Scientists map genes at work in human embryos' earliest days

September 4, 2015 by Melissa Healy, Los Angeles Times
A depiction of the double helical structure of DNA. Its four coding units (A, T, C, G) are color-coded in pink, orange, purple and yellow. Credit: NHGRI

A team of scientists in Sweden has broken open the genetic recipe for a human embryo's first three days of development, chronicling what happens in the crucial hours that follow the union of egg and sperm.

The order in which a human's 23,000 awaken and start the process of building a person has never been charted before. But therein lie some momentous turning points-moments that determine whether a fledgling embryo will grow and thrive or sputter and die, and moments at which the earliest seeds of disease can be sown.

Twenty-four hours after a single has been penetrated by a , it will split and become a two-cell zygote. At the end of two days, there will be four , and by day three, there will generally be eight cells. During the three-day initiation studied in the latest effort, an embryo is technically homeless: It has not yet implanted itself on the wall of a woman's uterus.

This unformed mass will develop into billions of highly diverse cells by the time a fetus has reached full term. Each of those cells is hatched and sent forth to perform its function on the instruction of genes that are all present at the embryo's creation. But those genes are not all active at the creation; they are activated sequentially.

Knowing which and how many of those genes go first could unlock a host of mysteries-not least of which is, how do two simple cells create a human?

Deconstructing the process could clarify whether some DNA long dismissed as "junk" has, in fact, a crucial function. It could make more efficient the process of turning the clock back on adult cells to create for the treatment of diseases.

Insights from the new research could also help infertility specialists decide which 4- and 5-day-old embryos (called blastocysts) should be transferred from a petri dish into a woman's uterus. And they may shed light on the origins of devastating genetic diseases, and how early they might be diagnosed or thwarted.

Published Thursday in the journal Nature Communications, the study found that only 32 of a typical human's 23,000 genes are switched on two days after fertilization. By day three, 129 genes have been activated.

The study's senior author, molecular geneticist Juha Kere of Sweden's Karolinksa Institute, called these genes "the ignition key" that turns on human embryonic . To chronicle their activation "is like dropping a stone into water and then watching the waves spread across the surface," he said.

Not all of those ignition keys were familiar to genetic scientists. Seven of the 129 genes that were active in a zygote's earliest days had not been discovered previously.

Some of those newly identified genes were found to interact with repeated DNA sequences long called "junk" because they do not hold the blueprint for the production of a protein. That observation suggests that some DNA sequences long thought to have no function at all may in fact be pivotal to getting the enterprise of fetal development off the ground. Having performed that crucial function, the research suggests, they may retire to a life of leisure.

To glean those insights, the team collected 348 single cells, oocytes (immature egg cells), zygotes (the single-cell organisms that result from a fertilized egg) and blastomeres (2- to 3-day-old embryos of two to 10 cells). All had been donated for research.

The scientists sequenced 372 samples-the 348 above plus 24 cell samples used as technical controls. Narrowing their focus to look only at the transition from single egg cell to four-cell zygotes and from four- to eight-cell zygotes, they generated 1.58 billion readings.

A study published in 2013, which looked at the zygote's transition from four to eight cells, suggested that a much larger number of genes - 2,495 - might be activated during this early phase of development. The authors argue that the methods they used to interpret their data probably yield a more realistic count.

If that is true, the act of creation that gives rise to a human being is accomplished with remarkable parsimony, the authors of the study suggest.

It may ultimately take thousands of genes, turning on and off in immensely complex patterns, to complete the production of a small human. But on the day after egg meets sperm, they write, just 32 genes "may suffice to initiate ," an elite group that rises to only 129 by day three.

Explore further: Study reveals the genetic start-up of a human embryo

More information: Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development, DOI: 10.1038/NCOMMS9207

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JVK
1 / 5 (3) Sep 05, 2015
"... the act of creation that gives rise to a human being is accomplished with remarkable parsimony."

