bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the Free Energy Landscape and Thermodynamics of Protein-Protein Association: HIV-1 Integrase Multimerization Induced by an Allosteric Inhibitor
Authors: Tse C. , Wickstrom L. , Kvaratskhelia M. , Gallicchio E. , Levy R. , Deng N. 
Published: June 2020

AbstractWe report the free energy landscape and thermodynamics of the protein-protein association responsible for the drug-induced multimerization of HIV-1 integrase (IN). Allosteric HIV-1 integrase inhibitors (ALLINIs) promote aberrant IN multimerization by bridging IN-IN intermolecular interactions. However, the thermodynamic driving forces and kinetics of the multimerization remain largely unknown. Here we explore the early steps in the IN multimerization by using umbrella sampling and unbiased molecular dynamics simulations in explicit solvent. In direct simulations, the two initially separated dimers spontaneously associate to form near-native complexes that resemble the crystal structure of the aberrant tetramer. Most strikingly, the effective interaction of the protein-protein association is very short-ranged: the two dimers associate rapidly within tens of nanoseconds when their binding surfaces are separated by d ≤ 4.3 Å (less than two water diameters). Beyond this distance, the oligomerization kinetics appears to be diffusion controlled with a much longer association time. The free energy profile also captured the crucial role of ALLINI in promoting multimerization, and explained why several CTD mutations are remarkably resistant to the drug-induced multimerization. The results also show that at small separation the protein-protein binding process contains two consecutive phases with distinct thermodynamic signatures. First, inter-protein water molecules are expelled to the bulk resulting in a small increase in entropy, as the solvent entropy gain from the water release is nearly cancelled by the loss of side chain entropies as the two proteins approach each other. At shorter distances, the two dry binding surfaces adapt to each other to optimize their interaction energy at the expense of further protein configurational entropy loss. While the binding interfaces feature clusters of hydrophobic residues, overall, the protein-protein association in this system is driven by enthalpy and opposed by entropy.Statement of SignificanceElucidating the energetics and thermodynamic aspects of protein-protein association is important for understanding this fundamental biophysical process. This study provided a more complete physical picture of the protein-protein association responsible for the drug-induced HIV-1 integrase multimerization. The results captured the critical role of the inhibitor, and accounted for the effects of mutations on the protein association. Remarkably, the effective range of the protein-protein attractive funnel is found to be very short, at less than two layers of water, despite the fact that the two binding partners carry opposite net charges. Lastly, entropy/enthalpy decomposition shows that the solvent release from the inter-protein region into the bulk is more than offset by the loss of the solute configurational entropy due to complexation.
Generation of clonal male and female mice through CRISPR/Cas9-mediated Y chromosome deletion in embryonic stem cells
Authors: Qin Yiren , Wong Bokey , Geng Fuqiang , Zhong Liangwen , Parada Luis F. , Wen Duancheng 
Published: June 2020

AbstractMice derived entirely from embryonic stem (ES) cells can be generated in one step through tetraploid complementation. Although XY male ES cell lines are commonly used in this system, occasionally, monosomic XO female all-ES mice are produced through spontaneous Y chromosome loss. Here, we describe an efficient method to obtain monosomic XO ES cells by CRISPR/Cas9-mediated deletion of the Y chromosome allowing generation of clonal male and female mice by tetraploid complementation. The monosomic XO female mice are viable and are able to produce normal male and female offspring. Direct generation of clonal male and female mice from the same mutant ES cells significantly accelerates the production of complex genetically modified mouse models by circumventing multiple rounds of outbreeding.
Effect of ligands on HP-induced unfolding and oligomerization of β-lactoglobulin
Authors: Minić S. , Annighöfer B. , Hélary A. , Hamdane D. , Hoa G. Hui Bon , Loupiac C. , Brûlet A. , Combet S. 
Published: June 2020

