scholarly journals Evolutionary Constraint on Visual and Nonvisual Mammalian Opsins

2021 ◽  
pp. 074873042199987
Author(s):  
Brian A. Upton ◽  
Nicolás M. Díaz ◽  
Shannon A. Gordon ◽  
Russell N. Van Gelder ◽  
Ethan D. Buhr ◽  
...  
Keyword(s):  
Mammalian Species ◽  
Light Sensitivity ◽  
Specific Gene ◽  
Human Populations ◽  
Evolutionary Constraint ◽  
Moderate Degree ◽  
Amino Acid Residues ◽  
Metabolic Physiology ◽  
Conservation Patterns ◽  
Cone Opsins

Animals have evolved light-sensitive G protein–coupled receptors, known as opsins, to detect coherent and ambient light for visual and nonvisual functions. These opsins have evolved to satisfy the particular lighting niches of the organisms that express them. While many unique patterns of evolution have been identified in mammals for rod and cone opsins, far less is known about the atypical mammalian opsins. Using genomic data from over 400 mammalian species from 22 orders, unique patterns of evolution for each mammalian opsins were identified, including photoisomerases, RGR-opsin (RGR) and peropsin (RRH), as well as atypical opsins, encephalopsin (OPN3), melanopsin (OPN4), and neuropsin (OPN5). The results demonstrate that OPN5 and rhodopsin show extreme conservation across all mammalian lineages. The cone opsins, SWS1 and LWS, and the nonvisual opsins, OPN3 and RRH, demonstrate a moderate degree of sequence conservation relative to other opsins, with some instances of lineage-specific gene loss. Finally, the photoisomerase, RGR, and the best-studied atypical opsin, OPN4, have high sequence diversity within mammals. These conservation patterns are maintained in human populations. Importantly, all mammalian opsins retain key amino acid residues important for conjugation to retinal-based chromophores, permitting light sensitivity. These patterns of evolution are discussed along with known functions of each atypical opsin, such as in circadian or metabolic physiology, to provide insight into the observed patterns of evolutionary constraint.

scholarly journals The effect of seasonal birth pulses on pathogen persistence in wild mammal populations

2014 ◽  
Vol 281 (1786) ◽  
pp. 20132962 ◽  
Author(s):  
A. J. Peel ◽  
J. R. C. Pulliam ◽  
A. D. Luis ◽  
R. K. Plowright ◽  
T. J. O'Shea ◽  
...  
Keyword(s):  
Communicable Disease ◽  
Mammalian Species ◽  
Human Populations ◽  
Community Size ◽  
Closed Population ◽  
Birth Pulse ◽  
Infection Dynamics ◽  
Pathogen Persistence ◽  
Host Life ◽  
Parameter Ranges

The notion of a critical community size (CCS), or population size that is likely to result in long-term persistence of a communicable disease, has been developed based on the empirical observations of acute immunizing infections in human populations, and extended for use in wildlife populations. Seasonal birth pulses are frequently observed in wildlife and are expected to impact infection dynamics, yet their effect on pathogen persistence and CCS have not been considered. To investigate this issue theoretically, we use stochastic epidemiological models to ask how host life-history traits and infection parameters interact to determine pathogen persistence within a closed population. We fit seasonal birth pulse models to data from diverse mammalian species in order to identify realistic parameter ranges. When varying the synchrony of the birth pulse with all other parameters being constant, our model predicted that the CCS can vary by more than two orders of magnitude. Tighter birth pulses tended to drive pathogen extinction by creating large amplitude oscillations in prevalence, especially with high demographic turnover and short infectious periods. Parameters affecting the relative timing of the epidemic and birth pulse peaks determined the intensity and direction of the effect of pre-existing immunity in the population on the pathogen's ability to persist beyond the initial epidemic following its introduction.

scholarly journals Amino Acid Residues in the Carboxy-Terminal Region of Cottontail Rabbit Papillomavirus E6 Influence Spontaneous Regression of Cutaneous Papillomas

