Unified theoretical description of the kinetics of protein aggregation

Solution conditions chosen for the production of amyloid can also promote formation of significant extents of amorphous protein aggregate. In one interpretation, the amyloid and amorphous aggregation pathways are considered to be in competition with each other. An alternative conceptualization involves considering amorphous aggregation as an obligatory intermediate process of the amyloid formation pathway. Here, we review recently developed macroscopic-level theories of protein aggregation that unify these two competing models into a single paradigm. Key features of the unified model included (1) a description of the amorphous aggregate as a second liquid phase with the degree of liquid-like character determined by the mobility of the monomer within it, and (2) heterogeneous growth pathways based on nucleation, growth, and fragmentation of amyloid occurring within different phases and at their interfacial boundary. Limiting-case behaviors of the protein aggregation reaction, either singly involving amyloid or amorphous aggregate production, and mixed-case behaviors, involving competitive and/or facilitated growth of amorphous and amyloid species, are presented and reviewed in context. This review principally describes an approach developed by Hirota and Hall 2019 (Hirota, N. and Hall, D. 2019. Protein Aggregation Kinetics: A Unified Theoretical Description. Chapter 7 of 'Protein Solubility and Amorphous Aggregation: From Academic Research to Applications in Drug Discovery and Bioindustry' edited by Y. Kuroda and F. Arisaka. CMC Publishers). Sections of that work are translated from the original Japanese and republished here with the full permission of CMC Publishing Corporation.

A note of appreciation for Prof. Cristobal dos Remedios on behalf of Biophysical Reviews

Following the initial five-year tenure (2009-2014) of the founding Chief Editor, Dr. Jean Garnier, Prof. Cristobal dos Remedios (University of Sydney) assumed responsibility for Biophysical Reviews as the second Chief Editor (2014-2019). Under his stewardship, Biophysical Reviews has become a six issue per year journal, publishing approximately 100 reviews per year. At the conclusion of his five-year tenure as Chief Editor (and at the age of 78), Cris is stepping down, leaving the journal well placed to apply for (and receive) an impact factor in 2020. On behalf of the journal, I would like to take the occasion of his retirement as Chief Editor to thank Cris for his dedicated service to Biophysical Reviews, and also welcome him to his new position as Emeritus Chief Editor.

Knowledge, help-seeking and efficacy to find respite services: an exploratory study in help-seeking carers of people with dementia in the context of aged care reforms

BACKGROUND

Research highlights the need for carers of people with dementia to acquire relevant and timely information to assist them to access appropriate respite services. Unfortunately, negative experiences of information-seeking can create additional stress for carers and contribute to delays in up-take, or not using respite services at all.

METHODS

Cross-sectional survey data was collected from a convenience sample of n = 84 carers of older people with dementia living in the Illawarra-Shoalhaven region of NSW, Australia. We assessed knowledge, attitudes, information seeking behaviours, and unmet need for respite services in 2016, following national aged care reforms.

RESULTS

Over the previous 12 months, 86% of carers sought respite service information. The majority (73%) of all carers reported an unmet need for respite services, and were relying on personal networks to provide support for respite information. Few utilised the new government gateway 'My Aged Care' phone line (11%) or website (25%). However, 35% used a pre-existing helpline to access short term or emergency respite. We found a preference for interpersonal information sources, including local doctor (65%), professionally and volunteer led carer support groups (49%), and family and friends (46%). Those using four or more information sources showed higher capacity to name local respite services. Respite service information seekers were more likely to be caring for someone with behavioural problems, to have received assistance to access services, and to have used respite services in the past 3 to 6 months.

CONCLUSIONS

New reforms in the Australian aged care sector have not adequately responded to the needs of carers of people with dementia for respite service information and support. Wider, community-based messaging promoting positive service options and the provision of active personal support is required to address the unmet need for respite in carers of people with dementia.