The act of virus-perturbed creation is accomplished with remarkable parsimony. Viruses are linked to all pathology via nutrient-dependent thermodynamic cycles of protein biosynthesis and degradation in species from microbes to humans. The accumulation of viral microRNAs eventually leads to pathology when nutrient-dependent microRNAs can no longer lead to RNA-mediated DNA repair.

See: http://www.icr.or...cle/8661
"Perhaps the evolutionists have placed the cart before the horse on this issue, as proposed by several creationist scientists.4,6 In fact, in an ironic twist, the evidence mentioned above indicates that viruses likely arose from their hosts and not the other way around. As molecular biologist and biochemist Peter Borger notes, "The most parsimonious answer is: the RNA viruses got their genes from their hosts..."
Vietvet
5 / 5 (2) Sep 05, 2015

Viruses are linked to all pathology

LMFAO!
JVK
1 / 5 (3) Sep 05, 2015
Viruses are linked to all pathology because they steal the energy that is required for proper RNA-mediated gene duplication and protein folding chemistry, which is stabilized by amino acid substitutions in the context of the physiology of reproduction.

Viral proteins may regulate human embryonic development http://phys.org/n...tml#nRlv
Vietvet
5 / 5 (3) Sep 06, 2015
"In other words, mammalian viruses may not have existed at all before the Curse, but after mankind's sin may have been allowed to develop from DNA sequence already present in the now-fallen people and animals of the earth. Again, cutting-edge genome research confirms the Genesis account of origins."
http://www.icr.or...cle/8661

Hear all the derisive laughter, JVK?

Vietvet
5 / 5 (2) Sep 06, 2015
Viruses are linked to all pathology because they steal the energy that is required for proper RNA-mediated gene duplication and protein folding chemistry, which is stabilized by amino acid substitutions in the context of the physiology of reproduction.

Where are the peer reviewed papers backing your claim?
JVK
1 / 5 (3) Sep 06, 2015
Why do you (Steven Taylor) expect me to provide biologically uninformed science idiots who denigrate my published works with more information about what is known to serious scientists, and also known to intelligent science fiction authors like Greg Bear?

See: http://rna-mediat...eg-bear/

See also: http://www.gregbe...2015.htm

From: Steven Taylor (aka Vietvet)
Location: United States
Date: 01/28/2015

James V. Kohl claims you incorporated his model of nutrient dependent, pheromone ecological adaptation in your Darwin novels. Any truth to that?
========================

Why is a biologically uninformed science idiot like Steven Taylor (aka Vietvet) continuing to denigrate my works, after Greg Bear incorporated them into his accurate representations of how ecological variation is linked to ecological adaptations in all living genera?
Vietvet
5 / 5 (3) Sep 06, 2015
@JVK

I asked for peer reviewed papers for your claim "Viruses are linked to all pathology" because I know they don't exist.
JVK
1 / 5 (3) Sep 06, 2015
You know nothing about cell type differentiation and pathology or healthy longevity because you are a biologically uninformed science idiot, not because the papers don't exist.

Modulation of GB virus B RNA abundance by microRNA-122: dependence on and escape from microRNA-122 restriction

Tubulin cofactors and Arl2 are cage-like chaperones that regulate the soluble αβ-tubulin pool for microtubule dynamics

A novel mycovirus from Aspergillus fumigatus contains four unique dsRNAs as its genome and is infectious as dsRNA

A ΩXaV motif in the Rift Valley fever virus NSs protein is essential for degrading p62, forming nuclear filaments and virulence

Cas9 specifies functional viral targets during CRISPR-Cas adaptation

Amino Acid Substitutions in Polymerase Basic Protein 2 Gene Contribute to the Pathogenicity of the Novel A/H7N9 Influenza Virus in Mammalian Hosts
Vietvet
5 / 5 (3) Sep 06, 2015
The causes of pathology are many, viruses account for a relatively few.

