664 results on '"Han, James"'
Search Results
2. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
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Jain, Shantanu, Bakolitsa, Constantina, Brenner, Steven E, Radivojac, Predrag, Moult, John, Repo, Susanna, Hoskins, Roger A, Andreoletti, Gaia, Barsky, Daniel, Chellapan, Ajithavalli, Chu, Hoyin, Dabbiru, Navya, Kollipara, Naveen K, Ly, Melissa, Neumann, Andrew J, Pal, Lipika R, Odell, Eric, Pandey, Gaurav, Peters-Petrulewicz, Robin C, Srinivasan, Rajgopal, Yee, Stephen F, Yeleswarapu, Sri Jyothsna, Zuhl, Maya, Adebali, Ogun, Patra, Ayoti, Beer, Michael A, Hosur, Raghavendra, Peng, Jian, Bernard, Brady M, Berry, Michael, Dong, Shengcheng, Boyle, Alan P, Adhikari, Aashish, Chen, Jingqi, Hu, Zhiqiang, Wang, Robert, Wang, Yaqiong, Miller, Maximilian, Wang, Yanran, Bromberg, Yana, Turina, Paola, Capriotti, Emidio, Han, James J, Ozturk, Kivilcim, Carter, Hannah, Babbi, Giulia, Bovo, Samuele, Di Lena, Pietro, Martelli, Pier Luigi, Savojardo, Castrense, Casadio, Rita, Cline, Melissa S, De Baets, Greet, Bonache, Sandra, Diez, Orland, Gutierrez-Enriquez, Sara, Fernandez, Alejandro, Montalban, Gemma, Ootes, Lars, Ozkan, Selen, Padilla, Natalia, Riera, Casandra, De la Cruz, Xavier, Diekhans, Mark, Huwe, Peter J, Wei, Qiong, Xu, Qifang, Dunbrack, Roland L, Gotea, Valer, Elnitski, Laura, Margolin, Gennady, Fariselli, Piero, Kulakovskiy, Ivan V, Makeev, Vsevolod J, Penzar, Dmitry D, Vorontsov, Ilya E, Favorov, Alexander V, Forman, Julia R, Hasenahuer, Marcia, Fornasari, Maria S, Parisi, Gustavo, Avsec, Ziga, Celik, Muhammed H, Thi, Yen Duong Nguyen, Gagneur, Julien, Shi, Fang-Yuan, Edwards, Matthew D, Guo, Yuchun, Tian, Kevin, Zeng, Haoyang, Gifford, David K, Goke, Jonathan, Zaucha, Jan, Gough, Julian, Ritchie, Graham RS, Frankish, Adam, Mudge, Jonathan M, Harrow, Jennifer, Young, Erin L, and Yu, Yao
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Biological Sciences ,Genetics ,Human Genome ,2.1 Biological and endogenous factors ,Good Health and Well Being ,Humans ,Computational Biology ,Mutation ,Missense ,Phenotype ,Critical Assessment of Genome Interpretation Consortium ,Environmental Sciences ,Information and Computing Sciences ,Bioinformatics - Abstract
BackgroundThe Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors.ResultsPerformance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic.ConclusionsResults show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.
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- 2024
3. Noise robustness and metabolic load determine the principles of central dogma regulation
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Lo, Teresa W., Choi, Han James, Huang, Dean, and Wiggins, Paul A.
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Quantitative Biology - Molecular Networks ,Physics - Biological Physics - Abstract
The processes of gene expression are inherently stochastic, even for essential genes required for growth. How does the cell maximize fitness in light of noise? To answer this question, we build a mathematical model to explore the trade-off between metabolic load and growth robustness. The model predicts novel principles of central dogma regulation: Optimal protein expression levels for many genes are in vast overabundance. Essential genes are transcribed above a lower limit of one message per cell cycle. Gene expression is achieved by load balancing between transcription and translation. We present evidence that each of these novel regulatory principles is observed. These results reveal that robustness and metabolic load determine the global regulatory principles that govern gene expression processes, and these principles have broad implications for cellular function., Comment: Main: 10 pages, 6 figures; Supplemental Material: 27 pages, 12 figures
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- 2023
4. SICNav: Safe and Interactive Crowd Navigation using Model Predictive Control and Bilevel Optimization
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Samavi, Sepehr, Han, James R., Shkurti, Florian, and Schoellig, Angela P.
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Computer Science - Robotics - Abstract
Robots need to predict and react to human motions to navigate through a crowd without collisions. Many existing methods decouple prediction from planning, which does not account for the interaction between robot and human motions and can lead to the robot getting stuck. We propose SICNav, a Model Predictive Control (MPC) method that jointly solves for robot motion and predicted crowd motion in closed-loop. We model each human in the crowd to be following an Optimal Reciprocal Collision Avoidance (ORCA) scheme and embed that model as a constraint in the robot's local planner, resulting in a bilevel nonlinear MPC optimization problem. We use a KKT-reformulation to cast the bilevel problem as a single level and use a nonlinear solver to optimize. Our MPC method can influence pedestrian motion while explicitly satisfying safety constraints in a single-robot multi-human environment. We analyze the performance of SICNav in two simulation environments and indoor experiments with a real robot to demonstrate safe robot motion that can influence the surrounding humans. We also validate the trajectory forecasting performance of ORCA on a human trajectory dataset., Comment: Currently under review for IEEE Transactions on Robotics (T-RO)
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- 2023
5. A Study of Class Competition and Interpersonal Patterns in the Urbanization Process : ——Taking takeout industry as an example
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Han, James Jiajun, Appolloni, Andrea, Series Editor, Caracciolo, Francesco, Series Editor, Ding, Zhuoqi, Series Editor, Gogas, Periklis, Series Editor, Huang, Gordon, Series Editor, Nartea, Gilbert, Series Editor, Ngo, Thanh, Series Editor, Striełkowski, Wadim, Series Editor, Dou, Peng, editor, and Zhang, Keying, editor
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- 2024
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6. Multi-modality imaging parameters that predict rapid tumor regression in head and neck radiotherapy
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Aliotta, Eric, Paudyal, Ramesh, Diplas, Bill, Han, James, Hu, Yu-Chi, Hun Oh, Jung, Hatzoglou, Vaios, Jensen, Naomi, Zhang, Peng, Aristophanous, Michalis, Riaz, Nadeem, Deasy, Joseph O., Lee, Nancy Y., and Shukla-Dave, Amita
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- 2024
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7. Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI‐5
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Monzon, Alexander Miguel, Carraro, Marco, Chiricosta, Luigi, Reggiani, Francesco, Han, James, Ozturk, Kivilcim, Wang, Yanran, Miller, Maximilian, Bromberg, Yana, Capriotti, Emidio, Savojardo, Castrense, Babbi, Giulia, Martelli, Pier L, Casadio, Rita, Katsonis, Panagiotis, Lichtarge, Olivier, Carter, Hannah, Kousi, Maria, Katsanis, Nicholas, Andreoletti, Gaia, Moult, John, Brenner, Steven E, Ferrari, Carlo, Leonardi, Emanuela, and Tosatto, Silvio CE
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Biological Sciences ,Bioinformatics and Computational Biology ,Schizophrenia ,Genetics ,Brain Disorders ,Mental Health ,Aetiology ,2.1 Biological and endogenous factors ,Mental health ,Autoantigens ,Cell Cycle Proteins ,Computational Biology ,Databases ,Genetic ,Genetic Predisposition to Disease ,Humans ,Mutation ,Missense ,Neural Networks ,Computer ,Phenotype ,Polymorphism ,Single Nucleotide ,bioinformatics tools ,community challenge ,critical assessment ,effect prediction ,missense mutations ,variant interpretation ,Clinical Sciences ,Genetics & Heredity ,Clinical sciences - Abstract
The CAGI-5 pericentriolar material 1 (PCM1) challenge aimed to predict the effect of 38 transgenic human missense mutations in the PCM1 protein implicated in schizophrenia. Participants were provided with 16 benign variants (negative controls), 10 hypomorphic, and 12 loss of function variants. Six groups participated and were asked to predict the probability of effect and standard deviation associated to each mutation. Here, we present the challenge assessment. Prediction performance was evaluated using different measures to conclude in a final ranking which highlights the strengths and weaknesses of each group. The results show a great variety of predictions where some methods performed significantly better than others. Benign variants played an important role as negative controls, highlighting predictors biased to identify disease phenotypes. The best predictor, Bromberg lab, used a neural-network-based method able to discriminate between neutral and non-neutral single nucleotide polymorphisms. The CAGI-5 PCM1 challenge allowed us to evaluate the state of the art techniques for interpreting the effect of novel variants for a difficult target protein.
