Vulnerability of individual fish to capture by trawling is influenced by capacity for anaerobic metabolism

The harvest of animals by humans may constitute one of the strongest evolutionary forces affecting wild populations. Vulnerability to harvest varies among individuals within species according to behavioural phenotypes, but we lack fundamental information regarding the physiological mechanisms underlying harvest-induced selection. It is unknown, for example, what physiological traits make some individual fish more susceptible to capture by commercial fisheries. Active fishing methods such as trawling pursue fish during harvest attempts, causing fish to use both aerobic steady-state swimming and anaerobic burst-type swimming to evade capture. Using simulated trawling procedures with schools of wild minnows Phoxinus phoxinus , we investigate two key questions to the study of fisheries-induced evolution that have been impossible to address using large-scale trawls: (i) are some individuals within a fish shoal consistently more susceptible to capture by trawling than others?; and (ii) if so, is this related to individual differences in swimming performance and metabolism? Results provide the first evidence of repeatable variation in susceptibility to trawling that is strongly related to anaerobic capacity and swimming ability. Maximum aerobic swim speed was also negatively correlated with vulnerability to trawling. Standard metabolic rate was highest among fish that were least vulnerable to trawling, but this relationship probably arose through correlations with anaerobic capacity. These results indicate that vulnerability to trawling is linked to anaerobic swimming performance and metabolic demand, drawing parallels with factors influencing susceptibility to natural predators. Selection on these traits by fisheries could induce shifts in the fundamental physiological makeup and function of descendent populations.

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Hypoxia Performance Curve: Assess a Whole-Organism Metabolic Shift from a Maximum Aerobic Capacity towards a Glycolytic Capacity in Fish

Metabolites ◽

10.3390/metabo11070447 ◽

2021 ◽

Vol 11 (7) ◽

pp. 447

Author(s):

Yangfan Zhang ◽

Bog E. So ◽

Anthony P. Farrell

Keyword(s):

Metabolic Rate ◽

Aerobic Capacity ◽

Metabolic Response ◽

Anaerobic Capacity ◽

Standard Metabolic Rate ◽

Individual Variability ◽

Aerobic Performance ◽

Performance Curve ◽

Individual Fish ◽

O2 Supply

The utility of measuring whole-animal performance to frame the metabolic response to environmental hypoxia is well established. Progressively reducing ambient oxygen (O2) will initially limit maximum metabolic rate as a result of a hypoxemic state and ultimately lead to a time-limited, tolerance state supported by substrate-level phosphorylation when the O2 supply can no longer meet basic needs (standard metabolic rate, SMR). The metabolic consequences of declining ambient O2 were conceptually framed for fishes initially by Fry’s hypoxic performance curve, which characterizes the hypoxemic state and its consequences to absolute aerobic scope (AAS), and Hochachka’s concept of scope for hypoxic survival, which characterizes time-limited life when SMR cannot be supported by O2 supply. Yet, despite these two conceptual frameworks, the toolbox to assess whole-animal metabolic performance remains rather limited. Here, we briefly review the ongoing debate concerning the need to standardize the most commonly used assessments of respiratory performance in hypoxic fishes, namely critical O2 (the ambient O2 level below which maintenance metabolism cannot be sustained) and the incipient lethal O2 (the ambient O2 level at which a fish loses the ability to maintain upright equilibrium), and then we advance the idea that the most useful addition to the toolbox will be the limiting-O2 concentration (LOC) performance curve. Using Fry & Hart’s (1948) hypoxia performance curve concept, an LOC curve was subsequently developed as an eco-physiological framework by Neil et al. and derived for a group of fish during a progressive hypoxia trial by Claireaux and Lagardère (1999). In the present review, we show how only minor modifications to available respirometry tools and techniques are needed to generate an LOC curve for individual fish. This individual approach to the LOC curve determination then increases its statistical robustness and importantly opens up the possibility of examining individual variability. Moreover, if peak aerobic performance at a given ambient O2 level of each individual is expressed as a percentage of its AAS, the water dissolved O2 that supports 50% of the individual’s AAS (DOAAS-50) can be interpolated much like the P50 for an O2 hemoglobin dissociation curve (when hemoglobin is 50% saturated with O2). Thus, critical O2, incipient lethal O2, DOAAS-50 and P50 and can be directly compared within and across species. While an LOC curve for individual fish represents a start to an ongoing need to seamlessly integrate aerobic to anaerobic capacity assessments in a single, multiplexed respirometry trial, we close with a comparative exploration of some of the known whole-organism anaerobic and aerobic capacity traits to examine for correlations among them and guide the next steps.

