Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans

Xenarthra (armadillos, sloths, and anteaters) constitutes one of the four major clades of placental mammals. Despite their phylogenetic distinctiveness in mammals, a reference phylogeny is still lacking for the 31 described species. Here we used Illumina shotgun sequencing to assemble 33 new complete mitochondrial genomes, establishing Xenarthra as the first major placental clade to be fully sequenced at the species level for mitogenomes. The resulting data set allowed the reconstruction of a robust phylogenetic framework and timescale that are consistent with previous studies conducted at the genus level using nuclear genes. Incorporating the full species diversity of extant xenarthrans points to a number of inconsistencies in xenarthran systematics and species definition. We propose to split armadillos in two distinct families Dasypodidae (dasypodines) and Chlamyphoridae (euphractines, chlamyphorines, and tolypeutines) to better reflect their ancient divergence, estimated around 42 million years ago. Species delimitation within long-nosed armadillos (genus Dasypus) appeared more complex than anticipated, with the discovery of a divergent lineage in French Guiana. Diversification analyses showed Xenarthra to be an ancient clade with a constant diversification rate through time with a species turnover driven by high but constant extinction. We also detected a significant negative correlation between speciation rate and past temperature fluctuations with an increase in speciation rate corresponding to the general cooling observed during the last 15 million years. Biogeographic reconstructions identified the tropical rainforest biome of Amazonia and the Guianan shield as the cradle of xenarthran evolutionary history with subsequent dispersions into more open and dry habitats.Fil: Gibb, Gillian C.. Universite de Montpellier; Francia. Massey Universit; Nueva ZelandaFil: Condamine, Fabien L.. University of Gothenburg; Suecia. Universite de Montpellier; Francia. University of Alberta; CanadáFil: Kuch, Melanie. McMaster University; CanadáFil: Enk, Jacob. McMaster University; CanadáFil: Moraes Barros, Nadia. Universidade Do Porto; Portugal. Universidade de Sao Paulo; BrasilFil: Superina, Mariella. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Medicina y Biología Experimental de Cuyo; ArgentinaFil: Poinar, Hendrik N.. McMaster University; CanadáFil: Delsuc, Frederic. Universite de Montpellier; Franci

Divide to conquer: A complex pattern of biodiversity depicted by vertebrate components in the Brazilian Atlantic Forest

The identification of northern and southern components in different vertebrate species led researchers to accept a two-component hypothesis for the Brazilian Atlantic forest (BAF). Nevertheless, neither a formal proposal nor a meta-analysis to confirm this coincidence was ever made. Our main objective here was therefore to systematically test in how many vertebrate components the BAF could be divided by analysing existing empirical data. We used two approaches: (1) mapping and comparing the proposed areas of vertebrate endemism in the BAF and (2) analysing studies mentioning spatial subdivisions in distinct forest-dependent vertebrates within the biome, by the use of panbiogeography. The four large-scale endemism area components together with the six small-scale panbiogeographical ones allowed the definition of three BAF greater regions, subdivided into nine vertebrate components, latitudinally and longitudinally organized. Empirical time estimates of the diversification events within the BAF were also reviewed. Diversification of these vertebrates occurred not only in the Pleistocene but also throughout the Miocene. Our results confirm the BAF's complex history, both in space and time. We propose that future research should be small-scale and focused in the vertebrate components identified herein. Given the BAF's heterogeneity, studying via sections will be much more useful in identifying the BAF's historical biogeography. © 2012 The Linnean Society of London

Avaliação dos processos de morte celular programada no epitélio da lente de cães idosos com catarata diabética e hipermadura

