scholarly journals Dorsal Pigmentation and Its Association with Functional Variation in MC1R in a Lizard from Different Elevations on the Qinghai–Tibetan Plateau

2020 ◽  
Vol 12 (12) ◽  
pp. 2303-2313
Author(s):  
Yuanting Jin ◽  
Haojie Tong ◽  
Gang Shao ◽  
Jiasheng Li ◽  
Yudie Lv ◽  
...  
Keyword(s):  
Amino Acid ◽  
Tibetan Plateau ◽  
Skin Pigmentation ◽  
Evolutionary Genetics ◽  
High Elevation ◽  
Melanin Synthesis ◽  
Nucleotide Polymorphisms ◽  
Functional Variation ◽  
Functional Link ◽  
Mc1r Gene

Abstract Identification of the role of the MC1R gene has provided major insights into variation in skin pigmentation in several organisms, including humans, but the evolutionary genetics of this variation is less well established. Variation in this gene and its relationship with degree of melanism was analyzed in one of the world’s highest-elevation lizards, Phrynocephalus theobaldi from the Qinghai–Tibetan Plateau. Individuals from the low-elevation group were shown to have darker dorsal pigmentation than individuals from a high-elevation group. The existence of climatic variation across these elevations was quantified, with lower elevations exhibiting higher air pressure, temperatures, and humidity, but less wind and insolation. Analysis of the MC1R gene in 214 individuals revealed amino acid differences at five sites between intraspecific sister lineages from different elevations, with two sites showing distinct fixed residues at low elevations. Three of the four single-nucleotide polymorphisms that underpinned these amino acid differences were highly significant outliers, relative to the generalized MC1R population structuring, suggestive of selection. Transfection of cells with an MC1R allele from a lighter high-elevation population caused a 43% reduction in agonist-induced cyclic AMP accumulation, and hence lowered melanin synthesis, relative to transfection with an allele from a darker low-elevation population. The high-elevation allele led to less efficient integration of the MC1R protein into melanocyte membranes. Our study identifies variation in the degree of melanism that can be explained by four or fewer MC1R substitutions. We establish a functional link between these substitutions and melanin synthesis and demonstrate elevation-associated shifts in their frequencies.

scholarly journals A SNP assay for assessing diversity in immune genes in the honey bee (Apis mellifera L.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Dora Henriques ◽  
Ana R. Lopes ◽  
Nor Chejanovsky ◽  
Anne Dalmon ◽  
Mariano Higes ◽  
...  
Keyword(s):  
Apis Mellifera ◽  
Honey Bee ◽  
Large Scale ◽  
Medium Density ◽  
Nucleotide Polymorphisms ◽  
Functional Variation ◽  
Immune Genes ◽  
Wide Range ◽  
Scale Range ◽  
Innate Immune Genes

AbstractWith a growing number of parasites and pathogens experiencing large-scale range expansions, monitoring diversity in immune genes of host populations has never been so important because it can inform on the adaptive potential to resist the invaders. Population surveys of immune genes are becoming common in many organisms, yet they are missing in the honey bee (Apis mellifera L.), a key managed pollinator species that has been severely affected by biological invasions. To fill the gap, here we identified single nucleotide polymorphisms (SNPs) in a wide range of honey bee immune genes and developed a medium-density assay targeting a subset of these genes. Using a discovery panel of 123 whole-genomes, representing seven A. mellifera subspecies and three evolutionary lineages, 180 immune genes were scanned for SNPs in exons, introns (< 4 bp from exons), 3’ and 5´UTR, and < 1 kb upstream of the transcription start site. After application of multiple filtering criteria and validation, the final medium-density assay combines 91 quality-proved functional SNPs marking 89 innate immune genes and these can be readily typed using the high-sample-throughput iPLEX MassARRAY system. This medium-density-SNP assay was applied to 156 samples from four countries and the admixture analysis clustered the samples according to their lineage and subspecies, suggesting that honey bee ancestry can be delineated from functional variation. In addition to allowing analysis of immunogenetic variation, this newly-developed SNP assay can be used for inferring genetic structure and admixture in the honey bee.

scholarly journals Genetic Relationships in the Toxin-Producing Fungal Endophyte, Alternaria oxytropis Using Polyketide Synthase and Non-Ribosomal Peptide Synthase Genes

2021 ◽  
Vol 7 (7) ◽  
pp. 538
Author(s):  
Rebecca Creamer ◽  
Deana Baucom Hille ◽  
Marwa Neyaz ◽  
Tesneem Nusayr ◽  
Christopher L. Schardl ◽  
...  
Keyword(s):  
Amino Acid ◽  
Polyketide Synthase ◽  
Genetic Relationships ◽  
Protein Sequences ◽  
Fungal Endophyte ◽  
Melanin Synthesis ◽  
Melanin Biosynthesis ◽  
Protein Levels ◽  
Oxytropis Sericea ◽  
And Function

