_    ___ ___      _                               
   / \  |_ _/ _ \ ___| |_ _ __ ___  __ _ _ __ ___  ___
  / _ \  | | | | / __| __| '__/ _ \/ _` | '_ ` _ \/ __|
 / ___ \ | | |_| \__ \ |_| | |  __/ (_| | | | | | \__ \
/_/   \_\___\___/|___/\__|_|  \___|\__,_|_| |_| |_|___/

Invidious > Channel > the bumbling biochemist

the bumbling biochemist	26800 subscribers    RSS
View channel on YouTube Videos Playlists

YT 1 hour 18 minutes 37 seconds the bumbling biochemist Biochemistry techniques - overview of some biochem, molecular biology, & structural biology methods YT 1 hour 1 minute the bumbling biochemist Lab equipment: What's what in wet work! YT 49 minutes 54 seconds the bumbling biochemist Inducible protein overexpression in bacteria with the T7 expression system

YT 26 minutes 31 seconds the bumbling biochemist Bacterial growth media (LB, TB, SOB, SOC, etc.) YT 7 minutes 3 seconds the bumbling biochemist Practical lab tip - prepare lots of SDS-PAGE samples in a PCR strip YT 19 minutes 25 seconds the bumbling biochemist Choosing a gel percentage for gel electrophoresis (polyacrylamide & agarose)

YT 45 minutes 31 seconds the bumbling biochemist Pull-down assays (co-IPs (co-immunoprecipitations), etc) - what, how, & what to look for YT 16 minutes 55 seconds the bumbling biochemist Why we use secondary antibodies (indirect detection method) - in western blots, etc. YT 4 minutes 15 seconds the bumbling biochemist Practical lab tips for working with protease inhibitor tablets

YT 16 minutes 1 second the bumbling biochemist Nucleic acid UV absorption & purity ratios (260/280 and 260/230) YT 29 minutes 20 seconds the bumbling biochemist cDNA (complementary DNA), its uses, & some nuances to take into account when molecular cloning YT 9 minutes 57 seconds the bumbling biochemist Tips for setting up, loading, & running PAGE gels

YT 6 minutes 19 seconds the bumbling biochemist "Clarification" steps in biochemistry YT 44 minutes 31 seconds the bumbling biochemist SLIC cloning (Sequence and Ligation Independent Cloning) theory & workflow YT 7 minutes 50 seconds the bumbling biochemist Ponceau staining - what, why, & how with some practical tips

YT 19 minutes 2 seconds the bumbling biochemist DpnI digest in PCR-based molecular cloning YT 20 minutes 13 seconds the bumbling biochemist Spin column nucleic acid purification - how it works YT 27 minutes 23 seconds the bumbling biochemist Minipreps (alkaline lysis plasmid purification) behind the scenes

YT 28 minutes 47 seconds the bumbling biochemist Significant figures (sig figs) - in measurements, calculations, etc. YT 5 minutes 23 seconds the bumbling biochemist Meniscus-measuring (without parallax error!) YT 20 minutes 12 seconds the bumbling biochemist DNA sequencing methods - an overview of Sanger, Illuminia, PacBio, and Oxford NanoPore

YT 20 minutes 48 seconds the bumbling biochemist Sequencing your plasmids (emphasis on Sanger sequencing) YT 24 minutes 17 seconds the bumbling biochemist Colony PCR - a quickish way to see if your cloning probably worked: a time, thumb, & resource-saver! YT 8 minutes 11 seconds the bumbling biochemist How a NanoDrop works

YT 26 minutes 28 seconds the bumbling biochemist Fusion partners for improving solubility & expression of recombinant proteins - SUMO, GST, MBP, etc. YT 49 minutes 39 seconds the bumbling biochemist Protein chromatography - an overview of affinity, ion exchange, and size exclusion chromatography YT 21 minutes 12 seconds the bumbling biochemist What do biochemists do? Lots of things! And what is biochemistry, anyway?

