scholarly journals Using deep learning to model the hierarchical structure and function of a cell

2018 ◽  
Vol 15 (4) ◽  
pp. 290-298 ◽  
Author(s):  
Jianzhu Ma ◽  
Michael Ku Yu ◽  
Samson Fong ◽  
Keiichiro Ono ◽  
Eric Sage ◽  
...  
Keyword(s):  
Deep Learning ◽  
Hierarchical Structure ◽  
Structure And Function ◽  
The Hierarchical Structure ◽  
A Cell ◽  
And Function

3. Proteins

2021 ◽  
pp. 34-51
Author(s):  
Mark Lorch
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Protein Structure ◽  
Protein Structures ◽  
Structure And Function ◽  
Vast Array ◽  
A Cell ◽  
Cellular Machinery ◽  
And Function ◽  
The Relationship

This chapter examines proteins, the dominant proportion of cellular machinery, and the relationship between protein structure and function. The multitude of biological processes needed to keep cells functioning are managed in the organism or cell by a massive cohort of proteins, together known as the proteome. The twenty amino acids that make up the bulk of proteins produce the vast array of protein structures. However, amino acids alone do not provide quite enough chemical variety to complete all of the biochemical activity of a cell, so the chapter also explores post-translation modifications. It finishes by looking as some dynamic aspects of proteins, including enzyme kinetics and the protein folding problem.

scholarly journals Genetic Analysis of Right Heart Structure and Function in 40,000 People

2021 ◽  
Author(s):  
James P. Pirruccello ◽  
Paolo Di Achille ◽  
Victor Nauffal ◽  
Mahan Nekoui ◽  
Samuel N. Friedman ◽  
...  
Keyword(s):  
Pulmonary Hypertension ◽  
Deep Learning ◽  
Right Ventricular ◽  
Congenital Heart ◽  
Left Ventricular ◽  
Structure And Function ◽  
Right Heart ◽  
Heart Chamber ◽  
The Right ◽  
And Function

The heart evolved hundreds of millions of years ago. During mammalian evolution, the cardiovascular system developed with complete separation between pulmonary and systemic circulations incorporated into a single pump with chambers dedicated to each circulation. A lower pressure right heart chamber supplies deoxygenated blood to the lungs, while a high pressure left heart chamber supplies oxygenated blood to the rest of the body. Due to the complexity of morphogenic cardiac looping and septation required to form these two chambers, congenital heart diseases often involve maldevelopment of the evolutionarily recent right heart chamber. Additionally, some diseases predominantly affect structures of the right heart, including arrhythmogenic right ventricular cardiomyopathy (ARVC) and pulmonary hypertension. To gain insight into right heart structure and function, we fine-tuned deep learning models to recognize the right atrium, the right ventricle, and the pulmonary artery, and then used those models to measure right heart structures in over 40,000 individuals from the UK Biobank with magnetic resonance imaging. We found associations between these measurements and clinical disease including pulmonary hypertension and dilated cardiomyopathy. We then conducted genome-wide association studies, identifying 104 distinct loci associated with at least one right heart measurement. Several of these loci were found near genes previously linked with congenital heart disease, such as NKX2-5, TBX3, WNT9B, and GATA4. We also observed interesting commonalities and differences in association patterns at genetic loci linked with both right and left ventricular measurements. Finally, we found that a polygenic predictor of right ventricular end systolic volume was associated with incident dilated cardiomyopathy (HR 1.28 per standard deviation; P = 2.4E-10), and remained a significant predictor of disease even after accounting for a left ventricular polygenic score. Harnessing deep learning to perform large-scale cardiac phenotyping, our results yield insights into the genetic and clinical determinants of right heart structure and function.

scholarly journals Engineering a cell-hydrogel-fibre composite to mimic the structure and function of the tendon synovial sheath

2021 ◽  
Vol 119 ◽  
pp. 140-154
Author(s):  
Angela Imere ◽  
Cosimo Ligorio ◽  
Marie O'Brien ◽  
Jason K.F. Wong ◽  
Marco Domingos ◽  
...  
Keyword(s):  
Fibre Composite ◽  
Structure And Function ◽  
A Cell ◽  
And Function

Small membrane proteins – elucidating the function of the needle in the haystack

2014 ◽  
Vol 395 (12) ◽  
pp. 1365-1377 ◽  
Author(s):  
Grant Kemp ◽  
Florian Cymer
Keyword(s):  
Amino Acids ◽  
Membrane Proteins ◽  
Soluble Proteins ◽  
Structure And Function ◽  
Ribosome Profiling ◽  
Water Soluble ◽  
Eukaryotic Cells ◽  
Large Numbers ◽  
A Cell ◽  
And Function

