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An Exome-seq Based Tool for Mapping and Selection of Candidate Genes in Maize Deletion Mutants

Genomics, Proteomics & Bioinformatics 2018年第6期16卷 439-450页

作者： Shangang Jia kyla morton Chi Zhang David Holding Department of Agronomy and Horticulture Center for Plant Science InnovationBeadle Center for BiotechnologyUniversity of Nebraska School of Biological Sciences Center for Plant Science InnovationBeadle Center for BiotechnologyUniversity of Nebraska

Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by gamma-irradiation showed clear segregation for the kernel phenotypes in B73 ? Mo17 F2 ears. To better understand the functional genomics of kernel development,we developed a mapping and gene identi?cation pipeline, bulked segregant exome sequencing(BSEx-seq), to map mutants with kernel phenotypes including opaque endosperm and reduced kernel size. BSEx-seq generates and compares the sequence of the exon fraction from mutant and normal plant F2 DNA pools. The comparison can derive mapping peaks, identify deletions within the mapping peak, and suggest candidate genes within the deleted regions. We then used the public kernel-speci?c expression data to narrow down the list of candidate genes/mutations and identi?ed deletions ranging from several kb to more than 1 Mb. A full deletion allele of the Opaque-2 gene was identi?ed in mutant 531, which occurs within a $200-kb deletion. Opaque mutant 1486 has a 6248-bp deletion in the mapping interval containing two candidate genes encoding RNA-directed DNA methylation 4(RdDM4) and AMP-binding protein, respectively. This study demonstrates the ef?-ciency and cost-effectiveness of BSEx-seq for causal mutation mapping and candidate gene selection,providing a new option in mapping-by-sequencing for maize functional genomics studies.

关键词： Maize functional genomics Mapping-by-sequencing Exome-seq Opaque mutant Bulked segregation analysis

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APIR:Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control

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Genomics, Proteomics & Bioinformatics 2024年第2期22卷 171-187页

作者： Yiling Elaine Chen Xinzhou Ge kyla Woyshner MeiLu McDermott Antigoni Manousopoulou Scott B.Ficarro Jarrod A.Marto Kexin Li Leo David Wang Jingyi Jessica Li Department of Statistics and Data Science University of CaliforniaLos AngelesCA 90095USA Department of Immuno-Oncology Beckman Research InstituteCity of Hope National Medical CenterDuarteCA 91010USA Department of Quantitative and Computational Biology University of Southern CaliforniaLos AngelesCA 90089USA Department of Cancer Biology and Blais Proteomics Center Dana-Farber Cancer InstituteDepartment of PathologyBrigham and Women’s Hospital and Harvard Medical SchoolBostonMA 02215USA Department of Pediatrics City of Hope National Medical CenterDuarteCA 91010USA Bioinformatics Interdepartmental Program University of CaliforniaLos AngelesCA 90095USA Department of Human Genetics University of CaliforniaLos AngelesCA 90095USA Department of Computational Medicine University of CaliforniaLos AngelesCA 90095USA Department of Biostatistics University of CaliforniaLos AngelesCA 90095USA

Advances in mass spectrometry(MS)have enabled high-throughput analysis of proteomes in biological *** state-of-the-art MS data analysis relies on database search algorithms to quantify proteins by identifying peptide–spectrum matches(PSMs),which convert mass spectra to peptide *** database search algorithms use distinct search strategies and thus may identify unique ***,no existing approaches can aggregate all user-specified database search algorithms with a guaranteed increase in the number of identified peptides and a control on the false discovery rate(FDR).To fill in this gap,we proposed a statistical framework,Aggregation of Peptide Identification Results(APIR),that is universally compatible with all database search ***,under an FDR threshold,APIR is guaranteed to identify at least as many,if not more,peptides as individual database search algorithms *** of APIR on a complex proteomics standard dataset showed that APIR outpowers individual database search algorithms and empirically controls the *** data studies showed that APIR can identify disease-related proteins and post-translational modifications missed by some individual database search *** APIR framework is easily extendable to aggregating discoveries made by multiple algorithms in other high-throughput biomedical data analysis,e.g.,differential gene expression analysis on RNA sequencing *** APIR R package is available at https://***/yiling0210/APIR.

关键词： Shotgun proteomics Peptide–spectrum match Peptide identification Aggregation of lists FDR control

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Evacuating a First Nation Due to Wildfire Smoke:The Case of Dene Tha’ First Nation

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International Journal of Disaster Risk Science 2020年第3期11卷 274-286页

作者： kyla D.Mottershead Tara K.McGee Amy Christianson Department of Earth and Atmospheric Sciences University of AlbertaEdmontonAB T6G 2E3Canada Canadian Forest Service Northern Forestry CentreEdmontonAB T6H 3S5Canada

Almost every year,First Nations are evacuated in Canada because of wildfire proximity and *** of wildfires,and remote locations,unique sociocultural characteristics,and limited emergency management resources present challenges for evacuation organizers and *** study explores how Dene Tha’First Nation evacuated their Tachécommunity in July 2012 due to wildfire smoke and how the evacuation process affected *** were completed with 31 evacuation organizers and residents to examine the factors that helped and hindered the evacuation *** of information about the nearby wildfire,smoke,and evacuation of the nearby small community of Zama City,combined with a generic evacuation plan,delayed and posed challenges during the evacuation of this Dene Tha’*** leadership and its role in community organizing,keeping families together,providing the social support they needed,and using familiar host communities,demonstrated and contributed to the community’s resilience during the *** to improve evacuations and emergency management in the community and other First Nations in Canada are identified and discussed.

