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Assessment of molecular markers and marker-assisted selection for drought tolerance in barley(Hordeum vulgare L.)

Journal of Integrative Agriculture 2024年第1期23卷 20-38页

作者： Akmaral Baidyussen Gulmira Khassanova Maral Utebayev satyvaldy Jatayev Rystay Kushanova sholpan Khalbayeva Aigul Amangeldiyeva Raushan Yerzhebayeva KulpashBulatova carly s.hramm Peter Anderson Colin L.D.Jenkins Kathleen Lsoole Yuri shavrukov Faculty of Agronomy S.Seifullin Kazakh AgroTechnical Research UniversityAstana 010000Kazakhstan A.I.Barayev Research and Production Centre of Grain Farming Shortandy 021601Kazakhstan Kazakh Research Institute of Agriculture and Plant Growing AlmalybakAlmaty District 040909Kazakhstan College of science and Engineering Biological SciencesFlinders UniversityAdelaideSA 5042Australia

This review updates the present status of the field of molecular markers and marker-assisted selection(MAs),using the example of drought tolerance in *** accuracy of selected quantitative trait loci(QTLs),candidate genes and suggested markers was assessed in the barley genome *** common strategies are described for molecular marker development,candidate gene identification and verification,and their possible applications in MAs to improve the grain yield and yield components in barley under drought *** strategies are based on the following five principles:(1)Molecular markers are designated as genomic‘tags’,and their‘prediction’is strongly dependent on their distance from a candidate gene on genetic or physical maps;(2)plants react differently under favourable and stressful conditions or depending on their stage of development;(3)each candidate gene must be verified by confirming its expression in the relevant conditions,e.g.,drought;(4)the molecular marker identified must be validated for MAs for tolerance to drought stress and improved grain yield;and(5)the small number of molecular markers realized for MAs in breeding,from among the many studies targeting candidate genes,can be explained by the complex nature of drought stress,and multiple stress-responsive genes in each barley genotype that are expressed differentially depending on many other factors.

关键词： barley candidate genes drought tolerance gene verification via expression grain yield marker-assisted selection(MAs) molecular markers quantitative trait loci(QTLs) strategy for MAs

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A generalized differential equation compartmental model of infectious disease transmission

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Infectious Disease Modelling 2021年第1期6卷 1073-1091页

作者： scott Greenhalgh carly Rozins siena College Department of Mathematics515 Loudon RoadLoudonvilleNY12211USA York University Department of Science and Technology Studies170 Campus WalkYork UniversityONCanada

For decades,mathematical models of disease transmission have provided researchers and public health officials with critical insights into the progression,control,and prevention of disease *** these models,one of the most fundamental is the sIR differential equation ***,this ubiquitous model has one significant and rarely acknowledged shortcoming:it is unable to account for a disease's true infectious period *** the misspecification of such a biological characteristic is known to significantly affect model behavior,there is a need to develop new modeling approaches that capture such ***,we illustrate an innovative take on compartmental models,derived from their general formulation as systems of nonlinear Volterra integral equations,to capture a broader range of infectious period distributions,yet maintain the desirable formulation as systems of differential *** work illustrates a compartmental model that captures any Erlang distributed duration of infection with only 3 differential equations,instead of the typical inflated model sizes required by traditional differential equation compartmental models,and a compartmental model that captures any mean,standard deviation,skewness,and kurtosis of an infectious period distribution with 4 differential *** significance of our work is that it opens up a new class of easyto-use compartmental models to predict disease outbreaks that do not require a complete overhaul of existing theory,and thus provides a starting point for multiple research avenues of investigation under the contexts of mathematics,public health,and evolutionary biology.

