Researchers have developed a sequencing methodology that enables doubtlessly a whole lot of plant chloroplast genomes to be sequenced without delay, facilitating research of molecular biology and evolution in crops. This methodology depends on environment friendly separation of chloroplast DNA utilizing brief DNA “baits” designed from already-sequenced chloroplast genomes. These molecular baits focus the chloroplast DNA earlier than sequencing, dramatically rising the variety of samples that may be sequenced.
Researchers on the University of Florida and Oberlin College have developed a sequencing methodology that can permit doubtlessly a whole lot of plant chloroplast genomes to be sequenced directly, facilitating research of molecular biology and evolution in crops.
Cell that’s answerable for photosynthesis and therefore offers all the sugar that a plant must develop and survive. The chloroplast is uncommon in containing its personal DNA genome, separate from the bigger and dominant genome that’s positioned in each cell’s nucleus.
Chloroplast DNA sequences are extensively utilized by plant biologists in genetic engineering and in reconstructing evolutionary relationships amongst vegetation. Until lately, although, chloroplast genome sequencing was a expensive and time-intensive endeavor, limiting its utility for plant evolutionary and molecular biologists. Instead, most researchers have been restricted to sequencing a small portion of the chloroplast genome, which in lots of instances is inadequate for figuring out evolutionary relationships, particularly in plant teams which can be evolutionarily younger.
In distinction, full chloroplast genome sequences harbor sufficient data to reconstruct each current and historic variations. New DNA sequencing applied sciences, termed “subsequent-era” sequencers, have made it significantly cheaper and simpler to sequence full chloroplast genomes. While present strategies utilizing subsequent-technology sequencers enable as much as forty eight chloroplast genomes to be sequenced at one time, the brand new technique will permit doubtlessly tons of of flowering plant chloroplast genomes to be sequenced without delay, considerably decreasing the per-pattern price of chloroplast genome sequencing.
This new methodology, reported within the February challenge of Applications in Plant Sciences, depends on environment friendly separation of chloroplast DNA from different DNA within the cell utilizing brief DNA “baits” that have been designed from chloroplast genomes which have already been sequenced. These molecular baits successfully focus the chloroplast DNA earlier than sequencing (a course of termed “focused enrichment”), dramatically growing the variety of samples that may be sequenced directly.
Greg Stull, a graduate pupil on the University of Florida and lead writer of the research, summarizes the flexibility of the brand new system: “With this methodology, it ought to be attainable for researchers to cheaply sequence tons of of chloroplast genomes for any flowering plant group of curiosity.”
The technique was particularly designed by the authors of the examine such that nearly any flowering plant chloroplast genome could be sequenced, no matter species. Flowering vegetation characterize the most important (~300,000 species) and most ecologically dominant group of land crops, and embody all main crop crops.
admin June 6th, 2014
Posted In: DNA sequencing
Single-cell genomics might present new perception into the biology of Malaria parasites, together with their virulence and ranges of drug resistance, to finally enhance therapy and management of the illness, based on new analysis funded by the Wellcome Trust and the National Institutes of Health.
The findings are revealed in a research by researchers on the Texas Biomedical Research Institute and revealed within the journal Genome Research.
Malaria infections generally include advanced mixtures of Plasmodium parasites which trigger the illness. These mixtures, often known as a number of genotype infections (MGI’s), can alter the influence of the an infection resulting from parasites competing with each other and may drive the unfold of drug resistance. MGI’s are extraordinarily widespread in areas with excessive ranges of malaria an infection however their biology is poorly understood.
“Up to 70 per cent of infections in sub-Saharan Africa are MGI’s and we presently do not know what number of genotypes are current and whether or not parasites come from a single mosquito chew or a number of mosquito bites” says Shalini Nair, first writer on the paper.
Current genome sequencing strategies contain the chemical disintegration of samples of pink blood cells from contaminated sufferers to acquire parasite DNA, that are then sequenced. This grouped sequencing can not account for variations between particular person parasites present in cells.
