scholarly journals Deciphering the Evolutionary History of Arowana Fishes (Teleostei, Osteoglossiformes, Osteoglossidae): Insight from Comparative Cytogenomics

2019 ◽  
Vol 20 (17) ◽  
pp. 4296 ◽  
Author(s):  
Cioffi ◽  
Ráb ◽  
Ezaz ◽  
Bertollo ◽  
Lavoué ◽  
...  
Keyword(s):  
South America ◽  
Indian Plate ◽  
Comparative Genomic ◽  
Nucleotide Polymorphisms ◽  
Dapi Staining ◽  
Single Nucleotide ◽  
Plate Movement ◽  
Array Technology ◽  
History Of ◽  
Cytogenetic Analyses

Arowanas (Osteoglossinae) are charismatic freshwater fishes with six species and two genera (Osteoglossum and Scleropages) distributed in South America, Asia, and Australia. In an attempt to provide a better assessment of the processes shaping their evolution, we employed a set of cytogenetic and genomic approaches, including i) molecular cytogenetic analyses using C- and CMA3/DAPI staining, repetitive DNA mapping, comparative genomic hybridization (CGH), and Zoo-FISH, along with ii) the genotypic analyses of single nucleotide polymorphisms (SNPs) generated by diversity array technology sequencing (DArTseq). We observed diploid chromosome numbers of 2n = 56 and 54 in O. bicirrhosum and O. ferreirai, respectively, and 2n = 50 in S. formosus, while S. jardinii and S. leichardti presented 2n = 48 and 44, respectively. A time-calibrated phylogenetic tree revealed that Osteoglossum and Scleropages divergence occurred approximately 50 million years ago (MYA), at the time of the final separation of Australia and South America (with Antarctica). Asian S. formosus and Australian Scleropages diverged about 35.5 MYA, substantially after the latest terrestrial connection between Australia and Southeast Asia through the Indian plate movement. Our combined data provided a comprehensive perspective of the cytogenomic diversity and evolution of arowana species on a timescale.

scholarly journals Different Within-Host Viral Evolution Dynamics in Severely Immunosuppressed Cases with Persistent SARS-CoV-2

Biomedicines ◽  
2021 ◽  
Vol 9 (7) ◽  
pp. 808
Author(s):  
Laura Pérez-Lago ◽  
Teresa Aldámiz-Echevarría ◽  
Rita García-Martínez ◽  
Leire Pérez-Latorre ◽  
Marta Herranz ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Evolutionary Dynamics ◽  
Viral Evolution ◽  
Special Focus ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
New Variant ◽  
History Of ◽  
Evolution Dynamics ◽  
The Uk

A successful Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant, B.1.1.7, has recently been reported in the UK, causing global alarm. Most likely, the new variant emerged in a persistently infected patient, justifying a special focus on these cases. Our aim in this study was to explore certain clinical profiles involving severe immunosuppression that may help explain the prolonged persistence of viable viruses. We present three severely immunosuppressed cases (A, B, and C) with a history of lymphoma and prolonged SARS-CoV-2 shedding (2, 4, and 6 months), two of whom finally died. Whole-genome sequencing of 9 and 10 specimens from Cases A and B revealed extensive within-patient acquisition of diversity, 12 and 28 new single nucleotide polymorphisms, respectively, which suggests ongoing SARS-CoV-2 replication. This diversity was not observed for Case C after analysing 5 sequential nasopharyngeal specimens and one plasma specimen, and was only observed in one bronchoaspirate specimen, although viral viability was still considered based on constant low Ct values throughout the disease and recovery of the virus in cell cultures. The acquired viral diversity in Cases A and B followed different dynamics. For Case A, new single nucleotide polymorphisms were quickly fixed (13–15 days) after emerging as minority variants, while for Case B, higher diversity was observed at a slower emergence: fixation pace (1–2 months). Slower SARS-CoV-2 evolutionary pace was observed for Case A following the administration of hyperimmune plasma. This work adds knowledge on SARS-CoV-2 prolonged shedding in severely immunocompromised patients and demonstrates viral viability, noteworthy acquired intra-patient diversity, and different SARS-CoV-2 evolutionary dynamics in persistent cases.

scholarly journals Early diversification and permeable species boundaries in the Mediterranean firs

