Patrick Pereira

Patrick Pereira
Instituto Federal de Educação, Ciência e Tecnologia do Pará Campus Braganca · Laboratório de Biologia Molecular e Neuroecologia

Msc

About

40
Publications
4,407
Reads
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78
Citations
Additional affiliations
January 2020 - present
McGill University
Position
  • PhD Student
January 2013 - present
Instituto Federal do Pará Campus Bragança
Position
  • Researcher
January 2012 - present
Education
February 2012 - April 2015
Instituto Federal do Pará Campus Bragança
Field of study
  • Tecnologia em Gestão Ambiental

Publications

Publications (40)
Data
Full-text available
Although Wilson ́s plovers (Charadrius wilsonia) are migratory, a resident population breeds in coastal northeastern Brazil and there population trend is described as decreasing by the IUCN Red List. Domestic dogs are a major predator of Wilson’s plover nests on an island in northeastern Brazil where dogs are kept to guard fishing equipment. Local...
Conference Paper
Full-text available
The aim of the present work is to estimate the number of neurons in hipocampal formation of Charadrius semipalmatus, a neartic shorebird of the plover group (Charadriidae family). We used immunohistochemistry with anti NeuN (MAB377) to define the cytoarchitectonic boundaries and obtain the stereological estimate of the number of neurons and volume...
Conference Paper
Full-text available
The aim of the present work is to describe the hipocampal formation of Charadrius semipalmatus, a neartic shorebird of the plover group (Charadriidae family). Using cresyl violet (Nissl technique) we defined the cytoarchitectonic boundaries and obtained the stereological estimate of the number of neurons, glial cells, total cells and the hipocampal...
Data
The presence of dogs on Islands that have birds nesting causes very intense impact over the ground nesting birds community. In this video we recorded one dog eating several nests in only five minutes.
Article
Full-text available
The semipalmated sandpiper Calidris pusilla and the spotted sandpiper Actitis macularia are long and short distance migrants, respectively. C. pusilla breeds in the sub-arctic and mid-arctic tundra of Canada and Alaska and winters on the north and east coasts of South America. A. macularia breeds in a broad distribution across most of North America...
Preprint
Full-text available
Background For the epic journey of autumn migration, long-distance migratory birds use innate and learned information and follow strict schedules imposed by genetic and epigenetic mechanisms, the details of which remain largely unknown. In addition, bird migration requires integrated action of different multisensory systems for learning and memory,...
Article
Full-text available
For the epic journey of autumn migration, long-distance migratory birds use innate and learned information and follow strict schedules imposed by genetic and epigenetic mechanisms, the details of which remain largely unknown. In addition, bird migration requires integrated action of different multisensory systems for learning and memory, and the hi...
Article
Full-text available
The number of parvalbumin neurons can be modified by social, multisensory, and cognitive stimuli in both mammals and birds, but nothing is known about their plasticity in long-distance migratory shorebirds. Here, in the spotted sandpiper (Actitis macularius), we investigated the plasticity of parvalbumin neurons of two brain areas during this speci...
Article
Full-text available
Microglial immunosurveillance of the brain parenchyma to detect local perturbations in homeostasis, in all species, results in the adoption of a spectrum of morphological changes that reflect functional adaptations. Here, we review the contribution of these changes in microglia morphology in distantly related species, in homeostatic and non-homeost...
Article
Full-text available
Abstract Based on previous evidence that environmental enrichment is associated with telencephalic cellular proliferation and that stable visuotopic tectal circuits are essential for discrimination of placement and identity of stationary or moving objects in the visual field, differential plasticity is expected in these areas. Here we tested this...
Article
Full-text available
Fish use spatial cognition based on allocentric cues to navigate, but little is known about how environmental enrichment (EE) affects learning and memory in correlation with hematological changes or gene expression in the fish brain. Here we investigated these questions in Colossoma macropomum (Teleostei). Fish were housed for 192 days in either EE...
Article
Full-text available
Semipalmated sandpiper (Calidris pusilla) migration to the southern hemisphere includes a 5‐day non‐stop flight over the Atlantic Ocean, whereas semipalmated plover (Charadrius semipalmatus) migration, to the same area, is largely over land, with stopovers for feeding and rest. We compared the number and 3‐D morphology of hippocampal astrocytes of...
Article
Full-text available
Little is known about environmental influences on radial glia-like (RGL) α cells (radial astrocytes) and their relation to neurogenesis. Because radial glia is involved in adult neurogenesis and astrogenesis, we investigated this association in two migratory shorebird species that complete their autumnal migration using contrasting strategies. Befo...
