A study on the morphoquantitative and cytological characteristics of the bulbar conjunctiva of the maned wolf (Chrysocyon brachyurus; Illiger, 1815).

The maned wolf, Chrysocyon brachyurus, is a near-threatened carnivore inhabiting the Brazilian Cerrado. Few studies have been conducted on this species, and even fewer have explored its ophthalmological characteristics. Vision is critical to wild canids; thus, this study aimed to provide a morphoquantitative description of the bulbar conjunctiva of the maned wolf using cytological and histological analyses. Ten healthy maned wolves from a conservational centre, including 4 females and 6 males aged 1-12 years (6.5 ± 2.8), were included in the study. The samples for cytological analysis were collected from the inferior conjunctival sac using a cytobrush, and conjunctival tissue was collected for histological analysis from the temporal canthus zone. The cytological samples were stained using the Papanicolaou method, and the histological sections were stained using haematoxylin and eosin, Periodic acid-Schiff, picrosirius red and Masson's trichrome stains. The cytological samples were studied for stain quality, and the different cell types were counted. Histological examination was used to determine tissue types in the conjunctiva and their proportions. Analyses revealed a stratified squamous epithelium with some goblet cells and eventual pigmentation in the basal layer. Loose connective tissue with the presence of some mononuclear and polymorphonuclear cells was also observed. The epithelium of the maned wolf's bulbar conjunctiva resembles that of dogs and other carnivore species; furthermore, its physiological and pathological responses were similar to those of other carnivore species.

MAVIS: merging, annotation, validation, and illustration of structural variants.

Summary: Reliably identifying genomic rearrangements and interpreting their impact is a key step in understanding their role in human cancers and inherited genetic diseases. Many short read algorithmic approaches exist but all have appreciable false negative rates. A common approach is to evaluate the union of multiple tools increasing sensitivity, followed by filtering to retain specificity. Here we describe an application framework for the rapid generation of structural variant consensus, unique in its ability to visualize the genetic impact and context as well as process both genome and transcriptome data. Availability and implementation: http://mavis.bcgsc.ca. Supplementary information: Supplementary data are available at Bioinformatics online.

The Genome of the Northern Sea Otter (Enhydra lutris kenyoni).

The northern sea otter inhabits coastal waters of the northern Pacific Ocean and is the largest member of the Mustelidae family. DNA sequencing methods that utilize microfluidic partitioned and non-partitioned library construction were used to establish the sea otter genome. The final assembly provided 2.426 Gbp of highly contiguous assembled genomic sequences with a scaffold N50 length of over 38 Mbp. We generated transcriptome data derived from a lymphoma to aid in the determination of functional elements. The assembled genome sequence and underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA388419.

The Genome of the Beluga Whale (Delphinapterus leucas).

The beluga whale is a cetacean that inhabits arctic and subarctic regions, and is the only living member of the genus Delphinapterus. The genome of the beluga whale was determined using DNA sequencing approaches that employed both microfluidic partitioning library and non-partitioned library construction. The former allowed for the construction of a highly contiguous assembly with a scaffold N50 length of over 19 Mbp and total reconstruction of 2.32 Gbp. To aid our understanding of the functional elements, transcriptome data was also derived from brain, duodenum, heart, lung, spleen, and liver tissue. Assembled sequence and all of the underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the Bioproject accession number PRJNA360851A.

Sealer: a scalable gap-closing application for finishing draft genomes.

BACKGROUND: While next-generation sequencing technologies have made sequencing genomes faster and more affordable, deciphering the complete genome sequence of an organism remains a significant bioinformatics challenge, especially for large genomes. Low sequence coverage, repetitive elements and short read length make de novo genome assembly difficult, often resulting in sequence and/or fragment "gaps" - uncharacterized nucleotide (N) stretches of unknown or estimated lengths. Some of these gaps can be closed by re-processing latent information in the raw reads. Even though there are several tools for closing gaps, they do not easily scale up to processing billion base pair genomes. RESULTS: Here we describe Sealer, a tool designed to close gaps within assembly scaffolds by navigating de Bruijn graphs represented by space-efficient Bloom filter data structures. We demonstrate how it scales to successfully close 50.8% and 13.8% of gaps in human (3 Gbp) and white spruce (20 Gbp) draft assemblies in under 30 and 27 h, respectively - a feat that is not possible with other leading tools with the breadth of data used in our study. CONCLUSION: Sealer is an automated finishing application that uses the succinct Bloom filter representation of a de Bruijn graph to close gaps in draft assemblies, including that of very large genomes. We expect Sealer to have broad utility for finishing genomes across the tree of life, from bacterial genomes to large plant genomes and beyond. Sealer is available for download at https://github.com/bcgsc/abyss/tree/sealer-release.

Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism.

White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation.

Uma breve leitura sobre experiência vivenciada por estagiários em unidade feminina da Febem / A brief lecture about the experience lived by students in a female unity of Febem

O objetivo deste artigo é relatar uma experiência e discutir alguns aspectos do adolescente em conflito com a lei, tais como relacionamentos familiares, sociais e o papel do psicólogo no trabalho com jovens infratores. Os temas emergiram durante o estágio realizado em dois semestres na Fundação Estadual do Bem-Estar do Menor – Unidade Feminina (FEBEM), situada no município de São Paulo. Os encontros foram realizados semanalmente com um grupo de quinze jovens e coordenado por três estagiários com o objetivo de proporcionar aos jovens um espaço de reflexão sobre seus projetos para o futuro. Consideramos fundamental desenvolver novas práticas em Psicologia Jurídica que ultrapassem a avaliação psicológica solicitada pelo judiciário. Valorizamos uma intervenção direcionada aos adolescentes infratores e suas demandas(AU)