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1.
Braz. j. biol ; 84: e248656, 2024. tab, graf
Artigo em Inglês | LILACS, VETINDEX | ID: biblio-1345542

RESUMO

Abstract Several species of Cichla successfully colonized lakes and reservoirs of Brazil, since the 1960's, causing serious damage to local wildlife. In this study, 135 peacock bass were collected in a reservoir complex in order to identify if they represented a single dominant species or multiple ones, as several Cichla species have been reported in the basin. Specimens were identified by color pattern, morphometric and meristic data, and using mitochondrial markers COI, 16S rDNA and Control Region (CR). Overlapping morphological data and similar coloration patterns prevented their identification using the taxonomic keys to species identification available in the literature. However, Bayesian and maximum likelihood from sequencing data demonstrated the occurrence of a single species, Cichla kelberi. A single haplotype was observed for the 16S and CR, while three were detected for COI, with a dominant haplotype present in 98.5% of the samples. The extreme low diversity of the transplanted C. kelberi evidenced a limited number of founding maternal lineages. The success of this colonization seems to rely mainly on abiotic factors, such as increased water transparency of lentic environments that favor visual predators that along with the absence of predators, have made C. kelberi a successful invader of these reservoirs.


Resumo Muitas espécies de Cichla colonizaram com sucesso lagos e reservatórios do Brasil desde os anos 1960, causando graves prejuízos à vida selvagem nesses locais. Neste estudo, 135 tucunarés foram coletados em um complexo de reservatórios a fim de identificar se representavam uma espécie dominante ou múltiplas espécies, uma vez que diversas espécies de Cichla foram registradas na bacia. Os espécimes foram identificados com base na coloração, dados morfométricos e merísticos, e por marcadores mitocondriais COI, 16S rDNA e Região Controle (RC). A sobreposição dos dados morfométricos e o padrão similar de coloração impediram a identificação utilizando as chaves de identificação disponíveis na literatura. Entretanto, as análises bayesiana e de máxima verossimilhança de dados moleculares demonstraram a ocorrência de uma única espécie, Cichla kelberi. Um único haplótipo foi observado para o 16S e RC, enquanto três foram detectados para o COI, com um haplótipo dominante presente em 98,5% das amostras. A baixa diversidade nos exemplares introduzidos de C. kelberi evidenciou um número limitado de linhagens maternas fundadoras. O sucesso da invasão parece depender de fatores abióticos, como a maior transparência da água de ambientes lênticos que favorece predadores visuais que, atrelado à ausência de predadores, fez do C. kelberi um invasor bem-sucedido nesses reservatórios.


Assuntos
Animais , Ciclídeos/genética , Filogenia , Variação Genética/genética , Haplótipos/genética , Lagos , Teorema de Bayes
2.
Braz. j. biol ; 84: e249664, 2024. tab, graf
Artigo em Inglês | LILACS, VETINDEX | ID: biblio-1345558

RESUMO

Abstract The impact of antibiotics on growth, cocoon production was assessed in addition to isolation and characterization of bacteria associated with silkworm gut of infected larvae. Larval rearing was maintained at recommended conditions of temperature and humidity. Silkworm larvae showing abnormal symptoms were collected from the control group and dissected for gut collection. Bacteria were isolated from the gut content by spreading on agar plates and incubated at 37 °C for 48 hrs. Bacterial identification and phylogenetic analysis were carried out by 16S rRNA gene sequencing. The isolated bacteria were subjected to antimicrobial susceptibility test (disc diffusion methods) by using Penicillin (10 µg/mL), Tetracycline (30 µg/mL), Amoxicillin (25 µg/mL), Ampicillin (10 µg/mL), and Erythromycin (15 µg/mL). All isolated strains showed positive results for the catalase test. We isolated and identified bacterial strains (n = 06) from the gut of healthy and diseased silkworm larvae. Based on the 16S rRNA gene sequence, isolated bacteria showed close relation with Serratia, Bacillus, and Pseudomonas spp. Notably, 83.3% of strains were resistant to Penicillin, Tetracycline, Amoxicillin, Ampicillin, and Erythromycin but 16.6% showed antibiotic susceptibility to the above-mentioned commonly used antibiotics. Silkworm larvae fed on penicillin-treated leaves showed significant improvement in larval weight, larval length, and cocoon production. Significantly higher larval weight (6.88g), larval length (5.84cm), and cocoon weight (1.33g) were recorded for larvae fed on leaves treated with penicillin as compared to other antibiotics. Isolated bacterial strains showed close relation with Serratia spp., Bacillus spp. and Pseudomonas spp.


