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This Carolina parakeet was collected sometime in the late 1800s.

Not very long ago, wild parrots lived in the forests of New York. The brightly-colored birds squawked among the treetops of old-growth riverine forests and swamps from Florida to New York and as far east as Colorado, gathering in flocks of hundreds at a time. Today, the great vociferous flocks are gone, and the bright green, red, and yellow plumage can be seen only in museums.

The last known Carolina parakeet was born sometime around 1883 and died in the Cincinnati Zoo in 1918, in the same ill-fated cage where the worlds last passenger pigeon had died in 1914. Inca, the last Carolina parakeet, had outlived his mate, Lady Jane, by around a year and as far as anyone knew, the pair had outlived their wild relatives by nearly a decade. No one had reported a credible sighting of a wild Carolina parakeet since 1910.

The Carolina parakeet has been extinct for roughly a century, and a new genetic study pins the blame squarely on humans.

The Last Stand Of Americas Parrots

As European settlers and their descendants pushed westward in the 1700s and 1800s, they cleared many of the forests the Carolina parakeet had once called home. They also shot the birds in droves to keep them away from grain fields and to collect their bright feathers for ladies hats. The Carolina parakeet made an easy target; flocking instinct would bring large numbers of birds back to the scene of a fresh kill, giving hunters another shot at them.

By the mid-1800s, Carolina parakeets were rare outside the swamps of Florida, and by 1900, they couldnt be found anywhere else. But even in their last bastion of habitat, Carolina parakeets seemed to be doing pretty well, under the circumstances. Farmers had stopped hunting them, because they turned out to be useful for keeping cockleburs in check (the Carolina parakeet was one of the only animals who could survive eating the poisonous plant, although the toxic glucoside accumulated in the birds flesh and made them deadly prey. Cats who ate Carolina parakeets usually died soon after). And naturalists described large flocks, with plenty of young birds and good access to nesting sites.

And then, abruptly, the Carolina parakeet simply vanished. A century later, ecologists still dont understand what happened. Maybe, some say, the species wasnt faring as well as it looked from the outside; population decline and habitat loss could have left them with a limited gene pool, doomed to fade away before too long. But maybe, others argue, the Carolina parakeet would have been just fine if they hadnt been exposed, in their last refuge, to deadly poultry diseases like Newcastle Disease from nearby farms.

If this is true, the very fact that the Carolina parakeet was finally tolerated to roam in the vicinity of human settlements proved its undoing, wrote the Audobon Society a few years ago. Theres no actual evidence to support the poultry disease hypothesis: no eyewitness report of sick parrots with symptoms of something like Newcastle Disease, and no smoking gun in the form of pathogen samples from a preserved parrot corpse. But a new study, published in the journal Current Biology, sequenced the Carolina parakeet genome for the first time and searched for signs of inbreeding or population decline and found none. That means the species wasnt doomed long before its disappearance, which means something must have tipped the balance.

Solving A Cold Case

Evolutionary biologist Carlez Laluzela-Fox and colleagues sampled nuclear DNA from the tibia (shin bone) and toe pads of a Carolina parakeet, killed and stuffed in the late 1800s and now owned by a private collector in Spain. They used the genome of the extinct species closest living relative, a South American parrot called the sun parakeet, as a reference to help them map the genome and understand what the sequences of adenine, thymine, guanine, and cytosine meant for the birds actual physiology.

Demographic declines leave specific signals in the genomes of the species, explained Laluzela-Fox in a statement to the press. If members of a species have spent several generations breeding with close genetic relatives, or if the overall breeding population was too small, geneticists can spot the signs in an organisms genome.

But the Carolina parakeet genome had none of those warning signs so its sudden extinction wasnt the end of a much longer decline. Something new had happened and the odds are good that it was our fault. That lends some support to the poultry disease idea, although its a long way from actually proving that sick chickens, and not some other problem, actually killed off the Carolina parakeets.

Meanwhile, Laluzela-Fox and colleagues say that the same process they used to look for signs of population decline in the Carolina parakeet genome could also help screen living species for warning signs and maybe solve more extinction cold cases, too.

