scholarly journals Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buffaloes (Bubalus bubalis)

2020 ◽  
Author(s):  
Dong Liang ◽  
Pengju Zhao ◽  
Jingfang Si ◽  
Lingzhao Fang ◽  
Erola Pairo-Castineira ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Population Genomics ◽  
Coat Color ◽  
Phylogenetic Analyses ◽  
Regulation Of Gene Expression ◽  
Fold Increase ◽  
Bubalus Bubalis ◽  
Proximal Promoter ◽  
Causative Mutation ◽  
Swamp Buffalo

Abstract Visible pigmentation phenotypes can be used to explore the regulation of gene expression and the evolution of coat color patterns in animals. Here, we performed whole-genome and RNA sequencing and applied genome-wide association study, comparative population genomics and biological experiments to show that the 2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (Bubalus bubalis). This LINE-1 insertion (3′ truncated and containing only 5′ UTR) functions as a strong proximal promoter that leads to a 10-fold increase in the transcription of ASIP in white buffalo skin. The 165 bp of 5′ UTR transcribed from the LINE-1 is spliced into the first coding exon of ASIP, resulting in a chimeric transcript. The increased expression of ASIP prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle ASIP gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe.

Does Dingo Predation or Buffalo Competition Regulate Feral Pig Populations in the Australian Wet-Dry Tropics? An Experimental Study.

1995 ◽  
Vol 22 (1) ◽  
pp. 65 ◽  
Author(s):  
L Corbett
Keyword(s):  
Experimental Study ◽  
Sus Scrofa ◽  
Interference Competition ◽  
Fold Increase ◽  
Bubalus Bubalis ◽  
Northern Australia ◽  
Dry Tropics ◽  
Swamp Buffalo ◽  
And Control ◽  
The Relationship

Dingo (Canis farniliaris dingo) predation on feral pigs (Sus scrofa) in response to experimental changes in prey populations was measured over seven years in the seasonally wet-dry tropics of northern Australia. Following the removal of feral swamp buffalo (Bubalus bubalis) from half of the 614-km*2 study area, the number of pigs doubled and there was a 3-fold increase of pig in dingo diet. The relationship between the functional response of the dingo and pig abundance was negative and significant for both the treatment and control areas. This indicated that dingoes were not regulating the pig population. Instead, dingo predation probably acted in concert with interference competition by buffalo which decreased access to critical subterranean food for pigs during the dry season and thus limited population growth in pigs.

scholarly journals Novel Antarctic yeast adapts to cold by switching energy metabolism and increasing small RNA synthesis

2021 ◽  
Author(s):  
D. Touchette ◽  
I. Altshuler ◽  
C. Gostinčar ◽  
P. Zalar ◽  
I. Raymond-Bouchard ◽  
...  
Keyword(s):  
Ethanol Production ◽  
Ethanol Fermentation ◽  
Phylogenetic Analyses ◽  
Regulation Of Gene Expression ◽  
Pentose Phosphate ◽  
Metabolic Switch ◽  
Antarctic Yeast ◽  
Fungal Adaptation ◽  
Pentose Phosphate Pathways ◽  
Post Transcriptional Regulation

AbstractThe novel extremophilic yeast Rhodotorula frigidialcoholis, formerly R. JG1b, was isolated from ice-cemented permafrost in University Valley (Antarctic), one of coldest and driest environments on Earth. Phenotypic and phylogenetic analyses classified R. frigidialcoholis as a novel species. To characterize its cold-adaptive strategies, we performed mRNA and sRNA transcriptomic analyses, phenotypic profiling, and assessed ethanol production at 0 and 23 °C. Downregulation of the ETC and citrate cycle genes, overexpression of fermentation and pentose phosphate pathways genes, growth without reduction of tetrazolium dye, and our discovery of ethanol production at 0 °C indicate that R. frigidialcoholis induces a metabolic switch from respiration to ethanol fermentation as adaptation in Antarctic permafrost. This is the first report of microbial ethanol fermentation utilized as the major energy pathway in response to cold and the coldest temperature reported for natural ethanol production. R. frigidialcoholis increased its diversity and abundance of sRNAs when grown at 0 versus 23 °C. This was consistent with increase in transcription of Dicer, a key protein for sRNA processing. Our results strongly imply that post-transcriptional regulation of gene expression and mRNA silencing may be a novel evolutionary fungal adaptation in the cryosphere.

scholarly journals KUALITAS SPERMATOZOA ASAL CAPUT, CORPUS, DAN CAUDA EPIDIDIMIS PADA KERBAU RAWA (Bubalus bubalis carabenensis)

