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Lou FCD



Posts: 5379
Joined: Jan. 2006

(Permalink) Posted: July 16 2008,08:10   

I've been meaning to do this for a while, but always manage to get sidetracked.

Long, long ago, before I took on the mantle of the man with the mop, I posted little interesting science bits that I'd come across in my travels about the web.  I'd give them their own threads, and sometimes they'd get some commentary and discussion, sometimes not.

Then I took to just posting them on the BW, to save from a bunch of empty threads, but then they just sort of got lost or buried amongst a big dump of trolling from PT or random matches of Mornington Crescent, or Ftk backwash or random silliness.

I'm starting this thread as a place for us all to just post links to Just Cool Science articles upon which we happen, and on which discussion may or may not take place.

It'll be nice to have a place for the occasional break from the TARD mines right here in our communal living room.

To that end, let me christen the thread with this from LiveScience:

Quote
Sexy People Sound Better
By Greg Soltis, LiveScience Staff
posted: 16 July 2008 06:54 am ET

People with voices deemed sexy and attractive tend to have greater body symmetry upon close inspection, suggesting that what we hear in a person can greatly affect what we see in them.

"The sound of a person's voice reveals a considerable amount of biological information," said Susan Hughes, an evolutionary psychologist from Albright College in Reading, Pa. "It can reflect the mate value of a person."

Hughes, whose new study is detailed in the June 2008 edition of the Journal of Nonverbal Behavior, cautions that an attractive voice does not necessarily indicate that this person has an attractive face.


More at the link.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Lou FCD



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(Permalink) Posted: July 16 2008,08:12   

And let me be clear:

I intend to be ruthless to trolls here.  This thread is for real science discussion.

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Louis



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(Permalink) Posted: July 16 2008,11:03   

Great idea Lou.

I've got a few things I wouldn't mind posting, but they are all behind journal pay screens (which I can access but many probably cannot). I'll post the abstracts and hope that's enough.

Here's one of the more AtBC relevant ones from this week's Nature:

Quote
Nature 454, 209-212 (10 July 2008)

The evolutionary origin of flatfish asymmetry, Matt Friedman

All adult flatfishes (Pleuronectiformes), including the gastronomically familiar plaice, sole, turbot and halibut, have highly asymmetrical skulls, with both eyes placed on one side of the head. This arrangement, one of the most extraordinary anatomical specializations among vertebrates, arises through migration of one eye during late larval development. Although the transformation of symmetrical larvae into asymmetrical juveniles is well documented1, 2, 3, 4, 5, 6, 7, the evolutionary origins of flatfish asymmetry are uncertain1, 2 because there are no transitional forms linking flatfishes with their symmetrical relatives8, 9. The supposed inviability of such intermediates gave pleuronectiforms a prominent role in evolutionary debates10, 11, 12, 13, 14, 15, 16, leading to attacks on natural selection11 and arguments for saltatory change14, 15. Here I show that Amphistium and the new genus Heteronectes, both extinct spiny-finned fishes from the Eocene epoch of Europe, are the most primitive pleuronectiforms known. The orbital region of the skull in both taxa is strongly asymmetrical, as in living flatfishes, but these genera retain many primitive characters unknown in extant forms. Most remarkably, orbital migration was incomplete in Amphistium and Heteronectes, with eyes remaining on opposite sides of the head in post-metamorphic individuals. This condition is intermediate between that in living pleuronectiforms and the arrangement found in other fishes. Amphistium and Heteronectes indicate that the evolution of the profound cranial asymmetry of extant flatfishes was gradual in nature.


What are the "rules" for this thread (apart from no trolls and knob gags)? I'll try to link things where practical/free. DOIs are the standard I find for linking things if people don't mind. Do you just want internet links? Or are abstracts like the above appropriate? Or less technical articles? Or is it a relative free for all wrt posting scientific stuff?

Louis

P.S. WHAT THE HELL IS WRONG WITH MORNINGTON CRESCENT AND RANDOMN SILLINESS!!!!one11eleven!!!?//????/?? No wait, forget I asked.

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Lou FCD



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(Permalink) Posted: July 16 2008,11:33   

If it's science, I'm good.

Just do be sure to remember to note if it's a pdf link.  Some folks don't care much for pdfs or something.

Me, personally, I love links to pdfs of the original papers.  A short translation into Carpenter's Son English would be appreciated.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Lou FCD



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(Permalink) Posted: July 16 2008,12:40   

From PLoS ONE:

A 28,000 Years Old Cro-Magnon mtDNA Sequence Differs from All Potentially Contaminating Modern Sequences

 
Quote
Abstract
Background

DNA sequences from ancient speciments may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal) and early modern (Cro-Magnoid) Europeans.