Foreword to 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', a special issue in Honour of Fumio Arisaka's 70th birthday

This issue of Biophysical Reviews, titled 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', is a collection of articles dedicated in honour of Professor Fumio Arisaka's 70th birthday. Initially, working in the fields of haemocyanin and actin filament assembly, Fumio went on to publish important work on the elucidation of structural and functional aspects of T4 phage biology. As his career has transitioned levels of complexity from proteins (hemocyanin) to large protein complexes (actin) to even more massive bio-nanomachinery (phage), it is fitting that the subject of this special issue is similarly reflective of his multiscale approach to structural biology. This festschrift contains articles spanning biophysical structure and function from the bio-molecular through to the bio-nanomachine level.

Oxytocin plasma levels predict the outcome of psychotherapy: A pilot study in chronic depression

BACKGROUND

Oxytocin is associated with bonding and social deficits in psychiatric disorders and has also been discussed as a potential therapeutic intervention to augment psychotherapy. The Cognitive Behavioral Analysis System of Psychotherapy (CBASP) is a specific form of psychotherapy for chronic depression, an illness in which interpersonal deficits play a major role. In this pilot study, we investigated whether Oxytocin plasma levels predict the clinical outcome of chronic depressive patients after CBASP.

METHODS

Sixteen patients with chronic depression participated in a 10-week CBASP inpatient program. Oxytocin plasma levels were measured before and after participants played a virtual ball-tossing game (Cyberball) that mimics social exclusion. Clinical outcome after CBASP was evaluated with the Beck Depression Inventory-II (BDI-II) and the 24-item Hamilton Depression Rating Scale (HAMD-24).

RESULTS

After CBASP, depressive symptoms decreased significantly: the response rates were 44% (BDI-II) and 50% (HAMD-24); and the remission rates, 38% (BDI-II) and 44% (HAMD-24). Lower oxytocin plasma levels at baseline correlated with smaller changes in BDI-II scores, but not with the change in HAMD-24 scores.

LIMITATIONS

The limitations of our study were the small sample size, concomitant and non-standardized pharmacotherapy, and lack of a controlled design and a follow-up period.

CONCLUSIONS

Our study provides first evidence that oxytocin plasma levels may predict the outcome of psychotherapy in chronic depression. These findings need to be replicated in larger randomized, controlled trials.

Heparin-dependent aggregation of hen egg white lysozyme reveals two distinct mechanisms of amyloid fibrillation

Heparin, a biopolymer possessing high negative charge density, is known to accelerate amyloid fibrillation by various proteins. Using hen egg white lysozyme, we studied the effects of heparin on protein aggregation at low pH, raised temperature, and applied ultrasonic irradiation, conditions under which amyloid fibrillation was promoted. Heparin exhibited complex bimodal concentration-dependent effects, either accelerating or inhibiting fibrillation at pH 2.0 and 60 °C. At concentrations lower than 20 μg/ml, heparin accelerated fibrillation through transient formation of hetero-oligomeric aggregates. Between 0.1 and 10 mg/ml, heparin rapidly induced amorphous heteroaggregation with little to no accompanying fibril formation. Above 10 mg/ml, heparin again induced fibrillation after a long lag time preceded by oligomeric aggregate formation. Compared with studies performed using monovalent and divalent anions, the results suggest two distinct mechanisms of heparin-induced fibrillation. At low heparin concentrations, initial hen egg white lysozyme cluster formation and subsequent fibrillation is promoted by counter ion binding and screening of repulsive charges. At high heparin concentrations, fibrillation is caused by a combination of salting out and macromolecular crowding effects probably independent of protein net charge. Both fibrillation mechanisms compete against amorphous aggregation, producing a complex heparin concentration-dependent phase diagram. Moreover, the results suggest an active role for amorphous oligomeric aggregates in triggering fibrillation, whereby breakdown of supersaturation takes place through heterogeneous nucleation of amyloid on amorphous aggregates.

Special Issue of Biophysical Reviews dedicated to the 19th IUPAB Conference in Edinburgh, Scotland (July 2017)

From the 16th to the 20th of July 2017, the 19th IUPAB (International Union of Pure and Applied Biophysics) world congress was held in Edinburgh, Scotland. Organized in conjunction with the 11th EBSA (European Biophysical Societies' Association) the meeting attracted over 1430 participants, had 35 scientific sessions and 10 plenary speakers. Each invited speaker was invited to contribute either a short review or a letter article that summarized the contents of their session. This special issue of Biophysical Reviews is dedicated to providing contextual background to some of the many talks presented at the meeting in Edinburgh. The reader is referred to supplementary issue 1 of volume 46 of the European Biophysics Journal for a complete listing of abstracts for all presented talks and posters.