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- 2019
8. Epileptiform activity predicts epileptogenesis in cerebral hemorrhage
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Tseun Han James Kong, Mohammad Abdul Azeem, Ayesha Naeem, Shawn Allen, Jennifer Ahjin Kim, and Aaron F. Struck
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epilepsy ,cerebral hemorrhage ,EEG ,neuro‐monitoring ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Abstract This retrospective case–controlled study was performed to evaluate whether Epileptiform Activity, suspected clinical seizures, and/or 2HELPS2B/S after nontraumatic Intraparenchymal Hemorrhage or Subarachnoid Hemorrhage can predict Epilepsy. Hundred and thirty‐two patients were included—29 (Epilepsy), 103 (Control Group). After matching, the average effect for all three risk factors was significant as follows: (1) Epileptiform Activity (p = 0.012, odds ratio 3.14), (2) suspected seizures (p = 0.021, odds ratio 3.78), and (3) 2HELPS2B/S score (p
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- 2022
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9. Difficult biliary cannulation: Historical perspective, practical updates, and guide for the endoscopist
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Berry, Rani, Han, James Y, and Tabibian, James H
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Biomedical and Clinical Sciences ,Clinical Sciences ,Biomedical Imaging ,Digestive Diseases ,Rare Diseases ,Oral and gastrointestinal ,Selective biliary cannulation ,Post-endoscopic retrograde cholangiopancreatography pancreatitis ,Periampullary diverticulum ,Precut technique ,Endoscopic ultrasound ,Rendezvous endoscopic retrograde cholangiopancreatography - Abstract
Despite improvements in endoscopic technologies and accessories, development of advanced endoscopy fellowship programs, and advances in ancillary imaging techniques, biliary cannulation in endoscopic retrograde cholangiopancreatography (ERCP) can still be unsuccessful in up to 20% of patients, even in referral centers. Once cannulation has been deemed to be difficult, the risk of post-ERCP pancreatitis and technical failure inherently increases. A number of factors, including endoscopist experience and patient anatomy, have been associated with difficult biliary cannulation, but predicting a case of difficult cannulation a priori is often not possible. Numerous techniques such as pancreatic guidewire and stenting, early pre-cut, and rendezvous may be employed when standard approaches fail. Data regarding the rate of success and adverse events of these techniques have been variable, though most studies suggest that pancreatic duct stenting generally reduces the rate of post-ERCP pancreatitis in instances of difficult biliary cannulation. Here we provide a review on difficult biliary cannulation and discuss how the choice of which techniques to employ and how to best employ them should be individualized and take into account the skill of the endoscopist, the disorder being treated, the anatomy of the patient, and the available biomedical literature.
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- 2019
10. Oysters at The Luke
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Han, James and Eville, Hardy
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News, opinion and commentary ,Sports and fitness - Abstract
Byline: James Han and Hardy Eville The Luke is a little bit of everything. Located at the foot of the Taft Apartments on College Street, it was once a ballroom [...]
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- 2024
11. Hemobilia: Etiology, diagnosis, and treatment
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Berry, Rani, Han, James Y, Kardashian, Ani A, LaRusso, Nicholas F, and Tabibian, James H
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Biomedical and Clinical Sciences ,Clinical Sciences ,Digestive Diseases ,Rare Diseases ,Clinical Research ,Liver Disease ,Oral and gastrointestinal ,Diagnosis ,Etiology ,Hemobilia ,Hepatopancreatobiliary interventions ,Imaging ,Upper gastrointestinal hemorrhage - Abstract
Hemobilia refers to bleeding from and/or into the biliary tract and is an uncommon but important cause of gastrointestinal hemorrhage. Reports of hemobilia date back to the 1600s, but due to its relative rarity and challenges in diagnosis, only in recent decades has hemobilia been more critically studied. The majority of cases of hemobilia are iatrogenic and caused by invasive procedures involving the liver, pancreas, bile ducts and/or the hepatopancreatobiliary vasculature, with trauma and malignancy representing the two other leading causes. A classic triad of right upper quadrant pain, jaundice, and overt upper gastrointestinal bleeding has been described (i.e. Quincke's triad), but this is present in only 25%-30% of patients with hemobilia. Therefore, prompt diagnosis depends critically on having a high index of suspicion, which may be based on a patient's clinical presentation and having recently undergone (peri-) biliary instrumentation or other predisposing factors. The treatment of hemobilia depends on its severity and suspected source and ranges from supportive care to advanced endoscopic, interventional radiologic, or surgical intervention. Here we provide a clinical overview and update regarding the etiology, diagnosis, and treatment of hemobilia geared for specialists and subspecialists alike.
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- 2018
12. Quality in Barrett's Esophagus: Diagnosis and Management
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Konda, Vani J.A., Ellison, Ashton, Codipilly, Don C., Han, James, Samarasena, Jason, and Iyer, Prasad G.
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- 2022
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13. Hemobilia: Perspective and Role of the Advanced Endoscopist
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Berry, Rani, Han, James, Girotra, Mohit, and Tabibian, James H
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Biomedical and Clinical Sciences ,Clinical Sciences ,Clinical Research ,Digestive Diseases ,Rare Diseases ,Liver Disease ,Oral and gastrointestinal ,Neurosciences ,Public Health and Health Services ,Clinical sciences - Abstract
Hemobilia refers to bleeding from and/or into the biliary tract and is an uncommon cause of gastrointestinal hemorrhage. Hemobilia has been documented since the 1600s, but due to its relative rarity, it has only been more critically examined in recent decades. Most cases of hemobilia are iatrogenic and caused by procedures involving the liver, pancreas, bile ducts, and/or the hepatopancreatobiliary vasculature, with trauma and malignancy representing the two other major causes. A classic triad of right upper quadrant pain, jaundice, and overt upper gastrointestinal bleeding has been described, but this is present in only 25-30% of patients with hemobilia. Historically, the gold standard for diagnosis and treatment has been angiography and interventional radiologic intervention, respectively. However, the paradigm is shifting, at least in select cases, towards first-line reliance on noninvasive imaging (e.g., computed tomography) and therapeutic endoscopy, owing to advances in and the less invasive nature of both, while saving interventional radiological and/or surgical intervention for refractory or imminently life-threatening cases.
