J.J. Emerson 艾偉傑 🖥️🧬
@jjemerson.bsky.social
Evolutionary geneticist at UCI. JJ_Emerson on http://ecoevo.social.
Relatedly, I think it's presumptuous to assume whether Puerto Rico would join or how their representatives would vote if they did. Nothing good ever comes from assuming a whole region's population is a monolith.
November 3, 2025 at 7:17 PM
Relatedly, I think it's presumptuous to assume whether Puerto Rico would join or how their representatives would vote if they did. Nothing good ever comes from assuming a whole region's population is a monolith.
12/12 This work provides a new map of variation for these "recalcitrant" regions, opening the door to studying how their variation affects essential biological functions. Check out the full paper here: genome.cshlp.org/content/35/9...
Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
October 31, 2025 at 9:37 PM
12/12 This work provides a new map of variation for these "recalcitrant" regions, opening the door to studying how their variation affects essential biological functions. Check out the full paper here: genome.cshlp.org/content/35/9...
11/12 The histone cluster was just one part. We also characterized the complex Stellate loci, which influence male fertility. Our new assembly also significantly improves the reference for the proximal side of the X chromosome, a notoriously difficult region.
October 31, 2025 at 9:37 PM
11/12 The histone cluster was just one part. We also characterized the complex Stellate loci, which influence male fertility. Our new assembly also significantly improves the reference for the proximal side of the X chromosome, a notoriously difficult region.
10/12 These anchors were critical. They gave us a window to map the complex structural changes (like duplications and deletions) happening in this locus. Without them, we couldn't have confidently made our observations about the scale of rearrangement in the cluster.
October 31, 2025 at 9:37 PM
10/12 These anchors were critical. They gave us a window to map the complex structural changes (like duplications and deletions) happening in this locus. Without them, we couldn't have confidently made our observations about the scale of rearrangement in the cluster.
9/12 I should also mention how we were able to analyze the histone cluster. Because it's so repetitive, just saying "it varies" is easy, but figuring out how it varies is the hard part. We first had to identify "landmark anchors", i.e. unique sequences to pin down the alignments.
October 31, 2025 at 9:37 PM
9/12 I should also mention how we were able to analyze the histone cluster. Because it's so repetitive, just saying "it varies" is easy, but figuring out how it varies is the hard part. We first had to identify "landmark anchors", i.e. unique sequences to pin down the alignments.
8/12 We also used our new map to compare variation within the histone cluster itself, revealing complex structural changes. This is just a sample; the paper is packed with new insights into the "dark matter" of the genome.
October 31, 2025 at 9:37 PM
8/12 We also used our new map to compare variation within the histone cluster itself, revealing complex structural changes. This is just a sample; the paper is packed with new insights into the "dark matter" of the genome.
7/12 This image (Fig. 5) shows this clearly. We measured high linkage disequilibrium (no meiotic crossing over) across the histone cluster. In contrast, the control segments flanking the cluster showed low linkage disequilibrium as expected. This suggests special processes in this locus.
October 31, 2025 at 9:37 PM
7/12 This image (Fig. 5) shows this clearly. We measured high linkage disequilibrium (no meiotic crossing over) across the histone cluster. In contrast, the control segments flanking the cluster showed low linkage disequilibrium as expected. This suggests special processes in this locus.
6/12 The lack of crossing over suggests that the histone cluster must undergo other mechanisms of recombination. This was especially surprising because Drosophila is famous for its high recombination rates, so finding nearly no crossing over in this critical, conserved cluster was unexpected.
October 31, 2025 at 9:37 PM
6/12 The lack of crossing over suggests that the histone cluster must undergo other mechanisms of recombination. This was especially surprising because Drosophila is famous for its high recombination rates, so finding nearly no crossing over in this critical, conserved cluster was unexpected.
5/12 My favorite part of this project: we found that the histone gene cluster, a critical repetitive region, seems to completely lack crossing over, despite a lot of variation in cluster structure between strains (see below). This was a puzzling observation.
October 31, 2025 at 9:37 PM
5/12 My favorite part of this project: we found that the histone gene cluster, a critical repetitive region, seems to completely lack crossing over, despite a lot of variation in cluster structure between strains (see below). This was a puzzling observation.
4/12 In this study, we tackled the Drosophila melanogaster genome. We developed a new pipeline to assemble and analyze genetic variation within these complex, repetitive regions.
October 31, 2025 at 9:37 PM
4/12 In this study, we tackled the Drosophila melanogaster genome. We developed a new pipeline to assemble and analyze genetic variation within these complex, repetitive regions.
