Proteogenomic analysis of mycobacterium smegmatis using high resolution mass spectrometry

Biochemical evidence is vital for accurate genome annotation. The integration of experimental data collected at the proteome level using high resolution mass spectrometry allows for improvements in genome annotation by providing evidence for novel gene models, while validating or modifying others. Here, we report the results of a proteogenomic analysis of a reference strain of Mycobacterium smegmatis (mc2155), a fast growing model organism for the pathogenic Mycobacterium tuberculosis—the causative agent for Tuberculosis. By integrating high throughput LC/MS/MS proteomic data with genomic six frame translation and ab initio gene prediction databases, a total of 2887 ORFs were identified, including 2810 ORFs annotated to a Reference protein, and 63 ORFs not previously annotated to a Reference protein. Further, the translational start site (TSS) was validated for 558 Reference proteome gene models, while upstream translational evidence was identified for 81. In addition, N-terminus derived peptide identifications allowed for downstream TSS modification of a further 24 gene models. We validated the existence of six previously described interrupted coding sequences at the peptide level, and provide evidence for four novel frameshift positions. Analysis of peptide posterior error probability (PEP) scores indicates high-confidence novel peptide identifications and shows that the genome of M. smegmatis mc2155 is not yet fully annotated. Data are available via ProteomeXchange with identifier PXD003500

Protocol for a prospective double-blind, randomised, placebo-controlled feasibility trial of octreotide infusion during liver transplantation

Introduction Liver transplantation is a complex operation that can provide significant improvements in quality of life and survival to the recipients. However, serious complications are common and include major haemorrhage, hypotension and renal failure. Blood transfusion and the development of acute kidney injury lead to both short-term and long-term poor patient outcomes, including an increased risk of death, graft failure, length of stay and reduced quality of life. Octreotide may reduce the incidence of renal dysfunction, perioperative haemorrhage and enhance intraoperative blood pressure. However, octreotide does have risks, including resistant bradycardia, hyperglycaemia and hypoglycaemia and QT prolongation. Hence, a randomised controlled trial of octreotide during liver transplantation is needed to determine the cost-efficacy and safety of its use; this study represents a feasibility study prior to this trial. Methods and analysis We describe a multicentre, double-blind, randomised, placebo-controlled feasibility study of continuous infusion of octreotide during liver transplantation surgery. We will recruit 30 adult patients at two liver transplant centres. A blinded infusion during surgery will be administered in a 2:1 ratio of octreotide:placebo. The primary outcomes will determine the feasibility of this study design. These include the recruitment ratio, correct administration of blinded study intervention, adverse event rates, patient and clinician enrolment refusal and completion of data collection. Secondary outcome measures of efficacy and safety will help shape future trials by assessing potential primary outcome measures and monitoring safety end points. No formal statistical tests are planned. This manuscript represents study protocol number 1.3, dated 2 June 2021. Ethics and dissemination This study has received Research Ethics Committee approval. The main study outcomes will be submitted to an open-access journal. Trial sponsor The Joint Research Office, University College London, UK. Neither the sponsor nor the funder have any role in study design, collection, management, analysis and interpretation of data, writing of the study report or the decision to submit the report for publication. Trial registration The study is registered with ClinicalTrials.gov (NCT04941911) with recruitment due to start in August 2021 with anticipated completion in July 2022. Clinical trials unit Surgical and Interventional Group, Division of Surgery & Interventional Science, University College London

Nuclear Spin Relaxation for Higher Spin

We study the relaxation of a spin I that is weakly coupled to a quantum mechanical environment. Starting from the microscopic description, we derive a system of coupled relaxation equations within the adiabatic approximation. These are valid for arbitrary I and also for a general stationary non--equilibrium state of the environment. In the case of equilibrium, the stationary solution of the equations becomes the correct Boltzmannian equilibrium distribution for given spin I. The relaxation towards the stationary solution is characterized by a set of relaxation times, the longest of which can be shorter, by a factor of up to 2I, than the relaxation time in the corresponding Bloch equations calculated in the standard perturbative way.Comment: 4 pages, Latex, 2 figure

An Improved Implementation and Abstract Interface for Hybrid

Hybrid is a formal theory implemented in Isabelle/HOL that provides an interface for representing and reasoning about object languages using higher-order abstract syntax (HOAS). This interface is built around an HOAS variable-binding operator that is constructed definitionally from a de Bruijn index representation. In this paper we make a variety of improvements to Hybrid, culminating in an abstract interface that on one hand makes Hybrid a more mathematically satisfactory theory, and on the other hand has important practical benefits. We start with a modification of Hybrid's type of terms that better hides its implementation in terms of de Bruijn indices, by excluding at the type level terms with dangling indices. We present an improved set of definitions, and a series of new lemmas that provide a complete characterization of Hybrid's primitives in terms of properties stated at the HOAS level. Benefits of this new package include a new proof of adequacy and improvements to reasoning about object logics. Such proofs are carried out at the higher level with no involvement of the lower level de Bruijn syntax.Comment: In Proceedings LFMTP 2011, arXiv:1110.668

Denial at the top table: status attributions and implications for marketing

Senior marketing management is seldom represented on the Board of Directors nowadays, reflecting a deteriorating status of the marketing profession. We examine some of the key reasons for marketing’s demise, and discuss how the status of marketing may be restored by demonstrating the value of marketing to the business community. We attribute marketing’s demise to several related key factors: narrow typecasting, marginalisation and limited involvement in product development, questionable marketing curricula, insensitivity toward environmental change, questionable professional standards and roles, and marketing’s apparent lack of accountability to CEOs. Each of these leads to failure to communicate, create, or deliver value within marketing. We argue that a continued inability to deal with marketing’s crisis of representation will further erode the status of the discipline both academically and professionally

