Netravathi Krishnappa
University of California, Berkeley
H-index: 14
North America-United States
About Netravathi Krishnappa
Netravathi Krishnappa, With an exceptional h-index of 14 and a recent h-index of 13 (since 2020), a distinguished researcher at University of California, Berkeley, specializes in the field of Molecular Genetics, Biotechnology, Next Generation Sequencing, CRISPR technology.
His recent articles reflect a diverse array of research interests and contributions to the field:
Functional annotation of variants of the BRCA2 gene via locally haploid human pluripotent stem cells
Peptide-mediated delivery of CRISPR enzymes for the efficient editing of primary human lymphocytes
Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species
Species-and site-specific genome editing in complex bacterial communities
Targeted genome editing of bacteria within microbial communities
Transcriptome analysis of alternative splicing-coupled nonsense-mediated mRNA decay in human cells reveals broad regulatory potential
Blueprint for a pop-up SARS-CoV-2 testing lab
Efficient isolation of protoplasts from rice calli with pause points and its application in transient gene expression and genome editing assays
Netravathi Krishnappa Information
University | University of California, Berkeley |
---|---|
Position | ___ |
Citations(all) | 3539 |
Citations(since 2020) | 2593 |
Cited By | 1852 |
hIndex(all) | 14 |
hIndex(since 2020) | 13 |
i10Index(all) | 14 |
i10Index(since 2020) | 13 |
University Profile Page | University of California, Berkeley |
Netravathi Krishnappa Skills & Research Interests
Molecular Genetics
Biotechnology
Next Generation Sequencing
CRISPR technology
Top articles of Netravathi Krishnappa
Functional annotation of variants of the BRCA2 gene via locally haploid human pluripotent stem cells
Authors
Hanqin Li,Rebecca Bartke,Lei Zhao,Yogendra Verma,Anna Horacek,Alma Rechav Ben-Natan,Gabriella R Pangilinan,Netravathi Krishnappa,Rasmus Nielsen,Dirk Hockemeyer
Journal
Nature Biomedical Engineering
Published Date
2024/2
Mutations in the BRCA2 gene are associated with sporadic and familial cancer, cause genomic instability and sensitize cancer cells to inhibition by the poly(ADP-ribose) polymerase (PARP). Here we show that human pluripotent stem cells (hPSCs) with one copy of BRCA2 deleted can be used to annotate variants of this gene and to test their sensitivities to PARP inhibition. By using Cas9 to edit the functional BRCA2 allele in the locally haploid hPSCs and in fibroblasts differentiated from them, we characterized essential regions in the gene to identify permissive and loss-of-function mutations. We also used Cas9 to directly test the function of individual amino acids, including amino acids encoded by clinical BRCA2 variants of uncertain significance, and identified alleles that are sensitive to PARP inhibitors used as a standard of care in BRCA2-deficient cancers. Locally haploid human pluripotent stem cells can …
Peptide-mediated delivery of CRISPR enzymes for the efficient editing of primary human lymphocytes
Authors
Dana V Foss,Joseph J Muldoon,David N Nguyen,Daniel Carr,Srishti U Sahu,John M Hunsinger,Stacia K Wyman,Netravathi Krishnappa,Rima Mendonsa,Elaine V Schanzer,Brian R Shy,Vivasvan S Vykunta,Vincent Allain,Zhongmei Li,Alexander Marson,Justin Eyquem,Ross C Wilson
Journal
Nature Biomedical Engineering
Published Date
2023/5
CRISPR-mediated genome editing of primary human lymphocytes is typically carried out via electroporation, which can be cytotoxic, cumbersome and costly. Here we show that the yields of edited primary human lymphocytes can be increased substantially by delivering a CRISPR ribonucleoprotein mixed with an amphiphilic peptide identified through screening. We evaluated the performance of this simple delivery method by knocking out genes in T cells, B cells and natural killer cells via the delivery of Cas9 or Cas12a ribonucleoproteins or an adenine base editor. We also show that peptide-mediated ribonucleoprotein delivery paired with an adeno-associated-virus-mediated homology-directed repair template can introduce a chimaeric antigen receptor gene at the T-cell receptor α constant locus, and that the engineered cells display antitumour potency in mice. The method is minimally perturbative, does not …
Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species
Authors
Andreja Kust,Jackie Zorz,Catalina Cruañas Paniker,Keith Bouma-Gregson,Netravathi Krishnappa,Jillian F Banfield,Spencer Diamond
Journal
bioRxiv
Published Date
2023
Cyanobacteria are central to biogeochemical cycling, climate change, and eutrophication. While they readily develop associations with environmental microorganisms, the question of whether they consistently recruit specific microbiomes remains unresolved. Here, we established in vitro cyanobacterial consortia by inoculating five different cyanobacterial strains with microbiomes from three freshwater environments to determine if similar non-cyanobacterial organisms were recruited into stable cyanobacteria-based communities. Using amplicon and genome-resolved metagenomic methods we determined that stable cyanobacterial communities largely share the same taxa, regardless of the host cyanobacterial species or inoculation source. Specifically, we identified a 25 species core microbiome, which was significantly enriched in functions for micronutrient biosynthesis, metabolite transport/exchange, and anoxygenic photosynthesis. Furthermore, core species were enriched in putative mobile genetic elements, including two large (> 100 kb) circularized and curated plasmids, encoding functions that may support cyanobacteria-heterotroph symbioses. The consistency observed across these systems indicate that cyanobacterial consortia maintained under similar conditions converge to a predictable structure, and support a core microbiome with taxonomic and functional similarity to core microbiomes of other phototroph-heterotroph symbiotic assemblages.
