Biochemistry and Microbiology at UVic
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Biochemistry and Microbiology at UVic
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Biochemistry and Microbiology - University of Victoria

 

This topic will highlight some of the research and events going on in our Department.

 

You can find our web page at: 

www.uvic.ca/science/biochem


You can find our Facebookpage at:

www.facebook.com/UVic.Biochem.Micro/

 

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Microbe reveals ‘major new branch’ of evolutionary tree, Halifax researchers say

Microbe reveals ‘major new branch’ of evolutionary tree, Halifax researchers say | Biochemistry and Microbiology at UVic | Scoop.it
A dirt sample taken from a wilderness area outside Halifax contained one-celled microbial organisms that no one even knew existed
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Launch of global effort to read genetic code of all complex life on earth | Wellcome Sanger Institute

Launch of global effort to read genetic code of all complex life on earth | Wellcome Sanger Institute | Biochemistry and Microbiology at UVic | Scoop.it
The Earth BioGenome Project (EBP), a global effort to sequence the genetic code, or genomes, of all 1.5 million known animal, plant, protozoan and fungal species on Earth, officially launched on 1 November) as key scientific partners and funders from around the glob
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Discovery and Preclinical Characterization of 5-[4,6-Bis({3-oxa-8-azabicyclo[3.2.1]octan-8-yl})-1,3,5-triazin-2-yl]-4-(difluoromethyl)pyridin-2-amine (PQR620), a Highly Potent and Selective mTORC1/...

Discovery and Preclinical Characterization of 5-[4,6-Bis({3-oxa-8-azabicyclo[3.2.1]octan-8-yl})-1,3,5-triazin-2-yl]-4-(difluoromethyl)pyridin-2-amine (PQR620), a Highly Potent and Selective mTORC1/... | Biochemistry and Microbiology at UVic | Scoop.it
Discovery and Preclinical Characterization of 5-[4,6-Bis({3-oxa-8-azabicyclo[3.2.1]octan-8-yl})-1,3,5-triazin-2-yl]-4-(difluoromethyl)pyridin-2-amine (PQR620), a Highly Potent and Selective mTORC1/2 Inhibitor for Cancer and Neurological Disorders
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600 free online courses you can take from universities worldwide —

600 free online courses you can take from universities worldwide — | Biochemistry and Microbiology at UVic | Scoop.it
If you haven’t heard, universities around the world are offering their courses online for free (or at least partially free).
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Targeted delivery of antisense oligonucleotides to pancreatic β-cells

Targeted delivery of antisense oligonucleotides to pancreatic β-cells | Biochemistry and Microbiology at UVic | Scoop.it
Antisense oligonucleotide (ASO) silencing of the expression of disease-associated genes is an attractive novel therapeutic approach, but treatments are limited by the ability to deliver ASOs to cells and tissues. Following systemic administration, ASOs preferentially accumulate in liver and kidney. Among the cell types refractory to ASO uptake is the pancreatic insulin-secreting β-cell. Here, we show that conjugation of ASOs to a ligand of the glucagon-like peptide-1 receptor (GLP1R) can productively deliver ASO cargo to pancreatic β-cells both in vitro and in vivo. Ligand-conjugated ASOs silenced target genes in pancreatic islets at doses that did not affect target gene expression in liver or other tissues, indicating enhanced tissue and cell type specificity. This finding has potential to broaden the use of ASO technology, opening up novel therapeutic opportunities, and presents an innovative approach for targeted delivery of ASOs to additional cell types.
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Protecting Pax6 3′ UTR from MicroRNA-7 Partially Restores PAX6 in Islets from an Aniridia Mouse Model - ScienceDirect

Protecting Pax6 3′ UTR from MicroRNA-7 Partially Restores PAX6 in Islets from an Aniridia Mouse Model - ScienceDirect | Biochemistry and Microbiology at UVic | Scoop.it
Aniridia is a rare congenital syndrome that is associated with reduced visual acuity and progressive loss of vision. Aniridia patients may also develo…
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Nice work Kevin, showing target protectors restoring Pax6 expression in deficient islets!
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Widespread position-specific conservation of synonymous rare codons within coding sequences

Widespread position-specific conservation of synonymous rare codons within coding sequences | Biochemistry and Microbiology at UVic | Scoop.it
Author summary Proteins are long linear polymers that must fold into complex three-dimensional shapes in order to carry out their cellular functions. Every protein is synthesized by the ribosome, which decodes each trinucleotide codon in an mRNA coding sequence in order to select the amino acid residue that will occupy each position in the protein sequence. Most amino acids can be encoded by more than one codon, but these synonymous codons are not used with equal frequency. Rare codons are associated with generally slower rates for protein synthesis, and for this reason have traditionally been considered mildly deleterious for efficient protein production. However, because synonymous codon substitutions do not change the sequence of the encoded protein, the majority view is that they merely reflect genomic ‘background noise’. To the contrary, here we show that the positions of many synonymous rare codons are conserved in mRNA sequences that encode structurally similar proteins from a diverse range of organisms. These results suggest that rare codons have a functional role related to the production of functional proteins, potentially to regulate the rate of protein synthesis and the earliest steps of protein folding, while synthesis is still underway.
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Ten simple rules for developing good reading habits during graduate school and beyond

