scholarly journals Screening of Gas Substrate and Medium Effects on 2,3-Butanediol Production with C. ljungdahlii and C. autoethanogenum Aided by Improved Autotrophic Cultivation Technique

Fermentation ◽  
2021 ◽  
Vol 7 (4) ◽  
pp. 264
Author(s):  
Luca Ricci ◽  
Valeria Agostino ◽  
Debora Fino ◽  
Angela Re
Keyword(s):  
Large Scale ◽  
Mineral Elements ◽  
Positive Influence ◽  
Model Organisms ◽  
Co2 Gas ◽  
Gas Fermentation ◽  
Screening Strategies ◽  
Genus Clostridium ◽  
Fair Comparison ◽  
Cultivation Technique

Gas fermentation by acetogens of the genus Clostridium is an attractive technology since it affords the production of biochemicals and biofuels from industrial waste gases while contributing to mitigate the carbon cycle alterations. The acetogenic model organisms C. ljungdahlii and C. autoethanogenum have already been used in large scale industrial fermentations. Among the natural products, ethanol production has already attained industrial scale. However, some acetogens are also natural producers of 2,3-butanediol (2,3-BDO), a platform chemical of relevant industrial interest. Here, we have developed a lab-scale screening campaign with the aim of enhancing 2,3-BDO production. Our study generated comparable data on growth and 2,3-BDO production of several batch gas fermentations using C. ljungdahlii and C. autoethanogenum grown on different gas substrates of primary applicative interest (CO2 · H2, CO · CO2, syngas) and on different media featuring different compositions as regards trace metals, mineral elements and vitamins. CO · CO2 fermentation was found to be preferable for the production of 2,3-BDO, and a fair comparison of the strains cultivated in comparable conditions revealed that C. ljungdahlii produced 3.43-fold higher titer of 2,3-BDO compared to C. autoethanogenum. Screening of different medium compositions revealed that mineral elements, Zinc and Iron exert a major positive influence on 2,3-BDO titer and productivity. Moreover, the CO2 influence on CO fermentation was explored by characterizing C. ljungdahlii response with respect to different gas ratios in the CO · CO2 gas mixtures. The screening strategies undertaken in this study led to the production of 2.03 ± 0.05 g/L of 2,3-BDO, which is unprecedented in serum bottle experiments.

Effectiveness the use of additive MEGA-VIT in the ration of mares of Shetland pony breed

2020 ◽  
pp. 60-67
Author(s):  
G. Uskov ◽  
A. Tsopanova ◽  
T. Perezhogina
Keyword(s):  
Physiological State ◽  
Mineral Elements ◽  
Positive Influence ◽  
Control Group ◽  
Physiological Indicators ◽  
Mineral Additive ◽  
Nutritional Needs ◽  
Young Horses ◽  
The Cost ◽  
Experimental Group

Complete feeding of ponies is provided on the basis of data on their nutritional needs depending on age, sex, physiological state and level of productivity (the amount of milk produced and the intensity of growth of young animals). Ponies are sensitive to a lack of vitamins and mineral elements in the feed. When there is a sufficient amount of organic and mineral substances, but a lack or absence of vitamins, horses and ponies have impaired metabolism. The purpose of this work is to study the effectiveness of the use of vitamin and mineral additive MEGA-VIT in the rations of pregnant and lactating mares of Shetland pony breed. It has been found during of the researches that the vitamin and mineral additive MEGA-VIT had a positive influence on the productive and physiological indicators of animals. The cost of spent feed for the entire period of experiment in the control group was 50,6 thousand rubles, and in the experimental group it was 11,8 thousand rubles more or 23,5 %. Revenue from the sale of young horses of the control group amounted to 400 thousand rubles, and experimental group – 440 thousand rubles, this is by 40 thousand rubles more than in control group. This led to the increase in profit in the experimental group of mares by 28,1 thousand rubles and accordingly the level of profitability by 3,2 %. It has been recommended on the results have been obtained on the base of researches to include 30 g/head/day in the rations of mares of Shetland pony breed during pregnancy, and 50 g/head/day during lactation.

MIC-Drop: A platform for large-scale in vivo CRISPR screens

Science ◽  
2021 ◽  
pp. eabi8870
Author(s):  
Saba Parvez ◽  
Chelsea Herdman ◽  
Manu Beerens ◽  
Korak Chakraborti ◽  
Zachary P. Harmer ◽  
...  
Keyword(s):  
Large Scale ◽  
Cultured Cells ◽  
Cardiac Development ◽  
Droplet Microfluidics ◽  
Model Organisms ◽  
Genetic Screens ◽  
Large Numbers ◽  
And Function ◽  
Genome Scale

CRISPR-Cas9 can be scaled up for large-scale screens in cultured cells, but CRISPR screens in animals have been challenging because generating, validating, and keeping track of large numbers of mutant animals is prohibitive. Here, we report Multiplexed Intermixed CRISPR Droplets (MIC-Drop), a platform combining droplet microfluidics, single-needle en masse CRISPR ribonucleoprotein injections, and DNA barcoding to enable large-scale functional genetic screens in zebrafish. The platform can efficiently identify genes responsible for morphological or behavioral phenotypes. In one application, we show MIC-Drop can identify small molecule targets. Furthermore, in a MIC-Drop screen of 188 poorly characterized genes, we discover several genes important for cardiac development and function. With the potential to scale to thousands of genes, MIC-Drop enables genome-scale reverse-genetic screens in model organisms.

