Jesper V. Olsen
Dec 1, 2005; 4:2010-2021
Technology

The dextransucrase DSR-OK from the Gram-positive bacterium Oenococcus kitaharae DSM17330 produces a dextran of the highest molar mass reported to date (∼109 g/mol). In this study, we selected a recombinant form, DSR-OKΔ1, to identify molecular determinants involved in the sugar polymerization mechanism and that confer its ability to produce a very-high-molar-mass polymer. In domain V of DSR-OK, we identified seven putative sugar-binding pockets characteristic of glycoside hydrolase 70 (GH70) glucansucrases that are known to be involved in glucan binding. We investigated their role in polymer synthesis through several approaches, including monitoring of dextran synthesis, affinity assays, sugar binding pocket deletions, site-directed mutagenesis, and construction of chimeric enzymes. Substitution of only two stacking aromatic residues in two consecutive sugar-binding pockets (variant DSR-OKΔ1-Y1162A-F1228A) induced quasi-complete loss of very-high-molar-mass dextran synthesis, resulting in production of only 10–13 kg/mol polymers. Moreover, the double mutation completely switched the semiprocessive mode of DSR-OKΔ1 toward a distributive one, highlighting the strong influence of these pockets on enzyme processivity. Finally, the position of each pocket relative to the active site also appeared to be important for polymer elongation. We propose that sugar-binding pockets spatially closer to the catalytic domain play a major role in the control of processivity. A deep structural characterization, if possible with large-molar-mass sugar ligands, would allow confirming this hypothesis.

7 May 2020 , Volume 96, Number 3

Invitation Only Research Event

Event participants

Anita Isaacs, Professor of Political Science, Haverford College; Co-Director, Migration Encounters Project
Juan Ricardo Ortega, Principal Advisor for Central America, Inter-American Development Bank
Chair: Amy Pope, Associate Fellow, Chatham House; US Deputy Homeland Security Adviser for the Obama Administration (2015-17)

7 May 2020 , Volume 96, Number 3

• The Hobbit Review
• Christmas Movies
• What We Watched: Sunshine/Silver Lining's Playbook/The Grey/Argo

O que é Candidíase? Candidíase, é uma infecção sistêmica causada pelo fungos da Candida albicans. A Candida albicans é um tipo de fungo (levedura) que vive em harmonia no organismo,…

The post Candidíase – Conheça as causas, sintomas e tratamentos appeared first on Saúde Próspera.

The spools of wire below contain the only known live recording of the legendary folk singer Woody Guthrie. A mathematician, Kevin Short, was part of a team that used signal processing techniques associated with chaotic music compression to recapture the live performance, which was often completely unintelligible. The modern techniques employed, instead of resulting in a cold, digital output, actually retained the original concert.s warmth and depth. As a result, Short and the team received a Grammy Award for their remarkable restoration of the recording. To begin the restoration the wire had to be manually pulled through a playback device and converted to a digital format. Since the pulling speed wasn.t constant there was distortion in the sound, frequently quite considerable. Algorithms corrected for the speed variations and reconfigured the sound waves to their original shape by using a background noise with a known frequency as a "clock." This clever correction also relied on sampling the sound selectively, and reconstructing and resampling the music between samples. Mathematics did more than help recreate a performance lost for almost 60 years: These methods are used to digitize treasured tapes of audiophiles everywhere. For More Information: "The Grammy in Mathematics," Julie J. Rehmeyer, Science News Online, February 9, 2008.

Hany Farid talks about fighting fake videos: "Mathematically, there's a lot of linear algebra, multivariate calculus, probability and statistics, and then a lot of techniques from pattern recognition, signal processing, and image processing."

Jeanette Ezzo
Oct 1, 2001; 14:
Articles

The Commerce & Economic Development Bureau today announced that the subsidy quota for three mask production lines have been reassigned.

Three production lines, previously approved under the Local Mask Production Subsidy Scheme, have withdrawn from the scheme, the Government said.

