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1.
Plant Mol Biol ; 114(2): 25, 2024 Mar 08.
Article in English | MEDLINE | ID: mdl-38457042

ABSTRACT

Knowing how chromosome recombination works is essential for plant breeding. It enables the design of crosses between different varieties to combine desirable traits and create new ones. This is because the meiotic crossovers between homologous chromatids are not purely random, and various strategies have been developed to describe and predict such exchange events. Recent studies have used methylation data to predict chromosomal recombination in rice using machine learning models. This approach proved successful due to the presence of a positive correlation between the CHH context cytosine methylation and recombination rates in rice chromosomes. This paper assesses the question if methylation can be used to predict recombination in four plant species: Arabidopsis, maize, sorghum, and tomato. The results indicate a positive association between CHH context methylation and recombination rates in certain plant species, with varying degrees of strength in their relationships. The CG and CHG methylation contexts show negative correlation with recombination. Methylation data was key effectively in predicting recombination in sorghum and tomato, with a mean determination coefficient of 0.65 ± 0.11 and 0.76 ± 0.05, respectively. In addition, the mean correlation values between predicted and experimental recombination rates were 0.83 ± 0.06 for sorghum and 0.90 ± 0.05 for tomato, confirming the significance of methylomes in both monocotyledonous and dicotyledonous species. The predictions for Arabidopsis and maize were not as accurate, likely due to the comparatively weaker relationships between methylation contexts and recombination, in contrast to sorghum and tomato, where stronger associations were observed. To enhance the accuracy of predictions, further evaluations using data sets closely related to each other might prove beneficial. In general, this methylome-based method holds great potential as a reliable strategy for predicting recombination rates in various plant species, offering valuable insights to breeders in their quest to develop novel and improved varieties.


Subject(s)
Arabidopsis , Arabidopsis/genetics , Epigenome , Plant Breeding , DNA Methylation , Plants/genetics , Recombination, Genetic/genetics , Gene Expression Regulation, Plant
2.
BMC Plant Biol ; 21(1): 312, 2021 Jul 02.
Article in English | MEDLINE | ID: mdl-34215182

ABSTRACT

BACKGROUND: Peanut smut is a disease caused by the fungus Thecaphora frezii Carranza & Lindquist to which most commercial cultivars in South America are highly susceptible. It is responsible for severely decreased yield and no effective chemical treatment is available to date. However, smut resistance has been identified in wild Arachis species and further transferred to peanut elite cultivars. To identify the genome regions conferring smut resistance within a tetraploid genetic background, this study evaluated a RIL population {susceptible Arachis hypogaea subsp. hypogaea (JS17304-7-B) × resistant synthetic amphidiploid (JS1806) [A. correntina (K 11905) × A. cardenasii (KSSc 36015)] × A. batizocoi (K 9484)4×} segregating for the trait. RESULTS: A SNP based genetic map arranged into 21 linkage groups belonging to the 20 peanut chromosomes was constructed with 1819 markers, spanning a genetic distance of 2531.81 cM. Two consistent quantitative trait loci (QTLs) were identified qSmIA08 and qSmIA02/B02, located on chromosome A08 and A02/B02, respectively. The QTL qSmIA08 at 15.20 cM/5.03 Mbp explained 17.53% of the phenotypic variance, while qSmIA02/B02 at 4.0 cM/3.56 Mbp explained 9.06% of the phenotypic variance. The combined genotypic effects of both QTLs reduced smut incidence by 57% and were stable over the 3 years of evaluation. The genome regions containing the QTLs are rich in genes encoding proteins involved in plant defense, providing new insights into the genetic architecture of peanut smut resistance. CONCLUSIONS: A major QTL and a minor QTL identified in this study provide new insights into the genetic architecture of peanut smut resistance that may aid in breeding new varieties resistant to peanut smut.


Subject(s)
Arachis/genetics , Arachis/microbiology , Chromosome Mapping , Disease Resistance/genetics , Plant Diseases/genetics , Plant Diseases/microbiology , Quantitative Trait Loci/genetics , Genetic Association Studies , Genetic Markers , Inbreeding , Phenotype , Polymorphism, Single Nucleotide/genetics , Recombination, Genetic/genetics
3.
Sci Rep ; 11(1): 13039, 2021 06 22.
Article in English | MEDLINE | ID: mdl-34158515

ABSTRACT

The Brazilian regions are still highly endemic areas for Canine morbillivirus [canine distemper virus (CDV)]. However, little is known regarding the genetic variability of the strain circulating in several Brazilian regions. Here, we report the first full-length genome and molecular characterization of CDV isolated from domestic dogs in the Brazilian Center-West region. Sequence alignment and phylogenetic analyses based on deduced amino acid and nucleotide sequences showed that the isolated strain is characterized as the South America-I/Europe genotype. However, it segregates into a CDV subgenotype branch. Interestingly, both H and F proteins have a gain of a potential N-glycosylation sites compared to the Onderstepoort vaccine strain. Therefore, this study provides a reference to further understand the epidemic and molecular characteristics of the CDV in Brazil.


