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Hands-on Workshops as An efective Means of Learning Advanced Technologies Including Genomics,Proteomics and Bioinformatics

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Genomics, Proteomics & Bioinformatics 2013年第6期11卷 368-377页

作者： Nichole Reisdorph Robert Stearman Katerina Kechris Tzu Lip Phang Richard Reisdorph jessica prenni David J.erle Christopher Coldren Kevin Schey Alexey Nesvizhskii Mark Geraci Department of Immunology National Jewish Health Department of Medicine Division of Pulmonary Sciences and Critical Care MedicineUniversity of Colorado School of Medicine Department of Biostatistics and Informatics Colorado School of Public Health Department of Pediatrics National Jewish Health Department of Biochemistry and Molecular Biology Proteomics and Metabolomics FacilityColorado State University Lung Biology Center Department of MedicineUniversity of California Bioinformatics PathgroupNashvilleTN 37027 USA Department of Biochemistry and Mass Spectrometry Research Center Vanderbilt School of Medicine Department of Pathology University of Michigan Medical School

Genomics and proteomics have emerged as key technologies in biomedical research, resulting in a surge of interest in training by investigators keen to incorporate these technologies into their research. At least two types of training can be envisioned in order to produce meaningful results, quality publications and successful grant applications：（1） immediate short-term training workshops and （2） long-term graduate education or visiting scientist programs. We aimed to fill the former need by providing a comprehensive hands-on training course in genomics, proteomics and informatics in a coherent, experimentally-based framework. This was accomplished through a National Heart, Lung, and Blood Institute （NHLBI）-sponsored 10-day Genomics and Proteomics Hands-on Workshop held at National Jewish Health （NJH） and the University of Colorado School of Medicine （UCD）. The course content included comprehensive lectures and laboratories in mass spectrometry and genomics technologies, extensive hands-on experience with instrumentation and software, video demonstrations, optional workshops, online sessions, invited keynote speakers, and local and national guest faculty. Here we describe the detailed curriculum and present the results of short- and long-term evaluations from course attendees. Our educational program consis- tently received positive reviews from participants and had a substantial impact on grant writing and review, manuscript submissions and publications.

关键词： Proteomics Mass spectrometry Genomics Bioinformatics Hands-on Workshops

How Sugars Might Coordinate Chloroplast and Nuclear Gene expression during Acclimation to High Light Intensities

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Molecular Plant 2014年第7期7卷 1121-1137页

作者： Rainer e. Haiusler Luisa Heinrichs jessica Schmitz Ulf-Ingo Flugge Department of Botany II Cologne Biocenter University of Cologne ZuIpicherstr. 47b 50674 Cologne Germany Present address: Plant Molecular Physiology and Biotechnology Heinrich-Heine-University Universitatsstrasse 1 40225 D~sseldorfGermany

The concept of retrograde control of nuclear gene expression assumes the generation of signals inside the chloroplasts, which are either released from or sensed inside of the organelle. In both cases, downstream signaling path- ways lead eventually to a differential regulation of nuclear gene expression and the production of proteins required in the chloroplast. This concept appears reasonable as the majority of the over 3000 predicted plastidial proteins are encoded by nuclear genes. Hence, the nucleus needs information on the status of the chloroplasts, such as during acclimation responses, which trigger massive changes in the protein composition of the thylakoid membrane and in the stroma. Here, we propose an additional control mechanism of nuclear- and plastome-encoded photosynthesis genes, taking advantage of pathways involved in sugar- or hormonal signaling. Sugars are major end products of photosynthesis and their con- tents respond very sensitively to changes in light intensities. Based on recent findings, we ask the question as to whether the carbohydrate status outside the chloroplast can be directly sensed within the chloroplast stroma. Sugars might syn- chronize the responsiveness of both genomes and thereby help to coordinate the expression of piastome- and nuclear- encoded photosynthesis genes in concert with other, more specific retrograde signals.

关键词： acclimation--physiological assimilate allocation/partitioning carbohydrate metabolism molecular physiology membrane proteins Arabidopsis.