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- 2018
14. Hypoxia-Directed Treatment of Human Papillomavirus–Related Oropharyngeal Carcinoma
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Lee, Nancy Y., primary, Sherman, Eric J., additional, Schöder, HeiKo, additional, Wray, Rick, additional, Boyle, Jay O., additional, Singh, Bhuvanesh, additional, Grkovski, Milan, additional, Paudyal, Ramesh, additional, Cunningham, Louise, additional, Zhang, Zhigang, additional, Hatzoglou, Vaios, additional, Katabi, Nora, additional, Diplas, Bill H., additional, Han, James, additional, Imber, Brandon S., additional, Pham, Khoi, additional, Yu, Yao, additional, Zakeri, Kaveh, additional, McBride, Sean M., additional, Kang, Jung J., additional, Tsai, C. Jillian, additional, Chen, Linda C., additional, Gelblum, Daphna Y., additional, Shah, Jatin P., additional, Ganly, Ian, additional, Cohen, Marc A., additional, Cracchiolo, Jennifer R., additional, Morris, Luc G.T., additional, Dunn, Lara A., additional, Michel, Loren S., additional, Fetten, James V., additional, Kripani, Anuja, additional, Pfister, David G., additional, Ho, Alan L., additional, Shukla-Dave, Amita, additional, Humm, John L., additional, Powell, Simon N., additional, Li, Bob T., additional, Reis-Filho, Jorge S., additional, Diaz, Luis A., additional, Wong, Richard J., additional, and Riaz, Nadeem, additional
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- 2024
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15. Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms
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Behera, Sairam, primary, Catreux, Severine, additional, Rossi, Massimiliano, additional, Truong, Sean, additional, Huang, Zhuoyi, additional, Ruehle, Michael, additional, Visvanath, Arun, additional, Parnaby, Gavin, additional, Roddey, Cooper, additional, Onuchic, Vitor, additional, Cameron, Daniel L, additional, English, Adam, additional, Mehtalia, Shyamal, additional, Han, James, additional, Mehio, Rami, additional, and Sedlazeck, Fritz J, additional
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- 2024
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16. Auto-segmentation of neck nodal metastases using self-distilled masked image transformer on longitudinal MR images
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Paudyal, Ramesh, primary, Jiang, Jue, additional, Han, James, additional, Diplas, Bill H, additional, Riaz, Nadeem, additional, Hatzoglou, Vaios, additional, Lee, Nancy, additional, Deasy, Joseph O, additional, Veeraraghavan, Harini, additional, and Shukla-Dave, Amita, additional
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- 2024
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17. Brachytherapy of the head and neck: An University of California Los Angeles guide to morbidity reduction
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Venkat, Puja, Han, James, and Demanes, D. Jeffrey
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- 2021
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18. Atelier Florian
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Eville, Hardy and Han, James
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News, opinion and commentary ,Sports and fitness - Abstract
Byline: Hardy Eville and James Han On a cold day in February, there's no better way to sustain yourself than comfort food. For us, that's Atelier Florian...even though we'd never [...]
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- 2024
19. Dope N Delicious
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Han, James and Eville, Hardy
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News, opinion and commentary ,Sports and fitness - Abstract
Byline: James Han and Hardy Eville If you take a walk down Dixwell Avenue, you'll find Dope N Delicious, a hole-in-the-wall spot with dark-tinted windows and an unassuming exterior. But [...]
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- 2023
20. Permanent Draft Genome Sequence of Desulfurococcus amylolyticus Strain Z-533T, a Peptide and Starch Degrader Isolated from Thermal Springs in the Kamchatka Peninsula and Kunashir Island, Russia
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Susanti, Dwi, Johnson, Eric F, Lapidus, Alla, Han, James, Reddy, TBK, Mukherjee, Supratim, Pillay, Manoj, Perevalova, Anna A, Ivanova, Natalia N, Woyke, Tanja, Kyrpides, Nikos C, and Mukhopadhyay, Biswarup
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Microbiology ,Biological Sciences ,Genetics ,Biotechnology - Abstract
Desulfurococcus amylolyticus Z-533T, a hyperthermophilic crenarcheon, ferments peptide and starch, generating acetate, isobutyrate, isovalerate, CO2, and hydrogen. Unlike D. amylolyticus Z-1312, it cannot use cellulose and is inhibited by hydrogen. The reported draft genome sequence of D. amylolyticus Z-533T will help to understand the molecular basis for these differences.
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- 2017
21. Oral IBGard™ Before Colonoscopy: A Single-Center Double-Blinded, Randomized, Placebo-Controlled Trial
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Han, James Y., Moosvi, Zain, Duh, Erica, Park, Sunhee, Albers, Gregory C., Samarasena, Jason B., and Karnes, William
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- 2021
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22. Treatment interruptions affect biochemical failure rates in prostate cancer patients treated with proton beam therapy: Report from the multi-institutional proton collaborative group registry
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Han, James E., Chang, John, Rosen, Lane, Hartsell, William, Tsai, Henry, Chen, Jonathan, Mishra, Mark V., Krauss, Daniel, Isabelle Choi, J., Simone, Charles B., II, and Hasan, Shaakir
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- 2020
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23. Permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, a thermoacidophilic sulfur-reducing crenarchaeon isolated from acidic hot springs of Hveravellir, Iceland.
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Susanti, Dwi, Johnson, Eric F, Lapidus, Alla, Han, James, Reddy, TBK, Pilay, Manoj, Ivanova, Natalia N, Markowitz, Victor M, Woyke, Tanja, Kyrpides, Nikos C, and Mukhopadhyay, Biswarup
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Acidic hot spring ,Desulfurococcus ,Sulfur-reducing crenarchaeon ,Thermophile ,Genetics ,Human Genome ,Biochemistry and Cell Biology - Abstract
This report presents the permanent draft genome sequence of Desulfurococcus mobilis type strain DSM 2161, an obligate anaerobic hyperthermophilic crenarchaeon that was isolated from acidic hot springs in Hveravellir, Iceland. D. mobilis utilizes peptides as carbon and energy sources and reduces elemental sulfur to H2S. A metabolic construction derived from the draft genome identified putative pathways for peptide degradation and sulfur respiration in this archaeon. Existence of several hydrogenase genes in the genome supported previous findings that H2 is produced during the growth of D. mobilis in the absence of sulfur. Interestingly, genes encoding glucose transport and utilization systems also exist in the D. mobilis genome though this archaeon does not utilize carbohydrate for growth. The draft genome of D. mobilis provides an additional mean for comparative genomic analysis of desulfurococci. In addition, our analysis on the Average Nucleotide Identity between D. mobilis and Desulfurococcus mucosus suggested that these two desulfurococci are two different strains of the same species.