关键词： Community resilience Evacuation planning First Nations Indigenous peoples Wildfire smoke

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Improving Your Oral English

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语数外学习(高中版高二年级) 2007年第10期 44-46页

作者： kyla Free

The most common question my students ask is "How can I improve my oral English?" My answer is always the same: practice. There is no quick way to learn another lan-guage.

关键词： Improving Your Oral English

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Improving Your Oral English

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语数外学习(高中版高三年级) 2007年第11期 44-46页

作者： kyla Free

The most common question my students ask is"Howcan I improve my oral English?"My answer is alwaysthe same: practice. There is no quick way to learn an-

关键词： Improving Your Oral English

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Impact of cardiologist intervention on guideline-directed use of statin therapy

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World Journal of Cardiology 2020年第8期12卷 419-426页

作者： Manouchkathe Cassagnol Ofek Hai Shaqeel A Sherali kyla D’Angelo David Bass Roman Zeltser Amgad N Makaryus Department of Cardiology NuHealth/Nassau University Medical CenterEast MeadowNY 11554United States Department of Clinical Health Professions College of Pharmacy and Health SciencesSt.John’s UniversityQueensNY 11430United States Donald and Barbara Zucker School of Medicine at Hofstra/Northwell HempsteadNY 11549United States St.Lawrence Health System PotsdamNY 13676United States

BACKGROUND Statins have an important and well-established role in the prevention of atherosclerotic cardiovascular disease(ASCVD).However,several studies have reported widespread underuse of statins in various practice settings and *** of relevant literature reveals opportunities for improvement in the implementation of guideline-directed statin therapy(GDST).AIM To examine the impact of cardiologist intervention on the use of GDST in the ambulatory *** Patients with at least one encounter at the adult Internal Medicine Clinic(IMC)and/or Cardiology Clinic(CC),who had an available serum cholesterol test performed,were *** 2 comparison groups were defined as:(1)Patients only seen by IMC;and(2)Patients seen by both IMC and *** were excluded if variables needed for calculation of ASCVD risk scores were lacking,and if demographic information lacked guideline-directed treatment *** were analyzed using student t-tests or χ^2,as *** of Variance was used to compare rates of adherence to *** A total of 268 patients met the inclusion criteria for this study;211 in the IMC group and 57 in the IMC-CC ***,56%of patients were female,mean age 56 years(±10.65,SD),22%Black or African American,56%Hispanic/Latino,14%had clinical ASCVD,13%current smokers,66%diabetic and 63%*** use was observed in 55%(n=147/268)of the entire patient *** the IMC-CC group,73.6%(n=42/57)of patients were prescribed statin therapy compared to 50.7%(n=107/211)of patients in the IMC group(P=0.002).In terms of appropriate statin use based on guidelines,there was no statistical difference between groups[IMC-CC group 61.4%(n=35/57)vs IMC group,55.5%(n=117/211),P=0.421].Patients in the IMC-CC group were older,had more cardiac risk factors and had higher proportions of non-white patients compared to the IMC group(P<0.02,all).CONCLUSION Although overall use of GDST was suboptimal,there was no statis

关键词： Statin use Guideline directed statin therapy Cardiologist Ambulatory care Adherence

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Caregiver burden is increased in Parkinson’s disease with mild cognitive impairment (PD-MCI)

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Translational Neurodegeneration 2017年第1期6卷 165-173页

作者： Ann J.Jones Roeline G.Kuijer Leslie Livingston Daniel Myall kyla Horne Michael MacAskill Toni Pitcher Paul T.Barrett Tim J.Anderson John C.Dalrymple-Alford New Zealand Brain Research Institute 66 Stewart StreetChristchurch 8011New Zealand Department of Psychology University of CanterburyChristchurchNew Zealand Department of Medicine University of OtagoChristchurchNew Zealand Cognadev UK Ltd.SandtonSouth Africa Department of Neurology Christchurch HospitalChristchurchNew Zealand Brain Research New Zealand Centre of Research Excellence ChristchurchNew Zealand