DNA recovery and analysis from skeletal material in modern forensic contexts

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Forensic Sciences Research 2019年第1期4卷 51-59页

作者： Krista e.Latham jessica J.Miller Biology Department Human Identification CenterUniversity of IndianapolisIndianapolisINUSA

The generation of a DNA profile from skeletal remains is an important part of the identifica-tion process in both mass disaster and unidentified person cases. Since bones and teeth are often the only biological materials remaining after exposure to environmental conditions, intense heat, certain traumatic events and in cases where a significant amount of time has passed since the death of the individual, the ability to purify large quantities of informative DNA from these hard tissues would be beneficial. Since sampling the hard tissues for gen-etic analysis is a destructive process, it is important to understand those environmental and intrinsic factors that contribute to DNA preservation. This will serve as a brief introduction to these topics, since skeletal sampling strategies and molecular taphonomy have been dis-cussed in depth elsewhere. Additionally advances in skeletal DNA extraction and analysis will be discussed. Currently there is great variation in the DNA isolation methods used by laboratories to purify DNA from the hard tissues;however, a standardized set of short tan-dem repeat (STR) loci is analyzed by many US laboratories to allow for comparisons across samples and jurisdictions. Recent advances have allowed for the generation of DNA profiles from smaller quantities of template DNA and have expanded the number of loci analyzed for greater discriminatory power and predictions regarding the geographic ancestry and phenotype of the individual. Finally, utilizing databases and expanding the number of com-parison samples will be discussed in light of their role in the identification process.

关键词： Forensic sciences forensic anthropology forensic genetics individual identification molecular taphonomy skeletal DNA extraction DNA profiles DNA databases

Comment on“In vivo flow cytometry reveals a circadian rhythm of circulating tumor cells”

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Light(Science & Applications) 2021年第10期10卷 1998-1999页

作者： Amber L.Williams jessica e.Fitzgerald Fernando Ivich eduardo DSontag Mark Niedre Department of Bioengineering Northeastern UniversityBostonMAUSA Department of electrical and Computer engineering Northeastern UniversityBostonMAUSA Laboratory of Systems Pharmacology Harvard Medical SchoolBostonMAUSA

Dear editor,Circulating tumor cells(CTCs)are instrumental in hematogenous metastasis and are widely studied using liquid biopsy *** involve analysis and characterization of CTCs from fractionally small blood samples drawn from *** biopsy implicitly assumes that the number and phenotypical distribution of CTCs in small blood samples is representative of the full peripheral blood volume,and furthermore that CTC numbers are approximately constant over the days and hours surrounding the blood draw.

关键词： biopsy metastasis furthermore

The immunomodulating effect of bifidobacteria is modified by the anticoagulant acenocoumarol

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Food Bioscience 2023年第2期52卷 1166-1174页

作者： Sabrina e.Assad Melisa Fragomeno Martin Rumbo jessica Minnaard Pablo F.Perez Centro de Investigacion y Desarrollo en Criotecnologia de Alimentos-UNLP-CONICeT CCT La PlataArgentina Catedra de Microbiologia FCEUNLPCalle 47 y 116CP 1900La PlataBs.AsArgentina Instituto de estudios Inmunologicos y Fisiopatologicos-UNLP-CONICeT-CCT La PlataArgentina

Bifidobacteria are health promoting microorganisms that can interact with drugs in the intestinal tract thus modifying the activation of immune cells and host *** study the effect of acenocoumarol on the interaction between bifidobacteria and THP-1 cells or intestinal epithelial *** bifidum CIDCA 5310 and *** CIDCA 5317 were grown in MRS broth in anaerobic *** experiments were done in the presence of ***-labeled bacteria were incubated with THP1 cells differentiated with PMA(THP1-PMA),and phagocytosis and intracellular localization of bacteria were assessed by flow cytometry and confocal laser microscopy,***,expression of macrophage surface molecules in THP1 and THP1-PMA cells was assessed by flow *** using the Caco-2 ccl20:luc reporter system innate immune response was analysed by determining luciferase expression induced by *** decreased phagocytosis of bifidobacteria but intracellular routing was not ***,anticoagulant reduced the expression of HLA-DR and CD64 induced by bifidobacteria in both THP1-PMA and THP1 ***,the decrease in the expression of CD206 and CD23 was dependent on differentiation status of THP1 *** increased CCL20 expression and it was partially abrogated by strain CIDCA *** of acenocoumarol modifies the interaction between bifidobacteria and eukaryotic cells thus suggesting that the expected modulation of immune response by probiotic foods can be different in persons under anticoagulant treatment.