The subsidy quota concerned has been allocated to SDL Skin (Asia), Safeguard HK and SwissTech.

SDL Skin (Asia) has been approved for obtaining a subsidy for a second production line and is expected to supply an average of 1.6 million masks every month to the Government. The production line may receive a subsidy of up to $1 million.

Safeguard HK has been approved for obtaining a subsidy for one production line and is expected to supply an average of 500,000 masks to the Government every month. The production line may receive up to $2 million.

SwissTech has been approved for obtaining a subsidy for one production line and is expected to supply an average of 2 million masks every month to the Government and produce a further 1 million masks on average monthly for the local market.

The production line may receive up to $3 million.

It is estimated that when all 20 subsidised lines under the scheme are in full production, they will collectively supply 33.85 million masks to the Government and a further 7.15 million to the local market monthly.

The companies which withdrew from the scheme were CareHK and Shang Manufactory.

The Government did not sign agreements with or make disbursements to these firms.

The CuMasks have undergone strict testing and certification processes before the product will be distributed to help people combat the COVID-19 virus, Secretary for Innovation & Technology Alfred Sit said today.

Mr Sit’s remarks came amid public concerns over the safety of the free reusable face masks that the Government plans to distribute to all Hong Kong citizens.

Addressing reporters after attending a radio programme this morning, Mr Sit said: “The product has gone through a very comprehensive and clear testing and certification process.

“The product can fully comply with the American Society for Testing & Materials (ASTM) F2100 Level 1 requirement, so that the product can fully meet the need of protecting our people from COVID-19.

“I have to emphasise that this whole process must be done by proper laboratories and that’s what we have done.”

Mr Sit noted that a dedicated website on the CuMask has been set up that contains information on the testing reports of the masks.

“For those people who may not have a complete understanding about our product, they may go to our website so that they can see the reports and certificates.

“I fully hope this product can help our people to combat COVID-19.That’s what we would like to do."

The AMS is pleased to announce that Scott Hershberger has been chosen as the 2020 AMS Mass Media Fellow. Scott studied mathematics and physics at Washington University in St. Louis and will graduate in May 2020. He will be working at Scientific American this summer.

The Mass Media Science and Engineering Fellows program is organized by the American Association for the Advancement of Science (AAAS). This program is designed to improve public understanding of science and technology by placing advanced undergraduate, graduate and postgraduate science, mathematics and engineering students in media outlets nationwide. The fellows work for ten weeks over the summer as reporters, researchers, and production assistants alongside media professionals to sharpen their communication skills and increase their understanding of the editorial process by which events and ideas become news.

Now in its 45th year, this fellowship program has placed more than 700 fellows in media organizations nationwide as they research, write, and report today’s headlines. The program is designed to report science-related issues in the media in easy-to-understand ways so as to improve public understanding and appreciation for science and technology.

For more information on the AMS Mass Media Fellowship, visit the website.

(Georgia Institute of Technology) The science behind sticky gecko's feet lets gecko adhesion materials pick up about anything. But cost-effective mass production of the materials was out of reach until now. A new method of making them could usher the spread of gecko-inspired grabbers to assembly lines and homes.

(To watch the full press conference with sign language interpretation, click here.)

Chief Executive Carrie Lam today said that Hong Kong’s needy and disadvantaged will receive masks as part of the Government’s new mask distribution programme.

Mrs Lam made the announcement during a press conference this afternoon and explained that millions of donated masks will also be distributed to those in need.

“I have outlined six measures to distribute masks freely to the people of Hong Kong, and of course in so doing, we will take special account of the disadvantaged, the elderly and street sleepers. 

“So apart from being a member of the Hong Kong population, they will receive reusable masks. They will receive disposable masks. We have this mask distribution program together with a large number of non-governmental organisations, charity groups and self-help groups.

“So we will continue to work with them to distribute another three million masks, which were donated to us.”

Mrs Lam emphasised that should there be a shortage of masks set aside for the needy, the Government will use its own supply to cover the shortfall.

