122 results match your criteria illumina novaseq

Comparative genomic characterization of multidrug-resistant Citrobacter spp. strains in Fennec fox imported to China.

Gut Pathog 2021 Oct 13;13(1):59. Epub 2021 Oct 13.

Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.

Background: To investigate the antimicrobial profiles and genomic characteristics of MDR-Citrobacter spp. strains isolated from Fennec fox imported from Sudan to China.

Methods: Four Citrobacter spp. Read More

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October 2021

Draft genome of Semisulcospira libertina, a species of freshwater snail.

Genomics Inform 2021 Sep 30;19(3):e32. Epub 2021 Sep 30.

Department of Orthopaedic Surgery, Gyeongsang National University Hospital, Jinju 52727, Korea.

Semisulcospira libertina, a species of freshwater snail, is widespread in East Asia. It is important as a food source. Additionally, it is a vector of clonorchiasis, paragonimiasis, metagonimiasis, and other parasites. Read More

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September 2021

Severe cases of osteogenesis imperfecta type VIII due to a homozygous mutation in P3H1 (LEPRE1) and review of the literature.

Adv Clin Exp Med 2021 Oct 12. Epub 2021 Oct 12.

Department of Pediatric Endocrinology, Faculty Of Medicine, Health Sciences University, Trabzon Kanuni Training and Research Hospital, Turkey.

Background: Osteogenesis imperfecta (OI) is a genetic disorder that causes skeletal fragility, multiple fractures and several extraskeletal disorders. Most cases of OI are caused by mutations in COL1A1/A2. Osteogenesis imperfecta type VIII typically causes a severe and fatal phenotype that presents at birth with severe osteopenia, congenital fractures and other clinical manifestations. Read More

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October 2021

Generation, characterization, and drug sensitivities of 12 patient-derived IDH1-mutant glioma cell cultures.

Neurooncol Adv 2021 Jan-Dec;3(1):vdab103. Epub 2021 Aug 2.

Department of Neurosurgery, Brain Tumor Center, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Zuid-Holland, The Netherlands.

Background: Mutations of the isocitrate dehydrogenase () gene occur in over 80% of low-grade gliomas and secondary glioblastomas. Despite considerable efforts, endogenous -mutated glioma models remain scarce. Availability of these models is key for the development of new therapeutic interventions. Read More

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Identification of Novel α and Fusions in NSCLC Plus Additional Novel Fusions in Other Solid Tumors by Whole Transcriptome Sequencing.

JTO Clin Res Rep 2021 Feb 24;2(2):100132. Epub 2020 Dec 24.

Division of Hematology-Oncology, Department of Medicine, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia.

Introduction: A novel fusion has recently been identified in NSCLC. We surveyed a large tumor database comprehensively profiled by whole transcriptome sequencing to investigate the incidence and distribution of fusions among various solid tumors.

Methods: Tumor samples submitted for clinical molecular profiling at Caris Life Sciences (Phoenix, AZ) that underwent whole transcriptome sequencing (NovaSeq [Illumina, San Diego, CA]) were retrospectively analyzed for fusion events. Read More

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February 2021

Characterization of Mitogenomes from Four Mucorales Species and Insights into Pathogenicity.

Mycoses 2021 Sep 27. Epub 2021 Sep 27.

Department of Medical Mycology, Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing, Jiangsu Province, 210042, China.

Background: Mucorales, as one major order of Zygomycetes fungi, can infect human beings and cause serious consequence. We have noticed the pathogenicity of Mucorales is closely related to energy metabolism, while mitochondria play the role of energy factories in almost all biological activities.

Methods: Virulence of M. Read More

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September 2021

The first complete genome sequence of species Shewanella decolorationis, from a bioremediation competent strain Ni1-3.

G3 (Bethesda) 2021 Sep;11(10)

Department of Environmental Engineering, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518071, P.R. China.

Shewanella decolorationis are Gram-negative γ-Proteobacteria with environmental bioremediation potential because they can perform anaerobic respiration using various types of pollutants as terminal electron acceptors. So far, three isolated and cultured strains of S. decolorationis have been reported. Read More

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September 2021

The complete chloroplast genome sequence of (Siebold & Zucc.) Miq. (Salicaceae).

Mitochondrial DNA B Resour 2021 17;6(10):2975-2976. Epub 2021 Sep 17.

Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, China.

(Siebold & Zucc.) Miq. which plays an important role in ecology, medicine and economy, is a deciduous species of Salicaceae. Read More

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September 2021

Genome Sequence of the Agrobacterium salinitolerans DG3-1 Isolated from Cotton Roots.

Mol Plant Microbe Interact 2021 Sep 17. Epub 2021 Sep 17.

