Publications by authors named "Gary Jones"

157 Publications

Identification of active deubiquitinases in the chicken tissues.

Proteomics 2021 Oct 13:e2100122. Epub 2021 Oct 13.

Department of Microbiology and Cell Science, College of Agricultural and Life Sciences, University of Florida, Gainesville, USA.

The existing protein annotation in chicken is mostly limited to computational predictions based on orthology to other proteins, which often leads to a significant underestimation of the function of these proteins. Genome-scale experimental annotation can provide insight into the actual enzymatic activities of chicken proteins. Amongst post-translational modifications, ubiquitination is of interest as anomalies in ubiquitination are implicated in such diseases as inflammatory disorders, infectious diseases, or malignancies. Ubiquitination is controlled by deubiquitinases (DUBs), which remove ubiquitin from protein substrates. However, the DUBs have not been systematically annotated and quantified in chicken tissues. Here we used a chemoproteomics approach, which is based on active-site probes specific to DUBs, and identified 26 active DUBs in the chicken spleen, cecum, and liver.
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http://dx.doi.org/10.1002/pmic.202100122DOI Listing
October 2021

California sea lions employ task-specific strategies for active touch sensing.

J Exp Biol 2021 Oct 5. Epub 2021 Oct 5.

Faculty of Science and Engineering, Manchester Metropolitan University, Chester Street, Manchester, M1 5GD, UK.

Active sensing is the process of moving sensors to extract task-specific information. Whisker touch is often referred to as an active sensory system since whiskers are moved with purposeful control. Even though whisker movements are found in many species, it is unknown if any animal can make task-specific movements with their whiskers. California sea lions (Zalophus californianus) make large, purposeful whisker movements and are capable of performing many whisker-related discrimination tasks. Therefore, California sea lions are an ideal species to explore the active nature of whisker touch sensing. Here, we show that California sea lions can make task-specific whisker movements. California sea lions move their whiskers with large amplitudes around object edges to judge size, make smaller, lateral stroking movements to judge texture and make very small whisker movements during a visual task. These findings, combined with the ease of training mammals and measuring whisker movements, makes whiskers an ideal system for studying mammalian perception, cognition and motor control.
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http://dx.doi.org/10.1242/jeb.243085DOI Listing
October 2021

Concurrent visual learning of adjacent and nonadjacent dependencies in adults and children.

Dev Psychol 2021 May;57(5):733-748

Department of Psychology, Nottingham Trent University.

Concurrent learning of adjacent and nonadjacent dependencies has been shown in adults only. This study extended this line of research by examining dependency-specific learning for both adjacent and nonadjacent dependencies concurrently in both adults and children. Seventy adults aged 18 to 64 (40 women, 30 men; Experiment 1) and 64 children aged 10 to 11 years (40 girls, 24 boys; Experiment 2) were tested with a new serial reaction time (SRT) task in which they were trained for 5-8 min on materials comprising equally probable adjacent and nonadjacent dependencies. They were then asked to discriminate between trained and untrained dependencies in a familiarity task. Both adults and children showed implicit concurrent learning of both adjacent and nonadjacent dependencies. The two dependency types were learned to the same extent. However, adults showed a rapid, sustainable, and dependency-specific sensitivity throughout the SRT task while children only showed a dependency-specific sensitivity to violations of expectations after exposure. When the two groups were statistically compared, only adults showed a dependency-specific learning effect after exposure. These findings are in line with the age-related improvement model of dependency learning. (PsycInfo Database Record (c) 2021 APA, all rights reserved).
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http://dx.doi.org/10.1037/dev0000998DOI Listing
May 2021

Practice patterns of corneal transplantation in Europe: first report by the European Cornea and Cell Transplantation Registry.

J Cataract Refract Surg 2021 Jul;47(7):865-869

From the University Eye Clinic, Maastricht University Medical Center+, The Netherlands (Dunker, Nuijts, Dickman); Translational Health Sciences, University of Bristol, United Kingdom (Armitage); Tissue and Eye Services, NHS Blood and Transplant, Bristol, United Kingdom (Armitage); European Eye Bank Association, Venice, Italy (Armitage, Jones); Department of Ophthalmology, Sahlgrenska University Hospital, Gothenburg, Sweden (Armitage); European Society of Cataract and Refractive Surgeons, Dublin, Ireland (Brocato, Nuijts, Lundström); Department of Ophthalmology, Royal Victoria Infirmary and Newcastle University, Newcastle upon Tyne, United Kingdom (Figueiredo); Dutch Transplant Foundation, Leiden, The Netherlands (Heemskerk, Konijn); Department of Ophthalmology, Aarhus University Hospital, Denmark (Hjortdal); European Society of Cornea and Ocular Surface Disease Specialists, Dublin, Ireland (Hjortdal); The Veneto Eye Bank Foundation, Venice, Italy (Jones); Department of Clinical Sciences, Ophthalmology, Faculty of Medicine, Lund University, Lund, Sweden (Lundström).

Purpose: To report practice patterns of corneal transplantation in Europe.

Setting: Corneal clinics in 10 European member states (MS), the United Kingdom, and Switzerland.

Design: Multinational registry study.

Methods: Corneal transplant procedures registered in the European Cornea and Cell Transplantation Registry were identified. Preoperative donor and recipient characteristics, indication and reason for transplantation, and surgical techniques were analyzed.