Methodology/Principal Findings

We typed the mitochondrial DNA (mtDNA) hypervariable region I in a 28,000 years old Cro-Magnoid individual from the Paglicci cave, in Italy (Paglicci 23) and in all the people who had contact with the sample since its discovery in 2003. The Paglicci 23 sequence, determined through the analysis of 152 clones, is the Cambridge reference sequence, and cannot possibly reflect contamination because it differs from all potentially contaminating modern sequences.

Conclusions/Significance:

The Paglicci 23 individual carried a mtDNA sequence that is still common in Europe, and which radically differs from those of the almost contemporary Neandertals, demonstrating a genealogical continuity across 28,000 years, from Cro-Magnoid to modern Europeans. Because all potential sources of modern DNA contamination are known, the Paglicci 23 sample will offer a unique opportunity to get insight for the first time into the nuclear genes of early modern Europeans.


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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

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Lou FCD



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(Permalink) Posted: July 16 2008,12:42   

Also from PLoS ONE:

Major Histocompatibility Complex Based Resistance to a Common Bacterial Pathogen of Amphibians

Quote
Abstract

Given their well-developed systems of innate and adaptive immunity, global population declines of amphibians are particularly perplexing. To investigate the role of the major histocompatibilty complex (MHC) in conferring pathogen resistance, we challenged Xenopus laevis tadpoles bearing different combinations of four MHC haplotypes (f, g, j, and r) with the bacterial pathogen Aeromonas hydrophila in two experiments. In the first, we exposed ff, fg, gg, gj, and jj tadpoles, obtained from breeding MHC homozygous parents, to one of three doses of A. hydrophila or heat-killed bacteria as a control. In the second, we exposed ff, fg, fr, gg, rg, and rr tadpoles, obtained from breeding MHC heterozygous parents and subsequently genotyped by PCR, to A. hydrophila, heat-killed bacteria or media alone as controls. We thereby determined whether the same patterns of MHC resistance emerged within as among families, independent of non-MHC heritable differences. Tadpoles with r or g MHC haplotypes were more likely to die than were those with f or j haplotypes. Growth rates varied among MHC types, independent of exposure dose. Heterozygous individuals with both susceptible and resistant haplotypes were intermediate to either homozygous genotype in both size and survival. The effect of the MHC on growth and survival was consistent between experiments and across families. MHC alleles differentially confer resistance to, or tolerance of, the bacterial pathogen, which affects tadpoles' growth and survival.


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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

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Lou FCD



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(Permalink) Posted: July 16 2008,14:38   

Quote (Lou FCD @ July 16 2008,09:10)
To that end, let me christen the thread with this from LiveScience:

   
Quote
Sexy People Sound Better
By Greg Soltis, LiveScience Staff
posted: 16 July 2008 06:54 am ET

People with voices deemed sexy and attractive tend to have greater body symmetry upon close inspection, suggesting that what we hear in a person can greatly affect what we see in them.

"The sound of a person's voice reveals a considerable amount of biological information," said Susan Hughes, an evolutionary psychologist from Albright College in Reading, Pa. "It can reflect the mate value of a person."

Hughes, whose new study is detailed in the June 2008 edition of the Journal of Nonverbal Behavior, cautions that an attractive voice does not necessarily indicate that this person has an attractive face.


More at the link.

An earlier paper on the subject by Susan Hughes.

Ratings of voice attractiveness predict sexual behavior and body configuration (.pdf)

 
Quote
Abstract

We investigated the relationship between ratings of voice attractiveness and sexually dimorphic differences in shoulder-to-hip ratios (SHR) and waist-to-hip ratios (WHR), as well as different features of sexual behavior. Opposite-sex voice attractiveness ratings were positively correlated with SHR in males and negatively correlated with WHR in females. For both sexes, ratings of opposite-sex voice attractiveness also predicted reported age of first sexual intercourse, number of sexual partners, number of extra-pair copulation (EPC) partners, and number of partners that they had intercourse with that were involved in another relationship (i.e., were themselves chosen as an EPC partner). Coupled with previous findings showing a relationship between voice attractiveness and bilateral symmetry, these results provide additional evidence that the sound of a person’s voice may serve as an important multidimensional fitness indicator.


Edited by Lou FCD on July 16 2008,15:39

--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

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Lou FCD



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(Permalink) Posted: July 16 2008,16:55   

Caveman's DNA Looks Modern at Science Now.

 
Quote
By Ann Gibbons
ScienceNOW Daily News
16 July 2008
When it comes to the extremely difficult task of sequencing caveman DNA, the third time may be the charm for David Caramelli. After two controversial attempts, the biological anthropologist at the University of Florence, Italy, and colleagues claim to have successfully sequenced mitochondrial DNA (mtDNA) from the fossils of a Cro-Magnon, a 28,000-year-old European ancestor of living humans. The mtDNA matches that of some modern Europeans but differs from that of Neandertals, shedding light on the fate of these ancient hominids.


