Bryan Pata was gunned down 15 years ago.

Miami lost to the Jacksonville Jaguars in London.

Governor Rena Lalgie announced that Major Duncan Simons will succeed Lt Col Ben Beasley BEM as Commanding Officer of the Royal Bermuda Regiment on June 1, 2024. Governor Lalgie said, “The Regiment plays a key role in ensuring the safety and security of Bermuda both on land and on water and Major Simons’ experience, gained […]

[Written by Stephen Wright] Bermuda swimmer Emma Harvey said making her debut at the Olympic Games was “100 per cent” worth a lifetime of hard work. Harvey competed in the women’s 100 metres backstroke heats at the Paris La Défense Arena today [July 29], finishing eighth in heat four in 1min 01.78sec. She placed 23rd […]

Bermuda’s Exclusive Economic Zone [EEZ] has been declared a Marine Mammal Sanctuary with particular emphasis on the endangered humpback whale, Minister of Environment, Planning and Infrastructure Strategy Marc Bean said this afternoon [Sept 21]. Minister Bean said: “The area of the new Bermuda Marine Mammal Sanctuary will be more than 170,000 square nautical miles, approximately […]

[Written by Stephen Wright] Whale researcher Andrew Stevenson will screen his two award-winning documentaries, ‘Where the Whales Sing’ and ‘The Secret Lives of the Humpbacks’ at the Speciality Cinema and Grill in Hamilton on Monday [December 4]. It will be the first time both documentaries are screened back-to-back, starting at 6.30 pm, with a 15-minute […]

[Updated with PDF] Former commanding officer of the Royal Bermuda Regiment [RBR] David Curley has been sentenced to six months in jail after admitting to a charge of official corruption A ZBM report said, “The 55-year-old former Lieutenant-Colonel had pleaded guilty to a charge of official corruption last July. His sentence totals 18 months, with […]

Apple is planning to launch an AI-powered smart home display as soon as March 2025, according to Bloomberg's Mark Gurman. The display will measure in at approximately six inches, and while it is similar to an iPad, it is square rather than rectangular and it has thick bezels around the edges. There is a camera at the top front so that it can be used for FaceTime, plus there are internal speakers for playing music and a built-in rechargeable battery.


Apple will offer the hub in silver and black, and it will use a touch-based interface. The operating system will look like a mix of the iPhone's StandBy mode and watchOS, though it will primarily be controlled by voice. Apple plans to integrate Apple Intelligence for accessing apps and controlling smart home products, and it was designed around App Intents, a Siri system that will be able to control apps and tasks.

Apple designed a customizable home screen with widgets that can be used to show things like the weather and upcoming appointments, a photo slideshow, or important home controls. A software-based dock will be available for launching apps, and multiple systems in different rooms will work as intercoms. Apple plans to focus on security as well, providing alerts and camera footage from connected smart home cameras.

Built-in sensors will be able to determine how close a person is standing to the device, and it can adjust features from there. When no one is nearby, for example, it might show the temperature, but as someone approaches, it can switch to an interface for adjusting the thermostat, much like Nest thermostats. It could also detect how many people are nearby using external sensors that plug into outlets throughout the home, but Apple may or may not manufacture these extra sensors.

In addition to offering smart home controls and FaceTiming features, the device will include several Apple apps like Safari, Apple News, Apple Music, Notes, Calendar, and Photos, but there will not be a dedicated App Store. Apple is designing different attachments, such as a plate for attaching it to the wall and a base with additional speakers for using it in a central location in the home.

Apple plans to position the smart display as a "command center," with the aim of furthering Apple's position in the smart home market. The smart home hub has been in development for more than three years, and Apple CEO Tim Cook has been pushing the engineering and design teams to prioritize the device. It will be a standalone device, but it is meant to work in concert with other Apple products and will require an ‌iPhone‌ for setup.

With the smart home hub, Apple is looking to compete with Amazon and Google, who have similar devices. Amazon has the Echo Hub, and Google offers the Nest Hub Max. Apple will likely need to price the device similarly to these products, and the Echo Hub costs $150, while the Nest Hub Max costs $230.

While Apple has considered creating its own line of smart home accessories like an indoor security camera, it is not yet clear if the company will do so. Apple could get into accessories if the smart home display is a success. Earlier this week, Apple analyst Ming-Chi Kuo said that Apple was working on a smart home camera with wireless connectivity and deep integration with ‌Apple Intelligence‌, with Apple planning to launch the device in 2026.

In the future, Apple plans to release a robotic version of the smart home hub that can move the screen around, Gurman reports.