2002 ◽  
Vol 76 (23) ◽  
pp. 11801-11808 ◽  
Author(s):  
Jiafen Hu ◽  
Nancy M. Cladel ◽  
Martin D. Pickel ◽  
Neil D. Christensen
Keyword(s):  
Amino Acid ◽  
Immune Responses ◽  
Single Amino Acid ◽  
Human Populations ◽  
Amino Acid Residues ◽  
High Frequencies ◽  
Host Immune Responses ◽  
Cottontail Rabbit ◽  
Single Amino Acid Change ◽  
Carboxy Terminal

ABSTRACT Previous studies have identified two different strains of cottontail rabbit papillomavirus (CRPV) that differ by approximately 5% in base pair sequence and that perform quite differently when used to challenge New Zealand White (NZW) rabbit skin. One strain caused persistent lesions (progressor strain), and the other induced papillomas that spontaneously regressed (regressor strain) at high frequencies (J. Salmon, M. Nonnenmacher, S. Caze, P. Flamant, O. Croissant, G. Orth, and F. Breitburd, J. Virol. 74:10766-10777, 2000; J. Salmon, N. Ramoz, P. Cassonnet, G. Orth, and F. Breitburd, Virology 235:228-234, 1997). We generated a panel of CRPV genomes that contained chimeric and mutant progressor and regressor strain E6 genes and assessed the outcome upon infection of both outbred and EIII/JC inbred NZW rabbits. The carboxy-terminal 77-amino-acid region of the regressor CRPV strain E6, which contained 15 amino acid residues that are different from those of the equivalent region of the persistent CRPV strain E6, played a dominant role in the conversion of the persistent CRPV strain to one showing high rates of spontaneous regressions. In addition, a single amino acid change (G252E) in the E6 protein of the CRPV progressor strain led to high frequencies of spontaneous regressions in inbred rabbits. These observations imply that small changes in the amino acid sequences of papillomavirus proteins can dramatically impact the outcome of natural host immune responses to these viral infections. The data imply that intrastrain differences between separate isolates of a single papillomavirus type (such as human papillomavirus type 16) may contribute to a collective variability in host immune responses in outbred human populations.

scholarly journals Signatures of genetic variation in human microRNAs point to processes of positive selection related to population-specific disease risks

2021 ◽  
Author(s):  
Pablo Villegas Mirón ◽  
Alicia Gallego ◽  
Jaume Bertranpetit ◽  
Hafid Laayouni ◽  
Yolanda Espinosa-Parrilla
Keyword(s):  
Genetic Variation ◽  
Disease Risk ◽  
In Silico Analysis ◽  
Human Populations ◽  
Evolutionary Constraint ◽  
Seed Region ◽  
Specific Disease ◽  
A Minor ◽  
Diversity Profiles

The occurrence of natural variation in human microRNAs has been the focus of numerous studies during the last twenty years. Most of them have been dedicated to study the role of specific mutations in diseases, like cancer, while a minor fraction seek to analyse the diversity profiles of microRNAs in the genomes of human populations. In the present study we analyse the latest human microRNA annotations in the light of the most updated catalog of genetic variation provided by the 1000 Genomes Project. We show by means of the in silico analysis of noncoding variation of microRNAs that the level of evolutionary constraint of these sequences is governed by the interplay of different factors, like their evolutionary age or the genomic location where they emerged. The role of mutations in the shaping of microRNA-driven regulatory interactions is emphasized with the acknowledgement that, while the whole microRNA sequence is highly conserved, the seed region shows a pattern of higher genetic diversity that appears to be caused by the dramatic frequency shifts of a fraction of human microRNAs. We highlight the participation of these microRNAs in population-specific processes by identifying that not only the seed, but also the loop, are particularly differentiated regions among human populations. The quantitative computational comparison of signatures of population differentiation showed that candidate microRNAs with the largest differences are enriched in variants implicated in gene expression levels (eQTLs), selective sweeps and pathological processes. We explore the implication of these evolutionary-driven microRNAs and their SNPs in human diseases, such as different types of cancer, and discuss their role in population-specific disease risk.

