Successful modification of the bacterial artificial chromosome (BAC) after two-step BAC engineering is confirmed in two separate polymerase chain reactions (PCRs). The first reaction (5' co-integrate PCR) uses a forward 5' co-integrate primer (a sequence located upstream of the 5' end of the A-box) and a reverse 3' primer on the vector (175PA+50AT) or within the reporter sequence or mutated region as appropriate. The second reaction (3' co-integrate PCR) uses a forward 5' primer on the recA gene (RecA1300S) and a reverse 3' co-integrate primer (a sequence located downstream from the 3' end of the B-box). Those colonies shown to be positive in PCR analysis are further tested for sensitivity to UV light. After the resolution, colonies that have lost the excised recombination vector including sacB and recA genes become UV light sensitive.

Bacterial artificial chromosome (BAC) clones are rendered electrocompetent and transformed with the recombinant shuttle vector, pLD53SCAB/AB-box. Cointegrates are selected by growth on chloramphenicol and ampicillin to ensure recombination of the shuttle vector into the BAC.

Plasmid DNA is prepared from the recombinant shuttle vector pLD53.SCAB/A-B created by cloning of the A and B homology arms for two-step bacterial artificial chromosome (BAC) engineering. To confirm that the A-box and B-box arms have been successfully incorporated into pLD53.SCAB, the pattern of enzyme digestion of the modified plasmid is compared with that of the unmodified pLD53.SCAB. Once the shuttle vector is shown to carry the proper sequences, it is ready for transfer into the BAC host.

This protocol describes the preparation of the shuttle vector before its introduction into bacterial artificial chromosome (BAC) host cells for BAC two-step engineering. The homology arm sequences, prepared previously, are introduced by ligation into the digested shuttle vector DNA to provide sites for recombination within the BAC clone. Crude lysates of individual bacterial transformants serve as templates in polymerase chain reaction (PCR) analysis to confirm the presence of the homology arms in the recombinant shuttle vector.

The 700-bp A homology arm (A-box) and the 700-bp B homology arm (B-box) are amplified by polymerase chain reaction (PCR) using purified bacterial artificial chromosome (BAC) DNA as template for two-step BAC engineering. The resulting A-box PCR product contains an AscI site at its 5' end (the 5' primer incorporates an AscI site, and the 3' primer does not incorporate any restriction sites). The B-box PCR product contains an XmaI site at its 3' end (the 5' primer does not incorporate any restriction sites, and the 3' primer incorporates an XmaI site). The amplification products are then digested with the appropriate restriction endonucleases to render them suitable for cloning into the shuttle vector.

In two-step bacterial artificial chromosome (BAC) engineering, a single plasmid is introduced into the BAC-carrying cell lines. The shuttle vector pLD53.SCAB (or pLD53.SCAEB) carries the recA gene and the R6K origin, which requires the protein to replicate. PIR2 cells, expressing , are typically used for the amplification of the vector and maintain about 15 copies/cell of the donor vector, which is relatively stable in this host.

Tissue engineering has a unique set of tools and technologies for developing preventive strategies, diagnostics, and treatments that can play an important role during the ongoing COVID-19 pandemic.

The post Danielle Boyer Makes STEAM Fun with The Engineering Design Club appeared first on SOLIDWORKS Education Blog.

The post Reverse Engineering to Fix the Laser Cutter appeared first on SOLIDWORKS Education Blog.

Repair site iFixit has shared x-ray photographs of the new Magic Keyboard for iPad Pro, and they reveal an accessory more complicated than it might appear from the outside.

In honor of a recently retired professor, a generous alumnus donation has enabled the creation of the Martin W. Trethewey Early Career Professorship.

The Penn State Department of Mechanical Engineering is honoring several outstanding undergraduate students through its annual awards.

Penn State senior Abigail Cowser was recently named one of 10 American Society of Civil Engineers "2020 New Faces of Civil Engineering - College Edition."

Fifteen graduating seniors from the College of Engineering have been selected to serve as student marshals for Penn State’s spring commencement ceremony, to be held virtually on May 9.

Overall, average scores were up two points since 2014 on the National Assessment of Educational Progress in Technology and Engineering Literacy.

When the novel coronavirus pandemic prompted the transition to remote learning at Penn State, faculty and administrators in the Department of Mechanical Engineering were prepared for the challenge.

After months of hard work and preparation, nearly a dozen Penn State Hazleton seniors are now one step closer to graduating after presenting their Capstone Research and Design Thesis projects.