Six-fold increase in historical Northern Hemisphere concurrent large heatwaves driven by warming and changing atmospheric circulations

2021 ◽  
pp. 1-39
Author(s):  
Cassandra D.W. Rogers ◽  
Kai Kornhuber ◽  
Sarah E. Perkins-Kirkpatrick ◽  
Paul C. Loikith ◽  
Deepti Singh
Keyword(s):  
Northern Hemisphere ◽  
Large Scale ◽  
Warm Season ◽  
Fold Increase ◽  
Circulation Pattern ◽  
Positive Influence ◽  
Climate Risks ◽  
Circulation Patterns ◽  
Multiple Regions ◽  
Barents And Kara Seas

AbstractSimultaneous heatwaves affecting multiple regions (referred to as concurrent heatwaves), pose compounding threats to various natural and societal systems, including global food chains, emergency response systems, and reinsurance industries. While anthropogenic climate change is increasing heatwave risks across most regions, the interactions between warming and circulation changes that yield concurrent heatwaves remain understudied. Here, we quantify historical (1979-2019) trends in concurrent heatwaves during the warm-season (May-September, MJJAS) across the Northern Hemisphere mid- to high-latitudes. We find a significant increase of ~46% in the mean spatial extent of concurrent heatwaves, ~17% increase in their maximum intensity, and ~6-fold increase in their frequency. Using Self-Organising Maps, we identify large-scale circulation patterns (300 hPa) associated with specific concurrent heatwave configurations across Northern Hemisphere regions. We show that observed changes in the frequency of specific circulation patterns preferentially increase the risk of concurrent heatwaves across particular regions. Patterns linking concurrent heatwaves across eastern North America, eastern and northern Europe, parts of Asia, and the Barents and Kara Seas, show the largest increases in frequency (~5.9 additional days per decade). We also quantify the relative contributions of circulation pattern changes and warming to overall observed concurrent heatwave day frequency trends. While warming has a predominant and positive influence on increasing concurrent heatwaves, circulation pattern changes have a varying influence and account for up to 0.8 additional concurrent heatwave days per decade. Identifying regions with an elevated risk of concurrent heatwaves and understanding their drivers is indispensable for evaluating projected climate risks on interconnected societal systems and fostering regional preparedness in a changing climate.

scholarly journals The daunting polygenicity of mental illness: making a new map

2018 ◽  
Vol 373 (1742) ◽  
pp. 20170031 ◽  
Author(s):  
Steven E. Hyman
Keyword(s):  
Mental Health ◽  
Large Scale ◽  
Computational Models ◽  
Model Organisms ◽  
Human Biology ◽  
Genetic Studies ◽  
Computational Tools ◽  
Experimental Systems ◽  
Terra Incognita ◽  
Phenotypic Complexity

An epochal opportunity to elucidate the pathogenic mechanisms of psychiatric disorders has emerged from advances in genomic technology, new computational tools and the growth of international consortia committed to data sharing. The resulting large-scale, unbiased genetic studies have begun to yield new biological insights and with them the hope that a half century of stasis in psychiatric therapeutics will come to an end. Yet a sobering picture is coming into view; it reveals daunting genetic and phenotypic complexity portending enormous challenges for neurobiology. Successful exploitation of results from genetics will require eschewal of long-successful reductionist approaches to investigation of gene function, a commitment to supplanting much research now conducted in model organisms with human biology, and development of new experimental systems and computational models to analyse polygenic causal influences. In short, psychiatric neuroscience must develop a new scientific map to guide investigation through a polygenic terra incognita . This article is part of a discussion meeting issue ‘Of mice and mental health: facilitating dialogue between basic and clinical neuroscientists’.