The legume Oxytropis sericea hosts a fungal endophyte, Alternaria oxytropis, which produces secondary metabolites (SM), including the toxin swainsonine. Polyketide synthase (PKS) and non-ribosomal peptide synthase (NRPS) enzymes are associated with biosynthesis of fungal SM. To better understand the origins of the SM, an unannotated genome of A. oxytropis was assessed for protein sequences similar to known PKS and NRPS enzymes of fungi. Contigs exhibiting identity with known genes were analyzed at nucleotide and protein levels using available databases. Software were used to identify PKS and NRPS domains and predict identity and function. Confirmation of sequence for selected gene sequences was accomplished using PCR. Thirteen PKS, 5 NRPS, and 4 PKS-NRPS hybrids were identified and characterized with functions including swainsonine and melanin biosynthesis. Phylogenetic relationships among closest amino acid matches with Alternaria spp. were identified for seven highly conserved PKS and NRPS, including melanin synthesis. Three PKS and NRPS were most closely related to other fungi within the Pleosporaceae family, while five PKS and PKS-NRPS were closely related to fungi in the Pleosporales order. However, seven PKS and PKS-NRPS showed no identity with fungi in the Pleosporales or the class Dothideomycetes, suggesting a different evolutionary origin for those genes.

Natural variation in rice starch synthase IIa affects enzyme and starch properties

2004 ◽  
Vol 31 (7) ◽  
pp. 671 ◽  
Author(s):  
Takayuki Umemoto ◽  
Noriaki Aoki ◽  
Hongxuan Lin ◽  
Yasunori Nakamura ◽  
Naoyoshi Inouchi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Natural Variation ◽  
Oryza Sativa L ◽  
Length Distribution ◽  
Starch Synthase ◽  
Rice Starch ◽  
Nucleotide Polymorphisms ◽  
Cultivated Rice ◽  
Chain Length Distribution ◽  
Starch Properties

The natural variation in starch synthase IIa (SSIIa) of rice (Oryza sativa L.) was characterised using near-isogenic lines (NILs). SSIIa is a candidate for the alk gene regulating the alkali disintegration of rice grains, since both genes are genetically mapped at the same position on chromosome 6 and related to starch properties. In this study, we report that the alkali-susceptible cultivar Nipponbare lacked SSIIa activity in endosperm. However, the activity was detected with NILs having the alk allele of alkali-tolerant Kasalath. SSIIa protein was present even in Nipponbare endosperm, but it was not associated with starch granules at the milky stage of endosperm. Three single-nucleotide polymorphisms (SNPs) predicting amino acid substitutions existed between the cDNA sequences of SSIIa of Nipponbare and Kasalath were genotyped with 65 rice cultivars and four wild relatives of cultivated rice. The results obtained explain the potential importance of two of the amino acid residues for starch association of rice SSIIa. An analysis of the chain-length distribution of β-limit dextrin of amylopectin showed that without SSIIa activity, the relative number of A-chains (the short chains without branches) increased and that of B1-chains (the short chains with branches) decreased. This suggests that, given the SSIIa defect, short A-chains could not reach a sufficient length for branching enzymes to act on them to produce B1-chains.

scholarly journals Pathogenic alleles in microtubule, secretory granule and extracellular matrix-related genes in familial keratoconus

2021 ◽  
Author(s):  
Vishal Shinde ◽  
Nara Sobreira ◽  
Elizabeth S Wohler ◽  
George Maiti ◽  
Nan Hu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Cell Cultures ◽  
Cell Biology ◽  
Stromal Cell ◽  
Primary Cilia ◽  
Single Amino Acid ◽  
European Ancestry ◽  
Base Substitution ◽  
Amino Acid Substitutions ◽  
Functional Link

Abstract Keratoconus is a common corneal defect with a complex genetic basis. By whole exome sequencing of affected members from 11 multiplex families of European ancestry, we identified 23 rare, heterozygous, potentially pathogenic variants in 8 genes. These include nonsynonymous single amino acid substitutions in HSPG2, EML6 and CENPF in two families each, and in NBEAL2, LRP1B, PIK3CG and MRGPRD in three families each; ITGAX had nonsynonymous single amino acid substitutions in two families and an indel with a base substitution producing a nonsense allele in the third family. Only HSPG2, EML6 and CENPF have been associated with ocular phenotypes previously. With the exception of MRGPRD and ITGAX, we detected the transcript and encoded protein of the remaining genes in the cornea and corneal cell cultures. Cultured stromal cells showed cytoplasmic punctate staining of NBEAL2, staining of the fibrillar cytoskeletal network by EML6, while CENPF localized to the basal body of primary cilia. We inhibited the expression of HSPG2, EML6, NBEAL2 and CENPF in stromal cell cultures and assayed for the expression of COL1A1 as a readout of corneal matrix production. An upregulation in COL1A1 after siRNA inhibition indicated their functional link to stromal cell biology. For ITGAX, encoding a leukocyte integrin, we assayed its level in the sera of 3 affected families compared with 10 unrelated controls to detect an increase in all affecteds. Our study identified genes that regulate the cytoskeleton, protein trafficking and secretion, barrier tissue function and response to injury and inflammation, as being relevant to keratoconus.

