Inheritance in plants can now be controlled specifically

A new application of the CRISPR/Cas molecular scissors promises major progress in crop cultivation. At Karlsruhe Institute of Technology (KIT), researchers from the team of molecular biologist Holger Puchta have succeeded in modifying the sequence of genes on a chromosome using CRISPR/Cas. For the first time worldwide, they took a known chromosome modification in the thale cress model plant and demonstrated how inversions of the gene sequence can be undone and inheritance can thus be controlled specifically. The results are published in Nature Communications.

About 5,000 years ago, genetic information of thale cress was modified. To date, it has spread widely and is of major interest to science. On the chromosome 4 of the plant, a so-called inversion occurred: The chromosome broke at two points and was reassembled again. The broken out section was reinserted, but rotated by 180°. As a result, the sequence of genes on this chromosome section was inverted. This chromosome mutation known as “Knob hk4S” in research is an example of the fact that evolution cannot only modify the genetic material of organisms, but determine it for a long term. “In inverted sections, genes cannot be exchanged between homologous chromosomes during inheritance,” molecular biologist Holger Puchta, KIT, explains.

Researchers Remove Obstacle to Crop Cultivation

Inversions do not only affect thale cress (Arabidopsis thaliana), a wild plant used as a model organism in genetics due to its completely decoded genome and its small chromosome number. Inversions can also be found in crop plants. They are an obstacle to cultivation that uses modifications of the genetic material to produce maximum yields and a good taste of the plant and to make the plant resistant to diseases, pests, and extreme climatic conditions.

For the first time, researchers from the Chair for Molecular Biology and Biochemistry held by Puchta at KIT’s Botanical Institute have now succeeded in undoing natural inversions. “We considerably extended the applications of the CRISPR/Cas molecular scissors,” Puchta says. “We no longer use the scissors for exchanging arms between chromosomes, but also for recombining genes on a single chromosome. For the first time, we have now demonstrated that it is possible to directly control inheritance processes. We can achieve genetic exchange in an area, in which this has been impossible before. With this, we have established chromosome engineering as a new type of crop cultivation.”

Molecular Scissors Precisely Cut the DNA

Together with researchers from the team of Professor Andreas Houben, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben, and Professor Paul Fransz from the University of Amsterdam, KIT scientists took the most prominent natural inversion hk4S on chromosome 4 of thale cress and demonstrated how this inversion can be undone and how genetic exchange can be achieved in cultivation. Their findings are reported in Nature Communications. The researchers also think that it is possible to use CRISPR/Cas to produce new inversions, which would be another step towards combining desired traits and eliminating undesired properties in crop cultivation.

Holger Puchta is considered a pioneer of genome editing with molecular scissors using the natural principle of mutation to precisely modify the genetic information in plants without introducing foreign DNA. His current project “Multidimensional CRISPR/Cas mediated engineering of plant breeding,” CRISBREED for short, now focuses on the recombination of plant chromosomes by means of CRISPR/Cas technology. CRISPR (stands for Clustered Regularly Interspaced Short Palindromic Repeats) represents a certain section on the DNA that carries the genetic information. Cas is an enzyme that recognizes this section and cuts the DNA precisely at that point in order to remove, insert, or exchange genes, recombine chromosomes, and for the first time modify the gene sequence on them.

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Materials provided by Karlsruher Institut für Technologie (KIT). Note: Content may be edited for style and length.

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GrammaTech Launches Tool for API Usage Error Detection

GrammaTech, a provider of software application security testing solutions, today announced it has released Swap Detector an open-source checker that detects API usage errors. The tool, developed as part of a research project sponsored by the Department of Homeland Security (DHS) Science and Technology Directorate (S&T) Static Tool Analysis Modernization Project (STAMP), improves application security testing for DevOps.

Modern software development involves the use of third-party APIs, libraries, and/or frameworks that are complex, rapidly evolving, and sometimes poorly documented. According to industry estimates, open source components can represent up to 90% of the code in the average application. Meanwhile, API usage errors are a common source of security and reliability vulnerabilities. Swap Detector enables developers and DevOps teams to identify errors due to swapped function arguments, which can also be present in deployed code.

