Phylogenetic relationships of the Mangrove Hummingbird, "Amazilia" boucardi (Apodiformes: Trochilidae) of Costa Rica / Relaciones filogenéticas del Colibrí manglero "Amazilia" boucardi (Apodiformes: Trochilidae) de Costa Rica

Abstract Introduction: A recent revision of the generic classification of the Trochilidae based on DNA sequences revealed many inconsistencies with the current generic classification, largely based on plumage characters subject to homoplasy, especially in the Trochilini, the largest tribe. A thorough generic reorganization brought the classification into accord with the phylogeny, but due to lack of genetic data, two species remained unclassified. One of these was the Mangrove Hummingbird, "Amazilia" boucardi, endemic to Costa Rica and included in the IUCN red list of threatened species. Objective: To obtain molecular evidence to clarify the generic relationships of "A." boucardi. Methods: We isolated DNA from tissues of this species and amplified 4 nuclear and 4 mitochondrial fragments and compared these with homologous fragments from 56 species in the Trochilini, constructing phylogenetic trees with maximum likelihood and Bayesian methods. Results: Our phylogenetic analyses confirmed the placement of boucardi in the Trochilini and definitely excluded it from Amazilia but placed it with high confidence in the genus Chrysuronia Bonaparte, 1850, within which its closest relative is C. coeruleogularis, which also inhabits mangroves. Conclusions: Our genetic data based on nuclear and mitochondrial regions clearly indicate the relationship of A. boucardi and L. coeruleogularis. Moreover, it is also supported by their habitat distribution in the mangroves of the Pacific coast of Costa Rica and Western Panama. Therefore, we suggested to exclude A. boucardi as "incertae sedis".

Resumen Introducción: Una revisión reciente de la clasificación de la familia Trochilidae con base en secuencias de ADN demostró muchas incongruencias con la clasificación genérica previa, que había sido hecho con base en caracteres del plumaje muy sujetos a homoplasia, especialmente en la tribu más grande, Trochillini. Una reorganización de los géneros logró llevar su clasificación genérica a la concordancia con la filogenia, pero debido a la ausencia de datos genéticos, dos especies permanecieron sin clasificar. Una de estas fue el colibrí de manglar Amazilia boucardi, una especie endémica de Costa Rica, considerada como amenazada en la lista roja de la UICN. Objetivo: Obtener evidencia molecular para esclarecer las relaciones genéricas de A. boucardi. Métodos: Se aisló ADN de tejidos de esta especie y se amplificaron 4 fragmentos de ADN del núcleo y 5 de la mitocondria, y se compararon con fragmentos homólogos de 56 especies en la tribu Trochillini, generando árboles filogenéticos con métodos de máxima verosimilitud y bayesiano. Resultados: Los análisis filogénticos obtenidos confirmaron la ubicación de boucardi en Trochilini y definitivamente la excluyó del género Amazilia, pero la ubicó con un alto grado de confianza en el género Chrysuronia Bonaparte, 1850, dentro los cuales su pariente más cercano es C. coeruleogularis, que también habita manglares. Conclusiones: Nuestros datos genéticos basados en regiones nucleares y mitocondriales indican claramente la relación entre A. boucardi and L. coeruleogularis. Es más, lo anterior se sustenta por su distribución en los manglares de la costa Pacífica de Costa Rica y oeste de Panamá. Por lo tanto, sugerimos excluir a A. boucardi como "incertae sedis".