“I am announcing that if we run out of donated masks, but there is still a need from this disadvantaged groups, we will use the government masks - the masks that we procured which are supposed to be for our own use - and share these with the needy groups in society.

“That's a way to ensure that, in a public health situation that we are now in, the needs of the disadvantaged groups will be fully taken care of.”

In addition to distributing donated masks, the Government announced other measures on mask supplies that include handing out single-use and reusable masks to all Hong Kong residents and students in need.

Such measures also call for increasing the supply of masks to staff of elderly homes and cleaning workers employed by the Government's outsourced service contractors, as well as providing masks to private medical practitioners.

The Government will distribute free reusable face masks to all Hong Kong citizens, the Innovation & Technology Bureau announced today.

The CuMask, made with six layers and special ergonomic features, was developed by the Hong Kong Research Institute of Textiles & Apparel.

Two of its layers contain copper which is capable of immobilising bacteria, common viruses and other harmful substances.

The mask complies with the American Society for Testing & Materials F2100 Level 1 Standard in terms of particle and bacterial filtration efficiency, resistance to penetration by synthetic blood, and flammability and pressure resistance.

It is also reusable for up to 60 washes.

The bureau said, except for babies and infants, all holders of valid Hong Kong identity cards are eligible to obtain a mask.

Citizens can register online from 7am tomorrow till June 6. Each registration can cater for a maximum of six persons.

Upon successful registration, the mask will be delivered to the door by Hongkong Post within two weeks.

Primary and kindergarten students will each be given two masks, which will be delivered directly to children's schools. Parents do not have to register.

The Government has also arranged to deliver over 140,000 of the masks to residential homes and social welfare institutions for their distribution to those including elderly and the homeless.

Click here for registration details.

The Innovation & Technology Bureau announced that as of 3pm today, the CuMask online registration system had received over 500,000 registrations, covering close to 1.38 million registrants in total. 

The bureau also responded to reports concerning the purpose of information collection and security of the registration system.

It noted that information provided by citizens in obtaining the masks will not be used for other purposes and that the Government will ensure the retention period of the personal data is no longer than the time required for the purposes for which the data is used.

The bureau pointed out that the registration system for masks operates on the Government's private cloud to ensure the stability and security of the system. 

In order to prevent intrusion and data leakage, multiple security measures have been put in place in compliance with the Government Information Technology Security Policy & Guidelines. 

These measures include a firewall, intrusion detection, anti-bot technology and installation of the latest anti-virus software with regular updates of virus definitions. 

The service has also passed an information security risk assessment and audit before launch.

The Privacy Commissioner for Personal Data has been consulted on the system's personal data processing arrangements. 

The system has also passed an independent third-party privacy impact assessment to ensure that the relevant service and system comply with the Personal Data (Privacy) Ordinance.

The bureau further explained that citizens need to provide their Hong Kong identity card number and date of birth for the registration system to match data with the Immigration Department’s system.

The process will be used to ascertain whether the registrant is a Hong Kong resident and check against any duplicated registrations. 

The local mobile number serves as a way to receive SMS messages on registration results and delivery, while the name and local address of the main registrant serves to verify whether the address exists and for arranging delivery. 

The bureau emphasised that the purposes of information collection have been clearly displayed on the front of the registration page for citizens to browse before registration.

Meanwhile, the bureau clarified the online rumours regarding the manufacturer of CuMask, noting that the CuMask is not manufactured by the Sun Hing Knitting Factory Limited nor Nan Fung Group.

The procurement of raw materials, coordination of production, sterilisation and packaging of the CuMask are being handled by the Hong Kong Research Institute of Textiles & Apparel, it said.

The bureau expressed regret about the rumours.

Chief Executive Carrie Lam inspected one of the CuMask production sites in Tsuen Wan today and expressed gratitude to those manufacturing the reusable masks for Hong Kong residents to fight against the COVID-19 epidemic.

She chatted with the staff and noted that many of them are retired textile industry workers who have re-joined the production workforce to combat the virus.

