Structure of the ATP synthase from Mycobacterium smegmatis provides targets for treating tuberculosis

The structure has been determined by electron cryomicroscopy of the adenosine triphosphate (ATP) synthase from Mycobacterium smegmatis. This analysis confirms features in a prior description of the structure of the enzyme, but it also describes other highly significant attributes not recognized before that are crucial for understanding the mechanism and regulation of the mycobacterial enzyme. First, we resolved not only the three main states in the catalytic cycle described before but also eight substates that portray structural and mechanistic changes occurring during a 360° catalytic cycle. Second, a mechanism of auto-inhibition of ATP hydrolysis involves not only the engagement of the C-terminal region of an α-subunit in a loop in the γ-subunit, as proposed before, but also a “fail-safe” mechanism involving the b′-subunit in the peripheral stalk that enhances engagement. A third unreported characteristic is that the fused bδ-subunit contains a duplicated domain in its N-terminal region where the two copies of the domain participate in similar modes of attachment of the two of three N-terminal regions of the α-subunits. The auto-inhibitory plus the associated “fail-safe” mechanisms and the modes of attachment of the α-subunits provide targets for development of innovative antitubercular drugs. The structure also provides support for an observation made in the bovine ATP synthase that the transmembrane proton-motive force that provides the energy to drive the rotary mechanism is delivered directly and tangentially to the rotor via a Grotthuss water chain in a polar L-shaped tunnel.

bddashboard: An infrastructure for biodiversity dashboards in R

The bdverse is a collection of packages that form a general framework for facilitating biodiversity science in R (programming language). Exploratory and diagnostic visualization can unveil hidden patterns and anomalies in data and allow quick and efficient exploration of massive datasets. The development of an interactive yet flexible dashboard that can be easily deployed locally or remotely is a highly valuable biodiversity informatics tool. To this end, we have developed 'bddashboard', which serves as an agile framework for biodiversity dashboard development. This project is built in R, using the Shiny package (RStudio, Inc 2021) that helps build interactive web apps in R. The following key components were developed: Core Interactive Components The basic building blocks of every dashboard are interactive plots, maps, and tables. We have explored all major visualization libraries in R and have concluded that 'plotly' (Sievert 2020) is the most mature and showcases the best value for effort. Additionally, we have concluded that 'leaflet' (Graul 2016) shows the most diverse and high-quality mapping features, and DT (DataTables library) (Xie et al. 2021) is best for rendering tabular data. Each component was modularized to better adjust it for biodiversity data and to enhance its flexibility. Field Selector The field selector is a unique module that makes each interactive component much more versatile. Users have different data and needs; thus, every combination or selection of fields can tell a different story. The field selector allows users to change the X and Y axis on plots, to choose the columns that are visible on a table, and to easily control map settings. All that in real-time, without reloading the page or disturbing the reactivity. The field selector automatically detects how many columns a plot needs and what type of columns can be passed to the X-axis or Y-axis. The field selector also displays the completeness of each field. Plot Navigation We developed the plot navigation module to prevent unwanted extreme cases. Technically, drawing 1,000 bars on a single bar plot is possible, but this visualization is not human-friendly. Navigation allows users to decide how many values they want to see on a single plot. This technique allows for fast drawing of extensive datasets without affecting page reactivity, dramatically improving performance and functioning as a fail-safe mechanism. Reactivity Reactivity creates the connection between different components. The changes in input values automatically flow to the plots, text, maps, and tables that use the input, and cause them to update. Reactivity facilitates drilling down functionality, which enhances the user’s ability to explore and investigate the data. We developed a novel and robust reactivity technique that allows us to add a new component and effectively connect it with all existing components within a dashboard tab, using only one line of code. Generic Biodiversity Tabs We developed five useful dashboard tabs (Fig. 1): (i) the Data Summary tab to give a quick overview of a dataset; (ii) the Data Completeness tab helps users get valuable information about missing records and missing Darwin Core fields; (iii) the Spatial tab is dedicated to spatial visualizations; (iv) the Taxonomic tab is designed to visualize taxonomy; and (v) the Temporal tab is designed to visualize time-related aspects. Performance and Agility To make a dashboard work smoothly and react quickly, hundreds of small and large modules, functions, and techniques must work together. Our goal was to minimize dashboard latency and maximize its data capacity. We used asynchronous modules to write non-blocking code, clusters in map components, and preprocessing and filtering data before passing it to plots to reduce the load. The 'bddashboard' package modularized architecture allows us to develop completely different interactive and reactive dashboards within mere minutes.