2016 ◽  
Vol 3 (3) ◽  
pp. 97
Author(s):  
Muhammad Riyadhi ◽  
Akbar Budiansa ◽  
Muhammad Rizal
Keyword(s):  
Artificial Insemination ◽  
Bubalus Bubalis ◽  
Spermatozoa Motility ◽  
Swamp Buffaloes ◽  
Swamp Buffalo

The purpose of this research was evaluate the quality of spermatozoa concentration in the caput, corpus and cauda of the swamp buffalo epididymis (Bubalus bubalis carabanensis).  Method of this research was to exploration to 13 epididymides of eight swamp buffaloes were obtained from Banjar and Banjarmasin slaughterhouses,evaluated the quality of spermatozoa in caput, corpus and cauda of epididymis.  Quality of collected-spermatozoa including spermatozoa motility, percentage of live spermatozoa, spermatozoa concentration and percentage of abnormality.  Result of this study showed that mean of each of caput spermatozoa motility, percentage of live spermatozoa, spermatozoa concentration and percentage of abnormality; 0%, 45.43% (31.87–72%), 189,62 x106 (40–480 x106) and 56.16 %(44.34–66.53%), corpus ;2.77% (1–9%), 58.73% (45.14 –76%), 152.31 x106 (45 – 345x106), and 47.61 %(23.92 – 60.15%), cauda;53.46% (20 – 70%), 74.32 % (56.68 – 83%), 1,459.62 x106 (825 – 2,340x106), and 34.60%(15.89 –50.04%). In conclusion, spermatozoaofcaudaepididymis could be used in artificial insemination program.Keywords: Spermatozoa, epididymis, swamp buffalo.

scholarly journals RNAs as proximity labeling media for identifying nuclear speckle positions relative to the genome

2018 ◽  
Author(s):  
Weizhong Chen ◽  
Zhangming Yan ◽  
Simin Li ◽  
Norman Huang ◽  
Xuerui Huang ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Genomic Sequence ◽  
Single Cells ◽  
Regulation Of Gene Expression ◽  
Nuclear Genome ◽  
Fold Increase ◽  
Nuclear Speckles ◽  
Nuclear Speckle ◽  
Interaction Sites ◽  
Genomic Regions

AbstractNuclear speckles are interchromatin structures enriched in RNA splicing factors. Determining their relative positions with respect to the folded nuclear genome could provide critical information on co-and post-transcriptional regulation of gene expression. However, it remains challenging to identify which parts of the nuclear genome are in proximity to nuclear speckles, due to physical separation between nuclear speckle cores and chromatin. We hypothesized that noncoding RNAs including small nuclear RNAs, 7SK and Malat1, which accumulate at the periphery of nuclear speckles (nsaRNA,nuclearspeckleassociated RNA), may extend to sufficient proximity to the nuclear genome. Leveraging a transcriptome-genome interaction assay (MARGI), we identified nsaRNA-interacting genomic sequences, which exhibited clustering patterns (nsaPeaks) in the genome, suggesting existence of relatively stable interaction sites for nsaRNAs in nuclear genome. Posttranscriptional pre-mRNAs, which are known to be clustered to nuclear speckles, exhibited proximity to nsaPeaks but rarely to other genomic regions. Furthermore, CDK9 proteins that localize to the vicinity of nuclear speckles produced ChIP-seq peaks that overlapped with nsaPeaks. Our combined DNA FISH and immunofluorescence analysis in 182 single cells revealed a 3-fold increase in odds for nuclear speckles to localize near an nsaPeak than its neighboring genomic sequence. These data suggest a model that nsaRNAs locate in sufficient proximity to nuclear genome and leave identifiable genomic footprints, thus revealing the parts of genome proximal to nuclear speckles.

scholarly journals Population Genomics of Bettongia lesueur: Admixing Increases Genetic Diversity with no Evidence of Outbreeding Depression

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 851 ◽  
Author(s):  
Kate Rick ◽  
Kym Ottewell ◽  
Cheryl Lohr ◽  
Rujiporn Thavornkanlapachai ◽  
Margaret Byrne ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Threatened Species ◽  
Population Genomics ◽  
Fold Increase ◽  
Recruitment Rate ◽  
Outbreeding Depression ◽  
Nucleotide Polymorphisms ◽  
Isolated Populations ◽  
Genomic Markers ◽  
Founder Populations

Small and isolated populations are subject to the loss of genetic variation as a consequence of inbreeding and genetic drift, which in turn, can affect the fitness and long-term viability of populations. Translocations can be used as an effective conservation tool to combat this loss of genetic diversity through establishing new populations of threatened species, and to increase total population size. Releasing animals from multiple genetically diverged sources is one method to optimize genetic diversity in translocated populations. However, admixture as a conservation tool is rarely utilized due to the risks of outbreeding depression. Using high-resolution genomic markers through double-digest restriction site-associated sequencing (ddRAD-seq) and life history data collected over nine years of monitoring, this study investigates the genetic and fitness consequences of admixing two genetically-distinct subspecies of Bettongia lesueur in a conservation translocation. Using single nucleotide polymorphisms (SNPs) identified from 215 individuals from multiple generations, we found an almost 2-fold increase in genetic diversity in the admixed translocation population compared to the founder populations, and this was maintained over time. Furthermore, hybrid class did not significantly impact on survivorship or the recruitment rate and therefore we found no indication of outbreeding depression. This study demonstrates the beneficial application of mixing multiple source populations in the conservation of threatened species for minimizing inbreeding and enhancing adaptive potential and overall fitness.

