Potential PCR amplification bias in identifying complex ecological patterns: Higher species compositional homogeneity revealed in smaller-size coral reef zooplankton by metatranscriptomics.

PCR-based high-throughput sequencing has permitted comprehensive resolution analyses of zooplankton diversity dynamics. However, significant methodological issues still surround analyses of complex bulk community samples, not least as in prevailing PCR-based approaches. Marine drifting animals-zooplankton-play essential ecological roles in the pelagic ecosystem, transferring energy and elements to higher trophic levels, such as fishes, cetaceans and others. In the present study, we collected 48 size-fractionated zooplankton samples in the vicinity of a coral reef island with environmental gradients. To investigate the spatiotemporal dynamics of zooplankton diversity patterns and the effect of PCR amplification biases across these complex communities, we first took metatranscriptomics approach. Comprehensive computational analyses revealed a clear pattern of higher/lower homogeneity in smaller/larger zooplankton compositions across samples respectively. Our study thus suggests changes in the role of dispersal across the sizes. Next, we applied in silico PCR to the metatranscriptomics datasets, in order to estimate the extent of PCR amplification bias. Irrespective of stringency criteria, we observed clear separations of size fraction sample clusters in both metatranscriptomics and in silico datasets. In contrast, the pattern-smaller-fractioned communities had higher compositional homogeneity than larger ones-was observed in the metatranscriptomics data but not in the in silico datasets. To investigate this discrepancy further, we analysed the mismatches of widely used mitochondrial CO1 primers and identified priming site mismatches likely driving PCR-based biases. Our results suggest the use of metatranscriptomics or, although less ideal, redesigning the CO1 primers is necessary to circumvent these issues.

Diversity and Ecology of Lobophora Species Associated with Coral Reef Systems in the Western Gulf of Thailand, including the Description of Two New Species.

The brown macroalgal genus Lobophora plays important ecological roles in many marine ecosystems. This group has received much attention over the past decade, and a considerable number of new species have been identified globally. However, our knowledge of the genus diversity and ecology along south-east Asian coasts are still limited. Given the growing body of research that uses a combination of molecular and morphological data to identify cryptic species, this study investigates the diversity of Lobophora in the western Gulf of Thailand using morphological and molecular data, as well as their interactions with scleractinian corals. A total of 36 Lobophora specimens were collected from 15 sites in the western Gulf of Thailand and used for molecular and morphological analyses. One mitochondrial (cox3) and two chloroplast (psbA and rbcL) genes were amplified and sequenced for molecular phylogenetic analyses. Based primarily on phylogenetic evidence, two new species were formally described, L. chumphonensis sp. nov. and L. thailandensis sp. nov. Additionally, L. lamourouxii was newly recorded from Thailand. Two new lineages of Lobophora obscura were identified, L. obscura12 and L. obscura13. Among the Lobophora species identified, three were found in interaction with corals, the most notable of which was the massive coral Porites. Lobophora chumphonensis sp. nov. only interacted with Porites by growing on bare coral skeleton between Porites colonies. Furthermore, L. obscura13 was observed under the branching coral Pocillopora. Our findings revealed that Lobophora presented both effects and absence of effects on coral. A thorough understanding of Lobophora diversity and ecology is essential for ongoing and future research on coral-macroalgal ecological relationships.

Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum.

High-throughput sequencing has enabled genome skimming approaches to produce complete mitochondrial genomes (mitogenomes) for species identification and phylogenomics purposes. In particular, the portable sequencing device from Oxford Nanopore Technologies (ONT) has the potential to facilitate hands-on training from sampling to sequencing and interpretation of mitogenomes. In this study, we present the results from sampling and sequencing of six gastropod mitogenomes (Aplysia argus, Cellana orientalis, Cellana toreuma, Conus ebraeus, Conus miles and Tylothais aculeata) from a graduate level biodiversity course. The students were able to produce mitogenomes from sampling to annotation using existing protocols and programs. Approximately 4 Gb of sequence was produced from 16 Flongle and one MinION flow cells, averaging 235 Mb and N50 = 4.4 kb per flow cell. Five of the six 14.1-18 kb mitogenomes were circlised containing all 13 core protein coding genes. Additional Illumina sequencing revealed that the ONT assemblies spanned over highly AT rich sequences in the control region that were otherwise missing in Illumina-assembled mitogenomes, but still contained a base error of one every 70.8-346.7 bp under the fast mode basecalling with the majority occurring at homopolymer regions. Our findings suggest that the portable MinION device can be used to rapidly produce low-cost mitogenomes onsite and tailored to genomics-based training in biodiversity research.