Discovery of a small protein-encoding cis-regulatory overlapping gene of the tumor suppressor gene Scribble in humans

Intensive gene annotation has revealed many functional and regulatory elements in the human genome. Although eukaryotic protein-coding genes are generally transcribed into monocistronic mRNAs, recent studies have discovered additional short open reading frames (sORFs) in mRNAs. Here, we performed proteogenomic data mining for hidden proteins categorized into sORF-encoded polypeptides (SEPs) in human cancers. We identified a new SEP-encoding overlapping sORF (oORF) on the cell polarity determinant Scribble (SCRIB) that is considered a proto-oncogene with tumor suppressor function in Hippo-YAP/TAZ, MAPK/ERK, and PI3K/Akt/mTOR signaling. Reanalysis of clinical human proteomic data revealed translational dysregulation of both SCRIB and its oORF, oSCRIB, during carcinogenesis. Biochemical analyses suggested that the translatable oSCRIB constitutively limits the capacity of eukaryotic ribosomes to translate the downstream SCRIB. These findings provide a new example of cis-regulatory oORFs that function as a ribosomal roadblock and potentially serve as a fail-safe mechanism to normal cells for non-excessive downstream gene expression, which is hijacked in cancer.

The Availability of Sharps Disposal Bins: A Survey of Airports in California

Background: Sharps waste, especially medical sharps waste, can put those who come into contact with it at risk for injury and exposure to blood-borne pathogens. Options for self-injectors to dispose of their sharps while traveling vary greatly – from sharps containers in limited locations in some public restrooms to large kiosks centrally located to no containers at all. Currently, there is a lack of published data on sharps disposal bins in commercial airports. We surveyed commercial airports in California to assess the current state of sharps waste disposal. Many people with diabetes routinely use sharps every day for injecting medications or for self-monitoring glucose concentrations and these people, along with others who self-inject medications, must have a safe mechanism for sharps disposal when travelling by air. Methods: A five-question survey was sent to 30 commercial airports in California. Responses were collected and then analyzed based on the following three metrics: (1) the percentage of airports that responded and indicated that they had any sharps disposal bins, (2) the percentage of airports that responded and indicated that they had sharps disposal bins in over half their restrooms, and (3) the average percentage of bathrooms that have available sharps disposal bins in airports that responded to our survey. Results: Out of 30 commercial airports in California, we received survey responses from 13 airport representatives and direct email responses from 5 airport representatives. Out of 18 total responses, 11 airports (61.1%) reported that they had some form of available sharps disposal options. Out of the 13 survey responses, 6 airports (46.2%) reported that they had sharps disposal in over 50% of their restrooms. Conclusion: There is a lack of consistency in sharps waste disposal options among commercial airports in California. While many commercial airports in California offer sharps waste disposal options, not all commercial airports have sharps waste disposal options in all their public restrooms. There is room for improved availability of sharps disposal bins in California’s commercial airports.

Recent Advances and Challenges in Nanodelivery Systems for Antimicrobial Peptides (AMPs)

Antimicrobial peptides (AMPs) can be used as alternative therapeutic agents to traditional antibiotics. These peptides have abundant natural template sources and can be isolated from animals, plants, and microorganisms. They are amphiphilic and mostly net positively charged, and they have a broad-spectrum inhibitory effect on bacteria, fungi, and viruses. AMPs possess significant rapid killing effects and do not interact with specific receptors on bacterial surfaces. As a result, drug resistance is rarely observed with treatments. AMPs, however, have some operational problems, such as a susceptibility to enzymatic (protease) degradation, toxicity in vivo, and unclear pharmacokinetics. However, nanodelivery systems loaded with AMPs provide a safe mechanism of packaging such peptides before they exert their antimicrobial actions, facilitate targeted delivery to the sites of infection, and control the release rate of peptides and reduce their toxic side effects. However, nanodelivery systems using AMPs are at an early stage of development and are still in the laboratory phase of development. There are also some challenges in incorporating AMPs into nanodelivery systems. Herein, an insight into the nanotechnology challenges in delivering AMPs, current advances, and remaining technological challenges are discussed in depth.

