Calit2’s Program in Nano-science, Nano-engineering, and Nano-medicine

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06.04.11 Invited Talk Review of Nano-cancer Project Title: Calit2’s Program in Nano-science, Nano-engineering, and Nano-medicine La Jolla, CA

Technology Business

Calit2’s Program in Nano-science, Nano-engineering, and Nano-medicine Invited Talk Review of Nano-cancer project April 11, 2006 Dr. Larry Smarr Director, California Institute for Telecommunications and Information Technologies Harry E. Gruber Professor, Dept. of Computer Science and Engineering Jacobs School of Engineering, UCSD

Two New Calit2 Buildings Will Provide Major New Laboratories to Their Campuses ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],UC Irvine www.calit2.net UC San Diego Richard C. Atkinson Hall Dedication Oct. 28, 2005

Calit2 Materials and Devices Laboratory: “Nano3” – Science, Engineering, Medicine Nano3 Facility CALIT2.UCSD 10,000 sq. feet State-of-the-Art Materials and Devices Laboratory Source: Bernd Fruhberger, Calit2

The First Shared Clean Room Facilities on the UCSD Campus ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Nano3 Facility CALIT2.UCSD Campus Recharge Facility – Operated by Professional Staff Limited Operation – April 2006 Fully Functional – September 2006 Source: Bernd Fruhberger, Calit2

Calit2 Nanomedicine Lab Facilities ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Source: Bernd Fruhberger, Calit2

NanoMedicine Lab: Current Projects ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Source: Bernd Fruhberger, Calit2

NanoMedicine Lab – Interface with Cleanrooms Raith50 E-beam Writing System In operation (March 2006) Example: Nanolithography Nanodimensional grid in PMMA resist e-beam Nanolithography is Used for Rapid Prototyping of Antibody Arrays to Optimize Size, Shape, and Spacing of the Antibody Coated Gold or TiO 2 Dots Source: Bernd Fruhberger, Calit2

NanoMedicine Lab – Interface with Materials Characterization Labs Nano3 Facility CALIT2.UCSD MultiMode Scanning Probe Microscope w/Nanoscope IV Controller In operation (March 2006) Example: Scanning Probe Microscopy Atomic Force Microscopy image of organometallic thin film (Cu-Phthalocyanine) ,[object Object],[object Object],Source: Bernd Fruhberger, Calit2

Adapting High Resolution Displays with Live Instrument Feeds to Cancer Research Source: David Lee, NCMIR, UCSD Calit2 OptIPuter Project

PI Larry Smarr Announced January 17, 2006

Marine Genome Sequencing Project Measuring the Genetic Diversity of Ocean Microbes CAMERA will include All Sorcerer II Metagenomic Data

Calit2’s Direct Access Core Architecture Will Create Next Generation Metagenomics Server Source: Phil Papadopoulos, SDSC, Calit2 + Web Services User Environment CAMERA Complex Flat File Server Farm TeraGrid Backplane (10000s of CPUs) W E B PORTAL Web Local Cluster Direct Access Lambda Cnxns Dedicated Compute Farm (1000 CPUs) Data- Base Farm 10 GigE Fabric

First Implementation of the CAMERA Complex Compute Database & Storage

This document describes the development of a diagnostic device to rapidly identify bacterial strains responsible for sepsis. Key points: - The device uses droplet digital PCR to amplify and quantify bacterial DNA signatures from patient blood samples. High resolution melt analysis is then used to generate strain-specific melt curves of the 16S rRNA gene. - A microfluidic chip is engineered to generate stable droplets and thermal gradients allowing acquisition of melt curves. Machine learning algorithms classify melt curves to identify bacterial strains. - The goal is to identify bacteria in patient blood samples within clinically relevant timeframes, shortening diagnostic time from 12 days to 3-4 hours for targeted antibiotic treatment. Results show a stable thermal gradient is achieved within the chip

Poster ESHG

Kirsten van Nimwegen

- The study provides a cost analysis of three next-generation sequencing applications: targeted gene panels (TGP), whole exome sequencing (WES), and whole genome sequencing (WGS). It finds per-sample costs of €333 for TGP, €792 for WES, and €1,669 for WGS. - Costs are mainly driven by consumables such as sequencing and sample preparation. The estimated $1,000 genome has not been achieved, though it may be approached under best-case assumptions of long-term, efficient use of equipment and considerable cost reductions. - The choice of sequencing approach in clinical practice should consider both costs and clinical effectiveness, not just costs alone.