Topological cell clustering in the ATLAS calorimeters and its performance in LHC Run 1

The reconstruction of the signal from hadrons and jets emerging from the proton-proton collisions at the Large Hadron Collider (LHC) and entering the ATLAS calorimeters is based on a three-dimensional topological clustering of individual calorimeter cell signals. The cluster formation follows cell signal-significance patterns generated by electromagnetic and hadronic showers. In this, the clustering algorithm implicitly performs a topological noise suppression by removing cells with insignificant signals which are not in close proximity to cells with significant signals. The resulting topological cell clusters have shape and location information, which is exploited to apply a local energy calibration and corrections depending on the nature of the cluster. Topological cell clustering is established as a well-performing calorimeter signal definition for jet and missing transverse momentum reconstruction in ATLAS.

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L, Yabsley B, Yacoob S, Yakabe R, Yamaguchi D, Yamaguchi Y, Yamamoto A, Yamamoto S, Yamanaka T, Yamauchi K, Yamazaki Y, Yan Z, Yang H, Yang H, Yang Y, Yang Z, Yao WM, Yap YC, Yasu Y, Yatsenko E, Wong KHY, Ye J, Ye S, Yeletskikh I, Yen AL, Yildirim E, Yorita K, Yoshida R, Yoshihara K, Young C, Young CJS, Youssef S, Yu DR, Yu J, Yu JM, Yu J, Yuan L, Yuen SPY, Yusuff I, Zabinski B, Zaidan R, Zaitsev AM, Zakharchuk N, Zalieckas J, Zaman A, Zambito S, Zanello L, Zanzi D, Zeitnitz C, Zeman M, Zemla A, Zeng JC, Zeng Q, Zengel K, Zenin O, Ženiš T, Zerwas D, Zhang D, Zhang F, Zhang G, Zhang H, Zhang J, Zhang L, Zhang R, Zhang R, Zhang X, Zhang Z, Zhao X, Zhao Y, Zhao Z, Zhemchugov A, Zhong J, Zhou B, Zhou C, Zhou L, Zhou L, Zhou M, Zhou N, Zhu CG, Zhu H, Zhu J, Zhu Y, Zhuang X, Zhukov K, Zibell A, Zieminska D, Zimine NI, Zimmermann C, Zimmermann S, Zinonos Z, Zinser M, Ziolkowski M, Živković L, Zobernig G, Zoccoli A, zur Nedden M, Zurzolo G, Zwalinski L. Performance of algorithms that reconstruct missing transverse momentum in [Formula: see text]= 8 TeV proton-proton collisions in the ATLAS detector

The reconstruction and calibration algorithms used to calculate missing transverse momentum ([Formula: see text] ) with the ATLAS detector exploit energy deposits in the calorimeter and tracks reconstructed in the inner detector as well as the muon spectrometer. Various strategies are used to suppress effects arising from additional proton-proton interactions, called pileup, concurrent with the hard-scatter processes. Tracking information is used to distinguish contributions from the pileup interactions using their vertex separation along the beam axis. The performance of the [Formula: see text] reconstruction algorithms, especially with respect to the amount of pileup, is evaluated using data collected in proton-proton collisions at a centre-of-mass energy of 8 [Formula: see text] during 2012, and results are shown for a data sample corresponding to an integrated luminosity of [Formula: see text]. The simulation and modelling of [Formula: see text]  in events containing a Z boson decaying to two charged leptons (electrons or muons) or a W boson decaying to a charged lepton and a neutrino are compared to data. The acceptance for different event topologies, with and without high transverse momentum neutrinos, is shown for a range of threshold criteria for [Formula: see text] , and estimates of the systematic uncertainties in the [Formula: see text]  measurements are presented.

