Category Archives: Genome

March 30, 2017 Credit: Institute of Molecular Biotechnology

Using a newly developed method, researchers at the Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA) have been able to shed light on the complexity of genome reorganization occurring during the first hours after fertilization in the single-cell mammalian embryo. Their findings have recently been published in the journal Nature. The team of researchers (from three continents) have discovered that the egg and sperm genomes that co-exist in the single-cell embryo or zygote have a unique structure compared to other interphase cells. Understanding this specialized chromatin "ground state" has the potential to provide insights into the yet mysterious process of epigenetic reprogramming to totipotency, the ability to give rise to all cell types.

Fusion of the egg and sperm, two highly differentiated cell types, leads to formation of the single-cell embryo or zygote. During the first hours after fertilization, the two separate genomes undergo reprogramming events that presumably function to erase the memory of the differentiated cell type and establish a state of totipotency. The mechanisms underlying totipotency remain poorly understood but are essential for generating a new organism from a fertilized egg.

A major advance in single-cell genomics

After fertilization, maternal and paternal genomes erase some of the epigenetic memory of the previously differentiated states in order to facilitate the beginning of new life as the zygote. In the first cell cycle after fertilization the maternal genome inherited from the oocyte (egg) and the paternal genome provided by sperm exist as separate nuclei in the zygote. The two genomes are marked by distinct epigenetic modifications acquired during reprogramming. Whether the 3-D chromatin structure of the maternal and paternal genomes is also distinct was not known.

An international team headed by Kiku Tachibana-Konwalski from IMBA in collaboration with researchers from the Massachusetts Institute of Technology (MIT) in Boston and the Lomonosov Moscow State University (MSU) aimed to uncover how chromatin structure is reorganized during the mammalian oocyte-to-zygote transition. Using next-generation sequencing, bioinformatics analysis and mathematical modeling performed by Maxim Imakaev in Leonid Mirny's lab, the researchers identified specific patterns that emerge during genome reorganization in mouse oocytes and zygotes.

The low availability of starting material made it necessary to develop a new single-nucleus Hi-C (snHi-C) method that made it possible to analyze the chromatin architecture in oocytes and single-cell embryos for the first time. Using this method, features of genomic organization including compartments, topologically associating domains (TADs) and chromatin loops were detected in single cells when averaged over the genome. "Our method allowed us to detect chromatin contacts ten times more efficiently than a previous method. Because of this we were able to find differences in genome folding on the level of single cells: these cell-to-cell variations were missed in conventional Hi-C due to the averaging over millions of cells," says Ilya Flyamer, former Vienna Biocenter (VBC) summer student and then Master student and one of the first authors of the study.

Contrasting behaviour of maternal and paternal chromatin

"Additionally, we found unique differences in the three-dimensional organization of the zygote's chromatin compared to other interphase cells. What was even more interesting is that maternal and paternal genomes of the zygote seem to have different organizations within the same cell. It seems like the chromatin architecture is reorganized after fertilization, and that this reorganization happens differentially for the maternal and the paternal genomes," explained Johanna Gassler, PhD student at IMBA and one of the first authors of the study.

Senior author and IMBA group leader Kiku Tachibana-Konwalski is fascinated by the secrets of the mammalian oocyte-to-zygote transition and has been studying the miracle of life, and in particular the very first molecular steps, for many years. She also hopes the findings will generate new insights for the emerging field of totipotency. "To place the power of the zygote into context: Reprogramming to pluripotency by the Yamanaka factors takes several days with limited efficiency, whilst reprogramming to totipotency occurs in the zygote within hours. How this is achieved remains one of the key unknowns in biology. By studying the chromatin state of zygotes, we aim to gain insights into this mechanism, which could also have applications for regenerative medicine," says Tachibana-Konwalski, underlining her excitement for the potential applications for her favourite research topic.

Explore further: The influence of the mother: Maternal epigenetic inheritance

More information: Ilya M. Flyamer et al. Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition, Nature (2017). DOI: 10.1038/nature21711

Three decades after being recognized as a group in need of conservation efforts, large fruit-eating bats still face an increasingly uncertain future on tropical islands as populations dwindle and threats close in, according ...

Changes in the distribution of land, marine and freshwater species as a result of climate change are affecting human wellbeing around the world, posing new health risks, economics threats and conflicts over resources.

Droplets and exhaled breath caught from the blowholes of killer whales along the Pacific coast are providing scientists with insights into whale health and revealing bacteria and fungi that may be a threat to the mammals.

The ability to generate oxygen through photosynthesisthat helpful service performed by plants and algae, making life possible for humans and animals on Earthevolved just once, roughly 2.3 billion years ago, in certain ...

Fang blennies are small fish with big teeth. Specifically, they have two large canine teeth that jut out of their lower jaw. Since blenny fish are only about two inches long, these "fangs" would be less than intimidating ...

Met Office technology used to study climate change is being used by scientists to predict the behaviour of vitalsorting and location of proteins cells in cells of the the human body.

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Read the original:
Unique genome architectures after fertilisation in single-cell embryos - Phys.Org

DINGO

Why is this the most interesting genome in the world?

Charles Darwin stated that the process of domestication can be divided into two steps that we now call unconscious and artificial selection.

Unconscious selection may be defined as non-intentional human selection, while artificial selection is the breeding of desirable traits. This is thought to be the process by which thousands of domestic plants and animals around the world have been produced and continue to be developed.

We aim, for the first time and in a unique case, to test Darwin's hypothesis and differentiate the genomic and genetic processes involved in unconscious and artificial selection. The Australian dingo is the ideal species to explore these questions because it represents an intermediate step along the evolutionary pathway from wild wolves to domestic dogs.

BOMBARDIER BEETLE

Why is this the most interesting genome in the world?

Bombardiers are among the world's most impressive chemists. Their genetic machinery provides for biochemical warfare.

They repel predators with rapid-fire, precisely-aimed explosive discharges of a toxic chemical mix at over 100 deg C, earning them lead roles in media and culture.

