scholarly journals Geographic patterns of koala retrovirus genetic diversity, endogenization and subtype distributions

2021 ◽  
Author(s):  
Michaela DJ Blyton ◽  
Paul Young ◽  
Ben D. Moore ◽  
Keith Chappell
Keyword(s):  
Hypervariable Region ◽  
Northern Australia ◽  
Geographic Patterns ◽  
Copy Numbers ◽  
Gene Copies ◽  
Unique System ◽  
Distinct Sequence ◽  
Subtype A ◽  
Local Transmission ◽  
Koala Retrovirus

Koala retrovirus subtype A is the youngest endogenized retrovirus, providing a unique system to elucidate retroviral-host co-evolution. We characterised KoRV geography using faecal DNA from 192 samples across 20 populations throughout the koala’s range. We reveal an abrupt change in KoRV genetics and incidence at the Victoria/NSW state border. In northern koalas, pol gene copies were ubiquitously present at greater than 5 per-cell, consistent with endogenous KoRV. In southern koalas, pol copies were detected in only 25.8% of koalas and always at copy numbers less than one, while the env gene was detected in all animals and in a majority at copy numbers of greater than one per-cell. These results suggest that southern koalas carry partial endogenous KoRV-like sequences. Deep sequencing of the env hypervariable region revealed three putatively endogenous KoRV-A sequences in northern koalas and a single, distinct sequence present in all southern koalas. Among northern populations, env sequence diversity decreased with distance from the equator, suggesting infectious KoRV-A invaded the koala genome in northern Australia and then spread south. The previously described exogenous KoRV subtypes (B-K), two novel subtypes (L and M), and intermediate or hybrid subtypes were detected in all northern koala populations but strikingly absent from all southern animals tested. Apart from KoRV-D, these exogenous subtypes were generally locally prevalent but geographically restricted, producing KoRV genetic differentiation among northern populations. This suggests that sporadic evolution and local transmission of the exogenous subtypes has occurred within northern Australia, but this has not extended into animals within southern Australia.

scholarly journals Somatic deletion of KDM1A/LSD1 gene is associated to advanced colorectal cancer stages

2019 ◽  
Vol 73 (2) ◽  
pp. 107-111 ◽  
Author(s):  
Ruth Ramírez-Ramírez ◽  
Melva Gutiérrez-Angulo ◽  
Jorge Peregrina-Sandoval ◽  
José Miguel Moreno-Ortiz ◽  
Ramon Antonio Franco-Topete ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Gene Deletion ◽  
In Situ Hybridisation ◽  
P Value ◽  
Histopathological Diagnosis ◽  
Fluorescence In Situ Hybridisation ◽  
Tissue Samples ◽  
Copy Numbers ◽  
Gene Copies ◽  
Advanced Stages

AimsKDM1A/LSD1 and ZNF217 are involved in a protein complex that participates in transcriptional regulation. ZNF217 has been analysed in numerous cancers and its amplification has been associated with advanced stages of disease; however, a similar role for KDM1A/LSD1 has not been uncovered. In this study, we estimated the number of KDM1A/LSD1 and ZNF217 gene copies in tissue samples from patients diagnosed with colorectal cancer (CRC), as well as its association with clinicopathological features in patients with CRC.MethodsParaffin-embedded tumour samples from 50 patients with CRC with a histopathological diagnosis of CRC were included. The number of copies of KDM1A/LSD1 and ZNF217 genes was determined by fluorescence in situ hybridisation (FISH). We also analysed the association between copy numbers of selected genes and clinicopathological data based on multivariate analysis.ResultsDeletion of the KDM1A/LSD1 gene occurred in 19 samples (38%), whereas ZNF217 gene amplification was identified in 11 samples (22%). We found a significant association between lymph node metastasis or advanced tumour stage and KDM1A/LSD1 gene deletion (p value=0.0003 and p value=0.011, respectively).ConclusionsKDM1A/LSD1 gene deletion could be considered a novel prognostic biomarker of late-stage CRC.