Interspecies Phylogenetic Analysis of / 生物医学与环境科学（英文）

Objective@#This study aims to investigate the infection of @*Method@#Infection of the definitive human host and intermediate fish host by @*Results@#In 2016-2020, the average population infection rate of Hunan was 1.38%, while in Tongdao County the rate was up to 26.90%, and the highest fish infection rate was detected in Qiyang County (99.44% in the dorsal fin of @*Conclusion@#The systematically study of

Molecular phylogeny of Monomorium pharaonis (Hymenoptera: Formicidae) based on rRNA sequences of mitochondrial gene

Many studies on forensic entomology have focussed on Diptera and lack the Hymenopteras population. Nonetheless, hymenopterans are part of the entomofaunal colonization of a corpse. Morphologically, it is difficult to identify and distinguish between them. In this study, using mitochondrial DNA knowledge, the molecular analysis was performed to classify the recovered species of hymenoptera collected from rabbit carcass, quickly and accurately. A molecular identification method with a 251-bp fragment of the 16S ribosomal gene RNA (16S rRNA) from a single ant species was evaluated. The maximum likelihood method analysis has recovered a generally well-supported phylogeny, with most taxa and species groups currently being recognized as monophyletic. The aculeate consists of some Hymenoptera’s best known. Their sister group has traditionally been considered in Ichneumonoidea. In addition, Trigonaloidea was found as the aculeates’ sister group and Crabronidae in Apoidea forming the Formicidae’s sister group. These results will play an important role in the implementation of the Saudi database forensically relevant ants.

Phylogeography of the banded butterflyfish, Chaetodon striatus, indicates high connectivity between biogeographic provinces and ecosystems in the western Atlantic

Among the four butterflyfishes of the genus Chaetodon present in the western Atlantic, the banded butterflyfish Chaetodon striatus has the largest distribution range, spanning 44 degrees of latitude (from Massachusetts, USA to Santa Catarina, Brazil). Although the ecology of the banded butterflyfish has been well studied over its entire range, nothing is known about its phylogeography and how biogeographic barriers structure its populations. To assess the level of genetic connectivity among populations from distinct biogeographic provinces and environmental conditions, we collected samples from seven localities: Puerto Rico, in the Caribbean, and Tamandaré, Salvador, Abrolhos, Trindade Island, Arraial do Cabo and Florianópolis, in Brazil. One nuclear (rag 2) and two mitochondrial (control region and cyt b) molecular markers were sequenced. Our findings are consistent with a recent population expansion, around 30-120 thousand years ago, which was found for all populations. Haplotype network analyses point to the Caribbean as a refugium before the population expansion. Results show no geographic pattern of genetic diversity. Indeed, a lack of population structure was found and no isolation was observed across oceanographic barriers, as well as between coral and rocky reef ecosystems. Furthermore, no directionality in the migration pattern was found among populations. Since ecological and environmental characteristics are very diverse across such a vast geographic range, the lack of genetic differentiation suggests that C. striatus evolved ecological plasticity rather than local adaptation in the western Atlantic.(AU)

O peixe-borboleta listrado, Chaetodon striatus, possui a maior distribuição geográfica dentre as quatro espécies de peixes-borboleta do gênero Chaetodon presentes no Oceano Atlântico Ocidental, abrangendo 44° de latitude (entre Massachusetts, EUA até o sul do Brasil). A ecologia alimentar desta espécie é bastante conhecida, considerando a ampla distribuição, porém, pouco se sabe sobre a filogeografia e como as barreiras biogeográficas estruturam as populações. Para acessar a conectividade genética entre as populações de diferentes províncias biogeográficas e diferentes condições ambientais, foram coletadas amostras de sete localidades: Porto Rico, no Caribe, e Tamandaré, Salvador, Abrolhos, Ilha da Trindade, Arraial do Cabo e Florianópolis, no Brasil. Foram sequenciados um gene nuclear (rag 2) e dois genes mitocondriais (região controle e cit B). Para todas as populações, foi identificada uma expansão populacional recente, em torno de 30-120 mil anos atrás. A análise de rede de haplótipos sugere que o Caribe serviu como refúgio antes desta expansão populacional. Os resultados indicam que não há padrão geográfico de diversidade genética. Apesar da existência de barreiras oceanográficas e diferenças na constituição dos recifes (rochosos e coralíneos), não foi encontrada estruturação populacional. Também, não encontramos padrão na direção de migração entre as populações. Os resultados sugerem que C. striatus apresenta plasticidade ecológica, uma vez que não há diferenciação genética entre as populações que habitam ecossistemas tão diferentes ao longo da ampla distribuição no Atlântico Ocidental.(AU)