Still no papers supporting your" viruses are linked to all pathology".
JVK
1 / 5 (3) Sep 06, 2015
Anti-entropic effects on the origin of life http://rna-mediat...of-life/
JVK
1 / 5 (3) Sep 06, 2015
See also: http://phys.org/n...nts.html Excerpt: "Having damaged DNA compromises our cells' ability to fight viral infection, while having healthy DNA boosts our cells' ability to catch viral DNA," .... "Our work implies that we may be able to engineer viruses that selectively kill cancer cells."

My comment: Healthy DNA is nutrient-dependent. RNA-mediated gene duplication is epigenetically linked to RNA-mediated amino acid substitutions that stabilize the organized genomes of all genera in the context of metabolic and genetic networks via the physiology of reproduction, which enables fixation of the amino acid substitutions and prevents fixation of mutations in populations.

Biologically uninformed neo-Darwinian evolutionary theorists tend to tout pseudoscientific nonsense that links viruses to beneficial mutations and natural selection to evolution instead of linking Darwin's "conditions of life" to ecological speciation.
Captain Stumpy
5 / 5 (3) Sep 07, 2015
See: //rna-mediat...eg-bear/
PSEUDOSCIENCE LINK
when you mix creationist and religious dogma with your site, it makes it a RELIGIOUS site and PSEUDOSCIENCE, NOT A SCIENCE SITE
reported
Why...continuing to denigrate my works
1- you cannot DENIGRATE PSEUDOSCIENCE, as it is NOT SCIENCE
2- if you feel threatened, try litigation: i warn you, however- creationist dogma is NOT SCIENCE, and the courts know this
https://en.wikipe...Arkansas

go to court and you will make Vietvet rich off of the countersuit
http://www.gregbe...2015.htm
greg does NOT validate your claims in this link
Anti-entropic effects on the origin of life
THIS LINK IS A PHISHING PSEUDOSCIENCE SITE
reported

continuing to try and justify your CLAIMS by linking to your personal phishing site filled with pseudoscience and religion is like claiming you are a Ferrari because you once stood in a garage in Italy

Captain Stumpy
5 / 5 (2) Sep 07, 2015
neo-Darwinian evolutionary theorists
still on about this kick?
you never could read or comprehend basic english very well... this is ONE MORE REASON that you are continually proven to be a religious fanatic pushing pseudoscience

My comment:
your "comments" historically have been:
1- blatant lies (mutations are pathological)
2- delusional (your model supplants Evolution Theory)
3- PSEUDOSCIENCE (your model)
4- incapable of discerning factual evidence from scientific studies (Lenski, Extavour)

you can continue to comment, but to date, you have YET to be able to interpret science with any clarity or validity.. your claims about the interpreted studies have been absolutely WRONG, and you push creationist religious diatribe

that makes you a proselytizing religious fundamentalist pseudoscience crackpot
not a "serious scientist"

working in a lab doesn't make you a serious scientist any more than standing in a field makes you a barn
JVK
1 / 5 (3) Sep 07, 2015
Neuroscientist David Edelman on Paradigm Shift (YES) and Origin of '3D Organismal Form'
http://www.huffin...746.html

Excerpt: "Infection, especially the viral one, but also bacterial and fungal infections, followed by symbiosis, is proposed to act as the major force that drives biological evolution toward higher complexity."