Subject(s)
Distemper Virus, Canine/genetics , Distemper Virus, Canine/isolation & purification , Dogs/virology , Genome, Viral , Amino Acid Sequence , Animals , Base Sequence , Brazil , Distemper/virology , Genes, Viral , Genotype , Glycosylation , Phylogeny , Recombination, Genetic/genetics , Selection, Genetic , Viral Proteins/chemistry , Viral Proteins/genetics
4.
Infect Genet Evol ; 92: 104854, 2021 08.
Article in English | MEDLINE | ID: mdl-33839313

ABSTRACT

The HIV-1 epidemic in southern Brazil is mostly caused by subtype C, which contrasts the dominance of subtype B in the other regions of the country. Santa Catarina (SC), although the smallest state in the southern region, presents one of the highest incidences and mortality rates in Brazil due to AIDS. This work investigated the HIV-1 molecular diversity and phylogenetic transmission networks in SC state by analyzing a database of 3070 sequences of the national genotyping service. HIV-1C proved to be the most frequent subtype, with a significant increase in prevalence over time. HIV-1B was observed to be associated with highly educated men, suggesting a compartmentalization from other subtypes. Such observation was confirmed by the high frequency of HIV-1B circulating in MSM transmission networks. Identified transmission clusters were majority composed by individuals living up to 25 km away and interstate linkages were mainly between southern neighbor states. In general, individuals between 25 and 40 years old and sequences sampled after 2014 were more likely to be in transmission chains, in agreement with the universal treatment protocol launched in 2014. The present study brings new insights about HIV-1 transmission dynamics in southern Brazil.


Subject(s)
HIV Infections/epidemiology , HIV Infections/transmission , HIV-1/genetics , Adolescent , Adult , Brazil/epidemiology , Epidemics , Female , Genotype , HIV Infections/virology , HIV Seropositivity/epidemiology , HIV Seropositivity/transmission , HIV Seropositivity/virology , Humans , Male , Middle Aged , Molecular Epidemiology/methods , Phylogeny , Recombination, Genetic/genetics , Young Adult
5.
Arch Virol ; 166(7): 2027-2031, 2021 Jul.
Article in English | MEDLINE | ID: mdl-33900470

ABSTRACT

To analyze the DNA virome associated with cacao (Theobroma cacao L.) trees showing virus-like symptoms in Brazil (BR) and Puerto Rico (PR) during 2018-2019, total DNA was isolated from symptomatic leaves and subjected to high-throughput Illumina sequencing. The assembled complete badnaviral genome sequences were verified by PCR amplification, cloning, and DNA sequencing. Based on pairwise distances and phylogenetic analysis, three badnaviral genomes were identified, and these viruses were found to be isolates of the previously described cacao mild mosaic virus (CaMMV). The three genomes were 7,520, 7,524, and 7,514 bp in size for the isolates CaMMV-BR321, CaMMV-BR322, and CaMMV-PR3, respectively. Each genome contained four predicted open reading frames: ORFs 1-3 and ORFY. The CaMMV-PR3 isolate was identified as a probable recombinant, with a CaMMV-BR-like virus as the major parent.


Subject(s)
Cacao/virology , Genome, Viral/genetics , Mosaic Viruses/genetics , Plant Diseases/virology , Recombination, Genetic/genetics , Badnavirus/genetics , Brazil , High-Throughput Nucleotide Sequencing , Open Reading Frames/genetics , Phylogeny , Puerto Rico , Sequence Analysis, DNA/methods , Whole Genome Sequencing/methods
6.
Bioessays ; 42(9): e2000037, 2020 09.
Article in English | MEDLINE | ID: mdl-32643212

