Asymmetry of cortical functional hierarchy in humans and macaques suggests phylogenetic conservation and adaptation

The human cerebral cortex is symmetrically organized along large-scale axes but also presents inter-hemispheric differences in structure and function. The quantified contralateral homologous difference, i.e., asymmetry, is a key feature of the human brain left-right axis supporting functional processes, such as language. Here, we assessed whether the asymmetry of cortical functional organization is heritable and phylogenetically conserved between humans and macaques. Our findings indicate asymmetric organization along an axis describing a hierarchical functional trajectory from perceptual/action to abstract cognition. Whereas language network showed leftward asymmetric organization, frontoparietal network showed rightward asymmetric organization. These asymmetries were heritable and comparable between humans and macaques, suggesting (phylo)genetic conservation. However, both language and frontoparietal networks showed a qualitatively larger asymmetry in humans relative to macaques and variable heritability in humans. This may reflect an evolutionary adaptation allowing for experience-dependent specialization, linked to higher-order cognitive functions uniquely developed in humans.

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Drug and metabolite-induced perturbations in nuclear structure and function: a review

Biochemistry and Cell Biology ◽

10.1139/o90-059 ◽

1990 ◽

Vol 68 (2) ◽

pp. 408-426 ◽

Cited By ~ 23

Author(s):

Klaus Brasch

Keyword(s):

Nuclear Structure ◽

Nuclear Matrix ◽

Large Scale ◽

Functional Organization ◽

Target Cells ◽

Cell Nuclei ◽

Structural Element ◽

Stimulatory Action ◽

Functional Aspects ◽

And Function

Clarification of large-scale organization in cell nuclei is central to a full understanding of the mechanisms which underlie replication, transcription, and interaction with the cytoplasmic compartment. Many drugs and natural biological agents affect such processes directly, through inhibitory or stimulatory action, and often reveal structural and functional aspects in nuclei not otherwise apparent. There is increasing evidence that the pore complex – lamina of the nuclear matrix is a primary structural element during interphase, which is pivotal to most nuclear processes. This communication reviews evidence based on studies with drugs, inhibitors, and natural biological processes, that the nuclear matrix concept is indeed valid. It is further shown that despite diversity in mode of action and affected target cells, many compounds induce related or complementary changes in nuclei and that such uniformity in pattern is attributable to the nuclear matrix. A general model of the functional organization of the nucleus is presented, to account for the perturbations observed after mass interference with either transcription, replication, or protein synthesis.Key words: nuclear structure, nuclear function, nuclear matrix.

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Integrative and conjugative elements and their hosts: composition, distribution, and organization

10.1101/135814 ◽

2017 ◽

Author(s):

Jean Cury ◽

Marie Touchon ◽

Eduardo P. C. Rocha

Keyword(s):

Large Scale ◽

Functional Organization ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Model Systems ◽

Integrative And Conjugative Elements ◽

Scale Characterization ◽

And Function ◽

Sequence Similarity Networks

AbstractConjugation of single-stranded DNA drives horizontal gene transfer between bacteria and was widely studied in conjugative plasmids. The organization and function of integrative and conjugative elements (ICE), even if they are more abundant, was only studied in a few model systems. Comparative genomics of ICE has been precluded by the difficulty in finding and delimiting these elements. Here, we present the results of a method that circumvents these problems by requiring only the identification of the conjugation genes and the species’ pan-genome. We delimited 200 ICEs and this allowed the first large-scale characterization of these elements. We quantified the presence in ICEs of a wide set of functions associated with the biology of mobile genetic elements, including some that are typically associated with plasmids, such as partition and replication. Protein sequence similarity networks and phylogenetic analyses show that ICEs are modular and that their gene repertoires can be grouped in function of their conjugation types, even if integrases were shown to be paraphyletic relative to the latter. We show that there are general trends in the functional organization of genes within ICEs and of ICEs within the bacterial chromosome paving the way for future functional and evolutionary analyses.

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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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Tool Selectivity in Left Occipitotemporal Cortex Develops without Vision

Journal of Cognitive Neuroscience ◽

10.1162/jocn_a_00411 ◽

2013 ◽

Vol 25 (8) ◽

pp. 1225-1234 ◽

Cited By ~ 48

Author(s):

Marius V. Peelen ◽

Stefania Bracci ◽

Xueming Lu ◽

Chenxi He ◽

Alfonso Caramazza ◽

...

Keyword(s):

Functional Organization ◽

Auditory Task ◽

Anatomical Location ◽

Resting State Functional Connectivity ◽

Frontoparietal Network ◽

Congenitally Blind ◽

Occipitotemporal Cortex ◽

Auditory Tasks ◽

Tool Motion ◽

Selective Activity

Previous studies have provided evidence for a tool-selective region in left lateral occipitotemporal cortex (LOTC). This region responds selectively to pictures of tools and to characteristic visual tool motion. The present human fMRI study tested whether visual experience is required for the development of tool-selective responses in left LOTC. Words referring to tools, animals, and nonmanipulable objects were presented auditorily to 14 congenitally blind and 16 sighted participants. Sighted participants additionally viewed pictures of these objects. In whole-brain group analyses, sighted participants showed tool-selective activity in left LOTC in both visual and auditory tasks. Importantly, virtually identical tool-selective LOTC activity was found in the congenitally blind group performing the auditory task. Furthermore, both groups showed equally strong tool-selective activity for auditory stimuli in a tool-selective LOTC region defined by the picture-viewing task in the sighted group. Detailed analyses in individual participants showed significant tool-selective LOTC activity in 13 of 14 blind participants and 14 of 16 sighted participants. The strength and anatomical location of this activity were indistinguishable across groups. Finally, both blind and sighted groups showed significant resting state functional connectivity between left LOTC and a bilateral frontoparietal network. Together, these results indicate that tool-selective activity in left LOTC develops without ever having seen a tool or its motion. This finding puts constraints on the possible role that this region could have in tool processing and, more generally, provides new insights into the principles shaping the functional organization of OTC.

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

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2015.0603 ◽

2015 ◽

Vol 282 (1813) ◽

pp. 20150603 ◽

Cited By ~ 27

Author(s):

Shaun S. Killen ◽

Julie J. H. Nati ◽

Cory D. Suski

Keyword(s):

Large Scale ◽

Swimming Performance ◽

Anaerobic Capacity ◽

Standard Metabolic Rate ◽

Metabolic Demand ◽

Evolutionary Forces ◽

Individual Fish ◽

Fundamental Information ◽

Behavioural Phenotypes ◽

And Function

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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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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