See also my comments on All in the (bigger) family
http://comments.s...6219.220

The sequencing of the octopus genome has since linked microbes to humans via the conserved molecular mechanisms of microRNA-mediated events and adhesion proteins linked to RNA-mediated DNA repair in the context of biophysically constrained protein folding chemistry in all living genera, which protects organized genomes from virus-driven entropic elasticity linked to genomic entropy.
Captain Stumpy
5 / 5 (2) Sep 08, 2015
Neuroscientist...
Huffington post is NOT a peer reviewed science journal
there is no evidence in ANY science study supporting creationist dogma
See also my comments on...
1- the most important part in the link you provide is this:
These postings do not necessarily represent the views/opinions of Science
2- being able to post to sciMag DOESN'T make your claims more legitimate any more than standing in a church makes you a preacher
See also: SciMag argument refute to jk SEP 8 here: http://phys.org/n...ion.html

there is NO science in the creationist movement
there is no honour spamming/trolling SciMag with religious dogma

just because you pay for a membership doesn't mean you are a scientist - that is like claiming you are a Marine Sniper because you read Guns and Ammo once
EPIC FAIL
JVK
1 / 5 (3) Sep 08, 2015
Suzan Mazur has continued to fight against the pseudoscience of evolutionary theory since she first learned from Lynn Margulis that neo-Darwinists invented the Modern Synthesis.

"[W]hat Haldane, Fisher, Sewell Wright, Hardy, Weinberg et al. did was invent.... Evolution was defined as "changes in gene frequencies in natural populations." The accumulation of genetic mutations was touted to be enough to change one species to another.... Assumptions, made but not verified, were taught as fact." http://www.huffin...211.html

Ms. Mazur has since learned about viruses:
"Having just published a book on the origin and synthesis of life, I was fascinated to learn that I'd missed interviewing one of the field's most provocative scientists -- virologist Luis Perez Villarreal -- who takes a "virus-first" perspective to life."
http://www.huffin...898.html
JVK
1 / 5 (3) Sep 08, 2015
there is NO science in the creationist movement


There is no science in neo-Darwinian theory.

"The entire evolution of the microbial world and the virus world, and the interaction between microbes and viruses and other life forms have been left out of the Modern Synthesis..."

http://www.huffin...216.html

Serious scientists are forced to examine biologically-based cause and effect. They must place what is known into the context of what is known about physics and chemistry. They cannot simply skip ~2 billion years of their time-frame and claim that they know how species evolved.

just because you pay for a membership doesn't mean you are a scientist


I am a medical laboratory scientist whose credentials come from the American Society for Clinical Pathology, and you are a biologically uninformed science idiot. Stop touting ignorance!
Captain Stumpy
5 / 5 (3) Sep 08, 2015
I am a medical laboratory scientist whose credentials come from the American Society for Clinical Pathology
1- appeal to authority argument is stupid when you don't have evidence
2- this does NOT substantiate creationist/religious claims any more than believing in the tooth fairy makes you a dentist
3- just because you're a lab tech doesn't mean you are a biologist
4- being a lab tech doesn't mean you have evidence supporting your claims, especially when they've been debunked by actual validated experiments and studies (Lenski, Extavour)
5- most important: believing you are special or correct doesn't make you either... neither does trying to post your credentials in an attempt to "appear" more educated, especially when you admitted to failing out of college and got caught LYING about your experience as a diagnostician (felony)

regardless of your claims of credentials, you've been demonstrated through EVIDENCE to be a chronic lying creationist troll
Captain Stumpy
5 / 5 (3) Sep 08, 2015
and you are a biologically uninformed science idiot. Stop touting ignorance!
One more point: you like to make this claim... except that YOU are the one with a 100% fail rate interpreting science, not i

YOU are the one who tried to say Extavour's work supported your anti-mutation claims and pheromone stupidity... except that everyone found out that you were WRONG, which is why you now denigrate people like Extavour, Lenski and Whittaker

YOU are the one caught lying about experience as well: experience as a diagnostician (FELONY) and you failed out of college - this is why you attack educated people: because they accomplished something you never could, regardless of your "mensa" claims

YOU are the one promoting creationist religious dogma that is proven to be NON SCIENCE!

these are not claims, but a FACT!

