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Tag: UCSF
Is Genome Editing the Next Step in Immunotherapy Innovation? Experts Think So
Just a few years ago, chimeric antigen receptor (CAR) T-cell therapy was brand new, offering a novel solution for populations of patients who were short on options and typically faced grim prognoses. But this weekend at the American Society of Hematology Annual Meeting and Exposition, a presentation saw experts in…
Postdoctoral Position in Genomics – Tcheandjieu Lab, US
Postdoctoral Position in Genomics: The Tcheandjieu Lab at the Gladstone Institutes/UCSF is inviting applications for a Postdoctoral position in Genomics. This role offers an exciting opportunity to work on diverse biobanks, utilizing genomic and multi-omic approaches to enhance our understanding of cardiovascular diseases. Located in the heart of Silicon Valley,…
Laura Zitella Discusses the Growing Arsenal of Bispecific Antibodies in DLBCL
In May 2023, the FDA granted accelerated approval to epcoritamab-bysp (Epkinly) for the treatment of adult patients with relapsed/refractory (R/R) diffuse large B-cell lymphoma (DLBCL), including DLBCL arising from indolent lymphoma, and high-grade B-cell lymphoma (HGBL), following 2 or more lines of systemic therapies. Shortly thereafter, in June 2023, the…
The Vitals / Laura Zitella Discusses the Growing Arsenal of Bispecific Antibodies in DLBCL
In May 2023, the FDA granted accelerated approval to epcoritamab-bysp (Epkinly) for the treatment of adult patients with relapsed/refractory (R/R) DLBCL, including DLBCL arising from indolent lymphoma, and high-grade B-cell lymphoma (HGBL), following 2 or more lines of systemic therapies. Shortly thereafter, in June 2023, the FDA granted accelerated approval…
Cancer Shredder Utilizes CRISPR, Targets Glioblastoma
Scientists at the Gladstone Institutes have published a paper in Cell Reports that describes a CRISPR-based technique for treating primary glioblastoma, a common and aggressive form of brain cancer. The paper, titled “Targeting the non-coding genome and temozolomide signature enables CRISPR-mediated glioma oncolysis,” describes the technique, which the researchers have…
CRISPR-powered ‘cancer shredding’ technique opens new possibility for treating most common and deadly brain cancer
Credit: Cell Reports (2023). DOI: 10.1016/j.celrep.2023.113339 The gene-editing technology CRISPR shows early promise as a therapeutic strategy for the aggressive and difficult-to-treat brain cancer known as primary glioblastoma, according to findings of a new study from Gladstone Institutes. The work is published in the journal Cell Reports. Using a novel…
CRISPR-Driven Method Offers New Hope for Treating Deadly Brain Cancer
SAN FRANCISCO—November 27, 2023—The gene-editing technology CRISPR shows early promise as a therapeutic strategy for the aggressive and difficult-to-treat brain cancer known as primary glioblastoma, according to findings of a new study from Gladstone Institutes. Using a novel technique they’ve dubbed “cancer shredding,” the researchers programmed CRISPR to zero-in on…
Oxford Nanopore and Day Zero Diagnostics Partner to Develop a New Class of Bloodstream Infection Diagnostics
OXFORD, England and BOSTON, Nov. 14, 2023 /PRNewswire/ — Oxford Nanopore, the company delivering a new generation of nanopore-based molecular sensing technology, and Day Zero Diagnostics (DZD), an infectious disease diagnostics company harnessing the power of whole-genome sequencing and AI to combat the rise of antibiotic-resistant infections, today announced a collaboration…
Filter out doublet and Clustering
Dear all, fellows, I used DoubletFinder from Chris github.com/chris-mcginnis-ucsf/DoubletFinder to filter out doublet cells for each sample individually and used standard seurat pipeline to normalize the data as using following functions because I cannot use SCTransform with seurat 5 as DoubletFinder did not upgrade to match with Seurat5 yet. NormalizeData(object…
[slurm-users] –partition requests ignored in scripts
“Bunis, Dan” <Daniel…@ucsf.edu> writes: > My colleagues and I have noticed that our compute cluster seems to > ignore ‘–partition’ requests when we give them as ‘#SBATCH > –partition=<partition_name>’ inside of our scripts, but it respects > them when given in-line within our sbatch calls as ‘sbatch > –partition=<partition_name> script.sh’. Based on some googling,…
Genome Browser Chimera Interface
Download Chimera Configure for automatic launch in web browsers UCSF Chimera is an interactive molecular modeling system that supports 3-D visualization of protein structures.It runs as an application on the user’s computer. The UCSC Genome Browser provides links to launch Chimera as a helper application for proteins with solved structures…
The Singh Lab – Junior/Assistant/Associate/Full Specialist in Bioinformatics or Computational Biology job in San Francisco, California at University of California – San Francisco
The Singh Lab – Junior/Assistant/Associate/Full Specialist in Bioinformatics or Computational Biology SCHOOL OF MEDICINE – Department of Anatomy Description The lab of Dr. Param Singh at UCSF (www.singhlabucsf.org) is looking for a Junior/Assistant/Associate/Full Specialist with expertise in bioinformatics or computational biology to join our team and contribute to new and…