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- 2016
24. ProDeGe: a computational protocol for fully automated decontamination of genomes
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Tennessen, Kristin, Andersen, Evan, Clingenpeel, Scott, Rinke, Christian, Lundberg, Derek S, Han, James, Dangl, Jeff L, Ivanova, Natalia, Woyke, Tanja, Kyrpides, Nikos, and Pati, Amrita
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Microbiology ,Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Biotechnology ,Infectious Diseases ,Generic health relevance ,Base Sequence ,Computational Biology ,Genome ,Metagenome ,Molecular Sequence Data ,Sequence Homology ,Nucleic Acid ,Environmental Sciences ,Technology ,Biological sciences ,Environmental sciences - Abstract
Single amplified genomes and genomes assembled from metagenomes have enabled the exploration of uncultured microorganisms at an unprecedented scale. However, both these types of products are plagued by contamination. Since these genomes are now being generated in a high-throughput manner and sequences from them are propagating into public databases to drive novel scientific discoveries, rigorous quality controls and decontamination protocols are urgently needed. Here, we present ProDeGe (Protocol for fully automated Decontamination of Genomes), the first computational protocol for fully automated decontamination of draft genomes. ProDeGe classifies sequences into two classes--clean and contaminant--using a combination of homology and feature-based methodologies. On average, 84% of sequence from the non-target organism is removed from the data set (specificity) and 84% of the sequence from the target organism is retained (sensitivity). The procedure operates successfully at a rate of ~0.30 CPU core hours per megabase of sequence and can be applied to any type of genome sequence.
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- 2016
25. Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050T (DSM 19838T) and Gramella portivictoriae UST040801-001T (DSM 23547T), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005
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Panschin, Irina, Huang, Sixing, Meier-Kolthoff, Jan P, Tindall, Brian J, Rohde, Manfred, Verbarg, Susanne, Lapidus, Alla, Han, James, Trong, Stephan, Haynes, Matthew, Reddy, TBK, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N, Mavromatis, Konstantinos, Markowitz, Victor, Woyke, Tanja, Göker, Markus, Klenk, Hans-Peter, Kyrpides, Nikos C, and Hahnke, Richard L
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Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,Life Below Water ,Carbohydrate active enzyme ,Polysaccharide ,Bioethanol ,Gliding motility ,Cellulose ,Marine ,Flavobacteriaceae ,Bacteroidetes ,GEBA ,KMG 1 ,KMG I - Abstract
Strains of the genus Gramella (family Flavobacteriacae, phylum Bacteroidetes) were isolated from marine habitats such as tidal flat sediments, coastal surface seawater and sea urchins. Flavobacteriaceae have been shown to be involved in the decomposition of plant and algal polysaccharides. However, the potential to decompose polysaccharides may differ tremendously even between species of the same genus. Gramella echinicola KMM 6050(T) (DSM 19838(T)) and Gramella portivictoriae UST040801-001(T) (DSM 23547(T)) have genomes of similar lengths, similar numbers of protein coding genes and RNA genes. Both genomes encode for a greater number of peptidases compared to 'G. forsetii'. In contrast to the genome of 'G. forsetii', both genomes comprised a smaller set of CAZymes. Seven polysaccharide utilization loci were identified in the genomes of DSM 19838(T) and DSM 23547(T). Both Gramella strains hydrolyzed starch, galactomannan, arabinoxylan and hydroxyethyl-cellulose, but not pectin, chitosan and cellulose (Avicel). Galactan and xylan were hydrolyzed by strain DSM 19838(T), whereas strain DSM 23547(T) hydrolyzed pachyman and carboxy-methyl cellulose. Conclusively, both Gramella type strains exhibit characteristic physiological, morphological and genomic differences that might be linked to their habitat. Furthermore, the identified enzymes mediating polysaccharide decomposition, are of biotechnological interest.
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- 2016
26. Chap's Grille
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Han, James and Eville, Hardy
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Restaurants ,News, opinion and commentary ,Sports and fitness - Abstract
Byline: James Han and Hardy Eville Chap's Grille is a place you can easily walk by and never walk into. Tucked among a cluster of other restaurants on an unassuming [...]
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- 2023
27. Pho Ketkeo
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Han, James and Eville, Hardy
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News, opinion and commentary ,Sports and fitness - Abstract
Byline: James Han and Hardy Eville After a long night of cooking and drinking more booze than water, Pho Ketkeo--or Pho Temple, according to the sign out front--calls out from [...]
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- 2023
28. Draft Genome Sequence of the Cellulolytic and Xylanolytic Thermophile Clostridium clariflavum Strain 4-2a
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Rooney, Elise A, Rowe, Kenneth T, Guseva, Anna, Huntemann, Marcel, Han, James K, Chen, Amy, Kyrpides, Nikos C, Mavromatis, Konstantinos, Markowitz, Victor M, Palaniappan, Krishna, Ivanova, Natalia, Pati, Amrita, Liolios, Konstantinos, Nordberg, Henrik P, Cantor, Michael N, Hua, Susan X, Shapiro, Nicole, Woyke, Tanja, Lynd, Lee R, and Izquierdo, Javier A
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Microbiology ,Biological Sciences ,Genetics ,Biotechnology ,Biochemistry and Cell Biology - Abstract
Clostridium clariflavum strain 4-2a, a novel strain isolated from a thermophilic biocompost pile, has demonstrated an extensive capability to utilize both cellulose and hemicellulose under thermophilic anaerobic conditions. Here, we report the draft genome of this strain.
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- 2015
29. High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1T (DSM 17521T) isolated from muddy waters of a drainage system in Chandigarh, India
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Mukherjee, Supratim, Lapidus, Alla, Shapiro, Nicole, Cheng, Jan-Fang, Han, James, Reddy, T.B.K., Huntemann, Marcel, Ivanova, Natalia, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Spring, Stefan, Göker, Markus, Woyke, Tanja, Tindall, Brian J., Klenk, Hans-Peter, and Pati, Amrita
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Aerobic ,Gram-negative ,non-motile ,obligate aerobe ,halotolerant ,menaquinone ,GEBA ,KMG-I - Abstract
Pontibacter roseus Suresh et al 2006 is a member of genus Pontibacter family Cytophagaceae, class Cytophagia. While the type species of the genus Pontibacter actiniarum was isolated in 2005 from a marine environment, subsequent species of the same genus have been found in different types of habitats ranging from seawater, sediment, desert soil, rhizosphere, contaminated sites, solar saltern andmuddy water. Here we describe the features of Pontibacter roseus strain SRC-1T along with its complete genome sequence and annotation from a culture of DSM 17521T. The 4,581,480 bp long draft genome consists of 12 scaffolds with 4,003 protein-coding and 50 RNA genes and is a part of Genomic encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project.
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- 2015
30. High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater
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Ramsay, Bradley D, Hwang, Chiachi, Woo, Hannah L, Carroll, Sue L, Lucas, Susan, Han, James, Lapidus, Alla L, Cheng, Jan-Fang, Goodwin, Lynne A, Pitluck, Samuel, Peters, Lin, Chertkov, Olga, Held, Brittany, Detter, John C, Han, Cliff S, Tapia, Roxanne, Land, Miriam L, Hauser, Loren J, Kyrpides, Nikos C, Ivanova, Natalia N, Mikhailova, Natalia, Pagani, Ioanna, Woyke, Tanja, Arkin, Adam P, Dehal, Paramvir, Chivian, Dylan, Criddle, Craig S, Wu, Weimin, Chakraborty, Romy, Hazen, Terry C, and Fields, Matthew W
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Microbiology ,Biological Sciences ,Genetics - Abstract
Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction.