So why is it that anyone with evidence proving you wrong is " touting ignorance"????
EVIDENCE is the key
NOT interpretations of evidence
Captain Stumpy
5 / 5 (2) Sep 08, 2015
I am a medical laboratory scientist ...Clinical Pathology
Translation: i am a lab tech
My most recent published work...
debunked by rational thought by a biology graduate: see - http://www.socioa...ew/24367

there is no room fro braggadocio and conjecture, especially religious motivated conjecture which is proven false already (see also: http://rspb.royal...full.pdf )

jvk is simple: Dunning-Kruger mixed with religious fundamentalism and a failure to comprehend the rigors of the scientific method

this hasn't stopped him from publishing "some" actual science, but like anyone else, he fails to comprehend that just because he is published, doesn't mean all his proclamations here are legit, supported or even real
JVK
1 / 5 (2) Sep 08, 2015
http://dx.doi.org...5.07.058

Excerpt: "Central to life is the faithful replication, inheritance, and maintenance of genomic DNA. The MRE11/RAD50/NBS1 (MRN) complex and ATM play a critical role in this biological mandate (Ciccia and Elledge, 2010). Cellular double-strand breaks (DSBs) are sensed by MRN and trigger the assembly of DNA damage response (DDR) foci that amplify global ATM signaling to induce cell-cycle arrest and DNA repair (Polo and Jackson, 2011). DNA viruses are an ancient and persistent threat to both cellular genome integrity and viability."

In the absence of nutrient-dependent RNA-mediated DNA repair, organized genomes do not exist. Everyone who is not a biologically uninformed science idiot realizes RNA-mediated amino acid substitutions are nutrient-dependent and that they protect organized genomes from virus-driven entropic elasticity, which links failed reproduction to genomic entropy as detailed in my atoms to ecosystems model.
JVK
1 / 5 (2) Sep 08, 2015
Why is only Captain Stumpy, a retired USAF Staff Sergeant (E-5) telling others that I am wrong about how nutrient-dependent cell type differentiation occurs in the context of the physiology of reproduction in all living genera and trying to convince people that others know more than I do about biologically-based cause and effect?

If anyone knew more than me, Greg Bear, Suzan Mazur, or the authors of "Viral and Cellular Genomes Activate Distinct DNA Damage Responses" -- the most recent review, they have had several decades to support their ridiculous theories with experimental evidence. Instead, not one other person or group has made accurate claims that fall outside the context of what we detailed in our 1996 Hormones and Behavior review: From Fertilization to Adult Sexual Behavior http://www.hawaii...ion.html See our section on molecular epigenetics.
Captain Stumpy
5 / 5 (2) Sep 08, 2015
Why is only Captain Stumpy, a retired USAF Staff Sergeant (E-5) telling others that I am wrong about
because i take the time and the rest of the population with a basic knowledge of biology knows you are an idiot pushing pseudoscience?
If anyone knew more than me
Dunning-Kruger to the rescue?
so... you are saying that everyone else ie wrong because your Mensa? you know more than everyone else because WHY?
i can refute that with a simple link: http://myxo.css.m...dex.html

want more?
http://extavourlab.com/

you still have NOT been able to give validated empirical evidence of pheromones
http://rspb.royal...full.pdf

so why should we think you know what you are talking about when you base an entire model on them, then include MUTATIONS but rant about mutations being pathological and always bad...?????
RealScience
5 / 5 (1) Sep 08, 2015
Why is only Captain Stumpy, a retired USAF Staff Sergeant (E-5) telling others that I am wrong ...

Because there is no need for others to - the good Captain is already doing a fine job of showing that you are wrong.

... and trying to convince people that others know more than I do about biologically-based cause and effect?

Again there is no need - you are doing a fine job yourself of showing that others know more than you do about biologically-based cause and effect.

LMAO!
JVK
1 / 5 (1) Sep 08, 2015
....the good Captain is already doing a fine job of showing that you are wrong.


Who do you think he is showing?

What do you think he is showing serious scientists?

See: Top-down causation: an integrating theme within and across the sciences? http://rsfs.royal...abstract

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