Single cell genomics permits the separation and isolation of cells to extract and sequence particular person parasite DNA and decide any variations between the parasites inside an an infection.
“Current sequencing methods actually restrict our understanding of parasite biology and malaria control, “It’s like making an attempt to grasp human genetics by making DNA from everybody in a village directly. The knowledge is all jumbled up, however what we actually need is data from people.”
The workforce used strategies of single cell-sorting and complete genome amplification to separate out particular person cells and amplify their DNA for sequencing immediately from contaminated pink blood cells. The use of single-cell genomics permits sequencing of particular person parasites straight from a affected person’s blood.
The method permits a complete description of the composition of MGIs, and can reveal data on the energy of an an infection and the event of drug-resistance, which may inform illness management interventions.
Though the expertise is presently too costly and demanding for routine use within the clinic, because the know-how matures the purposes for understanding malaria biology are huge.
Head of Genetics and Molecular Sciences mentioned: “Malaria stays one of many greatest killers on this planet at this time regardless of a long time of management efforts. Any perception into the basic genetics and total biology of the illness is efficacious to enhance future interventions and scale back charges of an infection and mortality.”
Two types of malaria parasites had been sequenced within the research; Plasmodium falciparum (liable for as much as seven-hundred, deaths per yr) and Plasmodium vivax (answerable for 20 million infections per yr).
admin May 28th, 2014
Posted In: DNA sequencing
Researchers led by bioengineers have generated essentially the most full genome sequences from single E. coli cells and particular person neurons from the brain. The breakthrough comes from a brand new single-cell genome sequencing method that confines genome amplification to fluid-crammed wells with a quantity of simply 12 nanoliters.
The research is revealed within the journal Nature Biotechnology on November 10, 2013.
“Our preliminary information recommend that neurons from the brain have completely different genetic compositions. This is a comparatively new concept, and our method will allow researchers to have a look at genomic variations between single cells with a lot finer element,” mentioned Kun Zhang, a professor within the Department of Bioengineering on the UC San Diego Jacobs School of Engineering and the corresponding creator on the paper.
The researchers report that the genome sequences of single cells generated utilizing the brand new method exhibited comparatively little “amplification bias,” which has been probably the most vital technological impediment going through single-cell genome sequencing up to now decade. This bias refers to the truth that the amplification step is uneven, with completely different areas of a genome being copied completely different numbers of instances. This imbalance complicates many downstream genomic analyses, together with meeting of genomes from scratch and figuring out DNA content material variations amongst cells from the identical particular person.
Sequencing the genomes of single cells is of nice curiosity to researchers working in many various fields. For instance, probing the genetic make-up of particular person cells would assist researchers determine and perceive a variety of organisms that can’t be simply grown within the lab from the micro organism that reside inside our digestive tracts and on our pores and skin, to the microscopic organisms that stay in ocean water. Single-cell genetic research are additionally getting used to review most cancers cells, stem cells and the human mind, which is made up of cells that more and more seem to have vital genomic variety.
“We now have the fantastic alternative to take a better-decision have a look at genomes inside single cells, extending our understanding of genomic mosaicism throughout the mind to the extent of DNA sequence, which right here revealed new somatic adjustments to the neuronal genome. This may present new insights into the conventional in addition to irregular mind, resembling happens in Alzheimer’s and Parkinson’s illness or Schizophrenia,” mentioned Jerold Chun, a co-creator and Professor within the Dorris Neuroscience Center at The Scripps Research Institute.
For instance, the brand new sequencing method recognized positive factors or lack of single copy DNA as small as M million base pairs, the best decision to this point for single-cell sequencing approaches. Recent single-cell sequencing research have used older strategies which may solely decipher DNA copy modifications which might be no less than three to 6 million base pairs.
The 12 nanoliter (nL) quantity microwells wherein amplification takes place are a few of the smallest quantity wells for use in revealed protocols for single-cell genome sequencing.
