scholarly journals Rapid Body-Wide Transcriptomic Turnover During Rhesus Macaque Perinatal Development

2021 ◽  
Vol 12 ◽  
Author(s):  
Wenqian Zhang ◽  
Wei Wang ◽  
Manman Zhao ◽  
Christoph W. Turck ◽  
Ying Zhu ◽  
...  
Keyword(s):  
Large Scale ◽  
Molecular Level ◽  
Rhesus Macaques ◽  
Transcriptome Data ◽  
Critical Periods ◽  
Peak Period ◽  
Perinatal Development ◽  
Primate Brain ◽  
Shape Pattern ◽  
Similar Peak

An hourglass cup-shape pattern of regulation at the molecular level was detected during the development of the primate brain. Specifically, a peak of temporally differentially expressed genes around the time of birth has been observed in the human brain. However, to what extend this peak of regulation exists among species has not been investigated in great detail. Here, by integrating multiple large-scale transcriptome data from rhesus macaques, we confirmed that a similar differential expression peak exists during the development of the macaque brain. We also found that a similar peak exists during the development of other organs, such as liver, testis, kidney and heart. Furthermore, we found that distinct pathways are regulated in the peak period of those organs. Our results highlight the importance of co-evolution of diverse organs during critical periods of perinatal development in primates.

scholarly journals Diffusion MRI data, sulcal anatomy, and tractography for eight species from the Primate Brain Bank

2021 ◽  
Author(s):  
Katherine L. Bryant ◽  
Dirk Jan Ardesch ◽  
Lea Roumazeilles ◽  
Lianne H. Scholtens ◽  
Alexandre A. Khrapitchev ◽  
...  
Keyword(s):  
Diffusion Mri ◽  
Large Scale ◽  
Structural Mri ◽  
Relative Volume ◽  
Primate Species ◽  
Brain Bank ◽  
Cingulum Bundle ◽  
Primate Brain ◽  
Multiple Levels ◽  
Comparative Neuroscience

AbstractLarge-scale comparative neuroscience requires data from many species and, ideally, at multiple levels of description. Here, we contribute to this endeavor by presenting diffusion and structural MRI data from eight primate species that have not or rarely been described in the literature. The selected samples from the Primate Brain Bank cover a prosimian, New and Old World monkeys, and a great ape. We present preliminary labelling of the cortical sulci and tractography of the optic radiation, dorsal part of the cingulum bundle, and dorsal parietal–frontal and ventral temporal-frontal longitudinal white matter tracts. Both dorsal and ventral association fiber systems could be observed in all samples, with the dorsal tracts occupying much less relative volume in the prosimian than in other species. We discuss the results in the context of known primate specializations and present hypotheses for further research. All data and results presented here are available online as a resource for the scientific community.

scholarly journals Noni fruit’s water spot appearance on the second day of harvest: a trade-off between resistance and energy

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Tian Wu ◽  
Danyan Hu ◽  
Qingfen Wang
Keyword(s):  
Statistical Analysis ◽  
Molecular Level ◽  
Morinda Citrifolia ◽  
Transcriptome Data ◽  
Trade Off ◽  
Kegg Pathways ◽  
Available Energy ◽  
Climacteric Fruit ◽  
The Relationship ◽  
Insight Into

Abstract Background Noni (Morinda citrifolia Linn.) is a tropical tree that bears climacteric fruit. Previous observations and research have shown that the second day (2 d) after harvest is the most important demarcation point when the fruit has the same appearance as the freshly picked fruit (0 d); however, they are beginning to become water spot appearance. We performed a conjoint analysis of metabolome and transcriptome data for noni fruit of 0 d and 2 d to reveal what happened to the fruit at the molecular level. Genes and metabolites were annotated to KEGG pathways and the co-annotated KEGG pathways were used as a statistical analysis. Results We found 25 pathways that were significantly altered at both metabolic and transcriptional levels, including a total of 285 differentially expressed genes (DEGs) and 11 differential metabolites through an integrative analysis of transcriptomics and metabolomics. The energy metabolism and pathways originating from phenylalanine were disturbed the most. The upregulated resistance metabolites and genes implied the increase of resistance and energy consumption in the postharvest noni fruit. Most genes involved in glycolysis were downregulated, further limiting the available energy. This lack of energy led noni fruit to water spot appearance, a prelude to softening. The metabolites and genes related to the resistance and energy interacted and restricted each other to keep noni fruit seemingly hard within two days after harvest, but actually the softening was already unstoppable. Conclusions This study provides a new insight into the relationship between the metabolites and genes of noni fruit, as well as a foundation for further clarification of the post-ripening mechanism in noni fruit.

scholarly journals A Mass-Temperature Decoupled Discretization Strategy for Large-Scale Molecular-Level Kinetic Model