Mrs Lam praised them for their commitment to serving the community and thanked them for their hard work.

The masks produced in the workshop will be delivered to a clean workspace for sterilising with ozone and packing before distribution. There is no need to wash the mask before it is used for the first time.

In the face of the tight supply of masks amid the epidemic, the Government set aside funds to subsidise projects on technology applications of reusable masks under the first round of the Anti-epidemic Fund.

The CuMask complies with the American Society for Testing & Materials F2100 Level 1 standard and can be washed up to 60 times. It can also be used for a longer period after replacing the filter.

Mrs Lam said she is pleased to note that CuMask is well received by the public and the registration process has been very smooth.

“CuMask is a home-grown scientific research achievement with local application. The whole process has involved co-operation between the Government, industry, academia and the research sector and is an outstanding example of the use of technology to improve people’s lives.

“It will also help solve the problem of the supply of face masks during an epidemic in the long run. I highly commend all the people who have participated in the relevant work and I am fully confident in the development of innovation and technology in Hong Kong.”

Mrs Lam appealed to the public to make use of the registration quota of up to six people to minimise delivery resources and enhance efficiency.

She added that relevant departments will deliver the masks as soon as possible.

The CuMask online registration system received over 720,000 registrations, covering two million registrants in total on the first day of registration on May 6, the Innovation & Technology Bureau announced today.

The bureau said the response is overwhelming and it is encouraged to see support for local invention.

"Our thanks go to support from all sides, including the Hong Kong Research Institute of Textiles & Apparel (HKRITA) which has been commissioned to oversee the project, the Crystal International Group Limited which is responsible for the production, the Novetex Textiles Limited in Tai Po Industrial Estate for providing clean room for sterilisation, The Mills and the TAL Apparel Limited for lending premises to set up workshops as well as the frontline workmen for their hard work over the past few months.

“This unrivalled challenge cannot be met without their joint efforts and the collaboration of the industry and our team,” the bureau stated.

The bureau commissioned the HKRITA to oversee the CuMask project in order to meet the imminent needs for masks in Hong Kong.

It pointed out that the Government Stores & Procurement Regulations do allow direct purchase to be made under extreme urgency.

The whole procurement process was conducted in accordance with the Government's procurement regulations and procedures and with confirmation that the conditions under the Agreement on Government Procurement of the World Trade Organization could be met.

The bureau further explained that in February and March this year, the Government contacted various suppliers of reusable masks. However, most stated that they had either stopped production, did not have enough stock, were unable to export materials due to export control, or unable to produce testing certification.

The epidemic at that time was serious and the supplies of anti-epidemic items were becoming scarce. Hong Kong did not have any raw materials or production lines.

Taking into account the aggressive procurement actions of anti-epidemic items by different countries, export control and suspension of production lines all over the world, the Government had to consider urgently the feasibility of manufacturing reusable masks that would be up to standard for use by the whole community.

On reviewing the reusable mask developed by the HKRITA, the Government considered that the design of the mask and materials used could meet the requirement, as there were supporting certifications proving its compliance with relevant international standards.

As for mass production, it depends on the availability of supply of raw materials. Having wide network in the industry, the HKRITA was able to acquire quality raw materials within a short period and put production lines in place.

The Government therefore commissioned the HKRITA to oversee the coordination of production through direct purchase with a view to supplying reusable masks to all Hong Kong residents as soon as possible.

The bureau added the HKRITA is a non-profit-making R&D centre fully subsidised by the Government, with most of their R&D projects funded by the Innovation & Technology Fund.

The HKRITA oversees the CuMask project on a non-profit-making basis. All expenses will be reimbursed to the HKRITA on the basis of actual spending.

People concerned with the effectiveness of the CuMask may browse the website for testing reports and patent information.