Alar, Xinjiang, China;

Agrobacterium salinitolerans DG3-1 is an endophytic bacterium isolated from cotton root tissue. Our previous work has shown that it can inhibit the growth of Fusarium and Verticillium wilt pathogens as well as increase the chlorophyll content of cotton leaves. Here, we reported the complete genome sequence of strain DG3-1, which was analyzed by sequence reads generated from Nanopore PromethION and Illumina NovaSeq PE150 platforms. Read More

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September 2021

The complete chloroplast genome characteristics of Buch.-Ham. ex DC. () from Yunnan, China.

Mitochondrial DNA B Resour 2021 6;6(10):2838-2840. Epub 2021 Sep 6.

Key Laboratory for Forest Resources Conservation and Utilisation in the Southwest Mountains of China Southwest Forestry University, Ministry of Education, Kunming, China.

Buch.-Ham. ex DC. Read More

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September 2021

Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study.

Nat Biotechnol 2021 09 9;39(9):1129-1140. Epub 2021 Sep 9.

Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.

Assessing the reproducibility, accuracy and utility of massively parallel DNA sequencing platforms remains an ongoing challenge. Here the Association of Biomolecular Resource Facilities (ABRF) Next-Generation Sequencing Study benchmarks the performance of a set of sequencing instruments (HiSeq/NovaSeq/paired-end 2 × 250-bp chemistry, Ion S5/Proton, PacBio circular consensus sequencing (CCS), Oxford Nanopore Technologies PromethION/MinION, BGISEQ-500/MGISEQ-2000 and GS111) on human and bacterial reference DNA samples. Among short-read instruments, HiSeq 4000 and X10 provided the most consistent, highest genome coverage, while BGI/MGISEQ provided the lowest sequencing error rates. Read More

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September 2021

Draft genome sequence of a multidrug-resistant novel candidate Pseudomonas sp. NCCP-436 isolated from faeces of a bovine host in Pakistan.

J Glob Antimicrob Resist 2021 Sep 5;27:91-94. Epub 2021 Sep 5.

National Culture Collection of Pakistan (NCCP), Bio-resources Conservation Institute (BCI), National Agricultural Research Centre (NARC), Park Road, Islamabad, Pakistan. Electronic address:

Objectives: Here we describe the first draft genome analysis of a CRISPR-carrying, multidrug-resistant, candidate novel Pseudomonas sp. NCCP-436 isolated from faeces of a neonatal diarrhoeic calf.

Methods: The genome of strain NCCP-436 was sequenced using an Illumina NovaSeq PE150 platform and analysed using various bioinformatic tools. Read More

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September 2021

Biological Ingredient Analysis of Traditional Herbal Patent Medicine Fuke Desheng Wan Using the Shotgun Metabarcoding Approach.

Front Pharmacol 2021 17;12:607197. Epub 2021 Aug 17.

Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.

With the widespread use of traditional medicine around the world, the safety and efficacy of traditional herbal patent medicine have become an increasing concern to the public. However, it is difficult to supervise the authenticity of herbal materials in mixed herbal products according to the current quality standards, especially for traditional herbal patent medicine, with a distinct variance in the dosage of herbal materials. This study utilized the shotgun metabarcoding approach to analyze the biological ingredients of Fuke Desheng Wan (FKDSW), which is an effective traditional herbal product for the treatment of dysmenorrhea. Read More

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Transcriptome analysis provides genome annotation and expression profiles in the central nervous system of Lymnaea stagnalis at different ages.

BMC Genomics 2021 Sep 3;22(1):637. Epub 2021 Sep 3.

Department of Biology, College of Arts and Sciences, Saint Louis University, St. Louis, MO, USA.

Background: The pond snail, Lymnaea stagnalis (L. stagnalis), has served as a valuable model organism for neurobiology studies due to its simple and easily accessible central nervous system (CNS). L. Read More

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September 2021

Emergence and Genetic Characterization of Plasmid-Encoded VIM-2-Producing with Novel Integron In Isolated from Cerebrospinal Fluid.

Infect Drug Resist 2021 24;14:3415-3424. Epub 2021 Aug 24.

Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China.

Purpose: To investigate the genomic and plasmid characteristics of a newly discovered strain with a -carrying plasmid and novel integron In isolated from a cerebrospinal fluid specimen in a teaching hospital.

Methods: Species identification was performed by MALDI-TOF MS, and was identified by PCR and Sanger sequencing. Whole-genome sequencing analysis was conducted using the Illumina NovaSeq 6000 and Oxford Nanopore platforms. Read More

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Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19.

Elife 2021 08 13;10. Epub 2021 Aug 13.