Results: A total of 12 913 corneal transplants were identified from 10 European Union MS, the United Kingdom, and Switzerland. Most countries were self-sufficient with regard to donor tissue. Fuchs endothelial corneal dystrophy was the most common indication (41%, n = 5325), followed by regraft (16%, n = 2108), pseudophakic bullous keratopathy (12%, n = 1594), and keratoconus (12%, n = 1506). Descemet stripping automated endothelial keratoplasty (DSAEK, 46%, n = 5918) was the most commonly performed technique, followed by penetrating keratoplasty (30%, n = 3886) and Descemet membrane endothelial keratoplasty (9%, n = 1838). Vision improvement was the main reason for corneal transplantation (90%, n = 11 591). Surgical technique and reason for transplantation differed between indications.

Conclusions: This report provides the most comprehensive overview of corneal transplantation practice patterns in Europe to date. Fuchs endothelial dystrophy is the most common indication, vision improvement the leading reason, and DSAEK the predominant technique for corneal transplantation.
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http://dx.doi.org/10.1097/j.jcrs.0000000000000574DOI Listing
July 2021

Defining the mechanism of PDI interaction with disulfide-free amyloidogenic proteins: Implications for exogenous protein expression and neurodegenerative disease.

Int J Biol Macromol 2021 Mar 28;174:175-184. Epub 2021 Jan 28.

School of Life Science, Liaoning University, Shenyang 110036, China. Electronic address:

Protein disulfide isomerase (PDI) is an important molecular chaperone capable of facilitating protein folding in addition to catalyzing the formation of a disulfide bond. To better understand the distinct substrate-screening principles of Pichia pastoris PDI (Protein disulfide isomerase) and the protective role of PDI in amyloidogenic diseases, we investigated the expression abundance and intracellular retention levels of three archetypal amyloidogenic disulfide bond-free proteins (Aβ42, α-synuclein (α-Syn) and SAA1) in P. pastoris GS115 strain without and with the overexpression of PpPDI (P. pastoris PDI). Intriguingly, amyloidogenic Aβ42 and α-Syn were detected only as intracellular proteins whereas amyloidogenic SAA1 was detected both as intracellular and extracellular proteins when these proteins were expressed in the PpPDI-overexpressing GS115 strain. The binding between PpPDI and each of the three amyloidogenic proteins was investigated by molecular docking and simulations. Three different patterns of PpPDI-substrate complexes were observed, suggesting that multiple modes of binding might exist for the binding between PpPDI and its amyloidogenic protein substrates, and this could represent different specificities and affinities of PpPDI toward its substrates. Further analysis of the proteomics data and functional annotations indicated that PpPDI could eliminate the need for misfolded proteins to be partitioned in ER-associated compartments.
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http://dx.doi.org/10.1016/j.ijbiomac.2021.01.172DOI Listing
March 2021

Mutational analysis of the Hsp70 substrate-binding domain: Correlating molecular-level changes with in vivo function.

Mol Microbiol 2021 06 4;115(6):1262-1276. Epub 2021 Jan 4.

Department of Biology, Maynooth University, Maynooth, Ireland.

Hsp70 is an evolutionarily conserved chaperone involved in maintaining protein homeostasis during normal growth and upon exposure to stresses. Mutations in the β6/β7 region of the substrate-binding domain (SBD) disrupt the SBD hydrophobic core resulting in impairment of the heat-shock response and prion propagation in yeast. To elucidate the mechanisms behind Hsp70 loss of function due to disruption of the SBD, we undertook targeted mutational analysis of key residues in the β6/β7 region. We demonstrate the critical functional role of the F475 residue across yeast cytosolic Hsp70-Ssa family. We identify the size of the hydrophobic side chain at 475 as the key factor in maintaining SBD stability and functionality. The introduction of amino acid variants to either residue 475, or close neighbor 483, caused instability and cleavage of the Hsp70 SBD and subsequent degradation. Interestingly, we found that Hsp70-Ssa cleavage may occur through a vacuolar carboxypeptidase (Pep4)-dependent mechanism rather than proteasomal. Mutations at 475 and 483 result in compromised ATPase function, which reduces protein re-folding activity and contributes to depletion of cytosolic Hsp70 in vivo. The combination of reduced functionality and stability of Hsp70-Ssa results in yeast cells that are compromised in their stress response and cannot propagate the [PSI ] prion.
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http://dx.doi.org/10.1111/mmi.14671DOI Listing
June 2021

Outcomes of corneal transplantation in Europe: report by the European Cornea and Cell Transplantation Registry.

J Cataract Refract Surg 2021 06;47(6):780-785

From the University Eye Clinic, Maastricht University Medical Center+, The Netherlands (Dunker, Nuijts, Dickman); Translational Health Sciences, University of Bristol, UK (W.J. Armitage); Tissue and Eye Services, NHS Blood and Transplant, Bristol, UK (W.J. Armitage); European Eye Bank Association (EEBA), Venice, Italy (W.J. Armitage, Jones); Department of Ophthalmology, Sahlgrenska University Hospital, Gothenburg, Sweden (M. Armitage); European Society of Cataract and Refractive Surgeons (ESCRS), Dublin, Ireland (Brocato, Lundström); Department of Ophthalmology, Royal Victoria Infirmary and Newcastle University, Newcastle upon Tyne, UK (Figueiredo); Dutch Transplant Foundation, Leiden, The Netherlands (Heemskerk); Department of Ophthalmology, Aarhus University Hospital, Denmark (Hjortdal); European Society of Cornea and Ocular Surface Disease Specialists (EuCornea), Dublin, Ireland (Hjortdal); The Veneto Eye Bank Foundation, Venice, Italy (Jones); Department of Clinical Sciences, Ophthalmology, Faculty of Medicine, Lund University, Lund, Sweden (Lundström).

Purpose: To analyze real-world graft survival and visual acuity outcomes of corneal transplantation in Europe.