The genomic study also solved another century-old mystery: how did the Carolina parakeet live on poisonous cockleburs, when their toxins even made the birds flesh too poisonous to eat? In the Carolina parakeets genome, Laluzela-Fox and colleagues found two proteins that interact with the toxic glucoside in cockleburs. They suggest that those proteins allowed the bird to safely enjoy its toxic treats.

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Scientists Sequenced The Genome Of The Carolina Parakeet, Americas Extinct Native Parrot - Forbes

In centuries past, large flocks of noisy, brightly colored parrots squawked their way across the United Statesfrom New England, to Florida, to eastern Colorado. The Carolina parakeet, or Conuropsis carolinensis, was the only parrot native to the eastern part of the country. But by the beginning of the 20th century, it had disappeared.

Experts believe that humans played a prominent role in the species extinction. The clearing of forests to make way for agricultural land destroyed the birds habitat and may have contributed to their loss. They were hunted for their vibrant feathers of green, yellow and red, which made a popular addition to ladies hats. Farmers considered them pests and killed them in large numbers; the parrots were easy targets, due to their unfortunate tendency to congregate around wounded flockmates.

But as Liz Langley reports for National Geographic, some experts have speculated that causes not directly driven by humanslike diseases spread by poultry and natural disasters that fragmented the Carolina parakeets habitatmay have contributed to the species decline. Hoping to shed new light on the issue, a team of researchers sequenced the Carolina parakeets genomeand found that human causes were likely the sole driver of the birds abrupt extinction.

To conduct their analysis, the team looked at the tibia bone and toe pads of a preserved parakeet specimen held in a private collection in Spain. Because its DNA was fragmented, the researchers also sequenced the genome of the Carolina parakeets closest living relative, the sun parakeet, which gave them a more complete picture of the extinct birds genetic profile.

The researchers were specifically looking for signs of a drawn-out decline that might have started before humans began hunting the birds extensivelysigns like inbreeding. They found that after the Last Glacial Period around 110,000 years ago, Carolina parakeets began experiencing a population decline that continued until recent timesbut the still-extant sun parakeets decline was stronger, according to the study.

Crucially, the researchers didnt discover evidence of inbreeding that you might expect to see in a species that has been endangered for some time, which suggests the parakeet suffered a very quick extinction process that left no traces in the genomes of the last specimens, the researchers write in Current Biology. And when extinction happens at a rapid pace, human action is common, study co-author Carles Lalueza tells Ryan F. Mandelbaum of Gizmodo.

Whats more, the study authors did not find a significant presence of bird viruses in the Carolina parakeets DNA, though they acknowledge that further research is needed to rule out poultry disease as a driver of the birds extinction. For now, however, they conclude that the parakeets extinction was an abrupt process and thus likely solely attributable to human causes.

Earlier this month, a separate team of researchers came to the same conclusion about the disappearance of the great auk, a large, flightless bird that appears to have been wiped out by rapacious hunters. These cases offer sobering insight into how quickly humans are capable of decimating a species; the Carolina parakeet, Lalueza tells Mandelbaum, likely went extinct within the order of [a] few decades.

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The Extinction of This U.S. Parrot Was Quick and Driven by Humans - Smithsonian.com

University of WisconsinMadison researchers have developed a computational tool that can accurately predict the three-dimensional interactions between regions of human chromosomes.

The predictive tool is a boon for researchers studying how cells control the activity of genes. The fine-tuned interaction between regulatory signals and the three-dimensional architecture of chromosomes helps explain how cells achieve their key functions, and how they go haywire, as happens in diseases such as cancer.

The experimental technique to measure these three-dimensional interactions, Hi-C, is expensive, which has limited high-quality data to just a few types of cells. In contrast, the new tool can predict these interactions using much more easily measurable and commonly available data. This could help biologists perform across many cell types more detailed research into tissue development, cancer and other diseases that are affected by this type of distant gene regulation.

Roy

Zhang

UWMadison researcher Sushmita Roy and her graduate studentShilu Zhang led the work, which was published Dec. 6 in Nature Communications. The researchers have made the tool freely available to other scientists and continue to improve the predictive power of the tool, which they named HiC-Reg after the resource-intensive experiments.