Transmission and virological studies of a malignant catarrhal fever syndrome in the Indonesian swamp buffalo (Bubalus bubalis)

1984 ◽  
Vol 61 (4) ◽  
pp. 113-116 ◽  
Author(s):  
D. HOFFMANN ◽  
S. SOBIRONINGSIH ◽  
B. C. CLARKE ◽  
P. J. YOUNG ◽  
I. SENDOW
Keyword(s):  
Bubalus Bubalis ◽  
Malignant Catarrhal Fever ◽  
Swamp Buffalo

221 EPIGENETIC DYNAMICS OF PLURIPOTENCY GENES IN THE CONTEXT OF DIFFERENTIATION AND NUCLEAR REPROGRAMMING DETERMINED BY Q2ChIP, A QUICK AND QUANTITATIVE CHROMATIN IMMUNOPRECIPITATION TECHNIQUE APPLICABLE TO SMALL CELL SAMPLES

2007 ◽  
Vol 19 (1) ◽  
pp. 227 ◽  
Author(s):  
J. A. Dahl ◽  
C. K. Taranger ◽  
P. Collas
Keyword(s):  
Gene Expression ◽  
Chromatin Immunoprecipitation ◽  
Regulation Of Gene Expression ◽  
Cell Extract ◽  
Proximal Promoter ◽  
Pcr Analysis ◽  
Cross Linking ◽  
Nuclear Reprogramming ◽  
Distal Enhancer ◽  
Developmentally Regulated

Interactions between proteins and DNA are essential for cellular functions such as genomic stability, DNA replication and repair, chromosome segregation, transcription, and epigenetic silencing of gene expression. Chromatin immunoprecipitation (ChIP) is a key technique for mapping histone modifications and transcription factor binding on DNA and thereby unraveling the role of epigenetics in the regulation of gene expression. Current ChIP protocols require extensive sample handling and large numbers of cells (5-10 million). primarily owing to ample loss of material during the procedure. We altered critical steps of conventional ChIP to develop a quick and quantitative (Q2) ChIP assay suitable for cell numbers 100- to 1000-fold lower than those required for conventional ChIP. Key modifications of the ChIP procedure include (i) formaldehyde DNA–protein cross-linking in suspended cells, (ii) cross-linking in the presence of 20 mM sodium butyrate to enhance specificity of precipitation of acetylated histones, (iii) transfer of washed precipitated immune complexes to a clean tube ('tube shift') to increase ChIP specificity by virtually eliminating nonspecifically bound chromatin, and (iv) combination of cross-link reversal, protein digestion, and DNA elution into a single 2-h step. We used Q2ChIP to monitor changes in 6 histone H3 modifications on the human developmentally regulated genes OCT4 (POU5F1), NANOG, and LMNA (lamin A) in the context of retinoic acid (RA)-mediated differentiation of embryonal carcinoma cells and upon reprogramming of kidney epithelial 293T cells to pluripotency in carcinoma cell extract (Taranger et al. 2005 Mol. Biol. Cell 16, 5719–5735). Real-time PCR analysis of precipitated DNA unravels an unexpected two-step heterochromatin assembly elicited by RA on the OCT4 proximal promoter, proximal enhancer, and distal enhancer, and on the NANOG promoter, whereby methylation of H3K9 and H3K27 is followed by H3K9 deacetylation. H3K4 di- and trimethylation remain relatively unaffected by RA treatment. In contrast, reprogramming of 293T cells in carcinoma extract promotes assembly of histone marks characteristic of transcriptional induction of OCT4 and NANOG, such as acetylation and demethylation of H3K9. The results argue toward ordered chromatin repackaging at developmentally regulated promoters upon differentiation or, conversely, nuclear reprogramming to pluripotency.

Ingestion Rates and Aspects of Water, Sodium and Energy Metabolism in Caged Swamp Buffalo, Bubalus Bubalis, From Isotope Dilution and Materials Balances.