The Hidden Mechanisms Behind Rapid Tumor Evolution: AR Amplification on Extrachromosomal DNA I Prostate Cancer
Read the Full Video Transcript Andrea Miyahira: Hi everyone, I’m Andrea Miyahira at the Prostate Cancer Foundation. Presenting today is Dr. Scott Dehm, a professor at the University of Minnesota on his recent paper, “Co-evolution of AR gene copy number and structural complexity in endocrine therapy resistant prostate cancer,” published…
Bioinformatics Programmer job in San Francisco, California at University of California – San Francisco
Bioinformatics Programmer Job Summary The laboratory of Matt State at the University of California, San Francisco is seeking a creative, independent, and team-oriented bioinformatics programmer to join our group. The State lab focuses on defining the etiology of childhood neuropsychiatric disorders, with particular interest in autism spectrum disorder, schizophrenia, OCD,…
Mechanisms of neurotransmitter transport and drug inhibition in human VMAT2
Kandel, E. R., Koester, J. D., Mack, S. H. & Siegelbaum, S. A. Principles of Neural Science 6th edn (McGraw Hill Professional, 2021). Ng, J., Papandreou, A., Heales, S. J. & Kurian, M. A. Monoamine neurotransmitter disorders—clinical advances and future perspectives. Nat. Rev. Neurol. 11, 567–584 (2015). Article CAS PubMed …
Bioinformatics Scientist/Research Software Engineer – UOD1104 at University of Dundee
We are seeking an individual with strong software development skills and a passion for research to join the Jalview (www.jalview.org) development team and help advance the state-of-the-art in biomolecular alignment visualisation and analysis. Jalview is a mature platform launched nearly a million times a year by students and researchers worldwide…
Complete Genomics demonstrates technical and commercial momentum in the sequencing market through new customers, partnerships and collaborations less than one year after launching in the U.S.
WASHINGTON, Oct. 31, 2023 /PRNewswire/ — Complete Genomics, a pioneering genomic sequencing company, announced today at the American Society of Human Genetics (ASHG) Annual Meeting, Nov. 1-5, in Washington details on the commercial and technical momentum it has demonstrated in the last 10 months since launching in the United States…
An Interview with Fyodor Urnov
By Jonathan D. Grinstein, PhD Fyodor Urnov, PhD, is a pioneer in the field of genome editing and one of the scientists most invested in expanding the availability and utility of CRISPR-based therapies to the broadest possible population. He envisions a world in which genome editing can treat the nearly…
Job:Data Scientist / Bioinformatician / Statistician at University of California San Francisco (UCSF)
Location: UCSF Mission Bay (Joan and Sanford I. Weill Neurosciences Building) Department: Psychiatry and Behavioral Sciences Hours: Monday – Friday, 9:00 am – 5:00 pm. Hybrid option available. JOB OVERVIEW: The laboratory of Matt State at the University of California San Francisco (UCSF) focuses in defining the etiology of childhood…
Structure of human TRPM8 channel
Reagents and chemicals pFastBac Dual His6 MBP N10 TEV LIC cloning vector (5 C) was purchased from Addgene (Addgene plasmid no. 30123; www.addgene.org/30123). All restriction enzymes, the pFastBac1 vector, and DH10Bac cells were purchased from Thermo Fisher Scientific. Sf9 cells were purchased from ATCC. Q5® High-Fidelity DNA Polymerase, the Monarch® DNA…
Tauopathy Transcriptomes Tell Tantalizing Tales
18 Oct 2023 Fibrillar tau accumulates in several neurodegenerative diseases. Are the same molecular mechanisms responsible, or does each tauopathy follow distinct pathways? Some of both, according to a preprint posted to bioRxiv on September 30. Researchers led by Jessica Rexach and Daniel Geschwind at the University of California, Los…
Breakthrough drug helps children with new-onset type 1 diabetes: Phase 3 trial
Credit: CC0 Public Domain Children who were recently diagnosed with type 1 diabetes need less supplemental insulin to keep their blood sugar in a healthy range if they use the immunotherapy drug teplizumab, a new study reports. Worldwide, about 8.4 million people have type 1 diabetes, an autoimmune disorder in…
Global CRISPR/CAS 9 Technology Market Size to Reach USD
Vancouver, Oct. 18, 2023 (GLOBE NEWSWIRE) — The global CRISPR/CAS 9 technology market size is expected to reach USD 13,072.73 Million at a steady revenue CAGR of 20.4% in 2032, according to latest analysis by Emergen Research. Steady CRISPR/CAS 9 market revenue growth is due to ability for researchers and…
University of California, San Francisco hiring BIOINFORMATICS PROGR 3 in San Francisco, California, United States
Diabetes Center Full Time 74609BR Job Summary Uses skills as a seasoned, experienced bioinformatics programming professional with a broad understanding of computational algorithms and systems; identifies and resolves a wide range of issues / software bugs. Demonstrates good judgment in selecting methods and techniques for obtaining solutions. Operates independentl y….
