Cientistas da Universidade de Rice desenvolvem método para acelerar a identificação de bactérias potencialmente perigosas. Com base em pequenho trechos de DNA e métodos informáticos cientistas desenvolveram formas de reduzir o tempo de idenitificar bactérias potencialmente perigosas.
Scientists at the University of Utah, ARUP Laboratories, and IDbyDNA, Inc., have developed ultra-fast, meta-genomics analysis software called Taxonomer that dramatically improves the accuracy and speed of pathogen detection
Samuel Viana's insight:
O sonho tornado possível graças à metagenómica: determinar computacionalmente o agente infeccioso de uma doença, tudo graças a uma aplicação chamada Taxonomer desenvolvida por cientistas da Universidade de Utah em parceria com laboratórios privados.
As células tronco (em inglês, "stem cells") são muito importantes em biologia do desenvolvimento e na medicina restituitiva uma vez que são capazes de se diferenciar em qualquer tipo de célula no organismo. Num futuro não muito distante, seria possível produzir qualquer tipo de órgão em laboratório o que evitaria o eterno problema de encontrar um dador compatível aquando dos transplantes. Este portal pretende ser uma porta de entrada para muitos estudos na área, integrando diversas bases de dados provenientes de estudos em feitos em humanos e ratos.
he new system will be superior to competing semiconductor-based sequencing systems with a raw error rate of less than one percent, data quality comparable to that of a HiSeq XTM Sequencing System. With output of approximately 1.2G per run, the platform will be ideal for numerous markets including academic research, oncology, infectious disease, inherited disease, and reproductive health.
Samuel Viana's insight:
A Illumina, líder mundial dos equipamentos de sequenciação lançou o seu novo sequenciador, ao preço mais acessível até agora: cinquenta mil euros. Destinado a laboratórios de média dimensão como análises clínicas: continuamos no caminho para a sequenciação individual e a medicina personalizada - a Illumina está aí para tornar realidade esse objectivo. É desta vez que iremos ter um sequnciador mais perto de todos nós ?
Bajo las condiciones extremas de los glaciares de la Antártida habitan unas bacterias capaces de sintetizar en su interior nanopartículas fluorescentes que podrían ser utilizadas para marcar células tumorales y rastrear la metástasis de diferentes tipos de cáncer.
Samuel Viana's insight:
Investigadores chilenos encontraram bactérias na Antárctida capazes de produzir pigmentos para identificar células cancerosas.
Single Nucleotide Polymorphisms (SNPs) are widely used molecular markers, and their use has increased massively since the inception of Next Generation Sequencing (NGS) technologies, which allow detection of large numbers of SNPs at low cost. However, both NGS data and their analysis are error-prone, which can lead to the generation of false positive (FP) SNPs. We explored the relationship between FP SNPs and seven factors involved in mapping-based variant calling — quality of the reference sequence, read length, choice of mapper and variant caller, mapping stringency and filtering of SNPs by read mapping quality and read depth. This resulted in 576 possible factor level combinations. We used error- and variant-free simulated reads to ensure that every SNP found was indeed a false positive.
Samuel Viana's insight:
Num trabalho liderado por um português, este estudo permite determinar até que ponto as actuais pipelines de análise e assemblagem pós-sequenciação pode gerar falsos SNPs.
A bad workman blames his tools. A bad life scientist blames bioinformatics. OK, so that’s a little unfair but so is the level of criticism levelled at bioinformatics by people who should know better. If you are a bioinformatician, it is inevitable that you will run up against the question of whether you ever do “real” science.
Samuel Viana's insight:
An opinion in which the wet-lab biologists should collaborate with their 'dry-lab' colleagues just like the bioinformaticians.
In rare instances, DNA is known to have jumped from one species to another. If a parasite’s DNA jumps to its host’s genome, it could leave evidence of that parasitic interaction that could be found millions of years later – a DNA ‘fossil’ of sorts. An international research team led from Uppsala University has discovered a new type of so-called transposable element that occurred in the genomes of certain birds and nematodes.
Trechos de DNA chamados transposões saltaram do DNA de nemátodes como a lombriga para os seus hospedeiros na altura. Encontram-se certos transposões provenientes de nemátodes no genoma de mamíferos mas essa "infecção" apenas se deu mais recentemente. O que parece provar que os nemátodes apenas foram capazes de parasitar mamíferos mais recentemente do que as aves.
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
Samuel Viana's insight:
Continuam a serem inventariadas novas espécies de procariotas. Este artigo faz uma revisão do ponto actual de "recenseamento" actual e avança com previsões relativamente à possibilidade de ainda serem encontradas novas espécies.
Um projecto que está recebendo fundos no Kickstartet prometer revolucionar o trabalho de laboratório. Em vez de confiar nos humanos para transferir pequenos quantidades que requerem extrema precisão usando micropipetas, esse trabalho pode ser confiado a um braço robótico baseado em tecnologias de código aberto. Digamos que é uma espécie de 'Bimby' que em vez de servir para cozinhas serve para laboratórios.