Resumo O impacto dos antibióticos no crescimento e na produção do casulo foi avaliado, além do isolamento e caracterização das bactérias associadas ao intestino de larvas infectadas do bicho-da-seda. A criação das larvas foi mantida nas condições recomendadas de temperatura e umidade. As larvas do bicho-da-seda com sintomas anormais foram coletadas do grupo controle e dissecadas para coleta do intestino. As bactérias foram isoladas do conteúdo intestinal por espalhamento em placas de ágar e incubadas a 37° C durante 48 horas. A identificação bacteriana e a análise filogenética foram realizadas pelo sequenciamento do gene 16S rRNA. As bactérias isoladas foram submetidas a teste de sensibilidade antimicrobiana (métodos de difusão em disco) com penicilina (10 µg / mL), tetraciclina (30 µg / mL), amoxicilina (25 µg / mL), ampicilina (10 µg / mL) e eritromicina (15 µg / mL). Todas as cepas isoladas apresentaram resultados positivos para o teste da catalase. Isolamos e identificamos cepas bacterianas (n = 06) do intestino de larvas de bicho-da-seda saudáveis e doentes. Com base na sequência do gene 16S rRNA, as bactérias isoladas mostraram estreita relação com Serratia, Bacillus e Pseudomonas spp. Notavelmente, 83,3% das cepas eram resistentes a penicilina, tetraciclina, amoxicilina, ampicilina e eritromicina, mas 16,6% mostraram suscetibilidade aos antibióticos comumente usados mencionados acima. As larvas do bicho-da-seda alimentadas com folhas tratadas com penicilina apresentaram melhora significativa no peso larval, comprimento larval e produção de casulo. Peso larval significativamente maior (6,88g), comprimento larval (5,84cm) e peso do casulo (1,33g) foram registrados para larvas alimentadas com folhas tratadas com penicilina, em comparação com outros antibióticos. Cepas bacterianas isoladas mostraram estreita relação com Serratia spp., Bacillus spp. e Pseudomonas spp.


Assuntos
Animais , Bombyx , Antibacterianos/farmacologia , Filogenia , Bactérias/genética , RNA Ribossômico 16S/genética , Testes de Sensibilidade Microbiana , Larva
3.
Braz. j. biol ; 84: e254253, 2024. tab, graf
Artigo em Inglês | LILACS, VETINDEX | ID: biblio-1350308

RESUMO

Abstract During the present study, specimens were collected from selected sites of Cholistan desert and Kalabagh Game Reserve, Punjab province, Pakistan. Each captured specimen was tagged with voucher number and morphometric measurements were taken. The average snout to vent length was 172.559±1.40 mm and average weight was 92.1±1.30 g. The DNA of Uromastyx hardwickii was amplified and sequenced using 16S rRNA primer set. The obtained DNA sequence has shown reliable and clear species identification. After trimming ambiguous bases, the obtained 16S rRNA fragment was 520 bp while 16S rRNA fragments aligned with closely matched sequence from NCBI comprised of 510 bp. Closely matched sequences of genus Uromastyx were retrieved from NCBI in blast searches. Neighbour-joining tree of genus Uromastyx was constructed based on p-distance using MEGA X. The mean intraspecific variation was 0.095±0.01 while intraspecific variation was ranging from 0-1%. Similarly, interspecific variation of Uromastyx hardwikii with Saara asmussi, Uromastyx alfredschmidti, Uromastyx geyri, Uromastyx thomasi, Uromastyx alfredschmidti was 0-12%, 0-19%, 0-19%, 0-20%, 12-19% respectively. The newly produced DNA was submitted to NCBI and accession number was obtained (MW052563.1). Results of current study provided information about the molecular and morphological identification of Genus Uromastyx. In our recommendation, comprehensive molecular based identification of Pakistan's reptiles is required to report any new or subspecies from country.


Resumo Durante o presente estudo, os espécimes foram coletados em locais selecionados do deserto do Cholistan e da Reserva de Caça de Kalabagh, província de Punjab, Paquistão. Cada espécime capturado foi etiquetado com o número do comprovante e medidas morfométricas foram realizadas. O comprimento médio do focinho à cloaca foi de 172,559 ± 1,40 mm, e o peso médio foi de 92,1 ± 1,30 g. O DNA de Uromastyx hardwickii foi amplificado e sequenciado usando o conjunto de primer 16S rRNA. A sequência de DNA obtida mostrou identificação de espécies confiável e clara. Após o corte de bases ambíguas, o fragmento de rRNA 16S obtido tinha 520 pb, enquanto os fragmentos de rRNA 16S alinhados com a sequência próxima do NCBI composta por 510 pb. Sequências semelhantes do gênero Uromastyx foram recuperadas do NCBI em pesquisas de explosão. A árvore de união de vizinhos do gênero Uromastyx foi construída com base na distância-p usando MEGA X. A variação intraespecífica média foi de 0,095 ± 0,01, enquanto a variação intraespecífica foi de 0-1%. Da mesma forma, a variação interespecífica de Uromastyx hardwikii com Saara asmussi, Uromastyx alfredschmidti, Uromastyx geyri, Uromastyx thomasi, Uromastyx alfredschmidti foi de 0-12%, 0-19%, 0-19%, 0-20%, 12-19%, respectivamente. O DNA recém-produzido foi submetido ao NCBI e o número de acesso foi obtido (MW052563.1). Os resultados do estudo atual forneceram informações sobre a identificação molecular e morfológica do Gênero Uromastyx. Em nossa recomendação, a identificação de base molecular abrangente de répteis do Paquistão é necessária para relatar qualquer nova ou subespécie do país.