scholarly journals Linking deeply-sourced volatile emissions to plateau growth dynamics in southeastern Tibetan Plateau

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Maoliang Zhang ◽  
Zhengfu Guo ◽  
Sheng Xu ◽  
Peter H. Barry ◽  
Yuji Sano ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Growth Dynamics ◽  
High Elevation ◽  
Fault System ◽  
The Tibetan Plateau ◽  
Southeastern Tibetan Plateau ◽  
Surface Uplift ◽  
Multi Stage ◽  
Geodynamic Processes ◽  
Underlying Mechanisms

AbstractThe episodic growth of high-elevation orogenic plateaux is controlled by a series of geodynamic processes. However, determining the underlying mechanisms that drive plateau growth dynamics over geological history and constraining the depths at which growth originates, remains challenging. Here we present He-CO2-N2 systematics of hydrothermal fluids that reveal the existence of a lithospheric-scale fault system in the southeastern Tibetan Plateau, whereby multi-stage plateau growth occurred in the geological past and continues to the present. He isotopes provide unambiguous evidence for the involvement of mantle-scale dynamics in lateral expansion and localized surface uplift of the Tibetan Plateau. The excellent correlation between 3He/4He values and strain rates, along the strike of Indian indentation into Asia, suggests non-uniform distribution of stresses between the plateau boundary and interior, which modulate southeastward growth of the Tibetan Plateau within the context of India-Asia convergence. Our results demonstrate that deeply-sourced volatile geochemistry can be used to constrain deep dynamic processes involved in orogenic plateau growth.

scholarly journals Molecular epidemiologic characteristics of hemagglutinin from five waves of avian influenza A (H7N9) virus infection, from 2013 to 2017, in Zhejiang Province, China

2021 ◽  
Author(s):  
Yi Sun ◽  
Haiyan Mao ◽  
Xiuyu Lou ◽  
Xinying Wang ◽  
Yin Chen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Influenza A ◽  
Zhejiang Province ◽  
Personal Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Amino Acid Mutations ◽  
Influenza Outbreaks ◽  
Epidemiological Characteristics ◽  
The Waves

AbstractThere have been five waves of influenza A (H7N9) epidemics in Zhejiang Province between 2013 and 2017. Although the epidemiological characteristics of the five waves have been reported, the molecular genetics aspects, including the phylogeny, evolution, and mutation of hemagglutinin (HA), have not been systematically investigated. A total of 154 H7N9 samples from Zhejiang Province were collected between 2013 and 2017 and sequenced using an Ion Torrent Personal Genome Machine. The starting dates of the waves were 16 March 2013, 1 July 2013, 1 July 2014, 1 July 2015, and 1 July 2016. Single-nucleotide polymorphisms (SNPs) and amino acid mutations were counted after the HA sequences were aligned. The evolution of H7N9 matched the temporal order of the five waves, among which wave 3 played an important role. The 55 SNPs and 14 amino acid mutations with high frequency identified among the five waves revealed the dynamic occurrence of mutation in the process of viral dissemination. Wave 3 contributed greatly to the subsequent epidemic of waves 4 and 5 of H7N9. Compared with wave 1, wave 5 was characterized by more mutations, including A143V and R148K, two mutations that have been reported to weaken the immune response. In addition, some amino acid mutations were observed in wave 5 that led to more lineages. It is necessary to strengthen the surveillance of subsequent H7N9 influenza outbreaks.

Characterisation of the melanocortin-1 receptor gene in alpaca and identification of possible markers associated with phenotypic variations in colour

2009 ◽  
Vol 49 (8) ◽  
pp. 675 ◽  
Author(s):  
N. L. Feeley ◽  
K. A. Munyard
Keyword(s):  
Mus Musculus ◽  
Bos Taurus ◽  
Receptor Gene ◽  
Nucleotide Polymorphisms ◽  
Wild Type ◽  
Single Nucleotide ◽  
Melanocortin 1 Receptor ◽  
Mc1r Gene ◽  
Pcr Products ◽  
Phenotypic Variations

