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991.
992.
Liu Jin Yue Sheng Ze Wen Hu Yu Qi Liu Qi Qiang Sheng Song Xiao Ling Liu Biao 《Transgenic research》2021,30(1):105-119
Transgenic Research - The releasing of transgenic soybeans (Glycine max (L.) Merr.) into farming systems raises concerns that transgenes might escape from the soybeans via pollen into... 相似文献
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Rodney T. Richardson Tyler D. Eaton Chia‐Hua Lin Garrett Cherry Reed M. Johnson Douglas B. Sponsler 《Molecular ecology》2021,30(1):310-323
Understanding animal foraging ecology requires large sample sizes spanning broad environmental and temporal gradients. For pollinators, this has been hampered by the laborious nature of morphologically identifying pollen. Identifying pollen from urban environments is particularly difficult due to the presence of diverse ornamental species associated with consumer horticulture. Metagenetic pollen analysis represents a potential solution to this issue. Building upon prior laboratory and bioinformatic methods, we applied quantitative multilocus metabarcoding to characterize the foraging ecology of honeybee colonies situated in urban, suburban, mixed suburban–agricultural and rural agricultural sites in central Ohio, USA. In cross‐validating a subset of our metabarcoding results using microscopic palynology, we find strong concordance between the molecular and microscopic methods. Our results suggest that forage from the agricultural site exhibited decreased taxonomic diversity and temporal turnover relative to the urban and suburban sites, though the generalization of this observation will require replication across additional sites and cities. Our work demonstrates the power of honeybees as environmental samplers of floral community composition at large spatial scales, aiding in the distinction of taxa characteristically associated with urban or agricultural land use from those distributed ubiquitously across the sampled landscapes. Observed patterns of high forage diversity and compositional turnover in our more urban sites are likely reflective of the fine‐grain heterogeneity and high beta diversity of urban floral landscapes at the scale of honeybee foraging. This provides guidance for future studies investigating how relationships between urbanization and measures of pollinator health are mediated by variation in floral resource dynamics across landscapes. 相似文献
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Barry J. Grant Lars Skjrven Xin‐Qiu Yao 《Protein science : a publication of the Protein Society》2021,30(1):20-30
Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database searching and retrieval, sequence and structure conservation analysis, ensemble normal mode analysis, protein structure and correlation network analysis, principal component, and related multivariate analysis methods. Here, we review recent package developments, including a new underlying segregation into separate packages for distinct analysis, and introduce a new method for structure analysis named ensemble difference distance matrix analysis (eDDM). The eDDM approach calculates and compares atomic distance matrices across large sets of homologous atomic structures to help identify the residue wise determinants underlying specific functional processes. An eDDM workflow is detailed along with an example application to a large protein family. As a new member of the Bio3D family, the Bio3D‐eddm package supports both experimental and theoretical simulation‐generated structures, is integrated with other methods for dissecting sequence‐structure–function relationships, and can be used in a highly automated and reproducible manner. Bio3D is distributed as an integrated set of platform independent open source R packages available from: http://thegrantlab.org/bio3d/ . 相似文献
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Elyeza Bakaze Beloved Mensah Dzomeku Jens‐Norbert Wünsche 《The Annals of applied biology》2021,178(1):98-108
Each year 25–75% of banana and plantain yields are lost because of rhizome damages caused by banana weevil (Cosmopolites sordidus) in growing regions of sub‐Saharan Africa. However, the specific plant defence response of the rhizome tissue in relation to the C. sordidus attack is unknown. Consequently, in this study, we evaluated whether plant defence substances in the rhizome are correlated with the degree of larval damage and whether applications of methyl jasmonate (MJ) elicit a greater induction of the plant defence potential against C. sordidus. Moreover, we attempted to reveal cellular modifications in response to the root feeding herbivore through histochemical staining. The banana cultivars “Km5” and “Mbwazirume” with tolerance and susceptibility to C. sordidus, respectively, were used in a pot experiment to evaluate percent rhizome damage, leaf chlorophyll content, total phenolic content (TPC), antioxidant capacity and cell morphology in response to C. sordidus attack and/or MJ applications compared to untreated control plants. We found that C. sordidus‐induced rhizome damage was 30% in the susceptible cultivar but less than 5% in the tolerant cultivar. The percent rhizome damage was not related to leaf chlorophyll content but showed a significant negative linear relationship to both TPC and antioxidant capacity. Larvae feeding induced a considerably greater increase of polyphenolic defence compounds in Km5 than in Mbwazirume; however, this response was opposite in the MJ treatment, suggesting that the phytohormone induced the susceptible plant to invest more into the synthesis of defence chemicals that in turn lead to reduced C. sordidus damage. Tissue staining demonstrated a greater deposition of lignin and suberin in C. sordidus challenged rhizome, presumably to seal off healthy tissue with a physical barrier from continued pest attack. It is concluded that MJ induces polyphenolics in susceptible Mbwazirume banana that reduced C. sordidus damage. 相似文献