Reef fishes biodiversity and conservation at the largest Brazilian coastal Marine Protected Area (MPA Costa dos Corais)

Abstract Coral reefs harbor one of the largest fish biodiversity on earth; yet information on reef fishes is still absent for many regions. We analyzed reef fish richness, distribution, and conservation on the largest Brazilian multiple use coastal MPA; which cover a large extent of coral reefs at the SWA. A total of 325 fish species have been listed for MPA Costa dos Corais, including Chondrichthyes (28 species) and Actinopterygii (297). Fish species were represented by 81 families and the most representative families were Carangidae (23 species), Labridae (21) and Gobiidae (15). The MPA fish richness represented 44% of all recorded fish species of the Southwestern Atlantic Ocean (SWA) highlighting the large-scale importance of this MPA. A total of 40 species (12%) are registered at Near Threatened (NT), Vulnerable (VU), Endangered (EN) or Critically Endangered (CR). This study reinforces the importance of MPA Costa dos Corais on reef fish biodiversity and conservation and emphasize the urgent need of conservation strategies.

Resumo Os recifes de coral abrigam uma das maiores biodiversidades de peixes do planeta; no entanto, as informações sobre peixes de recife ainda estão ausentes em muitas regiões. Analisamos a riqueza, distribuição e a conservação de peixes recifais na maior Área de Proteção Ambiental (APA) costeira de uso múltiplo do Brasil; área que possui grande extensão de recifes de corais no SWA. Um total de 325 espécies de peixes foram listadas para APA Costa dos Corais, incluindo Chondrichthyes (28 espécies) e Actinopterygii (297). As espécies de peixes foram representadas por 81 famílias e as famílias mais representativas foram Carangidae (23 espécies), Labridae (21) e Gobiidae (15). A riqueza de peixes da APA representou 44% de todas as espécies de peixes registradas no Oceano Atlântico Sudoeste (SWA), destacando a importância em grande escala desta APA. Um total de 40 espécies (12%) estão registradas como Quase Ameaçada (NT), Vulnerável (VU), Em Perigo (EN) ou Criticamente Em Perigo (CR). Este estudo reforça a importância da APA Costa dos Corais na biodiversidade e conservação dos peixes recifais e enfatiza a necessidade urgente de estratégias de conservação.

Enteral electrolytic solutions administered in continuous flow via naso-ruminal route in adult goats.

This study aimed to investigate the effects of maintenance enteral electrolytic solutions administered naso-ruminally in continuous flow in adult goats subjected to water and food restriction. Six adult non-pregnant and non-lactating female goats, aged between two and five years old, were used in a crossover (6 × 2) study. Solution 1 (SEE1) comprised: 4.5 g sodium chloride (NaCl); 1 g potassium chloride (KCl); 0.5 g magnesium chloride (MgCl); 1 g calcium chloride in 1,000 ml of water (measured osmolarity: 202 mOsm/l). Solution 2 (SEE2) comprised: 4.5 g of NaCl; 1 g of KCl; 0.5 g of MgCl; 2 g of calcium acetate in 1,000 ml of water (measured osmolarity: 212 mOsm/l). The solutions were administered naso-ruminally at a dose rate of 15 ml/kg/hr, for 12 hr. The animals were evaluated at times T-24, T0, T4, T8, T12, and T24. Both enteral electrolytic solutions were effective in expanding blood volume. SEE1 showed a low-intensity acidifying potential, while SEE2 showed behavior of a neutral enteral electrolytic solution.

Diversity patterns of reef fish along the Brazilian tropical coast.

Causal mechanisms for broad-scale reef fish diversity patterns are poorly understood and current knowledge is limited to trends of species richness. This work compared the effects of ecological drivers on components of fish diversity across reefs spanning over 2.000 km of the tropical Brazilian coastline. A quarter of communities' diversity is accountable to common and dominant species, while remaining species are rare. Low-latitude sites were more diverse in rare species. Communities along the coast share common and dominant species, which display high densities across all reefs, but differ in rare species that show abundance peaks in particular reef morphotypes. The disproportionate distribution of rare species reveals a higher vulnerability of these communities to impacts and stochastic density fluctuations. Uneven conservation efforts directed to these morphotypes pose a threat to the maintenance of a paramount component of the reef fish diversity represented by rare species.

