differential distribution
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2022 ◽  
Vol 4 (1) ◽  
Author(s):  
Aedan G K Roberts ◽  
Daniel R Catchpoole ◽  
Paul J Kennedy

ABSTRACT There is increasing evidence that changes in the variability or overall distribution of gene expression are important both in normal biology and in diseases, particularly cancer. Genes whose expression differs in variability or distribution without a difference in mean are ignored by traditional differential expression-based analyses. Using a Bayesian hierarchical model that provides tests for both differential variability and differential distribution for bulk RNA-seq data, we report here an investigation into differential variability and distribution in cancer. Analysis of eight paired tumour–normal datasets from The Cancer Genome Atlas confirms that differential variability and distribution analyses are able to identify cancer-related genes. We further demonstrate that differential variability identifies cancer-related genes that are missed by differential expression analysis, and that differential expression and differential variability identify functionally distinct sets of potentially cancer-related genes. These results suggest that differential variability analysis may provide insights into genetic aspects of cancer that would not be revealed by differential expression, and that differential distribution analysis may allow for more comprehensive identification of cancer-related genes than analyses based on changes in mean or variability alone.


Author(s):  
И.С. Бондарчук ◽  
С.С. Титов ◽  
С.С. Бондарчук

В работе предлагаются два новых эффективных алгоритма, реализованных коротким программным кодом в MS Excel, предназначенных для идентификации и характеризации размеров нано– и микропорошков частиц в виде обобщенного гамма или логнормального распределений по данным опытных гистограмм. Предлагаемый метод представляет собой новый и достаточно общий подход к решению обратных задач идентификации параметров дифференциальных функций распределения по экспериментальным данным на основе на минимизации функционала, представляющего собой коэффициент детерминации.Алгоритм реализован формулами (менее 10) наиболее распространенного инструментария (электронных таблиц MS Excel без использования макросов), позволяющего исследователям, не обладающими навыками профессиональных программистов, простоту проверки и воспроизведения представленного материала, а также возможность модификации кода для решения более широкого круга задач. Текст статьи и комментарии на рабочих листах скриншотов представляют собой готовые инструкции по решению задач идентификация функций распределения и характеризации размеров нано– и микропорошков. The paper proposes two new efficient algorithms, implemented by a short program code in MS Excel, designed to identify and characterize the sizes of nano- and micropowders of particles in the form of generalized gamma or lognormal distributions according to experimental histograms. The proposed method is a new general approach to solving inverse problems of identifying the parameters of differential distribution functions from experimental data based on minimizing the functional that is the coefficient of determination.The algorithm is implemented with formulas (less than 10) of the most common tools (MS Excel spreadsheets without the use of macros), which allow researchers without the skills of professional programmers to easily check and reproduce the presented material, as well as the ability to modify the code to solve a wider range of problems. The text of the article and comments on the worksheets of screenshots represent ready-made instructions for solving problems of identification of distribution functions and characterization of the sizes of nano- and micropowders.


2021 ◽  
Vol 12 ◽  
Author(s):  
Neha Jha ◽  
Dwight Hall ◽  
Akshay Kanakan ◽  
Priyanka Mehta ◽  
Ranjeet Maurya ◽  
...  

Globally, SARS-CoV-2 has moved from one tide to another with ebbs in between. Genomic surveillance has greatly aided the detection and tracking of the virus and the identification of the variants of concern (VOC). The knowledge and understanding from genomic surveillance is important for a populous country like India for public health and healthcare officials for advance planning. An integrative analysis of the publicly available datasets in GISAID from India reveals the differential distribution of clades, lineages, gender, and age over a year (Apr 2020–Mar 2021). The significant insights include the early evidence towards B.1.617 and B.1.1.7 lineages in the specific states of India. Pan-India longitudinal data highlighted that B.1.36* was the predominant clade in India until January–February 2021 after which it has gradually been replaced by the B.1.617.1 lineage, from December 2020 onward. Regional analysis of the spread of SARS-CoV-2 indicated that B.1.617.3 was first seen in India in the month of October in the state of Maharashtra, while the now most prevalent strain B.1.617.2 was first seen in Bihar and subsequently spread to the states of Maharashtra, Gujarat, and West Bengal. To enable a real time understanding of the transmission and evolution of the SARS-CoV-2 genomes, we built a transmission map available on https://covid19-indiana.soic.iupui.edu/India/EmergingLineages/April2020/to/March2021. Based on our analysis, the rate estimate for divergence in our dataset was 9.48 e-4 substitutions per site/year for SARS-CoV-2. This would enable pandemic preparedness with the addition of future sequencing data from India available in the public repositories for tracking and monitoring the VOCs and variants of interest (VOI). This would help aid decision making from the public health perspective.