More at the link.

ETA:  Original paper, A 28,000 Years Old Cro-Magnon mtDNA Sequence Differs from All Potentially Contaminating Modern Sequences, published in PLoS ONE.

Quote
Abstract
Background

DNA sequences from ancient speciments may in fact result from undetected contamination of the ancient specimens by modern DNA, and the problem is particularly challenging in studies of human fossils. Doubts on the authenticity of the available sequences have so far hampered genetic comparisons between anatomically archaic (Neandertal) and early modern (Cro-Magnoid) Europeans.

Methodology/Principal Findings

We typed the mitochondrial DNA (mtDNA) hypervariable region I in a 28,000 years old Cro-Magnoid individual from the Paglicci cave, in Italy (Paglicci 23) and in all the people who had contact with the sample since its discovery in 2003. The Paglicci 23 sequence, determined through the analysis of 152 clones, is the Cambridge reference sequence, and cannot possibly reflect contamination because it differs from all potentially contaminating modern sequences.

Conclusions/Significance:

The Paglicci 23 individual carried a mtDNA sequence that is still common in Europe, and which radically differs from those of the almost contemporary Neandertals, demonstrating a genealogical continuity across 28,000 years, from Cro-Magnoid to modern Europeans. Because all potential sources of modern DNA contamination are known, the Paglicci 23 sample will offer a unique opportunity to get insight for the first time into the nuclear genes of early modern Europeans.


Edited by Lou FCD on July 16 2008,18:00

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

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Lou FCD



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(Permalink) Posted: July 16 2008,17:16   

Empathy is 'Hard-Wired' in Children's Brains, at LiveScience, because the paper is behind a paywall.

Quote
Study author Jean Decety, a professor in the departments of Psychology and Psychiatry at the University of Chicago, reported that empathy appears to be "hard-wired" into the brains of normal children, as opposed to being solely the result of parental guidance or nurturing.

"Consistent with previous functional MRI studies of pain empathy with adults, the perception of other people in pain in children was associated with increased hemodymamic activity in the neural circuits involved in the processing of firsthand experience of pain...," Decety wrote.


and the actual abstract, from ScienceDirect:

Quote
Abstract

When we attend to other people in pain, the neural circuits underpinning the processing of first-hand experience of pain are activated in the observer. This basic somatic sensorimotor resonance plays a critical role in the primitive building block of empathy and moral reasoning that relies on the sharing of others' distress. However, the full-blown capacity of human empathy is more sophisticated than the mere simulation of the target's affective state. Indeed, empathy is about both sharing and understanding the emotional state of others in relation to oneself. In this functional magnetic resonance imaging (fMRI) study, 17 typically developing children (range 7–12 yr) were scanned while presented with short animated visual stimuli depicting painful and non-painful situations. These situations involved either a person whose pain was accidentally caused or a person whose pain was intentionally inflicted by another individual. After scanning, children rated how painful these situations appeared. Consistent with previous fMRI studies of pain empathy with adults, the perception of other people in pain in children was associated with increased hemodynamic activity in the neural circuits involved in the processing of first-hand experience of pain, including the insula, somatosensory cortex, anterior midcingulate cortex, periaqueductal gray, and supplementary motor area. Interestingly, when watching another person inflicting pain onto another, regions that are consistently engaged in representing social interaction and moral behavior (the temporo-parietal junction, the paracingulate, orbital medial frontal cortices, amygdala) were additionally recruited, and increased their connectivity with the fronto-parietal attention network. These results are important to set the standard for future studies with children who exhibit social cognitive disorders (e.g., antisocial personality disorder, conduct disorder) and are often deficient in experiencing empathy or guilt.


(What's up with scientists and paragraphs, by the way?  Is there a moratorium on carriage returns?)

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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Timothy McDougald



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(Permalink) Posted: July 16 2008,19:15   

This looks interesting
Control of segment number in vertebrate embryos:
Quote
The vertebrate body axis is subdivided into repeated segments, best exemplified by the vertebrae that derive from embryonic somites. The number of somites is precisely defined for any given species but varies widely from one species to another. To determine the mechanism controlling somite number, we have compared somitogenesis in zebrafish, chicken, mouse and corn snake embryos. Here we present evidence that in all of these species a similar 'clock-and-wavefront'1, 2, 3 mechanism operates to control somitogenesis; in all of them, somitogenesis is brought to an end through a process in which the presomitic mesoderm, having first increased in size, gradually shrinks until it is exhausted, terminating somite formation. In snake embryos, however, the segmentation clock rate is much faster relative to developmental rate than in other amniotes, leading to a greatly increased number of smaller-sized somites.