Yet the genomic basis of this extraordinary ability remains a mystery. The first bombardier genome will allow us to understand the genetic basis of bombardier chemical production, solving a longstanding evolutionary puzzle. This understanding will elucidate the currently unknown genetic basis of explosive chemical defence in the animal kingdom.

PINK PIGEON

Why is this the most interesting genome in the world?

The pink pigeon would be the first endangered bird species to be sequenced with PacBio's Iso-Seq method, which would make this species a blueprint for future conservation genomic research.

We are in a unique position to find out the reasons for the pink pigeon's continued decline; low genetic diversity reduces reproductive success and makes birds susceptible to infectious disease.

With recent advances in sequencing technology, such as the Iso-Seq method, we aim to identify the causative genetic variants responsible for the decline in population numbers. This is pivotal for the genetic rescue of the population through the reintroduction of beneficial genetic variants still present in captive individuals in zoos, thereby stopping the pink pigeon from becoming the next Dodo.

SOLAR-POWERED SLUG

Why is this the most interesting genome in the world?

The "solar-powered" sea slug Elysia timida is no beast of fiction. It is a real Mediterranean sacoglossan that can "steal" chloroplasts - the little solar panels where photosynthesis takes place - from its algal food source.

These "stolen" plastids are then stored in a still functional state in the slug's digestive gland cells, allowing the slug to endure at least three months of starvation. During this time, the chloroplasts continue photosynthesis and build up a starch reservoir that finally can be used by the slug.

This phenomenon, termed functional kleptoplasty, is unique among animals and, with this extraordinary evolutionary feature, E. timida stands for a climate- and eco-friendly lifestyle. However, the genetic basis enabling this lifestyle remains poorly understood.

See the solar sea slug stealing sustenance at http://www.pacb.com/smrt-science/smrt-grant/ pag2017/solar-powered-slug/

SOURCE: PACBIO

Read more:
Genome rivalry - The Straits Times

March 30, 2017 Human genes are riddled with a vast amount of DNA sequences which are known as jumping genes (colorful interconnected strings on the left). Without DHX9, these repetitive elements interact with each other to form entangled structures that can be detrimental to decoding the message. DHX9 is a nuclear enzyme that untangles this mess and creates neat mRNAs (thread) that are then used to make proteins (knitwork). Credit: Melica & timquo/ shutterstock.com; montage: MPI of Immunobiology & Epigenetics

Jumping genes are double-edged sword: By copying and integrating themselves into other parts of the genome these so-called transposons can lead to a variety of genetic disorders such as haemophilia or breast cancer. On the other hand the mobile DNA bits can create new genes and new gene expression programs. This is crucial for maintaining high genetic variability and adaptability to environmental changes. Scientists from the Max Planck Institute of Immunobiology and Epigenetics Freiburg in collaboration with the University of Freiburg have now found that an enzyme called DHX9 can neutralize the harmful structures formed by transposons and effectively increase the tolerance of the genome to include these jumping genes. By understanding this process better scientists can devise better therapies for diseases caused by transposons while retaining their evolutionary advantage.

Geneticists have long focused only on a very small part of DNA that contains blueprints for proteins. The non-coding remainder, around 97 percent in humans, was often dismissed as junk. But what was damned as junk before turned out to be the key regulator of genes determining where and how much protein should be synthesized. However, an even closer look into the "junk" revealed that it is also home for many more actors in the genome. One of these are the so-called transposons or jumping genes. Jumping genes are DNA sequences which are able to copy themselves and then insinuate the copies into distant sections of the genome.

"Our work revolves around a family of human transposons called Alu elements, which with more than 1.1 million copies, compose more than ten percent of our entire genome" says Tue Akta, co-first author of the study. To copy themselves, Alu elements are transcribed into RNA, reverse transcribed and then reintegrated into the genomic DNA at a different location. Once reintegrated, the short Alu elements have a vast amount of effects on the genome. "Depending on their site of insertion they can cause problematic mutations if they, for instance, jump into essential genes. Interestingly, Alu elements can cause a variety of genetic disorders such as haemophilia, breast cancer or familial hypercholesterolaemia, thus our work has to be explored further for therapeutic potential," says brahim Avar Ilk, co-first author of the study.

Jumping genes in evolution

Alu elements, are often referred to as "invaders" or "parasites" harming the genome stability. But at the same time Alu elements are also important drivers of evolution. Studies comparing primates and humans showed that more than five thousand Alu elements were newly inserted into the human genome during the past six million years. Scientists suggest that they act as a "creative destroyer" by separating parts of the genome into functional pieces that can be copied, moved around and re-used in other contexts. This ability to modify the DNA by more than 1.1 million Alu elements at the same time increases the possibility to create new genes as well as gene expression programs that probably allowed faster adaptation to the environment.

"We wondered how our genome deals with the outcome of this continuous copy-pasting and still avoids potentially fatal threats. Our discovery that DHX9 as the enzyme responsible for neutralizing harmful RNA structures produced during expression of our genes is very exciting as it opens a new angle to look into the complex biology hidden behind this abundant RNA helicase," says Asifa Akhtar, Max Planck Director and the lead investigator.

Untie the knot

DHX9 has the ability to unwind DNA and RNA duplexes and plays a central role in many processes in the cell like DNA replication, transcription or RNA processing. The Akhtar team in collaboration with Daniel Maticzka and Rolf Backofen from the bioinformatics research group of the University of Freiburg was able to show that in mice and humans DHX9 finds and removes disruptive RNA structures formed by dense Alu insertions. "If the distance between Alu elements in our genome is not large enough they interact with each other and form massive tangled RNA pieces", says brahim Avar Ilk. These huge cluttered structures can have fatal consequences, because essential RNA processing signals can be masked by them. DHX9 resolves the clutter and hands the now-untangled RNA over to further processing. "So without DHX9, our RNA turns into an entangled yarn that is no good for knitting," adds Tue Akta (see Fig. 1).