ABSTRACT

The distribution pattern of the meiotic machinery in known eukaryotes is most parsimoniously explained by the hypothesis that all eukaryotes are ancestrally sexual. However, this assumption is questioned by preliminary results, in culture conditions. These suggested that Acanthamoeba, an organism considered to be largely asexual, constitutively expresses meiosis genes nevertheless-at least in the lab. This apparent disconnect between the "meiosis toolkit" and sexual processes in Acanthamoeba led to the conclusion that the eukaryotic ancestor is asexual. In this review, the "meiosis toolkit" is rigorously defended, drawing on numerous research articles. Additionally, the claim of constitutive meiotic gene expression is probed in Acanthamoeba via the same transcriptomics data. The results show that the expression of the meiotic machinery is not constitutive in Acanthamoeba as claimed before. Furthermore, it is argued that this would have no implications for understanding the nature of the eukaryotic ancestor, regardless of the result.


Subject(s)
Eukaryota , Meiosis , Eukaryotic Cells , Gene Expression , Humans , Meiosis/genetics , Recombination, Genetic/genetics
7.
Mol Phylogenet Evol ; 136: 35-43, 2019 07.
Article in English | MEDLINE | ID: mdl-30914396

ABSTRACT

Hantaviruses (order Bunyavirales, family Hantaviridae) are important zoonotic pathogens. Because of the great diversity of their reservoir hosts, hantaviruses are excellent models to evaluate the dynamics of virus-host co-evolution. To understand the mechanisms behind the evolutionary history of hantaviruses through virus-reservoir interactions, it is important to know how the radiation and diversity of hantaviruses occurred. In this paper, we evaluate the pattern of hantavirus diversification based on a complete S segment representing major groups of hantaviruses found in the Americas. Phylogenetic analyses revealed a high degree of phylogeographic structure and a surprising pattern of geographical distribution of New World hantaviruses. The available data suggest that hantaviruses related to the Arvicolinae rodent subfamily in North America probably emerged and initially adapted from a shared common ancestor of the Tula virus. The first clade of hantaviruses associated with Neotominae occupied a stem lineage, especially those that emerged in Central America or Mexico. Hantaviruses from Central America and Mexico found in Neotominae rodents spread northward and probably gave rise to the first phylogroup of hantaviruses associated with Sigmodontinae in North America. Two preferential host-switching transmissions in hantaviruses apparently gave rise to two different paraphyletic group in Neotominae and Sigmodontinae. Our study supports a probable epicenter of diversification in Central America and/or Mexico for hantaviruses related to both the Neotominae and Sigmodontinae subfamilies.


Subject(s)
Orthohantavirus/classification , Phylogeography , Rodentia/virology , Animals , Central America , Hantavirus Infections/virology , Mexico , Phylogeny , Recombination, Genetic/genetics
8.
Microb Cell Fact ; 17(1): 189, 2018 Nov 28.
Article in English | MEDLINE | ID: mdl-30486842

ABSTRACT

BACKGROUND: In Streptomyces, understanding the switch from primary to secondary metabolism is important for maximizing the production of secondary metabolites such as antibiotics, as well as for optimizing recombinant glycoprotein production. Differences in Streptomyces lividans bacterial aggregation as well as recombinant glycoprotein production and O-mannosylation have been reported due to modifications in the shake flask design. We hypothetized that such differences are related to the metabolic switch that occurs under oxygen-limiting conditions in the cultures. RESULTS: Shake flask design was found to affect undecylprodigiosin (RED, a marker of secondary metabolism) production; the RED yield was 12 and 385 times greater in conventional normal Erlenmeyer flasks (NF) than in baffled flasks (BF) and coiled flasks (CF), respectively. In addition, oxygen transfer rates (OTR) and carbon dioxide transfer rates were almost 15 times greater in cultures in CF and BF as compared with those in NF. Based on these data, we obtained respiration quotients (RQ) consistent with aerobic metabolism for CF and BF, but an RQ suggestive of anaerobic metabolism for NF. CONCLUSION: Although the metabolic switch is usually related to limitations in phosphate and nitrogen in Streptomyces sp., our results reveal that it can also be activated by low OTR, dramatically affecting recombinant glycoprotein production and O-mannosylation and increasing RED synthesis in the process.