Edit to add the link goes to the abstract in Nature.

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Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Timothy McDougald



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Joined: Dec. 2006

(Permalink) Posted: July 16 2008,22:46   

Quote
Me, personally, I love links to pdfs of the original papers.


I almost forgot, if you like links to pdfs you should check out the links page at PT. There are a couple of sections with links to a wide variety of downloadable pdfs. It's a work in progress...

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Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Lou FCD



Posts: 5379
Joined: Jan. 2006

(Permalink) Posted: July 16 2008,22:52   

Quote (afarensis @ July 16 2008,23:46)
Quote
Me, personally, I love links to pdfs of the original papers.


I almost forgot, if you like links to pdfs you should check out the links page at PT. There are a couple of sections with links to a wide variety of downloadable pdfs. It's a work in progress...

Hey, thanks for that, and for hanging stuff up in this thread.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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JAM



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(Permalink) Posted: July 16 2008,23:52   

[quote=afarensis,July 16 2008,19:15]This looks interesting
Control of segment number in vertebrate embryos:
 
Quote
The vertebrate body axis is subdivided into repeated segments, best exemplified by the vertebrae that derive from embryonic somites. The number of somites is precisely defined for any given species...

Um...there's a slight problem there, as that claim is false.

It's false in fish:
http://www.nature.com/nature/journal/v183/n4672/abs/1831408b0.html

It's false in pigs:
http://www.genome.org/cgi/content/abstract/gr.6085507v1

It's false in people:
http://www3.interscience.wiley.com/journal....RETRY=0

  
Timothy McDougald



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Joined: Dec. 2006

(Permalink) Posted: July 17 2008,07:00   

Two more, both open access from PNAS:

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution:
Quote

Abstract

Lateral gene transfer is an important mechanism of natural variation among prokaryotes, but the significance of its quantitative contribution to genome evolution is debated. Here, we report networks that capture both vertical and lateral components of evolutionary history among 539,723 genes distributed across 181 sequenced prokaryotic genomes. Partitioning of these networks by an eigenspectrum analysis identifies community structure in prokaryotic gene-sharing networks, the modules of which do not correspond to a strictly hierarchical prokaryotic classification. Our results indicate that, on average, at least 81 ± 15% of the genes in each genome studied were involved in lateral gene transfer at some point in their history, even though they can be vertically inherited after acquisition, uncovering a substantial cumulative effect of lateral gene transfer on longer evolutionary time scales.


and

A germ-line-selective advantage rather than an increased mutation rate can explain some unexpectedly common human disease mutations

Quote
Abstract

Two nucleotide substitutions in the human FGFR2 gene (C755G or C758G) are responsible for virtually all sporadic cases of Apert syndrome. This condition is 100–1,000 times more common than genomic mutation frequency data predict. Here, we report on the C758G de novo Apert syndrome mutation. Using data on older donors, we show that spontaneous mutations are not uniformly distributed throughout normal testes. Instead, we find foci where C758G mutation frequencies are 3–4 orders of magnitude greater than the remaining tissue. We conclude this nucleotide site is not a mutation hot spot even after accounting for possible Luria–Delbruck “mutation jackpots.” An alternative explanation for such foci involving positive selection acting on adult self-renewing Ap spermatogonia experiencing the rare mutation could not be rejected. Further, the two youngest individuals studied (19 and 23 years old) had lower mutation frequencies and smaller foci at both mutation sites compared with the older individuals. This implies that the mutation frequency of foci increases as adults age, and thus selection could explain the paternal age effect for Apert syndrome and other genetic conditions. Our results, now including the analysis of two mutations in the same set of testes, suggest that positive selection can increase the relative frequency of premeiotic germ cells carrying such mutations, although individuals who inherit them have reduced fitness. In addition, we compared the anatomical distribution of C758G mutation foci with both new and old data on the C755G mutation in the same testis and found their positions were not correlated with one another.


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Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Henry J



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Joined: Mar. 2005

(Permalink) Posted: July 17 2008,13:31   

A mutation that's detrimental to the person, but that was advantageous to the success of the sperm that carried it? That is one weird result. :O

Henry

  
Arden Chatfield



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(Permalink) Posted: July 17 2008,22:56   

It might be a good idea to pushpin this thread to the top so that it doesn't go below the fold, or whateverthefuck the hip, succinct internet term is for that concept.

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"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
Nomad



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Joined: July 2007

(Permalink) Posted: July 17 2008,23:30   

Quote (Arden Chatfield @ July 17 2008,22:56)
It might be a good idea to pushpin this thread to the top so that it doesn't go below the fold, or whateverthefuck the hip, succinct internet term is for that concept.

The hip Internet term would be "sticky", or to describe the process of making the thread sticky, "stickied".  Yes, another word changed into a verb.