scholarly journals Phylogenetic Diversity of Koala Retrovirus within a Wild Koala Population

2016 ◽  
Vol 91 (3) ◽  
Author(s):  
K. J. Chappell ◽  
J. C. Brealey ◽  
A. A. Amarilla ◽  
D. Watterson ◽  
L. Hulse ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Diversity ◽  
Germ Line ◽  
Population Decline ◽  
Hypervariable Region ◽  
Sequence Divergence ◽  
The United States ◽  
High Prevalence ◽  
Amino Acid Sequence Divergence ◽  
Koala Retrovirus

ABSTRACT Koala populations are in serious decline across many areas of mainland Australia, with infectious disease a contributing factor. Koala retrovirus (KoRV) is a gammaretrovirus present in most wild koala populations and captive colonies. Five subtypes of KoRV (A to E) have been identified based on amino acid sequence divergence in a hypervariable region of the receptor binding domain of the envelope protein. However, analysis of viral genetic diversity has been conducted primarily on KoRV in captive koalas housed in zoos in Japan, the United States, and Germany. Wild koalas within Australia have not been comparably assessed. Here we report a detailed analysis of KoRV genetic diversity in samples collected from 18 wild koalas from southeast Queensland. By employing deep sequencing we identified 108 novel KoRV envelope sequences and determined their phylogenetic diversity. Genetic diversity in KoRV was abundant and fell into three major groups; two comprised the previously identified subtypes A and B, while the third contained the remaining hypervariable region subtypes (C, D, and E) as well as four hypervariable region subtypes that we newly define here (F, G, H, and I). In addition to the ubiquitous presence of KoRV-A, which may represent an exclusively endogenous variant, subtypes B, D, and F were found to be at high prevalence, while subtypes G, H, and I were present in a smaller number of animals. IMPORTANCE Koala retrovirus (KoRV) is thought to be a significant contributor to koala disease and population decline across mainland Australia. This study is the first to determine KoRV subtype prevalence among a wild koala population, and it significantly expands the total number of KoRV sequences available, providing a more precise picture of genetic diversity. This understanding of KoRV subtype prevalence and genetic diversity will be important for conservation efforts attempting to limit the spread of KoRV. Furthermore, KoRV is one of the only retroviruses shown to exist in both endogenous (transmitted vertically to offspring in the germ line DNA) and exogenous (horizontally transmitted between infected individuals) forms, a division of fundamental evolutionary importance.

scholarly journals Nonstarch Polysaccharides Modulate Bacterial Microbiota, Pathways for Butyrate Production, and Abundance of Pathogenic Escherichia coli in the Pig Gastrointestinal Tract

2010 ◽  
Vol 76 (11) ◽  
pp. 3692-3701 ◽  
Author(s):  
Barbara U. Metzler-Zebeli ◽  
Seema Hooda ◽  
Robert Pieper ◽  
Ruurd T. Zijlstra ◽  
Andrew G. van Kessel ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bacterial Community ◽  
High Viscosity ◽  
Gene Copy ◽  
Low Viscosity ◽  
Copy Numbers ◽  
Gene Copies ◽  
Nonstarch Polysaccharides ◽  
Gene Copy Numbers ◽  
Butyrate Production