HUMANOID CoRE, University of California San Diego, San Diego, United States.

Background: SARS-CoV-2, the virus responsible for COVID-19, causes widespread damage in the lungs in the setting of an overzealous immune response whose origin remains unclear.

Methods: We present a scalable, propagable, personalized, cost-effective adult stem cell-derived human lung organoid model that is complete with both proximal and distal airway epithelia. Monolayers derived from adult lung organoids (ALOs), primary airway cells, or hiPSC-derived alveolar type II (AT2) pneumocytes were infected with SARS-CoV-2 to create in vitro lung models of COVID-19. Read More

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First Report of Turnip Mosaic Virus in Peanut (Arachis hypogaea L.) in China.

Plant Dis 2021 Aug 29. Epub 2021 Aug 29.

Ningbo University, 47862, State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Fenghua Road 818, Ningbo, China, 315211;

Peanut (Arachis hypogaea L.) is an important source of edible oil in China but its yield and quality in agricultural production are affected by a number of diseases including those caused by viruses. The four viruses most commonly reported to affect the production of peanut worldwide are peanut stripe virus, cucumber mosaic virus, peanut stunt virus and peanut bud necrosis virus (Srinivasan et al. Read More

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First report of watermelon crinkle leaf-associated virus 1 and 2 infecting watermelon (Citrullus lanatus) plants in Brazil.

Plant Dis 2021 Aug 29. Epub 2021 Aug 29.

Universidade de Brasilia, 28127, Departamento de Biologia Celular, Brasilia, DF, Brazil;

Watermelon (Citrullus lanatus) is an important crop in Brazil both for export and domestic consumption. In this study, the cause of a severe leaf curling, distortions and vein clearing/yellowing disease of watermelon was investigated by high-throughput sequencing (HTS). The RNA extract of virus semi-purification preparation (Blawid et al. Read More

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Sequencing and de Novo Assembly of Abaca ( Née) var. Abuab Genome.

Genes (Basel) 2021 Aug 2;12(8). Epub 2021 Aug 2.

Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville, MD 20705, USA.

Abaca ( Née), an indigenous crop to the Philippines, is known to be the source of the strongest natural fiber. Despite its huge economic contributions, research on crop improvement is limited due to the lack of genomic data. In this study, the whole genome of the abaca var. Read More

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The complete chloroplast genome of a medicinal plant Burm.f. (Loranthaceae).

Mitochondrial DNA B Resour 2021 16;6(9):2635-2637. Epub 2021 Aug 16.

Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China.

is usually used as famous ethno-medicinal plant and popular drink in many provinces of China. In this study, the characterization of the complete chloroplast genome of was analyzed using the Illumina NovaSeq platform. The whole chloroplast genome sequence of is 131,825 including a large single-copy region (LSC, 76,069 bp), a small single-copy region (SSC, 8990 bp), and a pair of repeated regions (IRs, 23,383 bp, each). Read More

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First report of Grapevine enamovirus 1 in Vitis vinifera cultivar 'Meunier' in France.

Plant Dis 2021 Aug 22. Epub 2021 Aug 22.

Université de Strasbourg, INRAE, SVQV UMR-A 1131, F-68000 Colmar, France, Colmar, France;

Grapevine enamovirus 1 (GEV-1) is a member of the genus Enamovirus in the family Solemoviridae. GEV-1 was first described in 2017 in a few grapevine cultivars in Brazil (Silva et al. 2017) and subsequently in China (Ren et al. Read More

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Co-Occurrence of NDM-9 and MCR-1 in a Human Gut Colonized ST1011.

Infect Drug Resist 2021 10;14:3011-3017. Epub 2021 Aug 10.

Department of Infectious Diseases, The First Hospital of Taizhou, Taizhou, People's Republic of China.

Background: The emergence of the plasmid-borne colistin-resistant gene () poses a great threat to human health. What is worse, the recent observations of the coexistence of with carbapenemase encoding genes in some bacteria caused even more concern. Yet, there is a lack of observations of such strains in the human gut. Read More

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The complete chloroplast genome of Rehder, a sand binder in alpine hillslope, China.

Mitochondrial DNA B Resour 2021 28;6(9):2519-2520. Epub 2021 Jul 28.

College of Forestry, Sichuan Agricultural University, Chengdu, China.

The complete chloroplast genome of Rehder was assembled and subjected to phylogenetic analysis. The chloroplast genome of was 155,518 bp in length, containing a large single-copy region (84,373 bp), a small single-copy region (16,226 bp), and two inverted repeat regions (27,458 bp). The overall GC content of chloroplast genome was 36. Read More

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"More Guts Than Brains?"-The Role of Gut Microbiota in Idiopathic Intracranial Hypertension.