2021 ◽  
pp. 117348
Author(s):  
Zhengyu Chen ◽  
Dong Guan ◽  
Xiaojie Zhang ◽  
Ying Zhang ◽  
Suoqi Zhao ◽  
...  
Keyword(s):  
Kinetic Model ◽  
Large Scale ◽  
Molecular Level ◽  
Mass Temperature

scholarly journals A Mass-Temperature Decoupled Discretization Strategy for Large-Scale Molecular-Level Kinetic Model

2021 ◽  
Author(s):  
Zhengyu Chen ◽  
Dong Guan ◽  
Xiaojie Zhang ◽  
Ying Zhang ◽  
Suoqi Zhao ◽  
...  
Keyword(s):  
Kinetic Model ◽  
Differential Equations ◽  
Heat Balance ◽  
Large Scale ◽  
Molecular Level ◽  
Complex Mixture ◽  
Estimation Methods ◽  
Computational Time ◽  
Node Number ◽  
Mass Temperature

The molecular conversion of complex mixture involves a large number of species and reactions. The corresponding kinetic model is consist of a series of ordinary differential equations (ODEs) with severe stiffness, leading to an exponentially growing computational time. To reduce the computational time, we proposed a mass-temperature decoupled discretization strategy for a large-scale molecular-level kinetic model. The method separates the mass balance and heat balance calculations in the rigorous adiabatic reactor model and divided the reactor into several isothermal segments. After discretization, the differential equations for heat balance can be replaced by algebraic equations between nodes. We used a molecular-level diesel hydrotreating kinetic model as the case to validate the proposed method. We investigated the effects of temperature estimation methods and node number on the accuracy of the model. A good agreement between the discretization model and rigorous model was observed while the computational time was significantly shortened

Railway fuel and its impact on the forests in colonial India: The case of the Punjab, 1860–1884

2012 ◽  
Vol 47 (4) ◽  
pp. 1283-1309 ◽  
Author(s):  
PALLAVI V. DAS
Keyword(s):  
Environmental Degradation ◽  
Large Scale ◽  
National Level ◽  
Regional Level ◽  
Peak Period ◽  
Colonial State ◽  
Colonial India ◽  
Railway Line ◽  
State Response ◽  
The Impact

AbstractRecent studies have stressed the need for micro-histories of the environment so that important differences and similarities at local, regional and national level might be revealed. This paper analyses the process and patterns of environmental degradation at regional level by taking the case of deforestation in colonial Punjab by studying its implication at the level of empire. More specifically, it examines three aspects of how the operation and expansion of railways from 1869 to 1884, a peak period of railway expansion, affected the forests of the Punjab's plains. First, the paper analyses the reasons for large-scale railway expansion in the Punjab by discussing spatial and temporal expansion. Secondly, the impact of the railway firewood demand on the Punjab's forests between 1860 and 1884 is examined, specifically, the conditions that facilitated the increased dependence of the railways on firewood. Next follows an examination of the temporally varying nature of deforestation, given that railway firewood demand was determined by railway line openings. This section also includes a discussion on the nature of the colonial state response to the deforestation crisis and its role in maintaining the fuel supply to the railways. Finally, in the context of deforestation in the Punjab, the paper discusses how and why railway fuel changed from firewood to coal.

scholarly journals Molecular and Clinical Characterization of PD-1 in Breast Cancer Using Large-Scale Transcriptome Data

2020 ◽  
Vol 11 ◽  
Author(s):  
Qiang Liu ◽  
Ran Cheng ◽  
Xiangyi Kong ◽  
Zhongzhao Wang ◽  
Yi Fang ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Large Scale ◽  
Transcriptome Data

scholarly journals Gene Expression Patterns Underlying the Reinstatement of Plasticity in the Adult Visual System

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Ettore Tiraboschi ◽  
Ramon Guirado ◽  
Dario Greco ◽  
Petri Auvinen ◽  
Jose Fernando Maya-Vetencourt ◽  
...  
Keyword(s):  
Gene Expression ◽  
Visual Cortex ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Monocular Deprivation ◽  
Adult Brain ◽  
Gene Expression Patterns ◽  
Postnatal Life ◽  
Critical Periods

The nervous system is highly sensitive to experience during early postnatal life, but this phase of heightened plasticity decreases with age. Recent studies have demonstrated that developmental-like plasticity can be reactivated in the visual cortex of adult animals through environmental or pharmacological manipulations. These findings provide a unique opportunity to study the cellular and molecular mechanisms of adult plasticity. Here we used the monocular deprivation paradigm to investigate large-scale gene expression patterns underlying the reinstatement of plasticity produced by fluoxetine in the adult rat visual cortex. We found changes, confirmed with RT-PCRs, in gene expression in different biological themes, such as chromatin structure remodelling, transcription factors, molecules involved in synaptic plasticity, extracellular matrix, and excitatory and inhibitory neurotransmission. Our findings reveal a key role for several molecules such as the metalloproteases Mmp2 and Mmp9 or the glycoprotein Reelin and open up new insights into the mechanisms underlying the reopening of the critical periods in the adult brain.

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