Effects of Hypotonic and Isotonic Enteral Electrolyte Solutions Administered in Continuous Flow in Weaned Foals.

The effects of fluid therapy with maintenance enteral electrolytic solutions administered by nasogastric route in continuous flow have not previously been studied in weaned foals. This study primary goal was to compare the effects of two maintenance enteral electrolytic solutions administered by nasogastric route in continuous flow on the hydro electrolytic balance in weaned foals. This paper was a controlled trial in a cross-over design (6 × 2) performed in six foals with a mean age of 7.3 ± 1.4 months; each animal received two treatments, IsoES and HypoES, with an interval of 7 days between treatments. After 12 h of fasting, the animals were treated with enteral electrolyte solutions administered via nasogastric route in continuous flow in a volume of 15 mL/kg/h for 12 h. The evaluations were performed at T-12h (the beginning of the fasting), T0h (end of fasting and beginning of fluid therapy), T4h (4 h of fluid therapy), T8h (8 h of fluid therapy), T12h (end of fluid therapy), and T24h (12 h after the end of fluid therapy). Twelve hours of fasting resulted in a reduction (P < 0.05) in body weight, abdominal circumference, whereas serum sodium, SID and enophthalmos increased. Twelve hours of fluid therapy normalized these parameters and promoted increased urinary volume and decreased urinary density without causing electrolyte imbalances. Both enteral electrolytic solutions were effective in reestablishing clinical and laboratorial variables without causing electrolyte imbalances.

Two enteral solutions with different chloride concentrations administered by naso-ruminal route for fluid therapy in adult cattle / Comparação de duas soluções enterais com diferentes concentrações de cloreto administradas por via nasorruminal para hidratação em bovinos adultos

ABSTRACT: Six adult Holstein cows were used in this fluid therapy study. All animals were previously submitted to 24 hours of water and food abstaining period and submitted to both hydration treatments for eight hours in a crossover design 6x2. Two treatments with hypotonic solutions (190 mOsm/L) with low strong ion difference and different chloride concentrations solutions were executed. Physical, biochemical, blood gas analysis and urinary evaluation were executed in five different experimental times (T-24h, T0h, T4h, T8h e T24h). The hydration period caused plasmatic volume expansion. An increase in faeces humidity, excretion of Na+ and Cl- in urine, reduction of PCV, osmolarity, blood and urinary pH was observed. Both solutions can be used for fluid therapy for adult cattle and solution containing calcium chloride (SECaCl) was the most suitable for use in animals with hypochloraemia.

RESUMO: Seis vacas holandesas adultas foram utilizadas neste estudo de hidratação. Todos os animais foram submetidos previamente a 24 horas de jejum hídrico e alimentar e submetidos a ambos os tratamentos de hidratação por oito horas, em delineamento transversal 6x2. Foram realizados dois tratamentos com soluções hipotônicas balanceadas (190 mOsm/L) com diferentes concentrações de cloretos. Foram realizadas avaliações físicas, bioquímicas, hemogasometria e avaliação urinária em cinco diferentes tempos experimentais (T-24h, T0h, T4h, T8h e T24h). O período de hidratação causou expansão de volume plamático. Foi observado aumento da umidade das fezes e da excreção de Na+ e Cl- na urina, redução do volume globular, osmolaridade, pH sangüíneo e pH urinário. Ambas as soluções podem ser usadas para hidratação de bovinos adultos, sendo a solução que contém cloreto de cálcio (SECaCl) a mais indicada para o uso em animais com hipocloremia.

The use of optical coherence tomography for the detection of ocular toxicity by ethambutol.

OBJECTIVES: To evaluate, through (OCT), alterations in retinal thickness, secondary to use of ethambutol in the treatment of patients with tuberculosis. In addition to studying the use of simpler semiological tools, such as Amsler and Ishihara, in the screening of these cases. METHODS: Thirty patients with ethambutol were recruited from the reference service of tuberculosis treatment at the Federal University of Espírito Santo from May 2015 to July 2016. After clinical history, the following parameters were analyzed; best corrected visual acuity, biomicroscopy, tonometry, photomotor reflex testing, Ishihara test, Amsler's grid test, color digital retinography and optical coherence tomography with CIRRUS HD-OCT (Humphrey-Zeiss) every 2 months during treatment with ethambutol. They were divided into two groups according to the treatment: (1) standard group, two months of ethambutol; (2) extended group, nine to twelve months of ethambutol. RESULTS: There was a significant reduction in OCT thickness between the pre and post treatment times in ten eyes of the extended group, mean reduction of 7,8 microns and in seven eyes of the standard group, with an average of 5.57 microns. During the study, a significant reduction of retinal thickness was observed in both groups at two months of treatment, and the delta percentage was higher in those patients who presented reduction of visual acuity and / or change in the Ishihara test. CONCLUSION: There was a significant reduction in the thickness of the nerve fiber layer by OCT in the patients studied, being more pronounced in those submitted to the extended treatment regimen. This reduction was observed two months after the start of therapy, and was more significant in the cases that presented changes in the Ishihara test.