Ten simple rules for developing good reading habits during graduate school and beyond | Biochemistry and Microbiology at UVic | Scoop.it
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Gene editing restores dystrophin expression in a canine model of Duchenne muscular dystrophy

Gene editing restores dystrophin expression in a canine model of Duchenne muscular dystrophy | Biochemistry and Microbiology at UVic | Scoop.it
Mutations in the gene encoding dystrophin, a protein that maintains muscle integrity and function, cause Duchenne muscular dystrophy (DMD). The deltaE50-MD dog model of DMD harbors a mutation corresponding to a mutational “hot spot” in the human DMD gene. We used adeno-associated viruses to deliver CRISPR gene editing components to four dogs and examined dystrophin protein expression 6 weeks after intramuscular delivery (n=2) or 8 weeks after systemic delivery (n=2). After systemic delivery in skeletal muscle, dystrophin was restored to levels ranging from 3 to 90% of normal, depending on muscle type. In cardiac muscle, dystrophin levels in the dog receiving the highest dose reached 92% of normal. The treated dogs also showed improved muscle histology. These large animal data support the concept that, with further development, gene editing approaches may prove clinically useful for the treatment of DMD.
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University of Waterloo's Donna Strickland wins Nobel physics prize for laser research | CTV News

A Canadian professor ended a 55-year drought for female physicists when she was awarded the prestigious Nobel Prize for physics on Tuesday, becoming only the third woman to ever win it.
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Nobel Prize in Medicine awarded to James Allison and Tasuku Honjo

Nobel Prize in Medicine awarded to James Allison and Tasuku Honjo | Biochemistry and Microbiology at UVic | Scoop.it
American James Allison and Japan's Tasuku Honjo have won the 2018 Nobel Prize in Medicine for a pioneering approach to cancer treatment.
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Programmable protein circuits in living cells

Programmable protein circuits in living cells | Biochemistry and Microbiology at UVic | Scoop.it
Synthetic genetic and biological regulatory circuits can enable logic functions to form the basis of biological computing; synthetic biology can also be used to control cell behaviors (see the Perspective by Glass and Alon). Andrews et al. used mathematical models and computer algorithms to combine standardized components and build programmable genetic sequential logic circuits. Such circuits can perform regulatory functions much like the biological checkpoint circuits of living cells. Circuits composed of interacting proteins could be used to bypass gene regulation, interfacing directly with cellular pathways without genome modification. Gao et al. engineered proteases that regulate one another, respond to diverse inputs that include oncogene activation, process signals, and conditionally activate responses such as those leading to cell death. This platform should facilitate development of “smart” therapeutic circuits for future biomedical applications.

Science , this issue p. [eaap8987][1], p. [1252][2]; see also p. [1199][3]

Synthetic protein-level circuits could enable engineering of powerful new cellular behaviors. Rational protein circuit design would be facilitated by a composable protein-protein regulation system in which individual protein components can regulate one another to create a variety of different circuit architectures. In this study, we show that engineered viral proteases can function as composable protein components, which can together implement a broad variety of circuit-level functions in mammalian cells. In this system, termed CHOMP (circuits of hacked orthogonal modular proteases), input proteases dock with and cleave target proteases to inhibit their function. These components can be connected to generate regulatory cascades, binary logic gates, and dynamic analog signal-processing functions. To demonstrate the utility of this system, we rationally designed a circuit that induces cell death in response to upstream activators of the Ras oncogene. Because CHOMP circuits can perform complex functions yet be encoded as single transcripts and delivered without genomic integration, they offer a scalable platform to facilitate protein circuit engineering for biotechnological applications.