DHX9 does not do all the work by itself but has a "partner in crime" called ADAR, another enzyme that was previously shown to also be involved in the handling of tangled RNA structures especially during viral infections. "We suggest that this clearing unit evolved originally to fight against viral invasions. Their untangling activities were later reassigned and put into use in cells that are not under viral invasion, but are experiencing a surge in Alu element insertions", explains Asifa Akhtar the evolutionary implications of the data.

The great collaborative effort between the Max Planck Institute and the University of Freiburg leads the team to propose that DHX9 allowed the insertion of excessive amounts of Alu elements in our genome by simply counteracting harmful consequences of having too many of them side-by-side. Even though harboring so many disturbing jumping genes may seem like a waste of our cellular resources it pays for itself in the long run with genomic innovations that would otherwise be impossible. In other words, what is seen as a waste in our genome has never really been a waste, it is essentially a long, expensive road to complexity.

Explore further: A hidden code in our DNA explains how new pieces of genes are made

More information: Tue Akta et al. DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome, Nature (2017). DOI: 10.1038/nature21715

Journal reference: Nature

Provided by: Max Planck Society

We're all here because of mutations. Random changes in genes are what creates variety in a species, and this is what allows it to adapt to new environments and eventually evolve into completely new species. But most random ...

Scientists have discovered a previously unknown wellspring of genetic diversity in humans, chimps and most other primates. This diversity arises from a new component of itinerant sections of genetic code known as jumping ...

For more than 50 years, scientists have known of the existence of "jumping genes," strands of DNA material that can move from one location in the genome to another.

Almost 50 percent of our genome is made up of highly repetitive DNA, which makes it very difficult to be analysed. In fact, repeats are discarded in most genome-wide studies and thus, insights into this part of the genome ...

The human genome shares several peculiarities with the DNA of just about every other plant and animal. Our genetic blueprint contains numerous entities known as transposons, or "jumping genes," which have the ability to move ...

Moving genetic elements from one location to another in a genome makes for a very dynamic situation in terms of development and disease. An EU project has investigated a special type of micro transposable element and its ...

Three decades after being recognized as a group in need of conservation efforts, large fruit-eating bats still face an increasingly uncertain future on tropical islands as populations dwindle and threats close in, according ...

Changes in the distribution of land, marine and freshwater species as a result of climate change are affecting human wellbeing around the world, posing new health risks, economics threats and conflicts over resources.

Droplets and exhaled breath caught from the blowholes of killer whales along the Pacific coast are providing scientists with insights into whale health and revealing bacteria and fungi that may be a threat to the mammals.

The ability to generate oxygen through photosynthesisthat helpful service performed by plants and algae, making life possible for humans and animals on Earthevolved just once, roughly 2.3 billion years ago, in certain ...

Fang blennies are small fish with big teeth. Specifically, they have two large canine teeth that jut out of their lower jaw. Since blenny fish are only about two inches long, these "fangs" would be less than intimidating ...

Met Office technology used to study climate change is being used by scientists to predict the behaviour of vitalsorting and location of proteins cells in cells of the the human body.

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Read more from the original source:
An enzyme keeps the parasites of the genome in check and turns them into an evolutionary advantage - Phys.Org

A recent study conducted by scientists at the University of British Columbia (UBC) has unmasked more than two-dozen genes that provide the cannabis plant its varied flavor profile.

Published Thursday in the PLOS ONE journal, the study is part of an ongoing collaboration between researchers at UBC and Anandia Labs.

Investigating the various genes responsible for instilling our favorite strains with their distinct essence, UBC scientists have begun examining how specific terpenes and cannabinoid compounds interact to create todays appetizing strains, according to a press release from UBC:

The goal is to develop well-defined and highly-reproducible cannabis varieties. This is similar to the wine industry, which depends on defined varieties such as chardonnay or merlot for high-value products, said Jrg Bohlmann, a professor in the Michael Smith Laboratories and faculty of forestry at UBC. Our genomics work can inform breeders of commercial varieties which genes to pay attention to for specific flavor qualities.

PLOS ONE Study: Terpene Research

From limonene to myrcene, the researchers discovered approximately 30 terpene synthase genes that significantly contribute to todays diverse flavors in cannabis. Analogous to the wine industry and the genes that dictate their products flavor profile, The genes the researchers discovered play a role in producing natural products like limonene, myrcene, and pinene in the cannabis plants.

Terpene Research Results

Through this research, scientists hope to gain a greater understanding of how to cultivate well-defined and highly reproducible cannabis varieties, in addition to learning more about the synergistic interplay that confers the plants medicinal properties.

Photo courtesy of Allie Beckett

More here:
Cannabis Genome Research Examines Terpene Synthesis - Marijuana.com (blog)

Mitochondrial DNA (mtDNA or mDNA)[3] is the DNA located in mitochondria, cellular organelles within eukaryotic cells that convert chemical energy from food into a form that cells can use, adenosine triphosphate (ATP). Mitochondrial DNA is only a small portion of the DNA in a eukaryotic cell; most of the DNA can be found in the cell nucleus and, in plants and algae, also in plastids such as chloroplasts.

In humans, the 16,569 base pairs of mitochondrial DNA encode for only 37 genes.[4]Human mitochondrial DNA was the first significant part of the human genome to be sequenced. In most species, including humans, mtDNA is inherited solely from the mother.[5]

Since animal mtDNA evolves faster than nuclear genetic markers,[6][7][8] it represents a mainstay of phylogenetics and evolutionary biology. It also permits an examination of the relatedness of populations, and so has become important in anthropology and biogeography.