Three students received scholarships in industrial and mechanical engineering from the Material Handling Education Foundation for the 2020-21 academic year.

Michael Hillman, L. Robert and Mary L. Kimball Assistant Professor of Civil and Environmental Engineering at Penn State, received a NSF CAREER Award to develop new computational methods to simulate fracture.

Mark Alpert made a generous gift $200,000 in memory of his late wife, Claire, to establish the Mark E. and Claire L. Alpert Graduate Fellowship in the Department of Civil and Environmental Engineering at Penn State.

Agency: CHR Closing Date: 6/5/2020

Differentiating good IP from mediocre or bad IP is getting more difficult, in part because it depends upon how and where it is used and in part, because even the best IP may work better in one system than another—even in chips developed by the same vendor.  

So, how do you measure IP quality and why it is so complicated?

The answer depends on who is asking. Most of the time, the definition of IP quality depends on your vantage point.  If you are an R&D manager, IP quality means something. If you are a global supply manager, IP quality means something else. If you are an SoC start-up, your measure of quality is quite different from that of an established fabless company. If you are designing IP in-house, then your considerations are very different than being a commercial IP vendor. If you are designing an automotive SoC, then we are in a totally different category. How about as an IP vendor? How do you articulate IP quality metrics to your customers?

This varies greatly by the type of IP, as well. When it comes to interface (hard) IP and controllers, if you are an R&D manager, your goal is to design IP that meets the IP specifications and PPA (power, performance, and area) targets. You need to validate your design via silicon test chips. This applies to all hard PHYs, which must be mapped to a particular foundry process. For controllers that are in RTL form—we called these soft IP—you have to synthesize them into a particular target library in a particular foundry process in order to realize them in a physical form suitable for SoC integration. Of course, your design will need to go through a series of design validation steps via simulation, design verification and passing the necessary DRC checks, etc. In addition, you want to see the test silicon in various process corners to ensure the IP is robust and will perform well under normal process variations in the production wafers.

For someone in IP procurement, the measure of quality will be based on the maturity of the IP. This involves the number of designs that have been taped out using this IP and the history of bug reports and subsequent fixes. You will be looking for quality of the documentation and the technical deliverables. You will also benchmark the supplier’s standard operating procedures for bug reporting and technical support, as well as meeting delivery performance in prior programs. This is in addition to the technical teams doing their technical diligence.

An in-house team that is likely to design IP for a particular SoC project will be using an established design flow and will have legacy knowledge of last generation’s IP. They may be required to design the IP with some reusability in mind for future programs. However, such reusability requirements will not need to be as stringent and as broad as those of commercial IP vendors because there are likely to be established metrics and procedures in place to follow as part of the design team’s standard operating procedures. Many times, new development based on a prior design that has been proven in use will be started, given this stable starting point. All of these criteria help the team achieve a quality outcome more easily.

Then, if designing for an automotive SoC, additional heavy lifting is required.  Aside from ensuring that the IP meets the specifications of the protocol standards and passes the compliance testing, you also must pay attention to meeting functional safety requirements. This means adherence to ISO 26262 requirements and subsequently achieving ASIL certification. Oftentimes, even for IP, you must perform some AEC-Q100-related tests that are relevant to IP, such as ESD, LU, and HTOL.

To read more, please visit: https://semiengineering.com/why-ip-quality-is-so-difficult-to-determine/

•Lockheed Martin deploys the 3DEXPERIENCE platform as an engineering and manufacturing planning toolset •Multi-year collaboration aims to speed timelines and improve efficiencies of next generation products •Digital experience platform approach drives advances in complex, sophisticated aircraft innovation

Buildings account for nearly four-tenths of U.S. energy consumption through heating, cooling and other electricity use, according to the Energy Information Administration. And if that energy comes from fossil fuels, it releases more greenhouse gases that drive human-caused climate change.

Buildings account for nearly four-tenths of U.S. energy consumption through heating, cooling and other electricity use, according to the Energy Information Administration. And if that energy comes from fossil fuels, it releases more greenhouse gases that drive human-caused climate change.

Naval shipbuilder Navantia Australia, a subsidiary of Spain-based Navantia S.A., has opened a new design and engineering centre in Melbourne.

Buildings account for nearly four-tenths of U.S. energy consumption through heating, cooling and other electricity use, according to the Energy Information Administration. And if that energy comes from fossil fuels, it releases more greenhouse gases that drive human-caused climate change.