Enteral fluid therapy administered in continuous flow by naso-ruminal route using three maintenance electrolyte solutions: effects on physiological biomarkers and the hemogram of bovines / Hidratação enteral via nasorruminal em fluxo continuo utilizando três soluções eletrolíticas de manutenção: efeitos sobre os biomarcadores fisiológicos e o hemograma de bovinos

ABSTRACT: The aim of this study was to evaluate the effects of three enteral electrolyte solutions, each with different energy sources, administrated as continuous flow on the physiological parameters and blood count of healthy Holstein heifers. Six Holstein heifers were used in a crossover design. All animals received all three treatments: solution with calcium propionate, 4g of NaCl, 0.5g of KCl, 0.3g of MgCl2, and 10g of calcium propionate diluted in 1000mL of water (measured osmolarity: 299mOsm/L); solution with glycerol, 4g of NaCl, 0.5g of KCl, 0.3g of MgCl2, 1g of calcium acetate, and 10mL of glycerol in 1000mL of water (measured osmolarity: 287mOsm/L); solution with propylene glycol, 4g of NaCl, 0.5g of KCl, 0.3g of MgCl2, 1g of calcium acetate, and 15mL of propylene glycol in 1000mL of water (measured osmolarity: 378mOsm/L). Physical evaluations and blood samples were collected immediately before the initiation of fluid therapy, at 3-hour intervals over the 12-hour period of fluid therapy, and 12 hours after the end of fluid therapy. Animals presented no signs of stress or discomfort. All solutions resulted in a significant decrease in erythrocyte concentration, hemoglobin concentration, and hematocrit, without affecting the leukogram. Enteral fluid therapy administered as continuous flow via the naso-ruminal route was well-tolerated by animals with minimal effects on animal welfare, even when administered for 12 hours. This technique is indicated as an alternative route for parenteral maintenance fluid therapy. Electrolyte solutions proposed here were able to significantly expand blood volume.

RESUMO: Objetivou-se avaliar os efeitos de três soluções eletrolíticas enterais de manutenção com diferentes fontes de energia administradas em bovinos adultos por via nasorruminal em fluxo contínuo sobre parâmetros fisiológicos e hematológicos. Foram utilizadas seis novilhas holandesas em um delineamento crossover. Os animais foram submetidos a três tratamentos: Solução contendo Propionato de cálcio - 4g de NaCl, 0,5g de KCl, 0,3g de MgCl2 e 10g de propionato de cálcio para cada 1000mL (Osmolaridade mensurada: 299mOsm/L); Solução contendo Glicerol - 4g de NaCl, 0,5g de KCl, 0,3g de MgCl2, 1g de acetato de cálcio e 10mL de glicerol para cada 1000mL (Osmolaridade mensurada: 287mOsm/L); Solução contendo Propilenoglicol - 4g de NaCl, 0,5g de KCl, 0,3g de MgCl2, 1g de acetato de cálcio e 15mL de propilenoglicol para cada 1.000mL (Osmolaridade mensurada: 378mOsm/L). Foi realizado exame físico e colheita de sangue para os hemogramas imediatamente antes do início da hidratação e a cada três horas durante 12h de tratamento e mais uma colheita 12h após o final do período experimental, perfazendo seis colheitas ao total. Todas soluções promoveram ao longo das 12 horas de tratamento hemodiluição com redução nos valores de hemácias, concentração de hemoglobina e volume globular, sem, contudo, alterar o leucograma. A hidratação enteral em fluxo contínuo via nasorruminal, mostrou-se uma técnica bem tolerada pelos animais, como mínimos efeitos sobre o bem-estar, mesmo quando administrada por 12 horas, sendo, portanto, uma técnica indicada como uma opção à hidratação parenteral na terapia de manutenção de fluidos. As três soluções eletrolíticas aqui propostas são capazes de expandir significativamente a volemia.