“By decreasing amplification response volumes a thousand-fold to nanoliter ranges in 1000′s of microwells, we elevated the efficient focus of the template genome, resulting in improved amplification uniformity and diminished DNA contamination,” defined Jeff Gole, the primary creator on the paper. Gole labored on this challenge as a Ph.A. pupil in Kun Zhang’s bioengineering lab on the UC San Diego Jacobs School of Engineering. Gole is now a Scientist at Good Start Genetics in Cambridge, Mass.
Compared to essentially the most full beforehand printed single D. coli genome knowledge set, the brand new strategy recovered 50 p.c extra of the W. coli genome with A to thirteen-fold much less sequencing knowledge.
“The outcomes exhibit that MIDAS gives a way more environment friendly technique to assemble entire bacterial genomes from single cells with out tradition,” the authors write within the Nature Biotechnology paper.
The genomics researchers collaborated with supplies science graduate scholar Yu-Jui (Roger) Chiu on the microfabrication required to create the arrays of microwells. Chiu is engaged on his Ph.A. within the lab of UC San Diego electrical engineering professor Yu-Hwa Lo, who additionally directs the Nano3 Labs in UC San Diego’s Qualcomm Institute, the place microfabrication befell.
“This venture wouldn’t have succeeded with out the fabrication and instrumentation assist accessible on the Jacobs School and the Qualcomm Institute,” mentioned Zhang. “We are very enthusiastic about our preliminary outcomes in addition to the likelihood that researchers all over the world will be capable of use this strategy in many various contexts.”
admin May 28th, 2014
Posted In: DNA sequencing
DNA sequencing refers to determining the exact order of nucleotides (Adenine, Thiamine, Guanine, Cytosine) for the DNA in a cell. The major scientific advancement that occurred in this area was the completion of the Human Genome Project in 2003. The aim of this project was to sequence the entire DNA in a human cell and to determine which sections of DNA represent individual genes (protein-coding units).
and sent to the Human Genome centres where scientists performed DNA sequencing and analysis. Therefore the full sequence was published and researchers determined that within this sequence there was somewhere between 30,000 and 40,000 genes.
Some scientists still argue that the complete sequencing of the human genome is not complete because current technology has left many bases of repeat-rich heterochromatin and several small gaps unfinished. However, they seem to agree that the confirmed number of genes in the human is closer to 25,000.
Scientists are currently using this information to work on projects that compare genomes between human beings and other animals while other projects are investigating interactions between DNA sequences, gene products and environmental factors and analysing genetic variations between individuals in a population. An online system known as ENCODE (Encyclopaedia of DNA Elements) has also been invented that enables the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. In addition to the variation information catalogued by the International HapMap in 2007 and 100 Genomes project in 2012, researchers have built a reliable foundation for genetic research routed in the human genome sequence. The first genome-wide ENCODE papers were published in 2012 to help everyone in and outside the scientific community understand the meaning of these sequences.
Archiving of a lot of information on sequencing is operating under the International Nucleotide Sequence Database Collaboration (INSDC) which is currently preserving all sequences equally but it has been indicated that the rapid increase in the rate of global sequence production will soon lead to differentiated treatment of DNA sequences being submitted. This will be a major advancement in the storage and maintenance of the records. It will also contribute to easy retrieval of these sequences for different scientific purposes. Rapid advancement in sequencing technology, commonly referred to as the next generation sequencing, has contributed towards analyzing large numbers of DNA thus delivering large volumes of data over a short period of time. Sanger sequencing method which has been used for several years is no longer the only technique that can be applied for analysis of DNA.
Over the past several decades technical advances automated and refined the Sanger sequencing method. The new technologies that have been developed to further increase the efficiency of sequencing include flow cytometry, scanning microscopes, mass spectrophotometer and hybridization strategies. Next generation sequencing has been seen to be a major contributor towards
admin February 9th, 2014
Posted In: DNA sequencing
Tags: DNA sequencing