The Sequence Read Archive (SRA), NCBI’s largest growing repository of molecular data, archives raw sequencing data and alignment information from high-throughput sequencing platforms, including Roche 454 GS Systems®, Illumina’s Genome Analyzer®, and Complete Genomics® systems.
Researchers commonly use SRA data to make discoveries via comparison of data sets. Data sets can be compared through the SRA web interface, but if you want to integrate these downloads and file conversions into an already existing pipeline, or you simply prefer using a command-line interface, we recommend using the SRA Toolkit.
You’re not completely human, at least when it comes to the genetic material inside your cells. You—and everyone else—may harbor as many as 145 genes that have jumped from bacteria, other single-celled organisms, and viruses and made themselves at home in the human genome. That’s the conclusion of a new study, which provides some of the broadest evidence yet that, throughout evolutionary history, genes from other branches of life have become part of animal cells.
“This means that the tree of life isn’t the stereotypical tree with perfectly branching lineages,” says biologist Alastair Crisp of the University of Cambridge in the United Kingdom, an author of the new paper. “In reality, it’s more like one of those Amazonian strangler figs where the roots are all tangled and crossing back across each other.”
Scientists knew that horizontal gene transfer—the movement of genetic information between organisms other than parent-to-offspring inheritance—is commonplace in bacteria and simple eukaryotes. The process lets the organisms quickly share an antibiotic-resistance set of genes to adapt to an antibiotic, for instance. But whether genes have been horizontally transferred into higher organisms—like primates—has been disputed. Like in bacteria, it’s been proposed that animal cells could integrate foreign genetic material that’s introduced as small fragments of DNA or carried into cells by viruses. But proving that a bit of DNA in the human genome originally came from another organism is tricky.
Crisp and his colleagues analyzed the genome sequences of 40 different animal species, ranging from fruit flies and roundworms to zebrafish, gorillas, and humans. For each gene in the genomes, the scientists searched existing databases to find close matches—both among other animals and among nonanimals, including plants, fungi, bacteria, and viruses. When an animal’s gene more closely matched a gene from a nonanimal than any other animals, the researchers took a closer look, using computational methods to determine whether the initial database search had missed something.
In all, the researchers pinpointed hundreds of genes that appeared to have been transferred from bacteria, archaea, fungi, other microorganisms, and plants to animals, they report online today in Genome Biology. In the case of humans, they found 145 genes that seemed to have jumped from simpler organisms, including 17 that had been reported in the past as possible horizontal gene transfers.
“I think what this shows it that horizontal gene transfer is not just confined to microorganisms but has played a role in the evolution of many animals,” Crisp says, “perhaps even all animals.
The paper doesn’t give any hints as to how the genes—which now play established roles in metabolism, immune responses, and basic biochemistry—may have been transferred or the exact timeline of the jumps, he says. That will take more work.
A Microsoft está às necessidades futura de privacidade nos acessos aos dados bioinformáticos. Cada vez vão existir laboratórios, hospitais que vão trabalhar com dados obtidos de sequenciação e é necessário protegê-los como quaisquer outros dados clínicos.
Mystery Boy Brandon Keesing was incorrectly diagnosed with a degenerative muscular disease until revolutionary genetic sequencing gave him life-changing news.
Originally thought that Keesing has a mitochondrial disease, doctors had been wrong all along. Revolutionary advances in genetic sequencing proved he did not have mitochondrial disease at all. "In recent years the capacity to read the genetic code of every single gene — all 20,000 of them in the human body — has reached a point where it is now efficient, accurate, cost-effective to be able to do this," he says.
The new technique is called "next generation sequencing" — and where previously it took weeks or months to analyse the code of a single gene, today laboratory computers can decode all 20,000 genes in one go.
Almost immediately Westmead Children's Hospital researchers could pinpoint which one of Brandon's genes had a mutation. Professor Christodoulou illustrates how the technique works on a chart. "So here in the unaffected individual we have an 'A'. Here in the affected individual we have a 'G'. And that's precisely where the mistake is," he says.
Doctors using next generation sequencing discovered in fact that Brandon had congenital myasthenia — a different genetic disease which also affects the muscles. But although incurable, it is not usually fatal and can be treated with medication.
"The name of the gene that we found the mistakes in is called COLQ, and it has a completely different role," Professor Christodoulou says. "It has nothing to do with mitochondrial energy production. "What it is involved in is co-ordinating the communication of nerve cells with the muscle, so that the muscle, when it receives an impulse from a nerve cell, it contracts and relaxes appropriately.
"So the problem with the COLQ mistakes is that this process couldn't be co-ordinated properly. And that's what actually led to his progressive problems."
Finding that one gene in 20,000 has transformed Brandon's life. A simple drug quickly restored some of his muscle strength. As quickly as he had deteriorated as a toddler, he suddenly began making huge strides.
"We noticed it straight away. By the end of that week he got up off that bed and he walked," she says, wiping away tears. "That was unreal. I'll never forget that day. I was so happy for him and ... I just knew from that he was going to grow, he was going to enjoy his life that much more than what he had before. And he has."
Professor Christodoulou says it was a very gratifying outcome for doctors.
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