Genomics and homeostasis

2003 ◽  
Vol 284 (3) ◽  
pp. R611-R627 ◽  
Author(s):  
Allen W. Cowley
Keyword(s):  
Dna Sequences ◽  
Positional Cloning ◽  
Regulatory Pathways ◽  
Complex Functions ◽  
Challenges And Opportunities ◽  
The Galaxy ◽  
Systems Physiology ◽  
Living Organisms ◽  
New Hypothesis ◽  
Statistical Results

The Cannon lecture this year illustrates how knowledge of DNA sequences of complex living organisms is beginning to shape the landscape of physiology in the 21st century. Enormous challenges and opportunities now exist for physiologists to relate the galaxy of genes to normal and pathological functions. The first extensive genomic systems biology map for cardiovascular and renal function was completed last year as well as a new hypothesis-generating tool (“physiological profiling”) that enables us to hypothesize relationships between specific genes responsible for the regulation of regulatory pathways. Techniques of chromosomal substitution (consomic and congenic rats) are beginning to confirm statistical results from linkage analysis studies, narrow the regions of genetic interest for positional cloning, and provide genetically well-defined control strains for physiological studies. Patterns of gene expression identified by microarray and mapping of expressed genes to chromosomal sites are adding to the understanding of systems physiology. The previously unimaginable goal of connecting ∼36,000 genes to the complex functions of mammalian systems is indeed well underway.

Protein aggregation detection with fluorescent macromolecular and nanostructured probes: challenges and opportunities

2021 ◽  
Author(s):  
Matteo Cingolani ◽  
Liviana Mummolo ◽  
Francesca Lugli ◽  
Mirko Zaffagnini ◽  
Damiano Genovese
Keyword(s):  
Protein Aggregation ◽  
P Protein ◽  
Complex Functions ◽  
Challenges And Opportunities ◽  
External Stimuli

Protein aggregation is a phenomenon widespread in all organisms, that responds to a variety of external stimuli and is involved in complex functions such as storage and recycling of protein...

scholarly journals Societal impact of synthetic biology: responsible research and innovation (RRI)

2016 ◽  
Vol 60 (4) ◽  
pp. 371-379 ◽  
Author(s):  
Daniel Gregorowius ◽  
Anna Deplazes-Zemp
Keyword(s):  
Synthetic Biology ◽  
Technology Assessment ◽  
Ethical Issues ◽  
Responsible Research And Innovation ◽  
Societal Impact ◽  
Biotechnological Applications ◽  
Research And Innovation ◽  
Challenges And Opportunities ◽  
Living Organisms ◽  
Responsible Research

Synthetic biology is an emerging field at the interface between biology and engineering, which has generated many expectations for beneficial biomedical and biotechnological applications. At the same time, however, it has also raised concerns about risks or the aim of producing new forms of living organisms. Researchers from different disciplines as well as policymakers and the general public have expressed the need for a form of technology assessment that not only deals with technical aspects, but also includes societal and ethical issues. A recent and very influential model of technology assessment that tries to implement these aims is known as RRI (Responsible Research and Innovation). In this paper, we introduce this model and its historical precursor strategies. Based on the societal and ethical issues which are presented in the current literature, we discuss challenges and opportunities of applying the RRI model for the assessment of synthetic biology.

scholarly journals Modified HuffBit Compress Algorithm – An Application of R

2018 ◽  
Vol 15 (3) ◽  
Author(s):  
Nahida Habib ◽  
Kawsar Ahmed ◽  
Iffat Jabin ◽  
Mohammad Motiur Rahman
Keyword(s):  
Dna Sequences ◽  
Binary Tree ◽  
Deoxyribonucleic Acid ◽  
Repetitive Sequences ◽  
Huffman Codes ◽  
R Language ◽  
Living Organisms ◽  
Encoding Method ◽  
Dna Sequence Compression ◽  
Sequence Compression