YT 15 minutes 35 seconds the bumbling biochemist Structural biology resources - guide to my favorite software, articles, books, lectures, websites YT 31 minutes 36 seconds the bumbling biochemist What do structural biologists do? YT 28 minutes 53 seconds the bumbling biochemist X-ray crystallography maps (viewing & understanding 2Fo-Fc, Fo-Fc, etc.) & overview of phase problem

YT 21 minutes 44 seconds the bumbling biochemist X-ray crystallography and cryo-em (cryo-electron microscopy): an overview & comparison YT 30 minutes 58 seconds the bumbling biochemist It's just a model! Understanding x-ray crystallography & cryo-EM maps, models, and resolution YT 18 minutes 58 seconds the bumbling biochemist Viewing maps & evaluating resolution (global & local), B factor, contour, etc. - look in Pymol

YT 15 minutes 16 seconds the bumbling biochemist Resolution of molecular structures - an overview YT 55 minutes 20 seconds the bumbling biochemist Pyrrolysine and noncanonical incorporation with PylRS + PyltRNA & amber suppression YT 32 minutes 57 seconds the bumbling biochemist Using antibiotics as selectable markers for plasmids in the lab (antibiotic-based selection)

YT 9 minutes 36 seconds the bumbling biochemist Antibiotic types & resistance mechanisms: an overview YT 13 minutes 39 seconds the bumbling biochemist Housekeeping genes/proteins, internal references/loading controls & related terms: constitutive etc. YT 11 minutes 14 seconds the bumbling biochemist Endogenous vs. Exogenous - terminology, techniques, and biochemistry experimental considerations

YT 23 minutes 38 seconds the bumbling biochemist Lab equipment for heating, cooling, and incubating - what's what and which to use when YT 27 minutes 58 seconds the bumbling biochemist PCR (Polymerase Chain Reaction) - a comprehensive overview with tips to help it work well for you! YT 13 minutes 54 seconds the bumbling biochemist Hot start PCR & avoiding "nonspecific products"

YT 10 minutes 34 seconds the bumbling biochemist Role of heated lids in thermal cyclers (PCR machines) YT 6 minutes 18 seconds the bumbling biochemist Edge effects in multiwell plates YT 14 minutes 52 seconds the bumbling biochemist Fraction collection - practical tips and strategizing

YT 28 minutes 3 seconds the bumbling biochemist Colony PCR YT 13 minutes 56 seconds the bumbling biochemist “Preparative” vs “analytical” techniques & examples of when you might use what YT 37 minutes 54 seconds the bumbling biochemist Conditional degron tags

YT 36 minutes 12 seconds the bumbling biochemist Targeted protein degradation (via PROTACs, molecular glues, etc.) and stabilization (via DUBTACs) YT 14 minutes 3 seconds the bumbling biochemist Phenol red and pH buffering of cell culture media YT 7 minutes 39 seconds the bumbling biochemist Tips for efficiently balancing and preparing centrifuge tubes

YT 41 minutes 53 seconds the bumbling biochemist What gels and blots can and can’t tell you - interpreting (without overinterpreting) your results YT 20 minutes 23 seconds the bumbling biochemist Gel ladders - tips and tricks for using molecular weight markers YT 34 minutes 53 seconds the bumbling biochemist TRIzol extractions of RNA, DNA, and protein

YT 14 minutes 43 seconds the bumbling biochemist Troubleshooting and optimizing lab experiments YT 13 minutes 52 seconds the bumbling biochemist Homogenization and lysis (cellular disruption) - an overview of methods and practical considerations YT 10 minutes 32 seconds the bumbling biochemist Coprecipitants like GlycoBlue (and normal glycogen or LPA) in nucleic acid precipitation

YT 33 minutes 3 seconds the bumbling biochemist Splitting (aka passaging, subculturing) cells - what, why, & how YT 17 minutes 8 seconds the bumbling biochemist Harvesting cell culture - basics and practical tips YT 14 minutes 5 seconds the bumbling biochemist Pelleting tips and tricks

YT 33 minutes 10 seconds the bumbling biochemist Working with laboratory centrifuges and ultracentrifuges: practical tips, tricks, & best practices YT 10 minutes 35 seconds the bumbling biochemist Basics of lab centrifuges - rpm vs. rcf, swinging bucket vs. fixed angle, ultra vs. "normal", etc. YT 7 minutes 15 seconds the bumbling biochemist Making 70% ethanol solutions (the right way)