Genetic diversity in Mexican wild populations of the Great Curassow (Crax rubra) / Diversidad genética en poblaciones silvestres mexicanas del hocofaisán (Crax rubra)

Abstract The Great Curassow (Crax rubra) is a Neotropical bird with a wide distribution; it is classified under different threat categories and is listed as a vulnerable species by the IUCN. The Official Mexican Standard, the NOM-059-SEMARNAT-2010, indicates that the Great Curassow is a threatened species, and the subspecies Crax rubra griscomi, which is restricted to the island of Cozumel, is classified as critically endangered. Habitat loss and fragmentation, hunting, overexploitation, and illegal trade are among the main factors that have placed the bird at an endangered status. The objective of the present study was to determine the genetic structure and variation of the species within the Mexican populations of Crax rubra by using three mitochondrial markers, and one nuclear marker (COI, ND2, Cyt b, and MUSK). We used 47 samples obtained by noninvasive collection (feathers) including the two different color phases of the female plumage: dark brown and barred (rare in Mexico). Gene flow between the remaining populations is recent and extensive, even between the continental and the island population (C. r. griscomi). The results indicate that the subspecies C. r. rubra and C. r. griscomi do not present a marked genetic differentiation because the second exhibits an exclusive haplotype and a shared haplotype. With this study, we provide the first genetic-geographic approximation of the curassow in Mexico, where a gradual geographic differentiation is observed between the western and eastern populations of the Isthmus of Tehuantepec, and we provide a baseline for future studies. Finally, the information obtained indicates that important genetic diversity persists in the Mexican populations of the Great Curassow and that sufficient conservation within the ecosystems of these subspecies can be obtained by protecting them from overexploitation and by conserving and restoring their habitat.

Resumen El hocofaisán (Crax rubra) es un ave de la región Neotropical con amplia distribución, que se encuentra en diferentes categorías de riesgo, por la IUCN está catalogada como una especie Vulnerable. A nivel nacional, dentro de la NOM-059-SEMARNAT-2010 está considerada como una especie amenazada, y la subespecie Crax rubra griscomi restringida a la isla de Cozumel, está categorizada como en peligro de extinción. Entre los factores principales por los que se encuentra en grave riesgo, destacan la pérdida y fragmentación del hábitat, la cacería, la sobreexplotación, la extracción y el comercio ilegal. El objetivo del presente estudio es conocer la estructura y variación genética de la especie dentro de las poblaciones silvestres mexicanas de Crax rubra, mediante el uso de tres marcadores mitocondriales y uno nuclear (COI, ND2, Cyt b y MUSK). A partir de 47 muestras obtenidas mediante colecta no invasiva (plumas) que incluyen las dos fases de plumaje de la hembra: café oscura y barrada (rara en México). Se observó que el flujo génico entre las poblaciones remanentes es reciente y extenso, incluso entre las poblaciones continentales y la isleña (C. r. griscomi). Los resultados indican que las subespecies C. r. rubra y C. r. griscomi no presentan una marcada diferenciación genética dado que la segunda presentó un haplotipo exclusivo y uno compartido. Con el presente estudio brindamos la primera aproximación genético-geográfica del hocofaisán en México y una línea de base para futuros estudios, en el que se observa una diferenciación geográfica gradual entre las poblaciones del oeste y del este del Istmo de Tehuantepec. Finalmente, la información obtenida indica que en las poblaciones mexicanas del hocofaisán persiste una diversidad genética importante y que su conservación en los ecosistemas puede ser suficiente mediante la protección a la sobreexplotación, la conservación y restauración de su hábitat.

