scholarly journals ChroMo, an Application for Unsupervised Analysis of Chromosome Movements in Meiosis

Cells ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 2013
Author(s):  
Daniel León-Periñán ◽  
Alfonso Fernández-Álvarez
Keyword(s):  
Data Mining ◽  
Meiotic Prophase ◽  
Motif Discovery ◽  
Chromosome Morphology ◽  
Model Organisms ◽  
Physico Chemical ◽  
Time Series Segmentation ◽  
Cloud Application ◽  
High Throughput Imaging ◽  
Chromosome Movements

Nuclear movements during meiotic prophase, driven by cytoskeleton forces, are a broadly conserved mechanism in opisthokonts and plants to promote pairing between homologous chromosomes. These forces are transmitted to the chromosomes by specific associations between telomeres and the nuclear envelope during meiotic prophase. Defective chromosome movements (CMs) harm pairing and recombination dynamics between homologues, thereby affecting faithful gametogenesis. For this reason, modelling the behaviour of CMs and their possible microvariations as a result of mutations or physico-chemical stress is important to understand this crucial stage of meiosis. Current developments in high-throughput imaging and image processing are yielding large CM datasets that are suitable for data mining approaches. To facilitate adoption of data mining pipelines, we present ChroMo, an interactive, unsupervised cloud application specifically designed for exploring CM datasets from live imaging. ChroMo contains a wide selection of algorithms and visualizations for time-series segmentation, motif discovery, and assessment of causality networks. Using ChroMo to analyse meiotic CMs in fission yeast, we found previously undiscovered features of CMs and causality relationships between chromosome morphology and trajectory. ChroMo will be a useful tool for understanding the behaviour of meiotic CMs in yeast and other model organisms.

scholarly journals Chromatin accessibility and regulatory vocabulary across indicine cattle tissues

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Pâmela A. Alexandre ◽  
Marina Naval-Sánchez ◽  
Moira Menzies ◽  
Loan T. Nguyen ◽  
Laercio R. Porto-Neto ◽  
...  
Keyword(s):  
Motif Discovery ◽  
Target Genes ◽  
Developmental Stages ◽  
Bos Taurus ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Model Organisms ◽  
Open Chromatin ◽  
Health And Disease ◽  
Collaborative Efforts

Abstract Background Spatiotemporal changes in the chromatin accessibility landscape are essential to cell differentiation, development, health, and disease. The quest of identifying regulatory elements in open chromatin regions across different tissues and developmental stages is led by large international collaborative efforts mostly focusing on model organisms, such as ENCODE. Recently, the Functional Annotation of Animal Genomes (FAANG) has been established to unravel the regulatory elements in non-model organisms, including cattle. Now, we can transition from prediction to validation by experimentally identifying the regulatory elements in tropical indicine cattle. The identification of regulatory elements, their annotation and comparison with the taurine counterpart, holds high promise to link regulatory regions to adaptability traits and improve animal productivity and welfare. Results We generate open chromatin profiles for liver, muscle, and hypothalamus of indicine cattle through ATAC-seq. Using robust methods for motif discovery, motif enrichment and transcription factor binding sites, we identify potential master regulators of the epigenomic profile in these three tissues, namely HNF4, MEF2, and SOX factors, respectively. Integration with transcriptomic data allows us to confirm some of their target genes. Finally, by comparing our results with Bos taurus data we identify potential indicine-specific open chromatin regions and overlaps with indicine selective sweeps. Conclusions Our findings provide insights into the identification and analysis of regulatory elements in non-model organisms, the evolution of regulatory elements within two cattle subspecies as well as having an immediate impact on the animal genetics community in particular for a relevant productive species such as tropical cattle.

scholarly journals Conserved meiotic mechanisms in the cnidarian Clytia hemisphaerica revealed by Spo11 knockout

2022 ◽  
Author(s):  
Catriona Munro ◽  
Hugo Cadis ◽  
Evelyn Houliston ◽  
Jean-Ren&eacute Huynh
Keyword(s):  
Classical Model ◽  
Fruit Fly ◽  
Model Organisms ◽  
Oocyte Growth ◽  
Alternative Pathways ◽  
Functional Studies ◽  
Evolutionarily Conserved ◽  
Synaptonemal Complex Formation ◽  
Chromosome Movements

During meiosis, each duplicated chromosome pairs and recombines with its unique homolog to ensure the shuffling of genetic information across generations. Functional studies in classical model organisms have revealed a surprising diversity in the chronology and interdependency of the earliest meiotic steps such as chromosome movements, pairing, association via Synaptonemal Complex formation (synapsis), recombination and the formation of chiasmata. A key player is Spo11, an evolutionarily conserved topoisomerase-related transesterase that initiates meiotic recombination via the catalysis of programmed DNA double stranded breaks (DSBs). While DSBs are required for pairing and synapsis in budding yeast and mouse, alternative pathways are employed during female meiosis of the fruit fly and nematode Caenorhabditis elegans. Here, to provide a comparative perspective on meiotic regulation from a distinct animal clade, we chart gametogenesis in Clytia hemisphaerica jellyfish and examine the role of Spo11 using CRISPR-Cas9 mutants, generated clonally from F0 polyp colonies. Spo11 mutant females fail to assemble synaptonemal complexes and chiasmata, such that homologous chromosome pairs disperse during oocyte growth. Subsequent meiotic divisions are abnormal but produce viable progeny. Clytia thus shares an ancient eukaryotic dependence of synapsis and chromosome segregation on Spo11-generated DSBs. It provides a valuable additional experimental model for dissecting meiotic mechanisms during animal gametogenesis, and for building a comparative framework for distinguishing evolutionarily conserved versus flexible features of meiosis.