With a boost from beta, alpha thalassemia gene therapies blossom
If red blood cells are the ferryboats of the bloodstream, hemoglobin is the ferryman. With its two alpha globin and two beta globin subunits working in harmony, hemoglobin helps shuttle oxygen into cells and remove carbon dioxide waste products from them. But even one small defect — such as a…
When nature turns deadly: A look at Abrin
What is abrin? In certain parts of Asia and Australia, grows a flowering plant of the bean family Fabaceae, known as Abrus precatorius, also more commonly as jequirity bean or rosary pea [1]. It’s a delicate, perennial climber but extremely invasive and classified as a weed in several countries. However, what…
University of California, San Francisco hiring Bioinformatician in San Francisco, CA
MED-ZSFG-EXPMFull Time74386BRJob SummaryThe Rutishauser Lab, in the UCSF Division of Experimental Medicine, at Zuckerberg San Francisco General Hospital, is hiring an experienced Bioinformatics programming professional with a broad understanding of computational algorithms and systems to work on projects that utilize single cell RNA/TCR sequencing, epigenetic profiling, and multi-omics approaches to…
Templates from alpha fold predictions – Features and Functionality
DarioSB September 20, 2023, 10:45am #1 Dear all,is it possible to use an AlphaFold predicted structure as templates for picking?BestDario Hi Dario, You could use the molmap feature in ChimeraX to generate a volume of the alphafold structure (e.g. to 6 angstrom), save as an mrc file, import to cryosparc…
Zuckerberg’s philanthropy project plans AI system for life sciences research
Priscilla Chan (R) and her husband Mark Zuckerberg announce the Chan Zuckerberg Initiative to “cure, prevent or manage all disease” by the end of the century during a news conference at UCSF Mission Bay in San Francisco, California, U.S. September 21, 2016. REUTERS/Beck Diefenbach/File Photo Acquire Licensing Rights Sept 19…
How we measure success matters when evaluating HIV therapies
The human immunodeficiency virus (HIV) is a retrovirus that integrates into the human genome. This intact, integrated genome is referred to as a provirus and represents a latent or dormant form of the virus that can reactivate to make infectious virus. Antiretroviral therapy (ART) is extremely successful at blocking HIV…
Researchers identify a rare cause of male infertility and discover a potential cure
In a recent study published in the eBioMedicine journal, researchers investigated the genetic underpinning of asthenozoospermia, the leading cause of male fertility. Study: Deficiency in AK9 causes asthenozoospermia and male infertility by destabilising sperm nucleotide homeostasis. Image Credit: WHITE MARKERS/Shutterstock.com Their multidisciplinary examinations were able to identify adenylate kinase 9 (AK9), an enzyme…
Malignant phyllodes tumour with lymph node metastasis: a diagnostic conundrum resolved by next generation DNA sequencing
doi: 10.1111/his.15046. Online ahead of print. Affiliations Expand Affiliation 1 Department of Pathology, University of California San Francisco (UCSF), San Francisco, CA, USA. Item in Clipboard Christopher J Schwartz et al. Histopathology. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1111/his.15046. Online ahead of print. Affiliation 1 Department of…
MAPS PBC Announces Publication of Results from Confirmatory Phase 3 “MAPP2” Trial of MDMA-Assisted Therapy for PTSD in Nature Medicine
Study met primary and secondary endpoints confirming first Phase 3 study findings MAPP2 population reflects PTSD demographic with approximately half of study participants identifying as racially or ethnically diverse Company on track for NDA filing in 2023 SAN JOSE, Calif. , Sept. 14, 2023 /PRNewswire/ — MAPS Public Benefit Corporation…
Olorofim Aspergillus Infection Study – Full Text View
University of California Davis Health System Sacramento, California, United States, 95817 Contact: Thompson, George Thompson, George, Dr. 916-734-3815 grthompson@ucdavis.edu UCSF Helen Diller Medical Center at Parnassus Heights San Francisco, California, United States, 94143 Contact:…
Bioinformatics Programmer in San Francisco, CA for University of California San Francisco
Details Posted: 30-Aug-23 Location: San Francisco, California Type: Full-time Salary: Open The UCSF’s Helen Diller Family Comprehensive Cancer Center is seeking a person to serve as a Bioinformatics Programmer in the Computational Biology and Informatics (CBI) Core. The primary task for this person will be to analyze high-throughput data including…
Associate Specialist – Immunogenetics and Transplantation Laboratory (ITL) job with University of California San Francisco
Associate Specialist – Immunogenetics and Transplantation Laboratory (ITL) Department of Surgery University of California, San Francisco An Associate Specialist position is available in the Immunogenetics and Transplantation Laboratory (ITL, itl.ucsf.edu/ at the University of California, San Francisco (UCSF). This position will be working with Dr. Rajalingam and his team on…
Direct observation of the conformational states of PIEZO1
No statistical methods were used to predetermine sample size. The experiments were not randomized and investigators were not blinded to allocation during experiments and outcome assessment. Expression constructs The coding sequence of mouse PIEZO1 (E2JF22, UniprotKB entry) was codon-optimized, synthesized and cloned into the pcDNA3.1 plasmid. An amber stop codon…
A 15-year-old childhood cancer survivor becomes a cancer researcher
Robert McCabe of Anchorage, Alaska, is a 15-year-old avid bowler, a fan of baseball and basketball, and a rising high school sophomore who hopes to be an engineer one day. He is also a pediatric cancer survivor, and most recently, a pediatric cancer researcher. This summer, he helped to sequence…
A childhood cancer survivor becomes a cancer researcher
Robert McCabe of Anchorage, Alaska, is a 15-year-old avid bowler, a fan of baseball and basketball, and a rising high school sophomore who hopes to be an engineer one day. He is also a pediatric cancer survivor, and most recently, a pediatric cancer researcher. This summer, he helped to sequence…
Structural conservation of antibiotic interaction with ribosomes
Yonath, A. Antibiotics targeting ribosomes: resistance, selectivity, synergism and cellular regulation. Annu. Rev. Biochem. 74, 649–679 (2005). Article CAS PubMed Google Scholar Sohmen, D., Harms, J. M., Schlunzen, F. & Wilson, D. N. SnapShot: antibiotic inhibition of protein synthesis I. Cell 138, 1248 e1241 (2009). Article Google Scholar Wilson, D….