We can very cheaply predict the output of Hi-C experiments, which can help us prioritize other regions of the genome to follow up with more fine-tuned experiments, says Roy, a professor in the Wisconsin Institute for Discovery and the UWMadison Department of Biostatistics and Medical Informatics. This can be used as a resource to interpret regulatory variation in the genome.

The human genome consists of 23 pairs of chromosomes. A new study from UWMadisons Sushmita Roy describes a computational tool for researchers to better predict the three-dimensional interactions between chromosomes. Wikimedia Commons

A far cry from the neat, straight lines of DNA pictured in textbooks, real chromosomes fold, twist and bend to fit several linear feet of DNA into a tiny cell nucleus. These loops also bring distant regions of a chromosome together. Some of these regions carry regulatory information that can promote or repress the expression of distant genes. This intricate gene expression magnifies the complexity of traits that organisms exhibit.

Roy and other researchers have previously developed models that could predict whether or not two distant regions of a chromosome would interact. HiC-Reg builds on that model and not only predicts whether two regions will interact but also how strong that interaction might be. It provides a more complex and realistic model of how chromosomal regions interact and potentially regulate gene expression.

The packing of chromosomes into a nucleus allows distant regions of a chromosome to interact and affect one another. Consistently interacting regions are known as topologically associated domains, or TADs. This kind of fine-tuned gene regulation produces more complexity in the traits that organisms express. Navneet Matharu and Nadav Ahituv

To create HiC-Reg, Roys team fed a series of commonly available genomic data, such as the presence of proteins and chemical modifications that activate or repress gene expression, into a machine learning algorithm. It also included Hi-C data from the few cell lines for which it is available. The tool then learned relationships that enabled it to predict the Hi-C measurements for a new pair of genomic regions.

Lets try to use the data thats easy to measure to predict the information thats harder to gather, says Roy. The research was supported by the National Institutes of Health Big Data to Knowledge program, which allowed the team to mine this freely available but underutilized data. Were trying to leverage publicly available datasets as much as possible.

HiC-Reg correctly predicted between 40 percent and 80 percent of regional associations. The tool is more accurate than estimating the strength of interactions based on chromosomal distance alone or just mapping the interactions from a pair of regions in one cell line to the same pair of regions in another cell line. But the interactions were harder to predict in some cell types than in others, a limitation the researchers are now working to overcome.

The computationally intensive work relied on UWMadisons Center for High Throughput Computing, the UW Center for Predictive Computational Phenotyping and the Core Computational Technology research group at the Wisconsin Institute for Discovery.

Other researchers can now use HiC-Reg as-is to predict these three-dimensional interactions in their favorite cell line. Or, they can elect to re-train the program using their own datasets to improve its accuracy for their work.

Roy says that free access is consistent with the question that motivated this research: How can we help biologists gather this data?

This work was supported by the National Institutes of Health (BD2K grant U54 AI117924 and grant R01-HG010045-01).

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New tool predicts three-dimensional organization of human chromosomes - University of Wisconsin-Madison

Global Genome Editing Market: Overview

Also known as genome editing with engineered nucleases (GEEN), genome editing is a method of altering DNA within a cell in a safe manner. The technique is also used for removing, adding, or modifying DNA in the genome. By thus editing the genome, it is possible to change the primary characteristic features of an organism or a cell.

The global genome editing market can be segmented on the basis of delivery method, technology, application, and geography. By technology, the global genome editing market can be segmented into Flp-In, CRISPR, PiggyBac, and ZFN. Based on delivery method, in vivo and ex vivo can be the two broad segments of the global genome editing market. By application, the global genome editing market can be categorized into medicine, academic research, and biotechnology.

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Global Genome Editing Market: Key Trends

Since genome editing is gaining rising adoption in the domain of scientific research for attaining a better understanding of biological aspects of organisms and how they work, the global genome editing market is likely to promise considerable growth over the forthcoming years. More importantly, genome editing is being used by medical technologies, where it can be used for modifying human blood cells which can then be placed back in the body for treating conditions such as AIDS and leukemia. The technology can also be potentially utilized to combat infections such as MRSA as well as simple genetic disorders including hemophilia and muscular dystrophy.

