Good aquaculture practices (VietGAP) and sustainable aquaculture development in Viet Nam

The shrimp (black tiger and white leg shrimp) and catfish industries in Viet Nam continue to experience increasing growth due to rapid aquaculture development. However, disease outbreaks become a major issue. Moreover, seafood consumers at present are likely to be more concerned about how the products are produced and how to control/manage aquatic animal health instead of treatment. Hence, the main objective of this abstract is to focus on one of the solutions to address these problems/issues and ensure sustainable aquaculture development in Viet Nam

Isolation and characterization of chlorpyrifos-degrading bacteria in tea-growing soils

The excess use of pesticides in the agricultural sector has caused environmental pollution and affected the complete ecosystem. Among the various commonly used pesticides, chlorpyrifos (CPF) is widely used against multiple agrarian pests due to its effectiveness and higher insecticidal activities. However, along with its beneficial usage, CPF has various residual effects on the environment, causing multiple negative impacts on aquatic organisms and human health. Consequently, methods for eliminating CPF in the background are essential. Among the currently available approaches to CPF remediation, biological methods using microorganisms are eco-friendly and cost-effective. Therefore, this study was conducted to isolate and characterize chlorpyrifos-degrading bacteria from the tea-growing soil of Vietnam. For this, soil samples were collected from the 20 tea-growing areas of Vietnam. From the collected samples, three bacterial strains viz., Methylobacterium populi CNN2, Ensifer adhaerens VNN3, and Acinetobacter pittii CNN4 have been isolated by using streak plate method and identified based on 16S rRNA gene analysis. The study results showed that under laboratory conditions, E. adhaerens VNN3 had the highest CPF degradation ability and was followed by the strain M. populi CNN2. In liquid medium, CPF concentration (100 mg/L) was reduced by 95.2% and 81.4% by E.adhaerens VNN3 and M. populi CNN2, respectively, after 72 h. Further, under in-vitro conditions, the concentration of CPF was reduced from 500 mg/kg to 112 ± 1.73 (77.6%) and 197 ± 2.08 mg/kg (60.6%) by E. adhaerens VNN3 and M. populi CNN2, respectively. Based on the obtained results, it can be concluded that E. adhaerens VNN3 and M. populi CNN2 can be used for CPF-contaminated agricultural soil remediation

Characterization of arsenic-resistant endophytic Priestia megaterium R2.5.2 isolated from ferns in an arsenic-contaminated multi-metal mine in Vietnam

Bioremediation is a biological process to remove or neutralize environmental pollutants. This study was carried out to investing at the efficacy of arsenic resistant endophytic bacteria isolated from Pteris vittata, Pityrogramma calomelanos, Blenchum orientale, and Nephrolepis exaltata, which grow in a highly arsenic (As) contamination mining site in Vietnam. Their segmented roots, stems, and leaves were homogenized separately and inoculated on LB agar plates containing 5mM As(III) and As(V). A total of 31 arsenic resistant endophytic strains were selected, in which strain R2.5.2 isolated from the root of P. calomelanos had the highest arsenic resistant capability. Strain R2.5.2 tolerated up to 320 mM and 160 mM of arsenate and arsenite, respectively. The strain developed well on a media of 0.1 5% NaCl, at 20-40ºC and pH 5 9, and actively utilized most of the sugar sources. It had a high IAA biosynthesis capacity with an average concentration of 19.14 mg/L, tolerated to 0.5-16 mM concentration of Ag+, Hg2+, Co2+, Ni2+, Cu2+, Cr4+, and reduced As(V). Based on 16s rDNA, R2.5.2 was identified as Priestia megaterium. The ars C gene coding for arsenate reductase catalyzing reduction of As(V) was successfully amplified in P. megaterium R2.5.2.  The selected strain may have potential use for bioremediation practice

The impacts of lead recycling activities to human health and environment in Dong Mai craft village, Hung Yen, Vietnam

Lead (Pb) recycling activities in Dong Mai village, Chi Dao commune, Van Lam district, Hung Yen province have been taking place for more than 30 years. The development of recycling activities contributed to the improvement of the local economics. However, along with economic development, Dong Mai craft village is facing to serious pollution. Soil, air and water polluted by lead (Pb) caused food containing Pb at higher levels than allowed limit from 20 to 40 times. The pollution had the bad effect on human health in this village. The investigation results showed that 100 % of employee who participated on melting lead and 63.5 % of local children were poisoned by Pb. Besides, the local people got diseases relating to skin, eyes, etc. This situation requires the provincial authorities to find immediate solutions to reduce the impacts of Pb recycling activities to environment and human.Hoạt động tái chế chì của thôn Đông Mai, xã Chỉ Đạo, huyện Văn Lâm, tỉnh Hưng Yên đã diễn ra hơn 30 năm nay. Sự phát triển của nghề tái chế đã làm góp phần cải thiện kinh tế của địa phương. Tuy nhiên, cùng với sự phát triển kinh tế, làng nghề Đông Mai đã và đang đối mặt với ô nhiễm môi trường nghiêm trọng. Môi trường đất, nước không khí bị ô nhiễm bởi chì (Pb) dẫn đến thực phẩm nhiễm chì ở hàm lượng cao hơn mức cho phép từ 20- 40 lần. Sự ô nhiễm gây ra những ảnh hưởng xấu tới sức khỏe của người dân làng nghề. Kết quả điều tra cho thấy 100% công nhân tham gia nấu chì và 63.5% trẻ em địa phương bị nhiễm độc chì. Bên cạnh đó, người dân địa phương còn bị mắc của các loại bệnh ngoài da, bệnh về mắt, …. Tình trạng này đòi hỏi chính quyền địa phương phải tìm ra giải pháp khẩn cấp để giảm thiểu tác động của những hoạt động tái chế chì tới môi trường và con người

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types

Protein ubiquitination is a dynamic and reversibleprocess of adding single ubiquitin molecules orvarious ubiquitin chains to target proteins. Here,using multidimensional omic data of 9,125 tumorsamples across 33 cancer types from The CancerGenome Atlas, we perform comprehensive molecu-lar characterization of 929 ubiquitin-related genesand 95 deubiquitinase genes. Among them, we sys-tematically identify top somatic driver candidates,including mutatedFBXW7with cancer-type-specificpatterns and amplifiedMDM2showing a mutuallyexclusive pattern withBRAFmutations. Ubiquitinpathway genes tend to be upregulated in cancermediated by diverse mechanisms. By integratingpan-cancer multiomic data, we identify a group oftumor samples that exhibit worse prognosis. Thesesamples are consistently associated with the upre-gulation of cell-cycle and DNA repair pathways, char-acterized by mutatedTP53,MYC/TERTamplifica-tion, andAPC/PTENdeletion. Our analysishighlights the importance of the ubiquitin pathwayin cancer development and lays a foundation fordeveloping relevant therapeutic strategies