[1]: /lookup/doi/10.1126/science.aap8987
[2]: /lookup/doi/10.1126/science.aat5062
[3]: /lookup/volpage/361/1199?iss=6408
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TeSS (Training eSupport System)

TeSS (Training eSupport System) | Biochemistry and Microbiology at UVic | Scoop.it
Browse, discover and organise Life science training resources aggregated from ELIXIR nodes and other providers
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Of pale ales and proteins - University of Victoria

Of pale ales and proteins - University of Victoria | Biochemistry and Microbiology at UVic | Scoop.it
Through research conducted during a co-op work term, biochemistry undergraduate James Saville was able to help a Duncan brewery optimize the recipe for their IPA--determining the best hop type and timing to maximize flavour, while spending less money on the expensive ingredient.
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Nice story about one of our Coop students James Saville and his work experiences. Congratulations James!
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GenPipes: an open-source framework for distributed and scalable genomic analyses

With the decreasing cost of sequencing and the rapid developments in genomics technologies and protocols, the need for validated bioinformatics software that enables efficient large-scale data processing is growing. Here we present GenPipes, a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for High Performance Computing clusters and the cloud. GenPipes already implements 12 validated and scalable pipelines for various genomics applications, including RNA-Seq, ChIP-Seq, DNA-Seq, Methyl-Seq, Hi-C, capture Hi-C, metagenomics and PacBio long read assembly. The software is available under a GPLv3 open source license and is continuously updated to follow recent advances in genomics and bioinformatics. The framework has been already configured on several servers and a docker image is also available to facilitate additional installations. In summary, GenPipes offers genomic researchers a simple method to analyze different types of data, customizable to their needs and resources, as well as the flexibility to create their own workflows.
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Transcription factor dimerization activates the p300 acetyltransferase

Transcription factor dimerization activates the p300 acetyltransferase | Biochemistry and Microbiology at UVic | Scoop.it
The activation of the histone acetyltransferase p300 depends on the activation and oligomerization status of transcription factor ligands.
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really cool paper showing how TF dimerization leads to activation through trans acetylation
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Pathogen Perspectives: The Anti Vax Epidemic - Good Parents Getting Gamed . Episode 1. Autism and Vaccines

Pathogen Perspectives: The Anti Vax Epidemic - Good Parents Getting Gamed . Episode 1. Autism and Vaccines | Biochemistry and Microbiology at UVic | Scoop.it
I believe all parents want to do what's best for their kids. I really do. And even I, a virologist, had to deal with concerns abou
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Cranberry harvest creates sea of red in Richmond | CTV Vancouver News

Photos from Kelly Williams and Andrew Chin show an October cranberry harvest in Richmond.
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UVic #2 in Maclean's rankings - University of Victoria

UVic has maintained its second-place ranking among the top Canadian comprehensive universities in the 2019 Maclean's magazine rankings.
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Canada commits $558M for science discovery research | CBC News

Canada commits $558M for science discovery research | CBC News | Biochemistry and Microbiology at UVic | Scoop.it
Canada has announced the Natural Sciences and Engineering Research Council of Canada will be committing $558 million for discovery grants this year.
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good news for NSERC
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10 surprises from sequencing 25 new species –

10 surprises from sequencing 25 new species – | Biochemistry and Microbiology at UVic | Scoop.it
Sequencing human genomes is now routine at the Sanger Institute. Bacteria, yeast, worms, malaria, and other pathogens are also all regularly sequenced in their thousands. Our people are pretty well known for sequencing the human genome, but we’ve also contributed to the first sequencing of many others including the mouse, rat, zebrafish, pig and gorilla too.

The 25 genomes project is an entirely different beast. It’s posing some new, and frankly very odd, challenges. The diversity of the new species means we’ve had a steep learning curve. Here’s a peek at some of the weird and wonderful things we’ve discovered so far:

Via Cindy
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Nobel Prize in Chemistry Is Awarded to 3 Scientists for Using Evolution in Design of Molecules - The New York Times

Nobel Prize in Chemistry Is Awarded to 3 Scientists for Using Evolution in Design of Molecules - The New York Times | Biochemistry and Microbiology at UVic | Scoop.it
Frances H. Arnold of the U.S. received half the prize, while her compatriot George P. Smith and Gregory P. Winter of Britain shared the other half.
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Suppression of insulin feedback enhances the efficacy of PI3K inhibitors

Suppression of insulin feedback enhances the efficacy of PI3K inhibitors | Biochemistry and Microbiology at UVic | Scoop.it
Glucose–insulin feedback can reactivate PI3K in tumours treated with PI3K inhibitors, reducing therapeutic efficacy, but this effect can be reduced by using drugs or diet to suppress the insulin response.
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A sugar rush of DNA methylation

A sugar rush of DNA methylation | Biochemistry and Microbiology at UVic | Scoop.it
A new study in Nature identifies a molecular axis linking diabetes to cancer, whereby AMPK, which is inhibited in high glucose conditions, regulates the stability of TET2 DNA demethylase, thereby impacting DNA methylation and gene expression.
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Pathologists meet their match in tumour-spotting algorithm : Research Highlights

Pathologists meet their match in tumour-spotting algorithm : Research Highlights | Biochemistry and Microbiology at UVic | Scoop.it
Deep-learning model picks out two kinds of lung cancer by studying images of tissue.
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