Setting: Corneal clinics in 10 European Union member states, the United Kingdom, and Switzerland.

Design: Multinational registry study.

Methods: All corneal transplant procedures registered in the European Cornea and Cell Transplantation Registry (ECCTR) were identified. Graft survival of primary corneal transplants were analyzed using Kaplan-Meier survival curves with log-rank test and Cox regression. Corrected distance visual acuities (CDVAs) are reported at baseline and 2 years postoperatively using the Lundström distribution matrix.

Results: A total of 12 913 corneal transplants were identified. Overall, 32-year graft survival of corneal transplants was high (89%) but differed between indications, ranging from 98% in keratoconus and 80% for trauma. Overall, CDVA improved postoperatively, but the risk for losing vision ranged from 7% (baseline vision ≤0.1 Snellen) to 58% (baseline vision ≥1.0 Snellen).

Conclusions: This report provides a comprehensive overview of graft survival and visual outcomes of corneal transplantation in Europe. In addition, it provides real-world estimates of outcomes for a variety of indications and surgical techniques to support benchmarking and demonstrates the relationship between baseline and postoperative vision.
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http://dx.doi.org/10.1097/j.jcrs.0000000000000520DOI Listing
June 2021

One threat, different answers: the impact of COVID-19 pandemic on cornea donation and donor selection across Europe.

Br J Ophthalmol 2020 Nov 26. Epub 2020 Nov 26.

University Eye Clinic Maastricht, Maastricht University Medical Centre+, Maastricht, The Netherlands.

Objectives: To assess to which extent the COVID-19 pandemic affected corneal transplantation by virtue of donor selection algorithms in different European countries.

Design: Survey.

Setting: 110 eye banks in 26 European countries.

Participants: 64 eye banks covering 95% of European corneal transplantation activity.

Interventions: A questionnaire listing the number of corneas procured and distributed from February to May 2018-2020 was circulated to eye banks.

Main Outcome Measures: The primary outcome was the number of corneal procurements. Additional outcomes were national algorithms for donor selection, classified according to their stringency (donors with COVID-19 history, suspected for COVID-19, asymptomatic, PCR testing) and the pandemic severity in each country. We calculated Spearman's correlation coefficient to determine, two by two, the relationship between the 3-month decline in eye banking activity (procurement), the stringency of donor selection algorithm and the grading of pandemic severity (cases and deaths). A partial correlation was run to determine the relationship between decline and stringency while controlling for pandemic severity.

Results: Procurements decreased by 38%, 68% and 41%, respectively, in March, April and May 2020 compared with the mean of the previous 2 years, while grafts decreased, respectively, by 28%, 68% and 56% corresponding to 3866 untreated patients in 3 months. Significant disparities between countries and the decrease in activity correlated with stringency in donor selection independent of pandemic severity.

Conclusions: Our data demonstrate significant differences between countries regarding donor screening algorithms based on precautionary principles and, consequently, a decrease in the donor pool, already constrained by a long list of contraindications. Fundamental studies are needed to determine the risk of SARS-CoV-2 transmission by corneal transplantation and guide evidence-based recommendations for donor selection to justify their substantial medical and economic impact.
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http://dx.doi.org/10.1136/bjophthalmol-2020-317938DOI Listing
November 2020

Impact of COVID-19 on corneal donation and distribution.

Eur J Ophthalmol 2020 Aug 5:1120672120948746. Epub 2020 Aug 5.

Fondazione Banca degli Occhi del Veneto Onlus, Mestre, Venice, Italy.

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http://dx.doi.org/10.1177/1120672120948746DOI Listing
August 2020

Two-year-old children's processing of two-word sequences occurring 19 or more times per million and their influence on subsequent word learning.

J Exp Child Psychol 2020 11 20;199:104922. Epub 2020 Jul 20.

Georg-August-Universität Göttingen, 37073 Göttingen, Germany; Leibniz Science Campus Primate Cognition, 37077 Göttingen, Germany; Center for Brain and Cognition, 08018 Barcelona, Spain.

We know that 8-month-old infants track the statistical properties of a series of syllables and that 2- and 3-year-old children process familiar phrases more efficiently than unfamiliar phrases, but less is known about the intermediary level of two-word sequences. In Study 1, 2-year-olds (N = 45, mean age = 651 days) heard two-word sequences consisting of a prime word followed by a noun, with two pictures appearing on the screen (depicting the noun and a distractor). Eye tracking showed that children looked more quickly at the noun picture for two-word sequences occurring an average of 19 times per million and 206 times per million in child-directed speech than for novel sequences. In Study 2, corpus analyses showed that 2-year-olds' noun learning increased in line with the frequency of the two-word sequence that preceded it in caregiver speech utterances. This effect holds even after controlling nouns for frequency in caregiver speech, phonemic length, neighborhood density, phonotactic probability, and concreteness and after removing nouns produced in isolation by caregivers and nouns produced by children before being produced by caregivers. These studies show that young children's language processing is facilitated by known two-word sequences, allowing children to focus on more novel aspects of the utterance. Such efficiencies are far-reaching because nearly two thirds of child-directed utterances contain two-word sequences with frequencies of 19 or more per million.
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http://dx.doi.org/10.1016/j.jecp.2020.104922DOI Listing
November 2020

Does short-term memory develop?

Cognition 2020 05 28;198:104200. Epub 2020 Jan 28.

Cardiff University, UK.