Assuntos
Animais , Lagartos , Paquistão , Filogenia , Variação Genética/genética , RNA Ribossômico 16S
4.
Braz. j. biol ; 84: e253156, 2024. tab, graf
Artigo em Inglês | LILACS, VETINDEX | ID: biblio-1355904

RESUMO

Abstract Endophytic fungi are a ubiquituos group that colonize all plant species on earth. Studies comparing the location of endophytic fungi within the leaves and the sampling time in Manihot esculenta Crantz (cassava) are limited. In this study, mature leaves of M. esculenta from Panama were collected in order to compare the cultivable diversity of endophytic fungi and to determine their distribution within the leaves. A total of one hundred sixty endophytes belonging to 97 species representing 13 genera and 8 morphospecies determined as mycelia sterilia that containing 63 isolates were isolated. Cladosporium, Nigrospora, Periconia, and mycelia sterilia 1 and 3 were the most predominant isolated endophytes. We detected that endophytes varied across the sampling time, but not amongst locations within leaves. The endophytes composition across sampling and the location of endophytes within leaf was similar, except for Periconia and mycelia sterilia 3 and 7. The data generated in this study contribute to the knowledge on the biodiversity of endophytic fungi in Panama, and establish the bases for future research focused on understanding the function of endophytes in M. esculenta crops.


Resumo Os fungos endofíticos são um grupo ubiquituo que colonizam todas as espécies de plantas na terra. Os estudos que comparam a localização dos fungos endofíticos dentro das folhas de Manihot esculenta Crantz (mandioca) e o tempo de amostragem são muito escassos. Neste estudo, folhas maduras de M. esculenta foram coletadas do Panamá com a finalidade de comparar a diversidade cultivável de endófitos e determinar sua distribuição dentro das folhas. Um total de 170 endófitos foram isolados de 97 espécies que representam 13 gêneros e 8 morfoespécies determinadas como micélios esterilizados contendo 63 isolados. Os fungos Cladosporium, Nigrospora, Periconia e mycelia sterilia 1 e 3 foram os isolados mais predominantes. Também detectamos que os endófitos variaram ao longo do tempo de amostragem, mas não entre os locais dentro das folhas. A composição de endófitos na amostragem e localização de endófitos dentro da folha foi semelhante, exceto para Periconia e mycelia sterilia 3 e 7. Os dados gerados neste estudo contribuem para o conhecimento da biodiversidade de fungos endofíticos no Panamá e estabelecem as bases para pesquisas sobre o entendimento da função de endófitos em culturas de M. esculenta.


Assuntos
Ascomicetos , Manihot , Filogenia , Folhas de Planta , Biodiversidade , Endófitos , Fungos
6.
Braz. j. biol ; 84: e258626, 2024. tab, mapas, ilus
Artigo em Inglês | VETINDEX | ID: biblio-1384094

RESUMO

Ligula intestinalis is a cestode parasite that affects freshwater fish in different countries of the world. The current study aims to reveal the phylogenetic, genetic and haplotype diversity of mt-CO1 gene sequences sent to the NCBI database from different countries by using in-silico analysis. The 105 mt-CO1 (371 bp) gene sequences of L. intestinalis obtained from NCBI were used for bioinformatics analyses. Sequences were subjected to phylogenetic and haplotype analysis. As a result of the haplotype analysis of L. intestinalis, 38 haplotypes were obtained from 13 different countries. Hap24 constituted 44.76% of the obtained haplotype network. Changes in nucleotides between haplotypes occurred at 1-84 different points. China and Turkey have highest fixation index (Fst) values of 0.59761, while the lowest (-0.10526) was found between Russia and Turkey. This study provides a baseline for future studies on extensive scale on the epidemiology, ecological aspects, distribution pattern, transmission dynamics and population dispersion of L. intestinalis worldwide.


Ligula intestinalis é um parasita cestódeo que acomete peixes de água doce em diversos países do mundo. O presente estudo visa revelar a diversidade filogenética, genética e de haplótipos das sequências do gene mt-CO1 enviadas ao banco de dados do NCBI de diferentes países, por meio de análise in-silico. As sequências gênicas de 105 mt-CO1 (371 pb) de L. intestinalis obtidas do NCBI foram utilizadas para análises bioinformáticas. As sequências foram submetidas a análise filogenética e de haplótipos. Como resultado da análise de haplótipos de L. intestinalis, 38 haplótipos foram obtidos de 13 países diferentes. Hap24 constituiu 44,76% da rede de haplótipos obtida. Mudanças nos nucleotídeos entre os haplótipos ocorreram em 1-84 pontos diferentes. A China e a Turquia apresentam os maiores valores do índice de fixação (Fst), 0,59761, enquanto o menor (-0,10526) foi encontrado entre a Rússia e a Turquia. Este estudo fornece uma linha de base para futuros estudos em larga escala sobre epidemiologia, aspectos ecológicos, padrão de distribuição, dinâmica de transmissão e dispersão populacional de L. intestinalis em todo o mundo.


