Griffin:Trending

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Chalkboard

Intrinsically disordered regions (IDRs) in proteins are often targets of combinatorial posttranslational modifications 34158397

miR-429/PD-L1 Axis 33555514

N6-methyladenosine (m6A) is the most prevalent posttranscriptional modification on RNA.

O-GlcNAc (short for O-linked GlcNAc or O-linked β-N-acetylglucosamine) is a reversible enzymatic post-translational modification that is found on serine and threonine residues of nucleocytoplasmic proteins

younger age and a high number of tumor-infiltrating lymphocytes were predictive factors of a good response to immune checkpoint inhibitors 34136945


Selective inhibitors of mTORC1 activate 4EBP1 and suppress tumor growth 34168367

lymphoid lineage maturation bottleneck 34170284

HeLa Cells are heterogeneic/mixed population 34076552

base-pair resolution genome architecture 34108683

semiallogeneic (fetal) development dependent immuno-modulation (suppression) 34099889

enhancement (solid mass) targeting CAR(T) 34083764

host lineage quorum sensing (immunity) 34124789

body mass (adipose) dependent epigenetic modulation 32500354

Coffee consumption improves cognitive function 33125576

Autophagy (Mitophagy) promotes stemness 33172301

Exosome detection method via the ultrafast-isolation system (EXODUS) that allows automated label-free purification of exosomes from varied biofluids/ exosomal RNA profiling 33432243

Periodontal inflammation dependent neuropathology 33432590

Poly Adenylation trait loci mapping 33986536

ex vivo (transplantable cell populations) prime editing 33951479

hippocampal-thalamic-cortical network dependent systems consolidation (remote memory retrieval) 33782621

organoid engineering hPSC cardiac 33772245

3'UTR alternative polyadenylation (APA) quantitative trait loci (3'aQTLs) / polyadenylation quantitative trait loci 33986536

Genomic stability; DNA repair dependent genomic integrity / immune (hemopoietic) system (T Cell response) aging dynamics 33981041

RNA transcript dependent Homologous recombination (HR) DNA double-strand break (DSB) Repair 33981036

isoform composition of mRNA transcription dynamics splice site (intron/exon) selection 33979654

microbiota mutualist species fitness; interspecific dynamics of host-control 33521949

Intergenic Nonprotein Coding RNA 33978457

N6-Methyladenosine (m6A) dependent Spatial Patterning 33972392

nanoparticles water-insoluble hydrophobic polyethylenimines, low-molecular weight (MW) polyethylenimine (PEI) with high cholesterol substitution water-insoluble polymers RNAi vehicles 33964112

fate, migration, proliferation, progression 33971280

SF9 / baculovirus eukaryotic expression 0.3-8 mg/Liter yield 33971243

exogenic xenotransplantation 33782573

Mesenchymal fibro-adipogenic progenitor (FAP) stemness differentiation to skeletal muscle regeneration/repair 33529374

skeletal muscle ribosomal capacity

Stress/trauma exposure driven epigenomic (DNA methylation (DNAm)/ differentially methylated regions (DMR)) current 33529416

deep time metazoan global phylogeny

viral phylogenetics 33972780

miR-351-3p dependent mesenchymal stromal cell proliferation 33970551

genomic DNA promoter intrastrand hairpin (cruciforms)/ four-strand (G-quadruplex or i-motif) structures 33931265

Inflation (stem cell/transcriptional differentiation)-collapse (stretch-responsive/mechanical) dynamics / Inflation-collapse morphogenesis dynamics 33915079

BCAAs Isoleucine increases muscle mass 33289736

Therapeutic Intervention

platelets thrombosis Factor cascade 33471623

proteomics/kinome screen re: gluconeogenesis 33951476

Goat Milk 33555137

Heme catabolism 33903766

extracellular vesicle Proteomics 33905554

Ketone bodies are generated in the liver and allow for the maintenance of systemic caloric and energy homeostasis during fasting and caloric restriction. 33619377

genome-wide association study (GWAS) risk association Alzheimer’s disease (BIN1) and Parkinson’s disease (TMEM175) / GBA, APOE and SNCA 33589841

retrosplenial cortex (RSC) to dorsal hippocampus axis 33580135

Ferroptosis, redox lipid death signal 33542532

genome-wide association study (GWAS) risk association Alzheimer’s disease (BIN1) and Parkinson’s disease (TMEM175) / GBA, APOE and SNCA 33589841

retrosplenial cortex (RSC) to dorsal hippocampus axis 33580135

miR-138 dependent viral latency 33558653

adolescent stress dependent neuroimmune transcriptinomic modification (stress dependent epigenetic memory) 33558677

chromatin density; four major families of nucleosome remodeler complexes in mammals (SWI/SNF (switch/sucrose non-fermentable), ISWI (imitation switch), CHD (chromodomain helicase DNA binding) and INO80) are protein assemblies of a catalytic ATPase plus accessory subunits. 33558757