Batiraxcept May Not Improve Survival in Platinum-Resistant Ovarian Cancer
Batiraxcept did not significantly improve rates of survival without disease progression in patients with platinum-resistant ovarian cancer, according to high-level findings from a phase 3 trial. Batiraxcept did not significantly improve rates of survival without disease progression in patients with platinum-resistant ovarian cancer, according to high-level findings from a phase…
Aravive Announces Top-Line Results from Phase 3 AXLerate-OC Study of Batiraxcept in Platinum-Resistant Ovarian Cancer
Aravive, Inc. Trial did not meet primary endpoint of progression-free survival Cash at the end of Q2 of approximately $18M (unaudited) is expected to be sufficient to fund operations into early Q4 2023 HOUSTON, Aug. 02, 2023 (GLOBE NEWSWIRE) — Aravive, Inc. (Nasdaq: ARAV, “the Company”), a late clinical-stage oncology…
Aravive Announces Top-Line Results from Phase 3 AXLerate-OC
Trial did not meet primary endpoint of progression-free survival Cash at the end of Q2 of approximately $18M (unaudited) is expected to be sufficient to fund operations into early Q4 2023 HOUSTON, Aug. 02, 2023 (GLOBE NEWSWIRE) — Aravive, Inc. (Nasdaq: ARAV, “the Company”), a late clinical-stage oncology company developing…
Highlights from the 2023 Single-Cell and AI in Medicine Symposium
By Randall C. Willis with review and comments from Fabrice Chouraqui, Laurens Kruidenier, Chad Nusbaum, Diogo Camacho August 2, 2023 | “Technology and computation are revolutionizing the way we are creating and developing new drugs,” Cellarity CEO Fabrice Chouraqui announced to open the Second Single-Cell and AI in Medicine Symposium…
CRISPR Market is Expected to Reach $7.1 Billion | MarketsandMarkets.
/EIN News/ — Chicago, July 28, 2023 (GLOBE NEWSWIRE) — In the near future, the CRISPR industry is poised for transformative breakthroughs that will revolutionize medicine, agriculture, and biotechnology. With continuous advancements in CRISPR gene-editing technology, its application will become more widespread and accessible, unlocking unprecedented opportunities for precision medicine…
If You Never Got Sick From Covid, Thank Your Genes
Comment on this storyComment Even as Covid has faded into the background for most of the public, our curiosity about the virus’s idiosyncrasies hasn’t waned. Why does one member of a household suffer a hacking cough but another not even a sniffle? Why does long Covid afflict some and not…
cGMP CRISPR sgRNA and Non-viral DNA Payload Manufacturing Capacity Doubled
GenScript Biotech Corporation, the world’s leading provider of life-science research tools and services, has expanded its cGMP manufacturing capacity for sgRNA and non-viral DNA payloads with a new, state-of-the-art facility in Zhenjiang, Jiangsu, China. This latest expansion provides biopharma companies and gene and cell therapeutic discovery startups a fast-turnaround source…
Third Alzheimer’s Drug Can Slow Cognitive Decline by 35%
The new Alzheimer’s drug known as Donanemab was better at removing amyloid plaques compared to Aduhelm and Leqembi in the phase 3 trial. In an anticipated breakthrough, the Food and Drug Administration (FDA) is on the verge of approving a third new Alzheimer’s drug, marking a significant advancement in the…
Abivax announces the appointment of June Lee, M.D. and Troy Ignelzi as Members of the Board of Directors
EQS-News: ABIVAX / Key word(s): Personnel Abivax announces the appointment of June Lee, M.D. and Troy Ignelzi as Members of the Board of Directors 11.07.2023 / 18:00 CET/CESTThe issuer is solely responsible for the content of this announcement. Abivax announces the appointment of June Lee, M.D. and Troy Ignelzi as…
Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein
Hirotsu, Y. et al. SARS-CoV-2 Omicron sublineage BA.2 replaces BA.1.1: genomic surveillance in Japan from September 2021 to March 2022. J. Infect. 85, 174–211 (2022). Article CAS PubMed PubMed Central Google Scholar Lyngse, F. P. et al. Household transmission of SARS-CoV-2 Omicron variant of concern subvariants BA.1 and BA.2 in…
Was the Fruquintinib Trial for Metastatic CRC a Win?