关键词： Infectious disease models Volterra integral equations survival analysis Infectious period Mean residual waiting-time

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Population-standardized genetic risk score： the sNP-based method of choice for inherited risk assessment of prostate cancer

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Asian Journal of Andrology 2016年第4期18卷 520-524页

作者： carly A Conran Rong Na Haitao Chen Deke Jiang Xiaoling Lin s Lilly Zheng Charles B Brendler Jianfeng Xu Northshore University Healthsystem Program for Personalized Cancer Care 1001 University Place Evanston IL 60201 USA Fudan Institute of Urology Huashan Hospital Fudan University 12 Mid-Wulumuqi Road Shanghai 200040 P.R. China Center for Genomic Translational Medicine and Prevention School of Public Health Fudan University 138 Yixueyuan Road Shanghai 200032 RR. China.

several different approaches are available to clinicians for determining prostate cancer （PCa） risk. The clinical validity of various PCa risk assessment methods utilizing single nucleotide polymorphisms （sNPs） has been established; however, these sNP-based methods have not been compared. The objective of this study was to compare the three most commonly used sNP-based methods for PCa risk assessment. Participants were men （n = 1654） enrolled in a prospective study of PCa development. Genotypes of 59 PCa risk-associated sNPs were available in this cohort. Three methods of calculating sNP-based genetic risk scores （GRss） were used for the evaluation of individual disease risk such as risk allele count （GRs-RAC）, weighted risk allele count （GRs-wRAC）, and population-standardized genetic risk score （GRs-Ps）. Mean GRss were calculated, and performances were compared using area under the receiver operating characteristic curve （AUC） and positive predictive value （PPV）. All sNP-based methods were found to be independently associated with PCa （all P 〈 0.05; hence their clinical validity）. The mean GRss in men with or without PCa using GRs-RAC were 55.15 and 53.46, respectively, using GRs-wRAC were 7.42 and 6.97, respectively, and using GRs-Ps were 1.12 and 0.84, respectively （all P 〈 0.05 for differences between patients with or without PCa）. All three sNP-based methods performed similarly in discriminating PCa from non-PCa based on AUC and in predicting PCa risk based on PPV （all P 〉 0.05 for comparisons between the three methods）, and all three sNP-based methods had a significantly higher AUC than family history （all P 〈 0.05）. Results from this study suggest that while the three most commonly used sNP-based methods performed similarly in discriminating PCa from non-PCa at the population level, GRs-Ps is the method of choice for risk assessment at the individual level because its value （where 1.0 represents average population risk） can be easily interpreted regardless of

关键词： genetic risk score prostate cancer single nucleotide polymorphisms

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Current cancer therapies and their influence on glucose control

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World Journal of Diabetes 2021年第7期12卷 1010-1025页

作者： carly Yim Kerry Mansell Nassrein Hussein Terra Arnason Department of Medicine University of SaskatchewanSaskatoon S7N 0W8SaskatchewanCanada College of Pharmacy and Nutrition University of SaskatchewanSaskatoon S7N 5E5SaskatchewanCanada Department of Medicine Division of EndocrinologyUniversity of SaskatchewanSaskatoon S7N 0W8SaskatchewanCanada Departments of Anatomy and Cell Biology and Medicine Division of EndocrinologyUniversity of SaskatchewanSaskatoon S7N 0W8SaskatchewanCanada

This review focuses on the development of hyperglycemia arising from widely used cancer therapies spanning four drug *** groups of medications were selected due to their significant association with new onset hyperglycemia,or of potentially severe clinical consequences when *** classes include glucocorticoids that are frequently used in addition to chemotherapy treatments,and the antimetabolite class of 5-fluorouracil-related *** of these classes have been in use in cancer therapy since the *** considered are the phosphatidyl inositol-3-kinase(PI3K)/AKT/mammalian target of rapamycin(mTOR)-inhibitors that provide cancer response advantages by disrupting cell growth,proliferation and survival signaling pathways,and have been in clinical use as early as *** final class to be reviewed are the monoclonal antibodies selected to function as immune checkpoint inhibitors(ICIs).These were first used in 2011 for advanced melanoma and are rapidly becoming widely utilized in many solid *** each drug class,the literature has been reviewed to answer relevant questions about these medications related specifically to the characteristics of the hyperglycemia that develops with *** incidence of new glucose elevations in euglycemic individuals,as well as glycemic changes in those with established diabetes has been considered,as has the expected onset of hyperglycemia from their first *** comparison emphasizes that some classes exhibit very immediate impacts on glucose levels,whereas other classes can have lengthy delays of up to 1 year.A comparison of the spectrum of severity of hyperglycemic consequences stresses that the appearance of diabetic ketoacidosis is rare for all classes except for the *** are distinct differences in the reversibility of glucose elevations after treatment is stopped,as the mTOR inhibitors and ICI classes have persistent hyperglycemia long *** four highlighted drug categories differ in their