YT 24 minutes 53 seconds the bumbling biochemist Probing a western blot membrane for multiple things: multiplexing, stripping & re-probing, etc. YT 22 minutes 4 seconds the bumbling biochemist Preparing EDTA stock solutions YT 15 minutes 47 seconds the bumbling biochemist Chelators in the lab: EDTA & EGTA biochemistry

YT 27 minutes 22 seconds the bumbling biochemist Reproducing and adapting experimental protocols - get ready to Google! (and think critically) YT 10 minutes 51 seconds the bumbling biochemist Working with relative concentrations (in terms of stock solutions) YT 9 minutes 25 seconds the bumbling biochemist Parafilm "M" (M's a mystery...) and its many lab uses

YT 14 minutes 6 seconds the bumbling biochemist Best practices for working with molecular biology enzymes YT 25 minutes 28 seconds the bumbling biochemist Trypan blue dye exclusion test in cell counting YT 17 minutes 41 seconds the bumbling biochemist Laboratory water: What to know about lab H2O

YT 45 minutes 24 seconds the bumbling biochemist Biochemistry and molecular biology techniques - an overview YT 28 minutes 39 seconds the bumbling biochemist Pipette like a pro - basics & tips for using micropipettes & serological pipettes YT 10 minutes 47 seconds the bumbling biochemist Pipette types and tips - an intro/overview

YT 21 minutes 53 seconds the bumbling biochemist DMSO biochemistry YT 2 minutes 37 seconds the bumbling biochemist LabTips: prepping lots of gel samples edition YT 7 minutes 18 seconds the bumbling biochemist Cell scraping

YT 11 minutes 30 seconds the bumbling biochemist Cell detachment with trypsin/EDTA: the biochemistry going on when you take cells off! YT 12 minutes 13 seconds the bumbling biochemist Western blot blocking solutions YT 12 minutes 22 seconds the bumbling biochemist Mammalian cell culture media basics

YT 11 minutes 58 seconds the bumbling biochemist Filtering biochemical solutions - practical advice YT 19 minutes 54 seconds the bumbling biochemist Cryopreserving cell stocks YT 33 minutes 36 seconds the bumbling biochemist Western blots: the what's, why's, and which's, of the workflow

YT 20 minutes 30 seconds the bumbling biochemist HEK 293 cells: types and uses YT 17 minutes 40 seconds the bumbling biochemist Light-based readouts in biochemistry: colorimetric vs luminescent methods; light absorption, etc. YT 17 minutes 31 seconds the bumbling biochemist Luminescence and its uses in biochemistry

YT 17 minutes 4 seconds the bumbling biochemist Native PAGE (PolyAcrylamide Gel Electrophoresis) overview YT 16 minutes 12 seconds the bumbling biochemist Ames test for mutagenicity - the biochemistry behind it YT 7 minutes 55 seconds the bumbling biochemist Core facilities and shared research resources

YT 10 minutes 49 seconds the bumbling biochemist What's omics? A quick intro (from a non-pro) YT 20 minutes 46 seconds the bumbling biochemist Low melting point agarose YT 35 minutes 44 seconds the bumbling biochemist Fluorescent nucleic acid stains & fluorescence basics

YT 22 minutes 5 seconds the bumbling biochemist Gel extraction with the "crush and soak" method YT 7 minutes 47 seconds the bumbling biochemist Random tips for choosing & using micropipettes YT 7 minutes 53 seconds the bumbling biochemist Tips for when liquid jumps back & gets stuck in your micropipet tips! And how to prevent it

YT 20 minutes 56 seconds the bumbling biochemist DNA & RNA precipitation with alcohols & salts - theory, practice, & options (EtOH vs IsOH, etc.) YT 9 minutes 57 seconds the bumbling biochemist Nucleic acid precipitation with alcohol - an overview & discussion of co-precitants YT 9 minutes 55 seconds the bumbling biochemist Microcentrifuge tips and tricks

YT 14 minutes 15 seconds the bumbling biochemist Resuspending, diluting, & working with DNA & RNA oligos (primers you order, etc.) YT 11 minutes 5 seconds the bumbling biochemist Spin column purification of nucleic acids - the biochemistry of how they work YT 12 minutes 31 seconds the bumbling biochemist Some solid solutions to making solutions (or at least some bubbly tips)

YT 4 minutes 6 seconds the bumbling biochemist Random tips for working with DNA/RNA spin columns (like those in miniprep or PCR purification kits) YT 10 minutes 36 seconds the bumbling biochemist What to do when a plasmid comes for you: agar stab to plate to glycerol stock, miniprep & sequencing YT 22 minutes 21 seconds the bumbling biochemist Don't let your electrophoresis gels smile - gel electrophoresis voltage, heat, buffers etc.