Europe’s utilities are re-evaluating their business models due to the energy transition. Members of POWER-GEN Europe’s Advisory Board consider how a reliance on fossil fuels is no longer politically desirable, forcing utilities to transform their portfolios to adapt to radical change.

Buildings account for nearly four-tenths of U.S. energy consumption through heating, cooling and other electricity use, according to the Energy Information Administration. And if that energy comes from fossil fuels, it releases more greenhouse gases that drive human-caused climate change.

Samsung Engineering said on August 16 that it won two petrochemical power generation projects worth 550 billion won jointly with PTT Public Company Ltd., a Thai state-run oil company. This has been less than a week since the Korean company announced a large-scale oil refinery building project in Oman worth more than 1 trillion won. The project calls for building a petrochemical plant and an electricity generation plant in Rayong, Thailand's largest industrial city 150 kilometers southeast of ...

LOS ANGELES, CA – HARMAN International Industries, Inc. (NYSE:HAR), the premium audio and infotainment group, will have a major presence at the 137th Audio Engineering Society Convention as it returns to the Los Angeles Convention Center Thursday, October 9 through Sunday, October 12 for the first time in twelve years. HARMAN, the premiere sponsor of both the annual AES President’s Reception and the AES Student Zone, will present several research papers, highlight new Professional audio equipment, and demonstrate the company’s latest innovative music restoration technology, Clari-Fi, throughout the week.

With increasing public concern over climate change, interest is turning to geoengineering again. Is it time to take a serious look at engineering our climate?

As a leading technology company with applications across a range of industries including automotive, audio and enterprise technology, HARMAN has a strong focus on recognizing our talented in-house engineers, developers and designers who help bring ...

ABSTRACT

Selectable markers are indispensable for genetic engineering, yet their number and variety are limited. Most selection procedures for prototrophic cells rely on the introduction of antibiotic resistance genes. New minimally invasive tools are needed to facilitate sophisticated genetic manipulations. Here, we characterized three endogenous genes in the human fungal pathogen Aspergillus fumigatus for their potential as markers for targeted genomic insertions of DNAs of interest (DOIs). Since these genes are involved in uptake and metabolization of pyrimidines, resistance to the toxic effects of prodrugs 5-fluorocytosine and 5-fluorouracil can be used to select successfully integrated DOIs. We show that DOI integration, resulting in the inactivation of these genes, caused no adverse effects with respect to nutrient requirements, stress resistance, or virulence. Beside the individual use of markers for site-directed integration of reporter cassettes, including the 17-kb penicillin biosynthetic cluster, we demonstrate their sequential use by inserting three genes encoding fluorescent proteins into a single strain for simultaneous multicolor localization microscopy. In addition to A. fumigatus, we validated the applicability of this novel toolbox in Penicillium chrysogenum and Fusarium oxysporum. Enabling multiple targeted insertions of DOIs without the necessity for exogenous markers, this technology has the potential to significantly advance genetic engineering.

IMPORTANCE This work reports the discovery of a novel genetic toolbox comprising multiple, endogenous selectable markers for targeted genomic insertions of DNAs of interest (DOIs). Marker genes encode proteins involved in 5-fluorocytosine uptake and pyrimidine salvage activities mediating 5-fluorocytosine deamination as well as 5-fluorouracil phosphoribosylation. The requirement for their genomic replacement by DOIs to confer 5-fluorocytosine or 5-fluorouracil resistance for transformation selection enforces site-specific integrations. Due to the fact that the described markers are endogenously encoded, there is no necessity for the exogenous introduction of commonly employed markers such as auxotrophy-complementing genes or antibiotic resistance cassettes. Importantly, inactivation of the described marker genes had no adverse effects on nutrient requirements, growth, or virulence of the human pathogen Aspergillus fumigatus. Given the limited number and distinct types of selectable markers available for the genetic manipulation of prototrophic strains such as wild-type strains, we anticipate that the proposed methodology will significantly advance genetic as well as metabolic engineering of fungal species.