Abstract The databases of genomic sequences are growing at an explicative rate because of the increasing growth of living organisms. Compressing deoxyribonucleic acid (DNA) sequences is a momentous task as the databases are getting closest to its threshold. Various compression algorithms are developed for DNA sequence compression. An efficient DNA compression algorithm that works on both repetitive and non-repetitive sequences known as “HuffBit Compress” is based on the concept of Extended Binary Tree. In this paper, here is proposed and developed a modified version of “HuffBit Compress” algorithm to compress and decompress DNA sequences using the R language which will always give the Best Case of the compression ratio but it uses extra 6 bits to compress than best case of “HuffBit Compress” algorithm and can be named as the “Modified HuffBit Compress Algorithm”. The algorithm makes an extended binary tree based on the Huffman Codes and the maximum occurring bases (A, C, G, T). Experimenting with 6 sequences the proposed algorithm gives approximately 16.18 % improvement in compression ration over the “HuffBit Compress” algorithm and 11.12 % improvement in compression ration over the “2-Bits Encoding Method”.

scholarly journals Robust latent-variable interpretation of in vivo regression models by nested resampling

2019 ◽  
Author(s):  
Alexander W. Caulk ◽  
Kevin A. Janes
Keyword(s):  
Latent Variables ◽  
Latent Variable ◽  
Regression Models ◽  
Cultured Cells ◽  
Least Squares Regression ◽  
Phenotypic Data ◽  
Challenges And Opportunities ◽  
Living Organisms

ABSTRACTSimple multilinear methods, such as partial least squares regression (PLSR), are effective at interrelating dynamic, multivariate datasets of cell–molecular biology through high-dimensional arrays. However, data collected in vivo are more difficult, because animal-to-animal variability is often high, and each time-point measured is usually a terminal endpoint for that animal. Observations are further complicated by the nesting of cells within tissues or tissue sections, which themselves are nested within animals. Here, we introduce principled resampling strategies that preserve the tissue-animal hierarchy of individual replicates and compute the uncertainty of multidimensional decompositions applied to global averages. Using molecular–phenotypic data from the mouse aorta and colon, we find that interpretation of decomposed latent variables (LVs) changes when PLSR models are resampled. Lagging LVs, which statistically improve global-average models, are unstable in resampled iterations that preserve nesting relationships, arguing that these LVs should not be mined for biological insight. Interestingly, resampling is less discriminatory for multidimensional regressions of in vitro data, suggesting it is unnecessary when replicate-to-replicate variance is low. Our work illustrates the challenges and opportunities in translating systems-biology approaches from cultured cells to living organisms. Nested resampling adds a straightforward quality-control step aiding the interpretability of in vivo regression models.

scholarly journals Transcriptional Regulation in the G1-S Cell Cycle Stage in Fungi: Insights through Computational Analysis

2012 ◽  
Vol 6 (1) ◽  
pp. 43-54
Author(s):  
Viktor Martyanov ◽  
Robert H. Gross
Keyword(s):  
Cell Cycle ◽  
Transcription Factor ◽  
Transcriptional Regulation ◽  
Transcription Factors ◽  
Dna Sequences ◽  
Binding Sites ◽  
Positional Distribution ◽  
Upstream Sequence ◽  
Regulatory Pathways ◽  
Binding Factor

The transcription factor complexes Mlu1-box binding factor (MBF) and Swi4/6 cell cycle box binding factor (SBF) regulate the cell cycle in Saccharomyces cerevisiae. They activate hundreds of genes and are responsible for nor-mal cell cycle progression from G1 to S phase. We investigated the conservation of MBF and SBF binding sites during fungal evolution. Orthologs of S. cerevisiae targets of these transcription factors were identified in 37 fungal species and their upstream regions were analyzed for putative transcription factor binding sites. Both groups displayed enrichment in specific putative regulatory DNA sequences in their upstream regions and showed different preferred upstream motif loca-tions, variable patterns of evolutionary conservation of the motifs and enrichment in unique biological functions for the regulated genes. The results indicate that despite high sequence similarity of upstream DNA motifs putatively associated with G1-S transcriptional regulation by MBF and SBF transcription factors, there are important upstream sequence feature differences that may help differentiate the two seemingly similar regulatory modes. The incorporation of upstream motif sequence comparison, positional distribution and evolutionary variability of the motif can complement functional infor-mation about roles of the respective gene products and help elucidate transcriptional regulatory pathways and functions.

