The Respiratory Chain of Alkaliphilic Bacteria

Alkaliphilic bacteria that grow at extremely high pH are confronted by particular bioenergetic problems in carrying out oxidative phosphorylation. This project focused on the properties and adaptations of the respiratory chain. The respiratory chain as a whole, the redox poises of its components and several individual complexes of the respiratory chain of alkaliphilic Bacillus pseudofirmus OF4 have been characterized as part of this project and, importantly, this project has helped support the development of genetic tools that make B. pseudofirmus OF4 the most genetically tractable and, hence, most bioenergetically characterized extreme alkaliphile. Evidence has been obtained for a pivotal role of the cca3-type terminal oxidase in oxidative phosphorylation, especially at high pH and motifs that may be relevant to that special role have been identified

Alkaline pH homeostasis in bacteria: New insights

AbstractThe capacity of bacteria to survive and grow at alkaline pH values is of widespread importance in the epidemiology of pathogenic bacteria, in remediation and industrial settings, as well as in marine, plant-associated and extremely alkaline ecological niches. Alkali-tolerance and alkaliphily, in turn, strongly depend upon mechanisms for alkaline pH homeostasis, as shown in pH shift experiments and growth experiments in chemostats at different external pH values. Transcriptome and proteome analyses have recently complemented physiological and genetic studies, revealing numerous adaptations that contribute to alkaline pH homeostasis. These include elevated levels of transporters and enzymes that promote proton capture and retention (e.g., the ATP synthase and monovalent cation/proton antiporters), metabolic changes that lead to increased acid production, and changes in the cell surface layers that contribute to cytoplasmic proton retention. Targeted studies over the past decade have followed up the long-recognized importance of monovalent cations in active pH homeostasis. These studies show the centrality of monovalent cation/proton antiporters in this process while microbial genomics provides information about the constellation of such antiporters in individual strains. A comprehensive phylogenetic analysis of both eukaryotic and prokaryotic genome databases has identified orthologs from bacteria to humans that allow better understanding of the specific functions and physiological roles of the antiporters. Detailed information about the properties of multiple antiporters in individual strains is starting to explain how specific monovalent cation/proton antiporters play dominant roles in alkaline pH homeostasis in cells that have several additional antiporters catalyzing ostensibly similar reactions. New insights into the pH-dependent Na+/H+ antiporter NhaA that plays an important role in Escherichia coli have recently emerged from the determination of the structure of NhaA. This review highlights the approaches, major findings and unresolved problems in alkaline pH homeostasis, focusing on the small number of well-characterized alkali-tolerant and extremely alkaliphilic bacteria

Ionic selectivity and thermal adaptations within the voltage-gated sodium channel family of alkaliphilic Bacillus

Entry and extrusion of cations are essential processes in living cells. In alkaliphilic prokaryotes, high external pH activates voltage-gated sodium channels (Nav), which allows Na+ to enter and be used as substrate for cation/proton antiporters responsible for cytoplasmic pH homeostasis. Here, we describe a new member of the prokaryotic voltage-gated Na+ channel family (NsvBa; Non-selective voltage-gated, Bacillus alcalophilus) that is nonselective among Na+, Ca2+ and K+ ions. Mutations in NsvBa can convert the nonselective filter into one that discriminates for Na+ or divalent cations. Gain-of-function experiments demonstrate the portability of ion selectivity with filter mutations to other Bacillus Nav channels. Increasing pH and temperature shifts their activation threshold towards their native resting membrane potential. Furthermore, we find drugs that target Bacillus Nav channels also block the growth of the bacteria. This work identifies some of the adaptations to achieve ion discrimination and gating in Bacillus Nav channels. DOI: http://dx.doi.org/10.7554/eLife.04387.00

