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Welcome to The Visible Embryo, a comprehensive educational resource on human development from conception to birth.

The Visible Embryo provides visual references for changes in fetal development throughout pregnancy and can be navigated via fetal development or maternal changes.

The National Institutes of Child Health and Human Development awarded Phase I and Phase II Small Business Innovative Research Grants to develop The Visible Embryo. Initally designed to evaluate the internet as a teaching tool for first year medical students, The Visible Embryo is linked to over 600 educational institutions and is viewed by more than one million visitors each month.

Today, The Visible Embryo is linked to over 600 educational institutions and is viewed by more than 1 million visitors each month. The field of early embryology has grown to include the identification of the stem cell as not only critical to organogenesis in the embryo, but equally critical to organ function and repair in the adult human. The identification and understanding of genetic malfunction, inflammatory responses, and the progression in chronic disease, begins with a grounding in primary cellular and systemic functions manifested in the study of the early embryo.

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Pregnancy Timeline by SemestersFetal liver is producing blood cellsHead may position into pelvisBrain convolutions beginFull TermWhite fat begins to be madeWhite fat begins to be madeHead may position into pelvisImmune system beginningImmune system beginningPeriod of rapid brain growthBrain convolutions beginLungs begin to produce surfactantSensory brain waves begin to activateSensory brain waves begin to activateInner Ear Bones HardenBone marrow starts making blood cellsBone marrow starts making blood cellsBrown fat surrounds lymphatic systemFetal sexual organs visibleFinger and toe prints appearFinger and toe prints appearHeartbeat can be detectedHeartbeat can be detectedBasic Brain Structure in PlaceThe Appearance of SomitesFirst Detectable Brain WavesA Four Chambered HeartBeginning Cerebral HemispheresFemale Reproductive SystemEnd of Embryonic PeriodEnd of Embryonic PeriodFirst Thin Layer of Skin AppearsThird TrimesterSecond TrimesterFirst TrimesterFertilizationDevelopmental Timeline
CLICK ON weeks 0 - 40 and follow along every 2 weeks of fetal development
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Home | Pregnancy Timeline | News Alerts |News Archive Dec 15, 2014

Genomes are partitioned into domains based on histones. 10,000 of these histone loops were
frequently found linked to promoter and enhancer regions of gene activity. Each of the 10,000
loops is, therefore, a potential "switch" turning gene activation "on" or "off" and creating
new and unique cell types.   Image Credit: A. Sanchez/Baylor College of Medicine

VIDEO is available at: https://www.youtube.com/watch?v=dES-ozV65u4

 






 

 

3-D maps reveal genes fold like 'origami'

In a triumph for cell biology, researchers assembled the first high-resolution 3-D maps of entire folded genomes. These maps reveal a new basis for gene regulation — a kind of "genomic origami". The gene's structure allows for the same genome to fold and refold in order to produce different types of cells.

A central goal of the five-year project was to identify the loops in the human genome. The research was carried out at Baylor College of Medicine, Rice University, the Broad Institute, and Harvard University.


Loops form when two bits of DNA, that are far apart in the genome sequence, end up in close contact in a folded version of the genome within a cell's nucleus.


The research appears online in Cell.

Researchers used a technology called the"Hi-C" method to collect billions of snips of DNA. These were later analyzed for signs of loops. The team found that loops, and other genome folding patterns, are an essential part of gene regulation. Researchers sifted through billions of DNA pairs to catalog 10,000 loops.


"More and more, we're realizing that folding is regulation. When you see genes turn on or off, what lies behind that is a change in folding. It's a different way of thinking about how cells work."

Suhas Rao PhD, researcher at Baylor's Center for Genome Architecture, and study co-first author.

 

"Our maps of looping have revealed thousands of hidden switches that scientists didn't know about before. In the case of genes that can cause cancer or other diseases — knowing where these switches are is vital."

Miriam Huntley, doctoral student, Harvard's School of Engineering and Applied Sciences, Co-first author.


Senior author Erez Lieberman Aiden, assistant professor of genetics at Baylor and of computer science and computational and applied mathematics at Rice, said work began five years ago, shortly after he and his colleagues at the Broad Institute published a groundbreaking study introducing the Hi-C 3-D method for sequencing genomes.


"The 2009 study was a great proof of principle, but when we looked at the actual maps, we couldn't see fine details. It took us a few years to get the resolution to a biologically usable level. The new maps allow us to really see, for the first time, what folding looks like at the level of individual genes."

Erez Lieberman Aiden PhD, senior author, assistant professor of genetics at Baylor, and of computer science and computational and applied mathematics at Rice University


The work to refine "Hi-C" and produce full-genome maps with gene-level resolution continued when Aiden moved to Houston in 2013, established the Center for Genome Architecture at Baylor and joined the Center for Theoretical Biological Physics at Rice. Aiden credited Rao and Huntley with leading the effort, which involved a team of 11 researchers at Rice, Baylor, Broad and Harvard.

Identifying the loops themselves was yet another challenge. Fortunately, the group benefited from resources provided by NVIDIA, which named Aiden's lab a GPU Research Center in 2013 and provided essential hardware for the project. Huntley said new methods were also developed to speed the data processing and reduce experimental "noise," irregular fluctuations that tend to obscure weak signals in the data.

Huntley: "We faced a real challenge because we were asking, 'How do each of the millions of pieces of DNA in the database interact with each of the other millions of pieces?' Most of the tools that we used for this paper we had to create from scratch because the scale at which these experiments are performed is so unusual."

The big-data tools created for the study included parallelized pipelines for high-performance computer clusters, dynamic programming algorithms and custom data structures.

Rao said the group also relied heavily on data-visualization tools created by co-authors Neva Durand and James Robinson.

Rao: "When studying big data, there can be a tendency to try to solve problems by relying purely on statistical analyses to see what comes out, but our group has a different mentality. Even though there was so much data, we still wanted to be able to look at it, visualize it and make sense of it. I would say that almost every phenomenon we observed was first seen with the naked eye."

Abstract
Highlights
•Contact domains (∼185 kb) segregate into six subcompartments with distinct histone marks
•Loop anchors occur at domain boundaries and bind CTCF in a convergent orientation
•Loops correlate with gene activation and are conserved across cell types and species
•The inactive X chromosome contains large loops anchored at CTCF-binding repeats

Summary
We use in situ Hi-C to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1 kb resolution. We find that genomes are partitioned into contact domains (median length, 185 kb), which are associated with distinct patterns of histone marks and segregate into six subcompartments. We identify ∼10,000 loops. These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop anchors occur predominantly (>90%) in a convergent orientation, with the asymmetric motifs “facing” one another. The inactive X chromosome splits into two massive domains and contains large loops anchored at CTCF-binding repeats.

Additional co-authors include the Broad Institute's Eric Lander and Baylor's Elena Stamenova, Ivan Bochkov, Adrian Sanborn, Ido Machol and Arina Omer.

The research was supported by the National Science Foundation, the National Institutes of Health, the National Human Genome Research Institute, NVIDIA, IBM, Google, the Cancer Prevention and Research Institute of Texas and the McNair Medical Institute.

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