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Plant hormones, plant growth regulators

Orvosi Hetilap ◽

10.1556/oh.2014.29939 ◽

2014 ◽

Vol 155 (26) ◽

pp. 1011-1018 ◽

Cited By ~ 1

Author(s):

György Végvári ◽

Edina Vidéki

Keyword(s):

Nervous System ◽

Growth And Development ◽

Large Scale ◽

Essential Role ◽

Higher Plants ◽

Structure And Function ◽

Wide Sense ◽

Large Scale Integration ◽

Scale Integration ◽

And Function

Plants seem to be rather defenceless, they are unable to do motion, have no nervous system or immune system unlike animals. Besides this, plants do have hormones, though these substances are produced not in glands. In view of their complexity they lagged behind animals, however, plant organisms show large scale integration in their structure and function. In higher plants, such as in animals, the intercellular communication is fulfilled through chemical messengers. These specific compounds in plants are called phytohormones, or in a wide sense, bioregulators. Even a small quantity of these endogenous organic compounds are able to regulate the operation, growth and development of higher plants, and keep the connection between cells, tissues and synergy beween organs. Since they do not have nervous and immume systems, phytohormones play essential role in plants’ life. Orv. Hetil., 2014, 155(26), 1011–1018.

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Functional design of glycan-conjugated molecules using a chemoenzymatic approach

Bioscience Biotechnology and Biochemistry ◽

10.1093/bbb/zbab024 ◽

2021 ◽

Author(s):

Makoto Ogata

Keyword(s):

Molecular Weight ◽

Large Scale ◽

Biological Activities ◽

Natural Compounds ◽

Low Molecular Weight ◽

Functional Design ◽

Enzymatic Method ◽

Conjugated Molecules ◽

Design Synthesis ◽

And Function

Abstract Carbohydrates play important and diverse roles in the fundamental processes of life. We have established a method for accurately and a large scale synthesis of functional carbohydrates with diverse properties using a unique enzymatic method. Furthermore, various artificial glycan-conjugated molecules have been developed by adding these synthetic carbohydrates to macromolecules and to middle and low molecular weight molecules with different properties. These glycan-conjugated molecules have biological activities comparable to or higher than those of natural compounds, and present unique functions. In this review, several synthetic glycan-conjugated molecules are taken as examples to show design, synthesis and function.

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A widespread pathway for substitution of adenine by diaminopurine in phage genomes

Science ◽

10.1126/science.abe4882 ◽

2021 ◽

Vol 372 (6541) ◽

pp. 512-516

Author(s):

Yan Zhou ◽

Xuexia Xu ◽

Yifeng Wei ◽

Yu Cheng ◽

Yu Guo ◽

...

Keyword(s):

Large Scale ◽

Restriction Enzymes ◽

Diverse Range ◽

Host Restriction ◽

Form And Function ◽

Multienzyme System ◽

Dna Modifications ◽

Dna Production ◽

And Function

DNA modifications vary in form and function but generally do not alter Watson-Crick base pairing. Diaminopurine (Z) is an exception because it completely replaces adenine and forms three hydrogen bonds with thymine in cyanophage S-2L genomic DNA. However, the biosynthesis, prevalence, and importance of Z genomes remain unexplored. Here, we report a multienzyme system that supports Z-genome synthesis. We identified dozens of globally widespread phages harboring such enzymes, and we further verified the Z genome in one of these phages, Acinetobacter phage SH-Ab 15497, by using liquid chromatography with ultraviolet and mass spectrometry. The Z genome endows phages with evolutionary advantages for evading the attack of host restriction enzymes, and the characterization of its biosynthetic pathway enables Z-DNA production on a large scale for a diverse range of applications.