关键词： Cancer therapy Hyperglycemia adverse drug effects Immune checkpoint inhibitors mTOR inhibitors 5-fluorouracil analogs Glucocorticoids Diabetes mellitus

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Impact of bolus volume on small intestinal intra-luminal impedance in healthy subjects

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World Journal of Gastroenterology 2010年第17期16卷 2151-2157页

作者： Nam Q Nguyen Laura K Bryant carly M Burgstad Robert J Fraser Daniel sifrim Richard H Holloway Department of Gastroenterology & Hepatology Royal Adelaide HospitalAdelaide 5000Australia Investigation and Procedures Unit Repatriation General HospitalDaw Park 5041Australia Department of Medicine Centre for Gastroen-terological ResearchK.U.LeuvenLeuven 3000Belgium

AIM: To assess the impact of bolus volume on the characteristics of small intestinal (sI) impedance ***: Concurrent sI manometry-impedance measurements were performed on 12 healthy volunteers to assess the pattern of proximal jejunal fluid bolus movement over a 14 *** subject was given 34 boluses of normal saline (volume from 1 to 30 mL) via the feeding tube placed immediately above the proximal margin of the studied segment.A bolus-induced impedance event occurred if there was > 12% impedance drop from baseline,over ≥ 3 consecutive segments within 10 s of bolus injection.A minor or major imped-ance event was defined as a duration of impedance drop s or ≥ 60 s,***: The minimum volume required for a detectable sI impedance event was 2 mL.A direct linear relationship between the sI bolus volume and the occurrence of impedance events was noted until sI bolus volume reached 10 mL,a volume which always produced an impedance flow *** was a moderate correlation between the bolus volume and the duration of impedance drop (r = 0.63,P s (r = 0.50,P ses were associated with more major impedance events (≥ 10 mL boluses = 63%,3 mL boluses = 17%,and ses = 0%,P = 0.02).CONCLUsION: Bolus volume had an impact on the type and length of propagation of sI impedance events and a threshold of 2 mL is required to produce an event.

关键词： Bolus volume Health Impedance Luminal flow small intestine

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Physiological Response of the Resurrection Fern subjected to Environmental stress as shown by Plant Cell Membrane Integrity

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American Journal of Plant sciences 2022年第8期13卷 1081-1089页

作者： carly Balsam Ed Bush st. Joseph’s Academy Baton Rouge USA LsU AgCenter Baton Rouge USA

Resurrection fern has a unique ability to maintain cell wall integrity when the plant cell is desiccated. It uses proteins such as late embryogenesis proteins and heat shock proteins to maintain their cellular functions. The purpose of this experiment is to determine the effects of environmental stressors on the physiological response of the resurrection fern (Pleopeltis polypodioides). The physiological response of resurrection fern plants was subjected to various temperatures (-50°C, 0°C, 25°C, and 50°C) for 7 days. Results indicated that there was a significant difference between hydrated and desiccated ferns based on the temperature. Additionally, electrolyte leakage measurements confirmed cell damage following exposure to temperature extremes of -50°C and 50°C.