Subject(s)
Bioreactors/microbiology , Oxygen/pharmacology , Recombination, Genetic/genetics , Streptomyces lividans/metabolism , Kinetics , Metabolic Networks and Pathways/drug effects , Prodigiosin/analogs & derivatives , Prodigiosin/biosynthesis , Prodigiosin/chemistry , Spectroscopy, Fourier Transform Infrared , Streptomyces lividans/drug effects , Streptomyces lividans/growth & development
9.
Sci Rep ; 8(1): 15072, 2018 10 10.
Article in English | MEDLINE | ID: mdl-30305667

ABSTRACT

Mucositis is an inflammatory condition of the gut, caused by an adverse effect of chemotherapy drugs, such as 5-fluorouracil (5-FU). In an attempt to develop alternative treatments for the disease, several research groups have proposed the use of probiotics, in particular, Lactic Acid Bacteria (LAB). In this context, the use of recombinant LAB, for delivering anti-inflammatory compounds has also been explored. In previous work, we demonstrated that either Lactococcus lactis NZ9000 or a recombinant strain expressing an antimicrobial peptide involved in human gut homeostasis, the Pancreatitis-associated Protein (PAP), could ameliorate 5-FU-induced mucositis in mice. However, the impact of these strains on the gut microbiota still needs to be elucidated. Therefore, in the present study, we aimed to characterize the effects of both Lactococci strains in the gut microbiome of mice through a 16 S rRNA gene sequencing metagenomic approach. Our data show 5-FU caused a significant decrease in protective bacteria and increase of several bacteria associated with pro-inflammatory traits. The Lactococci strains were shown to reduce several potential opportunistic microbes, while PAP delivery was able to suppress the growth of Enterobacteriaceae during inflammation. We conclude the strain secreting antimicrobial PAP was more effective in the control of 5-FU-dysbiosis.


Subject(s)
Anti-Infective Agents/pharmacology , Gastrointestinal Microbiome/drug effects , Lactococcus lactis/physiology , Mucositis/microbiology , Mucositis/therapy , Pancreatitis-Associated Proteins/pharmacology , Recombination, Genetic/genetics , Animals , Biodiversity , Feces/microbiology , Female , Fluorouracil/pharmacology , Humans , Inflammation/microbiology , Inflammation/pathology , Mice, Inbred BALB C , Phylogeny
10.
Viruses ; 10(10)2018 09 24.
Article in English | MEDLINE | ID: mdl-30249971

ABSTRACT

Here we report the nearly full-length genome of a recombinant Saffold virus strain (SAFV-BR-193) isolated from a child with acute gastroenteritis. Evolutionary analysis performed using all available near-full length Saffold picornavirus genomes showed that the breakpoint found in the Brazilian strain (SAFV-BR-193) is indeed a recombination hotspot. Notably, this hotspot is located just one nucleotide after the ribosomal frameshift GGUUUUU motif in the SAFV genome. Empirical studies will be necessary to determine if this motif also affects the binding affinity of RNA-dependent RNA-polymerase (RdRp) and therefore increases the changes of RdRp swap between molecules during the synthesis of viral genomes.


Subject(s)
Cardiovirus Infections/virology , Cardiovirus/genetics , Frameshifting, Ribosomal/genetics , Gastroenteritis/virology , Recombination, Genetic/genetics , Acute Disease , Brazil , Child, Preschool , Feces/virology , Genome, Viral/genetics , Humans , Phylogeny , RNA-Dependent RNA Polymerase/genetics , Sequence Alignment
11.
Exp Parasitol ; 194: 24-31, 2018 Nov.
Article in English | MEDLINE | ID: mdl-30237050

ABSTRACT

The mechanisms underlying metronidazole (MTZ) resistance in Giardia duodenalis have been associated with decreased activity of the enzymes implicated in its activation including nitroductase-1, thioredoxin reductase and pyruvate-ferredoxin oxidoreductase (PFOR). MTZ activation generates radicals that can form adducts with proteins such as thioredoxin reductase and α- and -ß giardins as well as DNA damage resulting in trophozoite's death. The damage induced in DNA requires a straight forward response that may allow parasite survival. Here, we studied changes in histone H2A phosphorylation to evaluate the DNA repair response pathway after induction of double strand break (DSB) by MTZ in Giardia DNA. Our results showed that the DNA repair mechanisms after exposure of Giardia trophozoites to MTZ, involved a homologous recombination pathway. We observed a significant increase in the expression level of proteins GdDMC1B, which carries out Rad51 role in G. duodenalis, and GdMre11, after 12 h of exposure to 3.2 µM MTZ. This increase was concomitant with the generation of DSB in the DNA of trophozoites treated MTZ. Altogether, these results suggest that MTZ-induced DNA damage in Giardia triggers the DNA homologous recombination repair (DHRR) pathway, which may contribute to the parasite survival in the presence of MTZ.