关键词： Bifidobacterium Acenocoumarol THP-1 cells Caco-2 ccl20:luc reporter system Immune response Anticoagulant

A Comparative Study of the effect of Gold Seed Particle Preparation Method on Nanowire Growth

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Nano Research 2010年第7期3卷 506-519页

作者： Maria e.Messing Karla Hillerich jessica Bolinsson Kristian Storm Jonas Johansson Kimberly A.Dick Knut Deppert Solid State Physics Lund UniversityBox 118S-22100 LundSweden Polymer&Materials Chemistry Lund UniversityBox 124S-22100 LundSweden

Highly controlled particle-assisted growth of semiconductor nanowires has been performed for many years,and a number of novel nanowire-based devices have been *** control of the epitaxial growth is required to optimize the performance of devices,and gold seed particles are known to provide the most controlled *** nanowire growth from gold particles generated and deposited by various different methods has been reported,but no investigation has yet been performed to compare the effects of gold particle generation and deposition methods on nanowire *** this article we present a direct comparative study of the effect of the gold particle creation and deposition methods on nanowire growth characteristics and nanowire crystal structure,and investigate the limitations of the different generation and deposition methods used.

关键词： Nanowire growth nanoparticles gold epitaxy electron microscopy

Curcumin-loaded polymeric nanoparticles for neuro-protection in neonatal rats with hypoxic-ischemic encephalopathy

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Nano Research 2018年第10期11卷 5670-5688页

作者： Andrea Joseph Thomas Wood Chih-Chung Chen Kylie Corry jessica M. Snyder Sandra e. Juul Pratik Parikh elizabeth Nance Department of Chemical engineering University of Washington Seattle WA 98195 USA Division of Neonatology Department of Pediatrics University of Washington Seattle WA 98195 USA Department of Comparative Medicine University of Washington Seattle WA 98195 USA Department of Radiology University of Washington Seattle WA 98195 USA

Hypoxic-ischemic encephalopathy is the leading cause of permanent brain injury in term newborns and currently has no cure. Inflammatory processes play a key role in the progression of this disease and may be amenable to a targeted pharmaceutical intervention. Curcumin is a dietary compound with potent anti-inflammatory, antioxidant, and antiapoptotic properties but is limited in therapeutic applications due to its low aqueous solubility, low bioavailability, and rapid first-pass hepatic metabolism. To address these limitations, loading curcumin into poly（lactic-co-glycolic acid）-poly（ethylene glycol）（PLGA-PeG） nanoparticles may increase relevant pharmacokinetic parameters and allow for effective drug delivery to the brain. Using the Vannucci model of unilateral hypoxic-ischemic brain injury in neonatal rats, we studied the in vivo effect of curcumin-loaded PLGA-PeG nanoparticles on brain uptake and diffusion of curcumin and on neuroprotection. The curcumin-loaded nanoparticles were able to overcome the impaired blood-brain barrier, diffuse effectively through the brain parenchyma, localize in regions of injury, and deliver a protective effect in the injured neonatal brain. The application of curcumin and PLGA-PeG nanoparticle-mediated delivery to a clinically relevant model of neonatal brain injury provides greater opportunities for clinical translation of targeted therapies for hypoxic-ischemic encephalopathy.