关键词： Adaptive Mechanisms Plant stress Plant Cell Wall Cell Leakage

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Lower esophageal sphincter relaxation is impaired in older patients with dysphagia

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World Journal of Gastroenterology 2011年第10期17卷 1326-1331页

作者： Laura K Besanko carly M Burgstad Reme Mountifi eld Jane M Andrews Richard Heddle Helen Checklin Robert JL Fraser Investigation and Procedures Unit Repatriation General Hospital Department of Gastroenterology and Hepatology Royal Adelaide Hospital Discipline of Medicine University of Adelaide Adelaide 5000 South Australia Australia Department of Medicine Flinders University of South Australia Bedford Park 5042 South Australia Australia

AIM: To characterize the effects of age on the mechanisms underlying the common condition of esophageal dysphagia in older patients, using detailed manometric analysis. METHODs: A retrospective case-control audit was performed on 19 patients aged ≥ 80 years (mean age 85 ± 0.7 year) who underwent a manometric study for dysphagia (2004-2009). Data were compared with 19 younger dysphagic patients (32 ± 1.7 years). Detailed manometric analysis performed prospectively included basal lower esophageal sphincter pressure (BLEsP), pre-swallow and nadir LEsP, esophageal body pressures and peristaltic duration, during water swallows (5 mL) in right lateral (RL) and upright (UR) postures and with solids. Data are mean ± sE; a P-value s considered significant. REsULTs: Elderly dysphagic patients had higher BLEsP than younger patients (23.4 ± 3.8 vs 14.9 ± 1.2 mmHg; P swallow LEsP was elevated in the elderly in both postures (RL: 1 and 4 s P = 0.019 and P = 0.05; UR: P solids (P s, LEs nadir pressure was higher with liquids (RL: 2.3 ± 0.6 mmHg vs 0.7 ± 0.6 mmHg, P s 1.6 ± 0.5 mmHg, P = 0.01) with shorter relaxation after solids (7.9 ± 1.5 s vs 9.7 ± 0.4 s, P = 0.05). No age-related differences were seen in esophageal body pressures or peristalsis duration. CONCLUsION: Basal LEs pressure is elevated and swallow-induced relaxation impaired in elderly dysphagic patients. Its contribution to dysphagia and the effects of healthy ageing require further investigation.

关键词： Dysphagia Elderly Esophageal Motility Lower Esophageal sphincter Aging

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World Journal of Gastroenterology 2017年第15期23卷 2785-2794页

作者： Charles Cock Laura K Besanko carly M Burgstad Alison Thompson stamatiki Kritas Richard Heddle Robert JL Fraser Taher I Omari Investigation and Procedures Unit Repatriation General Hospital Department of Gastroenterology and Hepatology Flinders University of South Australia Gastroenterology Unit Women's and Children's Health Network Human Physiology School of MedicineFlinders University of South Australia

AIM To investigate the functional effects of abnormal esophagogastric(EGJ) measurements in asymptomatic healthy volunteers over eighty years of age. METHODs Data from 30 young controls(11 M, mean age 37 ± 11 years) and 15 aged subjects(9 M, 85 ± 4 years) were compared for novel metrics of EGJ-function: EGJcontractile integral(EGJ-CI), "total" EGJ-CI and bolus flow time(BFT). Data were acquired using a 3.2 mm, 25 pressure(1 cm spacing) and 12 impedance segment(2 cm) solid-state catheter(Unisensor and MMs solarGI system) across the EGJ. Five swallows each of 5 m L liquid(L) and viscous(V) bolus were analyzed. Mean values were compared using student's t test for normally distributed data or Mann Whitney U-test when non-normally distributed. A P value s considered *** EGJ-CI at rest was similar for older subjects compared to controls. "Total" EGJ-CI, measured during liquid swallowing, was increased in older individuals when compared to young controls(O 39 ± 7 mm *** vs C 18 ± 3 mm ***; P = 0.006). For both liquid and viscous bolus consistencies, IRP4 was increased(L: 11.9 ± 2.3 mm Hg vs 5.9 ± 1.0 mm Hg, P = 0.019 and V: 14.3 ± 2.4 mm Hg vs 7.3 ± 0.8 mm Hg; P = 0.02) and BFT was reduced(L: 1.7 ± 0.3 s vs 3.8 ± 0.2 s and V: 1.9 ± 0.3 s vs 3.8 ± 0.2 s; P subjects, when compared to young. A matrix of bolus flow and presence above the EGJ indicated reductions in bolus flow at the EGJ occurred due to both impaired bolus transport through the esophageal body(i.e., the bolus never reached the EGJ) and increased flow resistance at the EGJ(i.e., the bolus retained just above the EGJ).CONCLUsION Bolus flow through the EGJ is reduced in asymptomatic older individuals. Both ineffective esophageal bolus transport and increased EGJ resistance contribute to impaired bolus flow.

