Biology and Evolution

Puzzling observations from various eukaryotic genomes (part III)

We are continuing our discussion of eukaryotic genome evolution based on Dan Graur’s “Molecular and Genome Evolution”. In this post, we present a number of puzzling observations in various eukaryotic genomes. The title of each section also includes the page number of Graur’s book, where the observation is reported.

How do the eukaryotic genomes evolve? (part II)

We are continuing our discussion of eukaryotic genome evolution based on Dan Graur’s “Molecular and Genome Evolution”. In this post, we look at two key measures - genome size and gene size.

How do the eukaryotic genomes evolve? (part I)

In the previous post, I wrote about the book “Molecular and Genome Evolution” by Dan Graur. It contains thirteen chapters as shown below. Chapters 7-11 may be considered the heart of the book, where Graur discusses how the genomes evolve and how new genes come into existence. Among those, the chapters 6-8 present three mechanisms for genome evolution, namely DNA duplication, molecular tinkering and mobile elements. Subsequently, chapters 10 and 11 discuss evolutionary aspects of the prokaryotic and the eukaryotic genomes respectively.

Molecular and Genome Evolution by Dan Graur

Over the last two weeks, I have been reading Dan Graur’s book titled “Molecular and Genome Evolution”. This is a fantastic book that everyone should read before starting to work on any genome-related project. For the benefit of our readers, I will share some comments in this short post. If time permits, I will later follow up with a longer post on the book.

The Diversity of REcent and Ancient huMan (DREAM)

Population Genetics of Ancient Jewish Population in India

‘Ancient’ Bene Israel Jews and late-arrived Baghdadi Jews in India started the Bollywood movie industry. Many famous early Indian actresses also came from these communities. This is not common knowledge in India, because those actresses took Muslim (Firoza Begum) or Hindu (Sulochana, Pramila) screen names.

Transistors, Translation and tRNAs

Organoids and the Coming Medical Revolution - (ii)

Transfer RNAs and Neurodegenerative Disorders

Among all biomolecules within the cell, tRNAs got the least respect. Their supposed importance ended right after the ‘adaptors’ related to entries in the genetic code table were identified (mid-60s). Since then, the attention shifted to more complex RNAs like the rRNAs.

Organoids and the Coming Medical Revolution - (i)

Among various biotechnology inventions of the last few years with potential to revolutionize medicine, nothing excites us more than growing of three- dimensional human organoids on matrigel. Therefore, we plan to devote a number of posts on this topic to keep our readers aware of the practices, potentials and challenges.

Comments on Our New Paper - "Sequence Analysis and Comparative Study of the Protein Subunits of Archaeal RNase P"

How did life originate on earth? What chemical properties of living objects make them different from the non-living objects? Where did the genome come from in the first place? How was life before the emergence of the genetic code? Why does the genetic code have that specific form? What biochemical advantages do the proteins get by having methionine as their first amino acid? How did the metabolic pathway evolve to its current form? How did bacteria, archaea and eukaryotes evolve into distinct kingdoms? How did multi- cellularity evolve? How did our ability to hear and smell evolve? Where did the adaptive immune system come from?

Quasi-essential genes supporting yet undiscovered functions for life?

Venter’s group published a new paper on minimal genome.

Formin Is Associated with Left-Right Asymmetry in the Pond Snail and the Frog

This is another fascinating paper showing how little we know about the most basic questions, including ‘symmetry-breaking’ during animal development.

New Paper by Elhaik Shows that Ashkenazi Jews Came from Northeastern Turkey

Zika Oxitech Connection Can be Explained without Resorting to 'Conspiracies'

Zerohedge reported -

Rubbish DNA: The functionless fraction of the human genome

Here is a challenge. Guess the author’s name before looking at this new arxiv paper.

Solute Carrier Proteins and Their Therapeutic Implication

These days, when we analyze transcriptome data sets from vetebrates, one or other solute carrier gene often comes to the top. If have the same experience and spend a lot of time searching through various databases to find what they do, the following two reviews will come handy. The first author of both papers is Matthias A. Hediger, who is currently at Institute of Biochemistry and Molecular Medicine, University of Bern, Switzerland.

Wobble Modification and Human Diseases (3 old links)

A mitochondrial tRNA(Lys) gene mutation at nucleotide position 8344 is responsible for the myoclonus epilepsy associated with ragged-red fibers (MERRF) subgroup of mitochondrial encephalomyopathies. Here, we show that normally modified uridine at the anticodon wobble position remains unmodified in the purified mutant tRNA(Lys). We have reported a similar modification defect at the same position in two mutant mitochondrial tRNAs(Leu)(UUR) in another subgroup, mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS), indicating this defect is common in the two kinds of tRNA molecules with the respective mutations of the two major mitochondrial encephalomyopathies. We therefore suggest the defect in the anticodon is responsible, through the translational process, for the pathogenesis of mitochondrial diseases.

Agmatidine in Archael tRNA

Agmatidine (2-agmatinylcytidine, symbol C+ or agm2C) is a modified cytidine present in the wobble position of the anticodon of several archaeal AUA decoding tRNAs. Agmatidine is essential for correct decoding of the AUA codon in many archaea and is required for aminoacylation of tRNAIle2 with isoleucine. Agmatidine - wiki

Was July 20 a Turning Point for Stock Markets?

[Standard disclaimer - the following post is for entertainment only, and not financial advice of any sort.]

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