An International Campaign for Agricultural and Livestock Genomics (CALG)

2002 ◽  
Vol 06 (24) ◽  
pp. 958-965
Author(s):  
Jun Yu ◽  
Jian Wang ◽  
Huanming Yang
Keyword(s):  
Large Scale ◽  
Cost Effective ◽  
Model Organisms ◽  
Environmental Biology ◽  
Cdna Sequences ◽  
Governmental Agencies ◽  
Technology Innovations ◽  
A Genome ◽  
Starting Point ◽  
The Cost

A coordinated international effort to sequence agricultural and livestock genomes has come to its time. While human genome and genomes of many model organisms (related to human health and basic biological interests) have been sequenced or plugged in the sequencing pipelines, agronomically important crop and livestock genomes have not been given high enough priority. Although we are facing many challenges in policy-making, grant funding, regional task emphasis, research community consensus and technology innovations, many initiatives are being announced and formulated based on the cost-effective and large-scale sequencing procedure, known as whole genome shotgun (WGS) sequencing that produces draft sequences covering a genome from 95 percent to 99 percent. Identified genes from such draft sequences, coupled with other resources, such as molecular markers, large-insert clones and cDNA sequences, provide ample information and tools to further our knowledge in agricultural and environmental biology in the genome era that just comes to its accelerated period. If the campaign succeeds, molecular biologists, geneticists and field biologists from all countries, rich or poor, would be brought to the same starting point and expect another astronomical increase of basic genomic information, ready to convert effectively into knowledge that will ultimately change our lives and environment into a greater and better future. We call upon national and international governmental agencies and organizations as well as research foundations to support this unprecedented movement.

scholarly journals Climate-induced phenological shifts in a Batesian mimicry complex

2018 ◽  
Vol 116 (3) ◽  
pp. 929-933 ◽  
Author(s):  
Christopher Hassall ◽  
Jac Billington ◽  
Thomas N. Sherratt
Keyword(s):  
Large Scale ◽  
Computer Game ◽  
Species Traits ◽  
Batesian Mimicry ◽  
Model Organisms ◽  
Fitness Costs ◽  
Symbiotic Relationships ◽  
Phenological Shifts ◽  
Phenological Synchrony ◽  
Random Patterns

Climate-induced changes in spatial and temporal occurrence of species, as well as species traits such as body size, each have the potential to decouple symbiotic relationships. Past work has focused primarily on direct interactions, particularly those between predators and prey and between plants and pollinators, but studies have rarely demonstrated significant fitness costs to the interacting, coevolving organisms. Here, we demonstrate that changing phenological synchrony in the latter part of the 20th century has different fitness outcomes for the actors within a Batesian mimicry complex, where predators learn to differentiate harmful “model” organisms (stinging Hymenoptera) from harmless “mimics” (hoverflies, Diptera: Syrphidae). We define the mimetic relationships between 2,352 pairs of stinging Hymenoptera and their Syrphidae mimics based on a large-scale citizen science project and demonstrate that there is no relationship between the phenological shifts of models and their mimics. Using computer game-based experiments, we confirm that the fitness of models, mimics, and predators differs among phenological scenarios, creating a phenologically antagonistic system. Finally, we show that climate change is increasing the proportion of mimetic interactions in which models occur first and reducing mimic-first and random patterns of occurrence, potentially leading to complex fitness costs and benefits across all three actors. Our results provide strong evidence for an overlooked example of fitness consequences from changing phenological synchrony.

scholarly journals Hidden in plain sight: What remains to be discovered in the eukaryotic proteome?

2018 ◽  
Author(s):  
Valerie Wood ◽  
Antonia Lock ◽  
Midori A. Harris ◽  
Kim Rutherford ◽  
Jürg Bähler ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Fission Yeast ◽  
Genome Sequencing ◽  
Large Scale ◽  
Biological Process ◽  
Blind Spot ◽  
Model Organisms ◽  
Biological Processes ◽  
Health And Disease

AbstractThe first decade of genome sequencing stimulated an explosion in the characterization of unknown proteins. More recently, the pace of functional discovery has slowed, leaving around 20% of the proteins even in well-studied model organisms without informative descriptions of their biological roles. Remarkably, many uncharacterized proteins are conserved from yeasts to human, suggesting that they contribute to fundamental biological processes. To fully understand biological systems in health and disease, we need to account for every part of the system. Unstudied proteins thus represent a collective blind spot that limits the progress of both basic and applied biosciences.We use a simple yet powerful metric based on Gene Ontology (GO) biological process terms to define characterized and uncharacterized proteins for human, budding yeast, and fission yeast. We then identify a set of conserved but unstudied proteins in S. pombe, and classify them based on a combination of orthogonal attributes determined by large-scale experimental and comparative methods. Finally, we explore possible reasons why these proteins remain neglected, and propose courses of action to raise their profile and thereby reap the benefits of completing the catalog of proteins’ biological roles.

scholarly journals Phyletic distribution and diversification of the Phage Shock Protein stress response system in bacteria and archaea