  
Lou FCD



Posts: 5379
Joined: Jan. 2006

(Permalink) Posted: July 18 2008,08:59   

Quote (Arden Chatfield @ July 17 2008,23:56)
It might be a good idea to pushpin this thread to the top so that it doesn't go below the fold, or whateverthefuck the hip, succinct internet term is for that concept.

That's a lovely idea.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
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skeptic



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(Permalink) Posted: July 18 2008,20:30   

Here's my current most-recent favorite:

Science 9 May 2008:
Vol. 320. no. 5877, pp. 811 - 814
DOI: 10.1126/science.1156093

Prev | Table of Contents | Next
Reports
Regulation of the Cellular Heat Shock Response in Caenorhabditis elegans by Thermosensory Neurons
Veena Prahlad, Tyler Cornelius, Richard I. Morimoto*

Temperature pervasively affects all cellular processes. In response to a rapid increase in temperature, all cells undergo a heat shock response, an ancient and highly conserved program of stress-inducible gene expression, to reestablish cellular homeostasis. In isolated cells, the heat shock response is initiated by the presence of misfolded proteins and therefore thought to be cell-autonomous. In contrast, we show that within the metazoan Caenorhabditis elegans, the heat shock response of somatic cells is not cell-autonomous but rather depends on the thermosensory neuron, AFD, which senses ambient temperature and regulates temperature-dependent behavior. We propose a model whereby this loss of cell autonomy serves to integrate behavioral, metabolic, and stress-related responses to establish an organismal response to environmental change.

here's the link in case anyone can access the archives:

HSPs - May 2008

  
hereoisreal



Posts: 745
Joined: Feb. 2006

(Permalink) Posted: July 19 2008,21:56   

Lou:

>I'm starting this thread as a place for us all to just post links to Just Cool Science articles upon which we happen, and on which discussion may or may not take place.<

………………………………......................

One Cool site:

http://www.worldwidetelescope.org/

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Lou FCD



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(Permalink) Posted: July 22 2008,18:53   

I haven't located the original PNAS paper yet, but this movie was kind of cool.

The accompanying blurb, from LiveScience:

Quote
The Odorrana tormota frog opens and closes tubes in its ears when listening and calling at night. In this movie, the researchers shined a light under the frog's jaw to illuminate the inside of the mouth. The small circles of light on the side of the frog's head that brighten and dim show the opening and closing of the Eustachian tubes. Credit: National Academies of Science, PNAS (2008)


Edited by Lou FCD on July 22 2008,19:54

--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

Work-friendly photography
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Timothy McDougald



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(Permalink) Posted: July 22 2008,20:42   

Quote (Lou FCD @ July 22 2008,18:53)
I haven't located the original PNAS paper yet, but this movie was kind of cool.

The accompanying blurb, from LiveScience:

 
Quote
The Odorrana tormota frog opens and closes tubes in its ears when listening and calling at night. In this movie, the researchers shined a light under the frog's jaw to illuminate the inside of the mouth. The small circles of light on the side of the frog's head that brighten and dim show the opening and closing of the Eustachian tubes. Credit: National Academies of Science, PNAS (2008)

Yup, PNAS is bad about getting papers up on time. In the meantime, I have three that might be of interest (yes, I'm a literature hound)

The Ascent of the Abundant: How Mutational Networks Constrain Evolution:

Quote
Evolution by natural selection is fundamentally shaped by the fitness landscapes in which it occurs. Yet fitness landscapes are vast and complex, and thus we know relatively little about the long-range constraints they impose on evolutionary dynamics. Here, we exhaustively survey the structural landscapes of RNA molecules of lengths 12 to 18 nucleotides, and develop a network model to describe the relationship between sequence and structure. We find that phenotype abundance—the number of genotypes producing a particular phenotype—varies in a predictable manner and critically influences evolutionary dynamics. A study of naturally occurring functional RNA molecules using a new structural statistic suggests that these molecules are biased toward abundant phenotypes. This supports an “ascent of the abundant” hypothesis, in which evolution yields abundant phenotypes even when they are not the most fit.


and

Species richness and structure of three Neotropical bat assemblages:

Quote
We compared the assemblages of phyllostomid bats in three Neotropical rainforests with respect to species richness and assemblage structure and suggested a method to validate estimates of species richness for Neotropical bat assemblages based on mist-netting data. The fully inventoried bat assemblage at La Selva Biological Station (LS, 100 m elevation) in Costa Rica was used as a reference site to evaluate seven estimators of species richness. The Jackknife 2 method agreed best with the known bat species richness and thus was used to extrapolate species richness for an Amazonian bat assemblage (Tiputini Biodiversity Station; TBS, 200 m elevation) and an Andean premontane bat assemblage (Podocarpus National Park; BOM, 1000 m elevation) in Ecuador. Our results suggest that more than 100 bat species occur sympatrically at TBS and about 50 bat species coexist at BOM. TBS harbours one of the most species-rich bat assemblages known, including a highly diverse phyllostomid assemblage. Furthermore, we related assemblage structure to large-scale geographical patterns in floral diversity obtained from botanical literature. Assemblage structure of these three phyllostomid assemblages was influenced by differences in floral diversity at the three sites. At the Andean site, where understorey shrubs and epiphytes exhibit the highest diversity, the phyllostomid assemblage is mainly composed of understorey frugivores and nectarivorous species. By contrast, canopy frugivores are most abundant at the Amazonian site, coinciding with the high abundance of canopy fruiting trees. Assemblage patterns of other taxonomic groups also may reflect the geographical distribution patterns of floral elements in the Andean and Amazonian regions.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 94, 617–629.


and

The origin of snakes (Serpentes) as seen through
eye anatomy


Quote
Snakes evolved from lizards but have dramatically different eyes. These differences are cited widely as compelling evidence that snakes had fossorial and nocturnal ancestors. Their eyes, however, also exhibit similarities to those of aquatic vertebrates. We used a comparative analysis of ophthalmic data among vertebrate taxa to evaluate alternative hypotheses concerning the ecological origin of the distinctive features of the eyes of snakes. In parsimony and phenetic analyses, eye and orbital characters retrieved groupings more consistent with ecological adaptation rather than accepted phylogenetic relationships. Fossorial lizards and mammals cluster together, whereas snakes are widely separated from these taxa and instead cluster with primitively aquatic vertebrates. This indicates that the eyes of snakes most closely resemble those of aquatic vertebrates, and suggests that the early evolution of snakes occurred in aquatic environments. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society,
2004, 81, 469–482.


--------------
Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Peter Henderson



Posts: 298
Joined: Aug. 2007

(Permalink) Posted: July 23 2008,09:55   

I think this is one of the best science programmes on TV:

http://www.bbc.co.uk/science....o.shtml

Take a look at May's episode "we just don't know" (a phrase coined by Sir Patrick over the years).

A really fascinating discussion about the state of modern cosmology. Really worth watching. Far far better than any of the stupid reality shows that millions of brain dead people seem to watch these days e.g. Big brother, the X factor, America's got tallent, Gerry Springer, etc. etc. etc.

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: July 25 2008,12:34   

Origin of the nucleus and Ran-dependent transport to safeguard ribosome biogenesis in a chimeric cell

Quote
Background
The origin of the nucleus is a central problem about the origin of eukaryotes. The common ancestry of nuclear pore complexes (NPC) and vesicle coating complexes indicates that the nucleus evolved via the modification of a pre-existing endomembrane system. Such an autogenous scenario is cell biologically feasible, but it is not clear what were the selective or neutral mechanisms that had led to the origin of the nuclear compartment.

Results
A key selective force during the autogenous origin of the nucleus could have been the need to segregate ribosome factories from the cytoplasm where ribosomal proteins (RPs) of the protomitochondrium were synthesized. After its uptake by an anuclear cell the protomitochondrium transferred several of its RP genes to the host genome. Alphaproteobacterial RPs and archaebacterial-type host ribosomes were consequently synthesized in the same cytoplasm. This could have led to the formation of chimeric ribosomes. I propose that the nucleus evolved when the host cell compartmentalised its ribosome factories and the tightly linked genome to reduce ribosome chimerism. This was achieved in successive stages by first evolving karyopherin and RanGTP dependent chaperoning of RPs, followed by the evolution of a membrane network to serve as a diffusion barrier, and finally a hydrogel sieve to ensure selective permeability at nuclear pores. Computer simulations show that a gradual segregation of cytoplasm and nucleoplasm via these steps can progressively reduce ribosome chimerism.

Conclusions
Ribosome chimerism can provide a direct link between the selective forces for and the mechanisms of evolving nuclear transport and compartmentalisation. The detailed molecular scenario presented here provides a solution to the gradual evolution of nuclear compartmentalization from an anuclear stage. Reviewers This article was reviewed by Eugene V Koonin, Martijn Huynen, Anthony M. Poole and Patrick Forterre.



Interesting that according to this, we acquired a nucleus in response to the endosymbiosis with mitochondria. Where does that put plants?

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I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
nadandoenloprofundo



Posts: 1
Joined: July 2008

(Permalink) Posted: July 25 2008,14:41   

Well, I am not a scientist, however I do enjoy knowing about it. So for the ones that don´t have enough time to read a lot, I post a video.