What’s worse than getting broken up with over text? Getting broken up with over summarized text. Apple rolled out its Apple Intelligence suite of AI tools in October, and one feature has made headlines over and over again for its absurdity: Apple Intelligence notification summaries. What it is:…

The Better Breaks funding programme is focused on improving the range and availability of short break opportunities for disabled children and young people, particularly those with multiple support needs, including short break opportunities that families can enjoy together, or which allow parents and siblings to have time away from their caring responsibilities. This is the summary report.

The Short Breaks Fund helping to make breaks better and brighter for unpaid carers and cared-for people in Scotland. Launched in 2010 for one year, the fund has now been running for five years and has proved to be a lifeline for many carers. During the past five years the Scottish Government, through Shared Cared Scotland has distributed 12,547,409 to 697 projects to deliver innovative, tailor made breaks to groups and individuals.

By Brian VanHooker Published: November 12th, 2024

Hasbro has produced a 4-figure set for a 21-year old Timothy Zahn Star Wars books and it DOESN'T feature Thrawn?

Sugar gliders and bats are about as distantly related as any two mammals on Earth, but new Princeton research shows their wings are formed from the same genetic ingredients. 

Gemma Peacocke’s ‘A Strange Power’ is a 45-minute cantata about the tangled web of romance, free love, creation, and death in the early lives of Mary Wollstonecraft Godwin Shelley and her step-sister, Claire Clairmont. Scored for two sopranos, clarinet, piano, percussion, and cello, the work will be performed by Sputter Box with guest vocalist Charlotte Mundy. The program also features new works for the performers by other Princeton University graduate student composers Aliayta Foon-Dancoes, Devin Greenwood, Gemma Peacocke, and Onche Rajesh Ugbabe.

Students across the country are participating in NOVA's film production program to make videos about climate change solutions in their local communities.

The law requires public schools to display a poster of the Ten Commandments in every classroom.

If you have ever accidentally hit that key below the escape key during a game and a large, scary text… Continue reading All console commands for Brighter Shores

The post All console commands for Brighter Shores appeared first on ReadWrite.

This morning we awoke to one story dominating the tech news landscape: OpenAI is “expanding into search,” launching SearchGPT, a prototype that appears to be a direct competitor to Google (and Bing and Perplexity, not that they really matter). But despite the voluminous coverage, my initial take is that once the hype cycle passes – … Continue reading "What’s SearchGPT Really About? Moving Past the Training Data Dilemma."

A Louisiana law that sought to post the Ten Commandments in every schoolroom in the state has been shelved by a federal judge. U.S. District Court Judge John W. deGravelles, […]

The post Obama-Appointed Federal Judge Temporarily Blocks Ten Commandments Law appeared first on The Western Journal.

Qiang Tian
Oct 1, 2004; 3:960-969
Research

Candida albicans and Aspergillus fumigatus are dangerous fungal pathogens with high morbidity and mortality, particularly in immunocompromised patients. Innate immune-mediated programmed cell death (pyroptosis, apoptosis, necroptosis) is an integral part of host defense against pathogens. Inflammasomes, which are canonically formed upstream of pyroptosis, have been characterized as key mediators of fungal sensing and drivers of proinflammatory responses. However, the specific cell death pathways and key upstream sensors activated in the context of Candida and Aspergillus infections are unknown. Here, we report that C. albicans and A. fumigatus infection induced inflammatory programmed cell death in the form of pyroptosis, apoptosis, and necroptosis (PANoptosis). Further, we identified the innate immune sensor Z-DNA binding protein 1 (ZBP1) as the apical sensor of fungal infection responsible for activating the inflammasome/pyroptosis, apoptosis, and necroptosis. The Zα2 domain of ZBP1 was required to promote this inflammasome activation and PANoptosis. Overall, our results demonstrate that C. albicans and A. fumigatus induce PANoptosis and that ZBP1 plays a vital role in inflammasome activation and PANoptosis in response to fungal pathogens.

Russia's end games and Putin's dilemmas Expert comment NCapeling 14 February 2022

As warnings from Washington and London intensify, the period of maximum danger in the Ukraine standoff has begun. Even if conflict is avoided, the status quo has gone.

There are several reasons to believe conflict over the Ukraine is imminent. The military build-up is complete. Russia has added tactical support elements, including medical units, to its already large and comprehensive array of troops and equipment deployed to the east, north, and south of Ukraine.

Additional naval units have entered the Black Sea, military exercises with Belarusian forces have begun and, along with those on Russian territory, these can all provide cover for an intervention of some sort.

Far from being comforting, comments by Vladimir Putin and his entourage that it will not be Russia provoking a conflict are ominous. Russian media has ramped up domestic programming about the ‘imminent Ukrainian fascist threat’ to the motherland. And a recent US intelligence briefing alleges sophisticated preparations by Russian intelligence include releasing a video of a staged attack on Russian-speaking civilians in northern Ukraine.