J Neuroophthalmol 2021 Jul 13. Epub 2021 Jul 13.

Department of Ophthalmology (EB, BT, AK), Hillel Yaffe Medical Center, Hadera, Israel; Institute of Gastroenterology and Hepatology (YK), Hillel Yaffe Medical Center, Hadera, Israel; Department of Cell Biology and Cancer Science (DK, SC, NG-K), Rappaport Faculty of Medicine, Technion Israel Institute of Technology, Technion Integrated Cancer Center (TICC), Haifa, Israel; Sackler Faculty of Medicine (AK), Tel Aviv University, Tel Aviv, Israel; and Canadian Institute for Advanced Research (CIFAR) (NG-Z), Azrieli Global Scholar, MaRS Centre, Toronto, Canada.

Background: Idiopathic intracranial hypertension syndrome (IIH) is most common among obese women. Weight loss is an important factor in improving papilledema. Over the last decade, growing evidence has identified gut microbiota as a potential factor in the pathophysiology of obesity. Read More

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Structural and Functional Impacts of Microbiota on and Surrounding Seawater in Cultivation Farms along Coastal Areas of the Yellow Sea.

Microorganisms 2021 Jun 12;9(6). Epub 2021 Jun 12.

Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.

is the most important commercial edible red algae in China, carrying a variety of resident microbes at its surface. To understand microbiome diversity, community structure, interactions and functions with hosts in this regard, thalli and seawater sampleswere collected from Yantai and Rizhao cultivation farms in the Yellow Sea. The thalli and seawater samples ( = 12) were collected and studied using an Illumina NovaSeq 6000 platform and 16S ribosomal RNA (rRNA) gene sequencing, along with the consideration of environmental factors. Read More

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Examination of the Transcriptional Response to Overexpression in (Lamb.) Carr.

Biology (Basel) 2021 Jun 23;10(7). Epub 2021 Jun 23.

State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.

The study of somatic embryogenesis can provide insight into early plant development. We previously obtained -overexpressing embryonic cell lines of (Lamb.) Carr. Read More

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Characterization of the complete mitochondrial genome of , a wild saprobic mushroom in China.

Mitochondrial DNA B Resour 2021 Jun 14;6(7):1979-1981. Epub 2021 Jun 14.

College of Food Science and Engineering, Shanxi Agricultural University, Taigu, PR China.

The Glistening Inkcap () is a wild saprobic mushroom in China. In this study, we assembled and annotated its complete mitochondrial genome using raw data sequenced through Illumina NovaSeq 6000 platform (Illumina, San Diego, CA). The length of the . Read More

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Small RNA Sequencing of Aqueous Humor and Plasma in Patients With Primary Open-Angle Glaucoma.

Invest Ophthalmol Vis Sci 2021 06;62(7):24

University Eye Clinic Maastricht, Maastricht University Medical Center, Maastricht, The Netherlands.

Purpose: Identify differentially expressed microRNAs (miRNAs) in aqueous humor (AH) and blood of primary open-angle glaucoma (POAG) patients by using small RNA sequencing. These may provide insight into POAG pathophysiology or serve as diagnostic biomarker.

Methods: AH and plasma of nine POAG patients and 10 cataract control patients were small RNA sequenced on Illumina NovaSeq 6000. Read More

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Analysis of microbial community diversity of muscadine grape skins.

Food Res Int 2021 07 19;145:110417. Epub 2021 May 19.

Guangxi Crop Genetic Improvement and Biotechnology Key Lab, Guangxi Academy of Agricultural Sciences, Nanning 530007, Guangxi, China. Electronic address:

Microorganisms in grape skins play vital roles in grapevine health, productivity, wine quality and organoleptic properties. To investigate microbial diversity of muscadine grape skins, 16S and ITS sequences of 30 samples from six muscadine (Muscadinia rotundifolia Michx.) cultivars grown in Guangxi, China, were sequenced using Illumina Novaseq platform. Read More

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Association between premature ovarian insufficiency and gut microbiota.

BMC Pregnancy Childbirth 2021 Jun 5;21(1):418. Epub 2021 Jun 5.

Affiliated Shenzhen Maternity&Child Healthcare Hospital, Southern Medical University, No. 3012, Fuqiang Road, Futian District, Shenzhen City, 518000, Guangdong Province, China.

Background: Premature ovarian insufficiency (POI) is characterized by impairment of ovarian function on a continuum before the age of 40 years. POI is affected by multiple factors. Considering new insights from recent gut microbiome studies, this study aimed to investigate the relationship between gut microbial community structure and POI. Read More

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