Category Archives: Genome

Eukaryotic Genome
This is a short review over Eukaryotic Genomes (Chapter 19 of Campbell and Reece AP Biology book). It covers DNA structure, gene expression, and a little ove...

By: Muldrow AP Biology

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Eukaryotic Genome - Video

Marketing Genome Project - Building the Dark Horse Comics Booth at Comic-Con 2013
We had a great time at Comic-Con 2013 filming this video showing how the Marketing Genome Project constructs tradeshow booths for it #39;s clients. This video took 4 days to shoot and we used...

By: Pacific Creative Productions

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Marketing Genome Project - Building the Dark Horse Comics Booth at Comic-Con 2013 - Video

Genome mapping for just $10002232

By: Ali Replogle

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Genome mapping for just $10002232 - Video

Imagine having a child and knowing at birth what diseases he or she will face in life.

Its an ethical conundrum for parents: would you even want to know? This knowledge sounds almost too futuristic, and in many ways it is. But experts say genome sequencing technology is rapidly advancing and becoming less expensive, and it could shape the way we approach preventative care and the insurance industry.

Today, parents can receive newborn screens that check for diseases that need to be treated in infancy as well as genetic testing during early pregnancy that identify possible abnormalities.

The current cost of a complete genome sequencing using blood and saliva comes with a price tag of about $1,000, according to Jeffrey Kahn, deputy director for policy and administration at the Johns Hopkins Berman Institute of Bioethics.

It takes a few hours to produce now. As that gets faster and cheaper, it becomes something that is on a scale where it is almost worthwhile to do for everyone, Kahn says. It would be a big change, moving from that newborn screen to doing full genome sequencing on every child that is born.

But having access to a childs sequence today doesnt mean much. In fact, Kahn likens it to having all of the telephone numbers in the white pages without the names. The sequence would have to be run through software that could pick out certain gene mutations to determine predispositions.

The question then is: who should access this data, and for what purposes? he says.

Interpretation

In 2013, the Food and Drug Administration warned Google-backed (NASDAQ: GOOG) 23andMe to stop selling its $99 genetic tests sold at retailers because it had not received regulatory clearance. The FDA says products that are designed to diagnose or prevent disease are technically medical devices and need regulatory approval.

Misha Angrist, assistant professor at the Duke Institute for Genome Sciences & Policy, says the biggest bottleneck within the industry is interpretation.

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Genome Sequencing: Who Gets to Use the Data?

By Erinn Hutkin, Special to U-T San Diego 6 a.m.Feb. 4, 2014

Last year, actress and activist Angelina Jolie made headlines when she wrote an op-ed piece for the New York Times about why she chose to have a double mastectomy after undergoing a $3,000 genetic test showing she inherited faulty versions of the BRCA1 gene.

Her mother died of breast cancer at a relatively young age, and the test was an indicator that Jolie had a high risk of developing breast cancer in her lifetime.

Its just one example of how technology has allowed many people both high-profile and everyday Joes to learn more about their risks of developing genetic diseases through genome sequencing.

Sequencing is a laboratory process that uses a sample of a persons blood to help determine the DNA sequence of their genomes. DNA is passed down from a persons parents, and the testing can spot abnormalities or disorders that point to a high risk of developing certain genetic diseases, such as breast cancer, or rare disorders, such as Huntingtons disease.

The testing can be used to help doctors pinpoint the causes of certain disorders. It can also be used for cancer patients to make treatment more targeted and specific.

It does have an impact in helping doctors and patients make better decisions about their choices, said Dr. Mark Erlander, chief scientific officer at San Diego-based Trovagene Inc.

In the clinical world, he said, there are two main ways that sequencing is used.

The first is called germ-line sequencing, which he said is done to try to understand if a person is predisposed to certain diseases or disorders Alzheimers, for instance or the BRCA gene thats been linked to breast cancer.

When doing the sequencing, whats being looked for is an association or links, he said. He said this type of testing is typically done on people who are healthy but want to see if the risk of developing a certain disease is elevated.

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Genome sequencing highlights risks of diseases

Researchers from Yellow Sea Fisheries Research Institute, Chinese Academy of Fisheries Sciences, BGI-Shenzhen and other institutes have successfully decoded the first genome of a flatfish -- half-smooth tongue sole (Cynoglossus semilaevis), providing insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle. The data generated in this project also lay foundation on the genetic breeding of tongue sole. The latest study has been published online today in Nature Genetics. In another study published in Genome Research at the same time, the researchers also uncovered the epigenetic mechanism underlying the temperature-dependent sexual reversal as well as the trans-generational inheritance of such sexual reversal phenomena in tongue sole.

The genetic mechanisms underlying sex determination as well as the origin and evolution of sex chromosomes have fascinated biologists for decades. Half-smooth tongue sole is an important cultured marine flatfish along China coast, whose sex is primarily determined by the inheritance of sex chromosomes (genetic sex determination, GSD) but also affected by environmental temperature (environmental sex determination, ESD). In normal condition, the sex of tongue sole is determined by the ZW/ZZ sex determination system with female containing a heteromorphic W chromosome. However, if juvenile fish are reared in high temperature, the genetic females (ZW) can develop into phenotypic males (so-called pseudo-males). Interestingly, these sex-reversed pseudo-males are fertile and can mate with normal females to produce viable offspring. Astonishingly, most of their genetic female offspring (ZW) develop into pseudo-males, but without temperature induction. Thus, with its complex sex determination system governed by the interaction between genetic determination and environmental factors, tongue sole is an excellent model to understand the molecular mechanism of sex determination in fishes and the interplay of genome and environment.