2021 ◽  
Vol 13 ◽  
Author(s):  
Michinori Ezura ◽  
Akio Kikuchi ◽  
Nobuyuki Okamura ◽  
Aiko Ishiki ◽  
Takafumi Hasegawa ◽  
...  

Introduction: We aimed to determine whether in vivo tau deposits and monoamine oxidase B (MAO-B) detection using 18F-THK5351 positron emission tomography (PET) can assist in the differential distribution in patients with corticobasal syndrome (CBS), progressive supranuclear palsy (PSP), and Alzheimer’s disease (AD) and whether 18F-THK5351 retention of lesion sites in CBS and PSP can correlate with clinical parameters.Methods:18F-THK5351 PET was performed in 35 participants, including 7, 9, and 10 patients with CBS, PSP, and AD, respectively, and 9 age-matched normal controls. In CBS and PSP, cognitive and motor functions were assessed using the Montreal Cognitive Assessment, Addenbrooke’s Cognitive Examination–Revised, and Frontal Assessment Battery, Unified Parkinson’s Disease Rating Scale Motor Score, and PSP Rating Scale.Results:18F-THK5351 retention was observed in sites susceptible to disease-related pathologies in CBS, PSP, and AD. 18F-THK5351 uptake in the precentral gyrus clearly differentiated patients with CBS from those with PSP and AD. Furthermore, 18F-THK5351 uptake in the inferior temporal gyrus clearly differentiated patients with AD from those with CBS and PSP. Regional 18F-THK5351 retention was associated with the cognitive function in CBS and PSP.Conclusion: Measurement of the tau deposits and MAO-B density in the brain using 18F-THK5351 may be helpful for the differential diagnosis of tauopathies and for understanding disease stages.


2021 ◽  
Vol 12 ◽  
Author(s):  
Xuezhao Sun ◽  
Ian G. Andrew ◽  
Philip J. Harris ◽  
Simone O. Hoskin ◽  
Keith N. Joblin ◽  
...  

The cell walls of forage chicory (Cichorium intybus) leaves are known to contain high proportions of pectic polysaccharides. However, little is known about the distribution of pectic polysaacharides among walls of different cell types/tissues and within walls. In this study, immunolabelling with four monoclonal antibodies was used to map the distribution of pectic polysaccharides in the cell walls of the laminae and midribs of these leaves. The antibodies JIM5 and JIM7 are specific for partially methyl-esterified homogalacturonans; LM5 and LM6 are specific for (1→4)-β-galactan and (1→5)-α-arabinan side chains, respectively, of rhamnogalacturonan I. All four antibodies labelled the walls of the epidermal cells with different intensities. JIM5 and JIM7, but not LM5 or LM6, labelled the middle lamella, tricellular junctions, and the corners of intercellular spaces of ground, xylem and phloem parenchyma. LM5, but not LM6, strongly labelled the walls of the few sclerenchyma fibres in the phloem of the midrib and lamina vascular bundles. The LM5 epitope was absent from some phloem parenchyma cells. LM6, but not LM5, strongly labelled the walls of the stomatal guard cells. The differential distribution of pectic epitopes among walls of different cell types and within walls may reflect the deposition and modification of these polysaccharides which are involved in cell wall properties and cell development.


Author(s):  
Hans-Jürgen Ensikat ◽  
Maximilian Weigend

Biomineralization is a common phenomenon in plants and has been shown to be chemically, functionally and topologically diverse. Silica and calcium carbonate have long been known as structural plant biominerals and calcium phosphate (apatite)–long known from animals–has recently been reported. Strikingly, up to three different biominerals may occur in a single trichome in, e.g., Urticaceae and Loasaceae, and in combination with organic compounds, can form organic/inorganic composite materials. This article presents an extension of previous studies on the distribution of these biominerals in Loasaceae trichomes with a focus on their spatial (three-dimensional) distribution and co-localization with organic substances. Light microscopy and scanning electron microscopy with high-resolution EDX element analyses of sample surfaces and sections illustrate the differential distribution and composition of the different biomineral phases across cell surfaces and cell walls. Raman spectroscopy additionally permits the identification of organic and inorganic compounds side by side. All three biominerals may be found in a nearly pure inorganic phase, e.g., on the plant surfaces and in the barbs of the glochidiate trichomes, or in combination with a larger proportion of organic compounds (cellulose, pectin). The cell lumen may be additionally filled with amorphous mineral deposits. Water-solubility of the mineral fractions differs considerably. Plant trichomes provide an exciting model system for biomineralization and enable the in-vivo study of the formation of complex composite materials with different biomineral and organic compounds involved.


PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0257115
Author(s):  
Shivangi Thakur ◽  
Upendra Kumar ◽  
Rashmi Malik ◽  
Darshana Bisht ◽  
Priyanka Balyan ◽  
...  

Cymbopogon, commonly known as lemon grass, is one of the most important aromatic grasses having therapeutic and medicinal values. FISH signals on somatic chromosome spreads off Cymbopogon species indicated the localization of 45S rDNA on the terminal region of short arms of a chromosome pair. A considerable interspecific variation in the intensity of 45S rDNA hybridization signals was observed in the cultivars of Cymbopogon winterianus and Cymbopogon flexuosus. Furthermore, in all the varieties of C. winterianus namely Bio-13, Manjari and Medini, a differential distribution of 45S rDNA was observed in a heterologous pair of chromosomes 1. The development of C. winterianus var. Manjari through gamma radiation may be responsible for breakage of fragile rDNA site from one of the chromosomes of this heterologous chromosome pair. While, in other two varieties of C. winterianus (Bio-13 and Medini), this variability may be because of evolutionary speciation due to natural cross among two species of Cymbopogon which was fixed through clonal propagation. However, in both the situations these changes were fixed by vegetative method of propagation which is general mode of reproduction in the case of C. winterianus.


Toxins ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 814
Author(s):  
Leijane F. Sousa ◽  
Matthew L. Holding ◽  
Tiago H. M. Del-Rei ◽  
Marisa M. T. Rocha ◽  
Rosa H. V. Mourão ◽  
...  

Differences in snake venom composition occur across all taxonomic levels and it has been argued that this variation represents an adaptation that has evolved to facilitate the capture and digestion of prey and evasion of predators. Bothrops atrox is a terrestrial pitviper that is distributed across the Amazon region, where it occupies different habitats. Using statistical analyses and functional assays that incorporate individual variation, we analyzed the individual venom variability in B. atrox snakes from four different habitats (forest, pasture, degraded area, and floodplain) in and around the Amazon River in Brazil. We observed venom differentiation between spatially distinct B. atrox individuals from the different habitats, with venom variation due to both common (high abundance) and rare (low abundance) proteins. Moreover, differences in the composition of the venoms resulted in individual variability in functionality and heterogeneity in the lethality to mammals and birds, particularly among the floodplain snakes. Taken together, the data obtained from individual venoms of B. atrox snakes, captured in different habitats from the Brazilian Amazon, support the hypothesis that the differential distribution of protein isoforms results in functional distinctiveness and the ability of snakes with different venoms to have variable toxic effects on different prey.


2021 ◽  
Author(s):  
Meng-xiang Sun ◽  
Xiaorong Huang

During angiosperm male gametogenesis, microspores divide to produce a vegetative cell (VC) and a male germline (MG), each with a distinct cell fate. How the MG cell/VC fate is determined remains largely unknown. Here, we report that H3K27me3 is essential for VC fate commitment and H3K27me3 erasure contributes to the MG cell fate initiation in male gametophyte of Arabidopsis. The VC-targeted H3K27me3 erasure disturbed the VC development and resulted in the VC fate shifting towards a gamete destination, which suggests that MG cells require H3K27me3 erasure for triggering the gamete cell fate. Multi-omics and cytologic analysis confirmed the occurrence of extensive cell identity transition due to H3K27me3 erasure. Therefore, we experimentally confirm that the MG cell/VC fate is epigenetically regulated. The H3K27 methylation plays a critical role in the guidance of MG cell/VC fate determination for pollen fertility in Arabidopsis. Our work also provides new evidences for two previous hypotheses that the germline cell fate is specified by the differential distribution of yet unknown determinant, and VC maintains the microspore's default program, namely the H3K27me3 setting, whereas MG requires reprogramming.


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