Increasing DEA-X Waiver Trained Providers through Quality Improvement

Introduction New Mexico has long experienced challenges associated with opioid use disorder (OUD). In 2017, New Mexico had the seventeenth highest drug overdose death rate in the United States. Although this ranking has decreased since prior years, New Mexico experienced 16.7 overdose deaths involving opioids per 100,000 persons in 2017, compared to the national average of 14.6 per 100,000 persons. Additionally, New Mexico saw an 82% increase in opioid overdose related emergency department visits between 2013-2015, and this rate has stayed consistent since 2015.1 In 2017, of the 332 overdose deaths in New Mexico, the most common drugs causing overdose deaths were prescription opioids (51.5% - 171 deaths) followed by heroin (43.4% - 144 deaths).2 According to the New Mexico Department of Health Syringe Services Program, in 2016 6,976 of 9,649 enrollees (72%) indicated heroin use. Additionally, using data from the New Mexico Board of Pharmacy Prescription Monitoring Program it was estimated in 2017 that 12,400 patients (22%) with chronic opioid prescriptions were in need of treatment for OUD.3 Given that these estimates are limited to individuals captured by these two data sources, the estimate of 19,376 individuals in New Mexico experiencing OUD is a gross underestimate. Given the negative outcomes associated with OUD and the size of the population in need of treatment in New Mexico, there is a demand for more providers to offer OUD treatment. Medication-Assisted Treatment (MAT), including buprenorphine, is the mainstay maintenance therapy for OUD. In order to prescribe buprenorphine, providers must complete an 8 hour DEA-X waiver training. Given the heavy burden of OUD in New Mexico, our aim was to increase the number of General Internal Medicine (GIM) attending physicians at the University of New Mexico Hospital (UNMH) who have completed DEA-X waiver training to 50% by January 1st, 2020. Methods We identified the number of GIM attendings at UNMH who had already completed a DEA-X waiver training. In order to analyze the barriers to completing a DEA-X waiver training, we attended a monthly departmental GIM meeting where we explained the current need for more providers to prescribe buprenorphine in New Mexico and the process of our quality improvement project. Following the presentation, we surveyed 13 out of 20 GIM attendings via RedCap. The survey was comprised of 21 questions assessing attitudes toward OUD and buprenorphine, reservations about prescribing buprenorphine, and interest in obtaining a DEA-X waiver. Survey questions were designed on a five response Likert scale. Participants were asked to include their schedule availability for future DEA-X waiver trainings. Upon completion of the survey, we analyzed participant attitudes and barriers using a five-point Likert scale, by assigning 1 to strongly agree through 5 to strongly disagree. Common barriers were identified by grouping and summing the agreed and strongly agreed responses. Based on the provider availability submitted in the survey, we sent out a list of training dates to the GIM attendings. Results Of the 13 UNM GIM attendings surveyed, 12 (92%) thought OUD is a chronic disease. Thirteen (100%) thought increasing buprenorphine availability is important. Six (46%) expressed interest in getting DEA-X waiver trained. The top reservation classified by survey respondents who selected either Agree or Strongly Agree to completing the training was insufficient time available in the provider’s current patient schedule (10/13), followed by insufficient work time dedicated to complete the training (7/13). Office staff stigma was the least concerning reservation (3/13). Based on our interventions, the number of GIM attending physicians at UNMH with DEA X-waiver training increased from 3 to 6, which corresponds with a 100% increase. Conclusions Although 100% of GIM attendings surveyed thought increasing the availability of buprenorphine was important, only 45% were interested in getting DEA-X waiver training themselves. One of the major barriers identified was insufficient time to complete the training. One possible solution is to have clinic managers set aside time during normal work hours for this purpose. Our intervention for the first PDSA cycle was to educate the attendings on the importance of having a DEA-X waiver and to send participants information about local DEA-X waiver trainings. With this intervention, we exceeded our goal by achieving a 100% increase in GIM attendings with DEA-X waiver training. For our next PDSA cycle we plan to work with clinics to host a DEA-X waiver training on-site and during normal work hours or during a division faculty meeting to decrease some of the burden and increase the number of physicians trained. Furthermore, residents need to work with a supervising attending with a DEA-X waiver in order to prescribe Suboxone. 54% of attendings said that having residents who are DEA-X waiver trained would encourage them to become trained too. Therefore, increasing the number of resident physicians who have completed the DEA-X waiver training will in turn increase the amount of GIM attendings who become DEA-X waiver trained

A collaborative filtering similarity measure based on singularities.