ABSTRACT The impact of nonstarch polysaccharides (NSP) differing in their functional properties on intestinal bacterial community composition, prevalence of butyrate production pathway genes, and occurrence of Escherichia coli virulence factors was studied for eight ileum-cannulated growing pigs by use of terminal restriction fragment length polymorphism (TRFLP) and quantitative PCR. A cornstarch- and casein-based diet was supplemented with low-viscosity, low-fermentability cellulose (CEL), with high-viscosity, low-fermentability carboxymethylcellulose (CMC), with low-viscosity, high-fermentability oat β-glucan (LG), and with high-viscosity, high-fermentability oat β-glucan (HG). Only minor effects of NSP fractions on the ileal bacterial community were observed, but NSP clearly changed the digestion in the small intestine. Compared to what was observed for CMC, more fermentable substrate was transferred into the large intestine with CEL, LG, and HG, resulting in higher levels of postileal dry-matter disappearance. Linear discriminant analysis of NSP and TRFLP profiles and 16S rRNA gene copy numbers for major bacterial groups revealed that CMC resulted in a distinctive bacterial community in comparison to the other NSP, which was characterized by higher gene copy numbers for total bacteria, Bacteroides-Prevotella-Porphyromonas, Clostridium cluster XIVa, and Enterobacteriaceae and increased prevalences of E. coli virulence factors in feces. The numbers of butyryl-coenzyme A (CoA) CoA transferase gene copies were higher than those of butyrate kinase gene copies in feces, and these quantities were affected by NSP. The present results suggest that the NSP fractions clearly and distinctly affected the taxonomic composition and metabolic features of the fecal microbiota. However, the effects were more linked to the individual NSP and to their effect on nutrient flow into the large intestine than to their shared functional properties.

scholarly journals Transfection of mouse fibroblast cells with a promoterless herpes simplex virus thymidine kinase gene: number of integrated gene copies and structure of single and amplified gene sequences.

1985 ◽  
Vol 5 (2) ◽  
pp. 295-304 ◽  
Author(s):  
W Pülm ◽  
R Knippers
Keyword(s):  
Herpes Simplex Virus ◽  
Dna Replication ◽  
Herpes Simplex ◽  
Thymidine Kinase ◽  
Mouse Fibroblast ◽  
Copy Numbers ◽  
Gene Copies ◽  
Cell Clones ◽  
Simplex Virus ◽  
Tandem Arrays

Plasmids carrying the herpes simplex virus thymidine kinase (tk) gene were used to transfect thymidine kinase-deficient cells of the mouse fibroblast cell line LM(tk-). Individual cell clones were cultivated in selective hypoxanthine-aminopterin-thymidine medium to determine the number of integrated plasmid copies which was almost always in the range of one to three copies per genome. In contrast, cells transfected with plasmids carrying a promoterless "truncated" tk gene typically contained between 10 and 25 copies per genome. Surprisingly, when the truncated tk gene was transfected together with a simian virus 40 DNA segment, including its transcriptional enhancer, the number of integrated tk gene copies was always low, between one and three copies per genome. We have analyzed the genomic organization of integrated truncated tk genes by blot hybridization of restricted cellular DNA and concluded that integrated units of plasmid DNA molecules are arranged in tandem arrays which remain stable in most cases for many cell generations. In only 1 of ca. 20 cell clones did we observe a retraction and expansion of the number of integrated promoterless tk genes as a response to the removal or readdition of selective pressure. Surprisingly, the thymidine kinase activity determined in extracts from cells growing in selective hypoxanthine-aminopterin-thymidine medium (high numbers of integrated tk gene copies) was nearly the same as the enzymatic activity in cells growing in nonselective medium (low copy numbers). Moreover, Northern blots of polyadenylated RNA, extracted from cells growing under selective and nonselective conditions, showed that, in both cases, the major species of tk-specific transcripts was ca. 1.5 kilobases in size, as expected for a tk-specific mRNA containing the entire coding region of the gene. Thus, disproportionate DNA replication appeared not to be essential for an active tk gene expression in these cells. We discuss possible pathways leading to the formation of tandem arrays of integrated truncated tk genes and the conditions required for disproportionate DNA replication in the unique case in which we found a retraction and expansion of tk gene copy numbers as a response to selective growth conditions.

scholarly journals Koalas vaccinated against Koala retrovirus respond by producing increased levels of interferon-gamma