Nuclear and mitochondrial DNA are thought to be of separate evolutionary origin, with the mtDNA being derived from the circular genomes of the bacteria that were engulfed by the early ancestors of today's eukaryotic cells. This theory is called the endosymbiotic theory. Each mitochondrion is estimated to contain 210 mtDNA copies.[9] In the cells of extant organisms, the vast majority of the proteins present in the mitochondria (numbering approximately 1500 different types in mammals) are coded for by nuclear DNA, but the genes for some of them, if not most, are thought to have originally been of bacterial origin, having since been transferred to the eukaryotic nucleus during evolution.[10]

The reasons why mitochondria have retained some genes are debated. The existence in some species of mitochondrion-derived organelles lacking a genome[11] suggests that complete gene loss is possible, and transferring mitochondrial genes to the nucleus has several advantages.[12] The difficulty of targeting remotely-produced hydrophobic protein products to the mitochondrion is one hypothesis for why some genes are retained in mtDNA;[13]colocalisation for redox regulation is another, citing the desirability of localised control over mitochondrial machinery.[14] Recent analysis of a wide range of mtDNA genomes suggests that both these features may dictate mitochondrial gene retention.[10]

In most multicellular organisms, mtDNA is inherited from the mother (maternally inherited). Mechanisms for this include simple dilution (an egg contains on average 200,000 mtDNA molecules, whereas a healthy human sperm was reported to contain on average 5 molecules[15][16] ), degradation of sperm mtDNA in the male genital tract, in the fertilized egg, and, at least in a few organisms, failure of sperm mtDNA to enter the egg. Whatever the mechanism, this single parent (uniparental inheritance) pattern of mtDNA inheritance is found in most animals, most plants and in fungi as well.

In sexual reproduction, mitochondria are normally inherited exclusively from the mother; the mitochondria in mammalian sperm are usually destroyed by the egg cell after fertilization. Also, most mitochondria are present at the base of the sperm's tail, which is used for propelling the sperm cells; sometimes the tail is lost during fertilization. In 1999 it was reported that paternal sperm mitochondria (containing mtDNA) are marked with ubiquitin to select them for later destruction inside the embryo.[17] Some in vitro fertilization techniques, particularly injecting a sperm into an oocyte, may interfere with this.

The fact that mitochondrial DNA is maternally inherited enables genealogical researchers to trace maternal lineage far back in time. (Y-chromosomal DNA, paternally inherited, is used in an analogous way to determine the patrilineal history.) This is usually accomplished on human mitochondrial DNA by sequencing the hypervariable control regions (HVR1 or HVR2), and sometimes the complete molecule of the mitochondrial DNA, as a genealogical DNA test.[18] HVR1, for example, consists of about 440 base pairs. These 440 base pairs are then compared to the control regions of other individuals (either specific people or subjects in a database) to determine maternal lineage. Most often, the comparison is made to the revised Cambridge Reference Sequence. Vil et al. have published studies tracing the matrilineal descent of domestic dogs to wolves.[19] The concept of the Mitochondrial Eve is based on the same type of analysis, attempting to discover the origin of humanity by tracking the lineage back in time.

mtDNA is highly conserved, and its relatively slow mutation rates (compared to other DNA regions such as microsatellites) make it useful for studying the evolutionary relationshipsphylogenyof organisms. Biologists can determine and then compare mtDNA sequences among different species and use the comparisons to build an evolutionary tree for the species examined. However, due to the slow mutation rates it experiences, it is often hard to distinguish between closely related species to any large degree, so other methods of analysis must be used.

Entities undergoing uniparental inheritance and with little to no recombination may be expected to be subject to Muller's ratchet, the accumulation of deleterious mutations until functionality is lost. Animal populations of mitochondria avoid this buildup through a developmental process known as the mtDNA bottleneck. The bottleneck exploits stochastic processes in the cell to increase in the cell-to-cell variability in mutant load as an organism develops: a single egg cell with some proportion of mutant mtDNA thus produces an embryo where different cells have different mutant loads. Cell-level selection may then act to remove those cells with more mutant mtDNA, leading to a stabilisation or reduction in mutant load between generations. The mechanism underlying the bottleneck is debated,[20][21][22][23] with a recent mathematical and experimental metastudy providing evidence for a combination of random partitioning of mtDNAs at cell divisions and random turnover of mtDNA molecules within the cell.[24]

Doubly uniparental inheritance of mtDNA is observed in bivalve mollusks. In those species, females have only one type of mtDNA (F), whereas males have F type mtDNA in their somatic cells, but M type of mtDNA (which can be as much as 30% divergent) in germline cells.[25] Paternally inherited mitochondria have additionally been reported in some insects such as fruit flies,[26][27]honeybees,[28] and periodical cicadas.[29]

Male mitochondrial inheritance was recently discovered in Plymouth Rock chickens.[30] Evidence supports rare instances of male mitochondrial inheritance in some mammals as well. Specifically, documented occurrences exist for mice,[31][32] where the male-inherited mitochondria were subsequently rejected. It has also been found in sheep,[33] and in cloned cattle.[34] It has been found in a single case in a human male.[35]

Although many of these cases involve cloned embryos or subsequent rejection of the paternal mitochondria, others document in vivo inheritance and persistence under lab conditions.

An IVF technique known as mitochondrial donation or mitochondrial replacement therapy (MRT) results in offspring containing mtDNA from a donor female, and nuclear DNA from the mother and father. In the spindle transfer procedure, the nucleus of an egg is inserted into the cytoplasm of an egg from a donor female which has had its nucleus removed, but still contains the donor female's mtDNA. The composite egg is then fertilized with the male's sperm. The procedure is used when a woman with genetically defective mitochondria wishes to procreate and produce offspring with healthy mitochondria.[36] The first known child to be born as a result of mitochondrial donation was a boy born to a Jordanian couple in Mexico on 6 April 2016.[37]

In most multicellular organisms, the mtDNA - or mitogenome - is organized as a circular, covalently closed, double-stranded DNA. But in many unicellular (e.g. the ciliate Tetrahymena or the green alga Chlamydomonas reinhardtii) and in rare cases also in multicellular organisms (e.g. in some species of Cnidaria ) the mtDNA is found as linearly organized DNA. Most of these linear mtDNAs possess telomerase independent telomeres (i.e. the ends of the linear DNA) with different modes of replication, which have made them interesting objects of research, as many of these unicellular organisms with linear mtDNA are known pathogens.[38]