Assuntos
Animais , Parasitos , Filogenia , Variação Genética , Haplótipos , Peixes , Água Doce
7.
Braz. j. biol ; 84: e261849, 2024. ilus
Artigo em Inglês | VETINDEX | ID: biblio-1374691

RESUMO

Frequent outbreaks of avian influenza H9N2 virus in Pakistan revealed that this subtype has become endemic in the poultry industry and, besides economic losses, poses a threat to public health. The present study describes the molecular characterization and pathological alterations in naturally infected broiler chickens with the current H9N2 field strain and their phylogenomic dynamics. In this study, tissue samples (trachea, lung, kidney and intestine) from 100 commercial chicken flocks were collected from July 2018 to August 2019. Samples were subjected to molecular detection, phylogeny and subsequent pathological examination. The complete length of the HA gene was successfully amplified in five samples. Nucleotide sequencing revealed positive samples placed in a clade belonging to the B2 sub-lineage of the G1 genotype and categorized as LPAIV based on the amino acid sequence of the HA gene at the cleavage site (PAKSSR/G). Genetic analysis of the haemagglutinin (HA) gene revealed nt: 80.5%-99.5%; aa: 83.8%-98.9% homology to H9N2 strains reported previously from Pakistan, neighbouring countries, and (A/Quail/Hong Kong/G1/97). Gross lesions include a slight airsacculitis, mild hemorrhages, diffuse congestion and purulent exudate in tracheal mucosa, fibrinonecrotic cast in the trachea lumen and mild pulmonary congestion. Histopathological alterations include sloughing of epithelial cells and infiltration of inflammatory cells in the trachea, mononuclear cells (MNCs) infiltration, pulmonary congestion and exudate in the lumen of parabronchi, peritubular congestion in the kidneys with degeneration of tubular epithelial cells and degenerative changes in the intestinal villi epithelial cells and goblet cell hyperplasia. Immunohistochemistry analysis confirmed the presence of AIVH9N2 antigen in the trachea, lungs, kidney and intestine. Electron microscopy revealed ultrastructural changes in the trachea, including degenerated cilia, mitochondrial swelling and enlarged endoplasmic reticulum. Based on all essential analysis, the present study revealed the distribution of the H9N2 virus of G1 genotype in Punjab, Pakistan, with mild to moderate pathogenicity.


Surtos frequentes do vírus da gripe aviária H9N2 no Paquistão revelaram que esse subtipo se tornou endêmico na avicultura e, além das perdas econômicas, representa uma ameaça à saúde pública. O presente estudo descreve a caracterização molecular e as alterações patológicas em frangos de corte naturalmente infectados com a atual cepa H9N2 e sua dinâmica filogenômica. Neste estudo, amostras de tecidos (traqueia, pulmões, rim e intestino) de 100 lotes comerciais de frangos foram coletadas de julho de 2018 a agosto de 2019. As amostras foram submetidas à detecção molecular, filogenia e posterior exame patológico. O comprimento completo do gene HA foi amplificado com sucesso em cinco amostras. O sequenciamento de nucleotídeos revelou amostras positivas colocadas em um clado pertencente à sublinhagem B2 do genótipo G1 e categorizado como LPAIV com base na sequência de aminoácidos do gene da hemaglutinina (HA) no local de clivagem (PAKSSR/G). A análise genética do gene da HA revelou: nt = 80,5%-99,5%; aa = 83,8%-98,9% de homologia com cepas de H9N2 relatadas anteriormente no Paquistão e em países vizinhos (A/Quail/Hong Kong/G1/97). As lesões macroscópicas incluíram aerossaculite leve, hemorragias leves, congestão difusa e exsudato purulento na mucosa traqueal, cilindro fibrinonecrótico no lúmen da traqueia e congestão pulmonar leve. As alterações histopatológicas incluíram descamação de células epiteliais, infiltração de células inflamatórias na traqueia, infiltração de células mononucleares (MNCs), congestão pulmonar e exsudato no lúmen dos parabrônquios, congestão peritubular nos rins com degeneração das células epiteliais tubulares, alterações degenerativas nas células epiteliais das vilosidades intestinais e hiperplasia de células caliciformes. A análise imunoistoquímica confirmou a presença do antígeno AIVH9N2 na traqueia, nos pulmões, no rim e no intestino. A microscopia eletrônica revelou alterações ultraestruturais na traqueia, incluindo cílios degenerados, inchaço mitocondrial e retículo endoplasmático aumentado. Com base em todas as análises, o presente estudo revelou a distribuição do vírus H9N2 do genótipo G1 em Punjab, Paquistão, com patogenicidade de leve a moderada.