Such is the consistency by which performance on measures of short-term memory (STM) increase with age that developmental increases in STM capacity are largely accepted as fact. However, our analysis of a robust but almost ignored finding - that span for digit sequences (the traditional measure of STM) increases at a far greater rate than span for other verbal material - fundamentally undermines the assumption that increased performance in STM tasks is underpinned by developmental increases in capacity. We show that this digit superiority with age effect is explained by the relatively greater linguistic exposure to random sequences of digits versus other stimuli such as words. A simple associative learning process that learns incrementally from exposure to language accounts for the effect, without any need to invoke an STM mechanism, much less one that increases in capacity with age. By extension, using corpus data directed at 2-3 year old children, 4-6 year old children, and adults, we show that age-related performance increases with other types of verbal material are equally driven by the same basic associative learning process operating on the expanding exposure to language experienced by the child. Our results question the idea that tests such as digit span are measuring a dedicated system for the temporary maintenance and manipulation of verbal material, and as such have implications for our understanding of those aspects of typical and atypical development that are usually accounted for with respect to the operation of such a system.
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http://dx.doi.org/10.1016/j.cognition.2020.104200DOI Listing
May 2020

Involvement of Sulfur in the Biosynthesis of Essential Metabolites in Pathogenic Fungi of Animals, Particularly spp.: Molecular and Therapeutic Implications.

Front Microbiol 2019 13;10:2859. Epub 2019 Dec 13.

Department of Biology, Maynooth University, Maynooth, Ireland.

Fungal sulfur uptake is required for incorporation into the sidechains of the amino acids cysteine and methionine, and is also essential for the biosynthesis of the antioxidant glutathione (GSH), -adenosylmethionine (SAM), the key source of methyl groups in cellular transmethylation reactions, and -adenosylhomocysteine (SAH). Biosynthesis of redox-active gliotoxin in the opportunistic fungal pathogen has been elucidated over the past 10 years. Some fungi which produce gliotoxin-like molecular species have undergone unexpected molecular rewiring to accommodate this high-risk biosynthetic process. Specific disruption of gliotoxin biosynthesis, via deletion of , which encodes a γ-glutamyl cyclotransferase, leads to elevated intracellular antioxidant, ergothioneine (EGT), levels, and confirms crosstalk between the biosynthesis of both sulfur-containing moieties. Gliotoxin is ultimately formed by gliotoxin oxidoreductase GliT-mediated oxidation of dithiol gliotoxin (DTG). In fact, DTG is a substrate for both GliT and a -thiomethyltransferase, GtmA. GtmA converts DTG to bisdethiobis(methylthio)gliotoxin (BmGT), using 2 mol SAM and resultant SAH must be re-converted to SAM via the action of the Methyl/Met cycle. In the absence of GliT, DTG fluxes via GtmA to BmGT, which results in both SAM depletion and SAH overproduction. Thus, the negative regulation of gliotoxin biosynthesis via GtmA must be counter-balanced by GliT activity to avoid Methyl/Met cycle dysregulation, SAM depletion and consequences on global cellular biochemistry in . DTG also possesses potent Zn chelation properties which positions this sulfur-containing metabolite as a putative component of the Zn homeostasis system within fungi. EGT plays an essential role in high-level redox homeostasis and its presence requires significant consideration in future oxidative stress studies in pathogenic filamentous fungi. In certain filamentous fungi, sulfur is additionally indirectly required for the formation of EGT and the disulfide-bridge containing non-ribosomal peptide, gliotoxin, and related epipolythiodioxopiperazines. Ultimately, interference with emerging sulfur metabolite functionality may represent a new strategy for antifungal drug development.
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http://dx.doi.org/10.3389/fmicb.2019.02859DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6923255PMC
December 2019

Rapid deacetylation of yeast Hsp70 mediates the cellular response to heat stress.

Sci Rep 2019 11 7;9(1):16260. Epub 2019 Nov 7.

Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, USA.

Hsp70 is a highly conserved molecular chaperone critical for the folding of new and denatured proteins. While traditional models state that cells respond to stress by upregulating inducible HSPs, this response is relatively slow and is limited by transcriptional and translational machinery. Recent studies have identified a number of post-translational modifications (PTMs) on Hsp70 that act to fine-tune its function. We utilized mass spectrometry to determine whether yeast Hsp70 (Ssa1) is differentially modified upon heat shock. We uncovered four lysine residues on Ssa1, K86, K185, K354 and K562 that are deacetylated in response to heat shock. Mutation of these sites cause a substantial remodeling of the Hsp70 interaction network of co-chaperone partners and client proteins while preserving essential chaperone function. Acetylation/deacetylation at these residues alter expression of other heat-shock induced chaperones as well as directly influencing Hsf1 activity. Taken together our data suggest that cells may have the ability to respond to heat stress quickly though Hsp70 deacetylation, followed by a slower, more traditional transcriptional response.
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http://dx.doi.org/10.1038/s41598-019-52545-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6838335PMC
November 2019

Not quite the SSAme: unique roles for the yeast cytosolic Hsp70s.

Curr Genet 2019 Oct 24;65(5):1127-1134. Epub 2019 Apr 24.

Department of Biological Sciences, The University of North Carolina At Charlotte, Charlotte, NC, 28223, USA.

The Heat Shock Protein 70s (Hsp70s) are an essential family of proteins involved in folding of new proteins and triaging of damaged proteins for proteasomal-mediated degradation. They are highly conserved in all organisms, with each organism possessing multiple highly similar Hsp70 variants (isoforms). These isoforms have been previously thought to be identical in function differing only in their spatio-temporal expression pattern. The model organism Saccharomyces cerevisiae (baker's yeast) expresses four Hsp70 isoforms Ssa1, 2, 3 and 4. Here, we review recent findings that suggest that despite their similarity, Ssa isoforms may have unique cellular functions.
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http://dx.doi.org/10.1007/s00294-019-00978-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7262668PMC
October 2019

Visual Speech Benefit in Clear and Degraded Speech Depends on the Auditory Intelligibility of the Talker and the Number of Background Talkers.