Abstract Membrane proteins are important mediators between the cell and its environment or between different compartments within a cell. However, much less is known about the structure and function of membrane proteins compared to water-soluble proteins. Moreover, until recently a subset of membrane proteins, those shorter than 100 amino acids, have almost completely evaded detection as a result of technical difficulties. These small membrane proteins (SMPs) have been underrepresented in most genomic and proteomic screens of both pro- and eukaryotic cells and, hence, we know much less about their functions in both. Currently, through a combination of bioinformatics, ribosome profiling, and more sensitive proteomics, large numbers of SMPs are being identified and characterized. Herein we describe recent advances in identifying SMPs from genomic and proteomic datasets and describe examples where SMPs have been successfully characterized biochemically. Finally we give an overview of identified functions of SMPs and speculate on the possible roles SMPs play in the cell.

Epigenetic regulation of gene structure and function with a cell-permeable Cre recombinase

2001 ◽  
Vol 19 (10) ◽  
pp. 929-933 ◽  
Author(s):  
Daewoong Jo ◽  
Abudi Nashabi ◽  
Christie Doxsee ◽  
Qing Lin ◽  
Derya Unutmaz ◽  
...  
Keyword(s):  
Gene Structure ◽  
Epigenetic Regulation ◽  
Cre Recombinase ◽  
Structure And Function ◽  
A Cell ◽  
And Function

scholarly journals Neddylation regulation of mitochondrial structure and functions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Qiyin Zhou ◽  
Yawen Zheng ◽  
Yi Sun
Keyword(s):  
Structure And Function ◽  
Post Translational Modification ◽  
Exciting Field ◽  
E3 Ligases ◽  
Cellular Processes ◽  
Mitochondrial Regulation ◽  
A Cell ◽  
And Function ◽  
Multiple Signaling ◽  
Ring E3 Ligases

AbstractMitochondria are the powerhouse of a cell. The structure and function of mitochondria are precisely regulated by multiple signaling pathways. Neddylation, a post-translational modification, plays a crucial role in various cellular processes including cellular metabolism via modulating the activity, function and subcellular localization of its substrates. Recently, accumulated data demonstrated that neddylation is involved in regulation of morphology, trafficking and function of mitochondria. Mechanistic elucidation of how mitochondria is modulated by neddylation would further our understanding of mitochondrial regulation to a new level. In this review, we first briefly introduce mitochondria, then neddylation cascade, and known protein substrates subjected to neddylation modification. Next, we summarize current available data of how neddylation enzymes, its substrates (including cullins/Cullin-RING E3 ligases and non-cullins) and its inhibitor MLN4924 regulate the structure and function of mitochondria. Finally, we propose the future perspectives on this emerging and exciting field of mitochondrial research.

Interference Microscopy for Cellular Studies

2009 ◽  
pp. 656-672
Author(s):  
Alexey R. Brazhe ◽  
Nadezda A. Brazhe ◽  
Alexey N. Pavlov ◽  
Georgy V. Maksimov
Keyword(s):  
Optical Properties ◽  
Wavelet Analysis ◽  
Cell Structure ◽  
Structure And Function ◽  
Interference Microscopy ◽  
Data Series ◽  
Laser Interference ◽  
Non Invasive ◽  
A Cell ◽  
And Function

This chapter describes the application of interference microscopy and double-wavelet analysis to noninvasive study of cell structure and function. We present different techniques of phase and interference microscopy and discuss how variations in the intrinsic optical properties of a cell can be related to the intracellular processes. Particular emphasis is given to the newly developed phase modulation laser interference microscope. We show how this setup, combined with wavelet analysis of the obtained data series, can be applied to live cell imaging to investigate the rhythmic intracellular processes and their mutual interactions. We hope that the discussion will contribute to the understanding and learning of new methods for non-invasive investigation of intracellular processes.

Note on the Movements of the Mandibular and Maxillary Stylets of the Aphid, Myzus persicae (Sulzer)

1962 ◽  
Vol 94 (6) ◽  
pp. 653-654 ◽  
Author(s):  
R. H. E. Bradley ◽  
E. S. Sylvester ◽  
C. V. Wade
Keyword(s):  
Liquid Medium ◽  
Myzus Persicae ◽  
Plant Viruses ◽  
Structure And Function ◽  
Concerted Effort ◽  
A Cell ◽  
And Function

Lately there has been a concerted effort to elucidate the structure and function of the stylet bundle of suctorial insects. Aphids have received special attention because of their importance as vectors of plant viruses. Several workers have described their observations of stylets penetrating translucent tissues or membranes; for example, Bradley (1952), Mittler (1954), and van Hoof (1958).The movements most easily seen are rapid alternate oscillations at the stylet tips and a back and forth swinging of the entire stylet bundle as it enters a cell or other liquid medium.

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