The aim of this study was to determine if any correlation exists between melanocortin-1 receptor (MC1R) polymorphisms and skin and fibre colour in alpacas. Primers capable of amplifying the entire alpaca MC1R gene were designed from a comparative alignment of Bos taurus and Mus musculus MC1R gene sequences. The complete MC1R gene of 41 alpacas exhibiting a range of fibre colours, and which were sourced from farms across Australia, was sequenced from PCR products. Twenty-one single nucleotide polymorphisms were identified within MC1R. Two of these polymorphisms (A82G and C901T) have the potential to reduce eumelanin production by disrupting the activity of MC1R. No agreement was observed between fibre colour alone and MC1R genotype in the 41 animals in this study. However, when the animals were assigned to groups based on the presence or absence of eumelanin in their fibre and skin, only animals that had at least one allele with the A82/C901 combination expressed eumelanin. We propose that A82/C901 is the wild-type dominant ‘E’ MC1R allele, while alpacas with either G82/T901 or G82/Y901 are homozygous for the recessive ‘e’ MC1R allele and are therefore unable to produce eumelanin.

Roof of the World: Tibet, Pamirs

2013 ◽  
Author(s):  
Mike Searle
Keyword(s):  
Tibetan Plateau ◽  
High Elevation ◽  
Tien Shan ◽  
Palm Tree ◽  
The Tibetan Plateau ◽  
Wet Season ◽  
North West ◽  
Mountain Ranges ◽  
The North ◽  
The World

The Tibetan Plateau is by far the largest region of high elevation, averaging just above 5,000 metres above sea level, and the thickest crust, between 70 and 90 kilometres thick, anywhere in the world. This huge plateau region is very flat—lying in the internally drained parts of the Chang Tang in north and central Tibet, but in parts of the externally drained eastern Tibet, three or four mountain ranges larger and higher than the Alps rise above the frozen plateau. Some of the world’s largest and longest mountain ranges border the plateau, the ‘flaming mountains’ of the Tien Shan along the north-west, the Kun Lun along the north, the Longmen Shan in the east, and of course the mighty Himalaya forming the southern border of the plateau. The great trans-Himalayan mountain ranges of the Pamir and Karakoram are geologically part of the Asian plate and western Tibet but, as we have noted before, unlike Tibet, these ranges have incredibly high relief with 7- and 8-kilometre-high mountains and deeply eroded rivers and glacial valleys. The western part of the Tibetan Plateau is the highest, driest, and wildest area of Tibet. Here there is almost no rainfall and rivers that carry run-off from the bordering mountain ranges simply evaporate into saltpans or disappear underground. Rivers draining the Kun Lun flow north into the Takla Makan Desert, forming seasonal marshlands in the wet season and a dusty desert when the rivers run dry. The discovery of fossil tropical leaves, palm tree trunks, and even bones from miniature Miocene horses suggest that the climate may have been wetter in the past, but this is also dependent on the rise of the plateau. Exactly when Tibet rose to its present elevation is a matter of great debate. Nowadays the Indian Ocean monsoon winds sweep moisture-laden air over the Indian sub-continent during the summer months (late June–September). All the moisture is dumped as the summer monsoon, the torrential rains that sweep across India from south-east to north-west.

scholarly journals The cationic amino acid exporter Slc7a7 is induced and vital in zebrafish tissue macrophages with sustained efferocytic activity

2020 ◽  
Vol 133 (20) ◽  
pp. jcs249037
Author(s):  
Doris Lou Demy ◽  
Mireille Carrère ◽  
Ramil Noche ◽  
Muriel Tauzin ◽  
Marion Le Bris ◽  
...  
Keyword(s):  
Cell Death ◽  
Amino Acid ◽  
Neuronal Apoptosis ◽  
Amino Acid Transporter ◽  
Cationic Amino Acid Transporter ◽  
Adaptive Responses ◽  
Functional Link ◽  
Cationic Amino Acid ◽  
Zebrafish Larvae ◽  
Acid Transporter

ABSTRACTMost tissues harbor a substantial population of resident macrophages. Here, we elucidate a functional link between the Slc7a7 cationic amino acid transporter and tissue macrophages. We identified a mutant zebrafish devoid of microglia due to a mutation in the slc7a7 gene. We found that in Slc7a7-deficient larvae, macrophages do enter the retina and brain to become microglia, but then die during the developmental wave of neuronal apoptosis, which triggers intense efferocytic work from them. A similar macrophage demise occurs in other tissues, at stages where macrophages have to engulf many cell corpses, whether due to developmental or experimentally triggered cell death. We found that Slc7a7 is the main cationic amino acid transporter expressed in macrophages of zebrafish larvae, and that its expression is induced in tissue macrophages within 1–2 h upon efferocytosis. Our data indicate that Slc7a7 is vital not only for microglia but also for any steadily efferocytic tissue macrophages, and that slc7a7 gene induction is one of the adaptive responses that allow them to cope with the catabolism of numerous dead cells without compromising their own viability.

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