Trends Hear 2019 Jan-Dec;23:2331216519837866

1 Department of Psychology, Nottingham Trent University, UK.

Perceiving speech in background noise presents a significant challenge to listeners. Intelligibility can be improved by seeing the face of a talker. This is of particular value to hearing impaired people and users of cochlear implants. It is well known that auditory-only speech understanding depends on factors beyond audibility. How these factors impact on the audio-visual integration of speech is poorly understood. We investigated audio-visual integration when either the interfering background speech (Experiment 1) or intelligibility of the target talkers (Experiment 2) was manipulated. Clear speech was also contrasted with sine-wave vocoded speech to mimic the loss of temporal fine structure with a cochlear implant. Experiment 1 showed that for clear speech, the visual speech benefit was unaffected by the number of background talkers. For vocoded speech, a larger benefit was found when there was only one background talker. Experiment 2 showed that visual speech benefit depended upon the audio intelligibility of the talker and increased as intelligibility decreased. Degrading the speech by vocoding resulted in even greater benefit from visual speech information. A single "independent noise" signal detection theory model predicted the overall visual speech benefit in some conditions but could not predict the different levels of benefit across variations in the background or target talkers. This suggests that, similar to audio-only speech intelligibility, the integration of audio-visual speech cues may be functionally dependent on factors other than audibility and task difficulty, and that clinicians and researchers should carefully consider the characteristics of their stimuli when assessing audio-visual integration.
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http://dx.doi.org/10.1177/2331216519837866DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6435873PMC
November 2019

Using steered molecular dynamics to study the interaction between ADP and the nucleotide-binding domain of yeast Hsp70 protein Ssa1.

J Comput Aided Mol Des 2018 11 3;32(11):1217-1227. Epub 2018 Nov 3.

School of Environmental Science, College of Environment, Liaoning University, No. 66 Chongshan Middle Road, Huanggu District, Shenyang, 110036, Liaoning, China.

Genetics experiments have identified six mutations located in the subdomain IA (A17V, R23H, G32D, G32S, R34K, V372I) of Ssa1 that influence propagation of the yeast [PSI] prion. However, the underlining molecular mechanisms of these mutations are still unclear. The six mutation sites are present in the IA subdomain of the nucleotide-binding domain (NBD). The ATPase subdomain IA is a critical mediator of inter-domain allostery in Hsp70 molecular chaperones, so the mutation and changes in this subdomain may influence the function of the substrate-binding domain. In addition, ADP release is a rate-limiting step of the ATPase cycle and dysregulation of the ATPase cycle influences the propagation of the yeast [PSI] prion. In this work, steered molecular dynamics (SMD) simulations were performed to explore the interaction between ADP and NBD. Results suggest that during the SMD simulations, hydrophobic interactions are predominant and variations in the binding state of ADP within the mutants is a potential reason for in vivo effects on yeast [PSI] prion propagation. Additionally, we identify the primary residues in the ATPase domain that directly constitute the main hydrophobic interaction network and directly influence the ADP interaction state with the NBD of Ssa1. Furthermore, this in silico analysis reaffirms the importance of previously experimentally-determined residues in the Hsp70 ATPase domain involved in ADP binding and also identifies new residues potentially involved in this process.
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http://dx.doi.org/10.1007/s10822-018-0136-8DOI Listing
November 2018

The C-terminal GGAP motif of Hsp70 mediates substrate recognition and stress response in yeast.

J Biol Chem 2018 11 18;293(46):17663-17675. Epub 2018 Sep 18.

From the National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China. Electronic address:

The allosteric coupling of the highly conserved nucleotide- and substrate-binding domains of Hsp70 has been studied intensively. In contrast, the role of the disordered, highly variable C-terminal region of Hsp70 remains unclear. In many eukaryotic Hsp70s, the extreme C-terminal EEVD motif binds to the tetratricopeptide-repeat domains of Hsp70 co-chaperones. Here, we discovered that the TVEEVD sequence of cytoplasmic Hsp70 (Ssa1) functions as a SUMO-interacting motif. A second C-terminal motif of ∼15 amino acids between the α-helical lid and the extreme C terminus, previously identified in bacterial and eukaryotic organellar Hsp70s, is known to enhance chaperone function by transiently interacting with folding clients. Using structural analysis, interaction studies, fibril formation assays, and functional assays, we investigated the individual contributions of the α-helical bundle and the C-terminal disordered region of Ssa1 in the inhibition of fibril formation of the prion protein Ure2. Our results revealed that although the α-helical bundle of the Ssa1 substrate-binding domain (SBDα) does not directly bind to Ure2, the SBDα enhances the ability of Hsp70 to inhibit fibril formation. We found that a 20-residue C-terminal motif in Ssa1, containing GGAP and GGAP-like tetrapeptide repeats, can directly bind to Ure2, the Hsp40 co-chaperone Ydj1, and α-synuclein, but not to the SUMO-like protein SMT3 or BSA. Deletion or substitution of the Ssa1 GGAP motif impaired yeast cell tolerance to temperature and cell-wall damage stress. This study highlights that the C-terminal GGAP motif of Hsp70 is important for substrate recognition and mediation of the heat shock response.
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http://dx.doi.org/10.1074/jbc.RA118.002691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6240856PMC
November 2018

The same but different: the role of Hsp70 in heat shock response and prion propagation.