For human mitochondrial DNA (and probably for that of metazoans in general), 100-10,000 separate copies of mtDNA are usually present per somatic cell (egg and sperm cells are exceptions). In mammals, each double-stranded circular mtDNA molecule consists of 15,000-17,000[39]base pairs. The two strands of mtDNA are differentiated by their nucleotide content, with a guanine-rich strand referred to as the heavy strand (or H-strand) and a cytosine-rich strand referred to as the light strand (or L-strand). The heavy strand encodes 28 genes, and the light strand encodes 9 genes for a total of 37 genes.[4] Of the 37 genes, 13 are for proteins (polypeptides), 22 are for transfer RNA (tRNA) and two are for the small and large subunits of ribosomal RNA (rRNA).[40] The human mitogenome contains overlapping genes (ATP8 and ATP6 as well as ND4L and ND4: see the human mitochondrial genome map), a feature that is rare in animal genomes.[citation needed] The 37-gene pattern is also seen among most metazoans, although in some cases one or more of these genes is absent and the mtDNA size range is greater.

Great variation in mtDNA gene content and size exists among fungi and plants, although there appears to be a core subset of genes that are present in all eukaryotes (except for the few that have no mitochondria at all).[10] Some plant species have enormous mitochondrial genomes, with Silene conica mtDNA containing as many as 11,300,000 base pairs.[41] Surprisingly, even those huge mtDNAs contain the same number and kinds of genes as related plants with much smaller mtDNAs.[42] The genome of the mitochondrion of the cucumber (Cucumis sativus) consists of three circular chromosomes (lengths 1556, 84 and 45 kilobases), which are entirely or largely autonomous with regard to their replication.[43]

The smallest mitochondrial genome sequenced to date is the 5967 bp mtDNA of the parasite Plasmodium falciparum.[44]

There are six main genome types found in mitochondrial genomes. These genome types were classified by Kolesnikov & Gerasimov (2012)" and differ in various ways such as a circular versus linear genome, genome size, the presence of introns or plasmid like structures, and whether the genetic material is a singular molecule or collection of homogeneous or heterogeneous molecules.[45]

There is only one mitochondrial genome type found in animal cells. This genome contains one circular molecule with between 11-28kbp of genetic material (type 1).[45]

There are three different genome types found in plants and fungi. The first type is a circular genome that has introns (type 2) and may range from 19-1000kpb in length. The second genome type is a circular genome (about 20-1000kbp) that also has a plasmid-like structure (1kb) (type 3). The final genome type that can be found in plant and fungi is a linear genome made up of homogeneous DNA molecules (type 5).

Protists contain the most diverse mitochondrial genomes, with five different types found in this kingdom. Type 2, type 3 and type 5 mentioned in the plant and fungus genomes also exists in some protist, as well as two unique genome types. The first of these is a heterogeneous collection of circular DNA molecules (type 4) and the final genome type found in protists is a heterogeneous collection of linear molecules (type 6). Genome types 4 and 6 both range from 1-200kbp in size.

Endosymbiotic gene transfer, the process of genes that were coded in the mitochondrial genome being transferred to the cell's main genome likely explains why more complex organisms, such as humans, have smaller mitochondrial genomes than simpler organisms, such as protists.

Mitochondrial DNA is replicated by the DNA polymerase gamma complex which is composed of a 140 kDa catalytic DNA polymerase encoded by the POLG gene and two 55 kDa accessory subunits encoded by the POLG2 gene.[46] The replisome machinery is formed by DNA polymerase, TWINKLE and mitochondrial SSB proteins. TWINKLE is a helicase, which unwinds short stretches of dsDNA in the 5 to 3 direction.[47]

During embryogenesis, replication of mtDNA is strictly down-regulated from the fertilized oocyte through the preimplantation embryo.[48] The resulting reduction in per-cell copy number of mtDNA plays a role in the mitochondrial bottleneck, exploiting cell-to-cell variability to ameliorate the inheritance of damaging mutations.[24] At the blastocyst stage, the onset of mtDNA replication is specific to the cells of the trophectoderm.[48] In contrast, the cells of the inner cell mass restrict mtDNA replication until they receive the signals to differentiate to specific cell types.[48]

In animal mitochondria, each DNA strand is transcribed continuously and produces a polycistronic RNA molecule. Between most (but not all) protein-coding regions, tRNAs are present (see the human mitochondrial genome map). During transcription, the tRNAs acquire their characteristic L-shape that gets recognized and cleaved by specific enzymes. With the mitochondrial RNA processing, individual mRNA, rRNA, and tRNA sequences are released from the primary transcript.[49] Folded tRNAs therefore act as secondary structure punctuations.[50]

The concept that mtDNA is particularly susceptible to reactive oxygen species generated by the respiratory chain due to its proximity remains controversial.[51] mtDNA does not accumulate any more oxidative base damage than nuclear DNA.[52] It has been reported that at least some types of oxidative DNA damage are repaired more efficiently in mitochondria than they are in the nucleus.[53] mtDNA is packaged with proteins which appear to be as protective as proteins of the nuclear chromatin.[54] Moreover, mitochondria evolved a unique mechanism which maintains mtDNA integrity through degradation of excessively damaged genomes followed by replication of intact/repaired mtDNA. This mechanism is not present in the nucleus and is enabled by multiple copies of mtDNA present in mitochondria [55] The outcome of mutation in mtDNA may be an alteration in the coding instructions for some proteins,[56] which may have an effect on organism metabolism and/or fitness.