关键词： drug delivery neuroprotection brain penetrating neonatal hypoxia-ischemia curcumin nanotherapeutics

Fertility preservation in female cancer patients:a single center experience

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Chinese Journal of Cancer 2015年第1期34卷 56-60页

作者： Cristina Sigismondi enrico Papaleo Paola Viganò Simona Vailati Massimo Candiani jessica Ottolina Valentina e. Di Mattei Giorgia Mangili Gynecology Department Preservation of Fertility Unit IRCCS San Raffaele Hospital

Advances in cancer treatment allow women to be cured and live longer. However, the necessary chemotherapy and radiotherapy regimens have a negative impact on future fertility. Oncofertility has emerged as a new interdisciplinary field to address the issue of gonadotoxicity associated with cancer treatment and to facilitate fertility preservation, including oocyte and ovarian tissue cryopreservation. These fertility issues are often inadequately addressed, and referral rates to oncofertility centers are low. The aim of this study was to report the 3-year experience of the San Raffaele Oncofertility Unit. A total of 96 patients were referred to the Oncofertility Unit for evaluation after the diagnosis of cancer and before gonadotoxic treatment between April 2011 and June 2014. Of the 96 patients, 30(31.2%) were affected by breast cancers, 20(20.8%) by sarcomas, 28(29.2%) by hematologic malignancies, 13(13.5%) by central nervous system cancers, 3(3.1%) by bowel tumors, 1(1.0%) by Wilms' tumor, and 1(1.0%) by a thyroid tumor; 47(49.0%) were referred for oocyte cryopreservation before starting chemotherapy, 20(20.8%) were referred for ovarian tissue cryopreservation, and 29(30.2%) were not recruited. The mean time between the patients' counseling and oocyte retrieval was 15 days(range, 2–37 days). The mean time between the laparoscopic surgery and the beginning of treatment was 4 days(range, 2–10 days). The number of patients who were referred increased over time, whereas the rate of patients who were not recruited decreased, showing an improvement in referrals to the Oncofertility Unit and in the patients' counseling and understanding. Our results indicate that an effective multidisciplinary oncofertility team is necessary for prompt referrals and treatment.

关键词：癌症患者生育功能癌症治疗女性冷冻保存中枢神经系统平均时间卵巢组织

Investigating drivers of microbial activity and respiration in a forested bog

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Pedosphere 2020年第1期30卷 135-145页

作者： Kenna e.ReWCASTLe jessica A.M.MOORe Jeremiah A.HeNNING Melanie A.MAYeS Courtney M.PATTeRSON Gangsheng WANG Daniel B.MeTCALFe Aimée T.CLASSeN Rubenstein School of environment and Natural Resources University of VermontBurlington VT 05405(USA) ecology&evolutionary Biology University of TennesseeKnoxville TN 37996(USA) The Gund Institute for environment University of VermontBurlington VT 05405(USA) Department of Biology University of South AlabamaMobile AL 36688(USA) Climate Change Science Institute and environmental Sciences Division Oak Ridge National LaboratoryOak Ridge TN 37830(USA) Institute for environmental Genomics&Department of Microbiology and Plant Biology University of OklahomaNorman OK 73019(USA) The Department of Physical Geography and ecosystem Science Lund UniversityLund 22362(Sweden)

Northern peatlands store nearly one-third of terrestrial carbon(C)stocks while covering only 3%of the global landmass;nevertheless,the drivers of C cycling in these often-waterlogged ecosystems are different from those that control C dynamics in upland forested *** explore how multiple abiotic and biotic characteristics of bogs interact to shape microbial activity in a northern,forested bog,we added a labile C tracer(13C-labeled starch)to in situ peat mesocosms and correlated heterotrophic respiration with natural variation in several microbial predictor variables,such as enzyme activity and microbial biomass,as well as with a suite of abiotic variables and proximity to vascular plants *** found that peat moisture content was positively correlated with respiration and microbial activity,even when moisture levels exceeded total saturation,suggesting that access to organic matter substrates in drier environments may be limiting for microbial *** to black spruce trees decreased total and labile heterotrophic *** negative relationship may reflect the influence of tree evapotranspiration and peat shading effects;i.e.,microbial activity may decline as peat dries and cools near ***,we isolated the response of heterotrophic respiration to explore the variation in,and interactions among,multiple abiotic and biotic drivers that influence microbial *** approach allowed us to reveal the relative influence of individual drivers on C respiration in these globally important C sinks.

关键词： carbon cycling enzyme activity heterotrophic respiration labile carbon respiration ombrotrophic bog peat moisture plant proximity soil carbon sink