Different Transport Pathways of Individual Precursor Proteins in Mitochondria

Transport of mitochondrial precursor proteins into mitochondria of Neurospora crassa was studied in a cellfree reconstituted system. Precursors were synthesized in a reticulocyte lysate programmed with Neurospora mRNA and transported into isolated mitochondria in the absence of protein synthesis. Uptake of the following precursors was investigated: apocytochrome c, ADP/ATP carrier and subunit 9 of the oligomycin-sensitive ATPase. Addition of high concentrations of unlabelled chemically prepared apocytochrome c (1–10 μM) inhibited the appearance in the mitochondrial of labelled cytochrome c synthesized in vitro because the unlabelled protein dilutes the labelled one and because the translocation system has a limited capacity [apparent V is 1–3 pmol × min−1× (mg mitochondrial protein)−1]. Concentrations of added apocytochrome c exceeding the concentrations of precursor proteins synthesized in vitro by a factor of about 104 did not inhibit the transfer of ADP/ATP carrier or ATPase subunit 9 into mitochondria. Carbonylcyanide m-chlorophenylhydrazone, an uncoupler of oxidative phosphorylation, inhibited transfer in vitro of ADP/ATP carrier and of ATPase subunit 9, but not of cytochrome c. These findings suggest that cytochrome c and the other two proteins have different import pathways into mitochondria. It can be inferred from the data presented that different 'receptors' on the mitochondrial surface mediate the specific recognition of precursor proteins by mitochondria as a first step in the transport process

Changing a semantics: opportunism or courage?

The generalized models for higher-order logics introduced by Leon Henkin, and their multiple offspring over the years, have become a standard tool in many areas of logic. Even so, discussion has persisted about their technical status, and perhaps even their conceptual legitimacy. This paper gives a systematic view of generalized model techniques, discusses what they mean in mathematical and philosophical terms, and presents a few technical themes and results about their role in algebraic representation, calibrating provability, lowering complexity, understanding fixed-point logics, and achieving set-theoretic absoluteness. We also show how thinking about Henkin's approach to semantics of logical systems in this generality can yield new results, dispelling the impression of adhocness. This paper is dedicated to Leon Henkin, a deep logician who has changed the way we all work, while also being an always open, modest, and encouraging colleague and friend.Comment: 27 pages. To appear in: The life and work of Leon Henkin: Essays on his contributions (Studies in Universal Logic) eds: Manzano, M., Sain, I. and Alonso, E., 201

Spectroscopic and Mechanistic Studies of Heterodimetallic Forms of Metallo-β-lactamase NDM-1

In an effort to characterize the roles of each metal ion in metallo-β-lactamase NDM-1, heterodimetallic analogues (CoCo-, ZnCo-, and CoCd-) of the enzyme were generated and characterized. UV–vis, 1H NMR, EPR, and EXAFS spectroscopies were used to confirm the fidelity of the metal substitutions, including the presence of a homogeneous, heterodimetallic cluster, with a single-atom bridge. This marks the first preparation of a metallo-β-lactamase selectively substituted with a paramagnetic metal ion, Co(II), either in the Zn1 (CoCd-NDM-1) or in the Zn2 site (ZnCo-NDM-1), as well as both (CoCo-NDM-1). We then used these metal-substituted forms of the enzyme to probe the reaction mechanism, using steady-state and stopped-flow kinetics, stopped-flow fluorescence, and rapid-freeze-quench EPR. Both metal sites show significant effects on the kinetic constants, and both paramagnetic variants (CoCd- and ZnCo-NDM-1) showed significant structural changes on reaction with substrate. These changes are discussed in terms of a minimal kinetic mechanism that incorporates all of the data

SHV Lactamase Engineering Database: a reconciliation tool for SHV β-lactamases in public databases

<p>Abstract</p> <p>Background</p> <p>SHV β-lactamases confer resistance to a broad range of antibiotics by accumulating mutations. The number of SHV variants is steadily increasing. 117 SHV variants have been assigned in the SHV mutation table (<url>http://www.lahey.org/Studies/</url>). Besides, information about SHV β-lactamases can be found in the rapidly growing NCBI protein database. The SHV β-Lactamase Engineering Database (SHVED) has been developed to collect the SHV β-lactamase sequences from the NCBI protein database and the SHV mutation table. It serves as a tool for the detection and reconciliation of inconsistencies, and for the identification of new SHV variants and amino acid substitutions.</p> <p>Description</p> <p>The SHVED contains 200 protein entries with distinct sequences and 20 crystal structures. 83 protein sequences are included in the both the SHV mutation table and the NCBI protein database, while 35 and 82 protein sequences are only in the SHV mutation table and the NCBI protein database, respectively. Of these 82 sequences, 41 originate from microbial sources, and 22 of them are full-length sequences that harbour a mutation profile which has not been classified yet in the SHV mutation table. 27 protein entries from the NCBI protein database were found to have an inconsistency in SHV name identification. These inconsistencies were reconciled using information from the SHV mutation table and stored in the SHVED.</p> <p>The SHVED is accessible at <url>http://www.LacED.uni-stuttgart.de/classA/SHVED/</url>. It provides sequences, structures, and a multisequence alignment of SHV β-lactamases with the corrected annotation. Amino acid substitutions at each position are also provided. The SHVED is updated monthly and supplies all data for download.</p> <p>Conclusions</p> <p>The SHV β-Lactamase Engineering Database (SHVED) contains information about SHV variants with reconciled annotation. It serves as a tool for detection of inconsistencies in the NCBI protein database, helps to identify new mutations resulting in new SHV variants, and thus supports the investigation of sequence-function relationships of SHV β-lactamases.</p