A Novel Subsea Actuator to Electrify Small-Bore Valve

This paper presents the development and qualification of a novel Subsea Electric Actuator, especially designed for rotary small-bore valves. One of the main challenges was to design an electric actuator which is as compact as the existing hydraulic actuators, but able to provide a fail-safe mechanism by field-proven springs and full integration of all necessary components, including the electric drive and controls, inside of a compact enclosure. Furthermore, the design team had to considerably reduce its power consumption and weight in comparison to existing solutions. Finally, the system was designed for lean manufacturing, allowing considerable cost-saving benefits for all the partners due to extensive standardization work. The paper shows the engineering requirements obtained by interviewing different users, the design methodology applied and the qualification of the new system up to TRL 3 with Digital Twin and Rapid Prototyping. Finally, an outlook is presented with the planned TRL 4 and TRL 5 qualification tests and a summary of the technical and economic benefits for the users of this novel Subsea Valve Actuator.

Apoptotic and Non-Apoptotic Modalities of Thymoquinone-Induced Lymphoma Cell Death: Highlight of the Role of Cytosolic Calcium and Necroptosis

Targeting non-apoptotic modalities might be therapeutically promising in diffuse large B cell lymphoma (DLBCL) patients with compromised apoptotic pathways. Thymoquinone (TQ) has been reported to promote apoptosis in cancer cells, but little is known about its effect on non-apoptotic pathways. This work investigates TQ selectivity against DLBCL cell lines and the cell death mechanisms. TQ reduces cell viability and kills cell lines with minimal toxicity on normal hematological cells. Mechanistically, TQ promotes the mitochondrial caspase pathway and increases genotoxicity. However, insensitivity of most cell lines to caspase inhibition by z-VAD-fmk (benzyloxycarbonyl-Val-Ala-Asp-fluoromethyl ketone) pointed to a critical role of non-apoptotic signaling. In cells dying through non-apoptotic death, TQ increases endoplasmic reticulum (ER) stress markers and substantially increases cytosolic calcium ([Ca2+]c) through ER calcium depletion and activation of store-operated calcium entry (SOCE). Chelation of [Ca2+]c, but not SOCE inhibitors, reduces TQ-induced non-apoptotic cell death, highlighting the critical role of calcium in a non-apoptotic effect of TQ. Investigations showed that TQ-induced [Ca2+]c signaling is primarily initiated by necroptosis upstream to SOCE, and inhibition necroptosis by necrostatin-1 alone or with z-VAD-fmk blocks the cell death. Finally, TQ exhibits an improved selectivity profile over standard chemotherapy agents, suggesting a therapeutic relevance of the pro-necroptotic effect of TQ as a fail-safe mechanism for DLBCL therapies targeting apoptosis.

Methionine restriction breaks obligatory coupling of cell proliferation and death by an oncogene Src in Drosophila

Oncogenes often promote cell death as well as proliferation. How oncogenes drive these diametrically opposed phenomena remains to be solved. A key question is whether cell death occurs as a response to aberrant proliferation signals or through a proliferation-independent mechanism. Here, we reveal that Src, the first identified oncogene, simultaneously drives cell proliferation and death in an obligatorily coupled manner through parallel MAPK pathways. The two MAPK pathways diverge from a lynchpin protein Slpr. A MAPK p38 drives proliferation whereas another MAPK JNK drives apoptosis independently of proliferation signals. Src-p38-induced proliferation is regulated by methionine-mediated Tor signaling. Reduction of dietary methionine uncouples the obligatory coupling of cell proliferation and death, suppressing tumorigenesis and tumor-induced lethality. Our findings provide an insight into how cells evolved to have a fail-safe mechanism that thwarts tumorigenesis by the oncogene Src. We also exemplify a diet-based approach to circumvent oncogenesis by exploiting the fail-safe mechanism.