Last month, The Lancet published the results of a phase 3 trial that assessed the use of a highly selective, potent oral vascular endothelial growth factor receptor (VEGFR) inhibitor for patients with refractory metastatic colorectal cancer (CRC). The trial, dubbed FRESCO-2, found that use of fruquintinib “resulted in a significant…
Can Pre-Op MRI Staging Help Predict Prostate Cancer Recurrence after a Prostatectomy?
Emerging research suggests that pre-operative magnetic resonance imaging (MRI) findings may have comparable predictive efficacy to post-prostatectomy pathologic staging in assessing the risk of biochemical recurrence (BCR) of prostate cancer (PCa). For the retrospective study, recently published in the American Journal of Roentgenology, researchers assessed findings of extraprostatic extension (EPE)…
GenScript Doubles cGMP sgRNA and Non-Viral DNA Payload Manufacturing Capacity
“As a researcher in the gene and cell therapy field, I have experienced firsthand the challenges of finding GMP-grade materials for editing cells. In our lab, we have been leveraging non-viral CRISPR and payload materials to efficiently reprogram various types of immune cells, due to multiple advantages non-viral materials possess,…
06.07.2023 | Press Release | GenScript doubles production capacity for cGMP sgRNA and non-viral DNA payload
Additional 400,000 square feet at GenScript’s Zhenjiang cGMP facility, China provides biopharmaceutical companies and gene/cell therapy research startups with fast access to synthetic CRISPR sgRNA and non-viral single and double-stranded DNA payloads PISCATAWAY, NJ, July 6, 2023 /PRNewswire/ — GenScript Biotech Corporation, the global leader in life science research tools…
Regulation of the macrolide resistance ABC-F translation factor MsrD
Crowe-McAuliffe, C. et al. Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR. PNAS 115, 8978–8983 (2018). Article ADS CAS PubMed PubMed Central Google Scholar Crowe-McAuliffe, C. et al. Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens. Nat. Commun….
Multiple Sclerosis GWAS Points to Role for Central Nervous System in Disease Severity, Progression
NEW YORK – An international team led by investigators at the University of California San Francisco and the University of Cambridge has uncovered genetic risk variants with ties to multiple sclerosis (MS) severity. Unlike variants associated with MS susceptibility, which have been linked to the immune system, the new variants…
Module to RMSD two proteins with Python?
A UCSF Chimera option: (Taken from a more complicated script I wrote for use with pychimera here: script, pychimera) NB, pychimera takes a little more involved installation compared to pymol, but I really like it. The code below should work inside chimera’s python interpreter though I believe with no extra…
SandboxAQ launches new division to boost drug development
After several years of stealth development, SandboxAQ has announced its bio-pharma molecular simulation division, AQBioSim, and some of its customers. The division is helping bio-pharma and research institutions achieve breakthroughs in treatments for cancer, Alzheimer’s, Parkinson’s, and other conditions. The company is currently working with biopharma companies and university research…
Delve Bio Launches with $35M Series A to Advance its Metagenomic Sequencing Platform for Infectious Disease Diagnosis
Credit: KATERYNA KON/SCIENCE PHOTO LIBRARY/Getty Images Sporting an all-star team of scientific founders that includes Charles Chiu, MD, PhD, Joe DeRisi, PhD, Michael Wilson, MD, Pardis Sabeti, MD, DPhil, and Matthew Meyerson, MD, PhD, Delve Bio announced its launch via a $35 million Series A financing that will help commercialize…
Delve Bio Launches to Commercialize its Metagenomic Sequencing Platform for Infectious Disease Diagnosis
Platform developed at the UCSF Center for Next-Gen Precision Diagnostics $35M Series A financing led by Perceptive Xontogeny Venture Fund II Funds will enable broader access to mNGS testing and the development of a pipeline of next-generation tests. SAN FRANCISCO, June 20, 2023–(BUSINESS WIRE)–Delve Bio, a pioneer in metagenomic next-generation…
Human-Specific Features Found With CRISPR Screening on Stem Cells
NEW YORK – A team led by investigators at the University of California, San Francisco has combined loss-of-function screening and comparative genomics to tease out genetic dependencies that distinguish human stem cells from those in nonhuman primates. “Our findings demonstrate that human stem cells have evolved a distinct reliance on…
Infectious disease NGS test developer Delve Bio closes $35M Series A financing
Delve Bio on Tuesday announced that it has raised $35 million in a Series A financing to support the development of a metagenomic sequencing (mNGS) platform for infectious disease diagnostic testing. The company’s mNGS-based testing platform uses technology developed at the University of California San Francisco (UCSF) Center for Next-Gen…
Delve Bio Raises $35M in Series A Financing to Develop Metagenomic Sequencing Diagnostic Test