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- 2015
31. Draft genome sequence of Halomonas lutea strain YIM 91125T (DSM 23508T) isolated from the alkaline Lake Ebinur in Northwest China
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Gao, Xiao-Yang, Zhi, Xiao-Yang, Li, Hong-Wei, Zhou, Yu, Lapidus, Alla, Han, James, Haynes, Matthew, Lobos, Elizabeth, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N, Mavromatis, Konstantinos, Tindall, Brian J, Markowitz, Victor, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C, and Li, Wen-Jun
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Microbiology ,Biological Sciences ,Genetics ,Biotechnology ,Human Genome ,Halomonas lutea ,Aerobic ,Gram-negative ,Chemoorganotrophic ,Moderately halophilic ,Lake Ebinur - Abstract
Species of the genus Halomonas are halophilic and their flexible adaption to changes of salinity and temperature brings considerable potential biotechnology applications, such as degradation of organic pollutants and enzyme production. The type strain Halomonas lutea YIM 91125(T) was isolated from a hypersaline lake in China. The genome of strain YIM 91125(T) becomes the twelfth species sequenced in Halomonas, and the thirteenth species sequenced in Halomonadaceae. We described the features of H. lutea YIM 91125(T), together with the high quality draft genome sequence and annotation of its type strain. The 4,533,090 bp long genome of strain YIM 91125(T) with its 4,284 protein-coding and 84 RNA genes is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project. From the viewpoint of comparative genomics, H. lutea has a larger genome size and more specific genes, which indicated acquisition of function bringing better adaption to its environment. DDH analysis demonstrated that H. lutea is a distinctive species, and halophilic features and nitrogen metabolism related genes were discovered in its genome.
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- 2015
32. High quality draft genome sequence of Brachymonas chironomi AIMA4T (DSM 19884T) isolated from a Chironomus sp. egg mass
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Laviad, Sivan, Lapidus, Alla, Han, James, Haynes, Matthew, Reddy, TBK, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N, Mavromatis, Konstantinos, Lang, Elke, Rohde, Manfred, Markowitz, Victor, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C, and Halpern, Malka
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Microbiology ,Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Biotechnology ,Generic health relevance ,Brachymonas chironomi ,Comamonadaceae ,Chironomid ,Chironomus ,Egg mass ,Toxicant - Abstract
Brachymonas chironomi strain AIMA4(T) (Halpern et al., 2009) is a Gram-negative, non-motile, aerobic, chemoorganotroph bacterium. B. chironomi is a member of the Comamonadaceae, a family within the class Betaproteobacteria. This species was isolated from a chironomid (Diptera; Chironomidae) egg mass, sampled from a waste stabilization pond in northern Israel. Phylogenetic analysis based on the 16S rRNA gene sequences placed strain AIMA4(T) in the genus Brachymonas. Here we describe the features of this organism, together with the complete genome sequence and annotation. The DNA GC content is 63.5%. The chromosome length is 2,509,395 bp. It encodes 2,382 proteins and 68 RNA genes. Brachymonas chironomi genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.
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- 2015
33. High quality draft genome sequence of Meganema perideroedes str. Gr1T and a proposal for its reclassification to the family Meganemaceae fam. nov.
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McIlroy, Simon J, Lapidus, Alla, Thomsen, Trine R, Han, James, Haynes, Matthew, Lobos, Elizabeth, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N, Markowitz, Victor, Verbarg, Susanne, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos, and Nielsen, Per H
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Microbiology ,Biological Sciences ,Genetics ,Biotechnology ,Human Genome ,Activated sludge ,Bulking ,Facultative methylotroph ,Filamentous ,Meganema ,Meganemaceae ,Wastewater - Abstract
Meganema perideroedes Gr1(T) is a filamentous bacterium isolated from an activated sludge wastewater treatment plant where it is implicated in poor sludge settleability (bulking). M. perideroedes is the sole described species of the genus Meganema and of the proposed novel family "Meganemaceae". Here we describe the features of the type strain Gr1(T) along with its annotated genome sequence. The 3,409,949 bp long draft genome consists of 22 scaffolds with 3,033 protein-coding and 59 RNA genes and is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes KMG project. Notably, genome annotation indicated the potential for facultative methylotrophy. However, the ability to utilize methanol as a carbon source could not be empirically demonstrated for the type strain or for in situ Meganema spp. strains.
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- 2015
34. High quality draft genome sequence of Flavobacterium rivuli type strain WB 3.3-2T (DSM 21788T), a valuable source of polysaccharide decomposing enzymes
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Hahnke, Richard L, Stackebrandt, Erko, Meier-Kolthoff, Jan P, Tindall, Brian J, Huang, Sixing, Rohde, Manfred, Lapidus, Alla, Han, James, Trong, Stephan, Haynes, Matthew, Reddy, TBK, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N, Mavromatis, Konstantinos, Markowitz, Victor, Woyke, Tanja, Göker, Markus, Kyrpides, Nikos C, and Klenk, Hans-Peter
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Microbiology ,Biological Sciences ,Genetics ,Biotechnology ,Human Genome ,Carbohydrate active enzyme ,Polysaccharide utilization loci ,Gram-negative ,Non-motile ,Aerobic ,Hard water rivulet ,Flavobacteriaceae ,Bacteroidetes ,GEBA-KMG I ,Myroides - Abstract
Flavobacterium rivuli Ali et al. 2009 emend. Dong et al. 2013 is one of about 100 species in the genus Flavobacterium (family Flavobacteriacae, phylum Bacteroidetes) with a validly published name, and has been isolated from the spring of a hard water rivulet in Northern Germany. Including all type strains of the genus Myroides and Flavobacterium into the 16S rRNA gene sequence phylogeny revealed a clustering of members of the genus Myroides as a monophyletic group within the genus Flavobacterium. Furthermore, F. rivuli WB 3.3-2(T) and its next relatives seem more closely related to the genus Myroides than to the type species of the genus Flavobacterium, F. aquatile. The 4,489,248 bp long genome with its 3,391 protein-coding and 65 RNA genes is part of the G enomic E ncyclopedia of B acteria and A rchaea project. The genome of F. rivuli has almost as many genes encoding carbohydrate active enzymes (151 CAZymes) as genes encoding peptidases (177). Peptidases comprised mostly metallo (M) and serine (S) peptidases. Among CAZymes, 30 glycoside hydrolase families, 10 glycosyl transferase families, 7 carbohydrate binding module families and 7 carbohydrate esterase families were identified. Furthermore, we found four polysaccharide utilization loci (PUL) and one large CAZy rich gene cluster that might enable strain WB 3.3-2(T) to decompose plant and algae derived polysaccharides. Based on these results we propose F. rivuli as an interesting candidate for further physiological studies and the role of Bacteroidetes in the decomposition of complex polymers in the environment.
