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Addressing the Role of microRNAs in Reprogramming Leaf Growth during Drought Stress in Brachypodium distachyon

Molecular plant 2013年第2期6卷 423-443页

作者： Edoardo Bertolini Wim Verelst david Stephen Horner Luca Gianfranceschi Viviana piccolo Dirk Iné Mario Enrico pè Erica Mica Institute of Life Sciences Scuola Superiore Sant'Anna Piazza Martiri della Libertà 33 56127 Pisa Italy Department of plant Biotechnology and Bioinformatics Ghent University Technologiepark 927 9052 Ghent Belgium Department of plant Systems Biology VIB Technologiepark 927 9052 Gtlent. Belgium Department of BioSciences University of Milan via Celoria 26 20133 Milan Italy

plant responses to drought are regulated by complex genetic and epigenetic networks leading to rapid reprogramming of plant growth, miRNAs have been widely indicated as key players in the regulation of growth and development. The role of miRNAs in drought response was investigated in young leaves of Brachypodium dis- tachyon, a drought-tolerant monocot model species. Adopting an in vivo drought assay, shown to cause a dramatic reduction in leaf size, mostly due to reduced cell expansion, small RNA libraries were produced from proliferating and expanding leaf cells. Next-generation sequencing data were analyzed using an in-house bioinformatics pipeline allowing the identification of 66 annotated miRNA genes and 122 new high confidence predictions greatly expand- ing the number of known Brachypodium miRNAs. In addition, we identified four TAS3 loci and a large number of siRNA-producing loci that show characteristics suggesting that they may represent young miRNA genes. Most miR- NAs showed a high expression level, consistent with their involvement in early leaf development and cell identity. proliferating and expanding leaf cells respond differently to drought treatment and differential expression analyses suggest novel evidence for an miRNA regulatory network controlling cell division in both normal and stressed condi-tions and demonstrate that drought trigger a genetic reprogramming of leaf growth in which miRNAs are deeply involved.

关键词： miRNAs drought Brachypodium leaf development.

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Accommodating the bacterial decoding release factor as an alien protein among the RNAs at the active site of the ribosome

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Cell Research 2007年第7期17卷 591-607页

作者： Elizabeth S poole david J Young Marjan E Askarian-Amiri Debbie-Jane G Scarlett Warren p Tate Department of Biochemistry University of OtagoP.O.Box 56 DunedinNew Zealand

The decoding release factor (RF) triggers termination of protein synthesis by functionally mimicking a tRNA to spanthe decoding centre and the peptidyl transferase centre (pTC) of the ribosome. Structurally, it must fit into a site craftedfor a tRNA and surrounded by five other RNAs, namely the adjacent peptidyl tRNA carrying the completed polypeptide,the mRNA and the three rRNAs. This is achieved by extending a structural domain from the body of the protein thatresults in a critical conformational change allowing it to contact the pTC. A structural model of the bacterial terminationcomplex with the accommodated RF shows that it makes close contact with the first, second and third bases of the stopcodon in the mRNA with two separate loops of structure: the anticodon loop and the loop at the tip of helix α5. Theanticodon loop also makes contact with the base following the stop codon that is known to strongly influence termina-tion efficiency. It confirms the close contact of domain 3 of the protein with the key RNA structures of the pTC. ThemRNA signal for termination includes sequences upstream as well as downstream of the stop codon, and this may reflectstructural restrictions for specific combinations of tRNA and RF to be bound onto the ribosome together. An unbiasedSELEX approach has been investigated as a tool to identify potential rRNA-binding contacts of the bacterial RF in itsdifferent binding conformations within the active centre of the ribosome.

关键词： release factor protein synthesis termination tRNA functional mimicry molecular mimicry SELEX ribosome

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Effect of supplementation with n-3 polyunsaturated fatty acids and/or β-glucans on performance, feeding behaviour and immune status of Holstein Friesian bull calves during the pre-and post-weaning periods

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Journal of Animal Science and Biotechnology 2019年第2期10卷 475-490页

作者： Ruairi p.McDonnell John V.O’Doherty Bernadette Earley Anne Marie Clarke david A.Kenny School of Agriculture Food Science and Veterinary MedicineUniversity College DublinBelfieldDublin 4Ireland Teagasc Animal and Bioscience Research Department Animal and Grassland Research and Innovation Centre(AGRIC)GrangeDunsanyCo.MeathIreland present address:GippsDairy 71 Korumburra-Warragul RoadWarragulVIC 3820Australia.