NEW YORK – Delve Bio, a new startup with a star-studded team of scientific cofounders, said on Tuesday that it has launched with $35 million in Series A financing. The San Francisco-based firm will use the funding, led by Perceptive Advisors and joined by Section 32 and GV, to commercialize…
Nurix Therapeutics Presents Data from Studies of Its Targeted Protein Degraders in B Cell Malignancies and Initiates Expansion of NX-2127 Phase 1b Trial in Diffuse Large B Cell Lymphoma and Mantle Cell Lymphoma Indications
Nurix Therapeutics, Inc. Initiation of NX-2127 Phase 1b expansion cohort in patients with diffuse large B cell lymphoma (DLBCL) was informed by a rapid and sustained complete response; Phase 1b expansion cohort also initiated in patients with mantle cell lymphoma (MCL) Clinical biomarker data from Phase 1a trial of NX-5948…
Alternative Z-genome biosynthesis pathway shows evolutionary progression from Archaea to phage
Wyatt, G. R. & Cohen, S. S. A new pyrimidine base from bacteriophage nucleic acids. Nature 170, 1072–1073 (1952). Article CAS PubMed Google Scholar Kallen, R. G., Simon, M. & Marmur, J. The new occurrence of a new pyrimidine base replacing thymine in a bacteriophage DNA:5-hydroxymethyl uracil. J. Mol. Biol….
Whole-genome sequencing rule-out of suspected hospital-onset Rhizopus outbreaks
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Structural analysis of mitochondrial rRNA gene variants identified in patients with deafness
Introduction Aminoglycoside antibiotics (AGs) are some of the most commonly prescribed antibacterials, despite their well-known capacity to cause toxic side effects to the kidneys and inner ear (Huth et al., 2011). Although their use in the industrialized world is usually limited to severe infections, they remain very popular in the…
PFS Improvement Seen With Capivasertib/Fulvestrant in HR+/HER2- Breast Cancer
Hope S. Rugo, MD, FASCO, director of Breast Oncology and Clinical Trials Education and professor of medicine in the Division of Hematology and Oncology at the University of California San Francisco (UCSF) Helen Diller Family Comprehensive Cancer Center, discusses the methods, design, and key findings from the phase 3 CAPItello-291…
How do I calculate differential expression for RNA-seq values with the “limma” package and the “ebayes” function?
How do I calculate differential expression for RNA-seq values with the “limma” package and the “ebayes” function? 0 So for context, I have a set of TPM values (which I converted to log2(TPM+1) for multiple genes for different samples, and I need to calculate the differential expression for RNA-seq values….
Dr Kelley on the Need for Additional Second-line Therapies in Cholangiocarcinoma
R. Kate (Katie) Kelley, MD, professor, Clinical Medicine, the Department of Medicine, Hematology and Oncology, the University of California, San Francisco (UCSF), affiliated faculty member, the Cancer Immunotherapy Program, UCSF, discusses unmet needs and treatment challenges within the current standard-of-care for patients with cholangiocarcinoma. Treatment advancements with the addition of…
Nuclear export of pre-60S particles through the nuclear pore complex
Hampoelz, B., Andres-Pons, A., Kastritis, P. & Beck, M. Structure and assembly of the nuclear pore complex. Annu. Rev. Biophys. 48, 515–536 (2019). Article CAS PubMed Google Scholar Lin, D. H. & Hoelz, A. The structure of the nuclear pore complex (an update). Annu. Rev. Biochem. 88, 725–783 (2019). Article …
Differential Binding of NLRP3 to non-oxidized and Ox-mtDNA mediates NLRP3 Inflammasome Activation
NLRP3 expression and purification Both wild-type NLRP3 and CAPS mutants were cloned in the mammalian expression vector pcDNA3.1HisB. Plasmid was purified using Qiagen Giga Prep up to 2000 ng/μl and subsequently transfected into Expi293 with Expifectamine per manufacturer instructions. Expression was allowed to proceed for 3 days before harvesting. Cells were…
Bioinformatics Programmer 1 in San Francisco, CA for University of California San Francisco
Details Posted: 25-May-23 Location: San Francisco, California Type: Full-time Salary: Open Categories: Staff/Administrative Note: This is 1 year contract that offers full benefits (including medical, dental, vision along with retirement & pension plans). Under direct supervision, will analyze clinical datasets (with an emphasis on structured and unstructured data in electronic…
Indee Labs Announces Exclusive Distribution Deal for With Sunko Instruments in China
Indee Labs announces an exclusive marketing and distribution deal with Sunko Instruments in China for Hydropore Research Use Only. BERKELEY, Calif., May 25, 2023 /PRNewswire/ — Indee Labs is a biotechnology company developing the Hydropore™ for non-viral intracellular delivery. Sunko Instruments is a professional distributor of scientific and laboratory instruments in…
Structural basis of amine odorant perception by a mammal olfactory receptor
Liberles, S. D. & Buck, L. B. A second class of chemosensory receptors in the olfactory epithelium. Nature 442, 645–650 (2006). Article ADS CAS PubMed Google Scholar Buck, L. & Axel, R. A novel multigene family may encode odorant receptors: a molecular basis for odor recognition. Cell 65, 175–187 (1991)….