“Traditional static-analysis techniques do not take advantage of the vast wealth of information on what represents error-free coding practices available in the open-source domain,” says Alexey Loginov, Vice President of Research at GrammaTech. “With Swap Detector we applied Big Data analysis techniques, what we call Big Code analysis, to the Fedora RPM open-source repository to baseline correct API usage. This allowed us to develop error-detection capabilities that far exceed the scalability and accuracy of conventional approaches to program analysis.”

Swap Detector consumes input information about a call site, and optionally, function declaration information pertaining to that call site. If it detects a potential swapped-argument error at that call site, it outputs an appropriate warning message and a score for the warning. The Swap Detector interface integrates with a variety of static analysis tools, such as Clang Static Analyzer, Clang-Tidy, and PyLint. Although initially focused on C/C++ programs, Swap Detector is applicable to programs in other languages; and is especially beneficial for languages that are interpreted and not compiled.

Swap Detector uses multiple error-detection techniques, layered together to increase accuracy. For example, it compares argument names used in call sites with the parameter names used in corresponding declarations. In addition, it uses “Big Code” techniques, applying statistical information about usages of “known good” API-usage patterns collected from a large corpus of code, and flagging usages that are statistically anomalous as potential errors. To improve the precision of the reported warnings, Swap Detector applies false-positive reduction strategies to the output of both techniques.

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Author: <a href="">ProgrammableWeb PR</a>


Datadog launches Automated Error Tracking Service

Datadog, a cloud application monitoring, and security platform provider has launched Error Tracking. The new product automatically collects application errors in real-time. Then, it aggregates into action items for engineering teams to respond to.

“In modern applications, the number of errors can increase rapidly as we serve more users, make frontend code logic more complex with Single Page Applications, and increasingly rely on microservices and elastic infrastructure,” Renaud Boutet, Datadog Vice President of Product, commented in a press release. “Application engineers need a solution to prioritize issues in fast-moving situations that impact customer experience and revenues.”

Datadog Error Tracking processes data already available within its platform to provide the needed action items. This lowers the time to issue identification which keeps error fallout to a minimum. Multiple errors can be consolidated into a single issue that teams can remedy instead of tracking each error manually.

Key features of the new service include:

  • Automatic error extraction: automatically extracts errors for Datadog RUM users with no additional code
  • Errors view: visualization tool that uses tags and facets to group errors into related issues
  • Unminified stack traces: provides access to unminified source code to help pinpoint error causes
  • Seamless developer experience: works with existing CI/CD workflows with the Datadog CLI. Allows developers to track release and link source code to error events
  • Correlation across RUM sessions: includes data such as session ID, view ID, URL, browser, location, and OS to correlate error with data for triage purposes

To learn more, visit Datadog’s blog post announcement.

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Author: <a href="">ecarter</a>


Gov. Wolf Announces $96 Million for Small Businesses Impacted by COVID-19 – PA Department of Community & Economic Development

Application Period for Final Round of Funding Now Open

Harrisburg, PA – Governor Tom Wolf today announced that $96 million in state grants have been awarded to 4,933 Pennsylvania small businesses that were impacted by the COVID-19 public health crisis and subsequent business closure order.

Businesses in every Pennsylvania county received grants in this first of two rounds of funding, and 2,512 grants – or 51 percent – were awarded to historically disadvantaged businesses.

“As we continue to address this public health crisis, it’s critical that we also focus on our state’s economic recovery and supporting our small businesses across the state, which continue to be impacted by our necessary mitigation efforts,” Gov. Wolf said. “This funding will go a long way to help small businesses, including historically disadvantaged businesses, at a time when they need it most.”

The COVID-19 Relief Statewide Small Business Assistance funding was developed in partnership with state lawmakers and allocated through the state budget, which included $2.6 billion in federal stimulus funds through the Coronavirus Aid, Relief, and Economic Security (CARES) Act, of which $225 million was earmarked for relief for small businesses.

The Department of Community and Economic Development (DCED) distributed the funds to the Pennsylvania Community Development Financial Institutions (CDFIs), which are administering the grants through three programs: $100 million for the Main Street Business Revitalization Program, $100 million for the Historically Disadvantaged Business Revitalization Program, and $25 million for the Loan Payment Deferment and Loss Reserve Program.