Background: previous research in both calves and other species has suggested n-3 polyunsaturated fatty acids(pUFA) and β-glucans may have positive effects on immune function. This experiment measured performance,behaviour, metabolite and immunological responses to pre-weaning supplementation of dairy bull calves with n-3 pUFA in the form of fish oil and β-glucans derived from seaweed extract. 44 Holstein Friesian bull calves, aged 13.7± 2.5 d and weighing 48.0 ± 5.8 kg were artificially reared using an electronic feeding system. Each calf was offered5 L(120 g/L) per day of milk replacer(MR) and assigned to one of four treatments included in the MR,(1) Control(CON);(2) 40 g n-3 pUFA per day(FO);(3) 1 g β-glucans per day(GL) and(4) 40 g n-3 pUFA per day & 1 g/d β-glucans(FOGL) in a 2 × 2 factorial design. Milk replacer and concentrate was offered from d 0–62(pre-weaning),while concentrate provision continued for a further 31 d post-weaning period. Individual daily feed intake and feeding behaviour was recorded throughout, while bodyweight and blood analyte data were collected at regular ***: Overall mean concentrate DMI from d 0–93 was 1.39, 1.27, 1.00 and 0.72 kg/d for CON, FO, GL and FOGL calves, respectively(SEM = 0.037;p pplemented with GL were significantly lighter(p pasture(d 93) than un-supplemented calves, with a similar effect(p pared to un-supplemented contemporaries. Supplementation with GL reduced the number of unrewarded visits where milk was not consumed(p pplementation with FO increased mean drinking speed(p pplementation with GL resulted in greater concentrations of haptoglobin(p = 0.034), greater serum osmolality(p = 0.021) and lower lymphocyte levels(p = 0.027). In addition,cells from GL supplemented calves exhibited a lower response than un-supplemented contemporaries to both phytohaemagglutinin

关键词： Fish oil Fucoidan Immune function Laminarin preweaning Seaweed

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Machine learning property prediction for organic photovoltaic devices

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npj Computational Materials 2020年第1期6卷 279-286页

作者： Nastaran Meftahi Mykhailo Klymenko Andrew J.Christofferson Udo Bach david A.Winkler Salvy p.Russo ARC Centre of Excellence in Exciton Science School of ScienceRMIT UniversityMelbourneVIC 3001Australia School of Science College of ScienceEngineering and HealthRMIT UniversityMelbourneVIC 3001Australia ARC Centre of Excellence in Exciton Science Department of Chemical EngineeringMonash UniversityWellington RoadClaytonVIC 3800Australia La Trobe Institute for Molecular Science La Trobe UniversityKingsbury DriveBundooraVIC 3086Australia Monash Institute of pharmaceutical Sciences Monash UniversityParkvilleVIC 3052Australia School of pharmacy University of NottinghamNottingham NG72QLUK CSIRO Data61 PullenvaleQLD 4069Australia

Organic photovoltaic(OpV)materials are promising candidates for cheap,printable solar ***,there are a very large number of potential donors and acceptors,making selection of the best materials ***,we show that machine-learning approaches can leverage computationally expensive DFT calculations to estimate important OpV materials properties quickly and *** generate quantitative relationships between simple and interpretable chemical signature and one-hot descriptors and OpV power conversion efficiency(pCE),open circuit potential(Voc),short circuit density(Jsc),highest occupied molecular orbital(HOMO)energy,lowest unoccupied molecular orbital(LUMO)energy,and the HOMO–LUMO *** most robust and predictive models could predict pCE(computed by DFT)with a standard error of±0.5 for percentage pCE for both the training and test *** model is useful for pre-screening potential donor and acceptor materials for OpV applications,accelerating design of these devices for green energy applications.