Should Russia attack, its ‘fortress economy’ could weather a new round of sanctions for several years, not least given the growth in Russia’s hard currency reserves to $630 billion, under 20 per cent of which are now held in US dollars, and the high demand for – and global price of – oil and gas.

What does Putin really want?

Diplomacy is in high gear but, as Putin and other senior Russian figures have made clear, the US and European offers of new security confidence-building measures do not address Russia’s two core, stated demands – namely to withdraw US and NATO forces close to its borders in former Soviet and Warsaw Pact states, and to end NATO’s ‘open door’ policy to future enlargement.

For the Kremlin, enlargement to Ukraine would remove a critical buffer between Russia and the NATO alliance. If Putin’s objective, therefore, was simply to put down an unambiguous marker that Ukrainian membership of NATO is a red line, he has made progress.

He has reminded the world and Ukraine’s leadership of that country’s strategic vulnerability. US president Joe Biden and his European counterparts have stated NATO will not commit forces to defend Ukraine if it is attacked. And although they remain resolute on the ‘open door’ policy, there have been reminders NATO does not accept new members who risk importing a pre-existing conflict into the alliance.

If another Putin objective was to refocus US and, to a lesser extent, European attention away from China and back onto Russia and its security interests, he has succeeded. NATO has offered some new confidence-building measures around the conduct of military exercises and deployment of forces, while the US may be willing to enter negotiations for a new treaty with Russia to limit nuclear missiles deployed in Europe.

This would mean setting aside the growing threat posed by Chinese missiles that had partly motivated the Donald Trump administration to withdraw unilaterally from the Intermediate-Range Nuclear Forces (INF) Treaty.

But there is another scenario to consider – that although these two issues are both important, neither are Putin’s core objective, which instead is to right once and for all the historical ‘wrong’ of Ukraine’s separation from Russia in 1991.

As Putin made clear in a lengthy essay in July 2021, he sees an independent, sovereign Ukraine as a historical aberration, and he blames the US for the deepening discord and animosity between ‘brotherly’ Ukraine and Russia.

Not stated in the essay is that the emergence of a more democratic and functional Ukraine poses an existential threat to Putin’s own control over Russia. In contrast, reincorporating Ukraine into a ‘greater Russia’ would underpin his now constitutionally-mandated opportunity to reign until 2036, as well as being his biggest legacy.

The problem is it seems impossible to bring Ukraine permanently back into Russia’s sphere of influence without some form of new military intervention.

Putin’s options

Putin’s strategy to date has been limited to ensuring the breakaway Ukrainian portions of Donetsk and Lugansk gain a legal right to block any future efforts by the central Ukrainian government to join either the European Union (EU) or NATO.

The Kremlin sees expansive interpretation and implementation of the 2014-15 Minsk protocols allowing self-governance for these areas currently under Russian military control as a potential route to this outcome. But for Volodomyr Zelensky or any future Ukrainian president to accept this would be political suicide, and Kyiv has already resisted French and German pressure to make this concession under the Normandy Format of meetings they share with Russia.

If Putin has now decided to undermine Ukrainian sovereignty more explicitly, he can order a limited military intervention further into these occupied territories – and perhaps areas adjacent to them and Crimea – under the pretext of ‘protecting’ Russian-speaking communities there.

This would be relatively easy to achieve and, combined with a blockade of Ukraine’s Black Sea ports, could successfully destabilize the government in Kyiv. But such steps would trigger international economic sanctions and drive Ukraine even further towards the West.

A 21st century ‘blitzkrieg’ to take Ukrainian territory as far as the Dnipro River including Kyiv and all points east, would come closer to achieving Putin’s territorial and historic legacy. And this is now a feasible option given Russia’s military superiority. But how easily Russia could then hold the territory and consolidate its political control would be doubtful, and these moves also bring high-risk, long-term economic and diplomatic costs to Russia and to him personally.

No return to the status quo

On balance, Russian military intervention in the coming days or weeks is still less rather than more likely. Putin may yet accept a new, visible, bilateral accommodation with the US on the future of European security.

