2023

Lunar New Year 2023 2023-01-22

卯年の旧正月を祝うために四川風の年夜飯を拵えた。麻辣兎丁と麻婆豆腐と回鍋肉に、Pimm’s No.1 Cup プラチナジュビリー限定版と國窖1573をあしらった。

To celebrate the lunar New Year of the Rabbit, I cooked a Szechuanese Nianyefan, featuring Hot & Spicy Diced Rabbit, Mapo Tofu and Hui Guo Rou, accompanied by Pimm’s No.1 Cup Platinum Jubilee Edition and Guo Jiao 1573.

旧正月を機に韓国とベトナムの正月料理を作ってみた。

It is a great chance for me to try making some Korean and Vietnamese festive dishes.

トッククは、椎茸とカルビを煮込んだスープでトックを茹で上げ、錦糸卵（白身と黄身は別々で）とネギをトッピングしたものです。 トッククを作るのは初めてだったけどこんなに美味しいとは思わなかった。さほど手間がかからないし今後は日常的に作るようになるかもしれん😋

The Tteokguk was made by boiling Tteok (Korean rice cakes) in Shiitake mushrooms & beef Galbi soup and topping it with spring onions and thin strips of fried egg white & yolk. This is the first time I make Tteokguk and I never knew it’s so appetising. Since it does not require much effort I might routinely enjoy it from now on.

生春巻きの具材にバラ肉、海老、ビーフン、人参、胡瓜、もやし、レタス、ミント、コリアンダーとニラを使った。 ヌオックチャムのソースは、砂糖を魚醤に溶かし、搾りたてのライムの果汁と混ぜ、ニンニクの微塵切りとタイ産 bird’s eye 唐辛子の輪切りをあしらったものです。生のニラとコリアンダーが合うか心配だったけれど実際に食べてみたら意外と美味しかった。 バラ肉の脂っこさを和らげられるので相性抜群だった。

Gỏi cuốn (Vietnamese spring rolls) were made by rolling up dampened bánh tráng (rice paper) to wrap the ingredients of choice (I used a customary combination of pork belly, king prawns, rice vermicelli, carrot & cucumber strands, bean sprouts, lettuce, mint, coriander, and Chinese chive). To make the nước chấm sauce, dissolve sucrose in fish sauce, mix with freshly squeezed lime juice and garnish with finely chopped garlic and rings of bird’s eye chillies. Raw Chinese chives and coriander seemed intimidating to me at first but surprisingly I had no problem adapting to them and I realized how they are a perfect match for the pork belly by diminishing its greasiness.

残りのバラ肉は叉焼に仕上げてラーメンのトッピングにした。

The remaining pork belly were processed into Chashu and used as a topping for ramen.

2022

Personal Notes on RNA-seq 2022-07-29

• 1 Overview
• 2 Trimming
• 3 Mapping
  • 3.1 STAR
  • 3.2 HISAT2

1 Overview

Typical RNA-seq data analysis workflow:

1. Trimming, i.e. removal of the adapter sequences and poor-quality nucleotides. Quality control checks help to indicate whether trimming has been carried out appropriately.
2. Alignment to a reference genome
3. Gene quantification and normalization with reference to a file containing gene positions (GTF file)
4. Differential expression (DE) analysis across conditions

2 Trimming

3 Mapping

3.1 STAR

The --outSAMstrandField intronMotif option adds an XS attribute to the spliced alignments in the BAM file, which is required by Cufflinks for unstranded RNA-seq data (Dobin and Gingeras 2015).

3.2 HISAT2

HISAT2’s (Kim-2019?) alignment algorithm is based on a graph Ferragina Manzini index, which is faster and more memory-efficient than STAR.

HISAT2 binaries and indexes for H. sapians and a few model organisms are available for download from the official website.

Dobin, Alexander, and Thomas R. Gingeras. 2015. “Mapping RNA-Seq Reads with STAR.” Current Protocols in Bioinformatics 51 (1): 11.14.1–19. https://doi.org/https://doi.org/10.1002/0471250953.bi1114s51.