关键词： occupied property prediction

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STAT3 mediates C6-ceramide-induced cell death in chronic lymphocytic leukemia

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Signal Transduction and Targeted Therapy 2017年第1期2卷 61-72页

作者： Ushma A Doshi Jeremy Shaw Todd E Fox david F Claxton Thomas p Loughran Mark Kester Department of pharmacology Penn State College of MedicineHersheyPAUSA Department of Experimental pathology University of Virginia School of MedicineCharlottesvilleVAUSA Department of pharmacology University of Virginia School of MedicineCharlottesvilleVAUSA Division of Hematology and Oncology Penn State Milton S Hershey Medical Center and College of MedicineHersheyPAUSA Department of Medicine University of Virginia School of MedicineCharlottesvilleVAUSA NanoSTAR Institute University of VirginiaCharlottesvilleVAUSA

The pathogenesis of chronic lymphocytic leukemia(CLL)is poorly understood and it remains incurable with current *** have previously shown that nanoliposomal C6-ceramide(CNL)is an effective therapy in an in vivo murine model of ***,the key signaling pathways mediating CNL-induced cell death in CLL remains *** hypothesized that CNL targets STAT3,a critical regulator of hematopoietic *** observed that CNL treatment reduced phosphorylated STAT3 at both Y705 and S727 residues in CLL cell lines and patient ***,in turn,reduced STAT3 transcriptional activity and expression of critical STAT3-dependent survival factors like Mcl-1 and *** effect of CNL on STAT3 was further confirmed ex vivo as shown by reduced STAT3 phosphorylation in xenograft tumors obtained from mice treated with *** suppressed STAT3 phosphorylation at Y705 and S727 through reduction in BTK activity and MEK1/2 kinase/pKC activities,***,a synergistic reduction in CLL cell viability was observed on co-treatment with CNL and the BTK inhibitor,*** of an oncogenic form of STAT3 conferred partial resistance to CNL,providing confirmation that STAT3 mediates CNL-induced cell *** together,these findings provide the first body of evidence demonstrating ceramide regulation of STAT3 *** results are also the first to demonstrate an effect of ceramide on BTK,a critical kinase mediating the B-cell receptor signaling in CLL cells and suggest a novel and synergistic combination of CNL and BTK inhibitors for CLL treatment.

关键词： STAT3 lymphocytic media

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Up-regulation of mitochondrial chaperone TRAp1 in ulcerative colitis associated colorectal cancer

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World Journal of Gastroenterology 2014年第45期20卷 17037-17048页

作者： Ru Chen Sheng pan Keith Lai Lisa A Lai david A Crispin Mary p Bronner Teresa A Brentnall Department of Medicine University of Washington Department of Anatomic pathology Cleveland Clinic Foundation Division of Anatomic pathology University of Utah

AIM: To characterize tumor necrosis factor receptor-associated protein 1 (TRAp1) expression in the progression of ulcerative colitis (UC)-associated colorectal cancer.

关键词： Ulcerative colitis Colorectal cancer Inflammation Oxidative stress Tumor necrosis factor receptor-associated protein 1

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Cholera outbreak caused by drinking lake water contaminated with human faeces in Kaiso Village,Hoima District,Western Uganda,October 2015

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Infectious Diseases of poverty 2017年第1期6卷 1294-1300页

作者： david W.Oguttu A.Okullo G.Bwire p.Nsubuga A.R.Ario Uganda public Health Fellowship program-Field Epidemiology Track P.O.Box 7272KampalaUganda Ministry of Health KampalaUganda African Field Epidemiology Network KampalaUganda

Background:On 12 October 2015,a cholera outbreak involving 65 cases and two deaths was reported in a fishing village in Hoima District,Western *** initial response by the local health department,the outbreak *** conducted an investigation to identify the source and mode of transmission,and recommend evidenceled interventions to control and prevent cholera outbreaks in this ***:We defined a suspected case as the onset of acute watery diarrhoea from 1 October to 2 November 2015 in a resident of Kaiso Village.A confirmed case was a suspected case who had Vibrio cholerae isolated from *** found cases by record review and active community case *** performed descriptive epidemiologic analysis for hypothesis *** an unmatched case-control study,we compared exposure histories of 61 cases and 126 controls randomly selected among asymptomatic village *** also conducted an environmental assessment and obtained meteorological data from a weather ***:We identified 122 suspected cases,of which six were culture-confirmed,47 were confirmed positive with a rapid diagnostic test and two *** two deceased cases had onset of the disease on 2 October and 10 October,*** rainfall occurred on 7-11 October;a point-source outbreak occurred on 12-15 October,followed by continuous community transmission for two *** residents usually collected drinking water from three lakeshore points-A,B and C:9.8%(6/61)of case-persons and 31%(39/126)of control-persons were found to usually use point A,21%(13/61)of case-persons and 37%(46/126)of control-persons were found to usually use point B(OR=1.8,95%CI:0.64-5.3),and 69%(42/61)of case-persons and 33%(41/126)of control-persons were found to usually use point C(OR=6.7;95%CI:2.5-17)for water *** case-persons(61/61)and 93%(117/126)of control-persons reportedly never treated/boiled drinking water(OR=∞,95%CIFisher:1.0-∞).The village’s piped water syste