ABSTRACTTo probe intermediate states during unfolding and oligomerization of proteins remains a major challenge. High pressure (HP) is a powerful tool for studying these problems, revealing subtle structural changes in proteins not accessible by other means of denaturation. Bovine β-lactoglobulin (BLG), the main whey protein, has a strong propensity to bind various bioactive molecules, such as retinol and resveratrol, two ligands with different affinity and binding sites. By combiningin situHP-small-angle neutron scattering (SANS) and HP-UV/visible absorption spectroscopy, we report the specific effects of these ligands on 3D conformational and local changes in BLG induced by HP. Depending on BLG concentration, two different unfolding mechanisms are observedin situunder pressures up to ~300 MPa, mediated by the formation of disulfide bonds: either a complete protein unfolding, from native dimers to Gaussian chains, or a partial unfolding with oligomerization in tetramers. Retinol, which has a high affinity for BLG hydrophobic cavity, significantly stabilizes BLG both in 3D and local environments, by shifting the onset of protein unfolding by ~100 MPa. Increasing temperature from 30 to 37°C enhances the hydrophobic stabilization effects of retinol. In contrast, resveratrol, which has a low binding affinity for site(s) on the surface of the BLG, does not induce any significant effect on the structural changes of BLG due to pressure. HP treatment back and forth up to ~300 MPa causes irreversible covalent oligomerization of BLG.Ab initiomodeling of SANS shows that the oligomers formed from BLG/retinol complex are smaller and more elongated compared to BLG without ligand or in the presence of resveratrol. By combining HP-SANS and HP-UV/vis absorption spectroscopy, our strategy highlights the crucial role of BLG hydrophobic cavity and opens up new possibilities for the structural determination of HP-induced protein folding intermediates and irreversible oligomerization.STATEMENT OF SIGNIFICANCEHigh pressure (HP) is a powerful probe to access the intermediate states of proteins through subtle structural changes not accessible by other means of denaturation. Bovine β-lactoglobulin (BLG), the main whey protein, is able to bind various bioactive molecules, such as retinol and resveratrol, exhibiting different affinity and binding sites. By combining HP-small-angle neutron scattering and HP-UV/visible absorption spectroscopy, we highlight two different mechanisms during the unfolding and oligomerization of BLG depending on protein concentration. Above all, we show that retinol significantly prevents the unfolding and oligomerization of BLG, unlike resveratrol, emphasizing the crucial role of the hydrophobic cavity in BLG stabilization. Our strategy opens up new possibilities for the structural determination of protein intermediates and oligomers using HP.
Inhibition of fibrosis with multi-agent therapy in pulmonary fibrosis: Results of a drug library screening
Authors: Braun Cassandra Batzlaff , Girtman Megan , Jenson Paige , Bourne Michael H , Chae JuneMee , Kottom Theodore , Limper Andrew 
Published: June 2020

AbstractAimsSuccessful management of IPF will likely require multi-drug therapy as its pathogenesis is thought to be both driven by both pro-inflammatory and pro-fibrotic pathways. We hypothesized that the available anti-fibrotic agents, pirfenidone and nintedanib, may exhibit synergy in suppressing lung fibroblast extracellular matrix protein generation when administered in combination with other orally active agents.Materials and MethodsA fibroblastic cell line (AKR-2B) was stimulated with TGF-β1 and used to screen a library of over 1500 FDA approved drugs. Extracellular matrix protein generation was assessed via fibronectin ELISA assay and maintenance of cell viability confirmed with XTT assay.ResultsThe screening revealed sixty-two drugs from the repurposed drug-screening library that were shown to significantly suppress fibronectin expression and not result in cell death. Specifically drugs within the category of NSAIDs, steroids, azole antifungal agents, and antipyrine were associated with significant suppression of fibronectin on ELISA analysis. Surprisingly, we observed anti-fibrotic activity across a number of the azole antifungal compounds. We next assessed whether combination of azoles would exhibit synergy when combined with current anti-fibrotic therapies in the stimulated fibroblasts. As proof of concept, we demonstratedin vitrosynergy between oxiconazole and nintedanib in suppressing fibroblast generation of extracellular matrix fibronectin.ConclusionsThese results suggest an approach to identify potential combinations of therapy that may improve patient outcomes by reducing cost and potential toxicities during treatment.
Mapping the Multiscale Organisation of Escherichia Coli Chromosome in a Hi-C-integrated Model
Authors: Wasim Abdul , Gupta Ankit , Mondal Jagannath 
Published: June 2020