HTML
<object width="425" height="344"><param name="movie" value="http://www.youtube.com/v/Ivzs6ji7mMs&hl=en&fs=1"></param><param name="allowFullScreen" value="true"></param><embed src="http://www.youtube.com/v/Ivzs6ji7mMs&hl=en&fs=1" type="application/x-shockwave-flash" allowfullscreen="true" width="425" height="344"></embed></object>

  
qetzal



Posts: 309
Joined: Feb. 2006

(Permalink) Posted: July 25 2008,16:51   

Here's a very interesting abstract from Cell. Ran across it on one of the xkcd Science forums.

Quote
Drummond & Wilke (2008), Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution. Cell 134:341-352.

Strikingly consistent correlations between rates of coding-sequence evolution and gene expression levels are apparent across taxa, but the biological causes behind the selective pressures on coding-sequence evolution remain controversial. Here, we demonstrate conserved patterns of simple covariation between sequence evolution, codon usage, and mRNA level in E. coli, yeast, worm, fly, mouse, and human that suggest that all observed trends stem largely from a unified underlying selective pressure. In metazoans, these trends are strongest in tissues composed of neurons, whose structure and lifetime confer extreme sensitivity to protein misfolding. We propose, and demonstrate using a molecular-level evolutionary simulation, that selection against toxicity of misfolded proteins generated by ribosome errors suffices to create all of the observed covariation. The mechanistic model of molecular evolution that emerges yields testable biochemical predictions, calls into question the use of nonsynonymous-to-synonymous substitution ratios (Ka/Ks) to detect functional selection, and suggests how mistranslation may contribute to neurodegenerative disease.


I knew that codon usage correlated with gene expression levels, but I had no idea that evolutionary rates did as well! Unfortunately, I won't have full text access 'til I'm back on work on Mon. Can't wait to read it!

  
Timothy McDougald



Posts: 1015
Joined: Dec. 2006

(Permalink) Posted: July 25 2008,23:36   

Phylogenetic escalation and decline of plant defense strategies

Quote
As the basal resource in most food webs, plants have evolved myriad strategies to battle consumption by herbivores. Over the past 50 years, plant defense theories have been formulated to explain the remarkable variation in abundance, distribution, and diversity of secondary chemistry and other defensive traits. For example, classic theories of enemy-driven evolutionary dynamics have hypothesized that defensive traits escalate through the diversification process. Despite the fact that macroevolutionary patterns are an explicit part of defense theories, phylogenetic analyses have not been previously attempted to disentangle specific predictions concerning (i) investment in resistance traits, (ii) recovery after damage, and (iii) plant growth rate. We constructed a molecular phylogeny of 38 species of milkweed and tested four major predictions of defense theory using maximum-likelihood methods. We did not find support for the growth-rate hypothesis. Our key finding was a pattern of phyletic decline in the three most potent resistance traits (cardenolides, latex, and trichomes) and an escalation of regrowth ability. Our neontological approach complements more common paleontological approaches to discover directional trends in the evolution of life and points to the importance of natural enemies in the macroevolution of species. The finding of macroevolutionary escalating regowth ability and declining resistance provides a window into the ongoing coevolutionary dynamics between plants and herbivores and suggests a revision of classic plant defense theory. Where plants are primarily consumed by specialist herbivores, regrowth (or tolerance) may be favored over resistance traits during the diversification process.


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Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
Lou FCD



Posts: 5379
Joined: Jan. 2006

(Permalink) Posted: July 26 2008,08:04   

High Protein Bindingand Cidal Activity against Penicillin-Resistant S. pneumoniae: A Cefditoren In Vitro Pharmacodynamic Simulation, from PLoS ONE:

Quote
Background

Although protein binding is a reversible phenomenon, it is assumed that antibacterial activity is exclusively exerted by the free (unbound) fraction of antibiotics.

Methodology/Principal Findings

Activity of cefditoren, a highly protein bound 3rd generation cephalosporin, over 24h after an oral 400 mg cefditoren-pivoxil bid regimen was studied against six S. pneumoniae strains (penicillin/cefditoren MICs; µg/ml): S1 (0.12/0.25), S2 (0.25/0.25), S3 and S4 (0.5/0.5), S5 (1/0.5) and S6 (4/0.5). A computerized pharmacodynamic simulation with media consisting in 75% human serum and 25% broth (mean albumin concentrations = 4.85±0.12 g/dL) was performed. Protein binding was measured. The cumulative percentage of a 24h-period that drug concentrations exceeded the MIC for total (T>MIC) and unbound concentrations (fT>MIC), expressed as percentage of the dosing interval, were determined. Protein binding was 87.1%. Bactericidal activity (?99.9% initial inocula reduction) was obtained against strains S1 and S2 at 24h (T>MIC = 77.6%, fT>MIC = 23.7%). With T>MIC of 61.6% (fT>MIC = 1.7%), reductions against S3 and S4 ranged from 90% to 97% at 12h and 24h; against S5, reduction was 45.1% at 12h and up to 85.0% at 24h; and against S6, reduction was 91.8% at 12h, but due to regrowth of 52.9% at 24h. Cefditoren physiological concentrations exerted antibacterial activity against strains exhibiting MICs of 0.25 and 0.5 µg/ml under protein binding conditions similar to those in humans.