It is well known that posterior capsule opacification (PCO), one of the most common late postoperative complications of cataract surgery, is mainly caused by proliferation and differentiation of remaining lens epithelial cells (LECs) on the posterior lens capsule. Many authors suggest that alterations induced by the pathophysiology of cataracts, its metabolism and the use of 0.1% trypan blue (TB) must cause some degree of cellular damage on these cells, wicht would help to prevent and/or reduce the incidence of PCO after cataract surgery in humans. Therefore, the aim of this study was to evaluate the expression of cell death markers on LECs of older dogs with diabetic and hypermature cataracts, after capsulorhexis, both using 0.1% TB. Twenty samples collected from 13 dogs of different breeds, with ages varying from 8 to 12 years-old, with diabetic and hypermature cataracts, which had been subjected to phacoemulsification surgery (Phaco) using 0.1% TB for staining were studied. Animals were classified as dogs with diabetic (DC) and hypermature cataracts (HC), and expression of molecular markers for apoptosis and autophagy (caspase-3 and beclin-1) on LECs were obtained by immunofluorescence technique. The expression of caspase-3 and beclin-1 was observed in every studied sample and did not differ between groups. In conclusion, our findings suggest that apoptosis and autophagy processes occur to LECs in older dogs presenting diabetic and hypermature cataracts after Phaco utilizing 0.1% TB. Our results may be helpful to future studies of PCO in post-phacoemulsification surgery patients.A opacificação da cápsula posterior da lente do globo ocular é a complicação mais observada após a remoção da lente. Essa patologia é causada principalmente pela proliferação e diferenciação das células do epitélio anterior da lente em sua cápsula posterior. Muitos autores sugerem que alterações induzidas pelo metabolismo e/ou patofisiologia da catarata e o uso do corante de azul de tripan a 0,1% devam causar algum dano a essas células, o que supostamente ajudaria a prevenir e reduzir a incidência de tal complicação em humanos. Este trabalho avaliou a expressão de marcadores de morte celular no epitélio anterior da lente de cães idosos com catarata diabética e hipermadura, após capsulorrexe realizada com o emprego do azul de tripan a 0,1%. Foram estudadas vinte amostras colhidas de treze cães de diferentes raças, com idades variando de oito a doze anos, que apresentavam catarata diabética ou hipermadura e que foram submetidos à facoemulsificação utilizando corante de azul de tripan a 0,1%. Foram designados dois grupos: com catarata diabética (DC) e com catarata hipermadura (HC). A expressão molecular dos marcadores de morte celular por apoptose a autofagia (caspase-3 e beclina-1) no epitélio anterior da lente foi avaliada pela técnica de imunofluorescência. Observou-se que a expressão de caspase-3 e beclina-1 ocorreu em todas as amostras e não foi diferente entre os grupos. Os achados deste estudo sugerem que o processo de morte celular por apoptose e autofagia ocorre no epitélio anterior da lente de cães idosos com catarata diabética e hipermadura submetidos à facoemulsificação com o corante de azul de tripan a 0,1%. Este resultado pode ser útil para estudos futuros da opacidade da cápsula posterior da lente em cães submetidos à facoemulsificação

Aconselhamento telefônico para jovens usuários de crack

Este estudo buscou avaliar a utilização da Intervenção Breve Motivacional (IBM) em um serviço de aconselhamento telefônico, oferecida aos jovens no processo de cessação do consumo de crack. Foi realizado um estudo descritivo, a partir do levantamento dos registros de ligações de usuários no período de janeiro de 2006 a dezembro de 2007. Foram incluídos 40 registros de chamadas de jovens com idades entre 16 e 24 anos que consumiam crack, associado ou não com outras substâncias. Ao final do acompanhamento no sexto mês, 65% dos jovens haviam parado o consumo de crack. Do total, 57,5% estavam no estágio de preparação e ação na primeira ligação. As chances para recaída do uso de crack foram maiores nos seguimentos até 30 dias. A partir dos resultados obtidos pode-se sugerir que, a IBM associada ao aconselhamento telefônico representa uma alternativa de tratamento importante na cessação do uso de crack

Contribution of wildlife governmental centers to \ud conservation and biological study of sloths Bradypus \ud variegatus

Our study evaluated the anthropogenic threats to the common sloth in the Atlantic forest (AF) by analyzing data collected in wildlife governmental centers. Interesting, new biological data could also be reported. The main risks identified were the road network and falls, followed by domestic dogs and electric shocks. Tourism and preliminary evidences of locally distinct biological features were suggested as potential menaces to conservation of the AF common sloth populations. The birth season within the southeast appears to be the rainy season, but that is not the case in the northeast. Finally, the weight of adult individuals was reported not to vary between sexes. Data were confirmed by the highest number of individuals ever analyzed. Thus, although neotropical wildlife governmental centers usually cope with the lack of human resources, this study highlights that their records can be successfully used to add important biological information to the conservation and study of neotropical wildlife.The authors would like to thank to Camila L. Clozato, all the CETAS and DEPAVE-SP staff, and their collaborators, namely the Fire and Police Departments, health and environmental institutions, and citizens, who have been collecting animals and data across the years. We also acknowledge two anonymous reviewers for their helpful comments on an early version of this manuscript. S.M. Silva was supported by a Foundation for Science and Technology PhD grant (SFRH/ BD/40638/2007). N. Moraes-Barros was supported by CAPES. J. S. Morgante had a research grant from FAPESP (08/52207-0)

Rationale, study design, and analysis plan of the Alveolar Recruitment for ARDS Trial (ART): Study protocol for a randomized controlled trial

