Comparative genomics of mortal and immortal cnidarians unveils novel keys behind rejuvenation.

Turritopsis dohrnii is the only metazoan able to rejuvenate repeatedly after its medusae reproduce, hinting at biological immortality and challenging our understanding of aging. We present and compare whole-genome assemblies of T. dohrnii and the nonimmortal Turritopsis rubra using automatic and manual annotations, together with the transcriptome of life cycle reversal (LCR) process of T. dohrnii. We have identified variants and expansions of genes associated with replication, DNA repair, telomere maintenance, redox environment, stem cell population, and intercellular communication. Moreover, we have found silencing of polycomb repressive complex 2 targets and activation of pluripotency targets during LCR, which points to these transcription factors as pluripotency inducers in T. dohrnii. Accordingly, we propose these factors as key elements in the ability of T. dohrnii to undergo rejuvenation.

Occurrence of ß-lactam-resistant Staphylococcus aureus in milk from primiparous dairy cows in the northeastern region of Brazil.

The objective of the current study was to isolate and identify Staphylococcus (S.) aureus strains resistant to beta-lactam antibiotics from primiparous cows' milk. A total of 432 milk samples were collected from all primiparous dairy cows in early lactation that originated from 9 dairy properties. All samples were cultured in Mannitol salt agar enriched with egg yolk emulsion. Determination of genotypic resistance of S. aureus was achieved by polymerase chain reaction (PCR) for amplification of the blaZ, mecA, and mecC genes. Phenotypic resistance of S. aureus strains was evaluated by minimal inhibitory concentration (MIC) technique using broth microdilutions of penicillin G and oxacillin. From all the mammary quarters examined, S. aureus strains were detected in 27 out of 432 (6.25%) milk samples (CI95%, 4.33-8.84). From all dairy properties visited, only two out of 9 were found to have S. aureus. Hence, it was possible to evaluate genotypic and phenotypic resistance in 27 samples from two dairy farms. The isolates of S. aureus had a frequency of (20/27) 74.07% to blaZ gene (CI95%, 57.5-90.6), whereas mecA and mecC genes were not observed. According to MIC results, penicillin G had a 74.07% (20/27) resistance rate (CI95%, 57.5-90.6) and oxacillin had a 14.81% (4/27) resistance rate (CI95%, 1.4-28.2). Thus, the circulation of S. aureus strains resistant to beta-lactams has been confirmed in primiparous dairy cows in the northeastern region of Brazil, indicating the need for new management strategies involving the use of beta-lactam drugs to treat mastitis, discouraging and/or limiting their use. Also, it is important to highlight the need for further studies on epidemiology and traceability of the pathogen.

Differential mechanisms of tolerance to extreme environmental conditions in tardigrades.

Tardigrades, also known as water bears, are small aquatic animals that inhabit marine, fresh water or limno-terrestrial environments. While all tardigrades require surrounding water to grow and reproduce, species living in limno-terrestrial environments (e.g. Ramazzottius varieornatus) are able to undergo almost complete dehydration by entering an arrested state known as anhydrobiosis, which allows them to tolerate ionic radiation, extreme temperatures and intense pressure. Previous studies based on comparison of the genomes of R. varieornatus and Hypsibius dujardini - a less tolerant tardigrade - have pointed to potential mechanisms that may partially contribute to their remarkable ability to resist extreme physical conditions. In this work, we have further annotated the genomes of both tardigrades using a guided approach in search for novel mechanisms underlying the extremotolerance of R. varieornatus. We have found specific amplifications of several genes, including MRE11 and XPC, and numerous missense variants exclusive of R. varieornatus in CHEK1, POLK, UNG and TERT, all of them involved in important pathways for DNA repair and telomere maintenance. Taken collectively, these results point to genomic features that may contribute to the enhanced ability to resist extreme environmental conditions shown by R. varieornatus.