scholarly journals Presence of Toxoplasma gondii tissue cysts in human semen

2021 ◽  
Author(s):  
Wen Han Tong ◽  
Jana Hlaváčová ◽  
Samira Abdulai-Saiku ◽  
Šárka Kaňková ◽  
Jaroslav Flegr ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
Sexual Transmission ◽  
Congenital Toxoplasmosis ◽  
Protozoan Parasite ◽  
Specific Gene ◽  
Human Populations ◽  
Human Semen ◽  
Latently Infected ◽  
Clinically Significant ◽  
Toxoplasma Gondii Infection

Toxoplasma gondii is a widely prevalent protozoan parasite in human populations. This parasite is thought to be primarily transmitted through undercooked meat and contamination by cat feces. Here, we demonstrate that Toxoplasma gondii cysts can be found within human semen, thus suggesting a potential for sexual transmission. We visualized Toxoplasma gondii cysts in ejaculates of immune-competent and latently infected human volunteers. We confirmed the encystment by probing transcription of a bradyzoite-specific gene in these structures. These observations extend previous observations of the parasite in semen of several non-human host species, including rats, dogs, and sheep. Toxoplasma gondii infection is a clinically significant infection, in view of its high prevalence, its purported role in neuropsychiatric disorders such as schizophrenia, as well as in the more serious form of congenital toxoplasmosis. Our demonstration of intact Toxoplasma gondii cysts in the ejaculate supports the possibility of sexual transmission of the parasite and provides an impetus for further investigations.

scholarly journals Brain-specific homeobox Bsx specifies identity of pineal gland between serially homologous photoreceptive organs in zebrafish

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Hiroaki Mano ◽  
Yoichi Asaoka ◽  
Daisuke Kojima ◽  
Yoshitaka Fukada
Keyword(s):  
Gene Expression ◽  
Pineal Gland ◽  
Mammalian Species ◽  
Ectopic Expression ◽  
Tissue Level ◽  
Cellular Level ◽  
Specific Gene ◽  
Knock Down ◽  
Specific Gene Expression ◽  
Combinatorial Code

Abstract The pineal gland functioning as a photoreceptive organ in non-mammalian species is a serial homolog of the retina. Here we found that Brain-specific homeobox (Bsx) is a key regulator conferring individuality on the pineal gland between the two serially homologous photoreceptive organs in zebrafish. Bsx knock-down impaired the pineal development with reduced expression of exorh, the pineal-specific gene responsible for the photoreception, whereas it induced ectopic expression of rho, a retina-specific gene, in the pineal gland. Bsx remarkably transactivated the exorh promoter in combination with Otx5, but not with Crx, through its binding to distinct subtypes of PIRE, a DNA cis-element driving Crx/Otx-dependent pineal-specific gene expression. These results demonstrate that the identity of pineal photoreceptive neurons is determined by the combinatorial code of Bsx and Otx5, the former confers the pineal specificity at the tissue level and the latter determines the photoreceptor specificity at the cellular level.

scholarly journals Antigenic Evolution of Vaccine-Derived Polioviruses: Changes in Individual Epitopes and Relative Stability of the Overall Immunological Properties

2006 ◽  
Vol 80 (6) ◽  
pp. 2641-2653 ◽  
Author(s):  
Maria L. Yakovenko ◽  
Elena A. Cherkasova ◽  
Gennady V. Rezapkin ◽  
Olga E. Ivanova ◽  
Alexander P. Ivanov ◽  
...  
Keyword(s):  
Amino Acid ◽  
Rational Design ◽  
Driving Forces ◽  
Oral Poliovirus Vaccine ◽  
Enzyme Linked Immunosorbent Assay ◽  
Human Populations ◽  
Amino Acid Residues ◽  
Specific Amino Acid ◽  
Antigenic Sites ◽  
Neutralizing Capacity