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Miguel ngel Vega‐Ortega Jesús Llanderal‐Mendoza Patricia Gerez‐Fernndez Citlalli Lpez Binnqüist 《The Annals of applied biology》2021,178(1):80-97
Firewood and charcoal are used on a daily basis both in rural areas and in cities. This type of energy is produced by one of the most ancient traditional methods, known as coppice, which harvest tree sprouts. There is controversy about its effects on forests: it preserves populations and tree cover of species used, but reduces density, inhibits sexual reproduction and generates genetic erosion. We inquired if it was possible to identify a loss of genetic diversity in oak populations traditionally used for charcoal by the Zongolica Nahuas in Veracruz state, Mexico. We studied populations of Quercus laurina, Quercus calophylla and Quercus rugosa in three different altitudes. Molecular analysis with eight nuclear codominant microsatellites was performed to determine the diversity, structure and gene flow of these species. Results for Q. laurina were Na = 8.458, I = 1.766, Ho = 0.679, polymorphism = 100%, Fis = 0.079, with intraindividual variation of 81.55%. For Q. calophylla: Na = 7.250, I = 1.563, Ho = 0.646, polymorphism = 91.67%, Fis = 0.083, with intraindividual variation of 83.80%. For Q. rugosa: Na = 6.958, I = 1.510, Ho = 0.574, polymorphism = 91.67%, Fis = 0.204, with intraindividual variation of 81.99%; this species shows signals of an early genetic isolation process. Our findings indicate that Quercus genetic diversity for the three species is high and comparable with oak species in Mexico and worldwide. We conclude that at the present, coppice is preserving a historical diversity in adult trees kept alive through sprouting. Nonetheless, problems with coppice systems elsewhere, unregulated harvesting and expansion of pine plantation in the region suggest that further studies, hand in hand with a landscape management approach that improve charcoal and firewood production, may be valuable for Sierra de Zongolica genetic biodiversity conservation. 相似文献
999.
Large sample theory of semiparametric models based on maximum likelihood estimation (MLE) with shape constraint on the nonparametric component is well studied. Relatively less attention has been paid to the computational aspect of semiparametric MLE. The computation of semiparametric MLE based on existing approaches such as the expectation‐maximization (EM) algorithm can be computationally prohibitive when the missing rate is high. In this paper, we propose a computational framework for semiparametric MLE based on an inexact block coordinate ascent (BCA) algorithm. We show theoretically that the proposed algorithm converges. This computational framework can be applied to a wide range of data with different structures, such as panel count data, interval‐censored data, and degradation data, among others. Simulation studies demonstrate favorable performance compared with existing algorithms in terms of accuracy and speed. Two data sets are used to illustrate the proposed computational method. We further implement the proposed computational method in R package BCA1SG , available at CRAN. 相似文献
1000.
As the global burden of mental illness is estimated to become a severe issue in the near future, it demands the development of more effective treatments. Most psychiatric diseases are moderately to highly heritable and believed to involve many genes. Development of new treatment options demands more knowledge on the molecular basis of psychiatric diseases. Toward this end, we propose to develop new statistical methods with improved sensitivity and accuracy to identify disease‐related genes specialized for psychiatric diseases. The qualitative psychiatric diagnoses such as case control often suffer from high rates of misdiagnosis and oversimplify the disease phenotypes. Our proposed method utilizes endophenotypes, the quantitative traits hypothesized to underlie disease syndromes, to better characterize the heterogeneous phenotypes of psychiatric diseases. We employ the structural equation modeling using the liability‐index model to link multiple genetically regulated expressions from PrediXcan and the manifest variables including endophenotypes and case‐control status. The proposed method can be considered as a general method for multivariate regression, which is particularly helpful for psychiatric diseases. We derive penalized retrospective likelihood estimators to deal with the typical small sample size issue. Simulation results demonstrate the advantages of the proposed method and the real data analysis of Alzheimer's disease illustrates the practical utility of the techniques. Data used in preparation of this article were obtained from the Alzheimer's Disease Neuroimaging Initiative database. 相似文献