The dextransucrase DSR-OK from the Gram-positive bacterium Oenococcus kitaharae DSM17330 produces a dextran of the highest molar mass reported to date (∼109 g/mol). In this study, we selected a recombinant form, DSR-OKΔ1, to identify molecular determinants involved in the sugar polymerization mechanism and that confer its ability to produce a very-high-molar-mass polymer. In domain V of DSR-OK, we identified seven putative sugar-binding pockets characteristic of glycoside hydrolase 70 (GH70) glucansucrases that are known to be involved in glucan binding. We investigated their role in polymer synthesis through several approaches, including monitoring of dextran synthesis, affinity assays, sugar binding pocket deletions, site-directed mutagenesis, and construction of chimeric enzymes. Substitution of only two stacking aromatic residues in two consecutive sugar-binding pockets (variant DSR-OKΔ1-Y1162A-F1228A) induced quasi-complete loss of very-high-molar-mass dextran synthesis, resulting in production of only 10–13 kg/mol polymers. Moreover, the double mutation completely switched the semiprocessive mode of DSR-OKΔ1 toward a distributive one, highlighting the strong influence of these pockets on enzyme processivity. Finally, the position of each pocket relative to the active site also appeared to be important for polymer elongation. We propose that sugar-binding pockets spatially closer to the catalytic domain play a major role in the control of processivity. A deep structural characterization, if possible with large-molar-mass sugar ligands, would allow confirming this hypothesis.

(American Association for Cancer Research) Combining intratumoral electroporation of interleukin-12 (IL-12) DNA (tavokinogene telseplasmid, or TAVO) with the immune checkpoint inhibitor pembrolizumab (Keytruda) led to clinical responses in patients with immunologically quiescent advanced melanoma, according to results from a phase II trial.

(George Mason University) The team's work supports evidence-based decision making, informed by models, to rethink and facilitate hospital operations during the pandemic.

You can now add Fresno to the growing list of cities that are now requiring people to wear face masks in public places.

Restaurant workers in a reopened Dallas eatery say they are being asked to weigh their safety against their jobs.

Disposable masks can be used more than once, but it's important to make sure the mask isn't carrying coronavirus.

(The Korea Advanced Institute of Science and Technology (KAIST)) A research team led by Distinguished Professor Sang-Yup Lee reported the production of a microbial strain capable of the massive production of succinic acid with the highest production efficiency to date. This strategy of integrating systems metabolic engineering with enzyme engineering will be useful for the production of industrially competitive bio-based chemicals.

Xien Yu Chua
Apr 1, 2020; 19:730-743
Technological Innovation and Resources

Andreas Linden
Apr 24, 2020; 0:RA120.002028v1-mcp.RA120.002028
Research

Tsung-Heng Tsai
Mar 31, 2020; 0:RA119.001792v1-mcp.RA119.001792
Research

Karl A. T. Makepeace
Apr 1, 2020; 19:624-639
Research

Dorte B. Bekker-Jensen
Apr 1, 2020; 19:716-729
Technological Innovation and Resources

Cryptocurrency profits from sextortion spam funneled into wallets tied to other cybercrime and dark web market activity.