Background:There is limited evidence on caregiver outcomes associated with mild cognitive impairment in patients with Parkinson’s disease(PD-MCI)and the coping strategies used by these ***:To investigate this relationship,we examined levels of burden,depression,anxiety,coping strategies and positive aspects of caregiving in the informal caregivers of 96 PD *** PD patients were classified using MDS-Task Force Level II criteria as showing either normal cognition(PD-N;n=51),PD-MCI(n=30)or with dementia(PDD;n=15).Results:Mean Zarit Burden Interview(ZBI)score increased significantly between carers of PD-N(M=13.39,SD=12.22)compared to those of PD-MCI patients(M=22.00,SD=10.8),and between carers of PD-MCI and PDD patients(M=29.33,SD=9.59).Moreover,the proportion of carers showing clinically significant levels of burden(ZBI score≥21)also increased as the patients’cognitive status declined(18% for PD-N;60% for PD-MCI;and 80%for PDD)and was mirrored by an increasing amount of time spent providing care by the *** ZBI score was independent of patient neuropsychiatric symptoms,motor function,disease duration and time that caregivers spent *** use of different coping strategies increased with worsening ***,we found only equivocal evidence that the use of problem-focused,emotion-focused and dysfunctional coping mediated the association between patient cognitive status and caregiver burden,because the inverse models that used caregiver burden as the mediator were also ***:The study highlights the impact of Parkinson’s disease on those providing care when the patient’s cognition is poor,including those with *** well-being has important implications for caregiver support,nursing home placement and disease course.

关键词： Parkinson’s disease Mild cognitive impairment Zarit caregiver burden interview Coping Depression Anxiety Positive aspects of caregiving

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Evaluation of the Antimicrobial Activity of Endophytic Fungus Isolated from <i>Cocos nucifera</i>(L.) Cotyledon against Medically-Important Pathogens

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Journal of Biosciences and Medicines 2021年第1期9卷 86-97页

作者： Byran N. Fuego kyla G. Romano Charlmaine D. Pinlac Gary Antonio C. Lirio Major in Science Department of Elementary and Secondary Education College of Education Polytechnic University of the Philippines Manila Philippines Institute for Science and Technology Research Center for Life Sciences Research Polytechnic University of the Philippines Manila Philippines

The study aimed to evaluate the endophytic fungi isolated from Cocos nucifera (L.) cotyledon for their possible antimicrobial activity. A total of twelve endophytic fungal species were successfully isolated, from which five were selected and presumptively identified, including Aspergillus niger, Raffaelea sp., Aspergillus flavus, Cladosporium sp. and Pseudallescheria spp. based on their macro and microscopic characters. The agar blocks of actively growing pure culture were assessed for antibacterial activity against five human pathogenic bacterial and fungal strains: Escherichia coli (BIOTECH 1634), Bacillus subtilis (BIOTECH 1697), Staphylococcus aureus (BIOTECH 1592), Serratia marcescens (BIOTECH 1748), and Candida tropicalis (BIOTECH 2085). Among the selected five endophytic used for antimicrobial activity screening, the Raffaelea sp. (CN-EF 2) has shown a high zone of inhibition of 11 mm against Bacillus subtilis, 18 mm against Escherichia coli, 15 mm against Staphylococcus aureus, and 11 mm against Candida tropicalis. Correspondingly, Aspergillus niger (CN-EF 1) has shown a zone of inhibition of 16 mm against C. tropicalis. The endophytic fungus Raffaelea sp. was effective against all test organisms except for Serratia marcescens, while Aspergillus niger was only effective for pathogenic fungi C. albicans. Hence, further in-depth studies of the isolated endophytic fungi are needed to determine the mechanisms behind the endophytes’ inhibitory effects.

关键词： Endophytic Fungi Antimicrobial Activity Cocos nucifera L. Natural Product Agar Plug Diffusion Medically-Important Pathogens

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经济实惠的彩色打印机

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电子与电脑 1998年第7期5卷 30-41页

作者： kyla K.Carlson 宋荣

想与众不同吗?想使您的想法引人注目吗?想获得超群的工作效果吗?那就采纳专家的劝告:使用彩色,彩色会使一切更美好。很简单——购买一台彩色打印机就是使您的报告和文档拥有最佳效果的便宜而又简便易行的途径。

关键词：彩色打印机打印机产品评测

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Reservoir construction from the Newberry Volcano EGS Demonstration

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Journal of Groundwater Science and Engineering 2014年第3期2卷 1-7页

作者： Trenton T Cladouhos Susan Petty Yini Nordin Michael Moore kyla Grasso Matt Uddenberg Michael W Swyer Alta Rock Energy Inc.

The Newberry Volcano EGS Demonstration in central Oregon tests recent technological advances designed to reduce the cost of power generated by EGS in a hot,dry well(NWG 55-29) drilled in 2008. An EGS reservoir was created by injecting large volumes of cold water,causing existing fractures to slip in shear(known as hydroshearing) generating the seismic waves that can be used to map fracture location and size. At the Newberry Demonstration the final injectivity ranged between 1.4 and 1.7 L/s/MPa a ~6x improvement over the initial injectivity of the well. The injectivity improvement and seismic analysis indicate that previously impermeable fractures were enhanced during the NWG 55-29 stimulation.

关键词： EGS Stimulation Hydroshearing Microseismicity

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