ABSTRACT The Sabin oral poliovirus vaccine (OPV) readily undergoes changes in antigenic sites upon replication in humans. Here, a set of antigenically altered descendants of the three OPV serotypes (76 isolates) was characterized to determine the driving forces behind these changes and their biological implications. The amino acid residues of OPV derivatives that lie within or close to the known antigenic sites exhibited a marked tendency to be replaced by residues characteristic of homotypic wild polioviruses, and these changes may occur very early in OPV evolution. The specific amino acid alterations nicely correlated with serotype-specific changes in the reactivity of certain individual antigenic sites, as revealed by the recently devised monoclonal antibody-based enzyme-linked immunosorbent assay. In comparison to the original vaccine, small changes, if any, in the neutralizing capacity of human or rabbit sera were observed in highly diverged vaccine polioviruses of three serotypes, in spite of strong alterations of certain epitopes. We propose that the common antigenic alterations in evolving OPV strains largely reflect attempts to eliminate fitness-decreasing mutations acquired either during the original selection of the vaccine or already present in the parental strains. Variability of individual epitopes does not appear to be primarily caused by, or lead to, a significant immune evasion, enhancing only slightly, if at all, the capacity of OPV derivatives to overcome immunity in human populations. This study reveals some important patterns of poliovirus evolution and has obvious implications for the rational design of live viral vaccines.

Participation of multiple factors, including proliferin, in the inhibition of myogenic differentiation

1989 ◽  
Vol 9 (2) ◽  
pp. 430-441
Author(s):  
E L Wilder ◽  
D I Linzer
Keyword(s):  
Cell Lines ◽  
Myogenic Differentiation ◽  
Gene Promoter ◽  
Myogenic Cell ◽  
Cell Surface Receptor ◽  
Specific Gene ◽  
Amino Acid Residues ◽  
Surface Receptor ◽  
A Cell

Proliferin (PLF) is a secreted glycoprotein in the prolactin-growth hormone family in mice. PLF expression was detected in C3H 10T1/2 fibroblasts, but not in two 10T1/2-derived myogenic cell lines, and was restored in two nondifferentiating variants of one of these myogenic cell lines. Transient expression of one form of PLF (PLF1) inhibited expression from a muscle-specific gene promoter; a second form of PLF, which differed at three amino acid residues, displayed no activity in this transient assay. Introduction of a PLF1 expression construct into both muscle- and 10T1/2-derived myoblasts resulted in cell lines that were no longer myogenic or that differentiated only partially. Analysis of these cell lines revealed that differentiation could be obstructed at several steps and by one or more factors in addition to PLF. Although expected to function in vivo as an extracellular hormone, PLF did not appear to be acting through a cell surface receptor to inhibit differentiation in these cultured myoblasts.

Nucleolar localization of murine nuclear DNA helicase II (RNA helicase A)

1999 ◽  
Vol 112 (16) ◽  
pp. 2693-2703 ◽  
Author(s):  
S. Zhang ◽  
C. Herrmann ◽  
F. Grosse
Keyword(s):  
Nuclear Dna ◽  
Gene Dosage ◽  
Mammalian Species ◽  
Physiological Role ◽  
Dna Helicase ◽  
Rrna Synthesis ◽  
Nucleolar Localization ◽  
Specific Gene ◽  
Dna Helicase Ii ◽  
Pol I

Nuclear DNA helicase II (NDH II) is a highly conserved member of the DEXH superfamily of eukaryotic helicases, whose physiological role is still unclear. To explore the function of NDH II, we studied the intracellular distribution of NDH II of different mammalian species by immunofluorescence and compared these findings with the known role of the Drosophila homologue MLE that is involved in sex-specific gene dosage compensation. NDH II displayed an apparent nucleolar localization in murine cells, whereas in cells from all other mammalian species examined so far the protein was confined to the nucleoplasm and apparently excluded from the nucleoli. The nucleolar localization of mouse NDH II strongly suggests a role in ribosomal RNA biosynthesis. Immunoelectron microscopic studies revealed that the mouse NDH II was found at the dense fibrillar components of the nucleoli, and a significant percentage of NDH II molecules colocalized with the RNA polymerase I (Pol I) transcription factor UBF (upstream binding factor). Additionally, the nucleolar localization of NDH II coincided with a preferential immunolabeling pattern of nascent transcripts with bromouridine (BrUMP). Furthermore, mouse NDH II redistributed in mitosis in a manner highly correlated with Pol I activity. Conditions leading to the inhibition of Pol I activity in the interphase decreased the amount of NDH II in the nucleoli that diffused into the nucleoplasm and the cytosol. Contrary to the effect of inhibiting rRNA synthesis, treatment of mouse cells with the translation inhibitor cycloheximide did not compromise the nucleolar localization of murine NDH II.