Ferroptosis, redox lipid death signal 33542532

neuronal metastable proteome autophagy stasis 33891876

Melatonin 31894324

Processing bodies (P-bodies) 33586867

TRAFTACs: TRAnscription Factor TArgeting Chimeras (HaloTag-fused dCas9) 33836141

ncRNA autocrine/paracrine 33345445

SUMOylation 33526451

Epithelial mesenchymal Transition 33517270

comparative proteomics / host antiviral viral replication systems 33432153

epigenetic histone H3 methylation upstream 33900313

innate immune system response / transmembrane pores maturation / mechanistic cytokine release 33883744

Behavioral /mate choice-dependent niche (speciation) reinforcement 33766854

NGS based Tick-Borne Bacterial 16S Ribosomal RNA Detection from Whole Blood 33627320

human telomerase 33883742

Proinflammatory cytokine x homeostatic cytokine axis 33859404

recombinant multivalent hyperimmune globulins 33859400

pathogen exposure dependent polygenic shift adaptation 33854233

Multipotent adult progenitor cells (MAPC® cells) 33655577

Ubiquitin-dependent endosomal / lysosomal pathway coordination 33650289

Coconut Oil Supplementation inflammatory / dysfunction risk 33650755

Static magnetic field (SMF), with constant magnetic field strength and direction 2-4 T SMF improved bone microarchitecture and strength by stimulating bone formation and restraining bone resorption 33655538

photoreceptor-like Retinal organoids (ROs) 33662144

Durotaxis, the process by which cells follow gradients of extracellular mechanical stiffness 33290722

systemic lipopolysaccharide (LPS) morbidity 33677747

human primordial germ cell-like cells (hPGCLCs) expansion and epigenetic reprogramming 32954504

mesenchymal stromal/stem cell (MSC) support of astrocytic response 33381863

differentiation state specific Expression quantitative trait loci (eQTL) (genetic) variant trait-association 33664506

Phenotypic reversion / Donor cell memory 33848472

Nuclear mechanosensing 33875841

TNF-α dependent thiamin uptake abrogation

Peptide-major histocompatibility complex (pMHC) multimers enable the detection of antigen-specific T cells 33649568

Glucocorticoids are adrenocortical hormones maintaining homeostasis, including regulating whole-body energy metabolism in addition to stress response. In skeletal muscle, glucocorticoids can reduce the synthesis of muscle proteins and simultaneously accelerate the breakdown of proteins to regulate skeletal muscle mass and energy metabolism

caffeine-inducible telomerase reverse transcriptase (TERT) upregulation (mRNA/protein)-dependent cellular senescence and aging mitigation/telomere length extension/ 3720241

differentiation dependent gene transcription; initiation, promoter-proximal pausing, RNA polymerase II (Pol II) elongation. 33539786

Transit-amplifying cells (TACs) tissue-cell-type composition renewal via potentiating proliferative progenitor and specialization/ differentiated cell production emanation 33484640

Transit-amplifying cells (TACs) are an undifferentiated population in transition between SCs and differentiated cells. 24813615

Microglia are activated in many neurological diseases (systemic inflammation) and have been suggested to play an important role in the development 33476547

RNA signaling; ~150 post-transcriptional RNA modifications have been identified in all kingdoms of life. N6-methyladenosine (m6A) (epigenetic RNA feature), is a ligand for human adenosine A3 receptor (> affinity than unmodified adenosine) 33472058