Background: Acute respiratory distress syndrome (ARDS) is associated with high in-hospital mortality. Alveolar recruitment followed by ventilation at optimal titrated PEEP may reduce ventilator-induced lung injury and improve oxygenation in patients with ARDS, but the effects on mortality and other clinical outcomes remain unknown. This article reports the rationale, study design, and analysis plan of the Alveolar Recruitment for ARDS Trial (ART). Methods/Design: ART is a pragmatic, multicenter, randomized (concealed), controlled trial, which aims to determine if maximum stepwise alveolar recruitment associated with PEEP titration is able to increase 28-day survival in patients with ARDS compared to conventional treatment (ARDSNet strategy). We will enroll adult patients with ARDS of less than 72 h duration. The intervention group will receive an alveolar recruitment maneuver, with stepwise increases of PEEP achieving 45 cmH(2)O and peak pressure of 60 cmH2O, followed by ventilation with optimal PEEP titrated according to the static compliance of the respiratory system. In the control group, mechanical ventilation will follow a conventional protocol (ARDSNet). In both groups, we will use controlled volume mode with low tidal volumes (4 to 6 mL/kg of predicted body weight) and targeting plateau pressure <= 30 cmH2O. The primary outcome is 28-day survival, and the secondary outcomes are: length of ICU stay; length of hospital stay; pneumothorax requiring chest tube during first 7 days; barotrauma during first 7 days; mechanical ventilation-free days from days 1 to 28; ICU, in-hospital, and 6-month survival. ART is an event-guided trial planned to last until 520 events (deaths within 28 days) are observed. These events allow detection of a hazard ratio of 0.75, with 90% power and two-tailed type I error of 5%. All analysis will follow the intention-to-treat principle. Discussion: If the ART strategy with maximum recruitment and PEEP titration improves 28-day survival, this will represent a notable advance to the care of ARDS patients. Conversely, if the ART strategy is similar or inferior to the current evidence-based strategy (ARDSNet), this should also change current practice as many institutions routinely employ recruitment maneuvers and set PEEP levels according to some titration method.Hospital do Coracao (HCor) as part of the Program 'Hospitais de Excelencia a Servico do SUS (PROADI-SUS)'Brazilian Ministry of Healt

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

A simple protocol for the extraction and sequence analysis of DNA from study skin of museum collections

Museum collections have been widely used as sources of biological samples for molecular biology studies and there are several methodologies and techniques to obtain and analyze DNA from tissues archived in museums, but most of these protocols have been developed for a specific tissue or are commercial kits. We present a simple protocol for extracting and amplifying DNA segments from sloth museum specimens. With this simple protocol we analyzed DNA fragments from 64% of 64 skin samples from three-toed sloths (Bradypus variegatus and Bradypus tridactylus) archived in three different museums: 43 samples from the University of São Paulo Museum of Zoology (Museu de Zoologia da Universidade de São Paulo, MUZUSP) São Paulo, São Paulo, Brazil; 18 samples from the Emílio Goeldi Museum (Museu Paraense Emílio Goeldi, MPEG), Belém, Pará, Brazil; and 3 samples from the Museum of Vertebrate Zoology (MVZ) University of California, Berkeley, USA. The specimens sampled ranged in age from 18 to 108 years old. Our methodology allowed the recovery of up to 700 bp of mitochondrial DNA and 400 bp of nuclear genes. Thereafter, it is useful for genetic diversity studies of three-toed sloths and could be applied to other animals

A simple protocol for the extraction and sequence analysis of DNA from study skin of museum collections

Abstract Museum collections have been widely used as sources of biological samples for molecular biology studies and there are several methodologies and techniques to obtain and analyze DNA from tissues archived in museums, but most of these protocols have been developed for a specific tissue or are commercial kits. We present a simple protocol for extracting and amplifying DNA segments from sloth museum specimens. With this simple protocol we analyzed DNA fragments from 64% of 64 skin samples from three-toed sloths (Bradypus variegatus and Bradypus tridactylus) archived in three different museums: 43 samples from the University of São Paulo Museum of Zoology (Museu de Zoologia da Universidade de São Paulo, MUZUSP) São Paulo, São Paulo, Brazil; 18 samples from the Emílio Goeldi Museum (Museu Paraense Emílio Goeldi, MPEG), Belém, Pará, Brazil; and 3 samples from the Museum of Vertebrate Zoology (MVZ) University of California, Berkeley, USA. The specimens sampled ranged in age from 18 to 108 years old. Our methodology allowed the recovery of up to 700 bp of mitochondrial DNA and 400 bp of nuclear genes. Thereafter, it is useful for genetic diversity studies of three-toed sloths and could be applied to other animals