2020 ◽  
Vol 17 (1) ◽  
Author(s):  
Olusola Olagoke ◽  
Bonnie L. Quigley ◽  
Peter Timms
Keyword(s):  
Mrna Expression ◽  
Adaptive Immune Response ◽  
Interferon Γ ◽  
Northern Australia ◽  
Mrna Expression Level ◽  
Post Vaccination ◽  
Immune Genes ◽  
Adaptive Immune ◽  
Koala Retrovirus ◽  
Increased Susceptibility

Abstract Koala retrovirus (KoRV) is believed to be in an active state of endogenization into the koala genome. KoRV is present as both an endogenous and exogenous infection in all koalas in northern Australia. KoRV has been linked to koala pathologies including neoplasia and increased susceptibility to Chlamydia. A KoRV vaccine recently trialled in 10 northern koalas improved antibody response and reduced viral load. This communication reports the expression of key immune genes underlining the innate and adaptive immune response to vaccination in these northern koalas. The results showed that prior to vaccination, IL-8 was expressed at the highest levels, with at least 200-fold greater expression compared to other cytokines, while CD8 mRNA expression was significantly higher than CD4 mRNA expression level. Interferon-γ was up-regulated at both 4- and 8-weeks post-vaccination while IL-8 was down-regulated at 8-weeks post-vaccination.

scholarly journals Occurrence of Cyanobacteria and microcystins in hydroelectric reservoirs used for fish farming

2020 ◽  
Vol 18 (6) ◽  
pp. 983-994
Author(s):  
Maria Fernanda Falcone-Dias ◽  
Marianna Vaz Rodrigues ◽  
Jeppe Lund Nielsen ◽  
Nadieh de Jonge ◽  
Niels O. G. Jørgensen ◽  
...  
Keyword(s):  
Negative Impact ◽  
Aquatic Organisms ◽  
Fish Farming ◽  
Fish Farms ◽  
Hydroelectric Reservoirs ◽  
Copy Numbers ◽  
Gene Copies ◽  
Mcye Gene ◽  
Microcystin Production ◽  
Aquaculture Production

Abstract Fish farming can have a negative impact on water quality and aquatic organisms due to emerging blooms of Cyanobacteria and the production of cyanotoxins. In this study, the effect of aquaculture in hydroelectric reservoirs in Brazil was evaluated in six fish farms and in upstream and downstream water through analysis of the microbiome, Cyanobacteria and microcystin concentrations. Synechococcus and Microcystis were observed at all six locations, while Limnothrix was also observed abundantly at two locations. An increase in the relative abundance of Cyanobacteria inside the fish farms was observed at two locations, while an increase of Cyanobacteria was observed in downstream at five of the six locations. Microcystins were detected in significant and high values in all locations, with concentrations up to 1.59 μg/L. The trend in microcystin concentrations was mirrored in copy numbers of the mcyE gene (encodes microcystin synthetase) and presence of Microcystis, but not in any of the other observed cyanobacterial groups. In summary, the study shows that aquaculture production influenced the water microbiome inside and downstream the fish farms, and a direct correlation was found between mcyE gene copies, microcystin production and abundance of Microcystis, but not for the total abundance of Cyanobacteria.

Transfection of mouse fibroblast cells with a promoterless herpes simplex virus thymidine kinase gene: number of integrated gene copies and structure of single and amplified gene sequences

1985 ◽  
Vol 5 (2) ◽  
pp. 295-304
Author(s):  
W Pülm ◽  
R Knippers
Keyword(s):  
Herpes Simplex Virus ◽  
Dna Replication ◽  
Herpes Simplex ◽  
Thymidine Kinase ◽  
Mouse Fibroblast ◽  
Copy Numbers ◽  
Gene Copies ◽  
Cell Clones ◽  
Simplex Virus ◽  
Tandem Arrays