Alzheimer's disease (AD) is characterized by neuronal loss and accumulation of β-amyloid-protein (Aβ) in the brain parenchyma. Sleep impairment is associated with AD and affects about 25–40% of patients in the mild-to-moderate stages of the disease. Sleep deprivation leads to increased Aβ production; however, its mechanism remains largely unknown. We hypothesized that the increase in core body temperature induced by sleep deprivation may promote Aβ production. Here, we report temperature-dependent regulation of Aβ production. We found that an increase in temperature, from 37 °C to 39 °C, significantly increased Aβ production in amyloid precursor protein-overexpressing cells. We also found that high temperature (39 °C) significantly increased the expression levels of heat shock protein 90 (Hsp90) and the C-terminal fragment of presenilin 1 (PS1-CTF) and promoted γ-secretase complex formation. Interestingly, Hsp90 was associated with the components of the premature γ-secretase complex, anterior pharynx-defective-1 (APH-1), and nicastrin (NCT) but was not associated with PS1-CTF or presenilin enhancer-2. Hsp90 knockdown abolished the increased level of Aβ production and the increased formation of the γ-secretase complex at high temperature in culture. Furthermore, with in vivo experiments, we observed increases in the levels of Hsp90, PS1-CTF, NCT, and the γ-secretase complex in the cortex of mice housed at higher room temperature (30 °C) compared with those housed at standard room temperature (23 °C). Our results suggest that high temperature regulates Aβ production by modulating γ-secretase complex formation through the binding of Hsp90 to NCT/APH-1.

Weerapan Khovidhunkit
Jul 1, 2004; 45:1169-1196
Thematic Reviews

Zika virus (ZIKV) is a neurotropic flavivirus that causes several diseases including birth defects such as microcephaly. Intrinsic immunity is known to be a frontline defense against viruses through host anti-viral restriction factors. Limited knowledge is available on intrinsic immunity against ZIKV in brains. Amyloid precursor protein (APP) is predominantly expressed in brains and implicated in the pathogenesis of Alzheimer's diseases. We have found that ZIKV interacts with APP, and viral infection increases APP expression via enhancing protein stability. Moreover, we identified the viral peptide, HGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATLGGFGSLGL, which is capable of en-hancing APP expression. We observed that aging brain tissues with APP had protective effects on ZIKV infection by reducing the availability of the viruses. Also, knockdown of APP expression or blocking ZIKV-APP interactions enhanced ZIKV replication in human neural progenitor/stem cells. Finally, intracranial infection of ZIKV in APP-null neonatal mice resulted in higher mortality and viral yields. Taken together, these findings suggest that APP is a restriction factor that protects against ZIKV by serving as a decoy receptor, and plays a protective role in ZIKV-mediated brain injuries.

Stop codon read-through (SCR) is a process of continuation of translation beyond a stop codon. This phenomenon, which occurs only in certain mRNAs under specific conditions, leads to a longer isoform with properties different from that of the canonical isoform. MTCH2, which encodes a mitochondrial protein that regulates mitochondrial metabolism, was selected as a potential read-through candidate based on evolutionary conservation observed in the proximal region of its 3' UTR. Here, we demonstrate translational read-through across two evolutionarily conserved, in-frame stop codons of MTCH2 using luminescence- and fluorescence-based assays, and by analyzing ribosome-profiling and mass spectrometry (MS) data. This phenomenon generates two isoforms, MTCH2x and MTCH2xx (single- and double-SCR products, respectively), in addition to the canonical isoform MTCH2, from the same mRNA. Our experiments revealed that a cis-acting 12-nucleotide sequence in the proximal 3' UTR of MTCH2 is the necessary signal for SCR. Functional characterization showed that MTCH2 and MTCH2x were localized to mitochondria with a long t1/2 (>36 h). However, MTCH2xx was found predominantly in the cytoplasm. This mislocalization and its unique C terminus led to increased degradation, as shown by greatly reduced t1/2 (<1 h). MTCH2 read-through–deficient cells, generated using CRISPR-Cas9, showed increased MTCH2 expression and, consistent with this, decreased mitochondrial membrane potential. Thus, double-SCR of MTCH2 regulates its own expression levels contributing toward the maintenance of normal mitochondrial membrane potential.

Lutz Mattner
Theor. Probability and Math. Statist. 111 (), 45-122.
Abstract, references and article information

Reliable, specific polyclonal and monoclonal antibodies are important tools in research and medicine. However, the discovery of antibodies against their targets in their native forms is difficult. Here, we present a novel method for discovery of antibodies against membrane proteins in their native configuration in mammalian cells. The method involves the co-expression of an antibody library in a population of mammalian cells that express the target polypeptide within a natural membrane environment on the cell surface. Cells that secrete a single-chain fragment variable (scFv) that binds to the target membrane protein thereby become self-labeled, enabling enrichment and isolation by magnetic sorting and FRET-based flow sorting. Library sizes of up to 109 variants can be screened, thus allowing campaigns of naïve scFv libraries to be selected against membrane protein antigens in a Chinese hamster ovary cell system. We validate this method by screening a synthetic naïve human scFv library against Chinese hamster ovary cells expressing the oncogenic target epithelial cell adhesion molecule and identify a panel of three novel binders to this membrane protein, one with a dissociation constant (KD) as low as 0.8 nm. We further demonstrate that the identified antibodies have utility for killing epithelial cell adhesion molecule–positive cells when used as a targeting domain on chimeric antigen receptor T cells. Thus, we provide a new tool for identifying novel antibodies that act against membrane proteins, which could catalyze the discovery of new candidates for antibody-based therapies.