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- 2015
35. Genome sequence of the pink–pigmented marine bacterium Loktanella hongkongensis type strain (UST950701–009PT), a representative of the Roseobacter group
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Lau, Stanley CK, Riedel, Thomas, Fiebig, Anne, Han, James, Huntemann, Marcel, Petersen, Jörn, Ivanova, Natalia N, Markowitz, Victor, Woyke, Tanja, Göker, Markus, Kyrpides, Nikos C, Klenk, Hans-Peter, and Qian, Pei-Yuan
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Microbiology ,Biological Sciences ,Genetics ,Biotechnology ,Human Genome ,Biofilms ,Marine ,Roseobacter group ,Rhodobacteraceae ,Alphaproteobacteria ,Plasmids - Abstract
Loktanella hongkongensis UST950701-009P(T) is a Gram-negative, non-motile and rod-shaped bacterium isolated from a marine biofilm in the subtropical seawater of Hong Kong. When growing as a monospecies biofilm on polystyrene surfaces, this bacterium is able to induce larval settlement and metamorphosis of a ubiquitous polychaete tubeworm Hydroides elegans. The inductive cues are low-molecular weight compounds bound to the exopolymeric matrix of the bacterial cells. In the present study we describe the features of L. hongkongensis strain DSM 17492(T) together with its genome sequence and annotation and novel aspects of its phenotype. The 3,198,444 bp long genome sequence encodes 3104 protein-coding genes and 57 RNA genes. The two unambiguously identified extrachromosomal replicons contain replication modules of the RepB and the Rhodobacteraceae-specific DnaA-like type, respectively.
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- 2015
36. High quality draft genome sequence of Bacteroides barnesiae type strain BL2T (DSM 18169T) from chicken caecum
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Sakamoto, Mitsuo, Lapidus, Alla L, Han, James, Trong, Stephan, Haynes, Matthew, Reddy, TBK, Mikhailova, Natalia, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N, Pukall, Rüdiger, Markowitz, Victor M, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C, and Ohkuma, Moriya
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Microbiology ,Biological Sciences ,Genetics ,Microbiome ,Human Genome ,Biotechnology ,Strictly anaerobic ,Non-motile ,Rod-shaped ,Gram-negative ,Cecum ,Poultry ,Bacteroidaceae - Abstract
Bacteroides barnesiae Lan et al. 2006 is a species of the genus Bacteroides, which belongs to the family Bacteroidaceae. Strain BL2(T) is of interest because it was isolated from the gut of a chicken and the growing awareness that the anaerobic microbiota of the caecum is of benefit for the host and may impact poultry farming. The 3,621,509 bp long genome with its 3,059 protein-coding and 97 RNA genes is a part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.
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- 2015
37. High quality draft genome sequence of Corynebacterium ulceribovis type strain IMMIB-L1395T (DSM 45146T)
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Yassin, Atteyet F, Lapidus, Alla, Han, James, Reddy, TBK, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia, Markowitz, Victor, Woyke, Tanja, Klenk, Hans-Peter, and Kyrpides, Nikos C
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Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,Gram-positive ,Bovine skin ,Corynebacteriaceae ,Actinobacteria ,GEBA - Abstract
Corynebacterium ulceribovis strain IMMIB L-1395(T) (= DSM 45146(T)) is an aerobic to facultative anaerobic, Gram-positive, non-spore-forming, non-motile rod-shaped bacterium that was isolated from the skin of the udder of a cow, in Schleswig Holstein, Germany. The cell wall of C. ulceribovis contains corynemycolic acids. The cellular fatty acids are those described for the genus Corynebacterium, but tuberculostearic acid is not present. Here we describe the features of C. ulceribovis strain IMMIB L-1395(T), together with genome sequence information and its annotation. The 2,300,451 bp long genome containing 2,104 protein-coding genes and 54 RNA-encoding genes and is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.
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- 2015
38. High-quality draft genome sequence of Gracilimonas tropica CL-CB462T (DSM 19535T), isolated from a Synechococcus culture
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Choi, Dong Han, Ahn, Chisang, Jang, Gwang Il, Lapidus, Alla, Han, James, Reddy, TBK, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia, Markowitz, Victor, Rohde, Manfred, Tindall, Brian, Göker, Markus, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C, and Cho, Byung Cheol
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Microbiology ,Biological Sciences ,Genetics ,Biotechnology ,Human Genome ,Life Below Water ,Genome ,Gracilimonas tropica ,Marine ,Sphingobacteriia ,GEBA - Abstract
Gracilimonas tropica Choi et al. 2009 is a member of order Sphingobacteriales, class Sphingobacteriia. Three species of the genus Gracilimonas have been isolated from marine seawater or a salt mine and showed extremely halotolerant and mesophilic features, although close relatives are extremely halophilic or thermophilic. The type strain of the type species of Gracilimonas, G. tropica DSM19535(T), was isolated from a Synechococcus culture which was established from the tropical sea-surface water of the Pacific Ocean. The genome of the strain DSM19535(T) was sequenced through the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes project. Here, we describe the genomic features of the strain. The 3,831,242 bp long draft genome consists of 48 contigs with 3373 protein-coding and 53 RNA genes. The strain seems to adapt to phosphate limitation and requires amino acids from external environment. In addition, genomic analyses and pasteurization experiment suggested that G. tropica DSM19535(T) did not form spore.
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- 2015
39. Genome sequence of the Listia angolensis microsymbiont Microvirga lotononidis strain WSM3557T
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Reeve, Wayne, Ardley, Julie, Tian, Rui, De Meyer, Sofie, Terpolilli, Jason, Melino, Vanessa, Tiwari, Ravi, Yates, Ronald, O’Hara, Graham, Howieson, John, Ninawi, Mohamed, Zhang, Xiaojing, Bruce, David, Detter, Chris, Tapia, Roxanne, Han, Cliff, Wei, Chia-Lin, Huntemann, Marcel, Han, James, Chen, I-Min, Mavromatis, Konstantinos, Markowitz, Victor, Szeto, Ernest, Ivanova, Natalia, Pagani, Ioanna, Pati, Amrita, Goodwin, Lynne, Woyke, Tanja, and Kyrpides, Nikos
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Microbiology ,Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,Biotechnology ,root-nodule bacteria ,nitrogen fixation ,symbiotic specificity ,Alphaproteobacteria ,Biochemistry and Cell Biology - Abstract
Microvirga lotononidis is a recently described species of root-nodule bacteria that is an effective nitrogen- (N2) fixing microsymbiont of the symbiotically specific African legume Listia angolensis (Welw. ex Bak.) B.-E. van Wyk & Boatwr. M. lotononidis possesses several properties that are unusual in root-nodule bacteria, including pigmentation and the ability to grow at temperatures of up to 45°C. Strain WSM3557(T) is an aerobic, motile, Gram-negative, non-spore-forming rod isolated from a L. angolensis root nodule collected in Chipata, Zambia in 1963. This is the first report of a complete genome sequence for the genus Microvirga. Here we describe the features of Microvirga lotononidis strain WSM3557(T), together with genome sequence information and annotation. The 7,082,538 high-quality-draft genome is arranged in 18 scaffolds of 104 contigs, contains 6,956 protein-coding genes and 84 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.