7 May 2020 , Volume 96, Number 3

Purpose: PET using O-(2-[¹⁸F]Fluoroethyl)-L-tyrosine (¹⁸F-FET) is useful to detect residual tumor tissue after glioma resection. Recent animal experiments detected reactive changes of ¹⁸F-FET uptake at the rim of the resection cavity within the first two weeks after resection of gliomas. In the present study, we evaluated pre- and postoperative ¹⁸F-FET PET scans of glioma patients with particular emphasis on the identification of reactive changes after surgery. Methods: Forty-three patients with cerebral gliomas (9 low-grade, 34 high-grade; 9 primary tumors, 34 recurrent tumors) who had preoperative (time before surgery, median 23 d, range 6-44 d) and postoperative ¹⁸F-FET-PET (time after surgery, median 14, range 5–28 d) were included. PET scans (20-40 min p.i.) were evaluated visually for complete or incomplete resection (CR, IR) and compared with MRI. Changes of ¹⁸F-FET-uptake in residual tumor were evaluated by tumor-to-brain ratios (TBRmax) and in the vicinity of the resection cavity by maximum lesion-to-brain ratios (LBRmax). Results: Visual analysis of ¹⁸F-FET PET scans revealed CR in 16/43 patients and IR in the remaining patients. PET results were concordant with MRI in 69% of the patients. LBRmax of ¹⁸F-FET uptake in the vicinity of the resection cavity was significantly higher compared with preoperative values (1.59 ± 0.36 versus 1.14 ± 0.17; n = 43, p<0.001). In 11 patients (26%) a "flare phenomenon" was observed with a considerable increase of ¹⁸F-FET uptake compared with preoperative values in either the residual tumor (n = 5) or in areas remote from tumor in the preoperative PET scan (n = 6) (2.92 ± 1.24 versus 1.62 ± 0.75; p<0.001). Further follow-up in five patients showed decreasing ¹⁸F-FET uptake in the flare areas in four and progress in one case. Conclusion: Our study confirms that ¹⁸F-FET PET provides valuable information for assessing the success of glioma resection. Postoperative reactive changes at the rim of the resection cavity appear to be mild. However, in 23 % of the patients, a postoperative "flare phenomenon" was observed that warrants further investigation.

The presentation of peptides on class I human leukocyte antigen (HLA-I) molecules plays a central role in immune recognition of infected or malignant cells. In cancer, non-self HLA-I ligands can arise from many different alterations, including non-synonymous mutations, gene fusion, cancer-specific alternative mRNA splicing or aberrant post-translational modifications. Identifying HLA-I ligands remains a challenging task that requires either heavy experimental work for in vivo identification or optimized bioinformatics tools for accurate predictions. To date, no HLA-I ligand predictor includes post-translational modifications. To fill this gap, we curated phosphorylated HLA-I ligands from several immunopeptidomics studies (including six newly measured samples) covering 72 HLA-I alleles and retrieved a total of 2,066 unique phosphorylated peptides. We then expanded our motif deconvolution tool to identify precise binding motifs of phosphorylated HLA-I ligands. Our results reveal a clear enrichment of phosphorylated peptides among HLA-C ligands and demonstrate a prevalent role of both HLA-I motifs and kinase motifs on the presentation of phosphorylated peptides. These data further enabled us to develop and validate the first predictor of interactions between HLA-I molecules and phosphorylated peptides.

The human MASTL (Microtubule-associated serine/threonine kinase-like) gene encodes an essential protein in the cell cycle. MASTL is a key factor preventing early dephosphorylation of M-phase targets of Cdk1/CycB. Little is known about the mechanism of MASTL activation and regulation. MASTL contains a non-conserved insertion of 550 residues within its activation loop, splitting the kinase domain, and making it unique. Here, we show that this non-conserved middle region (NCMR) of the protein is crucial for target specificity and activity. We performed a phosphoproteomic assay with different MASTL constructs identifying key phosphorylation sites for its activation and determining whether they arise from autophosphorylation or exogenous kinases, thus generating an activation model. Hydrogen/deuterium exchange data complements this analysis revealing that the C-lobe in full-length MASTL forms a stable structure, whereas the N-lobe is dynamic and the NCMR and C-tail contain few localized regions with higher-order structure. Our results indicate that truncated versions of MASTL conserving a cryptic C-Lobe in the NCMR, display catalytic activity and different targets, thus establishing a possible link with truncated mutations observed in cancer-related databases.