Prion 2018 16;12(3-4):170-174. Epub 2018 Aug 16.

d Centre for Biomedical Science Research, School of Clinical and Applied Sciences , Leeds Beckett University , Leeds , UK.

The Hsp70 chaperone machinery is a key component of the heat-shock response and a modulator of prion propagation in yeast. A major factor in optimizing Hsp70 function is the highly coordinated activities of the nucleotide-binding and substrate-binding domains of the protein. Hsp70 inter-domain communication occurs through a bidirectional allosteric interaction network between the two domains. Recent findings identified the β6/β7 region of the substrate-binding domain as playing a critical role in optimizing Hsp70 function in both the stress response and prion propagation and highlighted the allosteric interaction interface between the domains. Importantly, while functional changes in Hsp70 can result in phenotypic consequences for both the stress response and prion propagation, there can be significant differences in the levels of phenotypic impact that such changes illicit.
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http://dx.doi.org/10.1080/19336896.2018.1507579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277183PMC
February 2019

Systems impact of zinc chelation by the epipolythiodioxopiperazine dithiol gliotoxin in Aspergillus fumigatus: a new direction in natural product functionality.

Metallomics 2018 06;10(6):854-866

Department of Biology, Maynooth University, Co. Kildare, Ireland.

The non-ribosomal peptide gliotoxin, which autoinduces its own biosynthesis, has potent anti-fungal activity, especially in the combined absence of the gliotoxin oxidoreductase GliT and bis-thiomethyltransferase GtmA. Dithiol gliotoxin (DTG) is a substrate for both of these enzymes. Herein we demonstrate that DTG chelates Zn2+ (m/z 424.94), rapidly chelates Zn2+ from Zn(4-(2-pyridylazo)-resorcinol) (Zn(PAR)2) and also inhibits a Zn2+-dependent alkaline phosphatase (AP). Zn2+ addition rescues AP function following DTG-associated inhibition, and pre-incubation of DTG with Zn2+ completely protects AP activity. Zn2+ (1-50 μM) also significantly relieves the potent gliotoxin-mediated inhibition of Aspergillus fumigatus ΔgliT::ΔgtmA (p < 0.05), which infers in vivo dithiol gliotoxin-mediated sequestration of free Zn2+ or chelation from intracellular metalloenzymes as inhibitory mechanisms. Quantitative proteomic analysis revealed that excess Zn2+ alters the effect of gliotoxin on A. fumigatus ΔgliT, with differential abundance of secondary metabolism-associated proteins in the combinatorial condition. GtmA abundance increased 18.8 fold upon co-addition of gliotoxin and Zn2+ compared to gliotoxin alone, possibly to compensate for disruption to GtmA activity, as seen in in vitro assays. Furthermore, DTG effected significant in vitro aggregation of a number of protein classes, including Zn2+-dependent enzymes, while proteins were protected from aggregation by pre-incubating DTG with Zn2+. We conclude that DTG can act in vivo as a Zn2+ chelator, which can significantly impede A. fumigatus growth in the absence of GliT and GtmA.
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http://dx.doi.org/10.1039/c8mt00052bDOI Listing
June 2018

Dysregulated gliotoxin biosynthesis attenuates the production of unrelated biosynthetic gene cluster-encoded metabolites in Aspergillus fumigatus.

Fungal Biol 2018 04 18;122(4):214-221. Epub 2017 Dec 18.

Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland; Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK. Electronic address:

Gliotoxin is an epipolythiodioxopiperazine (ETP) class toxin, contains a disulfide bridge that mediates its toxic effects via redox cycling and is produced by the opportunistic fungal pathogen Aspergillus fumigatus. The gliotoxin bis-thiomethyltransferase, GtmA, attenuates gliotoxin biosynthesis in A. fumigatus by conversion of dithiol gliotoxin to bis-thiomethylgliotoxin (BmGT). Here we show that disruption of dithiol gliotoxin bis-thiomethylation functionality in A. fumigatus results in significant remodelling of the A. fumigatus secondary metabolome upon extended culture. RP-HPLC and LC-MS/MS analysis revealed the reduced production of a plethora of unrelated biosynthetic gene cluster-encoded metabolites, including pseurotin A, fumagillin, fumitremorgin C and tryprostatin B, occurs in A. fumigatus ΔgtmA upon extended incubation. Parallel quantitative proteomic analysis of A. fumigatus wild-type and ΔgtmA during extended culture revealed cognate abundance alteration of proteins encoded by relevant biosynthetic gene clusters, allied to multiple alterations in hypoxia-related proteins. The data presented herein reveal a previously concealed functionality of GtmA in facilitating the biosynthesis of other BGC-encoded metabolites produced by A. fumigatus.
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http://dx.doi.org/10.1016/j.funbio.2017.12.007DOI Listing
April 2018

The β6/β7 region of the Hsp70 substrate-binding domain mediates heat-shock response and prion propagation.

Cell Mol Life Sci 2018 Apr 9;75(8):1445-1459. Epub 2017 Nov 9.

Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.