YT 13 minutes 34 seconds the bumbling biochemist C1V1 = C2V2 (aka M1V1=M2V2) is so useful for calculating solution volumes & concentrations! YT 24 minutes 34 seconds the bumbling biochemist Mastering master mixes - calculations & concepts YT 23 minutes 55 seconds the bumbling biochemist Bacterial transformation - chemically competent cells & heat shock

YT 28 minutes 27 seconds the bumbling biochemist Nucleic acid PAGE (Polyacrylamide Gel Electrophoresis), with emphasis on urea PAGE YT 12 minutes 14 seconds the bumbling biochemist Tips for loading PAGE gels - the strategy that works for me YT 3 minutes 39 seconds the bumbling biochemist Flash freeze fishing - and other tricks for snap freezing eppendorf tubes in liquid nitrogen

YT 14 minutes 55 seconds the bumbling biochemist Protein prep inventory-ing: keeping a detailed inventory of cell pellets and purified proteins YT 21 minutes 32 seconds the bumbling biochemist Keeping a detailed plasmid inventory YT 16 minutes 26 seconds the bumbling biochemist Why Kd doesn't depend on concentrations, but what you measure might; binding vs titration range, etc

YT 14 minutes 39 seconds the bumbling biochemist Lab labeling - some tips to labeling tubes, etc. effectively YT 2 minutes 52 seconds the bumbling biochemist The finger flick - an awesome lab trick! Finger vortexing & other mixing methods YT 4 minutes 19 seconds the bumbling biochemist Making a 80% glycerol stock solution - a simple lab hack that makes glycerol way easier to work with

YT 6 minutes 53 seconds the bumbling biochemist Pipetting viscous liquids - reverse pipetting, etc. YT 17 minutes 42 seconds the bumbling biochemist Miniprep science - what goes on in each step of a miniprep (alkaline lysis plasmid purification) YT 27 minutes 1 second the bumbling biochemist LB agar plates - theory & practice

YT 23 minutes 48 seconds the bumbling biochemist DH5α strains and a PSA to sequence your plasmids YT 24 minutes 2 seconds the bumbling biochemist Bacterial expression strains - esp BL21 strains with plasmids containing tRNAs for rare codons YT 44 minutes 37 seconds the bumbling biochemist Choosing vector plasmids and subcloning

YT 31 minutes 8 seconds the bumbling biochemist Choosing an experimental system in biochemistry YT 38 minutes 3 seconds the bumbling biochemist T7 RNA Polymerase & in vitro transcription (and more) YT 14 minutes 46 seconds the bumbling biochemist Making the most of experimental methods sections

YT 30 minutes 35 seconds the bumbling biochemist Ribosome toeprinting (aka primer extension inhibition) lets you see where ribosomes stall YT 19 minutes 21 seconds the bumbling biochemist Puromycin biochemistry & uses in biochemistry YT 10 minutes 30 seconds the bumbling biochemist rRNA (ribosomal RNA) depletion methods

YT 18 minutes 17 seconds the bumbling biochemist RNase inhibition & avoidance - RNase inhibitors, DEPC, RNaseZAP, etc. YT 19 minutes 2 seconds the bumbling biochemist Ribosome footprinting (aka profiling aka Ribo-seq) & polysome profiling - an overview & comparison YT 33 minutes 27 seconds the bumbling biochemist Antibiotic selection - mechanisms & usage of antibiotics & resistance genes in molecular cloning

YT 1 hour 2 minutes 53 seconds the bumbling biochemist Experimental techniques: overview of biochemistry, molecular biology & structural biology techniques YT 45 minutes 59 seconds the bumbling biochemist Lab equipment: Tour, terminology, & tips (biochemistry, structural, molecular biology focus) YT 31 minutes 3 seconds the bumbling biochemist Radiolabeling nucleic acids - the how & why of radiolabeling DNA & RNA w/emphasis on 5' end labeling