Subject(s)
Antiprotozoal Agents/pharmacology , DNA Damage/drug effects , DNA Repair/drug effects , Giardia lamblia/drug effects , Metronidazole/pharmacology , DNA, Protozoan/drug effects , DNA, Protozoan/genetics , Drug Resistance , Giardia lamblia/genetics , In Situ Nick-End Labeling , Inhibitory Concentration 50 , Phosphorylation/drug effects , Recombination, Genetic/genetics
12.
Ann Bot ; 121(3): 571-585, 2018 03 05.
Article in English | MEDLINE | ID: mdl-29293884

ABSTRACT

Background and Aims: Two main types of triploid limes are produced worldwide. The 'Tahiti' lime type (Citrus latifolia) is predominant, while the 'Tanepao' type (C. aurantiifolia) is produced to a lesser extent. Both types result from natural interspecific hybridization involving a diploid gamete of C. aurantiifolia 'Mexican' lime type (itself a direct interspecific C. micrantha × C. medica hybrid). The meiotic behaviour of a doubled-diploid 'Mexican' lime, the interspecific micrantha/medica recombination and the resulting diploid gamete structures were analysed to investigate the possibility that 'Tahiti' and 'Tanepao' varieties are derived from natural interploid hybridization. Methods: A population of 85 tetraploid hybrids was established between a doubled-diploid clementine and a doubled-diploid 'Mexican' lime and used to infer the genotypes of 'Mexican' lime diploid gametes. Meiotic behaviour was studied through combined segregation analysis of 35 simple sequenbce repeat (SSR) and single nucleotide polymorphismn (SNP) markers covering the nine citrus chromosomes and cytogenetic studies. It was supplemented by pollen viability assessment. Key Results: Pollen viability of the doubled-diploid Mexican lime (64 %) was much higher than that of the diploid. On average, 65 % of the chromosomes paired as bivalents and 31.4 % as tetravalents. Parental heterozygosity restitution ranged from 83 to 99 %. Disomic inheritance with high preferential pairing values was deduced for three chromosomes. Intermediate inheritances, with disomic trend, were found for five chromosomes, and an intermediate inheritance was observed for one chromosome. The average effective interspecific recombination rate was low (1.2 cM Mb-1). Conclusion: The doubled-diploid 'Mexican' lime had predominantly disomic segregation, producing interspecific diploid gamete structures with high C. medica/C. micrantha heterozygosity, compatible with the phylogenomic structures of triploid C. latifolia and C. aurantiifolia varieties. This disomic trend limits effective interspecific recombination and diversity of the diploid gamete population. Interploid reconstruction breeding using doubled-diploid lime as one parent is a promising approach for triploid lime diversification.


Subject(s)
Citrus aurantiifolia/genetics , Citrus/genetics , Diploidy , Hybridization, Genetic/genetics , Triploidy , Chromosome Mapping , Chromosomes, Plant/genetics , Cytogenetics , Genetic Markers/genetics , Genotyping Techniques , Microsatellite Repeats/genetics , Pollen/genetics , Polymorphism, Single Nucleotide/genetics , Recombination, Genetic/genetics
13.
Sci Rep ; 7(1): 8718, 2017 08 18.
Article in English | MEDLINE | ID: mdl-28821712

ABSTRACT

Mayaro virus (MAYV), causative agent of Mayaro Fever, is an arbovirus transmitted by Haemagogus mosquitoes. Despite recent attention due to the identification of several cases in South and Central America and the Caribbean, limited information on MAYV evolution and epidemiology exists and represents a barrier to prevention of further spread. We present a thorough spatiotemporal evolutionary study of MAYV full-genome sequences collected over the last sixty years within South America and Haiti, revealing recent recombination events and adaptation to a broad host and vector range, including Aedes mosquito species. We employed a Bayesian phylogeography approach to characterize the emergence of recombinants in Brazil and Haiti and report evidence in favor of the putative role of human mobility in facilitating recombination among MAYV strains from geographically distinct regions. Spatiotemporal characteristics of recombination events and the emergence of this previously neglected virus in Haiti, a known hub for pathogen spread to the Americas, warrants close monitoring of MAYV infection in the immediate future.