basophil-neuronal axis 33450207

2021

  • Compressional wave dependent central nervous system (CNS) development (hippocampal oxidative states/aminoacidergic neurotransmission) 33386696
  • ubiquitin-proteasome system Selective recognition
  • NLRP3 (NOD-, LRR- and pyrin domain-containing protein 3) inflammasome multiprotein complex dependent pro-inflammatory cytokines IL-1β and IL-18/ gasdermin D-mediated pyroptotic cell death
  • microtubule (MT) asymmetric distribution dynamics; cell polarity, centrosome positioning, focal adhesion dynamics
  • Prion protein (PrP) adopts (a)helical conformation (PrPC) or (b) beta sheet-rich, misfolded conformation (PrPSc). PrPSc form can alter templating "infect" PrPC and transition to misfolded states.
  • Alternative lengthening of telomeres (ALT) dependent break-induced replication (BIR),
  • Local nuclear protein synthesis (LNPS) / local nuclear translation
  • progenitor cell epigenetic fate conversion
  • Diapause / adaptive inactivation / reversible transcription development/reversion suspension
  • Ciliogenesis /axonemal outer dynein arm (ODA)
  • Intrinsic quiescence
  • Pulmonary endothelial barrier
  • Pluripotent stem cell trophic support systems
  • Mevalonate pathway
  • Thymus microenvironment-specific naive T cell mechanistic growth and maturation
  • Innate immune complement system sequential protein cleavage cascade activation
  • Ribosome biogenesis/ubiquitin-coordinated ribosome assembly
  • Regulatory T cells (follicular regulatory T (Tfr) cells) prevent emergence of B cell-driven autoantibodies and IgE-mediated allergies
  • Nonpeptidergic signaling
  • Efferocytosis
  • Major histocompatibility complex class II molecule antigen processing (endosomal processing efficiency)/ presentation machinery
  • Stress; in vivo non-enzymatic glycan chemistry; sugars, lipids, protein substrate (protein glycation, glycoxidation, and lipoxidation)
  • methyl donor, S-adenosylmethionine (SAM)
  • Ca2+ microdomain formation dependent prime T cell activation
  • Symmetric cell division; genetic information/cytoplasmic content partitioning between daughter cells
  • virus-host interaction; post-entry virus trafficking, uncoating and nuclear import
  • DNA double-strand break (DSB) repair by homologous recombination, DNA ends are resected (cut out) to overhanging single-stranded DNA (ssDNA). Homologous recombination = intrinsic coupling of Nucleosome (chromatin component) eviction with DNA-end resection.
  • Ferroptosis = programmed cell death via cellular accumulation of lipid peroxidation and lipid reactive oxygen species (ROS)
  • Posttranscriptional regulation; proliferation / maturation
  • ribosomal peptidyl-tRNA
  • Genetic transcription initiation rate/ burst duration; nonlinear (global gene bursting kinetics) gene regulatory function/cooperative gene control.
  • Pyroptosis
  • conditional essential
  • NLRP3 (NOD-, LRR-, and pyrin domain-containing protein 3) inflammasome kinetics
  • Protein Myristoylation
  • eukaryotic mRNA biogenesis; RNA polymerase II (Pol II/transcription machinery) / spliceosome component pre-mRNA branch site(s)recognition
  • Ubiquitin turnover
  • Rapid eye movement sleep (REMS) favors neuronal plasticity, brain development and memory
  • Metabolic heterogeneity
  • Prion-chaperoning machinery
  • Sister chromatid cohesion
  • Basal signaling, efficacy, precoupling, and allostery in GPCRs
  • Molecular chaperones
  • Mechanosensitive collaboration
  • Chromosomal Instability
  • Alternative telomere lengthening dynamics
  • Sphingolipid and ether lipid signatures
  • Genotoxic stress
  • Steatosis
  • Synaptic Transmission
  • Centriole Biogenesis

Autophagy

  • neuronal metastable proteome autophagy stasis 33891876
  • caloric restriction (CR) metabolomic, transcriptomic, proteomic signatures 33421383
  • Selective autophagy (aggnephagy) proteostasis; clearing accumulation and aggregation of ubiquitinated proteins. 33545068
  • Macroautophagy lysosome-mediated degradation
  • Autophagy is a form of intracellular metabolic recycling
  • Autophagy /catabolic (anabolic?) pathway(s) self-nourishment/maintenance/cellular homeostasis.
  • Autophagic flux / protective autophagy
  • Amino acid deprivation-induced autophagy
  • Chaperone-mediated autophagy (CMA) proteostasis network componentry (protein quality control)
  • Calorie restriction (CR) exerts multiple effects on health,including the amelioration of systemic insulin resistance.
  • Extracellular vesicles (EVs); large EVs (l-EVs, or microvesicles) / small EVs (s-EVs, or exosomes)
  • Extracellular growth factor-dependent communicate to ion channel modulating to intracellular organellar/ lysosomal function
  • Isocaloric moderately high-fat diet (IHF) prolongs (stasis of) lifespan 33440166
  • Retrograde lysosome transport
  • liver derivative ketone bodies /systemic caloric,energy homeostasis during fasting and caloric restriction. 33619377