Article
Full-text available
Carassius auratus is a teleost fish that has been largely used in behavioral studies. However, little is known about potential environmental influences on its performance of learning and memory tasks. Here, we investigated this question in C. auratus, and searched for potential correlation between exercise and visuospatial enrichment with the total...
Article
Full-text available
Seasonal migratory birds return to the same breeding and wintering grounds year after year, and migratory long-distance shorebirds are good examples of this. These tasks require learning and long-term spatial memory abilities that are integrated into a navigational system for repeatedly locating breeding, wintering, and stopover sites. Previous inv...
Data
Excel file shows all data related to astrocytes morphometric features with MMI > 0.55 and correspondent frequency distribution histograms for each morphometric variable. Because hierarchical cluster analysis was based on morphometric variables with multimodality index higher than 0.55, it is expected to find multimodal or at least bimodal distribut...
Data
Stereological parameters for the GFAP positive neurons in the right hippocampal formation of C. pusilla. ∑Q- = equals the total number of objects of interest counted using the optical dissector, SSF = section sampling fraction, ASF = area sampling fraction, TSF = thickness sampling fraction, a(frame) = area of counting frame, A(x,y step) = grid siz...
Data
Stereological parameters for the GFAP positive neurons in the left hippocampal formation of Calidris pusilla. ∑Q- = equals the total number of objects of interest counted using the optical dissector, SSF = section sampling fraction, ASF = area sampling fraction, LHF = left hippocampal formation.
Data
Stereological parameters for the GFAP positive neurons in the right hippocampal formation of C. pusilla. ∑Q- = equals the total number of objects of interest counted using the optical dissector, SSF = section sampling fraction, ASF = area sampling fraction, TSF = thickness sampling fraction, a(frame) = area of counting frame, A(x,y step) = grid siz...
Data
Stereological parameters for the GFAP positive neurons in the left hippocampal formation of C. pusilla. ∑Q- = equals the total number of objects of interest counted using the optical dissector, SSF = section sampling fraction, ASF = area sampling fraction, TSF = thickness sampling fraction, a(frame) = area of counting frame, A(x,y step) = grid size...
Preprint
Full-text available
The analysis of large numbers of sequences requires the reduction of ambiguities during the analytical work to ensure that the effort will focus only on confirmed sequences. Performing this work automatically may help to minimize potential errors associated with tedious manual correction, allowing more effective results. Basic local alignment searc...
Preprint
Full-text available
The analysis of large numbers of sequences requires the reduction of ambiguities during the analytical work to ensure that the effort will focus only on confirmed sequences. Performing this work automatically may help to minimize potential errors associated with tedious manual correction, allowing more effective results. Basic local alignment searc...
Article
Full-text available
Long distance migratory birds find their way by sensing and integrating information from a large number of cues in their environment. These cues are essential to navigate over thousands of kilometers and reach the same breeding, stopover, and wintering sites every year. The semipalmated sandpiper (Calidris pusilla) is a long-distance migrant that b...
Thesis
Full-text available
The species Charadrius semipalmatus and Charadrius collaris are from the Plovers group (Charadriidae Family). These species are migratory and non-migratory birds, respectively. In the migratory birds, the hippocampus is important to recover memories related to the stopping places, details about the breeding and the wintering grounds. The hippocampu...
Conference Paper
Full-text available
The aim of this paper is to quantify hippocampal formation neurogenesis of the spotted sandpiper (Actitis macularia) through stereological analyses during winter period. The immature neurons of hippocampal formation were immunolabelled by Anti-Doublecortin (C-18): SC-8066. The specimens were collected on Ilha de Canelas, Brazil (44°44'37.39"N e 66°...
Article
Full-text available
Abstract. Although Wilson ́s plovers (Charadrius wilsonia) are migratory, a resident population breeds in coastal northeastern Brazil and there population trend is described as decreasing by the IUCN Red List. Domestic dogs are a major predator of Wilson’s plover nests on an island in northeastern Brazil where dogs are kept to guard fishing equipme...
Conference Paper
Full-text available
The hippocampus is involved in spatial memory in birds and mammals and hence may be important in shorebirds for recalling landmarks and migratory routes. Studies about hippocampal changes induced by migration in sandpipers overwintering in tropical coastal regions are virtually nonexistent. The coastal regions of South America are relevant stopover...

