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The Bumbling Biochemist

The Bumbling Biochemist

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Category: 365 Days of Science

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Predicting protein protonation states with H++

July 28, 2024July 28, 2024

We’ve noticed some pH-dependent changes in our protein, so a free web-based tool that I’ve been exploring is H++. It […]

Differential Scanning Fluorimetry (DSF), aka Fluorescence Thermal Shift (FTS), aka Fast Thermal Melt

July 27, 2024January 26, 2026

Fluorescence Thermal Shift (FTS), aka Differential Scanning Fluorimetry (DSF) aka Fast Thermal Melt, is a way to measure the thermal […]

Autoinduction for recombinant protein overexpression

June 7, 2024January 21, 2026

Auto-induction is an alternative to IPTG-based induction for genes under regulation by a lac promoter. The media involves a mix […]

Notes on RT-qPCR vs RNA-seq

May 21, 2024May 21, 2024

RT-qPCR (reverse transcription quantitative PCR) lets you measure “gene expression” at the level of mRNA. Basically, you can see how […]

One-year teaching update

May 17, 2024May 17, 2024

I can’t believe it’s (almost) been a full academic year as a visiting professor at St. Mary’s College of California! […]

Lipid metabolism

April 21, 2024November 22, 2024

Page navigation: Videos; Graphics; Key points; Related posts; Recommended reading Videos Lipid anabolism (synthesis) Lipid catabolism (breakdown) Integrated lipid metabolism […]

Critically evaluating supplements, etc.: systematic reviews, meta-analyses, biases, evidence, etc.

April 1, 2024August 12, 2026

Don’t be fooled by biochemically-plausible-sounding claims! Use biochemistry knowledge with caution! Seek out systematic reviews & meta-analyses But remember: garbage […]

Advice for following and interpreting metabolic charts

March 29, 2024March 29, 2024

The biggest thing is to not be intimidated by them! Instead, after looking at the “start” and the “end” of […]

How alcohol affects metabolism

December 31, 2023January 1, 2024

At least some of the many ways… Ethanol metabolism is practically unregulated, but it produces metabolites (e.g. NADH & ATP) […]

Tips for scientific writing – write to be understood, not to “sound smart”

November 19, 2023November 19, 2023

note: be sure to check with your instructor if applicable because some might not like this

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