28 July 2020

The development of a chronic, low-grade inflammation originating from adipose tissue in obese subjects is widely recognized to induce insulin resistance, leading to the development of type 2 diabetes. The adipose tissue microenvironment drives specific metabolic reprogramming of adipose tissue macrophages, contributing to the induction of tissue inflammation. Uncoupling protein 2 (UCP2), a mitochondrial anion carrier, is thought to separately modulate inflammatory and metabolic processes in macrophages and is up-regulated in macrophages in the context of obesity and diabetes. Here, we investigate the role of UCP2 in macrophage activation in the context of obesity-induced adipose tissue inflammation and insulin resistance. Using a myeloid-specific knockout of UCP2 (Ucp2ΔLysM), we found that UCP2 deficiency significantly increases glycolysis and oxidative respiration, both unstimulated and after inflammatory conditions. Strikingly, fatty acid loading abolished the metabolic differences between Ucp2ΔLysM macrophages and their floxed controls. Furthermore, Ucp2ΔLysM macrophages show attenuated pro-inflammatory responses toward Toll-like receptor-2 and -4 stimulation. To test the relevance of macrophage-specific Ucp2 deletion in vivo, Ucp2ΔLysM and Ucp2fl/fl mice were rendered obese and insulin resistant through high-fat feeding. Although no differences in adipose tissue inflammation or insulin resistance was found between the two genotypes, adipose tissue macrophages isolated from diet-induced obese Ucp2ΔLysM mice showed decreased TNFα secretion after ex vivo lipopolysaccharide stimulation compared with their Ucp2fl/fl littermates. Together, these results demonstrate that although UCP2 regulates both metabolism and the inflammatory response of macrophages, its activity is not crucial in shaping macrophage activation in the adipose tissue during obesity-induced insulin resistance.

Yi Liu
Dec 1, 2020; 19:1968-1985
Research

Sean A Burnap
Dec 7, 2020; 0:RA120.002305v1-mcp.RA120.002305
Research

Daniel J. Geiszler
Dec 1, 2020; 0:TIR120.002216v1-mcp.TIR120.002216
Technological Innovation and Resources

Tuberculosis (TB), caused by the infection of Mycobacterium tuberculosis (MTB), is one of the leading causes of death worldwide, especially in children. However, the mechanisms by which MTB infects its cellular host, activates an immune response, and triggers inflammation remain unknown. Mitochondria play important roles in the initiation and activation of the nucleotide-binding oligomerization domain-like receptor with a pyrin domain 3 (NLRP3) inflammasome, where mitochondria-associated endoplasmic reticulum membranes (MAMs) may serve as the platform for inflammasome assembly and activation. Additionally, mitofusin 2 (MFN2) is implicated in the formation of MAMs, but, the roles of mitochondria and MFN2 in MTB infection have not been elucidated. Using mircroarry profiling of TB patients and in vitro MTB stimulation of macrophages, we observed an up-regulation of MFN2 in the peripheral blood mononuclear cells of active TB patients. Furthermore, we found that MTB stimulation by MTB-specific antigen ESAT-6 or lysate of MTB promoted MFN2 interaction with NLRP3 inflammasomes, resulting in the assembly and activation of the inflammasome and, subsequently, IL-1β secretion. These findings suggest that MFN2 and mitochondria play important role in the pathogen-host interaction during MTB infection.

Aloïs Dusuel
Dec 9, 2020; 0:jlr.RA120000704v1-jlr.RA120000704
Research Articles

Anja Jaeschke
Dec 9, 2020; 0:jlr.RA120001141v1-jlr.RA120001141
Research Articles

Functions of the gut microbiome have a growing number of implications for host metabolic health, with diet being one of the most significant influences on microbiome composition. Compelling links between diet and the gut microbiome suggest key roles for various macronutrients, including lipids, yet how individual classes of dietary lipids interact with the microbiome remains largely unknown. Sphingolipids are bioactive components of most foods and are also produced by prominent gut microbes. This makes sphingolipids intriguing candidates for shaping diet–microbiome interactions. Here, we used a click chemistry–based approach to track the incorporation of bioorthogonal dietary omega-alkynyl sphinganine (sphinganine alkyne [SAA]) into the murine gut microbial community (Bioorthogonal labeling). We identified microbial and SAA-specific metabolic products through fluorescence-based sorting of SAA-containing microbes (Sort), 16S rRNA gene sequencing to identify the sphingolipid-interacting microbes (Seq), and comparative metabolomics to identify products of SAA assimilation by the microbiome (Spec). Together, this approach, termed Bioorthogonal labeling-Sort-Seq-Spec (BOSSS), revealed that SAA assimilation is nearly exclusively performed by gut Bacteroides, indicating that sphingolipid-producing bacteria play a major role in processing dietary sphinganine. Comparative metabolomics of cecal microbiota from SAA-treated mice revealed conversion of SAA to a suite of dihydroceramides, consistent with metabolic activities of Bacteroides and Bifidobacterium. Additionally, other sphingolipid-interacting microbes were identified with a focus on an uncharacterized ability of Bacteroides and Bifidobacterium to metabolize dietary sphingolipids. We conclude that BOSSS provides a platform to study the flux of virtually any alkyne-labeled metabolite in diet–microbiome interactions.