Subject(s)
Alphavirus/physiology , Recombination, Genetic/genetics , Aedes/virology , Alphavirus/genetics , Alphavirus/isolation & purification , Animals , Bayes Theorem , Brazil , Codon/genetics , Genetic Code , Genome, Viral , Genotype , Humans , Likelihood Functions , Phylogeny , Phylogeography , Selection, Genetic , Time Factors
14.
AIDS Res Hum Retroviruses ; 33(9): 952-959, 2017 Sep.
Article in English | MEDLINE | ID: mdl-28443724

ABSTRACT

HIV-1 has the Vif protein, which binds to human antiviral proteins APOBEC3 to form complexes to be degraded by cellular proteolysis. To further explore HIV-1 diversity at the population level, we analyzed blood samples from 317 treatment-naive patients in Brazil. In this study, we explored the correlations of Vif polymorphisms with clinical parameters of the patients and found that mutation K22H is associated with low CD4+ cell counts and higher viral loads. Phylogenetic analysis of the vif gene indicated that subtype B was predominant in ∼77% (243/317) of the patients, followed by HIV-1 F ∼18% (56/317), and subtype C ∼4% (12/317); five samples were BF recombinants (∼1% of patients), and one was an AG recombinant. On the basis of the vif gene, we detected the presence of one AG and several previously unknown BF intersubtypes in this population. The global mean diversity, measured by pairwise distances, was 0.0931 ± 0.0006 among sequences of subtype B (n = 243), whereas the mean diversity of subtype C sequences (n = 12) was 0.0493 ± 0.001 and that of subtype F (n = 56) was 0.050 ± 0.001.


Subject(s)
Genetic Variation/genetics , HIV Infections/virology , HIV-1/genetics , Brazil , CD4 Lymphocyte Count/methods , Female , Humans , Phylogeny , Recombination, Genetic/genetics , vif Gene Products, Human Immunodeficiency Virus/genetics
15.
Food Chem Toxicol ; 101: 48-54, 2017 Mar.
Article in English | MEDLINE | ID: mdl-28069374

ABSTRACT

The significant contents of artepillin C (AC) in green propolis have prompted research on the biological activities of the compound. The present study evaluated the activity of this phenolic compound on DNA, assessing its genotoxic and antigenotoxic potentials in the somatic mutation and recombination test in Drosophila melanogaster. The standard (ST) and high-bioactivation (HB) crosses were used in the assessment of genotoxic potential, since they express cytochrome P450 metabolization enzymes differently. In the 0.1-1.6 mM concentration range, AC did not have any genotoxic action in either cross. Antigenotoxic potential was investigated using the ST cross. In co- and post-treatment protocols, AC 0.4, 0.8, and 1.6 mM did not modulate mutagenic action of ethyl methanesulphonate. However, though it did not influence the frequency of damage induced by mitomycin C in co-treatment, AC reduced genotoxicity of the mutagen when administered after damage, but only at 0.4 mM. This modulation is associated with the reduction of genetic damage caused by recombinational events. The results of the present study and literature findings indicate that the various responses elicited by AC, namely induction of DNA damage, production of genetic lesions, or activation of DNA repair mechanisms are functions of AC concentration.


Subject(s)
DNA Damage/drug effects , Drosophila melanogaster/drug effects , Phenylpropionates/toxicity , Recombination, Genetic/genetics , Animals , Cells, Cultured , DNA Damage/genetics , Drosophila melanogaster/genetics , Mutagenicity Tests/methods , Nucleic Acid Synthesis Inhibitors/toxicity
16.
BMC Bioinformatics ; 18(Suppl 14): 471, 2017 12 28.
Article in English | MEDLINE | ID: mdl-29297281