关键词： Aging Esophagus Impedance Manometry Pressure Esophagogastric junction

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Analysis of a single soybean microtubule’s persistence length

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Advances in Bioscience and Biotechnology 2013年第10期4卷 930-936页

作者： Mitra shojania Feizabadi Jimmy Barrientos carly Winton Department of Physics Seton Hall University South Orange USA

In this study, we have reported for the first time the persistence length of a single soybean microtubule in vitro. The measurement is based on analysis of thermal bending of a single soybean microtubule. similar to mammalian microtubules, the length dependency of the persistence length was also observed for this species of plant microtubule. The identification of two intrinsic aspects of plant microtubules: the persistence length and the compositional structure in terms of variety of beta tubulin isotypes, and the potential correlation between these two factors, provides evidence for the functionality mechanism of plant microtubules. In this work, these two fundamental factors have been further discussed for our case study: single soybean microtubule.

关键词： Microtubule soybean Persistence Length β Tubulin Isotype

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Race-specific genetic risk score is more accurate than nonrace-specific genetic risk score for predicting prostate cancer and high-grade diseases

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Asian Journal of Andrology 2016年第4期18卷 525-529页

作者： Rong Na Dingwei Ye Jun Qi Fang Liu Xiaoling Lin Brian T Helfand Charles B Brendler carly Conran Jian Gong Yishuo Wu Xu Gao Yaqing Chen s Lilly Zheng Zengnan Mo Qiang Ding Yinghao sun Jianfeng Xu Department of Urology Huashan Hospital Fudan University Shanghai China Fudan Institute of Urology Huashan Hospital Fudan University Shanghai China Program for Personalized Cancer Care NorthShore University HealthSystem Evanston Illinois USA Health Communication Institute School of Public Health Fudan University Shanghai China Department of Urology Shanghai Cancer Center Fudan University Shanghai China Department of Urology Xinhua Hospital Shanghai Jiaotong University School of Medicine Shanghai China Division of Urology NorthShore University HealthSystem Evanston Illinois USA Department of Urology Shanghai Changhai Hospital The Second Military Medical University Shanghai China Department of Medical Ultrasonic Xinhua Hospital Shanghai Jiaotong University School of Medicine Shanghai China Center for Genomic and Personalized Medicine Guangxi Medical University Nanning China

Genetic risk score （GRs） based on disease risk-associated single nucleotide polymorphisms （sNPs） is an informative tool that can be used to provide inherited information for specific diseases in addition to family history, However, it is still unknown whether only sNPs that are implicated in a specific racial group should be used when calculating GRss. The objective of this study is to compare the performance of race-specific GRs and nonrace-specitic GRs for predicting prostate cancer （PCa） among 1338 patients underwent prostate biopsy in shanghai, China. A race-specific GRs was calculated with seven PCa risk-associated sNPs implicated in East Asians （GRs7）, and a nonrace-specific GRs was calculated based on 76 PCa risk-associated sNPs implicated in at least one racial group （GRs76）. The means of GRs7 and GRs76 were 1.19 and 1.85, respectively, in the study population. Higher GRs7 and GRs76 were independent predictors for PCa and high-grade PCa in univariate and multivariate analyses. GRs7 had a better area under the receiver-operating curve （AUC） than GRs76 for discriminating PCa （0.602 vs 0.573） and high-grade PCa （0.603 vs 0.575） but did not reach statistical significance. GRs7 had a better （up to 13% at different cutoffs） positive predictive value （PPV） than GRs76. In conclusion, a race-specific GRs is more robust and has a better performance when predicting PCa in East Asian men than a GRs calculated using sNPs that are not shown to be associated with East Asians.

关键词： Chinese genetic risk score genome-wide association study prostate cancer single nucleotide polymorphism

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