Bacterial lipopolysaccharides (LPSs or endotoxins) can bind most proteins of the lipid transfer/LPS-binding protein (LT/LBP) family in host organisms. The LPS-bound LT/LBP proteins then trigger either an LPS-induced proinflammatory cascade or LPS binding to lipoproteins that are involved in endotoxin inactivation and detoxification. Cholesteryl ester transfer protein (CETP) is an LT/LBP member, but its impact on LPS metabolism and sepsis outcome is unclear. Here, we performed fluorescent LPS transfer assays to assess the ability of CETP to bind and transfer LPS. The effects of intravenous (iv) infusion of purified LPS or polymicrobial infection (cecal ligation and puncture [CLP]) were compared in transgenic mice expressing human CETP and wild-type mice naturally having no CETP activity. CETP displayed no LPS transfer activity in vitro, but it tended to reduce biliary excretion of LPS in vivo. The CETP expression in mice was associated with significantly lower basal plasma lipid levels and with higher mortality rates in both models of endotoxemia and sepsis. Furthermore, CETPTg plasma modified cytokine production of macrophages in vitro. In conclusion, despite having no direct LPS binding and transfer property, human CETP worsens sepsis outcomes in mice by altering the protective effects of plasma lipoproteins against endotoxemia, inflammation, and infection.

The LDL receptor-related protein-1 (LRP1) is highly expressed in numerous cell types, and its impairment is associated with obesity, diabetes, and fatty liver disease. However, the mechanisms linking LRP1 to metabolic disease are not completely understood. Here, we compared the metabolic phenotype of C57BL/6J wild type and LRP1 knock-in mice carrying an inactivating mutation in the distal NPxY motif after feeding a low fat (LF) diet or high fat diets with (HFHC) or without (HF) cholesterol supplementation. In response to HF feeding, both groups developed hyperglycemia, hyperinsulinemia, and hyperlipidemia, as well as increased adiposity with adipose tissue inflammation and liver steatosis. However, when animals were fed the HF diet supplemented with cholesterol, the LRP1 NPxY mutation prevents hypercholesterolemia, reduces adipose tissue and brain inflammation, and limits liver progression to steatohepatitis. Nevertheless, insulin signaling is impaired in LRP1 NPxY mutant hepatocytes and this mutation does not protect against HFHC-induced insulin resistance. The selective metabolic improvement observed in HFHC-fed LRP1 NPxY mutant mice is due to an apparent increase of hepatic LDL receptor levels, leading to an elevated rate of plasma lipoprotein clearance and lowering of plasma and hepatic cholesterol levels. The unique metabolic phenotypes displayed by LRP1 NPxY mutant mice in response to HF or HFHC diet feeding indicate an LRP1-cholesterol axis in modulating tissue inflammation. The LRP1 NPxY mutant mouse phenotype differs from phenotypes observed in mice with tissue-specific LRP1 inactivation, thus highlighting the importance of an integrative approach to evaluate how global LRP1 dysfunction contributes to metabolic disease development.

Coronavirus disease 2019 (COVID-19) is a highly contagious infection and threating the human lives in the world. The elevation of cytokines in blood is crucial to induce cytokine storm and immunosuppression in the transition of severity in COVID-19 patients. However, the comprehensive changes of serum proteins in COVID-19 patients throughout the SARS-CoV-2 infection is unknown. In this work, we developed a high-density antibody microarray and performed an in-depth proteomics analysis of serum samples collected from early COVID-19 (n = 15) and influenza (n = 13) patients. We identified a large set of differentially expressed proteins (n = 132) that participate in a landscape of inflammation and immune signaling related to the SARS-CoV-2 infection. Furthermore, the significant correlations of neutrophil and lymphocyte with the CCL2 and CXCL10 mediated cytokine signaling pathways was identified. These information are valuable for the understanding of COVID-19 pathogenesis, identification of biomarkers and development of the optimal anti-inflammation therapy.