Calit2-Living in the Future

Larry Smarr

The document summarizes activities at the California Institute for Telecommunications and Information Technology (Calit2). It describes two new buildings that provide laboratories and support over 1000 researchers working on projects including nanotechnology, virtual reality, and digital cinema. It highlights several projects Calit2 is involved in, such as prototyping extremely high bandwidth applications, borderless collaboration between global research centers, and wireless networks for disaster response.

Metagenomics Over Lambdas: Update on the CAMERA Project

Larry Smarr

Next-generation sequencing (NGS) and its application to breast cancer research is discussed. NGS allows for comprehensive profiling of microRNA (miRNA) expression, which can provide insights into tumorigenesis pathways. The document outlines the NGS process, including template preparation, sequencing/imaging, and complex data analysis using statistical methods and software. Key applications are identifying miRNA involvement in cancer driver genes and exploring miRNA expression patterns to discover potential diagnostic or prognostic biomarkers for breast cancer subtypes.

Viral Metagenomics (CABBIO 20150629 Buenos Aires)

bedutilh

This is a one-hour lecture about metagenomics, focusing on discovery of viruses and unknown sequence elements. It is part of a one-day workshop about metagenome assembly of crAssphage, a bacteriophage virus found in human gut. The hands-on workflow can be found at http://tbb.bio.uu.nl/dutilh/CABBIO/ and should be doable in one afternoon with supervision. There is also an iPython notebook about this here: https://github.com/linsalrob/CrAPy

Application of Whole Genome Sequencing in the infectious disease’ in vitro di...

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This document discusses the application of whole genome sequencing in infectious disease diagnostics. It provides examples of how genome sequencing has been used to identify bacterial species, detect antibiotic resistance genes, and study outbreaks. The document also discusses challenges around regulatory approval of genomic tests, data sharing policies, and database management. Overall, it argues that whole genome sequencing is a valuable tool but that standards must be developed to ensure high quality data.

2017 09-07 Global Virome Project

The End Within

The Global Virome Project is a 10-year global effort to identify and characterize naturally occurring viruses with pandemic potential. It aims to build a comprehensive database of the estimated 1.6 million viral species circulating in mammals and waterfowl. This will allow researchers to develop broad-spectrum countermeasures against future zoonotic viruses and identify high-risk viruses to prevent spillover. The project will sample viruses in 108 sites across 63 countries over 10 years, prioritizing countries and species based on viral discovery rates and zoonotic risk prediction models. The goal is to capture over 85% of the global mammalian virome to transform virology and pandemic preparedness.

Metagenomics sequencing

cdgenomics525

Sophie F. summer Poster Final

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This study demonstrates the utility of using Next Generation Sequencing (NGS) technology and DNA analysis to identify and analyze closely related insect species and populations. The researchers sequenced DNA from two mitochondrial genes and a nuclear gene from individuals of two closely related fly species, Bactrocera philippinensis and B. occipitalis. They obtained overlapping sequences from these genes that could be assembled into full gene sequences. Their goal is to ultimately sequence the entire genome of multiple individuals to better characterize populations and species through comparative genomic analysis. DNA-based methods provide advantages over traditional taxonomy by requiring less material and being consistent across life stages.

Image Based Transcriptomics: An Overview

Fredrick (Trace) Henry, PhD

This document discusses various approaches for spatial genomics including direct measurement techniques like RNA fluorescence in situ hybridization (RNA FISH) and multiplexed protein localization, as well as in situ sequencing methods like seqFISH, MERFISH, and fluorescent in situ sequencing (FISSEQ). It also covers computational inference methods that impute spatial gene expression patterns from bulk tissue sequencing data, and the commercial "Spatial Transcriptomics" approach that involves barcoding tissue sections on a slide and sequencing the resulting cDNA library.