2019 ◽  
Vol 125 (3) ◽  
pp. 495-507 ◽  
Author(s):  
Francisco Balao ◽  
María Teresa Lorenzo ◽  
José Manuel Sánchez-Robles ◽  
Ovidiu Paun ◽  
Juan Luis García-Castaño ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Taxonomic Status ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Early Diversification ◽  
Genome Wide ◽  
History Of ◽  
The Mediterranean ◽  
Independent Species

Abstract Background and Aims Inferring the evolutionary relationships of species and their boundaries is critical in order to understand patterns of diversification and their historical drivers. Despite Abies (Pinaceae) being the second most diverse group of conifers, the evolutionary history of Circum-Mediterranean firs (CMFs) remains under debate. Methods We used restriction site-associated DNA sequencing (RAD-seq) on all proposed CMF taxa to investigate their phylogenetic relationships and taxonomic status. Key Results Based on thousands of genome-wide single nucleotide polymorphisms (SNPs), we present here the first formal test of species delimitation, and the first fully resolved, complete species tree for CMFs. We discovered that all previously recognized taxa in the Mediterranean should be treated as independent species, with the exception of Abies tazaotana and Abies marocana. An unexpectedly early pulse of speciation in the Oligocene–Miocene boundary is here documented for the group, pre-dating previous hypotheses by millions of years, revealing a complex evolutionary history encompassing both ancient and recent gene flow between distant lineages. Conclusions Our phylogenomic results contribute to shed light on conifers’ diversification. Our efforts to resolve the CMF phylogenetic relationships help refine their taxonomy and our knowledge of their evolution.

scholarly journals Evidence GDF15 Plays a Role in Familial and Recurrent Hyperemesis Gravidarum

2018 ◽  
Vol 78 (09) ◽  
pp. 866-870 ◽  
Author(s):  
Marlena Fejzo ◽  
Daria Arzy ◽  
Rayna Tian ◽  
Kimber MacGibbon ◽  
Patrick Mullin
Keyword(s):  
Genome Wide Association Study ◽  
Risk Allele ◽  
Hyperemesis Gravidarum ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Severe Nausea ◽  
Single Nucleotide ◽  
Genome Wide ◽  
History Of ◽  
Study Support

Abstract Introduction Hyperemesis gravidarum (HG), a pregnancy complication characterized by severe nausea and vomiting in pregnancy, occurs in up to 2% of pregnancies. It is associated with both maternal and fetal morbidity. HG is highly heritable and recurs in approximately 80% of women. In a recent genome-wide association study, it was shown that placentation, appetite, and the cachexia gene GDF15 are linked to HG. The purpose of this study was to explore whether GDF15 alleles linked to overexpression of GDF15 protein segregate with the condition in families, and whether the GDF15 risk allele is associated with recurrence of HG. Methods We analyzed GDF15 overexpression alleles for segregation with disease using exome-sequencing data from 5 HG families. We compared the allele frequency of the GDF15 risk allele, rs16982345, in patients who had recurrence of HG with its frequency in those who did not have recurrence. Results Single nucleotide polymorphisms (SNPs) linked to higher levels of GDF15 segregated with disease in HG families. The GDF15 risk allele, rs16982345, was associated with an 8-fold higher risk of recurrence of HG. Conclusion The findings of this study support the hypothesis that GDF15 is involved in the pathogenesis of both familial and recurrent cases of HG. The findings may be applicable when counseling women with a familial history of HG or recurrent HG. The GDF15-GFRAL brainstem-activated pathway was recently identified and therapies to treat conditions of abnormal appetite are under development. Based on our findings, patients carrying GDF15 variants associated with GDF15 overexpression should be included in future studies of GDF15-GFRAL-based therapeutics. If safe, this approach could reduce maternal and fetal morbidity.

scholarly journals Spontaneous Mutations in thePlasmodium falciparumSarcoplasmic/ Endoplasmic Reticulum Ca2+-ATPase (PfATP6) Gene among Geographically Widespread Parasite Populations Unexposed to Artemisinin-Based Combination Therapies

