Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Engineered apoptotic nucleases for chromatin research.

  PMID 17626049 · PMC1935020 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  Inserting TEVP cleavage sites immediately downstream of the two caspase-3 sites in DFF45 (I1I2 mutant) makes DFF40 nuclease activity exclusively dependent on TEVP cleavage (DFF-T)

  recombinant cerevisiae coli western plasmid serial

• Tuberculosis vaccine strain Mycobacterium bovis BCG Russia is a natural recA mutant.

  PMID 18637199 · PMC2483709 · BMC microbiology · 2008 · 8 claims · 5 setups

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  A RecA- phenotype increases genetic stability and may help restrict ongoing genome evolution of BCG substrains while maintaining protective efficacy

  bovis bcg genomic cell-free allelic southern sequencing

• The exonuclease Xrn1 activates transcription and translation of mRNAs encoding membrane proteins.

  PMID 30899024 · PMC6428865 · Nature communications · 2019 · 7 claims · 8 setups

  Has reproduction · 85

  Xrn1 promotes translation of a specific group of mRNAs encoding membrane/secretome proteins, acting at translation initiation.

  cerevisiae yeast xrn1∆ western luciferase polysome

• Contribution of the C-terminal region within the catalytic core domain of HIV-1 integrase to yeast lethality, chromatin binding and viral replication.

  PMID 19014595 · PMC2615443 · Retrovirology · 2008 · 7 claims · 8 setups

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  IN mutants V165A, A179P and KR186,7AA in the C-terminal region of the catalytic core domain fail to induce the lethal phenotype in HP16 yeast

  saccharomyces hp16 293t cos-7 yeast immunoprecipitation chromatin

• The commonly-used DNA probe for diffusely-adherent Escherichia coli cross-reacts with a subset of enteroaggregative E. coli.

  PMID 20025771 · PMC2803494 · BMC microbiology · 2009 · 7 claims · 5 setups

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  The daaC probe cross-hybridizes with a specific subset of EAEC strains, namely those carrying the aafA gene (AAF/II fimbriae)

  coli hep-2 pslm862 eaec colony hep-2 pcr

• Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.

  PMID 18681975 · PMC2518929 · BMC microbiology · 2008 · 8 claims · 7 setups

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  E2348/69 possesses a type I restriction-modification system encoded by an hsdMSR-like operon identified by homology to known Hsd proteins.

  e2348 hep-2 blast colony transformation

• Grad-seq identifies KhpB as a global RNA-binding protein in Clostridioides difficile that regulates toxin production.

  PMID 37223250 · PMC10117727 · microLife · 2021 · 8 claims · 9 setups

  Has reproduction · 50

  Grad-seq resolves in-gradient sedimentation profiles for ~87-88% of annotated C. difficile transcripts and ~50% of annotated proteins, providing a comprehensive RNA-protein complexome resource

  difficile grad-seq rna-seq lc-ms

• Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

  PMID 16672049 · PMC1464126 · BMC genomics · 2006 · 8 claims · 7 setups

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  Seven genomic islands (VPaI-1 to VPaI-7, 10-81 kb) were identified in V. parahaemolyticus RIMD2210633 by aberrant GC content, presence of integrases/transposases, flanking direct repeats, and absence from related Vibrionaceae genomes.

  parahaemolyticus vulnificus clinical ecori-digested bioinformatic comparative pcr

• Evolutionary repair: Changes in multiple functional modules allow meiotic cohesin to support mitosis.

  PMID 32155147 · PMC7138332 · PLoS biology · 2020 · 8 claims · 8 setups

  Has reproduction · 90

  Replacing the mitotic kleisin Scc1 with the meiotic kleisin Rec8 impairs sister chromosome cohesion, advances genome replication timing, and reduces reproductive fitness by 45%.

  cerevisiae parallel evolved rec8-expressing competitive experimental whole-genome

• A Novel Algicidal Bacterium, Microbulbifer sp. YX04, Triggered Oxidative Damage and Autophagic Cell Death in Phaeocystis globosa, Which Causes Harmful Algal Blooms.