Mutations of mitochondrial DNA can lead to a number of illnesses including exercise intolerance and KearnsSayre syndrome (KSS), which causes a person to lose full function of heart, eye, and muscle movements. Some evidence suggests that they might be major contributors to the aging process and age-associated pathologies.[57] Particularly in the context of disease, the proportion of mutant mtDNA molecules in a cell is termed heteroplasmy. The within-cell and between-cell distributions of heteroplasmy dictate the onset and severity of disease [58] and are influenced by complicated stochastic processes within the cell and during development.[24][59]

Mutations in mitochondrial tRNAs can be responsible for severe diseases like the MELAS and MERRF syndromes.[60]

Mutations in nuclear genes that encode proteins that mitochondria use can also contribute to mitochondrial diseases. These diseases do not follow mitochondrial inheritance patterns, but instead follow Mendelian inheritance patterns.[61]

Recently a mutation in mtDNA has been used to help diagnose prostate cancer in patients with negative prostate biopsy.[62][63]

Though the idea is controversial, some evidence suggests a link between aging and mitochondrial genome dysfunction.[64] In essence, mutations in mtDNA upset a careful balance of reactive oxygen species (ROS) production and enzymatic ROS scavenging (by enzymes like superoxide dismutase, catalase, glutathione peroxidase and others). However, some mutations that increase ROS production (e.g., by reducing antioxidant defenses) in worms increase, rather than decrease, their longevity.[51] Also, naked mole rats, rodents about the size of mice, live about eight times longer than mice despite having reduced, compared to mice, antioxidant defenses and increased oxidative damage to biomolecules.[65] Once, there was thought to be a positive feedback loop at work (a 'Vicious Cycle'); as mitochondrial DNA accumulates genetic damage caused by free radicals, the mitochondria lose function and leak free radicals into the cytosol. A decrease in mitochondrial function reduces overall metabolic efficiency.[66] However, this concept was conclusively disproved when it was demonstrated that mice, which were genetically altered to accumulate mtDNA mutations at accelerated rate do age prematurely, but their tissues do not produce more ROS as predicted by the 'Vicious Cycle' hypothesis.[67] Supporting a link between longevity and mitochondrial DNA, some studies have found correlations between biochemical properties of the mitochondrial DNA and the longevity of species.[68] Extensive research is being conducted to further investigate this link and methods to combat aging. Presently, gene therapy and nutraceutical supplementation are popular areas of ongoing research.[69][70] Bjelakovic et al. analyzed the results of 78 studies between 1977 and 2012, involving a total of 296,707 participants, and concluded that antioxidant supplements do not reduce all-cause mortality nor extend lifespan, while some of them, such as beta carotene, vitamin E, and higher doses of vitamin A, may actually increase mortality.[71]

Deletion breakpoints frequently occur within or near regions showing non-canonical (non-B) conformations, namely hairpins, cruciforms and cloverleaf-like elements.[72] Moreover, there is data supporting the involvement of helix-distorting intrinsically curved regions and long G-tetrads in eliciting instability events. In addition, higher breakpoint densities were consistently observed within GC-skewed regions and in the close vicinity of the degenerate sequence motif YMMYMNNMMHM.[73]

Unlike nuclear DNA, which is inherited from both parents and in which genes are rearranged in the process of recombination, there is usually no change in mtDNA from parent to offspring. Although mtDNA also recombines, it does so with copies of itself within the same mitochondrion. Because of this and because the mutation rate of animal mtDNA is higher than that of nuclear DNA,[74] mtDNA is a powerful tool for tracking ancestry through females (matrilineage) and has been used in this role to track the ancestry of many species back hundreds of generations.

The rapid mutation rate (in animals) makes mtDNA useful for assessing genetic relationships of individuals or groups within a species and also for identifying and quantifying the phylogeny (evolutionary relationships; see phylogenetics) among different species. To do this, biologists determine and then compare the mtDNA sequences from different individuals or species. Data from the comparisons is used to construct a network of relationships among the sequences, which provides an estimate of the relationships among the individuals or species from which the mtDNAs were taken. mtDNA can be used to estimate the relationship between both closely related and distantly related species. Due to the high mutation rate of mtDNA in animals, the 3rd positions of the codons change relatively rapidly, and thus provide information about the genetic distances among closely related individuals or species. On the other hand, the substitution rate of mt-proteins is very low, thus amino acid changes accumulate slowly (with corresponding slow changes at 1st and 2nd codon positions) and thus they provide information about the genetic distances of distantly related species. Statistical models that treat substitution rates among codon positions separately, can thus be used to simultaneously estimate phylogenies that contain both closely and distantly related species[60]

Mitochondrial DNA was admitted into evidence for the first time ever in 1996 during State of Tennessee v. Paul Ware.[75]

In the 1998 court case of Commonwealth of Pennsylvania v. Patricia Lynne Rorrer,[76] mitochondrial DNA was admitted into evidence in the State of Pennsylvania for the first time.[77][78] The case was featured in episode 55 of season 5 of the true crime drama series Forensic Files (season 5).[citation needed]

Mitochondrial DNA was first admitted into evidence in California in the successful prosecution of David Westerfield for the 2002 kidnapping and murder of 7-year-old Danielle van Dam in San Diego: it was used for both human and dog identification.[79] This was the first trial in the U.S. to admit canine DNA.[80]

Mitochondrial DNA was discovered in the 1960s by Margit M. K. Nass and Sylvan Nass by electron microscopy as DNase-sensitive threads inside mitochondria,[81] and by Ellen Haslbrunner, Hans Tuppy and Gottfried Schatz by biochemical assays on highly purified mitochondrial fractions.[82]

Several specialized databases have been founded to collect mitochondrial genome sequences and other information. Although most of them focus on sequence data, some of them include phylogenetic or functional information.

Several specialized databases exist that report polymorphisms and mutations in the human mitochondrial DNA, together with the assessment of their pathogenicity.