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- 2014
40. High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169T (DSM 21076T) from a sea urchin in southern China
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Zhou, Yu, Li, Rui, Gao, Xiao-Yang, Lapidus, Alla, Han, James, Haynes, Matthew, Lobos, Elizabeth, Huntemann, Marcel, Pati, Amrita, Ivanova, Natalia N, Rohde, Manfred, Mavromatis, Konstantinos, Tindall, Brian J, Markowitz, Victor, Woyke, Tanja, Klenk, Hans-Peter, Kyrpides, Nikos C, and Li, Wen-Jun
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Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,strictly aerobic ,motile Gram-negative ,chemoorganotrophic ,slightly halophilic ,Halomonadaceae ,Biochemistry and Cell Biology - Abstract
Halomonas zhanjiangensis Chen et al. 2009 is a member of the genus Halomonas, family Halomonadaceae, class Gammaproteobacteria. Representatives of the genus Halomonas are a group of halophilic bacteria often isolated from salty environments. The type strain H. zhanjiangensis JSM 078169(T) was isolated from a sea urchin (Hemicentrotus pulcherrimus) collected from the South China Sea. The genome of strain JSM 078169(T) is the fourteenth sequenced genome in the genus Halomonas and the fifteenth in the family Halomonadaceae. The other thirteen genomes from the genus Halomonas are H. halocynthiae, H. venusta, H. alkaliphila, H. lutea, H. anticariensis, H. jeotgali, H. titanicae, H. desiderata, H. smyrnensis, H. salifodinae, H. boliviensis, H. elongata and H stevensii. Here, we describe the features of strain JSM 078169(T), together with the complete genome sequence and annotation from a culture of DSM 21076(T). The 4,060,520 bp long draft genome consists of 17 scaffolds with the 3,659 protein-coding and 80 RNA genes and is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.
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- 2014
41. High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6T), a diphenol degrader with genes involved in the catechol pathway
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Ntougias, Spyridon, Lapidus, Alla, Han, James, Mavromatis, Konstantinos, Pati, Amrita, Chen, Amy, Klenk, Hans-Peter, Woyke, Tanja, Fasseas, Constantinos, Kyrpides, Nikos C, and Zervakis, Georgios I
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Microbiology ,Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Biotechnology ,Human Genome ,alkaline two-phase olive mill waste ,Bacteroidetes ,Sphingobacteriaceae ,hemicellulose degradation ,beta-1 ,4-xylanase ,beta-1 ,4-xylosidase ,β-1 ,4-xylanase ,β-1 ,4-xylosidase ,Biochemistry and Cell Biology - Abstract
Olivibacter sitiensis Ntougias et al. 2007 is a member of the family Sphingobacteriaceae, phylum Bacteroidetes. Members of the genus Olivibacter are phylogenetically diverse and of significant interest. They occur in diverse habitats, such as rhizosphere and contaminated soils, viscous wastes, composts, biofilter clean-up facilities on contaminated sites and cave environments, and they are involved in the degradation of complex and toxic compounds. Here we describe the features of O. sitiensis AW-6(T), together with the permanent-draft genome sequence and annotation. The organism was sequenced under the Genomic Encyclopedia for Bacteria and Archaea (GEBA) project at the DOE Joint Genome Institute and is the first genome sequence of a species within the genus Olivibacter. The genome is 5,053,571 bp long and is comprised of 110 scaffolds with an average GC content of 44.61%. Of the 4,565 genes predicted, 4,501 were protein-coding genes and 64 were RNA genes. Most protein-coding genes (68.52%) were assigned to a putative function. The identification of 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase-coding genes indicates involvement of this organism in the catechol catabolic pathway. In addition, genes encoding for β-1,4-xylanases and β-1,4-xylosidases reveal the xylanolytic action of O. sitiensis.
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- 2014
42. Genome sequence of the Wenxinia marina type strain (DSM 24838T), a representative of the Roseobacter group isolated from oilfield sediments
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Riedel, Thomas, Fiebig, Anne, Han, James, Huntemann, Marcel, Spring, Stefan, Petersen, Jörn, Ivanova, Natalia N, Markowitz, Victor, Woyke, Tanja, Göker, Markus, Kyrpides, Nikos C, and Klenk, Hans-Peter
- Subjects
Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,aerobic ,heterotrophic ,rod-shaped ,quorum sensing ,autoinducer ,prophage-like structures ,Roseobacter group ,Rhodobacteraceae ,Alphaproteobacteria ,Biochemistry and Cell Biology - Abstract
Wenxinia marina Ying et al. 2007 is the type species of the genus Wenxinia, a representative of the Roseobacter group within the alphaproteobacterial family Rhodobacteraceae, isolated from oilfield sediments of the South China Sea. This family was shown to harbor the most abundant bacteria especially from coastal and polar waters, but was also found in microbial mats, sediments and attached to different kind of surfaces. Here we describe the features of W. marina strain HY34(T) together with the genome sequence and annotation of strain DSM 24838(T) and novel aspects of its phenotype. The 4,181,754 bp containing genome sequence encodes 4,047 protein-coding genes and 59 RNA genes. The genome of W. marina DSM 24838(T) was sequenced as part of the activities of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project funded by the DoE and the Transregional Collaborative Research Centre 51 (TRR51) funded by the German Research Foundation (DFG).
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- 2014
43. Genome sequence of Burkholderia mimosarum strain LMG 23256T, a Mimosa pigra microsymbiont from Anso, Taiwan
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Willems, Anne, Tian, Rui, Bräu, Lambert, Goodwin, Lynne, Han, James, Liolios, Konstantinos, Huntemann, Marcel, Pati, Amrita, Woyke, Tanja, Mavrommatis, Konstantinos, Markowitz, Victor, Ivanova, Natalia, Kyrpides, Nikos, and Reeve, Wayne
- Subjects
Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,root-nodule bacteria ,nitrogen fixation ,rhizobia ,Betaproteobacteria ,Biochemistry and Cell Biology - Abstract
Burkholderia mimosarum strain LMG 23256(T) is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Mimosa pigra (giant sensitive plant). LMG 23256(T) was isolated from a nodule recovered from the roots of the M. pigra growing in Anso, Taiwan. LMG 23256(T) is highly effective at fixing nitrogen with M. pigra. Here we describe the features of B. mimosarum strain LMG 23256(T), together with genome sequence information and its annotation. The 8,410,967 bp high-quality-draft genome is arranged into 268 scaffolds of 270 contigs containing 7,800 protein-coding genes and 85 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
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- 2014
44. Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2232 from Karijini National Park, Australia
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Walker, Robert, Watkin, Elizabeth, Tian, Rui, Bräu, Lambert, O’Hara, Graham, Goodwin, Lynne, Han, James, Reddy, Tatiparthi, Huntemann, Marcel, Pati, Amrita, Woyke, Tanja, Mavromatis, Konstantinos, Markowitz, Victor, Ivanova, Natalia, Kyrpides, Nikos, and Reeve, Wayne
- Subjects
Microbiology ,Biological Sciences ,Genetics ,Biotechnology ,Human Genome ,root-nodule bacteria ,nitrogen fixation ,rhizobia ,Betaproteobacteria ,Biochemistry and Cell Biology - Abstract
Burkholderia sp. strain WSM2232 is an aerobic, motile, Gram-negative, non-spore-forming acid-tolerant rod that was trapped in 2001 from acidic soil collected from Karijini National Park (Australia) using Gastrolobium capitatum as a host. WSM2232 was effective in nitrogen fixation with G. capitatum but subsequently lost symbiotic competence during long-term storage. Here we describe the features of Burkholderia sp. strain WSM2232, together with genome sequence information and its annotation. The 7,208,311 bp standard-draft genome is arranged into 72 scaffolds of 72 contigs containing 6,322 protein-coding genes and 61 RNA-only encoding genes. The loss of symbiotic capability can now be attributed to the loss of nodulation and nitrogen fixation genes from the genome. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