Hsp70 is a highly conserved chaperone that in addition to providing essential cellular functions and aiding in cell survival following exposure to a variety of stresses is also a key modulator of prion propagation. Hsp70 is composed of a nucleotide-binding domain (NBD) and substrate-binding domain (SBD). The key functions of Hsp70 are tightly regulated through an allosteric communication network that coordinates ATPase activity with substrate-binding activity. How Hsp70 conformational changes relate to functional change that results in heat shock and prion-related phenotypes is poorly understood. Here, we utilised the yeast [PSI ] system, coupled with SBD-targeted mutagenesis, to investigate how allosteric changes within key structural regions of the Hsp70 SBD result in functional changes in the protein that translate to phenotypic defects in prion propagation and ability to grow at elevated temperatures. We find that variants mutated within the β6 and β7 region of the SBD are defective in prion propagation and heat-shock phenotypes, due to conformational changes within the SBD. Structural analysis of the mutants identifies a potential NBD:SBD interface and key residues that may play important roles in signal transduction between domains. As a consequence of disrupting the β6/β7 region and the SBD overall, Hsp70 exhibits a variety of functional changes including dysregulation of ATPase activity, reduction in ability to refold proteins and changes to interaction affinity with specific co-chaperones and protein substrates. Our findings relate specific structural changes in Hsp70 to specific changes in functional properties that underpin important phenotypic changes in vivo. A thorough understanding of the molecular mechanisms of Hsp70 regulation and how specific modifications result in phenotypic change is essential for the development of new drugs targeting Hsp70 for therapeutic purposes.
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http://dx.doi.org/10.1007/s00018-017-2698-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5852193PMC
April 2018

Steered molecular dynamics simulation of the binding of the bovine auxilin J domain to the Hsc70 nucleotide-binding domain.

J Mol Model 2017 Oct 23;23(11):320. Epub 2017 Oct 23.

School of Environmental Science, Liaoning University, Shenyang, 110036, China.

The Hsp70 and Hsp40 chaperone machine plays critical roles in protein folding, membrane translocation, and protein degradation by binding and releasing protein substrates in a process that utilizes ATP. The activities of the Hsp70 family of chaperones are recruited and stimulated by the J domains of Hsp40 chaperones. However, structural information on the Hsp40-Hsp70 complex is lacking, and the molecular details of this interaction are yet to be elucidated. Here we used steered molecular dynamics (SMD) simulations to investigate the molecular interactions that occur during the dissociation of the auxilin J domain from the Hsc70 nucleotide-binding domain (NBD). The changes in energy observed during the SMD simulation suggest that electrostatic interactions are the dominant type of interaction. Additionally, we found that Hsp70 mainly interacts with auxilin through the surface residues Tyr866, Arg867, and Lys868 of helix II, His874, Asp876, Lys877, Thr879, and Gln881 of the HPD loop, and Phe891, Asn895, Asp896, and Asn903 of helix III. The conservative residues Tyr866, Arg867, Lys868, His874, Asp876, Lys877, and Phe891 were also found in a previous study to be indispensable to the catalytic activity of the DnaJ J domain and the binding of it with the NBD of DnaK. The in silico identification of the importance of auxilin residues Asn895, Asp896, and Asn903 agrees with previous mutagenesis and NMR data suggesting that helix III of the J domain of the T antigen interacts with Hsp70. Furthermore, our data indicate that Thr879 and Gln881 from the HPD loop are also important as they mediate the interaction between the bovine auxilin J domain and Hsc70.
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http://dx.doi.org/10.1007/s00894-017-3453-2DOI Listing
October 2017

Long-term associative learning predicts verbal short-term memory performance.

Mem Cognit 2018 02;46(2):216-229

School of Psychology, Cardiff University, Cardiff, UK.

Studies using tests such as digit span and nonword repetition have implicated short-term memory across a range of developmental domains. Such tests ostensibly assess specialized processes for the short-term manipulation and maintenance of information that are often argued to enable long-term learning. However, there is considerable evidence for an influence of long-term linguistic learning on performance in short-term memory tasks that brings into question the role of a specialized short-term memory system separate from long-term knowledge. Using natural language corpora, we show experimentally and computationally that performance on three widely used measures of short-term memory (digit span, nonword repetition, and sentence recall) can be predicted from simple associative learning operating on the linguistic environment to which a typical child may have been exposed. The findings support the broad view that short-term verbal memory performance reflects the application of long-term language knowledge to the experimental setting.
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http://dx.doi.org/10.3758/s13421-017-0759-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5809536PMC
February 2018

Diversity not quantity in caregiver speech: Using computational modeling to isolate the effects of the quantity and the diversity of the input on vocabulary growth.

Cogn Psychol 2017 11 10;98:1-21. Epub 2017 Aug 10.

Max Planck Institute for Psycholinguistics, Netherlands; University of Liverpool, UK.

Children who hear large amounts of diverse speech learn language more quickly than children who do not. However, high correlations between the amount and the diversity of the input in speech samples makes it difficult to isolate the influence of each. We overcame this problem by controlling the input to a computational model so that amount of exposure to linguistic input (quantity) and the quality of that input (lexical diversity) were independently manipulated. Sublexical, lexical, and multi-word knowledge were charted across development (Study 1), showing that while input quantity may be important early in learning, lexical diversity is ultimately more crucial, a prediction confirmed against children's data (Study 2). The model trained on a lexically diverse input also performed better on nonword repetition and sentence recall tests (Study 3) and was quicker to learn new words over time (Study 4). A language input that is rich in lexical diversity outperforms equivalent richness in quantity for learned sublexical and lexical knowledge, for well-established language tests, and for acquiring words that have never been encountered before.
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http://dx.doi.org/10.1016/j.cogpsych.2017.07.002DOI Listing
November 2017

Molecular dynamics simulations of Hsp40 J-domain mutants identifies disruption of the critical HPD-motif as the key factor for impaired curing in vivo of the yeast prion [URE3].

J Biomol Struct Dyn 2018 May 2;36(7):1764-1775. Epub 2017 Aug 2.

a School of Environmental Science, Liaoning University , Shenyang , China.