2010 ◽  
Vol 55 (1) ◽  
pp. 94-100 ◽  
Author(s):  
Kazuyuki Tanabe ◽  
Sedigheh Zakeri ◽  
Nirianne Marie Q. Palacpac ◽  
Manada Afsharpad ◽  
Milijaona Randrianarivelojosia ◽  
...  
Keyword(s):  
Amino Acid ◽  
South America ◽  
Artemisinin Resistance ◽  
Common Snps ◽  
Nucleotide Polymorphisms ◽  
Combination Therapies ◽  
Single Nucleotide ◽  
Baseline Information ◽  
A Minor ◽  
Parasite Populations

ABSTRACTRecent reports on the decline of the efficacy of artemisinin-based combination therapies (ACTs) indicate a serious threat to malaria control. The endoplasmic/sarcoplasmic reticulum Ca2+-ATPase ortholog ofPlasmodium falciparum(PfSERCA) has been suggested to be the target of artemisinin and its derivatives. It is assumed that continuous artemisinin pressure will affect polymorphism of the PfSERCA gene (serca) if the protein is the target. Here, we investigated the polymorphism ofsercain parasite populations unexposed to ACTs to obtain baseline information for the study of potential artemisinin-driven selection of resistant parasites. Analysis of 656 full-length sequences from 13 parasite populations in Africa, Asia, Oceania, and South America revealed 64 single nucleotide polymorphisms (SNPs), of which 43 were newly identified and 38 resulted in amino acid substitutions. No isolates showed L263E and S769N substitutions, which were reportedly associated with artemisinin resistance. Among the four continents, the number of SNPs was highest in Africa. In Africa, Asia, and Oceania, common SNPs, or those with a minor allele frequency of ≥0.05, were less prevalent, with most SNPs noted to be continent specific, whereas in South America, common SNPs were highly prevalent and often shared with those in Africa. Of 50 amino acid haplotypes observed, only one haplotype (3D7 sequence) was seen in all four continents (64%). Forty-eight haplotypes had frequencies of less than 5%, and 40 haplotypes were continent specific. The geographical difference in the diversity and distribution ofsercaSNPs and haplotypes lays the groundwork for assessing whether some artemisinin resistance-associated mutations and haplotypes are selected by ACTs.

Short Communication: Does Interleukin-28B Single Nucleotide Polymorphisms Influence the Natural History of Hepatitis B?

2012 ◽  
Vol 28 (10) ◽  
pp. 1262-1264 ◽  
Author(s):  
Luz Martín-Carbonero ◽  
Norma I. Rallón ◽  
José M. Benito ◽  
Eva Poveda ◽  
Juan González-Lahoz ◽  
...  
Keyword(s):  
Natural History ◽  
Hepatitis B ◽  
Single Nucleotide Polymorphisms ◽  
Short Communication ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Interleukin 28B ◽  
History Of

scholarly journals USA300 MRSA lineages persist on multiple body sites following infection

2017 ◽  
Author(s):  
Timothy D. Read ◽  
Robert A. Petit ◽  
Zachary Yin ◽  
Tuyaa Montgomery ◽  
Moira C. McNulty ◽  
...  
Keyword(s):  
Pairwise Distance ◽  
Comparative Genomic ◽  
Nucleotide Polymorphisms ◽  
Normal Flora ◽  
Single Nucleotide ◽  
Whole Genome Shotgun Sequencing ◽  
Initial Acquisition ◽  
Mrsa Infection ◽  
Initial Sampling ◽  
Hospital Acquired

AbstractBACKGROUNDUSA300 methicillin-resistant Staphylococcus aureus (MRSA) is a community- and hospital- acquired pathogen that frequently causes infections but also can survive on the human body asymptomatically as a part of the normal flora. We devised a comparative genomic strategy to track colonizing USA300 at different body sites after S. aureus infection.METHODSWe sampled ST8 S. aureus from subjects at the site of a first known MRSA infection. Within 60 days of this infection and again 12 months later, each subject was tested for asymptomatic colonization in the nose, throat and perirectal region. 93 S. aureus strains underwent whole genome shotgun sequencing.RESULTSGenome sequencing revealed that 23 patients carried USA300 intra-subject lineages (ISLs), defined as having an index infection isolate (III) and closely related strains. Pairwise distance between strains in different ISLs was 48 to 162 single nucleotide polymorphisms (SNPs), whereas within the same ISL it was 0 to 26 SNPs. At the initial sampling time among 23 subjects, we isolated S. aureus from the nose, throat and perirectal sites from 15, 11 and 15 of them, respectively. Twelve months later we isolated S. aureus within the same ISL from 9 subjects, with 6, 3 and 3 strains from the nose, throat and perirectal area, respectively. The median time from initial acquisition of the S. aureus USA300 strains to culture of the index infection was estimated at 18 weeks. Strains in ISLs from the same subject differed in plasmid and prophage content, and contained deletions that removed the mecA-containing SCCmec and ACME regions. Five strains contained frameshift mutations in agr toxin-regulating genes. Persistence of an ISL was not associated with clinical or demographic subject characteristics.CONCLUSIONClonal lineages of USA300 may continue to colonize people at one or more anatomic sites up to a year after an initial infection and experience loss of the SCCmec, loss and gain of other mobile genetic elements, and mutations in the agr operon.