Clinical analysis of 4 cases of Leigh syndrome in children / 临床儿科杂志

Objective To explore the clinical manifestation, diagnosis and prognosis of Leigh syndrome in children. Method Clinical data from 4 cases of Leigh syndrome conifrmed by genetic testing were retrospectively analyzed. The related literature were reviewed. Results In 4 cases, 3 were boys and one was a girl, 3 cases were onset in infant and one case was in school age. The main manifestations were mental retardation, low muscle tone, convulsions, feeding dififculties, drooping eyelids, extraocular muscle paralysis and nystagmus, irritation, activity intolerance etc. The brain magnetic resonance imaging (MRI) revealed symmetry long T1, T2 abnormal signal in brainstem, bilateral globus pallidus, thalamus, cerebellar dentate nuclei, and periaqueductal, 3 cases involved midbrain, one case involved thalamus, and one case involved cerebellar dentate nuclei;2 cases had encephalatrophy. Electromyography was normal in all cases. The levels of lactate in blood and cerebrospinal lfuid were increased. Mitochondrial DNA (mtDNA) detection found the mutation of mtDNA 8993 T>G in one case, and the mutation of mtDNA 9176 T>C in another 3 cases. The case onset in school age died of respiratory failure one month later, and another 3 cases were still in follow up, there were mental retardation, but no signiifcant setback. Conclusion The clinical manifestations of Leigh syndrome in children are diverse. The diagnosis is based on the typical clinical manifestations and MRI, blood and/or cerebrospinal lfuid lactate levels. The genetic testing is the golden standard for diagnosis.

Frequência da Mutação Mitocondrial C1494T, do Gene MT-RNR1, em Coortes de Ouvintes e Surdos Brasileiros / Frequency of Mitochondrial Mutation C1494T, of the Gene MT-RNR1, in Cohorts of Brazilian Hearing and Deaf People

Fatores ambientais e genéticos, ou mesmo ainteração destes, podem ser causadores da surdez sendo amesma o déficit sensorial mais frequente em humanos, sendoestimado que um a cada 500 recém-nascidos tenha perdaauditiva bilateral permanente, e que esta incidência aumentepara 3,5:1000 em indivíduos na adolescência. Determinadosfatores ambientais podem ser potencializados, quandodeterminadas mutações estão presentes no genoma. Éamplamente conhecida que a utilização de antibióticosaminoglicosídeos pode originar a surdez; especialmentequando o sujeito possuir mutações mitocondriaispredisponentes. A mutação C1494T do gene mitocondrial MTRNR1,o qual é responsável pela formação da subunidade12S do RNA ribossômico (12S rRNA), tem sido descritaassociada à perda auditiva pelo uso de antibióticosaminoglicosídeos. Objetivo: É o de investigar a prevalênciada mutação mitocondrial C1494T do gene MT-RNR1 em coortesde sujeitos ouvintes e surdos, das regiões Norte e Nordeste doEstado do Paraná, Brasil. Material e Método: Foraminvestigados 80 sujeitos ouvintes saudáveis e 80 surdos queapresentavam surdez pré-lingual, não sindrômica, de etiologiadesconhecida, sendo casos isolados dentro das famílias. Foiutilizada a técnica de PCR para amplificação da região, deum fragmento de 936 pb, na posição 1494, do gene MT-RNR1seguido de digestão pela enzima de restrição Hph I. Resultados:A mutação C1494T não foi encontrada nas amostras de sujeitosouvintes e de surdos. Conclusões: A mutação C1494T do geneMT-RNR1 pode ser considerada ausente ou rara nas populaçõesde sujeitos ouvintes e surdos das regiões Norte e Nordeste doestado do Paraná, Brasil...