Assuntos
Animais , Filogenia , Microscopia Eletrônica , Saúde Pública , Vírus da Influenza A Subtipo H9N2 , Influenza Aviária/genética , Paquistão
8.
Proc Biol Sci ; 290(1992): 20222435, 2023 Feb 08.
Artigo em Inglês | MEDLINE | ID: mdl-36722082

RESUMO

The secondary evolution of quadrupedality from bipedal ancestry is a rare evolutionary transition in tetrapods yet occurred convergently at least three times within ornithischian dinosaurs. Despite convergently evolving quadrupedal gait, ornithischians exhibited variable anatomy, particularly in the forelimbs, which underwent a major functional change from assisting in foraging and feeding in bipeds to becoming principal weight-bearing components of the locomotor system in quadrupeds. Here, we use three-dimensional multi-body dynamics models to demonstrate quantitatively that different quadrupedal ornithischian clades evolved distinct forelimb musculature, particularly around the shoulder. We find that major differences in glenohumeral abduction-adduction and long axis rotation muscle leverages were key drivers of mechanical disparity, thereby refuting previous hypotheses about functional convergence in major clades. Elbow muscle leverages were also disparate across the major ornithischian lineages, although high elbow extension muscle leverages were convergent between most quadrupeds. Unlike in ornithischian hind limbs, where differences are more closely tied to functional similarity than phylogenetic relatedness, mechanical disparity in ornithischian forelimbs appears to have been shaped primarily by phylogenetic constraints. Differences in ancestral bipedal taxa within each clade may have resulted in disparate ecomorphological constraints on the evolutionary pathways driving divergence in their quadrupedal descendants.


Assuntos
Dinossauros , Animais , Filogenia , Membro Anterior , Membro Posterior , Músculos
9.
Proc Biol Sci ; 290(1992): 20221062, 2023 Feb 08.
Artigo em Inglês | MEDLINE | ID: mdl-36722085

RESUMO

Mammalian omnivores are a broad group of species that are often treated uniformly in ecological studies. Here, we incorporate omnivorous dietary differences to investigate previously found mammalian macroevolutionary and macroecological trends. We investigate the frequency with which vertebrate prey, invertebrate prey, fibrous plant material and non-fibrous plant material co-occur in the diets of terrestrial mammals. We quantify the body size distributions and phylogenetic signal of different omnivorous diets and use multistate reversible jump Markov chain Monte Carlo methods to assess the transition rates between diets on the mammalian phylogenetic tree. We find omnivores that consume all four food types are relatively rare, as most omnivores consume only invertebrate prey and non-fibrous plants. In addition, omnivores that only consume invertebrate prey, many of which are from Rodentia, are on average smaller than omnivores that incorporate vertebrate prey. Our transition models have high rates from invertivorous omnivory to herbivory, and from vertivory to prey mixing and ultimately invertivory. We suggest prey type is an important aspect of omnivore macroevolution and macroecology, as it is correlated with body mass, evolutionary history and diet-related evolutionary transition rates. Future work should avoid lumping omnivores into one category given the ecological variety of omnivore diets and their strong evolutionary influence.


Assuntos
Dieta , Mamíferos , Animais , Filogenia , Resolução de Problemas , Tamanho Corporal
10.
J Genet ; 1022023.
Artigo em Inglês | MEDLINE | ID: mdl-36722212

RESUMO

The cicada species, Hyalessa fuscata and H. maculaticollis(Hemiptera: Cicadidae), share numerous morphological characters, and their status as distinct species remains controversial. We reconstructed a phylogeny based on two new mitogenomes of H. fuscata from Korea and H. maculaticollis from Japan, in combination with GenBank sequences of H. maculaticollis from China and Japan, and other closely related cicada species. Maximum likelihood and Bayesian inference phylogenies showed that H. fuscata from Korea is more closely related to H. maculaticollis from China than either is to H. maculaticollis from Japan. The time-calibrated Bayesian evolutionary analysis by sampling trees (BEAST) phylogeny indicated that the mainland and insular forms diverged approximately 1.7-2.6 million years ago. This coincides with the formation of the East China Sea land bridge between East Asia and the Japanese archipelago, which would provide a dispersal corridor for Hyalessa from the mainland via the Korean peninsula southeastward to Japan. East Asian H. fuscata is a geographic variant that may be considered synonymous with H. maculaticollis.


Assuntos
Hemípteros , Teorema de Bayes , Filogenia , República da Coreia , Hemípteros/genética , Animais
11.
Proc Biol Sci ; 290(1992): 20222085, 2023 Feb 08.
Artigo em Inglês | MEDLINE | ID: mdl-36722088

RESUMO

Whiskers are important tactile structures widely used across mammals for a variety of sensory functions, but it is not known how bats-representing about a fifth of all extant mammal species-use them. Nectar-eating bats typically have long vibrissae (long, stiff hairs) arranged in a forward-facing brush-like formation that is not present in most non-nectarivorous bats. They also commonly use a unique flight strategy to access their food-hovering flight. Here we investigated whether these species use their vibrissae to optimize their feeding by assisting fine flight control. We used behavioural experiments to test if bats' flight trajectory into the flower changed after vibrissa removal, and phylogenetic comparative methods to test whether vibrissa length is related to nectarivory. We found that bat flight trajectory was altered after vibrissae removal and that nectarivorous bats possess longer vibrissae than non-nectivorous species, providing evidence of an additional source of information in bats' diverse sensory toolkit.