Species-and site-specific genome editing in complex bacterial communities
Authors
Benjamin E Rubin*,Spencer Diamond*,Brady F Cress*,Alexander Crits-Christoph,Yue Clare Lou,Adair L Borges,Haridha Shivram,Christine He,Michael Xu,Zeyi Zhou,Sara J Smith,Rachel Rovinsky,Dylan CJ Smock,Kimberly Tang,Trenton K Owens,Netravathi Krishnappa,Rohan Sachdeva,Rodolphe Barrangou,Adam M Deutschbauer,Jillian F Banfield,Jennifer A Doudna (* denotes equal contribution)
Journal
Nature Microbiology
Published Date
2021/12/6
Understanding microbial gene functions relies on the application of experimental genetics in cultured microorganisms. However, the vast majority of bacteria and archaea remain uncultured, precluding the application of traditional genetic methods to these organisms and their interactions. Here, we characterize and validate a generalizable strategy for editing the genomes of specific organisms in microbial communities. We apply environmental transformation sequencing (ET-seq), in which nontargeted transposon insertions are mapped and quantified following delivery to a microbial community, to identify genetically tractable constituents. Next, DNA-editing all-in-one RNA-guided CRISPR–Cas transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-seq are used to enable organism- and locus-specific genetic manipulation in a community context. Using a combination of …
Targeted genome editing of bacteria within microbial communities
Authors
Benjamin E Rubin,Spencer Diamond,Brady F Cress,Alexander Crits-Christoph,Christine He,Michael Xu,Zeyi Zhou,Dylan C Smock,Kimberly Tang,Trenton K Owens,Netravathi Krishnappa,Rohan Sachdeva,Adam M Deutschbauer,Jillian F Banfield,Jennifer A Doudna
Journal
BioRxiv
Published Date
2020/7/17
Knowledge of microbial gene functions comes from manipulating the DNA of individual species in isolation from their natural communities. While this approach to microbial genetics has been foundational, its requirement for culturable microorganisms has left the majority of microbes and their interactions genetically unexplored. Here we describe a generalizable methodology for editing the genomes of specific organisms within a complex microbial community. First, we identified genetically tractable bacteria within a community using a new approach, Environmental Transformation Sequencing (ET-Seq), in which non-targeted transposon integrations were mapped and quantified following community delivery. ET-Seq was repeated with multiple delivery strategies for both a nine-member synthetic bacterial community and a ∼200-member microbial bioremediation community. We achieved insertions in 10 species not previously isolated and identified natural competence for foreign DNA integration that depends on the presence of the community. Second, we developed and used DNA-editing All-in-one RNA-guided CRISPR-Cas Transposase (DART) systems for targeted DNA insertion into organisms identified as tractable by ET-Seq, enabling organism- and locus-specific genetic manipulation within the community context. These results demonstrate a strategy for targeted genome editing of specific organisms within microbial communities, establishing a new paradigm for microbial manipulation relevant to research and applications in human, environmental, and industrial microbiomes.