scholarly journals A subcellular proteome atlas of the yeast Komagataella phaffii

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Minoska Valli ◽  
Karlheinz Grillitsch ◽  
Clemens Grünwald-Gruber ◽  
Nadine E Tatto ◽  
Bernhard Hrobath ◽  
...  
Keyword(s):  
Lipid Membranes ◽  
Ionization Mass ◽  
Heterologous Proteins ◽  
Regulatory Pathways ◽  
Komagataella Phaffii ◽  
Tandem Mass Tag ◽  
Interactive Map ◽  
Living Organisms ◽  
Cellular Compartments

ABSTRACT The compartmentalization of metabolic and regulatory pathways is a common pattern of living organisms. Eukaryotic cells are subdivided into several organelles enclosed by lipid membranes. Organelle proteomes define their functions. Yeasts, as simple eukaryotic single cell organisms, are valuable models for higher eukaryotes and frequently used for biotechnological applications. While the subcellular distribution of proteins is well studied in Saccharomyces cerevisiae, this is not the case for other yeasts like Komagataella phaffii (syn. Pichia pastoris). Different to most well-studied yeasts, K. phaffii can grow on methanol, which provides specific features for production of heterologous proteins and as a model for peroxisome biology. We isolated microsomes, very early Golgi, early Golgi, plasma membrane, vacuole, cytosol, peroxisomes and mitochondria of K. phaffii from glucose- and methanol-grown cultures, quantified their proteomes by liquid chromatography-electrospray ionization-mass spectrometry of either unlabeled or tandem mass tag-labeled samples. Classification of the proteins by their relative enrichment, allowed the separation of enriched proteins from potential contaminants in all cellular compartments except the peroxisomes. We discuss differences to S. cerevisiae, outline organelle specific findings and the major metabolic pathways and provide an interactive map of the subcellular localization of proteins in K. phaffii.

Hatchery Unit and Six Sigma Methodology

2021 ◽  
pp. 653-669
Author(s):  
Asawaree Anand Hable ◽  
Jaydip Rokade ◽  
Monika M. ◽  
Gopi M.
Keyword(s):  
Continuous Improvement ◽  
Six Sigma ◽  
Egg Quality ◽  
Cost Effective ◽  
Quality Standards ◽  
Poultry Industry ◽  
Defect Reduction ◽  
Challenges And Opportunities ◽  
Six Sigma Methodology ◽  
New Hypothesis

Six Sigma (6σ) is a process improvement methodology and can help in the betterment of the poultry industry. The steps are defined, measure, analyze, improve, and verify. It offers benefits like defect reduction and increased productivity. The new hypothesis is analyzed and improvements are tested and verified. Poultry is the most organized sector in animal agriculture in India, worth Euro 14,500 million. Poultry still has challenges and opportunities for improvement in productivity and quality standards. Six sigma can be applied to the poultry industry for continuous improvement and more economical benefits. The applications of 6σ to hatchery step in poultry may provide quality, uniformity, cost-effective process, minimum error, more customer satisfaction. The benefits offered are a reduction in egg damages, maintenance of egg quality, improvement in hatchability, improvement in hygiene, minimize microbial load and other inventories, improvement in capabilities and discipline of an employee, avoidance of backtracking. Six sigma applications to poultry industry need to be emphasized.