Global Genome Editing Market: Market Potential

As more easy-to-use and flexible genome technologies are being developed, greater potential of genome editing is being recognized across bioprocessing and treatment modalities. For instance, in May 2017, MilliporeSigma announced that it successfully developed a novel genome editing tool which can make the CRISPR system more productive, specific, and flexible. The researchers thus have a more number of experimental options along with faster results.

All this can lead to a growing rate of drug development, enabling access to more advanced therapies. Proxy-CRISPR, the new technique, makes access to earlier inaccessible aspects of the genome possible. As most of the existing CRISPR systems cannot manage without re-engineering of human cells, the new method is expected to gain more popularity by virtue of the elimination of the need for re-engineering, simplifying the procedures.

Several other market players are focusing on clinical studies with a view to produce effective treatments for different health conditions. For example, another major genome editing firm, Editas Medicine, Inc. announced the results of its pre-clinical study displaying the success of the CEP290 gene present in the retina of primates in the same month. With the positive results of the study, the companys belief in the vast potential of its candidate in the treatment of a genetically inherited retinal degenerative disease, Leber congenital amaurosis type 10, affecting childrens eyesight has been reinforced.

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Global Genome Editing Market: Regional Outlook

By geography, the global genome editing market can be segmented into Latin America, Europe, Asia Pacific, the Middle East and Africa, and North America. North America registered the highest growth in the past, and has been claiming the largest portion of the global genome editing market presently. The extraordinary growth of this region can be attributed to greater adoption of cutting edge technologies across several research organizations. The U.S., being the hub of research activities, is expected to emerge as the leading contributor. Asia Pacific is also likely to witness tremendous demand for genome editing over the forthcoming period, assisting the expansion of the global genome editing market.

Global Genome Editing Market: Competitive Analysis

CRISPR THERAPEUTICS, Caribou Biosciences, Inc., Sigma Aldrich Corporation, Sangamo, Intellia Therapeutics, Inc., Editas Medicine, Thermo Fisher Scientific, Inc., and Recombinetics, Inc are some of the key firms operating in the global genome editing market.

The study presents reliable qualitative and quantitative insights into:

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Genome Editing Market Exclusive insight on Transformation 2025 - Techi Labs

Gene therapies are experiencing a new era. CRISPR is current. CRISPR is trendy. CRISPR is on many researchers minds. But its sudden success has also triggered concerns about its safety. Can the proteome help solve these issues?

Although the landscape of genome editing has been evolving for nearly 50 years, it has only recently seen dramatic changes. After experiencing years of stagnation resulting from severe setbacks in clinical trials and a lack of efficiency, zinc-finger nucleases appeared on stage. This time, researchers were hampered by yet another problem: the patent landscape and design complexity. Licensed and commercialized for research by Sigma-Aldrich, the technology was costly which made it difficult to access as a general tool for researchers.

At the time, zinc-finger nucleases were a fantastic adventure, says Jens-Ole Bock, CEO of COBO Technologies. It was exciting to know that we had a tool that could do specific changes to the genome. But zinc-finger nucleases were expensive, very complex, and difficult to access. There were some alternatives on the market for a few years, and then CRISPR-Cas9 appeared. Suddenly we had this really great genome editing tool that was cheap, with a simple mode of action, and available for everyone to work with.

As a result of this democratization, research in the field of genome editing sped up dramatically and the CRISPR technology continues to evolve very fast. However, in 2018, a small number of publications raised concerns about the safety of CRISPR, revealing that the technology might cause severe side effects due to off-target mutations.

With CRISPR we now have a very effective and easy system that everyone is using, Bock says. There are more than 5000 publications a year in CRISPR research and we are now moving towards its clinical application. This also means that we need to focus on CRISPR safety concerns. If we want to move to the clinic, we need to understand exactly what is going on inside the cells when we apply CRISPR. What is the target? What happens in the target area? Are there off-target events? Is there immunogenicity? How is the biology of the cells affected?

In order to better anticipate the risks of genome editing tools, Bock and his colleagues founded COBO Technologies, a company that focuses exclusively on quality control of genome editing. The team has developed a platform called PIPPR that can address concerns about CRISPR safety on a proteome level, together with SCIEXs mass spectrometry SWATHAcquisition technology. The PIPPR platform offers a proteomic expression analysis solution for cells that have been genetically modified. Using SWATH Acquisition researchers can then visualize their results and identify and quantify between 3000-5000 proteins in any cell line, whether of plant or animal origin.