Characterization of physico-chemical properties of biodiesel components using smart data mining approaches

Fuel ◽  
2020 ◽  
Vol 266 ◽  
pp. 117075
Author(s):  
Danial Abooali ◽  
Reza Soleimani ◽  
Saeed Gholamreza-Ravi
Keyword(s):  
Data Mining ◽  
Chemical Properties ◽  
Physico Chemical ◽  
Smart Data

Bioinformatics Data Management and Data Mining

2008 ◽  
pp. 1714-1721
Author(s):  
Boris Galitsky
Keyword(s):  
Data Mining ◽  
Human Genetics ◽  
Genome Mapping ◽  
Biological Information ◽  
Model Organisms ◽  
Functional Study ◽  
Biological Research ◽  
Biochemical Processes ◽  
E Coli ◽  
Mapping Techniques

Bioinformatics is the science of storing, extracting, organizing, analyzing, interpreting, and utilizing information from biological sequences and molecules.  The focus of bioinformatics is the application of computer technology to the management of biological information. Specifically, it is the science of developing computer databases and algorithms to facilitate and expedite biological research, particularly in genomics. It has been mainly stimulated by advances in DNA sequencing and genome mapping techniques (Adams, Fields & Venter, 1994). Genomics is the discipline that studies genes and their functions, including the functional study of genes, their resulting proteins, and the role played by the proteins in the biochemical processes, as well as the study of human genetics by comparisons with model organisms such as mice, fruit flies, and the bacterium E. coli

Bioinformatics Data Management and Data Mining

2005 ◽  
pp. 29-34 ◽  
Author(s):  
Boris Galitsky
Keyword(s):  
Data Mining ◽  
Human Genetics ◽  
Genome Mapping ◽  
Biological Information ◽  
Model Organisms ◽  
Functional Study ◽  
Biological Research ◽  
Biochemical Processes ◽  
E Coli ◽  
Mapping Techniques

Bioinformatics is the science of storing, extracting, organizing, analyzing, interpreting, and utilizing information from biological sequences and molecules.  The focus of bioinformatics is the application of computer technology to the management of biological information. Specifically, it is the science of developing computer databases and algorithms to facilitate and expedite biological research, particularly in genomics. It has been mainly stimulated by advances in DNA sequencing and genome mapping techniques (Adams, Fields & Venter, 1994). Genomics is the discipline that studies genes and their functions, including the functional study of genes, their resulting proteins, and the role played by the proteins in the biochemical processes, as well as the study of human genetics by comparisons with model organisms such as mice, fruit flies, and the bacterium E. coli

Optimization of MRI Acquisition and Texture Analysis to Predict Physico-chemical Parameters of Loins by Data Mining

2017 ◽  
Vol 10 (4) ◽  
pp. 750-758 ◽  
Author(s):  
Trinidad Pérez-Palacios ◽  
Daniel Caballero ◽  
Teresa Antequera ◽  
Maria Luisa Durán ◽  
Mar Ávila ◽  
...  
Keyword(s):  
Data Mining ◽  
Texture Analysis ◽  
Chemical Parameters ◽  
Physico Chemical

MOTIF DISCOVERY WITH DATA MINING IN 3D PROTEIN STRUCTURE DATABASES: DISCOVERY, VALIDATION AND PREDICTION OF THE U-SHAPE ZINC BINDING ("HUF-ZINC") MOTIF

2013 ◽  
Vol 11 (01) ◽  
pp. 1340008 ◽  
Author(s):  
SEBASTIAN MAURER-STROH ◽  
HE GAO ◽  
HAO HAN ◽  
LIES BAETEN ◽  
JOOST SCHYMKOWITZ ◽  
...  
Keyword(s):  
Data Mining ◽  
Metal Ion ◽  
Motif Discovery ◽  
Enzymatic Catalysis ◽  
3D Structure ◽  
Structural Motif ◽  
Zinc Binding ◽  
Sequence Motif ◽  
3D Protein Structure ◽  
Binding Motifs

Data mining in protein databases, derivatives from more fundamental protein 3D structure and sequence databases, has considerable unearthed potential for the discovery of sequence motif—structural motif—function relationships as the finding of the U-shape (Huf-Zinc) motif, originally a small student's project, exemplifies. The metal ion zinc is critically involved in universal biological processes, ranging from protein-DNA complexes and transcription regulation to enzymatic catalysis and metabolic pathways. Proteins have evolved a series of motifs to specifically recognize and bind zinc ions. Many of these, so called zinc fingers, are structurally independent globular domains with discontinuous binding motifs made up of residues mostly far apart in sequence. Through a systematic approach starting from the BRIX structure fragment database, we discovered that there exists another predictable subset of zinc-binding motifs that not only have a conserved continuous sequence pattern but also share a characteristic local conformation, despite being included in totally different overall folds. While this does not allow general prediction of all Zn binding motifs, a HMM-based web server, Huf-Zinc, is available for prediction of these novel, as well as conventional, zinc finger motifs in protein sequences. The Huf-Zinc webserver can be freely accessed through this URL ( http://mendel.bii.a-star.edu.sg/METHODS/hufzinc/ ).

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