1982 ◽  
Vol 30 (5) ◽  
pp. 779 ◽  
Author(s):  
CK Williams ◽  
B Green
Keyword(s):  
Body Mass ◽  
Close Agreement ◽  
Bubalus Bubalis ◽  
The Body ◽  
High Rate ◽  
Evaporative Heat Loss ◽  
Northern Australia ◽  
Water Turnover ◽  
Daily Rate ◽  
Swamp Buffalo

Exchanges of DM, sodium, water and energy were estimated on caged swamp buffalo of body mass (W) 297 plus or minus 13 kg. Estimates of feed ingestion estimated from rates of 22Na and 3H turnover were in close agreement with estimates from weighing. Tritium equilibrated in 6 h and 22Na in 12 h. Tritium space was 78.9 plus or minus 1.6% of body mass at 6 h and 83.9 plus or minus 1.1% at 24 h. The body pool of exchangable Na was 40.56 plus or minus 1.79 mmol/kg W at 12 h, and 44.62 plus or minus 2.12 mmol/kg W at 24 h. The daily rate of water turnover was 34.72 plus or minus 2.33 litres or 326.1 plus or minus 17.2 ml/kg W0.82, about three times that expected on the basis of body size, reflecting adaptation to a tropical swamp habitat. It was due mainly to the high rate of imbibition, 30.78 plus or minus 2.15 litres daily or 289.1 plus or minus 16.3 ml/kg W0.82 daily. Daily rates of water loss were partitioned as: faecal, 9.99 plus or minus 0.761 (94.1 plus or minus 7.0 ml/kg W0.82); urinary, 10.39 plus or minus 0.76 litres (98.2 plus or minus 7.6 ml/kg W0.82); pulmocutaneous, 14.34 plus or minus 1.37 litres (133.8 plus or minus 8.9 ml/kg W0.82). Swamp buffalo are unlikely to be able to satisfy their water requirements from food alone during the dry season in northern Australia. The daily rate of Na turnover was 6.29 plus or minus 0.41 mmol/kg W0.75. Na in the faeces was low, 8.3 plus or minus 0.9 mmol/kg dry faeces, indicating very effective alimentary absorption of Na. Apparent digestible energy intake (DE) per day for maintenance was about 651 plus or minus 41 kJ/kg W0.75. Daily rates of evaporative heat loss were high, 481 plus or minus 33 kJ/kg W0.75, exceeding the non-evaporative component of the DE, 321 plus or minus 35 kJ/kg W0.75; evaporative processes may have contributed to the high maintenance DE.

scholarly journals Expression of a Shiga-Like Toxin during Plastic Colonization by Two Multidrug-Resistant Bacteria, Aeromonas hydrophila RIT668 and Citrobacter freundii RIT669, Isolated from Endangered Turtles (Clemmys guttata)

2020 ◽  
Vol 8 (8) ◽  
pp. 1172 ◽  
Author(s):  
Seema G. Thomas ◽  
Maryah A. Glover ◽  
Anutthaman Parthasarathy ◽  
Narayan H. Wong ◽  
Paul A. Shipman ◽  
...  
Keyword(s):  
Aeromonas Hydrophila ◽  
Biofilm Formation ◽  
Phylogenetic Analyses ◽  
Regulatory Protein ◽  
Antibiotic Resistance Genes ◽  
Fold Increase ◽  
Resistant Bacteria ◽  
Citrobacter Freundii ◽  
Protein Subunit ◽  
Clemmys Guttata

Aeromonas hydrophila RIT668 and Citrobacter freundii RIT669 were isolated from endangered spotted turtles (Clemmys guttata). Whole-genome sequencing, annotation and phylogenetic analyses of the genomes revealed that the closest relative of RIT668 is A. hydrophila ATCC 7966 and Citrobacter portucalensis A60 for RIT669. Resistome analysis showed that A. hydrophila and C. freundii harbor six and 19 different antibiotic resistance genes, respectively. Both bacteria colonize polyethylene and polypropylene, which are common plastics, found in the environment and are used to fabricate medical devices. The expression of six biofilm-related genes—biofilm peroxide resistance protein (bsmA), biofilm formation regulatory protein subunit R (bssR), biofilm formation regulatory protein subunit S (bssS), biofilm formation regulator (hmsP), toxin-antitoxin biofilm protein (tabA) and transcriptional activator of curli operon (csgD)—and two virulence factors—Vi antigen-related gene (viaB) and Shiga-like toxin (slt-II)—was investigated by RT-PCR. A. hydrophila displayed a >2-fold increase in slt-II expression in cells adhering to both polymers, C. freundii adhering on polyethylene displayed a >2-fold, and on polypropylene a >6-fold upregulation of slt-II. Thus, the two new isolates are potential pathogens owing to their drug resistance, surface colonization and upregulation of a slt-II-type diarrheal toxin on polymer surfaces.

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