Statistical studies of biomolecular sequences: score-based methods

1994 ◽  
Vol 344 (1310) ◽  
pp. 391-402 ◽  
Keyword(s):  
Dna Sequences ◽  
Protein Sequence ◽  
Sequence Data ◽  
Genome Composition ◽  
Sequence Comparisons ◽  
Multiple Sequence ◽  
Challenges And Opportunities ◽  
Protein Sequence Data ◽  
Statistical Studies ◽  
Massive Accumulation

The massive accumulation of DNA and protein sequence data poses challenges and opportunities in terms of interpretation and analysis. This presentation reviews the method of score-based sequence analysis with the objectives of discerning distinctive segments in single sequences and identifying significant common segments in sequence comparisons. A number of new results are described here for both the theory and its applications. These include distributional theory involving several high scoring segments in single sequences, distribution formulas for general scoring regimes in multiple sequence comparisons, bounds for periodic scoring assignments, sensitivity analysis of genome composition and refinements on predicting exons and genes in DNA sequences.

scholarly journals Spider web DNA: a new spin on noninvasive genetics of predator and prey

2014 ◽  
Author(s):  
Charles Cong Yang Xu ◽  
Ivy J Yen ◽  
Dean Bowman ◽  
Cameron R. Turner
Keyword(s):  
Dna Sequences ◽  
A Priori ◽  
Genetic Material ◽  
Environmental Dna ◽  
Acheta Domesticus ◽  
Spider Webs ◽  
Spider Web ◽  
Black Widow Spiders ◽  
Living Organisms ◽  
Promising Source

Noninvasive genetic approaches enable biomonitoring without the need to directly observe or disturb target organisms. Environmental DNA (eDNA) methods have recently extended this approach by assaying genetic material within bulk environmental samples without a priori knowledge about the presence of target biological material. This paper describes a novel and promising source of noninvasive spider DNA and insect eDNA from spider webs. Using black widow spiders (Latrodectus spp.) fed with house crickets (Acheta domesticus), we successfully extracted and amplified mitochondrial DNA sequences of both spider and prey from spider web. Detectability of spider DNA did not differ between assays with amplicon sizes from 135 to 497 base pairs. Spider DNA and prey eDNA remained detectable at least 88 days after living organisms were no longer present on the web. Spider web DNA may be an important tool in conservation research, pest management, biogeography studies, and biodiversity assessments.

scholarly journals DNA-based long-lived reaction-diffusion patterning in a host hydrogel

2019 ◽  
Author(s):  
Georg Urtel ◽  
André Estevez-Torres ◽  
Jean-Christophe Galas
Keyword(s):  
Dna Sequences ◽  
Reaction Diffusion ◽  
Life Time ◽  
Side Reactions ◽  
Chemical Information ◽  
Living Matter ◽  
Synthetic Material ◽  
Synthetic Life ◽  
Three Stages ◽  
Living Organisms

AbstractThe development of living organisms is a source of inspiration for the creation of synthetic life-like materials. Embryo development is divided into three stages that are inextricably linked: patterning, differentiation and growth. During patterning, sustained out-of-equilibrium molecular programs interpret underlying molecular cues to create well-defined concentration profiles. Implementing this patterning stage in an autonomous synthetic material is a challenge that at least requires a programmable and long-lasting out-of-equilibrium chemistry compatible with a host material. Here we show that DNA/enzyme reactions can create reaction-diffusion patterns that are extraordinary long-lasting both in solution and inside an autonomous hydrogel. The life-time and stability of these patterns - here traveling fronts and two-band patterns - are significantly increased by blocking parasitic side reactions and by dramatically reducing the diffusion coefficient of specific DNA sequences. Immersed in oil, hydrogels pattern autonomously with limited evaporation, but can also exchange chemical information from other gels when brought in contact. Our primitive metabolic material thus recapitulates two important properties of living matter: a certain degree of autonomy that makes each piece of material an ‘individual’ with its own metabolism and, at the same time, the capacity to interact with other ‘individuals’.

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