Conclusions/Significance

The results of this study suggest that, from the pharmacodynamic perspective, the presence of physiological albumin concentrations may not preclude antipneumococcal activity of highly bound cephalosporins as cefditoren.


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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

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dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: July 28 2008,17:06   

My wife (who is Japanese) brought home a DVD the other day of a Japanese game show called "The Most Useful School in the World". It's a mildly educational show that is packaged inside a quiz show format that could only be dreamed up, and survive, in Japan.

In this episode, one segment was on iguanas of the Galapagos islands. The show introduced as the guest "expert" a Japanese doctor who had become a nature photographer. Interestingly, they also showed Charles Darwin's picture during the segment intro and talked about evolution. Imagine a game show trying that in the US?

The doctor showed pictures of the land iguanas eating prickly pear cactus, and showed that in areas with abundant iguanas, the prickly pear grew on a short pedestal base putting fleshy parts out of reach of the iguanas, while in areas without a lot of iguanas, it grew directly on the ground. This was given as an example of evolution.

The next film showed some of the adaptations of the sea iguanas, and asked the contestants to guess which feature had been modified the most in going to sea. The correct answer (according to the show) was that the sea iguana's claws were longer and sharper, the better to hold them against strong currents under water. (They showed great footage of the iguanas feeding underwater, gnawing seaweed off of rocks.)

Now the weird part was that they claimed that recent weather changes that had increased the foliage on the islands had given rise to the opportunity for some form of hybridization between land and sea iguanas. The result was a land iguana with claws strong enough to climb the pedestal of a prickly pear, and thereby acquire more resources.

Since this wasn't a peer reviewed game show, I was leery of accepting this story at face value, but I am trying to run down some facts. I thought I'd bring it to your attention as an example of how evolution fares in the pop culture of other countries, and also a cool example of real time evolution (if true). If I can find the show on YouTube or similar Japanese site, I will send a link.

--------------
I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
qetzal



Posts: 309
Joined: Feb. 2006

(Permalink) Posted: July 29 2008,00:23   

I had a chance to read the Cell paper I mentioned a few days back. I thought it was fascinating, and I highly recommend it.

Basically, it appears that a number of things correlate with mRNA levels across species from E. coli, yeast, worms, flies, mice, to humans. These include the fraction of optimal codon usage (i.e., the fraction of codons that correspond to the most abundant tRNA for that amino acid), the evolutionary non-synonymous substitution rate, the synonymous substitution rate, and even the relative rate of transitions to transversions.

The authors use principal component analysis to argue that all of these are related to one main underlying feature. They then argue that this feature is the need to minimize translation errors that lead to protein misfolding. In essence, they argue that misfolded proteins are cytotoxic, presumably in rough proportion to their abundance.

For low abundance proteins, occasional misfolding contributes little to the total cytotoxic burden in the cell. But for high abundance proteins, even rare misfolding may be detrimental. Thus, they argue, highly expressed genes need to use optimal codons to minimize translation errors. Even synonymous substitutions in a highly expressed gene can be detrimental, because they will tend to change an optimal codon to a suboptimal codon. This will increase the rate of translational error, resulting in more misfolded proteins, and greater cytotoxicity.

They go on to show how all of the observed correlations with gene expression level can be explained by this underlying mechanism. They do simulated evolution studies in silico that reproduce the observed correlations, but only if they include a cost associated with protein misfolding. Then they go a step further and suggest that this effect shows tissue specific features in complex organisms. For example, they suggest that neural tissue may be particularly sensitive to cytotoxicity from misfolded proteins (think Alzheimer's, Parkinsons, CJD, etc.). They note that brain-specific genes appear to evolve relatively slowly as a group, and explain how their hypothesis accounts for this.

The authors suggest that, if they're right, this has wide ranging implications for our understanding of evolution. Among other things, we would need to take into account how this affects synonymous vs. non-synonymous substituion rates when estimating divergence based on molecular data.

Here's what I really liked about this paper. 1) It proposes a new mechanism that has fundamental implications for how evolution works and is constrained. (At least, it's new to me; an editorial in the same issue of Cell seems to think it's potentially quite important as well.) 2) It provides a unifying explanation for a number of seemingly unconnected observations. (It even provides possible insight into the mechanisms of type 2 diabetes!) 3) The authors make multiple predictions based on their proposal, all of which can be tested experimentally.

To me, this is a stellar example of how science really works. The contrast with ID is stark.

  
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