3/12 This was a massive effort, led by star PhD student Harsh Shukla. Huge congrats to Harsh on this fantastic achievement. This work was also possible thanks to Mahul Chakraborty (@mahulchak.bsky.social), a former postdoc in the lab now leading his own lab (chakrabortylab.org) at Texas A&M.
Chakraborty Lab – Texas A&M University
chakrabortylab.org
October 31, 2025 at 9:37 PM
3/12 This was a massive effort, led by star PhD student Harsh Shukla. Huge congrats to Harsh on this fantastic achievement. This work was also possible thanks to Mahul Chakraborty (@mahulchak.bsky.social), a former postdoc in the lab now leading his own lab (chakrabortylab.org) at Texas A&M.
2/12 These repetitive regions, such as centromeres, telomeres, and rRNA genes, are the "dark matter" of the genome. They are vital for cell survival but are often missing from standard genome assemblies, hiding their genetic variation from view.
October 31, 2025 at 9:37 PM
2/12 These repetitive regions, such as centromeres, telomeres, and rRNA genes, are the "dark matter" of the genome. They are vital for cell survival but are often missing from standard genome assemblies, hiding their genetic variation from view.
I just feel that if there weren't a competing unit standard, almost nobody would be confused as most of the time, you're working within the same unit tier and comparing apples to apples. Ah well, I guess that ship's sailed.
October 30, 2025 at 8:21 PM
I just feel that if there weren't a competing unit standard, almost nobody would be confused as most of the time, you're working within the same unit tier and comparing apples to apples. Ah well, I guess that ship's sailed.
OMG, I feel like I just mainlined some nostalgia from childhood by seeing that door. Wow, the memories of the ever changing door decorations tied to seasonal milestones. I think I need to go play with some G1 Transformers, now.
October 30, 2025 at 7:17 PM
OMG, I feel like I just mainlined some nostalgia from childhood by seeing that door. Wow, the memories of the ever changing door decorations tied to seasonal milestones. I think I need to go play with some G1 Transformers, now.
And not RAM, but rather flash memory. RAM has stayed stubbornly base 2. My bad.
October 30, 2025 at 6:29 PM
And not RAM, but rather flash memory. RAM has stayed stubbornly base 2. My bad.
Well, not just 2.4%, but only 2.4% as the base 1,000, which grows exponentially, of course. It starts to really matters in the higher capacities.
October 30, 2025 at 6:23 PM
Well, not just 2.4%, but only 2.4% as the base 1,000, which grows exponentially, of course. It starts to really matters in the higher capacities.
So the marketing won. But computers didn't change.
October 30, 2025 at 6:22 PM
So the marketing won. But computers didn't change.
This system predated the base 10. And since 2^10 is 2.4% greater than 10^3, it was used to market 2.4% less hardware capacity for RAM and storage without violating truth in advertising laws before standardization made that impossible. However, the common notation was applied to base-10, not 2.
October 30, 2025 at 6:22 PM
This system predated the base 10. And since 2^10 is 2.4% greater than 10^3, it was used to market 2.4% less hardware capacity for RAM and storage without violating truth in advertising laws before standardization made that impossible. However, the common notation was applied to base-10, not 2.
1 byte = 2^(0*10) bytes
1 KiB = 2^(1*10) bytes
1 MiB = 2^(2*10) bytes
1 GiB = 2^(3*10) bytes
1 TiB = 2^(4*10) bytes
Yeah, that nasty 10 sneaks in there, for sure. But it lets binary be binary while making it almost intuitive to our decimal-trained brains expecting base-10 thousands, millions, etc.
1 KiB = 2^(1*10) bytes
1 MiB = 2^(2*10) bytes
1 GiB = 2^(3*10) bytes
1 TiB = 2^(4*10) bytes
Yeah, that nasty 10 sneaks in there, for sure. But it lets binary be binary while making it almost intuitive to our decimal-trained brains expecting base-10 thousands, millions, etc.
October 30, 2025 at 6:19 PM
1 byte = 2^(0*10) bytes
1 KiB = 2^(1*10) bytes
1 MiB = 2^(2*10) bytes
1 GiB = 2^(3*10) bytes
1 TiB = 2^(4*10) bytes
Yeah, that nasty 10 sneaks in there, for sure. But it lets binary be binary while making it almost intuitive to our decimal-trained brains expecting base-10 thousands, millions, etc.
1 KiB = 2^(1*10) bytes
1 MiB = 2^(2*10) bytes
1 GiB = 2^(3*10) bytes
1 TiB = 2^(4*10) bytes
Yeah, that nasty 10 sneaks in there, for sure. But it lets binary be binary while making it almost intuitive to our decimal-trained brains expecting base-10 thousands, millions, etc.
Rich is wrong! Not very common in cities, however.
October 29, 2025 at 9:07 PM
Rich is wrong! Not very common in cities, however.