Lymphocyte reconstitution following autologous stem cell transplantation for progressive MS

BACKGROUND

Autologous stem cell transplantation (ASCT) for progressive multiple sclerosis (MS) may reset the immune repertoire.

OBJECTIVE

The objective of this paper is to analyse lymphocyte recovery in patients with progressive MS treated with ASCT.

METHODS

Patients with progressive MS not responding to conventional treatment underwent ASCT following conditioning with high-dose cyclophosphamide and antithymocyte globulin. Lymphocyte subset analysis was performed before ASCT and for two years following ASCT. Neurological function was assessed by the EDSS before ASCT and for three years post-ASCT.

RESULTS

CD4+ T-cells fell significantly post-transplant and did not return to baseline levels. Recent thymic emigrants and naïve T-cells fell sharply post-transplant but returned to baseline by nine months and twelve months, respectively. T-regulatory cells declined post-transplant and did not return to baseline levels. Th1 and Th2 cells did not change significantly while Th17 cells fell post-transplant but recovered to baseline by six months. Neurological function remained stable in the majority of patients. Progression-free survival was 69% at three years.

CONCLUSION

This study demonstrates major changes in the composition of lymphocyte subsets following ASCT for progressive MS. In particular, ablation and subsequent recovery of thymic output is consistent with the concept that ASCT can reset the immune repertoire in MS patients.

Foreword to 'Quantitative and analytical relations in biochemistry'-a special issue in honour of Donald J. Winzor's 80th birthday

The purpose of this special issue is to honour Professor Donald J. Winzor's long career as a researcher and scientific mentor, and to celebrate the milestone of his 80th birthday. Throughout his career, Don has been renowned for his development of clever approximations to difficult quantitative relations governing a range of biophysical measurements. The theme of this special issue, 'Quantitative and analytical relations in biochemistry', was chosen to reflect this aspect of Don's scientific approach.

Test of CP invariance in vector-boson fusion production of the Higgs boson using the Optimal Observable method in the ditau decay channel with the ATLAS detector

A test of CP invariance in Higgs boson production via vector-boson fusion using the method of the Optimal Observable is presented. The analysis exploits the decay mode of the Higgs boson into a pair of [Formula: see text] leptons and is based on 20.3 [Formula: see text] of proton-proton collision data at [Formula: see text] = 8 [Formula: see text] collected by the ATLAS experiment at the LHC. Contributions from CP-violating interactions between the Higgs boson and electroweak gauge bosons are described in an effective field theory framework, in which the strength of CP violation is governed by a single parameter [Formula: see text]. The mean values and distributions of CP-odd observables agree with the expectation in the Standard Model and show no sign of CP violation. The CP-mixing parameter [Formula: see text] is constrained to the interval [Formula: see text] at 68% confidence level, consistent with the Standard Model expectation of [Formula: see text].

Measurement of amyloid formation by turbidity assay-seeing through the cloud

Detection of amyloid growth is commonly carried out by measurement of solution turbidity, a low-cost assay procedure based on the intrinsic light scattering properties of the protein aggregate. Here, we review the biophysical chemistry associated with the turbidimetric assay methodology, exploring the reviewed literature using a series of pedagogical kinetic simulations. In turn, these simulations are used to interrogate the literature concerned with in vitro drug screening and the assessment of amyloid aggregation mechanisms.

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Performance of pile-up mitigation techniques for jets in [Formula: see text] collisions at [Formula: see text] TeV using the ATLAS detector

The large rate of multiple simultaneous proton-proton interactions, or pile-up, generated by the Large Hadron Collider in Run 1 required the development of many new techniques to mitigate the adverse effects of these conditions. This paper describes the methods employed in the ATLAS experiment to correct for the impact of pile-up on jet energy and jet shapes, and for the presence of spurious additional jets, with a primary focus on the large 20.3 [Formula: see text] data sample collected at a centre-of-mass energy of [Formula: see text]. The energy correction techniques that incorporate sophisticated estimates of the average pile-up energy density and tracking information are presented. Jet-to-vertex association techniques are discussed and projections of performance for the future are considered. Lastly, the extension of these techniques to mitigate the effect of pile-up on jet shapes using subtraction and grooming procedures is presented.