Human adenoviruses have many attractive features for gene therapy applications. However, the high prevalence of preexisting immunity against these viruses in general populations worldwide has greatly limited their clinical utility. In addition, the most commonly used human adenovirus, human adenovirus subgroup C serotype 5 (HAd5), when systemically administered, triggers systemic inflammation and toxicity, with the liver being the most severely affected organ. Here, we evaluated the utility and safety of a new low-seroprevalence gorilla adenovirus (GAd; GC46) as a gene transfer vector in mice. Biodistribution studies revealed that systemically administered GAd had a selective and robust lung endothelial cell (EC) tropism with minimal vector expression throughout many other organs and tissues. Administration of a high dose of GAd accomplished extensive transgene expression in the lung yet elicited no detectable inflammatory histopathology in this organ. Furthermore, GAd, unlike HAd5, did not exhibit hepatotropism or induce liver inflammatory toxicity in mice, demonstrating the exceptional safety profile of the vector vis-à-vis systemic utility. We further demonstrated that the GAd capsid fiber shared the flexibility of the HAd5 equivalent for permitting genetic modification; GAd with the pan-EC-targeting ligand myeloid cell-binding peptide (MBP) incorporated in the capsid displayed a reduced lung tropism and efficiently retargeted gene expression to vascular beds in other organs.

IMPORTANCE In the aggregate, our mouse studies suggest that GAd is a promising gene therapy vector that utilizes lung ECs as a source of therapeutic payload production and a highly desirable toxicity profile. Further genetic engineering of the GAd capsid holds the promise of in vivo vector tropism modification and targeting.

Actuation remains a significant challenge in soft robotics. Actuation by light has important advantages: Objects can be actuated from a distance, distinct frequencies can be used to actuate and control distinct modes with minimal interference, and significant power can be transmitted over long distances through corrosion-free, lightweight fiber optic cables....

South Africa is a mineral-rich country with a diverse geology and a long history of mining. The rich history of mining activities includes the extraction of coal from the Ecca Group Sediments of the Karoo Supergroup (250 Ma), gold and uranium from the Witwatersrand Supergroup (2900 Ma), as well as platinum, uranium, tin and lead from the layered Bushveld Igneous Complex (BIC) (2150 Ma). The extraction of gold, copper, tin, lead and rare earth minerals also took place in the Archean rocks of Swazium age (3500–3000 Ma). The historical mining records have either not been accurately recorded or have been lost over time. This has resulted in significant geohazard risk during infrastructure development, especially in and around historical mining towns, such as Johannesburg and Ermelo. These geohazard risks require careful appraisal and quantification prior to any infrastructure design or construction.

This case study aims to set out the development aspects of the Multi-Faceted Geophysical Modelling Systems approach, which was used by the South African National Roads Agency SOC Ltd (SANRAL) during an investigation of undermined ground for the historical coal-mining town of Ermelo in South Africa. The N11/N2 ring road was planned to go around Ermelo to ensure mobility between major routes, whilst still maintaining town access.

The systems approach used a combination of airborne geophysics (Versatile Time Domain Electromagnetic System (VTEM^TM) and magnetics), generally used in mining exploration, land-based and borehole geophysics, borehole water testing, and ground-truthing. The approach was continuous and iterative, building on the data at hand and reducing unnecessary investigations while eliminating the possibility of anomalies being missed, as in the case of conventional discrete drilling. The investigation ensured that 100% of the route was comprehensively investigated with a high confidence in the geological and geophysical data, and concomitant mitigation of infrastructure risk.

The Multi-Faceted Geophysical Modelling Systems approach was successfully used to identify a previously unknown 1 x 1 m mining stope cavity at 90 m depth and a 3 x 5 m access tunnel at 24 m depth in a timely and cost-effective manner. Seven reverse-circulation percussion boreholes confirmed the structural integrity of these underground cavities, as well as the structural geology along the centreline. Based on the great success achieved in identifying shallow anomalies, this Multi-Faceted Geophysical Modelling Systems approach is now being considered for field trails on the dolomitic formations and the Wild Coast greenfields road project where there are large historical slumps and many fault lines.

Thematic collection: This article is part of the Ground-related risk to transportation infrastructure collection available at https://www.lyellcollection.org/cc/Ground-related-risk-to-transportation-infrastructure

Ubiquitin (UB) transfer cascades consisting of E1, E2, and E3 enzymes constitute a complex network that regulates a myriad of biologic processes by modifying protein substrates. Deubiquitinating enzymes (DUBs) reverse UB modifications or trim UB chains of diverse linkages. Additionally, many cellular proteins carry UB-binding domains (UBDs) that translate the signals encoded in UB chains to target proteins for degradation by proteasomes or in autophagosomes, as well as affect nonproteolytic outcomes such as kinase activation, DNA repair, and transcriptional regulation. Dysregulation of the UB transfer pathways and malfunctions of DUBs and UBDs play causative roles in the development of many diseases. A greater understanding of the mechanism of UB chain assembly and the signals encoded in UB chains should aid in our understanding of disease pathogenesis and guide the development of novel therapeutics. The recent flourish of protein-engineering approaches such as unnatural amino acid incorporation, protein semisynthesis by expressed protein ligation, and high throughput selection by phage and yeast cell surface display has generated designer proteins as powerful tools to interrogate cell signaling mediated by protein ubiquitination. In this study, we highlight recent achievements of protein engineering on mapping, probing, and manipulating UB transfer in the cell.