Valor prognóstico dos polimorfismos fincionais nos genes da mmp-1, mmp-13 e il-8 no carcinoma epidermóide oral e de orofaringe / Fincionais prognostic value of polymorphisms in the genes of MMP-1, MMP-13 and IL-8 in oral squamous cell carcinoma and oropharyngeal

Tumores malignos têm a habilidade de invadir tecidos normais e de se espalharem para sítios anatômicos distantes, originando a metástase, o maior fator de mortalidade do câncer. As metaloproteinases de matriz (MMP)-l e MMP-13 têm sido associadas à invasão tumoral e à metástase, pois a MMP-1 degrada colágeno tipo I, que é o substrato mais abundante no estroma tumoral e a MMP-13 degrada colágeno tipo IV, dentre outros, que está presente na membrana basal dos vasos. Pesquisas mostram que a IL-8 é um potente fator angiogênico e está associada ao crescimento tumoral, à metástase e ao pobre prognóstico do câncer. O presente trabalho se propõe a verificar a existência e a frequência dos polimorfismos nos genes das MMPs-1 (rs2071230 e rs470558), -13 (rs2252070) e da IL-8 (rs4073 e rs2227532) e investigar o possível valor prognóstico dos mesmos em uma série de casos de carcinoma epidermóide oral e de orofaringe (CEOO). Foram genotipados por meio de PCR em tempo real 98 amostras de pacientes com carcinoma epidermóide e 134 amostras controle. Todos os polimorfismos estavam em equilíbrio de Hardy-Weinberg, exceto o SNP IL-8 (rs2227532). O genótipo homozigoto polimórfico GG da MMP-1 (rs2071230) revelou ser um fator de risco pouco mais de 8 vezes para o desenvolvimento do carcinoma epidermóide, enquanto o genótipo polimórfico GG da MMP-13 (rs2252070) diminuiu o risco de desenvolver CEOO em aproximado de 3 vezes. Verificou-se diferença na distribuição dos genótipos em relação à localização da lesão, sendo o genótipo CC da MMP-1 (rs470558) mais frequente em lesões intraorais e o CT em orofaringe e o genótipo TT da IL-8 (rs4073) mais comum em lesões intraorais e com estadiamento clínico III e IV. Os indivíduos portadores do genótipo GG da MMP-13 (rs2252070) apresentaram menor tempo de sobrevida livre de doença e sobrevida global. Conclui-se que o SNP (rs2252070) da MMP-13 possui valor prognóstico em pacientes com carcinoma epidermóide oral e de orofaringe.

Malignant tumors have the ability to invade normal tissues and spread to distant anatomic sites, leading to metastasis, the whole factor for cancer mortality. Matrix metalloproteinases (MMP)-l and MMP-13 have been associated with tumor invasion and metastasis because MMP-1 degrades type I collagen, which is the most abundant substrate in the tumor stroma and MMP-13 degrades type IV collagen, among others, that is present in the basement membrane of the vessels. Research shows that IL-8 is a potent angiogenic factor and is associated with tumor growth, metastasis and poor prognosis of cancer. This study aims to verify the existence and frequency of polymorphisms in genes of MMP-1 (rs2071230 and rs470558), -13 (rs2252070) and IL-8 (rs4073 and rs2227532) and investigate the possible prognostic value of the same in cases of squamous cell carcinoma. Ninety eight samples from patients with oral and oropharyngeal squamous cell carcinoma and 134 control samples were genotyped by real-time PCR. All polymorphisms were in Hardy-Weinberg equilibrium, except SNP (rs2227532) of IL-8. The polymorphic homozygote genotype GG of MMP-1 (rs2071230) was found to be a risk factor just over 8 times for the development of oral and oropharyngeal squamous cell carcinoma, while the GG genotype polymorphism of MMP-13 (rs2252070) showed a protective effect of approximately 3 times. CC genotype of MMP-1 (rs470558) was most frequent in intraoral and CT in oropharyngeal lesions. TT genotype of the IL-8 (rs4073) was most common in intraoral lesions and III and IV clinical staging. Patients with GG genotype of MMP-13 (rs2252070) had fewer disease-free survival and overall survival. We conclude that the SNP (rs2252070) of MMP-13 has prognostic value in patients with oral and oropharyngeal squamous cell carcinoma.