Serological response to Neospora caninum infection in goats and agreement between three diagnostic techniques to detect caprine neosporosis / Resposta sorológica à infecção por Neospora caninum em cabras e concordância entre três técnicas diagnósticas para detecção de neosporose caprina

The present study aimed to measure the serological response of goats infected with Neospora caninum by assessing the diagnostic performance and agreement between three techniques (indirect immunofluorescent antibody test, IFAT; Neospora agglutitation test, NAT; enzyme-linked immunosorbent assay, ELISA). The panel of sera were comprised of 500 samples of goats, and 60 reference serum samples. These reference and field serum samples were tested by ELISA, NAT, and IFAT. In the field serum samples tested, the seroprevalences of anti-N. caninum antibodies were 3.2%, 4.6%, and 6.4% in the NAT, IFAT and ELISA, respectively. Using the IFAT as the gold standard, the NAT and the ELISA agreement was considered weak (k=0.28) and strong (k=0.75), respectively. When the IFAT performance was used for comparison purposes, the ELISA showed 91.3% sensitivity and 97.7%, specificity with a PPV of 65.2% and a NPV of 99.6%; The NAT presented sensitivity of 26.1% and specificity of 97.9% with a PPV of 37.5% and a NPV of 96.5%. Accordingly, the IFAT should remain the assay of choice for studies about N. caninum infection in goats in individual serum samples. A combination of serological assays with high sensitivity and specificity is recommended in serosurveys of caprine neosporosis.(AU)

Objetivou-se avaliar a resposta sorológica de caprinos infectados com Neospora caninum mediante o estudo da performance e concordância de três técnicas sorológicas (RIFI, NAT e ELISA). O painel de soros testes foi composto por 500 amostras de caprinos e ainda 60 soros classificados como de referência. Todos os soros de referência e de campo foram testados por ELISA, NAT e RIFI. Nos soros de campo, as soroprevalências de anticorpos anti-N. caninum foram de 3,2% no NAT, 4,6% na RIFI e 6,4% no ELISA. Utilizando a RIFI como técnica de referência, a concordância de NAT e ELISA foi considerada fraca (k=0,28) e substancial (k=0,75), respectivamente. Ainda utilizando a RIFI como comparação, foram obtidos valores de sensibilidade de 91,3% e 97,7% de especificidade no ELISA, e valores preditivos positivo de 65,2% e negativo de 99,6%; NAT apresentou resultados de sensibilidade de 26,1% e de especificidade de 97,9% com valores preditivos positivo de 37,5% e negativo de 96,5%. Com base nos resultados deste trabalho, sugerimos que a RIFI permaneça como técnica de escolha no estudo da neosporose caprina em amostras individuais, resguardando as recomendações e pontos de corte adotados neste estudo. Indicamos a associação de técnicas sorológicas de alta sensibilidade e especificidade.(AU)

Giant tortoise genomes provide insights into longevity and age-related disease.

Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George-the iconic last member of Chelonoidis abingdonii-and the Aldabra giant tortoise (Aldabrachelys gigantea). Comparison of these genomes with those of related species, using both unsupervised and supervised analyses, led us to detect lineage-specific variants affecting DNA repair genes, inflammatory mediators and genes related to cancer development. Our study also hints at specific evolutionary strategies linked to increased lifespan, and expands our understanding of the genomic determinants of ageing. These new genome sequences also provide important resources to help the efforts for restoration of giant tortoise populations.

Genome Sequencing and Analysis Methods in Chronic Lymphocytic Leukemia.

The genomic sequencing of chronic lymphocytic leukemia (CLL) samples has provided exciting new venues for the understanding and treatment of this prevalent disease. This feat is possible thanks to high-throughput sequencing methods, such as Illumina sequencing. The interpretation of these data sources requires not only appropriate software and hardware, but also understanding the biology and technology behind the sequencing process. Here, we provide a primer to understand each step in the analysis of point mutations from whole-genome or whole-exome sequencing experiments of tumor and normal samples.

nVenn: generalized, quasi-proportional Venn and Euler diagrams.