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Plant Phenotyping, a new scientific discipline to quantify plant traits

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Parks kmer metagenomics

dparks1134

K-mers in metagenomics K-mers play a critical role in the exploration of metagenomic data. They have been widely used to assign taxonomic attributions to the short genomic fragments characteristic of shotgun (metagenomic) sequencing. These approaches provide an assembly-free method for profiling microbial communities, and have helped elucidate the factors driving microbial community composition across biogeochemical gradients. Advances in sequencing technology are now making it cost-effective to sequence microbial communities at sufficient depths to allow for the assembly of high-quality contigs. This has made it possible to adopt k-mer based approaches to enable reliable binning of contigs originating from a single microbial population within a community. In this session, I will present both an overview of how k-mers can be used to assign taxonomic attributions to short metagenomic reads, and discuss how these approaches have advanced to a point where population genomes can be recovered en masse from even complex microbial communities.

Errors and Limitaions of Next Generation Sequencing

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This document discusses some key errors and limitations of next-generation sequencing (NGS). It notes that while NGS has significantly reduced costs and improved throughput, it also has some drawbacks compared to previous sequencing technologies. Specifically, it outlines issues related to low quality bases, PCR errors during amplification, and high error rates that can make rare mutations difficult to detect. Limitations include short read lengths that hamper assembly of repetitive regions, contamination risks, incomplete representation of repeats, difficulties assembling segmental duplications and genes fragmented across scaffolds. The document emphasizes the need for validation of genome assemblies and development of hybrid approaches combining long and short reads to overcome these challenges.

Machine Learning

Indian Institute of Science Education and Research

The presentation includes preliminary information about the big data mainly metagenomic data and discussions related to the hurdles in analyzing using conventional approaches. In the later part, brief introduction about machine learning approaches using biological example for each. In the last, work done with special focus on implementation of a machine learning approach Random Forest for the functional annotation and taxonomic classification of metagenomic data.

Biochemistry: A pivotal aspects in forensic science

VanshikaVarshney5

In the above presentation, you will know the importance of biochemistry in forensic science. Biochemistry is not all about the chemicals, it is about your life, your environment. Basically, it belongs to you. in this presentation, you can know about the biochemical techniques which are majority used in forensic science and various research occurs in the field of forensic science which is related with biochemistry.

Gerbig, Christoph: Can we see a covid-19 impact in atmospheric GHGs? A diagno...

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CAMERA Presentation at KNAW ICoMM Colloquium May 2008

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Applications of microarray

sana shakeel

Microarrays can be used for gene expression profiling, comparative genomics, disease diagnosis, drug discovery, and toxicological research. It allows researchers to examine thousands of genes simultaneously and see changes in gene expression patterns. Microarrays have applications in areas like cancer classification, pharmacogenomics, and toxicogenomics. While a powerful tool, microarrays also have limitations like being expensive to create and requiring time to develop.

Genome metagenomics sequencing – next generation technology

CD Genomics-- Biotechnology Services Company

Spatial transcriptome profiling by MERFISH reveals sub-cellular RNA compartme...

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The document summarizes research using Multiplexed Error-robust FISH (MERFISH), a technique that uses error-correcting barcodes to enable simultaneous spatial transcriptomic profiling of thousands of genes. MERFISH allows identification of subcellular localization of RNAs and spatial organization of single cell clusters. It also enables derivation of "RNA velocity" to predict the future transcriptional state of cells by discriminating between nuclear and cytoplasmic mRNA. When combined with computational analyses, MERFISH provides high-resolution insights into gene expression patterns within tissues at both the cellular and subcellular levels.

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Parks kmer metagenomics

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7. NanoMedicine Lab – Interface with Cleanrooms Raith50 E-beam Writing System In operation (March 2006) Example: Nanolithography Nanodimensional grid in PMMA resist e-beam Nanolithography is Used for Rapid Prototyping of Antibody Arrays to Optimize Size, Shape, and Spacing of the Antibody Coated Gold or TiO 2 Dots Source: Bernd Fruhberger, Calit2

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10. PI Larry Smarr Announced January 17, 2006

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