Lineage/Differentiation

  • stemness dependent exosomal trafficking of miRNA 33945431
  • cis-regulatory element spatial cue dependent cell fate commitment/molecular identity determination 33852891
  • stromal differentiation 33658717
  • 3D organoid culture technology ; Human induced pluripotent stem cells (iPSCs) to studies of organ development, disease modeling, drug screening and cell replacement therapy.
  • Astrocytic lineage dependent pituitary amygdala hippocampus axis
  • CNS, oligodendrocyte precursor cells differentiate into oligodendrocytes to wrap their plasma membranes around neuronal axons, generating mature neural networks with myelin sheaths according to spatial and temporal patterns
  • ezrin-radixin-moesin (ERM) dependent plasma membrane-actin cytoskeleton apical structure/junction formation (i.e. microvilli)
  • Hematopoietic stem cell (HSCs) systemic (re)entry/replenishment cell cycle program initiation
  • Leukocyte extravasation
  • Osteoclast derivative lysosomal secretion-dependent proton (H+)/acid hydrolase mediated bone resorption/bone homeostasis. 33484199
  • Regulatory T cell homeostasis
  • Enteroendocrine cells
  • Macrophage polarization
  • Thymic epithelial cells (TECs) centric T cell development; T cell receptor (TCR) repertoire/lineage differentiation. Medullary thymic epithelial cells (mTECs) dependent thymocyte selection/self-tolerance. 33817835
  • Trophoblast cells-> spiral artery remodeling in hemochorial placentation. trophoblast cell lineage development/ modulator of the syncytiotrophoblast lineage. Nutrients between the mother and the fetus during pregnancy is predominantly governed by the syncytiotrophoblast lining at the outer surface of the placental villi. Mechanisms of extrasencory syncytiotrophoblast nutrient status and support.
  • trophoblastic lineage; BeWo, JEG-3, HTR-8/SVneo, AC1-M59, AC1-M32, ACH-3P and Swan71
  • Sequential myeloid transition
  • viability nascency enhancement; Human pluripotent stem cells (hPSCs) chroman 1, emricasan, polyamines, and trans-ISRIB (CEPT) enhanced cell survival of genetically stable hPSCs by simultaneously blocking several stress mechanisms that otherwise compromise cell structure and function 33941937

Engineering

  • biologically active recombinant protein from E. coli 33927995
  • permeability enhancement / liposomal / cationic? 33913042


Epigenomics

  • chromatin accessibility 34017130
  • Histone modifications histone modifications characteristic of active promoters, enhancers and gene bodies (H3K4me3, H3K27ac and H3K36me3) and inactive regions (H3K27me3) 33846645
  • Histone crotonylation / crotonyl-coenzyme A (CoA) 33450185
  • transcription memory / nascent/daughter epigenomic memory ; Hammer-seq (hairpin-assisted mapping of methylation of replicated DNA) 33686219
  • chromatin ubiquitylation 33664452
  • intracellular oxidative stress- skeletal muscle DNA methylome axis
  • chromatin stability dynamics
  • DNA demethylation / methylation
  • Epitranscriptomic mechanisms
  • Genome structural variation (SV) determinant quantitative trait/epitranscriptomic programming
  • Memory formation
  • progenitor network determinants
  • Nucleosome Remodeling
  • MicroRNAs (miRNAs) are small regulatory RNAs of relatively long half-life in non-proliferative human cells
  • genotypic locus susceptibility mapping
  • Chromatin remodelling via genomic DNA hydroxymethylation distribution (transcription memory) 33960278
  • adolescent stress dependent neuroimmune transcriptinomic modification (stress dependent epigenetic memory) 33558677
  • chromatin density; four major families of nucleosome remodeler complexes in mammals (SWI/SNF (switch/sucrose non-fermentable), ISWI (imitation switch), CHD (chromodomain helicase DNA binding) and INO80) are protein assemblies of a catalytic ATPase plus accessory subunits. 33558757

Metagenomics

  • RNA modification ( N6-methyladenosine (m6A)/ RNA m 6 A reader YTHDC1) dependent chromatin modification and retrotransposon repression 33658714
  • Phenotypic plasticity
  • Ex vivo chimerism 33861963
  • non-random (translational amino acid replacement genomic segment clustering) distribution 33953399
  • deep-time palaeogenomics 33597750

Microbiology

  • Host-microbiota compartment boundary nowcasting
  • Endotoxemic mechanisms
  • Gram negative bacterial phylogenetic host/phage dependent evolutionary divergence (CRISPR/Cas systems)/genetic variance determines host response severity/trajectory
  • Intra-host (pleomorphic) anaerobic bacteria quorum sensing (QS) networks
  • Latency reservoirs
  • Periodontal disease (p gingivalis) dependent coronary artery endothelial dysfunction 33677586
  • Prokaryotic/viral stage-specific quorum sensing / Autoinduction / density; Epigenetic (host histone methylation) response
  • type I interferon (IFN-1) response
  • Viral immune evasion evolution trajectories
  • Viral entry genetic variance (entry glycan/glycoprotein tropism) preferential viral entry tropism determines immunopathogenic disease severity trajectory
  • viral/bacterial mediated host immune response signature pathology predisposition / dysbiosis susceptibility 33883226
  • forward line quorum sensing; intra-/ inter-community parasites-host axis communication mechanisms extracellular vesicles (EVs) /heterogenous nanoparticles containing protein, lipid, nucleic acid, metabolites/(~30-5000 nm)/ biogenesis 33933651