Deafness is the most common sensory deficit inhumans, which may be caused by environmental and geneticfactors or even by a combination of both. It has been estimatedthat one in every 500 newborns has bilateral permanent hearingloss, and this incidence increases to 3.5:1,000 individuals inadolescence. Certain environmental factors may be enhancedwhen specific mutations are present in the genome. It is widelyknown that the use aminoglycoside antibiotics may lead tohearing loss, especially if the individual has predisposingmitochondrial mutations. Mutation C1494T of themitochondrial gene MT-RNR1 which causes the formation ofthe subunit 12S of the ribosome RNA (12S rRNA), has beenassociated with hearing loss due to the use of aminoglycosideantibiotics. Objective: This study investigates the occurrenceof mitochondrial mutation C1494T in the gene MT-RNR1 incohorts of hearing and deaf people in northern and northwesternregions of Paraná state, Brazil. Material and Methods: Eightyhearing people and eighty deaf people were analyzed. Thelatter were characterized as pre-lingual, non-syndromic, ofunknown etiology, being isolated cases within the family. PCRtechnique was used for amplification of the fragment 936 bpof the gene MT-RNR1 at position 1494, followed by digestionwith restriction enzyme Hph I. Results: Mutation C1494T wasnot detected in the samples of hearing and deaf people.Conclusions: Mutation C1494T of the gene MT-RNR1 may beabsent or rare in populations of hearing and deaf people innorthern and northwestern regions of Paraná state, Brazil...

Dose-effect relationship of mRNA level of human sensitive mitochondrial genes in lymphoblastoid cells induced by 60Co γ-rays / 中华放射医学与防护杂志

Objective To investigate the dose-effect relationship of mRNA level of sensitive mitochondrial genes in human lymphoblastoid cells induced by ionizing radiation.Methods Seven human sensitive genes,including ND3,Cyt b,COX Ⅰ,COX Ⅱ,COX Ⅲ,ATPase6 and ATPase8 were chosen.Changes of mRNA level of these genes were detected by RT-PCR and Real-Time PCR at 24 h after irradiation in human lymphoblastoid cells,which were exposed to 0 - 15 Gy of 60 Co γ-rays.Results The expression of these 7 genes at mRNA level was up-regulated 24 h after irradiation in human lymphoblastoid cells.The level of gene expression of COX Ⅰ,which belongs to complex Ⅳ of mitochondrial respiratory chain,was most obvious,and the peak occurred after irradiation of 8 Gy,which was 13 times of the control group.A good dose-effect relationship was showed for COX Ⅲ gene expression at dose range of 3 -10 Gy as well as 3 - 15 Gy for other 3 genes including ND3,ATPase6 and ATPase8.Conclusions Gene expression levels of COX Ⅲ,ND3,ATPase6 and ATPase8 24h post-irradiation at certain irradiation dose range could be used for radiation damage biomarkers.

Mitochondrial genome organization and cytoplasmic male sterility in plants.

Plant mitochondrial genomes are much larger and more complex than those of other eukaryotic organisms. They contain a very active recombination system and have a multipartite genome organization with a master circle resolving into two or more subgenomic circles by recombination through repeated sequences. Their protein coding capacity is very low and is comparable to that of animal and fungal systems. Several subunits of mitochondrial functional complexes, a complete set of tRNAs and 26S, 18S and 5S rRNAs are coded by the plant mitochondrial genome. The protein coding genes contain group II introns. The organelle genome contains stretches of DNA sequences homologous to chloroplast DNA. It also contains actively transcribed DNA sequences having open reading frames. Plasmid like DNA molecules are found in mitochondria of some plants Cytoplasmic male sterility in plants, characterized by failure to produce functional pollen grains, is a maternally inherited trait. This phenomenon has been found in many species of plants and is conveniently used for hybrid plant production. The genetic determinants for cytoplasmic male sterility reside in the mitochondrial genome. Some species of plants exhibit more than one type of cytoplasmic male sterility. Several nuclear genes are known to control expression of cytoplasmic male sterility. Different cytoplasmic male sterility types are distinguished by their specific nuclear genes (rfs) which restore pollen fertility. Cytoplasmic male sterility types are also characterized by mitochondrial DNA restriction fragment length polymorphism patterns, variations in mitochondrial RNAs, differences in protein synthetic profiles, differences in sensitivity to fungal toxins and insecticides, presence of plasmid DNAs or RNAs and also presence of certain unique sequences in the genome. Recently nuclear male sterility systems based on (i) over expression of agrobacterial rol C gene and (ii) anther specific expression of an RNase gene have been developed in tobacco and Brassica by genetic engineering methods.