Mallory-Denk-bodies (MDBs) are hepatic protein aggregates associated with inflammation both clinically and in MDB-inducing models. Similar protein aggregation in neurodegenerative diseases also triggers inflammation and NF-B activation. However, the precise mechanism that links protein aggregation to NF-B-activation and inflammatory response remains unclear. Herein we find that treating primary hepatocytes with MDB-inducing agents (N-methylprotoporphyrin (NMPP), protoporphyrin IX (PPIX), or Zinc-protoporphyrin IX (ZnPP)) elicited an IBα-loss with consequent NF-B activation. Four known mechanisms of IBα-loss i.e. the canonical ubiquitin-dependent proteasomal degradation (UPD), autophagic-lysosomal degradation, calpain degradation and translational inhibition, were all probed and excluded. Immunofluorescence analyses of ZnPP-treated cells coupled with 8 M urea/CHAPS-extraction revealed that this IBα-loss was due to its sequestration along with IBβ into insoluble aggregates, thereby releasing NF-B. Through affinity pulldown, proximity biotinylation by antibody recognition, and other proteomic analyses, we verified that NF-B subunit p65, which stably interacts with IBα under normal conditions, no longer binds to it upon ZnPP-treatment. Additionally, we identified 10 proteins that interact with IBα under baseline conditions, aggregate upon ZnPP-treatment, and maintain the interaction with IBα after ZnPP-treatment, either by cosequestering into insoluble aggregates or through a different mechanism. Of these 10 proteins, the nucleoporins Nup153 and Nup358/RanBP2 were identified through RNA-interference, as mediators of IBα-nuclear import. The concurrent aggregation of IBα, NUP153, and RanBP2 upon ZnPP-treatment, synergistically precluded the nuclear entry of IBα and its consequent binding and termination of NF-B activation. This novel mechanism may account for the protein aggregate-induced inflammation observed in liver diseases, thus identifying novel targets for therapeutic intervention. Because of inherent commonalities this MDB cell model is a bona fide protoporphyric model, making these findings equally relevant to the liver inflammation associated with clinical protoporphyria.

Ankylosing Spondylitis (AS) is a common, inflammatory rheumatic disease, which primarily affects the axial skeleton and is associated with sacroiliitis, uveitis and enthesitis. Unlike other autoimmune rheumatic diseases, such as rheumatoid arthritis or systemic lupus erythematosus, autoantibodies have not yet been reported to be a feature of AS. We therefore wished to determine if plasma from patients with AS contained autoantibodies and if so, characterize and quantify this response in comparison to patients with Rheumatoid Arthritis (RA) and healthy controls. Two high-density nucleic acid programmable protein arrays expressing a total of 3498 proteins were screened with plasma from 25 patients with AS, 17 with RA and 25 healthy controls. Autoantigens identified were subjected to Ingenuity Pathway Analysis in order to determine patterns of signalling cascades or tissue origin. 44% of patients with Ankylosing Spondylitis demonstrated a broad autoantibody response, as compared to 33% of patients with RA and only 8% of healthy controls. Individuals with AS demonstrated autoantibody responses to shared autoantigens, and 60% of autoantigens identified in the AS cohort were restricted to that group. The AS patients autoantibody responses were targeted towards connective, skeletal and muscular tissue, unlike those of RA patients or healthy controls. Thus, patients with AS show evidence of systemic humoral autoimmunity and multispecific autoantibody production. Nucleic Acid Programmable Protein Arrays constitute a powerful tool to study autoimmune diseases.

Paramphistomosis, caused by the rumen fluke, Calicophoron daubneyi, is a parasitic infection of ruminant livestock which has seen a rapid rise in prevalence throughout Western Europe in recent years. Following ingestion of metacercariae (parasite cysts) by the mammalian host, newly-excysted juveniles (NEJs) emerge and invade the duodenal submucosa which causes significant pathology in heavy infections. The immature larvae then migrate upwards, along the gastrointestinal tract, and enter the rumen where they mature and begin to produce eggs. Despite their emergence, and sporadic outbreaks of acute disease, we know little about the molecular mechanisms used by C. daubneyi to establish infection, acquire nutrients and to avoid the host immune response. Here, transcriptome analysis of four intra-mammalian life-cycle stages, integrated with secretome analysis of the NEJ and adult parasites (responsible for acute and chronic disease respectively), revealed how the expression and secretion of selected families of virulence factors and immunomodulators are regulated in accordance with fluke development and migration. Our data show that whilst a family of cathepsins B with varying S2 sub-site residues (indicating distinct substrate specificities) are differentially secreted by NEJs and adult flukes, cathepsins L and F are secreted in low abundance by NEJs only. We found that C. daubneyi has an expanded family of aspartic peptidases, which is up-regulated in adult worms, although they are underrepresented in the secretome. The most abundant proteins in adult fluke secretions were helminth defence molecules (HDMs) that likely establish an immune environment permissive to fluke survival and/or neutralise pathogen-associated molecular patterns (PAMPs) such as bacterial lipopolysaccharide in the microbiome-rich rumen. The distinct collection of molecules secreted by C. daubneyi allowed the development of the first coproantigen-based ELISA for paramphistomosis which, importantly, did not recognise antigens from other helminths commonly found as co-infections with rumen fluke.