Microbiome/Dysbiosis/Inflammation

  • microbiome-gut-brain axis sensory mechanisms 33953396

Organelle/Sub Structures

ECM

  • extracellular matrix viscoelasticity 33707778

Mitochondria

  • Low-grade mitochondrial stress; ergogenic mitohormesis
  • Caffeine induces cAMP/PKA/AMPK signaling dependent mitochondrial fission.
  • Central nervous system (CNS) specific Mitochondrial biogenesis/integrity 33415987
  • Mitochondria are an autonomous/spatially segregated parallel functioning genome within eukaryotic nuclear genomic.
  • Mitochondria organizational genome unit = nucleoid = mitochondrial DNA (mtDNA) + architectural proteins.
  • Mitochondrial respiration; ATP, respiration generates biosynthetic precursors (ie aspartate)/ essential substrates for nucleotide synthesis.
  • mitochondrial oxidative stress derivative clearance 33665835
  • Oxidative phosphorylation (OXPHOS) 33852893
  • Mitochondrial fission signatures toward autophagy or biogenesis 33953403

TGN

  • Nucleocytoplasmic transport (NCT) 34059832

Neoplasia

  • successive clonal population expansion via sequential acquisition of (? / somatic mutations) 33571445
  • Meiotic programs are potentially dangerous to genome stability and could be disastrous if activated in proliferative cells. 33658710


RNA

Transcriptinomics

  • single-cell RNA sequencing (scRNA-seq) 33721368

Noncoding ncRNA

  • Small nuclear ribonucleoprotein particle (snRNP)
  • Long non-coding RNAs (lncRNAs)
  • Small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs)
  • Circular RNAs (circRNAs)
  • First exons of enhancer-generated long noncoding RNAs (elncRNAs) elncRNAs / promoter-antisense long noncoding RNAs (pa-lncRNAs) pa-lncRNAs-dependent (cis-regulatory element) splice machinery activity /extragenic transcription modulation. 33767452
  • Humans genome lncRNA 30,000–60,000 long noncoding RNAs (lncRNAs) 33958760
  • miR-138 dependent viral latency 33558653

Phase Separation

  • chromosome/chromatin architecture; phase-separation dependent sub cellular/sub nuclear structures
  • Nanocluster Reorganization
  • phase separation dependent exonuclease endonuclease catalytic regulation outer shell at the droplet periphery selective environment
  • CaRriers of the Trans-Golgi network to the cell Surface (CARTS)
  • spatial distinction interactomes

Post transcription/translation

  • Adhesion G protein-coupled receptors (aGPCRs)/family B2 GPCRs 33497605
  • polyadenylation mechanics 33619322
  • targeted protein degradation technologies; Trim-Away https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5733393/
  • targeted protein degradation technologies; Small-molecule degraders such as proteolysis-targeting chimeras (PROTACs) induce the degradation of neo-substrates by hijacking E3 ubiquitin ligases 33567268
  • phosphorylation code dependent central signalling hub integration 33658715


Temporal Development

  • Central nervous system (CNS) neurodegeneration/organismal aging through peripheral tissues; skeletal muscle proteasome stress influences amylase/maltose-mediated adaptive response-dependent retinal and brain stress (aging). 33773104

Vesicular Traffic

  • exosome-derived miRNA sequencing to predict viral host seroconversion 33666247
  • Regenerative role of mesenchymal stem cell (MSC)-derived extracellular vesicles (MSC-EVs) 33369392
  • Ribonucleoprotein complex-dependent extracellular RNA (exRNAs)/ncRNA/miRNA extracellular vesicle (EV) assembly units transmission from systemic circulation to Central Nervous System (CNS) via blood-brain barrier (BBB) traverse.
  • mesenchymal stem cell exosomal derivatives trafficking
  • Microfilament/Microtubule dependent endosomal trafficking mechanisms
  • Urinary extracellular vesicle (uEVs) traffic/excretion
  • extracellular vesicle monitoring of small-molecule chemical occupancy and protein expression (ExoSCOPE) 33686255