Mass spectrometry (MS) and proteomics offer comprehensive characterization and identification of microorganisms and discovery of protein biomarkers that are applicable for diagnostics of infectious diseases. The use of biomarkers for diagnostics is widely applied in the clinic and the use of peptide biomarkers is increasingly being investigated for applications in the clinical laboratory. Respiratory-tract infections are a predominant cause for medical treatment, although, clinical assessments and standard clinical laboratory protocols are time-consuming and often inadequate for reliable diagnoses. Novel methods, preferably applied directly to clinical samples, excluding cultivation steps, are needed to improve diagnostics of infectious diseases, provide adequate treatment and reduce the use of antibiotics and associated development of antibiotic resistance. This study applied nano-liquid chromatography (LC) coupled with tandem MS, with a bioinformatics pipeline and an in-house database of curated high-quality reference genome sequences to identify species-unique peptides as potential biomarkers for four bacterial pathogens commonly found in respiratory tract infections (RTIs): Staphylococcus aureus; Moraxella catarrhalis; Haemophilus influenzae and Streptococcus pneumoniae. The species-unique peptides were initially identified in pure cultures of bacterial reference strains, reflecting the genomic variation in the four species and, furthermore, in clinical respiratory tract samples, without prior cultivation, elucidating proteins expressed in clinical conditions of infection. For each of the four bacterial pathogens, the peptide biomarker candidates most predominantly found in clinical samples, are presented. Data are available via ProteomeXchange with identifier PXD014522. As proof-of-principle, the most promising species-unique peptides were applied in targeted tandem MS-analyses of clinical samples and their relevance for identifications of the pathogens, i.e. proteotyping, was validated, thus demonstrating their potential as peptide biomarker candidates for diagnostics of infectious diseases.

For more than two decades naturally presented, human leukocyte antigen (HLA)-restricted peptides (immunopeptidome) have been eluted and sequenced using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Since, identified disease-associated HLA ligands have been characterized and evaluated as potential active substances. Treatments based on HLA-presented peptides have shown promising results in clinical application as personalized T cell-based immunotherapy. Peptide vaccination cocktails are produced as investigational medicinal products under GMP conditions. To support clinical trials based on HLA-presented tumor-associated antigens, in this study the sensitive LC-MS/MS HLA class I antigen identification pipeline was fully validated for our technical equipment according to the current US Food and Drug Administration (FDA) and European Medicines Agency (EMA) guidelines.

The immunopeptidomes of JY cells with or without spiked-in, isotope labeled peptides, of peripheral blood mononuclear cells of healthy volunteers as well as a chronic lymphocytic leukemia and a bladder cancer sample were reliably identified using a data-dependent acquisition method. As the LC-MS/MS pipeline is used for identification purposes, the validation parameters include accuracy, precision, specificity, limit of detection and robustness.

Dynamic tyrosine phosphorylation is fundamental to a myriad of cellular processes. However, the inherently low abundance of tyrosine phosphorylation in the proteome and the inefficient enrichment of phosphotyrosine(pTyr)-containing peptides has led to poor pTyr peptide identification and quantitation, critically hindering researchers' ability to elucidate signaling pathways regulated by tyrosine phosphorylation in systems where cellular material is limited. The most popular approaches to wide-scale characterization of the tyrosine phosphoproteome use pTyr enrichment with pan-specific, anti-pTyr antibodies from a large amount of starting material. Methods that decrease the amount of starting material and increase the characterization depth of the tyrosine phosphoproteome while maintaining quantitative accuracy and precision would enable the discovery of tyrosine phosphorylation networks in rarer cell populations. To achieve these goals, the BOOST (Broad-spectrum Optimization Of Selective Triggering) method leveraging the multiplexing capability of tandem mass tags (TMT) and the use of pervanadate (PV) boost channels (cells treated with the broad-spectrum tyrosine phosphatase inhibitor PV) selectively increased the relative abundance of pTyr-containing peptides. After PV boost channels facilitated selective fragmentation of pTyr-containing peptides, TMT reporter ions delivered accurate quantitation of each peptide for the experimental samples while the quantitation from PV boost channels was ignored. This method yielded up to 6.3-fold boost in pTyr quantification depth of statistically significant data derived from contrived ratios, compared with TMT without PV boost channels or intensity-based label-free (LF) quantitation while maintaining quantitative accuracy and precision, allowing quantitation of over 2300 unique pTyr peptides from only 1 mg of T cell receptor-stimulated Jurkat T cells. The BOOST strategy can potentially be applied in analyses of other post-translational modifications where treatments that broadly elevate the levels of those modifications across the proteome are available.