Ongoing Investigation of RLY-4008 Highlights Evolving Treatment Options for FGFR2+ Cholangiocarcinoma
R. Kate (Katie) Kelley, MD The selective FGFR2 inhibitor RLY-4008 has generated higher response rates compared with historical data for prior pan-FGFR inhibitors in patients with cholangiocarcinoma harboring FGFR2 fusions or alterations who have not been exposed to a prior FGFR inhibitor, according to R. Kate (Katie) Kelley, MD. Data…
Bioconductor – arrayQuality
This package is for version 2.11 of Bioconductor; for the stable, up-to-date release version, see arrayQuality. Assessing array quality on spotted arrays Bioconductor version: 2.11 Functions for performing print-run and array level quality assessment. Author: Agnes Paquet and Jean Yee Hwa Yang <yeehwa at stat.berkeley.edu> Maintainer: Agnes Paquet…
[chimerax-users] How to describe methods
[chimerax-users] How to describe methods Tom Goddard goddard at sonic.net Tue May 9 14:25:27 PDT 2023 Hi Jim, As Elaine says, ChimeraX is using ColabFold, which is an optimized version of AlphaFold. So you should cite ColabFold (and AlphaFold and ChimeraX). Also your description of the template use is a…
ATP6V0C gene variants were identified in individuals with epilepsy, with or without developmental delay
Steering Committee on Quality Improvement and Management, Subcommittee on Febrile Seizures American Academy of Pediatrics. Febrile seizures clinical practice guideline for the long-term management of the child with simple febrile seizures. Pediatrics. 2008;121:1281–6. Camfield P, Camfield C. Febrile seizures and genetic epilepsy with febrile seizures plus (GEFS+). Epileptic Disord. 2015;17:124–33….
Research Technologist – Stem Cell Core – San Francisco
Category:ScienceLab/Area:Stem Cell Core Description: The Stem Cell Core is a state-of-the-art facility providing comprehensive pluripotent stem cell related services (standard and customized), training and consultations. Our focus includes reprogramming of somatic cells into iPSCs, differentiation of iPSCs into various cell lineages and genome editing in iPSCs. Our mission is to…
[chimerax-users] unifold
[chimerax-users] unifold Roger Leng rleng at ualberta.ca Fri May 5 10:58:35 PDT 2023 Many thanks, Elaine. I agree with your point. I find Alphafold is very close to “exactly” detecting two or three protein interactions. I used an example ” p53-MDM2 interaction” (structure and experiments) to test Alphafold Program. Also,…
Structural atlas of a human gut crassvirus
Shkoporov, A. N. & Hill, C. Bacteriophages of the human gut: the “known unknown” of the microbiome. Cell Host Microbe 25, 195–209 (2019). Article CAS PubMed Google Scholar Dutilh, B. E. et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat. Commun. 5, 4498…
PERSONALIS, INC. Management’s Discussion and Analysis of Financial Condition and Results of Operations. (form 10-Q)
The following discussion and analysis of our financial condition and results of operations should be read in conjunction with our condensed consolidated financial statements and the related notes and other financial information included elsewhere in this Quarterly Report on Form 10-Q and our Annual Report on Form 10-K for the…
Structural insights into the broad protection against H1 influenza viruses by a computationally optimized hemagglutinin vaccine
Centers for Disease Control and Prevention. Past Seasons Vaccine Effectiveness Estimates, www.cdc.gov/flu/vaccines-work/past-seasons-estimates.html (2022). Accessed 10 March 2022. Centers for Disease Control and Prevention. Pandemic influenza—past pandemics, www.cdc.gov/flu/pandemic-resources/basics/past-pandemics.html (2022). Accessed 10 March 2022. Erbelding, E. J. et al. A universal influenza vaccine: the strategic plan for the National Institute of Allergy…
IGI Wins $70 Million to Study Microbiome Engineering for Health, Climate Challenges
A research initiative co-led by Nobel laureate and CRISPR pioneer Jennifer Doudna, PhD, has been awarded $70 million to address health and climate challenges by combining the genome editing technology with genome-resolved metagenomics through the microbiome. TED’s Audacious Project, a collaborative funding effort designed to help solve grand-scale social impact…
Mirusviruses link herpesviruses to giant viruses
Vincent, F., Sheyn, U., Porat, Z., Schatz, D. & Vardi, A. Visualizing active viral infection reveals diverse cell fates in synchronized algal bloom demise. Proc. Natl Acad. Sci. USA 118, e2021586118 (2021). Article CAS PubMed PubMed Central Google Scholar Suttle, C. A. Marine viruses — major players in the global…
IGI’s ‘Audacious’ New Frontier for CRISPR: Editing Microbiomes for Climate and Health
The Audacious Project, an initiative housed at TED, encourages the world’s greatest changemakers to dream bigger. A new initiative led by Jennifer Doudna and Jill Banfield at the Innovative Genomics Institute and announced today at the TED Conference in Vancouver is a big dream that uses the smallest tools: microbes. The research initiative, “Engineering…
Aer Therapeutics raises $36M to tackle lung diseases
Aer Therapeutics, a joint University College Dublin (UCD) and University of California, San Francisco (UCSF) biopharmaceutical spin-out company developing novel inhaled treatments for muco-obstructive lung diseases, has announced the closing of a $36 million Series A financing round.Funding was received from a syndicate of premier life science industry investors, including…
Sensory specializations drive octopus and squid behaviour
van Giesen, L., Kilian, P. B., Allard, C. A. H. & Bellono, N. W. Molecular basis of chemotactile sensation in octopus. Cell 183, 594–604.e14 (2020). Article PubMed PubMed Central Google Scholar Noviello, C. M. et al. Structure and gating mechanism of the α7 nicotinic acetylcholine receptor. Cell 184, 2121–2134 (2021)….