scholarly journals By Animal, Water, or Wind: Can Dispersal Mode Predict Genetic Connectivity in Riverine Plant Species?

2021 ◽  
Vol 12 ◽  
Author(s):  
Alison G. Nazareno ◽  
L. Lacey Knowles ◽  
Christopher W. Dick ◽  
Lúcia G. Lohmann
Keyword(s):  
Gene Flow ◽  
Seed Dispersal ◽  
Plant Species ◽  
Amazon Basin ◽  
Geographic Distance ◽  
Genetic Connectivity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Deforestation Rates ◽  
History Of

Seed dispersal is crucial to gene flow among plant populations. Although the effects of geographic distance and barriers to gene flow are well studied in many systems, it is unclear how seed dispersal mediates gene flow in conjunction with interacting effects of geographic distance and barriers. To test whether distinct seed dispersal modes (i.e., hydrochory, anemochory, and zoochory) have a consistent effect on the level of genetic connectivity (i.e., gene flow) among populations of riverine plant species, we used unlinked single-nucleotide polymorphisms (SNPs) for eight co-distributed plant species sampled across the Rio Branco, a putative biogeographic barrier in the Amazon basin. We found that animal-dispersed plant species exhibited higher levels of genetic diversity and lack of inbreeding as a result of the stronger genetic connectivity than plant species whose seeds are dispersed by water or wind. Interestingly, our results also indicated that the Rio Branco facilitates gene dispersal for all plant species analyzed, irrespective of their mode of dispersal. Even at a small spatial scale, our findings suggest that ecology rather than geography play a key role in shaping the evolutionary history of plants in the Amazon basin. These results may help improve conservation and management policies in Amazonian riparian forests, where degradation and deforestation rates are high.

scholarly journals Polymorphism of MUC1 gene in Vietnamese gastric cancer patients: a case-control study

2019 ◽  
Author(s):  
Lan Thi Ngoc Nguyen ◽  
Dzung Thi Ngoc Dang ◽  
Van Thanh Ta ◽  
Huy Quang Dang ◽  
Chuc Van Tran ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Family History ◽  
Single Nucleotide Polymorphisms ◽  
Cancer Patients ◽  
Nucleotide Polymorphisms ◽  
Mucin 1 ◽  
Single Nucleotide ◽  
History Of ◽  
Gastric Cancer Patients ◽  
Multifactor Regression

Abstract Background Gastric cancer is a malignant type of cancer associated with many factors such as environment, behavior, infection, and genetics, which include Single Nucleotide Polymorphism. A few studies revealed polymorphisms of the Mucin 1 gene have a role and significance as a susceptible factor contributing to gastric cancer. The aim of this research is to evaluate the association between Single Nucleotide Polymorphisms of the Mucin 1 gene and Vietnamese gastric cancer patients.Methods 302 gastric cancer patients and 304 controls were interviewed for social-economic characteristics, smoking and drinking status, personal and family history of gastric diseases. Genotyping was done using polymerase chain reaction-restriction fragment length polymorphism analysis. The association of Single Nucleotide Polymorphisms with gastric cancer was evaluated using multifactor regression models.Results AA genotype for rs4072037 was found to be highly associated with gastric cancer (OR: 2.07 (95% CI: 1.46-2.90). GG genotype for rs2070803 increased the risk of gastric cancer (OR:1.96 (95% CI: 1.37-2.78). These genotypes in combination with other factors such as old age, male gender, alcoholism and personal history of gastric disease also showed an increased risk of having gastric cancer.Conclusions rs4072037 and rs2070803 of Mucin 1 genes are two genotypic risk factors of gastric cancer. Those in combination with other factors such as gender, family history, smoking and drinking habits significantly increase the risk of gastric cancer.