Questions

Question (1)
Question
Hi.
Any way to use Trinity with GPU?
I have an Nvidea Tesla k40 and an cluster with 72 cores and 125GB of RAM
Commonly i use this command line:
Trinity -seqType fq --max_memory 125G -single Filename.fastq -CPU 72
I want to know how i can use my GPU to run o Trinity?
Thank you!

Network

Cited By

Projects

Projects (3)
Project
É de conhecimento científico que peixes possuem a capacidade de memória e aprendizagem, estas funções estão relacionadas com o telencéfalo, porção cerebral dos peixes que se assemelha ao hipocampo de mamíferos. No presente trabalho investigamos possíveis relações do ambiente nos resultados em teste de memória e reconhecimento de objeto e possíveis alterações no número de células gliais e neuronais no telencéfalo de peixes da espécie Carassius auratus. Para isso, mantivemos os peixes em ambientação durante 183 dias, dispostos em dois aquários que foram denominados de ambiente enriquecido (AE) com n=16 e ambiente padrão (AP) com n=10, ambos possuíam dimensão de 110 x 55 x 55 cm. Os dois aquários possuíam bombas de filtro biológicos com lâmpada ultravioleta, termômetros, pedras de aeração e ciclo claro/escuro de 12 horas. Somente o ambiente enriquecido continha brinquedos, plantas naturais e corrente de água para exercício voluntário durante 12 horas por dia. Oxigênio, pH e temperatura foram medidos e mantidos dentro dos padrões aceitáveis para a espécie. Para realização dos testes comportamentais utilizamos outro aquário em formato de labirinto em cruz, com pistas visuais distintas em dois de seus 4 braços, quadrado para o braço correto e círculo para o braço incorreto. O teste consistia em 30 sessões, se dava por encerrado caso os animais fizessem 3 acertos consecutivos ou 7 alternados. A taxa de aprendizagem entre os peixes EE e IE revelou diferenças significativas. Os resultados preliminares apontam que o ambiente pode influenciar na aprendizagem e memória espacial em Carassius auratus e pode estar associado ao número de células no telencéfalo.
Project
A presente proposta se dedica a investigar a neuroecologia de espécies de pássaros migrantes de longa distância com diferentes estratégias de migração e ao mesmo tempo a fauna de invertebrados que compõe a dieta desses animais nos diferentes pontos de invernada. O hipocampo, uma área cerebral chave para reconhecimento das rotas de migração foi estudado recentemente em nosso laboratório na Universidade Federal do Pará em duas espécies de maçaricos que após o período reprodutivo migram para as áreas de invernada da América do Sul e do Caribe. Escolhemos estudar o Calidris pusilla que viaja entre seu habitat de reprodução no verão canadense para áreas de invernada no Brasil em um voo sem paradas de aproximadamente 4000 km, comprando-o ao Actitis macularia que migra na mesma direção com voos interrompidos por paradas múltiplas em sítios selecionados para repouso e alimentação. Encontramos diferenças marcantes no número de células da glia no hipocampo dessas espécies sugerindo que pressões ambientais diferentes podem alterar de forma distinta o número de células da glia na formação hipocampal, modificando a relação neurônio/micróglia de forma distinta em cada espécie. De fato encontramos que embora o número de neurônios tenha sido igual em ambas as espécies o número de micróglias e o volume hipocampal são 6 significativamente maiores em Actitis macularia, e que a razão entre o número de neurônios e o número de micróglias num caso e noutro é duas vezes maior em C. pusilla quando comparado ao A. macularia. Difícil dizer com o presente conjunto de evidências indiretas se essa relação e suas diferenças estão ou não associadas à resposta adaptativa expressa no padrão de migração sendo um dos objetivos do presente projeto esclarecer essas e outras questões relacionadas. Mantendo-se em mente para análises comparativas subsequentes que as pressões ambientais e a estimulação multissensorial, somatomotoras e visuoespaciais são bastante diferentes nas duas espécies, é importante para esclarecer de que forma esse processo afeta a formação hipocampal, estimar em observações futuras de forma comparativa, a relação neurônio/glia e a taxa de neurogênese e gliogênese antes e depois do processo migratório se completar. Além disso investigaremos as bases moleculares do processo migratório diferenciado dessas espécies esperando-se que isso possa esclarecer em detalhe a contribuição do hipocampo nesse processo. Com o andamento do projeto, outros pássaros marinhos migrantes podem ser investigados, por exemplo, Charidrius semipalmatus, comumente encontradas próximos aos bando de C. pusilla. Este estudo talvez permita generalizações acerca dos mecanismos neurais envolvidos na migração de longa distância assim como acerca do papel do hipocampo e da plasticidade que garantem navegação adequada durante a viagem entre os sítios de alta latitude de reprodução no Canadá e áreas tropicais de invernada no Brasil. Além disso é determinante investigar as características ambientais de cada local de parada documentando possíveis impactos naturais ou antrópicos sobre as espécies que servem de alimento para estes pássaros migrantes e que podem alterar a rota migratória em função da redução da oferta de alimento. O presente projeto visa portanto implantar na Região Costeira do Estado do Pará município de Bragança, junto ao Instituto Federal do Pará, Campus de Bragança, a Unidade de Pesquisa em Neuroecologia de Aves Marinhas em parceria com a Unidade Avançada de Pesquisa em Aves (AFAR) da Universidade de Western Ontario - Canadá e a Universidade Federal do Pará campi de Belém e de Bragança. Esse esforço complementa trabalho excepcional que já vem sendo realizado pelo Instituto de Estudos Costeiros (IECOS) da UFPA em Bragança onde o estudo da biodiversidade e da ecologia dos manguezais avança a passos largos
Project
Investigar os mecanismos neurais que permitem respostas adaptativas às diferentes estratégias de migração de espécies irmãs de aves migratórias marinhas, Charadrius semipalmatus, Charadrius collaris e Charadrius wilsonia que partilham de forma transitória os recursos contidos nos substratos aquático, terrestre e aéreo dos manguezais da Região Norte do Brasil.