There is a growing need to understand how the proteome changes during different CRISPR applications, explains Bock. We need a powerful method that is robust, fast and sensitive, to both confirm expected changes and to check for unexpected changes in proteins and different pathways. PIPPR, powered by SWATHAcquisition, is the first platform to really address this and will make it possible for researchers to see and compare expression levels of more than 3000 proteins in their cell line projects. Using this detailed, large-scale proteome information, the efficacy and safety of genetic modifications can now be assessed.

COBO Technologies customers work with genome editing tools and often want to understand how the cells biological makeup is modified when they have applied CRISPR. By looking at the expression of proteins in the edited cell line and comparing these to the wildtype cell line, the team can identify changes that may have occurred during genome editing.

The team at COBO Technologies has developed a full package service that enables customers to use validated reagents to extract proteins from their modified cells. Once extracted, the proteins are sent to COBO Technologies where they undergo a robust analysis using SWATHAcquisition. Within four weeks, the customers will receive a full bioinformatic analysis of the cells proteins.

Some of the companys customers use the PIPPRplatform and SWATHAcquisition technology to compare the proteome of their modified cell line with that of the wild type cell line. This allows them to see what impact the genetic modification had at a proteome level.

Other customers are more interested in seeing the effect of different genome editing tools on their cell line and comparing these with each other. They want to know whether there is a difference between the two, whether we get different proteomic profiles. Has anything changed? Is there toxicity in one, but not the other? Might we have immunogenicity issues with some CRISPR tools, but not with others? All of this information can be gained by looking at the proteome level, which is especially important when working with CRISPR safety, says Bock.

Since before the initial release in 2010, SWATHAcquisition has been continually developed in collaboration with customers, says Ferran Snchez, Marketing Development Manager at SCIEX. SWATH Acquisition ultimately immortalizes a sample by creating a digital data record of all observable species. As a data-independent acquisition strategy, SWATH Acquisition collects mass spectrometry (MS) and MS/MS information on every detectable peak leaving you with an option to re-interrogate your sample data should new questions arise tomorrow. The extra dimension of data interpretation achieved provides increased confidence in identification for both quantitative and qualitative discovery workflows.

Moreover, the combination of the two technologies allows researchers to save time. We are working in a research environment where time is a big thing, says Bock. Researchers are doing a lot of things and we need technology that is fast, robust, and efficient because CRISPR safety is becoming increasingly important as we move into clinical phases.

With SWATH Acquisition, a single generic MS acquisition method is used all of the time, explains Snchez. This means you select your compounds of interest from the digital map after you collect your comprehensive MS and MS/MS data on your sample. Should your data analysis present new questions, you can simply re-interrogate the data youve already collected rather than updating your acquisition method and re-analyzing your sample from step one. Once your SWATH Acquisition method is optimized for a sample type, the same method can be used for analysis across many similar samples no matter what analytes youre studying, saving tremendous time.

As basic genome editing moves closer from bench to bedside, more and more studies have to be done into the safety of CRISPR and other genome editing methods. Currently, interventions are used for diseases for which the genetic background is very clear and patient stratification is possible.

Furthermore, while most drugs today follow clear regulations, there has yet to be a standard laid down for CRISPR. This is especially important for CRISPR safety as the technology moves from research to clinical phases.

We are at an extremely early stage, says Bock. At the moment, we are merely looking at what standards to define at the DNA level. But once we have defined these, we need to describe standards for the RNA level, and later the proteome level. We are at a very early stage regarding the safety and efficacy of CRISPR.

Do you want to be at the forefront of CRISPR safety research? Get in touch with SCIEX at [emailprotected] and learn how you can use SWATHAcquisition to advance your studies. To request more information on the PIPPR platform, contact COBO Technologies at j[emailprotected]

Images via Shutterstock.com, SCIEX, and COBO Technologies

Author: Larissa Warneck, Science Journalist at Labiotech.eu

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Taking CRISPR Safety to the Next... - Labiotech.eu