scholarly journals Associations of hypertension Diabetes Smoking History and SNPs with Responses to Aflibercept Treatment for tAMD and PCV

2019 ◽  
pp. 170-177
Author(s):  
Tanaka K ◽  
Furuya K ◽  
Mori R ◽  
Kawamura A ◽  
Yuzawa M ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Initial Treatment ◽  
Smoking History ◽  
Diabetic Patients ◽  
Therapeutic Effects ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
History Of ◽  
One Year ◽  
The One

Purpose: To determine the correlation between therapeutic effects of IVA treatment on typical AMD (tAMD), and polypoidal choroidal vasculopathy (PCV) and the history of hypertension, diabetes mellitus, smoking history and single nucleotide polymorphisms (SNPs).Methods: Prospective, interventional study. Subjects were assigned to 125 untreated patients with exudative AMD (tAMD: 58 patients, PCV: 67 patients, male: 91:34, mean age 73.4 years). Among the tAMD patients, there were 28 bimonthly injections 30 who received pro re nata (PRN) injections after three monthly injections. Among the PCV patients, 33 were treated with bimonthly injections and 34 received PRN injections after three monthly injections. Therapeutic effects were evaluated by best-corrected visual acuity (BCVA), central retinal thickness (CRT), subfoveal choroidal thickness (CCT), and exudative change after 3 months and 1 year from initial treatment, and also the history of hypertension, diabetes mellitus, smoking and five SNPs (rs10490924, rs800292, rs699947, rs1061170, rs13278062).Results: Improvements of BCVA, CRT were observed in all groups at 1 year after initial treatment. The one-yearchange in CRT showed significant improvement in nonsmokers than smokers in tAMD. The one-year change in CRT indicated a significant improvement in non-diabetic patients in PCV. There was more exudation at both 3 months and 1 year who had smoking history in tAMD. With respect to the rs1061170 mutation of tAMD, in the case with TT type, significant residual exudation was noted at both 3 and 12 months.Conclusions: The history of smoking and diabetes could be influence to IVA treatment for AMD.

scholarly journals Novel Associations Between Brca1 Variants C.181 T>G (Rs28897672) and Ovarian Cancer Risk in Saudi Females

2019 ◽  
Vol 38 (1) ◽  
pp. 13-21 ◽  
Author(s):  
Nora Alyahri ◽  
Saba Abdi ◽  
Wajahatullah Khan ◽  
Mohamed Elrobh ◽  
Mohammed H. Addar ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Brca1 Gene ◽  
P Value ◽  
Ovarian Cancer Risk ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
High Risk Women ◽  
History Of ◽  
Polymerase Chain ◽  
Cancer Tissues

Summary Background: Mutations in BRCA1 gene have been implicated in ovarian cancers, and BRCA testing may be conducted in high-risk women. This study was designed to determine the frequency of three single nucleotide polymorphisms (SNPs) variants in BRCA1 gene and BRCA1 expression in Saudi females with ovarian cancer. Methods: Expression levels of mRNA of BRCA1 gene were studied in 10 ovarian cancer and 10 normal ovarian tissues, by quantitative real time polymerase chain reaction (qPCR). The study also included 28 females who had suffered from ovarian cancer and had been successfully operated upon and 90 healthy females with no history of cancer. Blood was drawn in EDTA tubes and used for extraction of DNA. The genotyping was carried out using Taqman® SNP Genotyping kit by RT-PCR. The variants investigated included c.871 T>C (rs799917), c.1040 G>A (rs4986852), c.181 T>G (rs28897672) in BRCA1 gene. Results: The c.181 T>G (rs28897672) showed significantly different genotype and allele frequencies between the patients and the control subjects (p value = 0.002 and 0.02, respectively). The genotype TG was significantly protective (OR = 0.36, p value = 0.024). The mRNA expression of BRCA1 gene was found to be low in the ovarian cancer tissues. Conclusions: This study showed that c.181 T>G in BRCA1 genes is associated with the development of ovarian cancer in Saudis. More studies are needed to unveil other SNPs that may be associated with ovarian cancer and to understand the mechanism(s) involved in reducing the expression of BRCA1 gene in ovarian cancer tissues.

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