2020

Michaelmas Term

Tutorial: Insertion of Membrane Proteins Week 8

Tutorial: Protein-Nucleic Acid Interactions Week 7

Lab: Metabolic Modelling Week 7

Lab: Gene Expression Practical Paper 6 Questions Week 6

Worksheet: Data Handling — Biophysical Methods Week 7

Tutorial: Protein-Protein Interactions Week 6

Tutorial: Membrane Protein: Structure and Stability Week 5

Lab: Gene Control Practical Week 5

Tutorial: Crystallography: A Case Study Week 4

Tutorial: Assessing The Quality Structural Models Week 3

Bioinformatics: Download and Sync with the Entire PDB Database Week 2

Bioinformatics: Sequence Alignment: Gap Penalty Week -4

Bioinformatics: FASTA Parser Implemented in Rust with Nom Week -5

Trinity Term

Tutorial: Redox-Based Modulation of Enzyme Activity Week 8

Tutorial: Improving Photosynthesis by Photorespiratory Bypasses Week 7

Lab: Computational Genomics Practical (TT 2020) Week 6

Tutorial: Genetic Manipulation of the Calvin Cycle Week 6

Tutorial: Coordination of PS I and PS II Week 5

Tutorial: Fuel Selection During Exercise Week 4

Tutorial: Insulin and Ketone Bodies Week 3

Tutorial: Glucagon and Insulin Week 2

Tutorial: Supplying Fuels to the Brain During Starvation Week 1

Hilary Term

Lab: Immunoassay (in Silico) Week 8

Tutorial: How Has Ras Signalling Been Studied in C. Elegans Week 8

Tutorial: What is the Point of Studying Developmental Biology Week 7

Bioinformatics: Random Notes on Bioinformatics Week 6

Bioinformatics: Visualising the Resolution Revolution of Electron Microscopy Week 6

Tutorial: Three Biophysical Methods Week 6

Bioinformatics: Visualizing Protein Structures Using Plotly Week 5

Tutorial: Electron Microscopy and X-Ray Crystallography Week 5

Learning objectives To understand the methodological principle of electron microscopy in its different applications (e.g. TEM, SEM, tomography, single-particle), and X-ray crystallography  To be able to evaluate, which method of structural analysis would be most feasible with which kind of biological specimen (e.g. whole cells, viruses, protein complexes, peptides). To gain a conception of the resolution ranges attainable by EM methods as compared to X-ray crystallography. To be aware of the computational methods that combine EM maps and crystallogrographic data

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Tutorial: Bacterial Cell Division Week 4

discussing both Gram positive and negative bacteria with different morphologies, how they divide and chose examples of antibiotics, comparing their different effects

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Bioinformatics: Isoelectric Point Calculation Week 4

Notes: Molecular Cloning Week 3

Bioinformatics: Sequence Alignment Week 3

Lab: Protein Purification Practical Week 3

Fun: Vim Week 2

Notes: Techniques Week 2

Tutorial: MCB Toolbox Week 2

Special: 2019–20 outbreak of novel coronavirus '2019-nCoV' Week 1

Tutorial: Vectors Used in Bacterial and Eukaryotic Host Cells Week 1

What are the key similarities and differences between vectors used in bacterial and eukaryotic host cells? What can such vectors be used for?

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2019

Michaelmas Term

Tutorial: Antibiotics and Protein Synthesis Week 8

Explain how antibiotics and genetic mutations have helped in our understanding of the mechanism of protein synthesis on the ribosome.

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Tutorial: RNA Splicing Week 7

What are the roles of small nuclear RNAs (SnRNAs) in pre-mRNA splicing and what are the mechanisms that control alternative splicing?

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Tutorial: NMR Week 6

Tutorial: Biophysical Techniques Week 5

You have expressed and purified a protein in a recombinant system. How would you confirm that the protein was the one expected from the DNA sequence. (ESI-MS) How would you determine that the protein was folded and its solution behaviour. (CD, Thermofluor, Intrinsic fluorescence, DSC, SEC MALS, AUC, DLS) How can we quantify the binding between two macromolecules? Discuss how you could use the following techniques to determine a KD for an interaction? What are their limitations in practice? What would decide which techniques you could apply to an interaction? (Surface Plasmon resonance, Fluorimetry/Fluorescence anisotropy, Microscale thermophoresis (MST), Isothermal titration calorimetry (ITC), Stopped flow, NMR, AUC) References: Use Campbell's Biophysical Techniques; for MST use Wienken et al 2010 Nature Communications 10.1038/ncomms1093

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Tutorial: Paper VI 2011 Week 5

Tutorial: Protein Expression and Purification Week 4

You want to over-express a protein secreted by the malarial parasite. It is cysteine-rich and has no known structure. Outline an expression and purification strategy, using both traditional and high-throughput methods, to produce a sample suitable for protein crystallography. Include a description of how you would assess the quality of the purified protein. OR What strategies could you employ during protein expression and purification to minimise heterogeneity in a sample required for structural studies?

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Tutorial: Protein Structure and Function Week 3

Choose 3 structural papers. They can be crystallography, NMR, CryoEM etc. Explain why the protein is important and what the structure tells you about function (why you find it interesting) but most importantly go to the methods section (it may be supplementary information especially if you choose high profile paper) and explain how the protein was purified. The techniques will be those covered in Matt Higgins' lecture series. Bring notes no essay.

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Tutorial: Principle of electron transfer and proton transport Week 2

What mechanisms are employed by mitochondrial electron transfer proteins to generate a proton-motive force (pmf)? Using the concept of membrane capacitance, explain why the dominant component of the pmf in mitochondria is an electrical potential rather than a pH gradient.

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Lab: Specific Radioactivity Week 1

Specific radioactivity of ATP and glucose.

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Worksheet: Radioactivity Worksheet Week 5

Tutorial: Principle of chemiosmotic mechanism Week 1

What is the evidence that the chemiosmotic mechanism applies to oxidative phosphorylation and photophosphorylation?

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