Vibralactone, a hybrid compound derived from phenols and a prenyl group, is a strong pancreatic lipase inhibitor with a rare fused bicyclic β-lactone skeleton. Recently, a researcher reported a vibralactone derivative (compound C1) that caused inhibition of pancreatic lipase with a half-maximal inhibitory concentration of 14 nM determined by structure-based optimization, suggesting a potential candidate as a new antiobesity treatment. In the present study, we sought to identify the main gene encoding prenyltransferase in Stereum vibrans, which is responsible for the prenylation of phenol leading to vibralactone synthesis. Two RNA silencing transformants of the identified gene (vib-PT) were obtained through Agrobacterium tumefaciens-mediated transformation. Compared to wild-type strains, the transformants showed a decrease in vib-PT expression ranging from 11.0 to 56.0% at 5, 10, and 15 days in reverse transcription-quantitative PCR analysis, along with a reduction in primary vibralactone production of 37 to 64% at 15 and 21 days, respectively, as determined using ultra-high-performance liquid chromatography-mass spectrometry analysis. A soluble and enzymatically active fusion Vib-PT protein was obtained by expressing vib-PT in Escherichia coli, and the enzyme’s optimal reaction conditions and catalytic efficiency (K_m/k_cat) were determined. In vitro experiments established that Vib-PT catalyzed the C-prenylation at C-3 of 4-hydroxy-benzaldehyde and the O-prenylation at the 4-hydroxy of 4-hydroxy-benzenemethanol in the presence of dimethylallyl diphosphate. Moreover, Vib-PT shows promiscuity toward aromatic compounds and prenyl donors.

IMPORTANCE Vibralactone is a lead compound with a novel skeleton structure that shows strong inhibitory activity against pancreatic lipase. Vibralactone is not encoded by the genome directly but rather is synthesized from phenol, followed by prenylation and other enzyme reactions. Here, we used an RNA silencing approach to identify and characterize a prenyltransferase in a basidiomycete species that is responsible for the synthesis of vibralactone. The identified gene, vib-PT, was expressed in Escherichia coli to obtain a soluble and enzymatically active fusion Vib-PT protein. In vitro characterization of the enzyme demonstrated the catalytic mechanism of prenylation and broad substrate range for different aromatic acceptors and prenyl donors. These characteristics highlight the possibility of Vib-PT to generate prenylated derivatives of aromatics and other compounds as improved bioactive agents or potential prodrugs.

Human macrophages equipped with chimeric antigen receptor constructs infiltrate solid tumors, ingest malignant tissue, and stimulate adaptive immunity in mouse models. Several new biotech companies are racing to bring the technology into clinical trials.

Tissue engineering has a unique set of tools and technologies for developing preventive strategies, diagnostics, and treatments that can play an important role during the ongoing COVID-19 pandemic.

On April 17, 2012, a federal grand jury returned a four count indictment charging Beverly S. Beavers and James E. Beavers of Knoxville, Tenn., with conspiracy to defraud the United States and filing false claims for tax refunds, the Justice Department and the Internal Revenue Service (IRS) announced today.

The Justice Department announced today that Multi/Tech Engineering Services Inc., an engineering firm based in Salem, Ore., has agreed to pay more than $60,000 to settle a lawsuit alleging that it had violated the Fair Housing Act by designing Gateway Village Apartments with steps and other features that made it inaccessible to people with disabilities.

Bilfinger SE, an international engineering and services company based in Mannheim, Germany, has agreed to pay a $32 million penalty to resolve charges that it violated the Foreign Corrupt Practices Act (FCPA) by bribing government officials of the Federal Republic of Nigeria to obtain and retain contracts

APEC member economies launched the APEC Women in STEM Principles and Actions, a set of suggested principles and actions for encouraging women’s participation in the fields of science, technology, engineering, and mathematics, commonly referred to as STEM.