Recommender systems play an important role in reducing the negative impact of informa- tion overload on those websites where users have the possibility of voting for their prefer- ences on items. The most normal technique for dealing with the recommendation mechanism is to use collaborative filtering, in which it is essential to discover the most similar users to whom you desire to make recommendations. The hypothesis of this paper is that the results obtained by applying traditional similarities measures can be improved by taking contextual information, drawn from the entire body of users, and using it to cal- culate the singularity which exists, for each item, in the votes cast by each pair of users that you wish to compare. As such, the greater the measure of singularity result between the votes cast by two given users, the greater the impact this will have on the similarity. The results, tested on the Movielens, Netflix and FilmAffinity databases, corroborate the excellent behaviour of the singularity measure proposed

A New Type of Proton Coordination in an F1Fo-ATP Synthase Rotor Ring

The high-resolution structure of the rotor ring from alkaliphilic Bacillus pseudofirmus OF4 reveals a new type of ion binding in F1Fo-ATP synthases

2020-05-02/03 DAILY UNM GLOBAL HEALTH COVID-19 BRIEFING

Executive Summary: More NM cases. Free Shiprock testing. Prison release demands. 8 state parks reopen. Higher US deaths. NY PPE case dismissed. Orthopedic Tx down. European deaths down. UK mortality factors. People leaving large cities. Ending lockdown strategies. Public mask impact. Taiwan tracing. Homeless shelter prevalence. Homeless shelter outbreak. 50-state R0. COVID-19 decades later. US county tracking site. Hospital management model. COVID-19 behavioral transformation. Practice guidelines for: cardiology, IBD surgery, and rheumatic physical inactivity. Roche antibody test approved. Abbott antibody test EU-certified. Home anosmia assessment. CVD and ACE/ARBs. Tocilizumab early evidence. Tocilizumab systematic review. WHO vaccines trial. HCQ slower viral clearance. CBC predicts severity. Kidney disease meta-analysis. Innate/adaptive immunity timing. Combating misinformation. Mental health living reviews

pH Dependent Antimicrobial Peptides and Proteins, Their Mechanisms of Action and Potential as Therapeutic Agents

Antimicrobial peptides (AMPs) are potent antibiotics of the innate immune system that have been extensively investigated as a potential solution to the global problem of infectious diseases caused by pathogenic microbes. A group of AMPs that are increasingly being reported are those that utilise pH dependent antimicrobial mechanisms and here, we review research into this area. This review shows that these antimicrobial molecules are produced by a diverse spectrum of creatures, including vertebrates and invertebrates, and are primarily cationic although a number of anionic examples are known. Some of these molecules exhibit high pH optima for their antimicrobial activity but in most cases, these AMPs show activity against microbes that present low pH optima, which reflects the acidic pH generally found at their sites of action, particularly the skin. The modes of action used by these molecules are based on a number of major structure / function relationships, which include metal ion binding, changes to net charge and conformational plasticity, and primarily involve the protonation of histidine, aspartic acid and glutamic acid residues at low pH. The pH dependent activity of pore forming antimicrobial proteins involves mechanisms that generally differ fundamentally to those used by pH dependent AMPs, which can be described by the carpet, toroidal pore and barrel-stave pore models of membrane interaction. A number of pH dependent AMPs and antimicrobial proteins have been developed for medical purposes and have successfully completed clinical trials, including kappacins, LL-37, histatins and lactoferrin, along with a number of their derivatives. Major examples of the therapeutic application of these antimicrobial molecules include wound healing as well as the treatment of multiple cancers and infections due to viruses, bacteria and fungi. In general, these applications involve topical administration, such as the use of mouth washes, cream formulations and hydrogel delivery systems. Nonetheless, many pH dependent AMPs and antimicrobial proteins have yet to be fully characterized and these molecules, as a whole, represent an untapped source of novel biologically active agents that could aid fulfillment of the urgent need for alternatives to conventional antibiotics, helping to avert a return to the pre-antibiotic era