Mutational Analysis of Two Stefin A Epitopes

1999 ◽  
Vol 380 (6) ◽  
Author(s):  
N. Kopitar-Jerala ◽  
R. Jerala ◽  
B. Turk ◽  
F. Gubensek ◽  
V. Turk
Keyword(s):  
Monoclonal Antibodies ◽  
Tertiary Structure ◽  
Mutational Analysis ◽  
Sequence Similarity ◽  
Mammalian Species ◽  
Cross Reactivity ◽  
Binding Affinities ◽  
Amino Acid Residues ◽  
Stefin A ◽  
Carboxy Terminal

AbstractStefin A, an intracellular inhibitor of cysteine proteinases, is expressed most abundantly in epithelial cells and in cells of lymphatic origin. In order to study its role in normal and pathological conditions we have prepared and characterized monoclonal antibodies against recombinant stefin A. Two high affinity monoclonal antibodies (mAbs) (A22 and C52) were tested for binding to free and papain-complexed stefin A and to a chimeric inhibitor, consisting of 61 amino acid residues of stefin A and 37 carboxy-terminal residues of stefin B. mAb A22 recognized not only free stefin A but also stefin A in complex with papain. The mAbs were further tested for their cross-reactivity against stefin A and B isolated from different mammalian species. On the basis of sequence similarity and tertiary structure of human stefin A we have prepared three mutants–Glu33Lys, Asp61Gly and Asn62Tyr–and their reactivity with the mAbs was tested. The binding affinities of mAb A22 for the Asp61Gly and Asn62Tyr mutants were significantly lower, indicating that the two amino acids are part of the stefin A epitope recognized by A22. The binding of both mAbs to the mutants Gly4Arg and Gly4Glu was comparable to wild-type stefin A.

scholarly journals Adaptation and Constraint in the Atypical Chemokine Receptor Family in Mammals

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Li Pan ◽  
Jianliang Lv ◽  
Zhongwang Zhang ◽  
Yongguang Zhang
Keyword(s):  
Ligand Binding ◽  
Chemokine Receptors ◽  
Homo Sapiens ◽  
Mammalian Species ◽  
Evolutionary Analysis ◽  
Amino Acid Residues ◽  
Mammal Species ◽  
And Function ◽  
G Protein Coupled ◽  
Receptor Family

Atypical chemokine receptors (ACKRs) are a subclass of G protein-coupled receptors characterized by promiscuity of ligand binding and an obvious inability to signal after ligand binding. Although some discoveries regarding this family in Homo sapiens and other species have been reported in some studies, the evolution and function of multiple ACKR in mammals have not yet been clearly understood. We performed an evolutionary analysis of ACKR genes (ACKR1, ACKR2, ACKR3, and ACKR4) in mammals. Ninety-two full-length ACKR genes from 27 mammal species were retrieved from the Genbank and Ensemble databases. Phylogenetic analysis showed that there were four well-conserved subfamilies in mammals. Synteny analysis revealed that ACKR genes formed conserved linkage groups with their adjacent genes across mammalian species, facilitating the identification of ACKRs in as yet unannotated genome datasets. Analysis of the site-specific profiles established by posterior probability revealed the positive-selection sites to be distributed mainly in the ligand binding region of ACKR1. This study highlights the molecular evolution of the ACKR gene family in mammals and identifies the critical amino acid residues likely to be relevant to ligand binding. Further experimental verification of these findings may provide valuable information regarding the ACKR’s biochemical and physiological functions.

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