Assuntos
Quirópteros , Animais , Vibrissas , Filogenia , Flores , Alimentos
12.
Nat Commun ; 14(1): 549, 2023 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-36725857

RESUMO

The genetics underlying tuberculosis (TB) pathophysiology are poorly understood. Human genome-wide association studies have failed so far to reveal reproducible susceptibility loci, attributed in part to the influence of the underlying Mycobacterium tuberculosis (Mtb) bacterial genotype on the outcome of the infection. Several studies have found associations of human genetic polymorphisms with Mtb phylo-lineages, but studies analysing genome-genome interactions are needed. By implementing a phylogenetic tree-based Mtb-to-human analysis for 714 TB patients from Thailand, we identify eight putative genetic interaction points (P < 5 × 10-8) including human loci DAP and RIMS3, both linked to the IFNγ cytokine and host immune system, as well as FSTL5, previously associated with susceptibility to TB. Many of the corresponding Mtb markers are lineage specific. The genome-to-genome analysis reveals a complex interactome picture, supports host-pathogen adaptation and co-evolution in TB, and has potential applications to large-scale studies across many TB endemic populations matched for host-pathogen genomic diversity.


Assuntos
Mycobacterium tuberculosis , Tuberculose , Humanos , Estudo de Associação Genômica Ampla , Filogenia , Tuberculose/microbiologia , Mycobacterium tuberculosis/genética , Genoma , Interações Hospedeiro-Patógeno/genética
13.
Sci Rep ; 13(1): 1828, 2023 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-36725981

RESUMO

The present study aimed to detect molecularly the presence of co-infections by vector-borne agents (VBA) in ring-tailed coatis' (Nasua nasua) blood samples from Iguaçu National Park (INP), southern Brazil, and assess the phylogenetic positioning of the detected agents. DNA blood samples were submitted to molecular screening and characterization for Anaplasmataceae agents, Piroplasmids, Hepatozoon sp., hemotropic mycoplasmas, and Bartonella spp. In total, 42 (85.7%) coatis were positive for hemotropic Mycoplasma sp., 12 (24.5%) for Bartonella machadoae, 7 (14.3%) for Anaplasma sp. closely related to 'Candidatus Anaplasma brasiliensis', and 3 (6%) for Hepatozoon procyonis. The most prevalent co-infections observed was from bacterial VBA: while 18.3% were co-infected by hemotropic Mycoplasma sp. and Bartonella sp., 12.2% were co-infected by Anaplasma sp. and hemotropic Mycoplasma sp. Only two animals (4%) presented co-infections by three VBA (Bartonella sp., Anaplasma sp. and hemotropic Mycoplasma sp.). The coati is a wild carnivore found in INP, mainly in areas visited by tourists. These animals are frequently seen searching for food in garbage dumps or in tourists' belongings. The present study expands the host specificity range of B. machadoae, which has been isolated only from rodents until the present moment. Since the zoonotic potential and transmission routes of the detected VBA are not yet known, surveillance in this area is much needed.


Assuntos
Bartonella , Coinfecção , Mycoplasma , Procyonidae , Animais , Procyonidae/microbiologia , Brasil/epidemiologia , Filogenia , Coinfecção/epidemiologia , Parques Recreativos , Bartonella/genética , Anaplasma/genética
14.
BMC Plant Biol ; 23(1): 70, 2023 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-36726056

RESUMO

The subgenus Rhizirideum in the genus Allium consists of 38 species worldwide and forms five sections (A. sect. Rhizomatosa, A. sect. Tenuissima, A. sect. Rhizirideum, A. sect. Eduardia, and A. sect. Caespitosoprason), A. sect. Caespitosoprason being merged into A. sect. Rhizomatosa recently. Previous studies on this subgenus mainly focused on separate sections. To investigate the inter-section and inter-subgenera phylogenetic relationships and adaptive evolution of A. subg. Rhizirideum, we selected thirteen representative species, which cover five sections of this subgenus and can represent four typical phenotypes of it. We conducted the comparative plastome analysis with our thirteen plastomes. And phylogenetic inferences with CDSs and complete sequences of plastomes of our thirteen species and another fifty-four related species were also performed. As a result, the A. subg. Rhizirideum plastomes were relatively conservative in structure, IR/SC borders, codon usage, and repeat sequence. In phylogenetic results, the inter-subgenera relationships among A. subg. Rhizirideum and other genus Allium subgenera were generally similar to the previous reports. In contrast, the inter-section relationships within our subgenus A. subg. Rhizirideum were newly resolved in this study. A. sect. Rhizomatosa and A. sect. Tenuissima were sister branches, which were then clustered with A. sect. Rhizirideum and A. sect. Eduardia successively. However, Allium Polyrhizum Turcz. ex Regel, type species of A. sect. Caespitosoprason, was resolved as the basal taxon of A. subg. Rhizirideum. Allium siphonanthum J. M. Xu was also found in clade A. subg. Cyathophora instead of clade A. subg. Rhizirideum. The selective pressure analysis was also conducted, and most protein-coding genes were under purifying selection. At the same time, just one gene, ycf2, was found under positive selection, and another three genes (rbcL, ycf1a, ycf1b) presented relaxed selection, which were all involved in the photosynthesis. The low temperature, dry climate, and high altitude of the extreme habitats where A. subg. Rhizirideum species grow might impose intense natural selection forces on their plastome genes for photosynthesis. In summary, our research provides new insights into the phylogeny and adaptive evolution of A. subg. Rhizirideum. Moreover, we suggest that the positions of the A. subg. Rhizirideum species A. polyrhizum and A. siphonanthum should be reconsidered.