Genetic screens using Saccharomyces cerevisiae have identified an array of Hsp40 (Ydj1p) J-domain mutants that are impaired in the ability to cure the yeast [URE3] prion through disrupting functional interactions with Hsp70. However, biochemical analysis of some of these Hsp40 J-domain mutants has so far failed to provide major insight into the specific functional changes in Hsp40-Hsp70 interactions. To explore the detailed structural and dynamic properties of the Hsp40 J-domain, 20 ns molecular dynamic simulations of 4 mutants (D9A, D36A, A30T, and F45S) and wild-type J-domain were performed, followed by Hsp70 docking simulations. Results demonstrated that although the Hsp70 interaction mechanism of the mutants may vary, the major structural change was targeted to the critical HPD motif of the J-domain. Our computational analysis fits well with previous yeast genetics studies regarding highlighting the importance of J-domain function in prion propagation. During the molecular dynamics simulations several important residues were identified and predicted to play an essential role in J-domain structure. Among these residues, Y26 and F45 were confirmed, using both in silico and in vivo methods, as being critical for Ydj1p function.
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http://dx.doi.org/10.1080/07391102.2017.1334594DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6312664PMC
May 2018

Aspergillus fumigatus protein phosphatase PpzA is involved in iron assimilation, secondary metabolite production, and virulence.

Cell Microbiol 2017 12 17;19(12). Epub 2017 Aug 17.

Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.

Metal restriction imposed by mammalian hosts during an infection is a common mechanism of defence to reduce or avoid the pathogen infection. Metals are essential for organism survival due to its involvement in several biological processes. Aspergillus fumigatus causes invasive aspergillosis, a disease that typically manifests in immunocompromised patients. A. fumigatus PpzA, the catalytic subunit of protein phosphatase Z (PPZ), has been recently identified as associated with iron assimilation. A. fumigatus has 2 high-affinity mechanisms of iron acquisition during infection: reductive iron assimilation and siderophore-mediated iron uptake. It has been shown that siderophore production is important for A. fumigatus virulence, differently to the reductive iron uptake system. Transcriptomic and proteomic comparisons between ∆ppzA and wild-type strains under iron starvation showed that PpzA has a broad influence on genes involved in secondary metabolism. Liquid chromatography-mass spectrometry under standard and iron starvation conditions confirmed that the ΔppzA mutant had reduced production of pyripyropene A, fumagillin, fumiquinazoline A, triacetyl-fusarinine C, and helvolic acid. The ΔppzA was shown to be avirulent in a neutropenic murine model of invasive pulmonary aspergillosis. PpzA plays an important role at the interface between iron starvation, regulation of SM production, and pathogenicity in A. fumigatus.
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http://dx.doi.org/10.1111/cmi.12770DOI Listing
December 2017

Credentialing is 15 years behind.

Authors:
Gary J Jones

Nurs Stand 2017 Jun;31(42):32

I was pleased to see the RCN inviting applications for the credentialing scheme (news, 31 May). I note the piece indicated that credentialing will provide formal recognition of high quality advanced-level nursing practice.
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http://dx.doi.org/10.7748/ns.31.42.32.s33DOI Listing
June 2017

Parental Perceptions of Obesity and Obesity Risk Associated With Childhood Acute Lymphoblastic Leukemia.

J Pediatr Hematol Oncol 2017 07;39(5):370-375

Children's Mercy Hospital, Kansas City, MO.

The prevalence of obesity and related comorbidities in survivors of childhood acute lymphoblastic leukemia (ALL) is well established and ranges anywhere from 29% to 69% depending on the study. We sought to explore the awareness of parents of survivors of childhood ALL regarding the increased risk of obesity and their perceptions regarding the overall health of their child. One hundred twenty-one parents of 99 survivors of pediatric ALL completed surveys regarding perceptions of obesity risk in survivors. Eighty percent of parents of overweight and obese survivors correctly identified their child as "a little overweight" or "overweight." Few parents recalled discussing weight gain (21%) or obesity risk (36%) with their practitioner. Parents that did recall having these discussions and/or reported a decreased level of posttherapy activity in their child were more likely to be concerned about their child's weight status. Improved awareness and education regarding the risk of obesity and associated comorbid conditions may provide an avenue for future prevention of obesity in survivors of pediatric ALL. Discussion and education regarding a healthy lifestyle, including proper diet and exercise, should be incorporated early in routine patient visits.
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http://dx.doi.org/10.1097/MPH.0000000000000852DOI Listing
July 2017

The double life of the ribosome: When its protein folding activity supports prion propagation.

Prion 2017 Mar;11(2):89-97

f Université de Rennes 1, CNRS UMR 6290 IGDR , Rennes , France.

It is no longer necessary to demonstrate that ribosome is the central machinery of protein synthesis. But it is less known that it is also key player of the protein folding process through another conserved function: the protein folding activity of the ribosome (PFAR). This ribozyme activity, discovered more than 2 decades ago, depends upon the domain V of the large rRNA within the large subunit of the ribosome. Surprisingly, we discovered that anti-prion compounds are also potent PFAR inhibitors, highlighting an unexpected link between PFAR and prion propagation. In this review, we discuss the ancestral origin of PFAR in the light of the ancient RNA world hypothesis. We also consider how this ribosomal activity fits into the landscape of cellular protein chaperones involved in the appearance and propagation of prions and other amyloids in mammals. Finally, we examine how drugs targeting the protein folding activity of the ribosome could be active against mammalian prion and other protein aggregation-based diseases, making PFAR a promising therapeutic target for various human protein misfolding diseases.
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http://dx.doi.org/10.1080/19336896.2017.1303587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5399909PMC
March 2017
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