YT 26 minutes 35 seconds the bumbling biochemist Lab antibody considerations - monoclonal vs polyclonal, production, usages, epitope tags, etc. YT 44 minutes 41 seconds the bumbling biochemist northern blots, Southern blots, western blots, & more - similarities, differences, uses, etc. YT 31 minutes 45 seconds the bumbling biochemist Desalting & buffer exchange gel filtration columns - theory, practice, & comparison to other methods

YT 32 minutes 44 seconds the bumbling biochemist Restriction enzymes - what they are & practical stuff about using them in the lab YT 16 minutes 47 seconds the bumbling biochemist Protein chromatography as a museum - a little geeky fun... YT 41 minutes 49 seconds the bumbling biochemist Size Exclusion Chromatography (aka Gel Filtration): theory & practice of preparative & analytical

YT 32 minutes 17 seconds the bumbling biochemist Ion exchange chromatography protein purification and isoelectric point (pI) YT 27 minutes 53 seconds the bumbling biochemist Coomassie Brilliant Blue Dye - the science of SDS-PAGE staining YT 41 minutes 9 seconds the bumbling biochemist Casting polyacrylamide gels - in theory (the polymerization reaction) & practice

YT 20 minutes 53 seconds the bumbling biochemist Liquid Scintillation Counting - a scintillating look inside of a way to measure radioactive decay! YT 24 minutes 39 seconds the bumbling biochemist Cryoprotecting, flash freezing, and storing protein samples: cryoprotectants, vitrification, etc. YT 24 minutes 32 seconds the bumbling biochemist Centrifugal ultrafiltration (spin concentrators) for protein (or nucleic acid) concentrating

YT 31 minutes 56 seconds the bumbling biochemist Protein dialysis in biochemistry - theory & practice YT 37 minutes 34 seconds the bumbling biochemist Strep-tag affinity chromatography protein purification - theory & practice YT 36 minutes 40 seconds the bumbling biochemist Phage display - theory, techniques, & uses

YT 20 minutes 8 seconds the bumbling biochemist Experiment-ing: organizedly planning out, preparing for, performing, & writing notes for experiments YT 33 minutes 22 seconds the bumbling biochemist Interpreting & working with protein chromatography chromatograms - w/practical look on an AKTA YT 22 minutes 12 seconds the bumbling biochemist Prepping proteins for purification: a practical look at lysis, sonication, ultracentrifugation, etc.

YT 20 minutes 47 seconds the bumbling biochemist Figuring out sig figs - working with significant figures YT 45 minutes 58 seconds the bumbling biochemist Protein chromatography - types, tips, & example workflow for protein purification YT 31 minutes 49 seconds the bumbling biochemist Western blot workflow - theory & practice

YT 39 minutes 8 seconds the bumbling biochemist RT-qPCR (Reverse Transcription/Real Time - quantitative Polymerase Chain Reaction) theory & practice YT 42 minutes 40 seconds the bumbling biochemist Gene expression - levels of regulation & measurement techniques YT 35 minutes 43 seconds the bumbling biochemist Phenotype, genotype, forward vs. reverse genetics - tricky terms & tons of techniques

YT 23 minutes 1 second the bumbling biochemist Bacterial growth media - terms, types (LB, TB, SOC, etc.), and usages in biochemistry YT 39 minutes 58 seconds the bumbling biochemist Recombinant protein expression in bacteria using the inducible T7/pET system YT 43 minutes 4 seconds the bumbling biochemist Baculovirus Expression Vector Systems - expressing proteins in insect cells - theory & practice

YT 35 minutes 51 seconds the bumbling biochemist Molecular cloning overview - techniques & workflow YT 20 minutes 45 seconds the bumbling biochemist Blue-white screening biochemistry YT 32 minutes 15 seconds the bumbling biochemist Codon Optimization & Codon Usage Bias

YT 20 minutes 35 seconds the bumbling biochemist Specific activity & enzyme activity units (those pesky U's) - an explanation & rant YT 35 minutes 56 seconds the bumbling biochemist Cell-free protein expression & the biochemistry of the PURE expression system YT 25 minutes 59 seconds the bumbling biochemist RNA interference (RNAi): microRNA (miRNA), siRNA, Argonaute (Ago) proteins, & a comparison to CRISPR

YT 29 minutes 27 seconds the bumbling biochemist Vapor diffusion crystallization - theory & practice of hanging & sitting drop crystallization YT 51 minutes 32 seconds the bumbling biochemist Biochemical approaches to studying protein-protein & protein-nucleic acid interactions YT 23 minutes 51 seconds the bumbling biochemist Agarose science - composition, gelification, hysteresis, syneresis, modifications, etc.