State-of-the-art proteomics-grade mass spectrometers can measure peptide precursors and their fragments with ppm mass accuracy at sequencing speeds of tens of peptides per second with attomolar sensitivity. Here we describe a compact and robust quadrupole-orbitrap mass spectrometer equipped with a front-end High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Interface. The performance of the Orbitrap Exploris 480 mass spectrometer is evaluated in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes in combination with FAIMS. We demonstrate that different compensation voltages (CVs) for FAIMS are optimal for DDA and DIA, respectively. Combining DIA with FAIMS using single CVs, the instrument surpasses 2500 peptides identified per minute. This enables quantification of >5000 proteins with short online LC gradients delivered by the Evosep One LC system allowing acquisition of 60 samples per day. The raw sensitivity of the instrument is evaluated by analyzing 5 ng of a HeLa digest from which >1000 proteins were reproducibly identified with 5 min LC gradients using DIA-FAIMS. To demonstrate the versatility of the instrument, we recorded an organ-wide map of proteome expression across 12 rat tissues quantified by tandem mass tags and label-free quantification using DIA with FAIMS to a depth of >10,000 proteins.

An experimental and computational approach for identification of protein-protein interactions by ex vivo chemical crosslinking and mass spectrometry (CLMS) has been developed that takes advantage of the specific characteristics of cyanurbiotindipropionylsuccinimide (CBDPS), an affinity-tagged isotopically coded mass spectrometry (MS)-cleavable crosslinking reagent. Utilizing this reagent in combination with a crosslinker-specific data-dependent acquisition strategy based on MS2 scans, and a software pipeline designed for integrating crosslinker-specific mass spectral information led to demonstrated improvements in the application of the CLMS technique, in terms of the detection, acquisition, and identification of crosslinker-modified peptides. This approach was evaluated on intact yeast mitochondria, and the results showed that hundreds of unique protein-protein interactions could be identified on an organelle proteome-wide scale. Both known and previously unknown protein-protein interactions were identified. These interactions were assessed based on their known sub-compartmental localizations. Additionally, the identified crosslinking distance constraints are in good agreement with existing structural models of protein complexes involved in the mitochondrial electron transport chain.

This week David Price is in the presenter chair for the jolliest tech podcast of the year. David is joined by Miriam Harris, staff writer at Digital Arts, to talk about the design trends set to shape 2017. Then online editor at Techworld Scott Carey runs through the hottest tech gifts this Christmas, including games consoles, VR, Amazon gadgets and Star Wars merch (14:30). Finally, staff writer at PC Advisor Dom Preston makes his UKTW debut to chat about the latest Star Wars movie, Rogue One, which includes spoilers (29:00). This is the last UK Tech Weekly podcast of the year. Thank you for listening and we will be back in 2017 to chat about the hottest tech topics all over again.  

See acast.com/privacy for privacy and opt-out information.

We finally get the IoT acronym the pod has been waiting for as we discuss Bitcoin and 17th century Dutch finance. Charlotte Jee informs Henry Burrell, David Price and Scott Carey.

Scott then leads us down the winding road of the so-called platform wars, in a week when Google blocked the Amazon Echo Show from streaming YouTube. Is this a bump in the road or will services be cut from rival hardware?

And finally, led by David, the pod discusses its favourite tech of the year and what you might consider buying for friends and family for Christmas.

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Once more for 2017 as Henry Burrell, Karen Khan and Scott Carey bid farewell to this wonderful year (ahem) with musings on Apple's sexy new iMac Pro. Who is it for, how much is it and does this mean there is no Mac Pro in 2018?

We then tackle Netflix's Twitter shaming of its users and why Spotify got away with it earlier in the year. How comfortable are we all when we realise how much data companies really have on us?

In light of this, Apple bought Shazam - most likely for the data sets as much as the tech and the talent. What form will it take in Apple as another UK tech company is acquired?

See acast.com/privacy for privacy and opt-out information.