Assuntos
Allium , Amaryllidaceae , Genomas de Plastídeos , Allium/genética , Amaryllidaceae/genética , Filogenia , Sequências Repetitivas de Ácido Nucleico , Evolução Molecular
15.
BMC Genomics ; 24(1): 58, 2023 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-36726084

RESUMO

BACKGROUND: Toona is a critical genus in the Meliaceae, and the plants of this group are an asset for both restorative and restorative purposes, the most flexible of which are Toona sinensis and Toona ciliata. To concentrate on the advancement of mitochondrial(Mt) genome variety in T.sinensis and T.ciliata, the Mt genomes of the two species were sequenced in high throughput independently, after de novo assembly and annotation to construct a Mt genome map for comparison in genome structure. Find their repetitive sequences and analyze them in comparison with the chloroplast genome, along with Maximum-likelihood(ML) phylogenetic analysis with 16 other relatives. RESULTS: (1) T. sinensis and T.ciliata are both circular structures with lengths of 683482 bp and 68300 bp, respectively. They share a high degree of similarity in encoding genes and have AT preferences. All of them have the largest Phe concentration and are the most frequently used codons. (2) Both of their Mt genome are highly preserved in terms of structural and functional genes, while the main variability is reflected in the length of tRNA, the number of genes, and the value of RSCU. (3) T. siniensis and T. ciliata were detected to have 94 and 87 SSRs, respectively, of which mononucleotides accounted for the absolute proportion. Besides, the vast majority of their SSRs were found to be poly-A or poly-T. (4)10 and 11 migrating fragments were identified in the comparison with the chloroplast genome, respectively. (5) In the ML evolutionary tree, T.sinensis and T.ciliata clustered individually into a small branch with 100% support, reflecting two species of Toona are very similarly related to each other. CONCLUSIONS: This research provides a basis for the exploitation of T.sinensis and T.ciliata in terms of medicinal, edible, and timber resources to avoid confusion; at the same time, it can explore the evolutionary relationship between the Toona and related species, which does not only have an important practical value, but also provides a theoretical basis for future hybrid breeding of forest trees, molecular markers, and evolutionary aspects of plants, which has great scientific significance.


Assuntos
Genoma Mitocondrial , Meliaceae , Toona/genética , Filogenia , Melhoramento Vegetal , Meliaceae/genética
16.
Front Biosci (Landmark Ed) ; 28(1): 13, 2023 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-36722280

RESUMO

Following gene expansion during evolution, today's phylogenetic tree of the NR2F family of nuclear orphan receptors in mammals is represented by three different isoforms: NR2F1, NR2F2, and NR2F6. Structural analysis of the NR2F family members has revealed that NR2F1 and NR2F2 are closely related and grouped together apart from NR2F6, which is more divergent in its biochemical characteristics. In this review, we highlight current knowledge on the cellular functions of NR2F family members. NR2F family members have been reported to be causally involved in carcinogenesis. Mechanistically, NR2F proteins are localized in the nucleus, where they bind to target DNA enhancer sequences and have been implicated in the regulation of de novo gene transcription, though this is not sufficiently understood. Based on apparently divergent and non-uniform expression patterns of the NR2F isoforms in different tissues and cell types, non-redundant functions of the individual family members appear to exist. Notably, NR2F2 appears to be more closely related functionally to NR2F6 than NR2F1. Along these lines, NR2F2 and NR2F6 have been reported to be involved in cellular neoplasia. Furthermore, enhanced expression of NR2F isoforms has been established as prognostic biomarkers in various cancer entities. Therefore, it is tempting to speculate that NR2F isoforms represent innovative targets for therapeutic intervention in defined types of cancer. Thus, NR2F family nuclear receptors can be viewed as gatekeepers balancing cell type-specific regulation of proliferation and the suppression of terminal differentiation in health and disease.