Plasmids carrying the herpes simplex virus thymidine kinase (tk) gene were used to transfect thymidine kinase-deficient cells of the mouse fibroblast cell line LM(tk-). Individual cell clones were cultivated in selective hypoxanthine-aminopterin-thymidine medium to determine the number of integrated plasmid copies which was almost always in the range of one to three copies per genome. In contrast, cells transfected with plasmids carrying a promoterless "truncated" tk gene typically contained between 10 and 25 copies per genome. Surprisingly, when the truncated tk gene was transfected together with a simian virus 40 DNA segment, including its transcriptional enhancer, the number of integrated tk gene copies was always low, between one and three copies per genome. We have analyzed the genomic organization of integrated truncated tk genes by blot hybridization of restricted cellular DNA and concluded that integrated units of plasmid DNA molecules are arranged in tandem arrays which remain stable in most cases for many cell generations. In only 1 of ca. 20 cell clones did we observe a retraction and expansion of the number of integrated promoterless tk genes as a response to the removal or readdition of selective pressure. Surprisingly, the thymidine kinase activity determined in extracts from cells growing in selective hypoxanthine-aminopterin-thymidine medium (high numbers of integrated tk gene copies) was nearly the same as the enzymatic activity in cells growing in nonselective medium (low copy numbers). Moreover, Northern blots of polyadenylated RNA, extracted from cells growing under selective and nonselective conditions, showed that, in both cases, the major species of tk-specific transcripts was ca. 1.5 kilobases in size, as expected for a tk-specific mRNA containing the entire coding region of the gene. Thus, disproportionate DNA replication appeared not to be essential for an active tk gene expression in these cells. We discuss possible pathways leading to the formation of tandem arrays of integrated truncated tk genes and the conditions required for disproportionate DNA replication in the unique case in which we found a retraction and expansion of tk gene copy numbers as a response to selective growth conditions.

scholarly journals Comparison of Different Approaches To QuantifyStaphylococcus aureus Cells by Real-Time Quantitative PCR and Application of This Technique for Examination of Cheese

2001 ◽  
Vol 67 (7) ◽  
pp. 3122-3126 ◽  
Author(s):  
Ingeborg Hein ◽  
Angelika Lehner ◽  
Petra Rieck ◽  
Kurt Klein ◽  
Ernst Brandl ◽  
...  
Keyword(s):  
Real Time ◽  
Quantitative Pcr ◽  
Taqman Probe ◽  
Gene Copy ◽  
Real Time Quantitative Pcr ◽  
Copy Numbers ◽  
Gene Copies ◽  
Different Types ◽  
Pure Cultures ◽  
Gene Copy Numbers

ABSTRACT Two different real-time quantitative PCR (RTQ-PCR) approaches were applied for PCR-based quantification of Staphylococcus aureus cells by targeting the thermonuclease (nuc) gene. Purified DNA extracts from pure cultures ofS. aureus were quantified in a LightCycler system using SYBR Green I. Quantification proved to be less sensitive (60nuc gene copies/μl) than using a fluorigenic TaqMan probe (6 nuc gene copies/μl). Comparison of the LightCycler system and the well-established ABI Prism 7700 SDS with TaqMan probes revealed no statistically significant differences with respect to sensitivity and reproducibility. Application of the RTQ-PCR assay to quantify S. aureus cells in artificially contaminated cheeses of different types achieved sensitivities from 1.5 � 102 to 6.4 � 102 copies of the nuc gene/2 g, depending on the cheese matrix. The coefficients of correlation between log CFU and nuc gene copy numbers ranged from 0.979 to 0.998, thus enabling calculation of the number of CFU of S. aureus in cheese by performing RTQ-PCR.

scholarly journals From the sxtA4 Gene to Saxitoxin Production: What Controls the Variability Among Alexandrium minutum and Alexandrium pacificum Strains?