YT 19 minutes 59 seconds the bumbling biochemist Kd (equilibrium dissociation constant) & how binding assays let us find it YT 36 minutes 53 seconds the bumbling biochemist X-ray crystallography & resolution YT 18 minutes 21 seconds the bumbling biochemist Hot Start PCR, heated lids, polymerase options, etc. - basically random PCR stuff...

YT 29 minutes 27 seconds the bumbling biochemist PCR (Polymerase Chain Reaction) - theory & practical tips YT 40 minutes 19 seconds the bumbling biochemist Unnatural/non-canonical amino acid incorporation by "genetic code expansion" inspired by pyrrolysine YT 34 minutes 36 seconds the bumbling biochemist His-Tag Protein Purification theory & practice - Immobilized Metal Affinity Chromatography (IMAC)

YT 19 minutes 46 seconds the bumbling biochemist Protein UV absorption - starring tryptophan, Beer's Law, & more YT 32 minutes 27 seconds the bumbling biochemist EMSA (gel shift assay) - Electrophoretic Mobility Shift Assay. Theory, pros, cons, & controls! YT 9 minutes 1 second the bumbling biochemist Why your plasmid runs weird on an agarose gel: DNA topology meets agarose gel electrophoresis

YT 21 minutes 21 seconds the bumbling biochemist Formaldehyde protein/nucleic acid & protein/protein crosslinking biochemistry YT 31 minutes 39 seconds the bumbling biochemist Choosing and preparing pH buffers - practical stuff YT 8 minutes 5 seconds the bumbling biochemist pH buffers - an overview

YT 16 minutes 15 seconds the bumbling biochemist Protein-protein crosslinking - an overview with emphasis on structural biology uses YT 10 minutes 12 seconds the bumbling biochemist Blue Native PAGE (BN-PAGE) behind the scenes YT 26 minutes 27 seconds the bumbling biochemist Native PAGE (PolyAcrylamide Gel Electrophoresis) & Blue Native PAGE

YT 29 minutes 43 seconds the bumbling biochemist Protein charge and isoelectric point (pI) - "basic" vs "acidic" etc. YT 26 minutes 46 seconds the bumbling biochemist Protease types, mechanisms, and inhibitors YT 26 minutes 51 seconds the bumbling biochemist Size Exclusion Chromatography (SEC) (aka Gel Filtration): preparative & analytical on the AKTA

YT 20 minutes the bumbling biochemist Proteases and their inhibitors - a biochemist's overview of the what, where, when, & how YT 54 minutes 34 seconds the bumbling biochemist Biochemistry resources - a guide to my favorite books, articles, sites, software, etc. YT 21 minutes 1 second the bumbling biochemist Making stock solutions - how and why

YT 33 minutes 49 seconds the bumbling biochemist Determining concentration & purity of RNA & DNA with UV spectroscopy: Beer's Law and Beyond! YT 37 minutes 44 seconds the bumbling biochemist Minipreps: alkaline lysis based plasmid purification YT 29 minutes 36 seconds the bumbling biochemist RNA extraction biochemistry (the TRIzol aka TRI aka guanidinium thiocyanate–phenol–chloroform way)

YT 22 minutes the bumbling biochemist Percent weight-volume (% w/v): where it comes from, why I hate it, & better alternatives (molarity!) YT 28 minutes 46 seconds the bumbling biochemist Casting polyacrylamide gels - practice & theory of acrylamide polymerization YT 27 minutes 26 seconds the bumbling biochemist Bacterial transformation - heat shock with chemically competent cells

YT 7 minutes 43 seconds the bumbling biochemist HDX-MS (Hydrogen Deuterium eXchange Mass Spectrometry) basic overview YT 27 minutes 15 seconds the bumbling biochemist Meet the AKTA! Fast Protein Liquid Chromatography (extended version w/extra tips for frequent users)