Motivation: Venn and Euler diagrams are extensively used for the visualization of relationships between experiments and datasets. However, representing more than three datasets while keeping the proportions of each region is still not feasible with existing tools. Results: We present an algorithm to render all the regions of a generalized n-dimensional Venn diagram, while keeping the area of each region approximately proportional to the number of elements included. In addition, missing regions in Euler diagrams lead to simplified representations. The algorithm generates an n-dimensional Venn diagram and inserts circles of given areas in each region. Then, the diagram is rearranged with a dynamic, self-correcting simulation in which each set border is contracted until it contacts the circles inside. This algorithm is implemented in a C++ tool (nVenn) with or without a web interface. The web interface also provides the ability to analyze the regions of the diagram. Availability and implementation: The source code and pre-compiled binaries of nVenn are available at https://github.com/vqf/nVenn. A web interface for up to six sets can be accessed at http://degradome.uniovi.es/cgi-bin/nVenn/nvenn.cgi. Supplementary information: Supplementary data are available at Bioinformatics online.

The Novel Evolution of the Sperm Whale Genome.

The sperm whale, made famous by Moby Dick, is one of the most fascinating of all ocean-dwelling species given their unique life history, novel physiological adaptations to hunting squid at extreme ocean depths, and their position as one of the earliest branching toothed whales (Odontoceti). We assembled the sperm whale (Physeter macrocephalus) genome and resequenced individuals from multiple ocean basins to identify new candidate genes for adaptation to an aquatic environment and infer demographic history. Genes crucial for skin integrity appeared to be particularly important in both the sperm whale and other cetaceans. We also find sperm whales experienced a steep population decline during the early Pleistocene epoch. These genomic data add new comparative insight into the evolution of whales.

Incidence and vertical transmission rate of Neospora caninum in sheep.

The infection by Neospora caninum in sheep can lead to abortion and the birth of weak and debilitated lambs. The aim of this study was to assess the incidence of natural infection by Neospora caninum and the vertical transmission rate among sheep. A flock of 50 sheep was monitored for serum antibody titres against N. caninum and seroconversion over a period of six months using an indirect ELISA technique. The offspring of the herd was also investigated regarding anti-N. caninum antibodies to determine the vertical transmission rate through the indirect immunofluorescence technique. The initial and final prevalences of infection by N. caninum were 26.0% (13/50) and 72.0% (36/50), respectively, and the incidence of infection by N. caninum in the present study was 62.2% (23/37). The vertical transmission rate found was 15.4% (2/13). A high incidence of infection by N. caninum in sheep was observed, and this is the first report assessing the incidence of N. caninum among naturally infected sheep.

The Degradome database: expanding roles of mammalian proteases in life and disease.

Since the definition of the degradome as the complete repertoire of proteases in a given organism, the combined effort of numerous laboratories has greatly expanded our knowledge of its roles in biology and pathology. Once the genomic sequences of several important model organisms were made available, we presented the Degradome database containing the curated sets of known protease genes in human, chimpanzee, mouse and rat. Here, we describe the updated Degradome database, featuring 81 new protease genes and 7 new protease families. Notably, in this short time span, the number of known hereditary diseases caused by mutations in protease genes has increased from 77 to 119. This increase reflects the growing interest on the roles of the degradome in multiple diseases, including cancer and ageing. Finally, we have leveraged the widespread adoption of new webtools to provide interactive graphic views that show information about proteases in the global context of the degradome. The Degradome database can be accessed through its web interface at http://degradome.uniovi.es.

Occurrence of Toxoplasma gondii DNA in sheep naturally infected and slaughtered in abattoirs in Pernambuco, Brazil / Ocorrência de DNA de Toxoplasma gondii em ovelhas naturalmente infectadas e abatidas em matadouros de Pernambuco

The aim of the present study was to assess the occurrence of antibodies to Toxoplasma gondii and to detect genomic DNA of the parasite in the reproductive organs, fetuses and fetal membranes of sheep in slaughterhouses in the state of Pernambuco, Brazil. The Indirect Immunofluorescence technique (IFA) was used for screening. The Polymerase Chain Reaction (PCR) was used to detect DNA of T. gondii in the animals that were positive in the serology. In the serology, 13/50 samples were positive and genomic DNA of T. gondii was detected in one uterus, tube, ovary, placenta and fetus (heart, brain and umbilical cord) sample from a sheep that was positive in the serology. The present study provides evidence of the occurrence of T. gondii DNA in the organs of the reproductive system, placenta and fetus of a naturally infected sheep.