ABSTRACT

BACKGROUND: Zika virus (ZIKV) is an emerging human pathogen. Since its arrival in the Western hemisphere, from Africa via Asia, it has become a serious threat to pregnant women, causing microcephaly and other neuropathies in developing fetuses. The mechanisms behind these teratogenic effects are unknown, although epidemiological evidence suggests that microcephaly is not associated with the original, African lineage of ZIKV. The sequences of 196 published ZIKV genomes were used to assess whether recently proposed mechanistic explanations for microcephaly are supported by molecular level changes that may have increased its virulence since the virus left Africa. For this we performed phylogenetic, recombination, adaptive evolution and tetramer frequency analyses, and compared protein sequences for the presence of protease cleavage sites, Pfam domains, glycosylation sites, signal peptides, trans-membrane protein domains, and phosphorylation sites. RESULTS: Recombination events within or between Asian and Brazilian lineages were not observed, and likewise there were no differences in protease cleavage, glycosylation sites, signal peptides or trans-membrane domains between African and Brazilian strains. The frequency of Retinoic Acid Response Element (RARE) sequences was increased in Brazilian strains. Genetic adaptation was also apparent by tetramer signatures that had undergone major changes in the past but has stabilized in the Brazilian lineage despite subsequent geographic spread, suggesting the viral population presently propagates in the same host species in various regions. Evidence for selection pressure was recognized for several amino acid sites in the Brazilian lineage compared to the African lineage, mainly in nonstructural proteins, especially protein NS4B. A number of these positively selected mutations resulted in an increased potential to be phosphorylated in the Brazilian lineage compared to the African linage, which may have increased their potential to interfere with neural fetal development. CONCLUSIONS: ZIKV seems to have adapted to a limited number of hosts, including humans, during which its virulence increased. Its protein NS4B, together with NS4A, has recently been shown to inhibit Akt-mTOR signaling in human fetal neural stem cells, a key pathway for brain development. We hypothesize that positive selection of novel phosphorylation sites in the protein NS4B of the Brazilian lineage could interfere with phosphorylation of Akt and mTOR, impairing Akt-mTOR signaling and this may result in an increased risk for developmental neuropathies.


Subject(s)
Genome, Viral , Microcephaly/virology , Zika Virus/genetics , Zika Virus/physiology , Adaptation, Physiological/genetics , Africa , Asia , Base Sequence , Brazil , Cell Line , Codon/genetics , Female , Genetic Variation , Host-Pathogen Interactions/genetics , Humans , Microcephaly/immunology , Phosphorylation , Phylogeny , Pregnancy , RNA Stability/genetics , Recombination, Genetic/genetics , Selection, Genetic , Virulence/genetics , Zika Virus/pathogenicity , Zika Virus Infection/immunology , Zika Virus Infection/virology
17.
Genet Mol Res ; 15(4)2016 Oct 17.
Article in English | MEDLINE | ID: mdl-27813561

ABSTRACT

The stigma exertion rate is a polygenic inherited trait that is important for increased seed yield in hybrid rice breeding. To identify quantitative trait loci (QTL) associated with high stigma exertion rate, we conducted QTL mapping using 134 recombinant inbred lines derived from XieqingzaoB and Zhonghui9308, which have high and low stigma exertion rates, respectively. A total of eight QTLs (qSES6, qSSE11, qDSE1a, qDSE1b, qDSE10, qDSE11, qTSE1, and qTSE11) for single stigma exertion, double stigma exertion, and total stigma exertion were detected. The locations of qSSE11 and qTSE11 have not been previously reported, and the qDSE11 allele from parent XQZB exhibited a positive additive effect. In addition, three QTLs (qSNP1, qSNP3a, and qSNP3b), for spikelet number per panicle were identified. Of note, one QTL (qSNP1) was detected in two different environments (Hainan and Zhejiang). To evaluate the advantage of exerted stigma for cross-pollination, single, dual, and total stigma exertion should be considered separately for future genetic improvement in the production of rice hybrid seeds. In addition, this study provides information for fine mapping, gene cloning, and marker assisted selection, with emphasis on the latter.


Subject(s)
Chromosome Mapping/methods , Oryza/anatomy & histology , Oryza/genetics , Quantitative Trait Loci/genetics , Analysis of Variance , Chromosomes, Plant/genetics , Environment , Genetics, Population , Inbreeding , Models, Genetic , Polymorphism, Single Nucleotide/genetics , Quantitative Trait, Heritable , Recombination, Genetic/genetics , Temperature
18.
Genet Mol Res ; 15(4)2016 Oct 17.
Article in English | MEDLINE | ID: mdl-27813562

ABSTRACT

Chlorophyll (CHL) is present in many plant organs, and its metabolism is strongly regulated throughout plant development. Understanding the fate of CHL in senescent leaves or during fruit ripening is a complex process. The stay-green (SGR) protein has been shown to affect CHL degradation. In this study, we used the conserved sequences of STAY-GREEN domain protein (NP_567673) in Arabidopsis thaliana as a probe to search SGR family genes in the genome-wide melon protein database. Four candidate SGR family genes were identified in melon (Cucumis melo L. Hetao). The phylogenetic evolution, gene structure, and conserved motifs were subsequently analyzed. In order to verify the function of CmSGR genes in CHL degradation, CmSGR1 and CmSGR2 were transiently overexpressed and silenced using different plasmids in melon. Overexpression of CmSGR1 or CmSGR2 induced leaf yellowing or fruit ripening, while silencing of CmSGR1 or CmSGR2 via RNA interference delayed CHL breakdown during fruit ripening or leaf senescence compared with the wild type. Next, the expression profile was analyzed, and we found that CmSGR genes were expressed ubiquitously. Moreover, CmSGR1 and CmSGR2 were upregulated, and promoted fruit ripening. CmSGR3 and CmSGR4 were more highly expressed in leaves, cotyledon, and stem compared with CmSGR1 or CmSGR2. Thus, we conclude that CmSGR genes are crucial for fruit ripening and leaf senescence. CmSGR protein structure and function were further clarified to provide a theoretical foundation and valuable information for improved performance of melon.