2021 ◽  
Vol 12 ◽  
Author(s):  
Solène Geffroy ◽  
Marc-Marie Lechat ◽  
Mickael Le Gac ◽  
Georges-Augustin Rovillon ◽  
Dominique Marie ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Size ◽  
Copy Number ◽  
Gene Copy Number ◽  
Toxin Production ◽  
Gene Copy ◽  
Alexandrium Minutum ◽  
Copy Numbers ◽  
Gene Copies ◽  
Paralytic Shellfish

Paralytic shellfish poisoning (PSP) is a human foodborne syndrome caused by the consumption of shellfish that accumulate paralytic shellfish toxins (PSTs, saxitoxin group). In PST-producing dinoflagellates such as Alexandrium spp., toxin synthesis is encoded in the nuclear genome via a gene cluster (sxt). Toxin production is supposedly associated with the presence of a 4th domain in the sxtA gene (sxtA4), one of the core genes of the PST gene cluster. It is postulated that gene expression in dinoflagellates is partially constitutive, with both transcriptional and post-transcriptional processes potentially co-occurring. Therefore, gene structure and expression mode are two important features to explore in order to fully understand toxin production processes in dinoflagellates. In this study, we determined the intracellular toxin contents of twenty European Alexandrium minutum and Alexandrium pacificum strains that we compared with their genome size and sxtA4 gene copy numbers. We observed a significant correlation between the sxtA4 gene copy number and toxin content, as well as a moderate positive correlation between the sxtA4 gene copy number and genome size. The 18 toxic strains had several sxtA4 gene copies (9–187), whereas only one copy was found in the two observed non-toxin producing strains. Exploration of allelic frequencies and expression of sxtA4 mRNA in 11 A. minutum strains showed both a differential expression and specific allelic forms in the non-toxic strains compared with the toxic ones. Also, the toxic strains exhibited a polymorphic sxtA4 mRNA sequence between strains and between gene copies within strains. Finally, our study supported the hypothesis of a genetic determinism of toxin synthesis (i.e., the existence of several genetic isoforms of the sxtA4 gene and their copy numbers), and was also consistent with the hypothesis that constitutive gene expression and moderation by transcriptional and post-transcriptional regulation mechanisms are the cause of the observed variability in the production of toxins by A. minutum.

scholarly journals Geographic patterns and correlates of the decline of granivorous birds in northern Australia

2005 ◽  
Vol 32 (5) ◽  
pp. 399 ◽  
Author(s):  
Donald C. Franklin ◽  
Peter J. Whitehead ◽  
Guy Pardon ◽  
Janet Matthews ◽  
Philip McMahon ◽  
...  
Keyword(s):  
Linear Models ◽  
Spatial Scales ◽  
Grazing Intensity ◽  
Strong Correlations ◽  
Northern Australia ◽  
Intensity Measure ◽  
Generalised Linear Models ◽  
The North ◽  
Geographic Patterns ◽  
Topographic Variation

A geographic index of the decline in the distribution and abundance of granivorous birds in tropical northern Australia shows that declines are greatest in Queensland and especially in the south-eastern tropics and in inland areas, and lowest in the north Kimberley and east Arnhem districts. In this paper, we use generalised linear models to investigate interrelationships among an index of decline in 1° by 1° cells and measures of grazing intensity and contemporary patterns of burning, together with the environmental variables of rainfall, vegetation and topographic patterning in the landscape. Grazing intensity was the single strongest human effect but strong correlations between grazing intensity and other human influences suggest that these may have been subsumed within the grazing intensity measure. Impacts of grazing may be worse where pastoral settlement occurred earlier. Topographic variation appeared to be a mitigating effect, suggesting a role for ‘topographic refuges’ from human activities. Relationships among granivore declines, grazing and rainfall are difficult to disentangle using inferential statistics, but a consistent effect is that declines are more severe in areas with greater year-to-year variation in rainfall. We do not suggest that our analyses are conclusive. However, they do support the proposition that better understanding of the causes of decline at finer spatial scales will emerge most strongly in studies that link habitat quality with granivore demography at inland sites of highly variable year-to-year rainfall and with strongly contrasting grazing histories.

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