Objetivou-se estudar a ocorrência de anticorpos contra Toxoplasma gondii e detectar o DNA genômico do parasito em órgãos reprodutivos, fetos e anexos fetais de ovelhas em matadouros no estado de Pernambuco, Brasil. Foram coletadas amostras de soro sanguíneo, útero, trompas e ovários, além de fetos e placentas. Para a triagem utilizou-se a técnica de Imunofluorescência Indireta (RIFI) e para a detecção do DNA de T. gondii empregou-se a Reação em Cadeia da Polimerase (PCR) nos animais positivos na sorologia e em todos os fetos e anexos fetais. Na sorologia, 13/50 amostras foram positivas e o DNA genômico de T. gondii foi detectado em uma amostra de útero, trompa, ovário, placenta e feto (coração, cérebro e cordão umbilical) de uma ovelha positiva na sorologia. A identidade molecular dos produtos amplificados foi confirmada por sequenciamento. Neste estudo comprova-se a ocorrência do DNA de T. gondii em órgãos do sistema reprodutivo, placenta e feto de ovelha naturalmente infectada.

Mycoplasma agalactiae in semen and milk of goat from Pernambuco state, Brazil / Mycoplasma agalactiae em sêmen e leite de caprinos do estado de Pernambuco

In goat and sheep flocks, mycoplasmosis is a disease that may cause severe economical losses associated with polyarthritis, mastitis, agalactia, conjunctivitis, pneumonia and reproductive failure. The latter may involve repeat breeding, granular vulvovaginitis, infertility and abortions. The aim of the present study was to assess the occurrence of Mycoplasma agalactiae (Ma) in semen and milk samples from naturally infected goat in the semiarid region from Pernambuco State, Northeast from Brazil. Thirty-nine semen samples and 81 milk samples were submitted to DNA extraction using a commercially available kit and following the manufacturer's instructions. The polymerase chain reaction (PCR) was then performed in accordance with protocols described in the literature. The results of the present study revealed the presence of Ma in the DNA of 17.9% (7/39) of the semen samples and 3.7% (3/81) of the milk samples. The results obtained in the present study confirm the elimination of the DNA of Ma in the semen and milk samples. The presence of this agent in goat flocks is considered very risky in terms of reproductive disorders and contagious agalactia outbreaks in the Northeast region of Brazil.

Em caprinos e ovinos as micoplasmoses causam sérias perdas econômicas associadas com poliartrites, mastites, agalaxia, conjuntivite, pneumonias e falhas reprodutivas. Esta última pode envolver repetição de cio, vulvovaginite granular, infertilidade e abortos. O objetivo desse estudo foi verificar a ocorrência de Mycoplasma agalactiae (Ma) em sêmen e leite de caprinos naturalmente infectados procedentes de regiões semiáridas do Estado de Pernambuco, Nordeste do Brasil. Foram usadas 39 amostras de sêmen e 81 de leite, as quais foram submetidas à extração do DNA genômico usando um kit comercial, seguindo as instruções do fabricante. A reação da PCR foi realizada de acordo com protocolo previamente descrito na literatura. Os resultados revelaram a presença de DNA de Ma nas amostras de sêmen com uma frequência de 17,9% (7/39) e no leite a frequência encontrada foi de 3,7% (3/81). Os resultados obtidos no presente estudo confirmam a eliminação de DNA de Ma nas amostras de sêmen e leite analisadas. A presença deste agente nos rebanhos caprinos pode ser considerada um risco para doenças reprodutivas e surtos de agalaxia contagiosa na região Nordeste do Brasil.