# gene: bacteria and archaea CRISPR everywhere in nature

<< Single-celled bacteria and archaea use CRISPR systems to defend themselves against viruses known as bacteriophages. (..) Until now, researchers had identified six types of CRISPR system, designated I–VI. >>

AA << developed an algorithm called FLSHclust, which analyses genetic sequences in public databases. (..) By looking at the predicted function of the clusters, the researchers found around 130,000 genes associated in some way with CRISPR, 188 of which had never been seen before, >>️️

<< It’s a treasure trove for biochemists, >> Lennart Randau.

Sara Reardon. ‘Treasure trove’ of new CRISPR systems holds promise for genome editing. Nature. doi: 10.1038/ d41586-023-03697-w. Nov 23, 2023. 

https://www.nature.com/articles/d41586-023-03697-w

Han Altae-Tran, Soumya Kannan, Feng Zhang, et al. Uncovering the functional diversity of rare CRISPR-Cas systems with deep terascale clustering. 

Science, Vol 382, Issue 6673. doi: 10.1126/ science.adi1910. Nov 23, 2023. 

https://www.science.org/doi/10.1126/science.adi1910

Also: 'CRISPR' in https://flashontrack.blogspot.com/search?q=crispr  

Keywords: genome, gene, crispr, crispr system, ai, artificial intelligence

# behav: a single gene can drive aggression (in wild songbird)

<< In 2014, the lab (Donna Maney lab) identified a hormone receptor—estrogen receptor alpha (ER-alpha)—that appeared connected to the differences in the sparrows' aggression and parenting behaviors in the wild. The white-striped birds express this receptor at much higher levels than the tan-striped birds, and the more the expression, the more aggressive the bird. >>

In the recent work << results showed that when expression of that one gene was blocked, the aggression of the white-striped birds went down so they behaved like the tan-striped ones. >>

Carol Clark. Study shows how a single gene drives aggression in wild songbird.  Emory University. Aug 18, 2020.

https://phys.org/news/2020-08-gene-aggression-wild-songbird.html   

Jennifer R. Merritt, Kathleen E. Grogan, et al. A supergene-linked estrogen receptor drives alternative phenotypes in a polymorphic songbird. PNAS doi: 10.1073/ pnas.2011347117 Aug 17, 2020.

https://www.pnas.org/content/early/2020/08/14/2011347117

# gst: apropos of 'fleeting (transient) interactions'

AA << captured highly transient interactions between transcription factors-proteins that control gene expression-and target genes in the genome and showed that these typically missed interactions have important practical implications. >>

<< Our approaches to capturing transient transcription factor-target interactions genome-wide can be applied to validate dynamic interactions of transcription factors for any pathway of interest in agriculture or medicine, >> Gloria Coruzzi. 

Biologists capture fleeting interactions between regulatory proteins and their genome-wide targets. New York University. Mar 2, 2020.

https://m.phys.org/news/2020-03-biologists-capture-fleeting-interactions-regulatory.html

José M. Alvarez, Anna-Lena Schinke, et al. Transient genome-wide interactions of the master transcription factor NLP7 initiate a rapid nitrogen-response cascade. Nat Commun 11, 1157. doi: 10.1038/s41467-020-14979-6. Mar 2, 2020

https://www.nature.com/articles/s41467-020-14979-6

# gst: measuring biological noise of gene expression

<< Essential genes are often expressed with high variability during the development of cells. Scientists call this phenomenon "biological noise" and suspect that it is also decisive for the fate of cells, i.e. the developmental pathway a cell takes. Max Planck researcher Dominic Grun now presents a method based on single-cell data to quantify this variability in gene expression.  >>

Dominic Grun << hopes to gain a better understanding of the extent to which noise regulates development or is even necessary for the differentiation of cells. >>

How gene expression noise shapes cell fate. Max Planck Society. Nov 18, 2019. 

https://m.phys.org/news/2019-11-gene-noise-cell-fate.html   

Grun D. Revealing dynamics of gene expression variability in cell state space. Nat Methods (2019) doi:10.1038/s41592-019-0632-3. Nov 18, 2019.

https://www.nature.com/articles/s41592-019-0632-3

Also

keyword 'noise' in Notes:

https://inkpi.blogspot.com/search?q=noise

keyword 'noise' in FonT:

https://flashontrack.blogspot.com/search?q=noise

# evol: echolocation, a prime example of convergent evolution

<< Echolocation is a prime example of convergent evolution, the independent gain of similar features in species of different lineages. >>

<< Distantly related species entering similar biological niches often adapt by evolving similar morphological and physiological characters. How much genomic molecular convergence (particularly of highly constrained coding sequence) contributes to convergent phenotypic evolution, such as echolocation in bats and whales, is a long-standing fundamental question.  >>

AA << find that the gene set most overrepresented (q-value = 2.2e-3) with convergent substitutions in echolocators, affecting 18 genes, regulates development of the cochlear ganglion, a structure with empirically supported relevance to echolocation. >>

Amir Marcovitz, Yatish Turakhia, et al. A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales.
PNAS doi: 10.1073/pnas.1818532116   Sep 30, 2019    https://www.pnas.org/content/early/2019/09/27/1818532116 

Krista Conger. Scientists uncover genetic similarities among species that use sound to navigate. Stanford University Medical Center. Oct 4, 2019.   https://m.phys.org/news/2019-10-scientists-uncover-genetic-similarities-species.html