Open searching has proven to be an effective strategy for identifying both known and unknown modifications in shotgun proteomics experiments. Rather than being limited to a small set of user-specified modifications, open searches identify peptides with any mass shift that may correspond to a single modification or a combination of several modifications. Here we present PTM-Shepherd, a bioinformatics tool that automates characterization of PTM profiles detected in open searches based on attributes such as amino acid localization, fragmentation spectra similarity, retention time shifts, and relative modification rates. PTM-Shepherd can also perform multi-experiment comparisons for studying changes in modification profiles, e.g. in data generated in different laboratories or under different conditions. We demonstrate how PTM-Shepherd improves the analysis of data from formalin-fixed paraffin-embedded samples, detects extreme underalkylation of cysteine in some datasets, discovers an artefactual modification introduced during peptide synthesis, and uncovers site-specific biases in sample preparation artifacts in a multi-center proteomics profiling study.

We have previously shown that multimers of plasma pentraxin-3 (PTX3) were predictive of survival in patients with sepsis. To characterize the release kinetics and cellular source of plasma protein changes in sepsis, serial samples were obtained from healthy volunteers (n=10, 3 time-points) injected with low-dose endotoxin (LPS) and analyzed using data-independent acquisition (DIA) MS. The human plasma proteome response was compared to an LPS-induced endotoxemia model in mice. Proteomic analysis of human plasma revealed a rapid neutrophil degranulation signature, followed by a rise in acute phase proteins. Changes in circulating PTX3 correlated with increases in neutrophil-derived proteins following LPS injection. Time course analysis of the plasma proteome in mice showed a time-dependent increase in multimeric PTX3, alongside increases in neutrophil-derived myeloperoxidase (MPO) upon LPS treatment. The mechanisms of oxidation-induced multimerisation of PTX3 were explored in two genetic mouse models: MPO global knock-out mice and LysM CreNox2KO mice, in which NADPH oxidase 2 (Nox2) is only deficient in myeloid cells. Nox2 is the enzyme responsible for the oxidative burst in neutrophils. Increases in plasma multimeric PTX3 were not significantly different between wildtype and MPO or LysM CreNox2KO knock-out mice. Thus, PTX3 may already be stored and released in a multimeric form. Through in vivo neutrophil depletion and multiplexed vascular proteomics, PTX3 multimer deposition within the aorta was confirmed to be neutrophil-dependent. Proteomic analysis of aortas from LPS-injected mice returned PTX3 as the most upregulated protein, where multimeric PTX3 was deposited as early as 2 h post-LPS along with other neutrophil-derived proteins. In conclusion, the rise in multimeric PTX3 upon LPS injection correlates with neutrophil-related protein changes in plasma and in aortas. MPO and myeloid Nox2 are not required for the multimerisation of PTX3; instead, neutrophil extravasation is responsible for the LPS-induced deposition of multimeric PTX3 in the aorta.

Faithful replication of the mitochondrial genome is carried out by a set of key nuclear-encoded proteins. DNA polymerase γ is a core component of the mtDNA replisome and the only replicative DNA polymerase localized to mitochondria. The asynchronous mechanism of mtDNA replication predicts that the replication machinery encounters dsDNA and unique physical barriers such as structured genes, G-quadruplexes, and other obstacles. In vitro experiments here provide evidence that the polymerase γ heterotrimer is well-adapted to efficiently synthesize DNA, despite the presence of many naturally occurring roadblocks. However, we identified a specific G-quadruplex–forming sequence at the heavy-strand promoter (HSP1) that has the potential to cause significant stalling of mtDNA replication. Furthermore, this structured region of DNA corresponds to the break site for a large (3,895 bp) deletion observed in mitochondrial disease patients. The presence of this deletion in humans correlates with UV exposure, and we have found that efficiency of polymerase γ DNA synthesis is reduced after this quadruplex is exposed to UV in vitro.

Discrimination -- prejudiced actions toward people based on their identity -- may cause stress that impairs gut health and lead to the growth of unhealthy bacteria that promote inflammation, a new study has found.

A federal judge has blocked a new bill in Louisiana that would require the Bible's Ten Commandments to be displayed in the state's publicly-funded schools.