Read the original post:
Mitochondrial DNA - Wikipedia

The Scientist

Aedes aegypti Genome Assembled From Scratch | The Scientist ... The Scientist Aedes aegypti is the main vector of the Zika virus. Now, scientists at the Baylor College of Medicine in Houston, Texas, and their colleagues have successfully ... Scientists find a low-cost way to build genomes from scratchEngadget Scientists drastically reduce costs for building and sequencing ...The Tech Portal all 5 news articles »

See the original post here:
Aedes aegypti Genome Assembled From Scratch | The Scientist ... - The Scientist

MOUNTAIN VIEW, Calif., March 29, 2017 /PRNewswire/ --Cellecta, Inc. today announced the launch of the Driver-Map Human Genome-Wide Gene Expression Profiling kit, a targeted RNA expression profiling assay designed to easily provide a molecular snapshot of all known 19,000 human protein-coding genes from complex samples starting from as little as 10 pg of total RNA.

The multiplex RT-PCR-based, followed by next-generation sequencing (NGS) method used in the Driver-Map Expression Profiling kit allows researchers access to the specially designed and experimentally validated gene-specific primer pairs to run samples in their own laboratories. This enables them to generate data that is more sensitive and easier to analyze when compared to conventional genome-wide expression profiling approaches such as RNA-Seq and microarray platforms.

"The simple, robust Driver-Map assay is ideal for use in characterization of complex biological samples," said Alex Chenchik, Ph.D., president and chief scientific officer of Cellecta. "Some novel applications for this gold-standard RT-PCR technology include biomarker discovery with whole blood without a globin or rRNA depletion step, detection of circulating tumor cells (CTC) in whole blood without previous CTC enrichment, high sensitivity profiling of tumor, stromal and infiltrating immune cell types from a complex tumor microenvironment, and expression profiling of patient-derived xenograft (PDX) models without interference from mouse background cells."

The Driver-Map Expression Profiling assay is highly reproducible, even starting with minimal amounts of RNA sample. Noteworthy features of this assay include:

The Driver-Map assay kit includes a complete set of gene-specific and PCR-NGS primers, buffers, spike-in ERCC and positive control RNAs as well as all other reagents required to profile 24 samples and prepare them for digital expression profiling using NGS on an Illumina sequencing platform. NGS reagents are not included in the Driver-Map assay kit.

The Driver-Map Human Genome-Wide Gene Expression Profiling kit (Catalog # DM-hgw) is available now. For more information, please visit http://www.driver-map.com

About Cellecta:

Cellecta, Inc., a trusted provider of genomic products and services, is an industry leader in RNAi and CRISPR technologies for the discovery and characterization of novel therapeutic targets, and genetic profiling for biomarker discovery. Numerous scientific papers have been published citing Cellecta's functional genomics portfolio offering gene knockout and knockdown screens, custom and genome-wide RNAi and CRISPR libraries, cell engineering, RNAi and CRISPR construct services, and mutation and expression profiling of disease samples.

Cellecta, Inc. is headquartered in Mountain View, California. Further information about the company and its functional genomic products and services may be found online at http://www.cellecta.com

Cellecta, Inc. Paul Diehl, 650-938-4050 152593@email4pr.com or Media: Ruth Mercado, 650-938-4080 152593@email4pr.com

To view the original version on PR Newswire, visit:http://www.prnewswire.com/news-releases/cellecta-inc-launches-driver-map-human-genome-wide-gene-expression-profiling-kit-for-19000-human-genes-300430932.html

SOURCE Cellecta, Inc.

http://www.cellecta.com

Read more:
Cellecta, Inc. Launches Driver-Map Human Genome-Wide Gene Expression Profiling Kit for 19000 Human Genes - PR Newswire (press release)

VANCOUVER, British Columbia--(BUSINESS WIRE)--STEMCELL Technologies announces the development of CloneR, a novel medium formulation to aid researchers in their ability to successfully genome edit human pluripotent stem cells. This supplement represents a dramatic improvement over existing technologies.

Editing the pluripotent stem cell genome relies heavily on the survival of single cells to establish clonal cell lines. CloneR is a medium supplement designed for greatly enhancing the cloning efficiency and single-cell survival of pluripotent stem cells. Unlike current methods, CloneR will enable the robust generation of clonal cell lines without single-cell adaptation, thus minimizing the risk of acquiring genetic abnormalities. Such irregularities bear a close resemblance to those found in many human cancers, raising safety concerns for the use of these cells in regenerative medicine.

As the market-leader for the development of innovative products for pluripotent stem cell research, we are delighted to announce the imminent launch of CloneR, says Dr. Allen Eaves, CEO and President of STEMCELL Technologies. We are confident that this new invention will enable researchers by improving their capacity for disease modeling, drug screening and the development of cell and gene therapies for regenerative medicine.

CloneR will build upon STEMCELLs extensive portfolio of products to support pluripotent stem cell research, including mTeSR1, the most widely published feeder-free maintenance medium on the market. The CloneR supplement will be manufactured using STEMCELLs rigorous raw material screening and quality control processes certified under ISO 13485, Medical Devices Standards. This will ensure that the final product is of the highest quality, with maximal performance and minimal lot-to-lot variability.

To receive a notification of the product launch, sign up here: http://www.stemcell.com/CloneR

About STEMCELL Technologies

STEMCELL Technologies helps power leading-edge life science research globally. The company offers highly specialized cell culture media, cell separation products, instruments, accessory products and educational tools that support scientists performing stem cell, immunology, cancer, regenerative medicine and cellular therapy research.

The rest is here:
STEMCELL Technologies to Launch CloneR to Facilitate Genome Editing of Human Pluripotent Stem Cells - Business Wire (press release)

Where earlier approaches saw researchers using computers to stick small pieces of genetic code together, the new technique takes advantages of folding maps (which show how a 6.5ft long genome can cram into a cell's nucleus) to quickly build out a sequence. As you only need short reads of DNA to make this happen, the cost is much lower. You also don't need to know much about your sample organism going in.

As an example of what's possible, the team completely assembled the three chromosomes for the Aedes aegypti mosquito for the first time. More complex organisms would require more work, of course, but the dramatically lower cost makes that more practical than ever. Provided the approach finds widespread use, it could be incredibly valuable for both biology and medicine.