Assuntos
Carcinogênese , Núcleo Celular , Animais , Filogenia , Ciclo Celular , Mamíferos
17.
Singapore Med J ; 64(1): 45-52, 2023 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-36722516

RESUMO

Microbiome is associated with a wide range of diseases. The gut microbiome is also a dynamic reflection of health status, which can be modified, thus representing great potential to exploit the mechanisms that influence human physiology. Recent years have seen a dramatic rise in gut microbiome studies, which has been enabled by the rapidly evolving high-throughput sequencing methods (i.e. 16S rRNA sequencing and shotgun sequencing). As the emerging technologies for microbiome research continue to evolve (i.e. metatranscriptomics, metabolomics, culturomics, synthetic biology), microbiome research has moved beyond phylogenetic descriptions and towards mechanistic analyses. In this review, we highlight different approaches to study the microbiome, in particular, the current limitations and future promise of these techniques. This review aims to provide clinicians with a framework for studying the microbiome, as well as to accelerate the adoption of these techniques in clinical practice.


Assuntos
Microbioma Gastrointestinal , Humanos , Filogenia , RNA Ribossômico 16S/genética , Nível de Saúde
18.
BMC Plant Biol ; 23(1): 66, 2023 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-36721081

RESUMO

BACKGROUND: The evolutionarily conserved Polycomb Repressive Complex 2 (PRC2) plays a vital role in epigenetic gene repression by depositing tri-methylation on lysine residue K27 of histone H3 (H3K27me3) at the target loci, thus participating in diverse biological processes. However, few reports about PRC2 are available in plant species with large and complicated genomes, like cotton. RESULTS: Here, we performed a genome-wide identification and comprehensive analysis of cotton PRC2 core components, especially in upland cotton (Gossypium hirsutum). Firstly, a total of 8 and 16 PRC2 core components were identified in diploid and tetraploid cotton species, respectively. These components were classified into four groups, E(z), Su(z)12, ESC and p55, and the members in the same group displayed good collinearity, similar gene structure and domain organization. Next, we cloned G. hirsutum PRC2 (GhPRC2) core components, and found that most of GhPRC2 proteins were localized in the nucleus, and interacted with each other to form multi-subunit complexes. Moreover, we analyzed the expression profile of GhPRC2 genes. The transcriptome data and quantitative real-time PCR (qRT-PCR) assays indicated that GhPRC2 genes were ubiquitously but differentially expressed in various tissues, with high expression levels in reproductive organs like petals, stamens and pistils. And the expressions of several GhPRC2 genes, especially E(z) group genes, were responsive to various abiotic and biotic stresses, including drought, salinity, extreme temperature, and Verticillium dahliae (Vd) infection. CONCLUSION: We identified PRC2 core components in upland cotton, and systematically investigated their classifications, phylogenetic and synteny relationships, gene structures, domain organizations, subcellular localizations, protein interactions, tissue-specific and stresses-responsive expression patterns. Our results will provide insights into the evolution and composition of cotton PRC2, and lay the foundation for further investigation of their biological functions and regulatory mechanisms.


Assuntos
Núcleo Celular , Gossypium , Gossypium/genética , Filogenia , Diploide , Secas
19.
BMC Genomics ; 24(1): 56, 2023 Jan 31.
Artigo em Inglês | MEDLINE | ID: mdl-36721120

RESUMO

BACKGROUND: Toxicodendron vernicifluum, belonging to the family Anacardiaceae, is an important commercial arbor species, which can provide us with the raw lacquer, an excellent adhesive and painting material used to make lacquer ware. Compared with diploid, triploid lacquer tree has a higher yield of raw lacquer and stronger resistance to stress. Triploid T. vernicifluum was a newly discovered natural triploid lacquer tree. However, the taxonomy of triploid T. vernicifluum has remained uncertain. Here, we sequenced and analyzed the complete chloroplast (cp) genome of triploid T. vernicifluum and compared it with related species of Toxicodendron genus based on chloroplast genome and SSR markers. RESULTS: The plastome of triploid T. vernicifluum is 158,221 bp in length, including a pair of inverted repeats (IRs) of 26,462 bp, separated by a large single-copy region of 86,951 bp and a small single-copy region of 18,346 bp. In total, 132 genes including 87 protein-coding genes, 37 tRNA genes and 8 rRNA genes were identified in the triploid T. vernicifluum. Among these, 16 genes were duplicated in the IR regions, 14 genes contain one intron, while three genes contain two introns. After nucleotide substitutions, seven small inversions were analyzed in the chloroplast genomes, eight hotspot regions were found, which could be useful molecular genetic markers for future population genetics. Phylogenetic analyses showed that triploid T. vernicifluum was a sister to T. vernicifluum cv. Dahongpao and T. vernicifluum cv. Hongpigaobachi. Moreover, phylogenetic clustering based on the SSR markers showed that all the samples of triploid T. vernicifluum, T. vernicifluum cv. Dahongpao and T. vernicifluum cv. Hongpigaobachi in one group, while the samples of T. vernicifluum and T. succedaneum in another group, which is consistent with the cp genome and morphological analysis. CONCLUSIONS: The current genomic datasets provide pivotal genetic resources to determine the phylogenetic relationships, variety identification, breeding and resource exploitation, and future genetic diversity-related studies of T. vernicifluum.


Assuntos
Genoma de Cloroplastos , Toxicodendron , Triploidia , Laca , Filogenia , Melhoramento Vegetal
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