  PMID 35019679 · PMC8754136 · Microbiology spectrum · 2022 · 8 claims · 9 setups

  Has reproduction · 36

  Microbulbifer sp. YX04 shows high algicidal activity against P. globosa, peaking at 93.2% in the declining growth phase

  phaeocystis strain yx04 globosa algicidal 16s scanning

• Genetic diversity among Enterococcus faecalis.

  PMID 17611618 · PMC1899230 · PloS one · 2007 · 7 claims · 7 setups

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  Virulence and antibiotic resistance traits are distributed across many diverse E. faecalis lineages rather than confined to one clade

  faecalis multi-locus dot pcr

• N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.

  PMID 36422864 · PMC9731578 · eLife · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  Pho92 specifically binds m6A-modified RNA via its YTH domain, both in vitro and in vivo

  cerevisiae diploid yeast recombinant affinity rt-qpcr chip-seq

• A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein.

  PMID 17183673 · PMC1762436 · PloS one · 2006 · 8 claims · 7 setups

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  HCNCp is a novel invariant (non-variant) cyst protein belonging to a new family of high-cysteine membrane proteins (HCMp) abundant in the Giardia genome

  giardia serial northern western

• Use of suppression subtractive hybridisation to extend our knowledge of genome diversity in Campylobacter jejuni.

  PMID 17470265 · PMC1868759 · BMC genomics · 2007 · 8 claims · 6 setups

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  There is a clear correlation between MLST clonal complex and the distribution of metabolic genes involved in alternative terminal electron acceptor use.

  jejuni ssh panel suppression blastx dot-blot

• The Cohesin Ring Uses Its Hinge to Organize DNA Using Non-topological as well as Topological Mechanisms.

  PMID 29754816 · PMC6371919 · Cell · 2018 · 8 claims · 8 setups

  Has reproduction · 80

  Sister chromatid cohesion is mediated by co-entrapment of both sister DNAs inside a single hetero-trimeric cohesin ring, perfectly correlating CD formation with cohesion

  cerevisiae smc1 minichromosome agarose western

• Polymorphism and epitope sharing between the alleles of merozoite surface protein-1 of Plasmodium falciparum among Indian isolates.

  PMID 17659072 · PMC1950510 · Malaria journal · 2007 · 7 claims · 6 setups

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  PfMAD20 is the predominant PfMSP-1 allelic type among Indian field isolates

  falciparum escherichia coli-expressed recombinant pcr recombinant sds-page

• Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates.

  PMID 17408487 · PMC1853099 · BMC microbiology · 2007 · 8 claims · 8 setups

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  Arginase activity varies more than 100-fold among H. pylori clinical isolates and laboratory-adapted strains

  minimally-passaged pylori coli arginase urease heterologous

• Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination.

  PMID 19031011 · PMC2756966 · Journal of structural and functional genomics · 2009 · 8 claims · 6 setups

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  A discovery-oriented pipeline using standardized single-condition methods (one expression system, one detergent, one SEC buffer) can efficiently triage large numbers of eukaryotic IMP targets to identify well-behaved candidates for crystallization

  cerevisiae ddm-solubilized sec-included tmhmm ligase-independent small-scale

• Profiling humoral immune responses to P. falciparum infection with protein microarrays.

  PMID 18937256 · PMC3021802 · Proteomics · 2008 · 7 claims · 5 setups

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  A protein microarray platform of 250 Pf proteins, individually expressed cell-free and printed unpurified, can profile serum antibody responses across donor groups of differing immune status

  sera coli genomic microarray immuno-dot elisa

• Asthma investigators begin to reap the fruits of genomics.

  PMID 14611649 · PMC329104 · Genome biology · 2003 · 7 claims · 8 setups

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  Microarray profiling of animal models of allergic asthma can identify novel differentially expressed candidate genes involved in inflammation and airway remodeling.

  monkey models lung inbred cdna oligonucleotide northern