2021 ◽  
Author(s):  
Philipp F. Popp ◽  
Vadim M. Gumerov ◽  
Ekaterina P. Andrianova ◽  
Lisa Bewersdorf ◽  
Thorsten Mascher ◽  
...  
Keyword(s):  
Stress Response ◽  
Large Scale ◽  
Cell Envelope ◽  
Model Organisms ◽  
Microbial World ◽  
Natural Classification ◽  
Response System ◽  
Core Proteins ◽  
Envelope Stress

AbstractThe bacterial cell envelope is an essential structure that protects the cell from environmental threats, while simultaneously serving as communication interface and diffusion barrier. Therefore, maintaining cell envelope integrity is of vital importance for all microorganisms. Not surprisingly, evolution has shaped conserved protection networks that connect stress perception, transmembrane signal transduction and mediation of cellular responses upon cell envelope stress. The phage shock protein (PSP) stress response is one of such conserved protection networks. Most of the knowledge about the Psp response comes from studies in the Gram-negative model bacterium, Escherichia coli where the Psp system consists of several well-defined protein components. Homologous systems were identified in representatives of Proteobacteria, Actinobacteria, and Firmicutes; however, the Psp system distribution in the microbial world remains largely unknown. By carrying out a large-scale, unbiased comparative genomics analysis, we found components of the Psp system in many bacterial and archaeal phyla and demonstrated that the PSP system deviates dramatically from the proteobacterial prototype. Two of its core proteins, PspA and PspC, have been integrated in various (often phylum-specifically) conserved protein networks during evolution. Based on protein sequence and gene neighborhood analyses of pspA and pspC homologs, we built a natural classification system of PSP networks in bacteria and archaea. We performed a comprehensive in vivo protein interaction screen for the PSP network newly identified in the Gram-positive model organism Bacillus subtilis and found a strong interconnected PSP response system, illustrating the validity of our approach. Our study highlights the diversity of PSP organization and function across many bacterial and archaeal phyla and will serve as foundation for future studies of this envelope stress response beyond model organisms.

scholarly journals Deconstructing Gastrulation at the Single Cell Level

2021 ◽  
Author(s):  
Tomer Stern ◽  
Sebastian J Streichan ◽  
Stanislav Y Shvartsman ◽  
Eric F Wieschaus
Keyword(s):  
Large Scale ◽  
Drosophila Embryo ◽  
Cell Segmentation ◽  
Model Organisms ◽  
Specific Cell ◽  
Cell Behaviors ◽  
Animal Development ◽  
Wide Range ◽  
Cell Groups ◽  
Epithelial Sheets

Gastrulation movements in all animal embryos start with regulated deformations of patterned epithelial sheets. Current studies of gastrulation use a wide range of model organisms and emphasize either large-scale tissue processes or dynamics of individual cells and cell groups. Here we take a step towards bridging these complementary strategies and deconstruct early stages of gastrulation in the entire Drosophila embryo, where transcriptional patterns in the blastoderm give rise to region-specific cell behaviors. Our approach relies on an integrated computational framework for cell segmentation and tracking and on efficient algorithms for event detection. Our results reveal how thousands of cell shape changes, divisions, and intercalations drive large-scale deformations of the patterned blastoderm, setting the stage for systems-level dissection of a pivotal step in animal development.

scholarly journals iProteinDB: an integrative database of Drosophila post-translational modifications

2018 ◽  
Author(s):  
Yanhui Hu ◽  
Richelle Sopko ◽  
Verena Chung ◽  
Romain A. Studer ◽  
Sean D. Landry ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Protein Function ◽  
Large Scale ◽  
Model Organisms ◽  
General Strategy ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Functional Sites ◽  
Evolutionarily Conserved ◽  
And Function

AbstractPost-translational modification (PTM) serves as a regulatory mechanism for protein function, influencing stability, protein interactions, activity and localization, and is critical in many signaling pathways. The best characterized PTM is phosphorylation, whereby a phosphate is added to an acceptor residue, commonly serine, threonine and tyrosine. As proteins are often phosphorylated at multiple sites, identifying those sites that are important for function is a challenging problem. Considering that many phosphorylation sites may be non-functional, prioritizing evolutionarily conserved phosphosites provides a general strategy to identify the putative functional sites with regards to regulation and function. To facilitate the identification of conserved phosphosites, we generated a large-scale phosphoproteomics dataset from Drosophila embryos collected from six closely-related species. We built iProteinDB (https://www.flyrnai.org/tools/iproteindb/), a resource integrating these data with other high-throughput PTM datasets, including vertebrates, and manually curated information for Drosophila. At iProteinDB, scientists can view the PTM landscape for any Drosophila protein and identify predicted functional phosphosites based on a comparative analysis of data from closely-related Drosophila species. Further, iProteinDB enables comparison of PTM data from Drosophila to that of orthologous proteins from other model organisms, including human, mouse, rat, Xenopus laevis, Danio rerio, and Caenorhabditis elegans.

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