In the case of the mosquito, scientists hope the genomes will reveal the vulnerabilities that let the Zika virus spread. You could see gene-modified mosquitoes that resist the virus and stop it from spreading. Alternately, this could uncover patient-specific genetic changes that expose humans to certain diseases -- it wouldn't be a mystery why one person falls ill while another is healthy. And when it's relatively affordable to build a genome out of curiosity, biologists could catalog many species instead of the most vital examples.

Go here to see the original:
Scientists find a low-cost way to build genomes from scratch - Engadget

Scientists at Baylor College of Medicine, Rice University, Texas Children's Hospital, and the Broad Institute of MIT and Harvard say they have developed a new way to sequence genomes, which can assemble the genome of an organism entirely from scratch, much cheaper and faster.

The multi-institutional team reports a methodcalled 3D genome assemblythat can create a human reference genome, entirely from scratch, for less than $10,000. The ability to quickly and easily generate a reference genome from scratch would open the door to creating reference genomes for everything from patients to tumors to all species on earth. The group published their study ("De Novo Assembly of the Aedes aegypti Genome Using Hi-C Yields Chromosome-Length Scaffolds") in Science.

To illustrate the power of 3D genome assembly, the researchers have assembled the 1.2-billion-letter genome of the Aedes aegypti mosquito, which carries the Zika virus, producing the first end-to-end assembly of each of its three chromosomes. The new genome will enable scientists to better combat the Zika outbreak by identifying vulnerabilities in the mosquito that the virus uses to spread.

Despite the decline in the cost of DNA sequencing, determining the sequence of each chromosome from scratch via de novo genome assembly remains extremely expensive because chromosomes can be hundreds of millions of base pairs long. In contrast, today's inexpensive DNA sequencing technologies produce short reads, or hundred-base-pair-long snippets of DNA sequence, which are designed to be compared to an existing reference genome. Actually generating a reference genome and assembling all those long chromosomes involves combining many different technologies at a cost of hundreds of thousands of dollars. Unfortunately, because human genomes differ from one another, the use of a reference genome generated from one person in the process of diagnosing a different person can mask the true genetic changes responsible for a patient's condition.

"As physicians, we sometimes encounter patients who we know must carry some sort of genetic change, but we can't figure out what it is," said Aviva Presser Aiden, Ph.D., M.D., a physician-scientist in the Pediatric Global Health Program at Texas Children's Hospital and a co-author of the new study. "To figure out what's going on, we need technologies that can report a patient's entire genome. But, we also can't afford to spend millions of dollars on every patient's genome."

To tackle the challenge, the team developed a new approach, called 3D assembly, which determines the sequence of each chromosome by studying how the chromosomes fold inside the nucleus of a cell.

"Our method is quite different from traditional genome assembly," said Olga Dudchenko, Ph.D., postdoctoral fellow at the Center for Genome Architecture at Baylor College of Medicine, who led the research. "Several years ago, our team developed an experimental approach that allows us to determine how the 2-meter-long human genome folds up to fit inside the nucleus of a human cell. In this new study, we show that, just as these folding maps trace the contour of the genome as it folds inside the nucleus, they can also guide us through the sequence itself."

By carefully tracing the genome as it folds, the team found that they could stitch together hundreds of millions of short DNA reads into the sequences of entire chromosomes. Since the method only uses short reads, it reduces the cost of de novo genome assembly, which is likely to accelerate the use of de novo genomes in the clinic.

"Sequencing a patient's genome from scratch using 3D assembly is so inexpensive that it's comparable in cost to an MRI," said Dr. Dudchenko, who also is a fellow at Rice University's Center for Theoretical Biological Physics. "Generating a de novo genome for a sick patient has become realistic."

Unlike the genetic tests used in the clinic today, de novo assembly of a patient genome does not rely on the reference genome produced by the Human Genome Project. "Our new method doesn't depend on previous knowledge about the individual or the species that is being sequenced," Dr. Dudchenko noted. "It's like being able to perform a human genome project on whomever you want, whenever you want."

"Or whatever you want," added Erez Lieberman Aiden, Ph.D., director of the Center for Genome Architecture at Baylor and corresponding author on the new work. "Because the genome is generated from scratch, 3D assembly can be applied to a wide array of species, from grizzly bears to tomato plants. And it is pretty easy. A motivated high school student with access to a nearby biology lab can assemble a reference-quality genome of an actual species, like a butterfly, for the cost of a science fair project."

The effort took on added urgency with the outbreak of Zika virus, which is carried by the A. aegypti mosquito. Researchers hoped to use the mosquito's genome to identify a strategy to combat the disease, but the Aedes genome had not been well characterized, and its chromosomes are much longer than those of humans.

"We had been discussing these ideas for years, writing a chunk of code here, doing a proof-of-principle assembly there," explained Dr. Lieberman Aiden, also assistant professor of molecular and human genetics at Baylor, computer science at Rice and a senior investigator at the Center for Theoretical Biological Physics. "So we had assembly data for A. aegypti just sitting on our computers. Suddenly, there's an outbreak of Zika virus, and the genomics community was galvanized to get going on Aedes. That was a turning point."

"With the Zika outbreak, we knew that we needed to do everything in our power to share the Aedes genome assembly, and our methods, as soon as possible," according to Dr. Dudchenko."This de novo genome assembly is just a first step in the battle against Zika, but it's one that can help inform the community's broader effort."

The team also assembled the genome of the Culex quinquefasciatus mosquito, the principal vector for West Nile virus. "Culex is another important genome to have, since it is responsible for transmitting so many diseases," said Dr. Lieberman Aiden. "Still, trying to guess what genome is going to be critical ahead of time is not a good plan. Instead, we need to be able to respond quickly to unexpected events. Whether it is a patient with a medical emergency or the outbreak of an epidemic, these methods will allow us to assemble de novo genomes in days, instead of years."

Read more:
3D Assembly of Zika Genome Could Have Significant Impact on Human Reference Genome - Genetic Engineering & Biotechnology News