关键词： Cholera Outbreak Faeces Lake water Uganda

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Training data selection for accuracy and transferability of interatomic potentials

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npj Computational Materials 2022年第1期8卷 1795-1803页

作者： david Montes de Oca Zapiain Mitchell A.Wood Nicholas Lubbers Carlos Zp.ereyra Aidan p.Thompson Danny perez Sandia National Laboratories AlbuquerqueNM87185USA Computer Computationaland Statistical Sciences DivisionLos Alamos National LaboratoryLos AlamosNM87545USA Mechanical and Aerospace Engineering University of California DavisDavisCA95616USA Theoretical Division Los Alamos National LaboratoryLos AlamosNM87545USA

Advances in machine learning(ML)have enabled the development of interatomic potentials that promise the accuracy of first principles methods and the low-cost,parallel efficiency of empirical ***,ML-based potentials struggle to achieve transferability,i.e.,provide consistent accuracy across configurations that differ from those used during *** order to realize the promise of ML-based potentials,systematic and scalable approaches to generate diverse training sets need to be *** work creates a diverse training set for tungsten in an automated manner using an entropy optimization ***,multiple polynomial and neural network potentials are trained on the entropy-optimized dataset.A corresponding set of potentials are trained on an expert-curated dataset for tungsten for *** models trained to the entropy-optimized data exhibited superior transferability compared to the expert-curated ***,the models trained to the expert-curated set exhibited a significant decrease in performance when evaluated on out-of-sample configurations.

关键词： entropy transfer configuration

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Hepatic abscess associated with Salmonella serotype B in a chronic alcoholic patient

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Hepatobiliary & pancreatic Diseases International 2013年第4期12卷 440-442页

作者： Sidhartha S Tulachan Charles E Wilkins Anthony F Cutrona david Gemmel Thomas p Marnejon Department of Internal Medicine St Elizabeth Health Center1044 Belmont AvenueYoungstown OH 44501 USA Department of Infectious Disease St Elizabeth Health Center1044 Belmont AvenueYoungstown OH 44501 USA Department of Research St Elizabeth Health Center1044 Belmont AvenueYoungstown OH 44501 USA

BACKGROUND: Hepatic abscess secondary to Salmonella is extremely rare in the United States and other Western countries. METHODS: A 43-year-old Caucasian man, with a history of chronic alcohol abuse, was admitted to the hospital for intermittent abdominal pain, fever and diarrhea. Clinical radiological and laboratory results were analyzed. Medical literature in pubMed pertaining to similar cases was reviewed. RESULTS: Stool culture was positive for Salmonella serotype B and a CT scan of the abdomen with contrast was consistent with a solitary hepatic abscess. Appropriate intravenous antibiotics followed by oral maintenance therapy for six weeks resulted in a complete clinical recovery and radiographic resolution. CONCLUSIONS: The cause of Salmonella hepatic abscess in our patient was most likely associated with decreased mucosal resistance to the bacteria, seeding of infection via transient portal bacteremia and loss of host immunity. Our case highlights the fact that appropriate antibiotic alone is sufficient in the management of a solitary hepatic abscess less than 3-5 cm.

关键词： hepatic abscess Salmonella alcoholic hypochlorhydria antibiotics

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Synchronous colorectal liver metastases:therapeutic considerations

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Hepatobiliary Surgery and Nutrition 2021年第5期10卷 711-713页

作者： Michael R.Driedger Sean p.Cleary david M.Nagorney Division of Hepatobiliary and pancreatic Surgery Atrium HealthCharlotteNCUSA Division of Hepatobiliary and pancreatic Surgery Mayo ClinicRochesterMNUSA

More than 50%of patients will develop colorectal cancer(CRC)liver metastases(CRCLM)during the course of their disease,while 15-25%of patients will have metastatic disease present at the time of initial *** of CRCLM is possible in approximately one-in-four patients and 5-year overall survival(OS)rates have improved to nearly 60%in selected patients who undergo resection.

关键词： colorectal metastases patients

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