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- 2014
45. Genome sequence of the Medicago-nodulating Ensifer meliloti commercial inoculant strain RRI128
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Reeve, Wayne, Ballard, Ross, Drew, Elizabeth, Tian, Rui, Bräu, Lambert, Goodwin, Lynne, Huntemann, Marcel, Han, James, Tatiparthi, Reddy, Chen, Amy, Mavrommatis, Konstantinos, Markowitz, Victor, Palaniappan, Krishna, Ivanova, Natalia, Pati, Amrita, Woyke, Tanja, and Kyrpides, Nikos
- Subjects
Microbiology ,Biological Sciences ,Genetics ,Human Genome ,Biotechnology ,root-nodule bacteria ,nitrogen fixation ,rhizobia ,Alphaproteobacteria ,Biochemistry and Cell Biology - Abstract
Ensifer meliloti strain RRI128 is an aerobic, motile, Gram-negative, non-spore-forming rod. RRI128 was isolated from a nodule recovered from the roots of barrel medic (Medicago truncatula) grown in the greenhouse and inoculated with soil collected from Victoria, Australia. The strain is used in commercial inoculants in Australia. RRI128 nodulates and forms an effective symbiosis with a diverse range of lucerne cultivars (Medicago sativa) and several species of annual medic (M. truncatula, Medicago littoralis and Medicago tornata), but forms an ineffective symbiosis with Medicago polymorpha. Here we describe the features of E. meliloti strain RRI128, together with genome sequence information and annotation. The 6,900,273 bp draft genome is arranged into 156 scaffolds of 157 contigs, contains 6,683 protein-coding genes and 87 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
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- 2014
46. The complete genome sequence of Clostridium indolis DSM 755T
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Biddle, Amy S, Leschine, Susan, Huntemann, Marcel, Han, James, Chen, Amy, Kyrpides, Nikos, Markowitz, Victor, Palaniappan, Krishna, Ivanova, Natalia, Mikhailova, Natalia, Ovchinnikova, Galina, Schaumberg, Andrew, Pati, Amrita, Stamatis, Dimitrios, Reddy, Tatiparthi, Lobos, Elizabeth, Goodwin, Lynne, Nordberg, Henrik P, Cantor, Michael N, Hua, Susan X, Woyke, Tanja, and Blanchard, Jeffrey L
- Subjects
Microbiology ,Biological Sciences ,Ecology ,Genetics ,Human Genome ,2.2 Factors relating to the physical environment ,Infection ,Clostridium indolis ,citrate ,lactate ,aromatic degradation ,nitrogen fixation ,bacterial microcompartments ,Biochemistry and Cell Biology - Abstract
Clostridium indolis DSM 755(T) is a bacterium commonly found in soils and the feces of birds and mammals. Despite its prevalence, little is known about the ecology or physiology of this species. However, close relatives, C. saccharolyticum and C. hathewayi, have demonstrated interesting metabolic potentials related to plant degradation and human health. The genome of C. indolis DSM 755(T) reveals an abundance of genes in functional groups associated with the transport and utilization of carbohydrates, as well as citrate, lactate, and aromatics. Ecologically relevant gene clusters related to nitrogen fixation and a unique type of bacterial microcompartment, the CoAT BMC, are also detected. Our genome analysis suggests hypotheses to be tested in future culture based work to better understand the physiology of this poorly described species.
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- 2014
47. Genome sequence of Microvirga lupini strain LUT6T, a novel Lupinus alphaproteobacterial microsymbiont from Texas
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Reeve, Wayne, Parker, Matthew, Tian, Rui, Goodwin, Lynne, Teshima, Hazuki, Tapia, Roxanne, Han, Cliff, Han, James, Liolios, Konstantinos, Huntemann, Marcel, Pati, Amrita, Woyke, Tanja, Mavromatis, Konstantinos, Markowitz, Victor, Ivanova, Natalia, and Kyrpides, Nikos
- Subjects
Microbiology ,Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Human Genome ,root-nodule bacteria ,nitrogen fixation ,rhizobia ,Alphaproteobacteria ,Biochemistry and Cell Biology - Abstract
Microvirga lupini LUT6(T) is an aerobic, non-motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Lupinus texensis. LUT6(T) was isolated in 2006 from a nodule recovered from the roots of the annual L. texensis growing in Travis Co., Texas. LUT6(T) forms a highly specific nitrogen-fixing symbiosis with endemic L. texensis and no other Lupinus species can form an effective nitrogen-fixing symbiosis with this isolate. Here we describe the features of M. lupini LUT6(T), together with genome sequence information and its annotation. The 9,633,614 bp improved high quality draft genome is arranged into 160 scaffolds of 1,366 contigs containing 10,864 protein-coding genes and 87 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of a DOE Joint Genome Institute 2010 Community Sequencing Project.
- Published
- 2014
48. Metastatic Testicular Embryonal Carcinoma Presenting as Gastrointestinal Hemorrhage
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Park, Nathan, Han, James, Shah, Sagar, Chahine, Anastasia, and Samarasena, Jason
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- 2021
- Full Text
- View/download PDF
49. Single Cell Genomics and Transcriptomics for Unicellular Eukaryotes
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Ciobanu, Doina, Clum, Alicia, Singh, Vasanth, Salamov, Asaf, Han, James, Copeland, Alex, Grigoriev, Igor, James, Timothy, Singer, Steven, Woyke, Tanja, Malmstrom, Rex, and Cheng, Jan-Fang
- Abstract
Despite their small size, unicellular eukaryotes have complex genomes with a high degree of plasticity that allow them to adapt quickly to environmental changes. Unicellular eukaryotes live with prokaryotes and higher eukaryotes, frequently in symbiotic or parasitic niches. To this day their contribution to the dynamics of the environmental communities remains to be understood. Unfortunately, the vast majority of eukaryotic microorganisms are either uncultured or unculturable, making genome sequencing impossible using traditional approaches. We have developed an approach to isolate unicellular eukaryotes of interest from environmental samples, and to sequence and analyze their genomes and transcriptomes. We have tested our methods with six species: an uncharacterized protist from cellulose-enriched compost identified as Platyophrya, a close relative of P. vorax; the fungus Metschnikowia bicuspidate, a parasite of water flea Daphnia; the mycoparasitic fungi Piptocephalis cylindrospora, a parasite of Cokeromyces and Mucor; Caulochytrium protosteloides, a parasite of Sordaria; Rozella allomycis, a parasite of the water mold Allomyces; and the microalgae Chlamydomonas reinhardtii. Here, we present the four components of our approach: pre-sequencing methods, sequence analysis for single cell genome assembly, sequence analysis of single cell transcriptomes, and genome annotation. This technology has the potential to uncover the complexity of single cell eukaryotes and their role in the environmental samples.
- Published
- 2014
50. Complete genome sequence of Micromonospora L.5, a potential plant-growth regulating actinomycete, originally isolated from Casuarina equisetifolia root nodules
- Author
-
Hirsch, Ann M., Alvarado, Johana, Bruce, David, Chertkov, Olga, Hoff, Peter L. De, Detter, Chris, Fujishige, Nancy A., Goodwin, Lynne, Han, James, Han, Shunsheng, Ivanova, Natalia, Land, Miriam L., Lum, Michelle R., Martinez, Claudia, Milani-Nejad, Nima, Nolan, Matt, Pati, Amrita, Pitluck, Sam, Woyke, Tanja, and Valdes, Maria
- Subjects
Micromonospora L5 ,actinomycete ,Casuarina Equisetifolia root nodules ,Illumina GAii - Published
- 2014
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