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Tree Diversity Reduces Fungal Endophyte Richness and Diversity in a Large-Scale Temperate Forest Experiment

Diversity ◽

10.3390/d11120234 ◽

2019 ◽

Vol 11 (12) ◽

pp. 234 ◽

Cited By ~ 2

Author(s):

Eric A. Griffin ◽

Joshua G. Harrison ◽

Melissa K. McCormick ◽

Karin T. Burghardt ◽

John D. Parker

Keyword(s):

Phylogenetic Diversity ◽

Large Scale ◽

High Throughput Sequencing ◽

Spatial Scales ◽

Fungal Endophytes ◽

Fungal Endophyte ◽

Tree Diversity ◽

Trophic Levels ◽

Community Diversity ◽

And Function

Although decades of research have typically demonstrated a positive correlation between biodiversity of primary producers and associated trophic levels, the ecological drivers of this association are poorly understood. Recent evidence suggests that the plant microbiome, or the fungi and bacteria found on and inside plant hosts, may be cryptic yet important drivers of important processes, including primary production and trophic interactions. Here, using high-throughput sequencing, we characterized foliar fungal community diversity, composition, and function from 15 broadleaved tree species (N = 545) in a recently established, large-scale temperate tree diversity experiment using over 17,000 seedlings. Specifically, we tested whether increases in tree richness and phylogenetic diversity would increase fungal endophyte diversity (the “Diversity Begets Diversity” hypothesis), as well as alter community composition (the “Tree Diversity–Endophyte Community” hypothesis) and function (the “Tree Diversity–Endophyte Function” hypothesis) at different spatial scales. We demonstrated that increasing tree richness and phylogenetic diversity decreased fungal species and functional guild richness and diversity, including pathogens, saprotrophs, and parasites, within the first three years of a forest diversity experiment. These patterns were consistent at the neighborhood and tree plot scale. Our results suggest that fungal endophytes, unlike other trophic levels (e.g., herbivores as well as epiphytic bacteria), respond negatively to increasing plant diversity.

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

Science ◽

10.1126/science.abi8870 ◽

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.

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Neural system-enriched gene expression: relationship to biological pathways and neurological diseases

Physiological Genomics ◽

10.1152/physiolgenomics.00220.2003 ◽

2004 ◽

Vol 18 (2) ◽

pp. 167-183 ◽

Cited By ~ 12

Author(s):

Jianhua Zhang ◽

Amy Moseley ◽

Anil G. Jegga ◽

Ashima Gupta ◽

David P. Witte ◽

...

Keyword(s):

