNF1B, P = 1.32 × 10-8), and rs1517037 at 18q21.32 (GRP, P = 3.28 × 10-8). rs78417682 is not statistically significantly associated with pancreatic cancer in PANDoRA. Expression quantitative trait locus analysis in three independent pancreatic data sets provides molecular support of NOC2L as a pancreatic cancer susceptibility gene.
Influence of substrate on ultrafast water transport property of multilayer graphene coatings

Kueh TC, Yu H, Soh AK, Wu HA, Hung YM

Nanotechnology, 2020 Sep 11;31(37):375704.
PMID: 32480382 DOI: 10.1088/1361-6528/ab9864

The ultrafast water transport in graphene nanoplatelets (GNPs) coating is attributed to the low friction passages formed by pristine graphene and the hydrophilic functional groups which provide a strong interaction force to the water molecules. Here, we examine the influence of the supporting substrate on the ultrafast water transport property of multilayer graphene coatings experimentally and by computational modelling. Thermally cured GNPs manifesting ultrafast water permeation are coated on different substrate materials, namely aluminium, copper, iron and glass. The physical and chemical structures of the GNPs coatings which are affected by the substrate materials are characterized using various spectroscopy techniques. Experimentally, the water permeation and absorption tests evidence the significant influence of the substrate on the rapid water permeation property of GNPs-coating. The water transport rates of the GNPs coatings correspond to the wettability and the free surface energy of their substrates where the most hydrophilic substrate induces the highest water transport rate. In addition, we conduct molecular dynamics (MD) simulations to investigate the transport rate of water molecules through multilayer GNPs adjacent to different substrate materials. The MD simulations results agree well with the experimental results inferring the strong influence of the substrate materials on the fast water transport of GNPs. Therefore, selection of substrate has to be taken into consideration when the GNPs-coating is placed into applications.
Phylogeny and evolution of the Drosophila nasuta subgroup based on mitochondrial ND4 and ND4L gene sequences

Yu H, Wang W, Fang S, Zhang YP, Lin FJ, Geng ZC

Mol Phylogenet Evol, 1999 Dec;13(3):556-65.
PMID: 10620413

The sequences of the mitochondrial ND4 gene (1339 bp) and the ND4L gene (290 bp) were determined for all the 14 extant taxa of the Drosophila nasuta subgroup. The average A + T content of ND4 genes is 76.5% and that of ND4L genes is 83.5%. A total of 114 variable sites were scored. The ND4 gene sequence divergence ranged from 0 to 5.4% within the subgroup. The substitution rate of the ND4 gene is about 1.25% per million years. The base substitution of the genes is strongly transition biased. Neighbor-joining and parsimony were used to construct a phylogeny based on the resultant sequence data set. According to these trees, five distinct mtDNA clades can be identified. D. niveifrons represents the most diverged lineage. D. sulfurigaster bilimbata and D. kepulauana form two independent lineages. The other two clades are the kohkoa complex and the albomicans complex. The kohkoa complex consists of D. sulfurigaster sulfurigaster, D. pulaua, D. kohkoa, and Taxon-F. The albomicans complex can be divided into two groups: D. nasuta, D. sulfurigaster neonasuta, D. sulfurigaster albostrigata, and D. albomicans from Chiangmai form one group; and D. pallidifrons, Taxon-I, Taxon-J, and D. albomicans from China form the other group. High genetic differentiation was found among D. albomicans populations. Based on our phylogenetic results, we hypothesize that D. niveifrons diverged first from the D. nasuta subgroup in Papua New Guinea about 3.5 Mya. The ancestral population spread to the north and when it reached Borneo, it diversified sequentially into the kohkoa complex, D. s. bilimbata, and D. kepulauana. About 1 Mya, another radiation occurred when the ancestral populations reached the Indo-China Peninsula, forming the albomicans complex. Discrepancy between morphological groupings and phylogenetic results suggests that the male morphological traits may not be orthologous.
Fulltext Identification and genomic analysis of temperate Halomonas bacteriophage vB_HmeY_H4907 from the surface sediment of the Mariana Trench at a depth of 8,900 m

Su Y, Zhang W, Liang Y, Wang H, Liu Y, Zheng K, et al.

Microbiol Spectr, 2023 Sep 20;11(5):e0191223.
PMID: 37728551 DOI: 10.1128/spectrum.01912-23

Viruses play crucial roles in the ecosystem by modulating the host community structure, mediating biogeochemical cycles, and compensating for the metabolism of host cells. Mariana Trench, the world's deepest hadal habitat, harbors a variety of unique microorganisms that have adapted to its extreme conditions of low temperatures, high pressure, and nutrient scarcity. However, our knowledge about isolated hadal phage strains in the hadal trench is still limited. This study reported the discovery of a temperate phage, vB_HmeY_H4907, infecting Halomonas meridiana H4907, isolated from surface sediment from the Mariana Trench at a depth of 8,900 m. To our best knowledge, it is the deepest isolated siphovirus from the ocean. Its 40,452 bp linear dsDNA genome has 57.64% GC content and 55 open reading frames, and it is highly homologous to its host. Phylogenetic analysis and average nucleotide sequence identification reveal that vB_HmeY_H4907 is separated from the isolated phages and represents a new family, Suviridae, with eight predicted proviruses and six uncultured viral genomes. They are widely distributed in the ocean, suggesting a prevalence of this viral family in the deep sea. These findings expand our understanding of the phylogenetic diversity and genomic features of hadal lysogenic phages, provide essential information for further studies of phage-host interactions and evolution, and may reveal new insights into the lysogenic lifestyles of viruses inhabiting the hadal ocean. IMPORTANCE Halomonas phage vB_HmeY_H4907 is the deepest isolated siphovirus from the ocean, and it represents a novel abundant viral family in the ocean. This study provides insights into the genomic, phylogenetic, and ecological characteristics of the new viral family, namely, Suviridae.

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