“The COVID-19 pandemic unexpectedly affected small businesses across the commonwealth, an unfortunate circumstance that could not have been predicted or prepared for,” said DCED Secretary Dennis Davin. “However, through the collective action of the Wolf Administration, the General Assembly, and the CDFI Network, Pennsylvania’s hardest hit and most at-risk businesses will be able to access the funding they need to shore up their resources and regain sound financial footing as we move into recovery.”

The second and final round of funding is open starting today through 11:59 PM on Friday, August 28. Eligible applicants not awarded in the first round do not need to reapply and will be rolled into the next round for consideration. More information on the COVID-19 Relief Statewide Small Business Assistance Program, including how to apply, is available on DCED’s website.

“The PA CDFI Network targeted these funds to reach the smallest and most vulnerable businesses across the state and we received an immense response with close to 50,000 applications submitted in the first round and more than $860 million in total requests,” said Daniel Betancourt, chairman of the PA CDFI Network and President & CEO of Community First Fund. “We are grateful to be part of this first step with Governor Wolf and the Pennsylvania Legislature to get much needed resources to the small businesses that have been so adversely impacted by the pandemic.”

The grants may be used to cover operating expenses during the shutdown and transition to re-opening, and for technical assistance including training and guidance for business owners as they stabilize and relaunch their businesses.

“These grants and the relief they will provide are testament to what we can do when we prioritize the right initiatives,” said state Sen. Vincent Hughes (D-Philadelphia, Montgomery), Democratic chairman of the Senate Appropriations Committee. “It is because of collaboration and a collective focus that today we were able to deliver help to the auto body shops, the barbershops, the beauticians, the pizza shop owners, the soul food establishments and other businesses across the commonwealth. It is critical to understand that there is still a great deal of need and must continue to direct resources and aid to our small business community to help it recover from the devastation of the pandemic.”

“I could not be more proud or more grateful for the great work of DCED and Pennsylvania’s CDFI Network in delivering substantive, fair, equitable, need-based assistance to our state’s main street and historically disadvantaged small businesses. Our program design and the accountability it provides to taxpayers and to our federal funders is a model for the nation,” said state Sen. John Blake (D-Lackawanna, Luzerne, Monroe), Democratic chairman of the Senate Finance Committee. “I appeal to the US Congress and to our colleagues on both sides of the aisle in Harrisburg to recognize the success of this program in assisting small businesses devastated by the pandemic and to invest further in the program so we can help even more of them.”

“Our business community has been severely impacted by the COVID-19 pandemic and is in need of immediate assistance. The grant program is targeted to help small businesses manage costs, handle expenses, and stay in operation in this exceptionally difficult time,” said state Sen. Jim Brewster (D-Allegheny, Westmoreland). “Since COVID struck our state and debilitated our business community, I have been advocating for bridge grants and sought millions in aid for impacted businesses and workers. The small business assistance grants are one of the tools we can use to bolster business, maintain jobs and help workers at a time of immense distress.”

“For minority and women-owned businesses in Pennsylvania COVID-19 didn’t create a crisis, it laid bare the crisis our minority entrepreneurs have been facing for decades,” said state Rep. Jake Wheatley Jr (D-Allegheny), Democratic chairman of the House Finance Committee. “While I’m glad to see the positive impact of these grants and I urge all local community businesses to apply for the next round of grants, we need to expand investment in programs like this because it’s long past time for the legislature to address the systemic flaws that are leaving too many marginalized people behind.”

“The burden that COVID-19 has put on business owners, employees and families in southeast Pennsylvania gets heavier every day,” said state Rep. Chris Sappey (D-Chester). “At this point, when we talk about addressing the pandemic, we must not only fight it with masks and social distancing, but we also must equally and strongly support our business community, where this fight for our health and safety actually is taking place. Commerce and industry must survive this virus, as well. Pennsylvania needs this aid now, and my office is eager to work with any business that needs help applying.”

For more information about the Department of Community and Economic Development, visit the DCED website, and be sure to stay up-to-date with all of our agency news on Facebook, Twitter