Transcriptome analysis of alternative splicing-coupled nonsense-mediated mRNA decay in human cells reveals broad regulatory potential
Authors
Courtney E French,Gang Wei,James PB Lloyd,Zhiqiang Hu,Angela N Brooks,Steven E Brenner
Journal
bioRxiv
Published Date
2020/7/2
To explore the regulatory potential of nonsense-mediated mRNA decay (NMD) coupled with alternative splicing, we globally surveyed the transcripts targeted by this pathway via RNA-Seq analysis of HeLa cells in which NMD had been inhibited. We identified putative NMD-targeted transcripts as those with a termination codon more than 50 nucleotides upstream of an exon-exon junction (premature termination as defined by the ‘50nt rule’) and that significantly increased in abundance upon NMD inhibition. We additionally controlled for potential transcriptional up-regulation by requiring the putative NMD targets to increase in abundance substantially more than the isoforms from the same gene that do not contain a premature termination codon. This resulted in a conservative set of 2,793 transcripts derived from 2,116 genes as physiological NMD targets (9.2% of expressed transcripts and >20% of alternatively spliced genes). Our analysis identified previously inferred unproductive isoforms and numerous heretofore-uncharacterized ones. NMD-targeted transcripts were derived from genes involved in many functional categories, and are particularly enriched for RNA splicing genes as well as for those harboring ultraconserved elements. By investigating the features of all transcripts impacted by NMD, we find that the 50nt rule is a strong predictor of NMD degradation while 3’ UTR length on its own generally has only a small effect in this human cell line. Additionally, thousands more transcripts without a premature termination codon in the main coding sequence contain a uORF and display significantly increased abundance upon NMD inhibition …
Blueprint for a pop-up SARS-CoV-2 testing lab
Journal
Nature Biotechnology
Published Date
2020/7
NE, TG, MKK, GMC, JMT and HR are shareholders in and/or employees of Helix Nanotechnologies Inc., which is developing gene-encoded vaccines for SARS-CoV-2. A full list of GMC’s technology transfer, advisory roles and funding sources can be found at http://arep. med. harvard. edu/gmc/tech. html. JMT is a shareholder and employee of SmartPharm Therapeutics, which is developing gene-encoded antibody vaccines for SARS-CoV-2.
Efficient isolation of protoplasts from rice calli with pause points and its application in transient gene expression and genome editing assays
Authors
Snigdha Poddar,Jaclyn Tanaka,Jamie HD Cate,Brian Staskawicz,Myeong-Je Cho
Journal
Plant Methods
Published Date
2020/12
Background An efficient in vivo transient transfection system using protoplasts is an important tool to study gene expression, metabolic pathways, and multiple mutagenesis parameters in plants. Although rice protoplasts can be isolated from germinated seedlings or cell suspension culture, preparation of those donor tissues can be inefficient, time-consuming, and laborious. Additionally, the lengthy process of protoplast isolation and transfection needs to be completed in a single day. Results Here we report a protocol for the isolation of protoplasts directly from rice calli, without using seedlings or suspension culture. The method is developed to employ discretionary pause points during protoplast isolation and before transfection. Protoplasts maintained within a sucrose cushion partway through isolation, for completion on a subsequent day, per the first pause point, are referred to as S protoplasts. Fully isolated …
Netravathi Krishnappa FAQs
What is Netravathi Krishnappa's h-index at University of California, Berkeley?
The h-index of Netravathi Krishnappa has been 13 since 2020 and 14 in total.
What are Netravathi Krishnappa's top articles?
The articles with the titles of
Functional annotation of variants of the BRCA2 gene via locally haploid human pluripotent stem cells
Peptide-mediated delivery of CRISPR enzymes for the efficient editing of primary human lymphocytes
Model cyanobacterial consortia reveal a consistent core microbiome independent of inoculation source or cyanobacterial host species
Species-and site-specific genome editing in complex bacterial communities
Targeted genome editing of bacteria within microbial communities
Transcriptome analysis of alternative splicing-coupled nonsense-mediated mRNA decay in human cells reveals broad regulatory potential
Blueprint for a pop-up SARS-CoV-2 testing lab
Efficient isolation of protoplasts from rice calli with pause points and its application in transient gene expression and genome editing assays
are the top articles of Netravathi Krishnappa at University of California, Berkeley.
What are Netravathi Krishnappa's research interests?
The research interests of Netravathi Krishnappa are: Molecular Genetics, Biotechnology, Next Generation Sequencing, CRISPR technology
What is Netravathi Krishnappa's total number of citations?
Netravathi Krishnappa has 3,539 citations in total.