Subject(s)
Cucumis melo/genetics , Genes, Plant , Multigene Family , Agrobacterium/metabolism , Amino Acid Motifs , Amino Acid Sequence , Amino Acids/metabolism , Conserved Sequence , Exons/genetics , Fruit/genetics , Gene Expression Profiling , Gene Expression Regulation, Developmental , Gene Expression Regulation, Plant , Introns/genetics , Phylogeny , Plant Proteins/chemistry , Plant Proteins/genetics , Plant Proteins/metabolism , Recombination, Genetic/genetics , Sequence Alignment , Species Specificity
19.
Food Chem Toxicol ; 96: 117-21, 2016 Oct.
Article in English | MEDLINE | ID: mdl-27484244

ABSTRACT

Propolis is a resinous, complex mixture of compounds collected by the bee species Apis mellifera. This study investigated the genotoxicity of green and brown propolis collected in southeast Brazil using the somatic mutation and recombination test (SMART) in Drosophila melanogaster. The effect of five concentrations (0.5, 1.0, 2.0, 4.0, and 7.5 mg/mL) of both propolis types was analyzed in standard (ST) and high-bioactivation (HB) crosses, which have normal and high levels of cytochrome P450 enzymes, respectively. The results show that the types of propolis evaluated have no mutagenic action, in either cross. Moreover, chromatography findings revealed that the propolis types analyzed have different chemical compositions. Brown propolis had lower levels of polyphenols (∼7.2 mg/mL), compared to the green type (34.9 mg/g). Taken together, the findings of the present study and literature reports point to the safety in consuming low amounts of propolis, considering the risk of genetic damage, and confirm the absence of mutagenic and recombinagenic actions of the propolis types investigated.


Subject(s)
Drosophila melanogaster/drug effects , Drosophila melanogaster/genetics , Larva/drug effects , Mutagens/toxicity , Propolis/toxicity , Recombination, Genetic/genetics , Wings, Animal/drug effects , Animals , Anti-Infective Agents/toxicity , Bees/chemistry , Female , Larva/genetics , Male , Wings, Animal/metabolism
20.
Biogerontology ; 17(5-6): 883-892, 2016 11.
Article in English | MEDLINE | ID: mdl-27488377

ABSTRACT

An extremely high (about 100 %) increase in longevity is reported for a subset of recombinant inbred lines (RILs) of Drosophila melanogaster subjected to a cyclic heat stress throughout the adult life. Previous work showed that both longevity and heat sensitivity highly differed among RILs. The novel heat stress treatment used in this study consisted of 5 min at 38 °C applicated approximately every 125 min throughout the adult life starting at the age of 2 days. In spite of the exceptionally high increase in longevity in a set of RILs, the same heat stress treatment reduced rather than increased longevity in other RILs, suggesting that heat-induced hormesis is dependent on the genotype and/or the genetic background. Further, one quantitative trait locus (QTL) was identified for heat-induced hormesis on chromosome 2 (bands 28A1-34D2) in one RIL panel (RIL-D48) but it was not significant in its reciprocal panel (RIL-SH2). The level of heat-induced hormesis showed a sexual dimorphism, with a higher number of lines exhibiting higher hormesis effects in males than in females. The new heat stress treatment in this study suggests that longevity can be further extended than previously suggested by applying a cyclic and mild stress throughout the life, depending on the genotype.


Subject(s)
Aging/genetics , Drosophila melanogaster/genetics , Heat-Shock Response/genetics , Longevity/genetics , Animals , Animals, Inbred Strains/genetics , Drosophila Proteins/genetics , Female , Gene Expression Regulation, Developmental/genetics , Hormesis/genetics , Male , Quantitative Trait Loci/genetics , Recombination, Genetic/genetics , Sex Characteristics , Thermotolerance/genetics
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