New method for lower respiratory tract infection diagnosis in critically ill children
Lower respiratory tract infection (LRTI), which includes conditions such as pneumonia, has long been the leading cause of death from communicable agents and a leading cause of death in children worldwide. But despite its prevalence, LRTI is tricky for doctors to treat effectively because the current diagnostic approach often fails…
Cryo-EM structure of the transposon-associated TnpB enzyme
Sample preparation The genes encoding ISDra2 TnpB (TnpB from D. radiodurans ISDra2; residues 1 to 408) and the 247-nt ωRNA were synthesized by Eurofin Genomics and cloned into the modified pETDuet vector (Novagen). The N-terminally MBP-tagged TnpB and ωRNA were co-expressed in Escherichia coli Rosetta2 (DE3). The E. coli cells were cultured…
Intranasal trimeric sherpabody inhibits SARS-CoV-2 including recent immunoevasive Omicron subvariants
Research reported in this study complies with all relevant ethical regulations, and our animal study protocol has been approved by the Animal Experimental Board of Finland (license number ESAVI/28687/2020. Phage panning Sherpabody phage display library (size ~1011 cfu) was obtained from Next Biomed Therapies Oy. To develop sherpabodies specific for SARS-CoV-2…
Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS | BMC Bioinformatics
The Molecular Dynamics (MD) is one of the techniques incorporated into bioinformatics, specifically by structural bioinformatics. With that, it is possible to obtain kinetic and thermodynamic characteristics of biomolecular structures. For example, macromolecular stability, identification of allosteric sites, elucidation of mechanisms of enzymatic activity, molecular recognition and properties of complexes…
Senior Bioinformatics Programmer in San Francisco, CA for University of California San Francisco
Details Posted: 18-Mar-23 Location: San Francisco, California Type: Full-time Salary: Open The Krogan lab at the Quantitative Biosciences Institute (QBI) at UCSF is looking for a seasoned, experienced, analytical Senior Bioinformatics Programmer with a broad understanding of computational algorithms, systems and their application to omics and related systems-level biological data…
Multiancestry genomic and transcriptomic analysis of gastric cancer
Bray, F. et al. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 68, 394–424 (2018). Article PubMed Google Scholar Sung, H. et al. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers…
University of California, San Francisco hiring Bioinformatics Programmer II in San Francisco, California, United States
NeurologyFull Time65411BRJob SummaryA bright, hardworking individual with very strong communication and organizational skills is sought by the Hollenbach Lab in the Department of Neurology at the University of California at San Francisco, to serve as a staff bioinformatician providing support for ongoing research projects related to the immunogenetics of disease,…
Gene Synthesis Market is expected to surpass US$ 4.5 billion by 2033 | FMI Study
During the forecast period, the global Gene Synthesis Market is expected to grow at a steady rate of 19.2%. The market is expected to be worth US$ 779.4 million in 2023. The estimate is that by 2033, it will have surpassed US$ 4.5 billion. The current biotechnology system relies heavily…
Structural basis for bacterial energy extraction from atmospheric hydrogen
Statistics and reproducibility Huc purification and PAGE analysis Huc was purified from M. smegmatis cells on eight separate occasions throughout the course of the study. The yield of purified Huc (mg per litre of culture) varied by a factor of five between purifications. The relative abundance of the Huc oligomer…
Uncommon test solved a Mission medical mystery
A mystery disease wound its way through the Mission this January, wreaking runny noses and headaches upon its victims. But when doctors had patients test for likely diseases — Covid-19, flu, Respiratory Syncytial Virus (RSV) — results turned up negative for all three. What was…
Structure Predictions | IISER-Pune2_India – iGEM 2022
Summary What are we trying to achieve?We are trying to create accurate models of our final protein products. These models will help us verify that our sequences are correct, since we know of similar structures from literature, and these models will help us run many protein interactions simulations to infer…