Gene Expression ◽

Nervous System ◽

Intracellular Signaling ◽

Large Scale ◽

Expression Profiles ◽

Gene List ◽

Structure And Function ◽

System Structure ◽

Psychiatric Disease ◽

And Function

To understand the commitment of the genome to nervous system differentiation and function, we sought to compare nervous system gene expression to that of a wide variety of other tissues by gene expression database construction and mining. Gene expression profiles of 10 different adult nervous tissues were compared with that of 72 other tissues. Using ANOVA, we identified 1,361 genes whose expression was higher in the nervous system than other organs and, separately, 600 genes whose expression was at least threefold higher in one or more regions of the nervous system compared with their median expression across all organs. Of the 600 genes, 381 overlapped with the 1,361-gene list. Limited in situ gene expression analysis confirmed that identified genes did represent nervous system-enriched gene expression, and we therefore sought to evaluate the validity and significance of these top-ranked nervous system genes using known gene literature and gene ontology categorization criteria. Diverse functional categories were present in the 381 genes, including genes involved in intracellular signaling, cytoskeleton structure and function, enzymes, RNA metabolism and transcription, membrane proteins, as well as cell differentiation, death, proliferation, and division. We searched existing public sites and identified 110 known genes related to mental retardation, neurological disease, and neurodegeneration. Twenty-one of the 381 genes were within the 110-gene list, compared with a random expectation of 5. This suggests that the 381 genes provide a candidate set for further analyses in neurological and psychiatric disease studies and that as a field, we are as yet, far from a large-scale understanding of the genes that are critical for nervous system structure and function. Together, our data indicate the power of profiling an individual biologic system in a multisystem context to gain insight into the genomic basis of its structure and function.

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A Potential of microRNAs for High-Content Screening

Journal of Nucleic Acids ◽

10.4061/2011/870903 ◽

2011 ◽

Vol 2011 ◽

pp. 1-15 ◽

Cited By ~ 9

Author(s):

Andrius Serva ◽

Christoph Claas ◽

Vytaute Starkuviene

Keyword(s):

Large Scale ◽

Cellular Processes ◽

Comprehensive Knowledge ◽

Functional Models ◽

Rapid Accumulation ◽

Health And Disease ◽

Temporal And Spatial ◽

And Function ◽

Functional Analyses ◽

Immense Potential

In the last years miRNAs have increasingly been recognised as potent posttranscriptional regulators of gene expression. Possibly, miRNAs exert their action on virtually any biological process by simultaneous regulation of numerous genes. The importance of miRNA-based regulation in health and disease has inspired research to investigate diverse aspects of miRNA origin, biogenesis, and function. Despite the recent rapid accumulation of experimental data, and the emergence of functional models, the complexity of miRNA-based regulation is still far from being well understood. In particular, we lack comprehensive knowledge as to which cellular processes are regulated by which miRNAs, and, furthermore, how temporal and spatial interactions of miRNAs to their targets occur. Results from large-scale functional analyses have immense potential to address these questions. In this review, we discuss the latest progress in application of high-content and high-throughput functional analysis for the systematic elucidation of the biological roles of miRNAs.

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Direct observation of the setular web that fuses thoracopodal setae of a calanoid copepod into a collapsible fan

10.1101/808196 ◽

2019 ◽

Author(s):

George von Dassow ◽

Richard B. Emlet

Keyword(s):

Food Webs ◽

Carbon Flux ◽

High Speed ◽

Calanoid Copepod ◽

Swimming Performance ◽

Structure And Function ◽

High Speed Video ◽

Aquatic Food ◽

And Function ◽

Oceanic Carbon

SummaryCopepods are numerically dominant planktonic grazers throughout the waters of Earth, preyed upon in turn by a wide diversity of pelagic animals (1,2). Their feeding and swimming performance thus has global importance to aquatic food webs and oceanic carbon flux. These crustaceans swim and feed using cuticle-covered, segmented, muscular appendages whose reach is extended greatly by setae, extracellular chitinous extensions with diverse structure and function (3). Plumose setae, with subsidiary setules arranged like barbs on a feather, have well-documented roles in generating feeding and swimming currents (4,5). Recent work showed that plumose setae of barnacle cyprid thoracopods are permanently linked by setules into a single fan that opens and closes as one sheet during high-speed swimming (6). Intersetular linkage across cyprid thoracopods may greatly decrease leakage between extended setae, ensure even spread of setae within the fan, and promote ordered collapse of the fan to avoid entanglement of adjacent appendages. Here we demonstrate similar setular webbing amongst thoracopod setae in the calanoid copepod Acartia sp. High-speed video directly documents the existence of such links, and reveals that individuals experience apparently-irreparable degradation of the setal array due to de-linkage, with likely consequences for swimming performance.

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