In this study, the researchers sequenced and assembled the genomes of one male (ZZ) and one female (ZW) tongue sole, respectively. Based on the difference of sequencing depth of Z/W linked-scaffolds between female and male, together with the high-resolution genetic map constructed by SSR and SNP, they assembled the Z and W chromosome of tongue sole at high quality. Using the Z-W homologous genes, they estimated that the age of the tongue sole sex chromosome pair is relatively young (about 30 million years), which contrasts with the age of hundreds of millions of years for the mammalian and avian sex chromosomes. Interestingly, researchers found that the sex chromosomes of tongue sole are derived from the same ancestral vertebrate protochromosome as the avian W and Z chromosomes. Furthermore, the same gene on the Z chromosome, dmrt1, which is the male-determining gene in birds, showed convergent evolution of features that are compatible with a similar function in tongue sole.

To understanding the regulatory mechanisms involved in the temperature-dependent sex reversal as well as the inheritance of sex reversal in tongue sole, researchers then analyzed the gonadal DNA methylomes and transcriptomes of normal males (ZZ), pseudo-males (ZW), normal females (ZW), and the offspring of a pseudo-male crossed with a female. They found that, after phenotypic sexual reversal, the genome-wide methylation patterns of genetic females have been accurately shaped to the patterns of normal males. Furthermore, the methylation changes after sex reversal were enriched in genes in the sex determination pathway. By comparing parental and offspring samples, researchers also found that the methylation changes between parental pseudo-males and females were inherited by offspring pseudo-males, probably explaining why the offspring genetic females of pseudo-males can undergo sexual reversal without temperature induction. For organisms with sex chromosomes, a challenge for the sex-reversed individuals is the unequal gene dosage on sex chromosomes when compared with normal individuals. For example, pseudo-males (ZW) of tongue sole lack one Z chromosome compared with normal males (ZZ), and contain one extra W chromosome with female-specific genes. Thus, how to revolve gene dosage inequality on sex chromosomes is a fundamental question for sex reversal. Researchers found that, dosage compensation only occurs in a restricted, methylated cytosine enriched Z chromosomal region in pseudo-male testes, achieving equal expression level in normal male testes. Some spermatogenesis-related genes were found in this region. For the W chromosome, they observed that many W-linked genes are still actively expressed in pseudo-males. The researchers speculate that the expression of these W-linked genes may compensate the dosage of their counterparts on the Z chromosomes. However, female-specific genes, such as figla, were suppressed in pseudo-males by methylation regulation. In conclusion, the researchers propose that epigenetic regulation plays multiple crucial roles in sexual reversal of tongue sole fish.

Flatfish are characterized by a transition from pelagic to benthic habitats when they metamorphose from free swimming larvae to bottom-dwelling fish, accompanied by a series of biological and phenotypic changes, such as eye migration, displacement of internal organs, the difference of pigmentation and the sensitivity of light. By comparing the transcriptomes of pelagic and benthic fish, the researchers revealed that the differentially expressed genes between these two developmental stages are enriched in genes potentially involved in adaptation to a benthic lifestyle. They also identified 15 positively selected genes, which have putative roles in metamorphosis. In addition, they found that the expression levels of rod pigment (rh1) and cone pigment (lws1) genes, which are responsible for scotopic vision and long-wavelength-sensitivity, respectively, were significantly up-regulated in benthic stages, whereas the expression of the middle-wavelength-sensitive pigment gene (rh2) was significantly up-regulated in pelagic stages. Moreover, they also found that several crystallin genes were lost or became pseudogenes. They speculate that these changes reveal the adaptation of the tongue sole visual system after shifting to the benthic environment with weak light conditions. As compensation, tongue sole have developed a strong lateral -line sense organ and especially, the papillae-a specific mechanoreceptorsense organ during evolution.

Dr. Guojie Zhang, who is the leading author of both papers from China National Genebank of BGI, said: "The evolution of sex is one of the major transitions in evolution, that has significantly enhanced the adaptation ability of the species. However, our knowledge of sex determination mechanisms is still very limited. Vertebrates have various sex-determination mechanisms. The sex determination process of many vertebrate species is regulated by environmental cues, like temperature. Investigation of the molecular mechanisms underlying this process will shed new lights on the understanding of the interaction between functional gene networks and their regulations by environmental factors, and increase our knowledge on how genome evolution drives species diversification and diversity."

Story Source:

The above story is based on materials provided by BGI Shenzhen. Note: Materials may be edited for content and length.

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Two papers unraveled the mystery of sex determination and benthic adaptation of the flatfish

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By: Cindy Jared

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Backtrack r3 genome cracking zip rar password using fcrackZip in secs 2014 - Video

- Daidai Genome (Short ver.) [Matt]
Guess who #39;s (sorta) back? Hellishly rusty, though, so here #39;s hoping my future uploads improve... Producer: MezameP Mix: Lan (http://www.youtube.com/user/Tobi...

By: MattTheLeek

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- Daidai Genome (Short ver.) [Matt] - Video

Winter Symposium 2014 - Health Sector Research Opportunities (Q A)
Session 2: Health Sector Sam Abraham and Bonnie Henry Questions and Answers session.

By: Genome BC

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Winter Symposium 2014 - Health Sector Research Opportunities (Q&A) - Video

OriGene Webinar Series: Genome Editing with CRISPR/Cas9
OriGene offers CRISPR/Cas9, the latest and effective tool for genome editing. This webinar covers the basics of the CRISPR/Cas9 system, as well as the applic...

By: OriGene Technologies Inc.

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OriGene Webinar Series: Genome Editing with CRISPR/Cas9 - Video