ABSTRACTThe chromosome of Escherichia Coli (E. coli) is riddled with multi-faceted complexity and its nature of organization is slowly getting recognised. The emergence of chromosome conformation capture techniques and super-resolution microscopy are providing newer ways to explore chromosome organization, and dynamics and its effect on gene expression. Here we combine a beads-on-a-spring polymer-based framework with recently reported high-resolution Hi-C data of E. coli chromosome to develop a comprehensive model of E. coli chromosome at 5 kilo base-pair resolution. The model captures a self-organised chromosome composed of linearly organised genetic loci, and segregated macrodomains within a ring-like helicoid architecture, with no net chirality. Additionally, a genome-wide map identifies multiple chromosomal interaction domains (CIDs) and corroborates well with a transcription-centric model of the E. coli chromosome. The investigation further demonstrates that while only a small fraction of the Hi-C contacts is dictating the underlying chromosomal organization, a random-walk polymer chain devoid of Hi-C encoded contact information would fail to map the key genomic interactions unique to E. coli. Collectively, the present work, integrated with Hi-C interaction, elucidates the organization of bacterial chromosome at multiple scales, ranging from identifying a helical, macro-domain-segregated morphology at coarse-grained scale to a manifestation of CIDs at a fine-grained scale.
Site-specific Crosslinking Coupled with Mass Spectrometry as a Structural Tool in Studies of the Human α1Glycine Receptor
Authors: Veeramachaneni Rathna J. , Donelan Chelsee A. , Tomcho Kayce A. , Aggarwal Shaili , Lapinsky David J. , Cascio Michael 
Published: June 2020

AbstractRecent advances in mass spectrometry coupled with chemical crosslinking (CX-MS) can be applied for the structural interrogation of macromolecular complexes to identify statedependent distance constraints and provides a powerful complementary technique to other structural methods. In this study, we develop a CX-MS approach to identify the sites of crosslinking from a single targeted location within the human glycine receptor (GlyR) in a single apo/resting state. The GlyR belongs to the family of pentameric ligand-gated ion channel receptors that function in fast neuronal transmission. A single cysteine residue was re-introduced intoCys nullGlyR construct at position 41 within the extracellular domain of an overexpressed human a1 homomeric GlyR. After purification and reconstitution into vesicles, a methanethiosulfonate benzophenone heterobifunctional crosslinker was attached via formation of a disulfide bond, and the resting receptor is subsequently photocrosslinked. Monomeric and oligomeric bands from SDS-PAGE gels were then trypsinized and analyzed by tandem MS in bottom-up studies. Dozens of intra- and inter-subunit sites of crosslinking were differentiated and identified from single gel bands (pmols of purified GlyR), showing the utility of this approach to identify a diverse array of distance constraints of GlyR in its resting state. These studies highlight the potential of CX-MS as an experimental approach to identify state-dependent crosslinks of full length integral membrane protein assemblies in a native-like lipid environment.
Secondary single-cell transcriptomic analysis reveals common molecular signatures of cerebrovascular injury between traumatic brain injury and aging
Authors: Guo Xinying , Zhang Bangyan , Gomez-Pinilla Fernando , Gao Fan , Zhao Zhen 
Published: June 2020

AbstractCerebrovascular injury is a common pathological feature of a spectrum of neurological disorders including traumatic brain injury (TBI), stroke, Alzheimer’s disease (AD), as well as aging. Vascular manifestations among these conditions are similar indeed, including the breakdown of the blood-brain barrier (BBB). However, whether there is a common molecular mechanism underlying the vascular changes among these conditions remains elusive. Here, we report secondary transcriptomic analysis on cerebrovascular cells based single-cell RNA-seq datasets of mouse models of mild TBI and aging, with a focus on endothelial cells and pericytes. We identify several molecular signatures commonly found between mTBI and aging vasculature, includingAdamts1, Rpl23a, Tmem252, Car4, Serpine2, andNdnfin endothelial cells, andRps29andSepp1in pericytes. These markers may represent the shared endophenotype of microvascular injury and be considered as cerebrovascular injury responsive genes. Additionally, pathway analysis on differentially expressed genes demonstrated alterations in common pathways between mTBI and aging, including vascular development and extracellular matrix pathways in endothelial cells. Hence, our analysis suggests that cerebrovascular injury triggered by different neurological conditions may share common molecular signatures, which may only be detected at the single-cell transcriptome level.
Genotype-first approach to the detection of hereditary breast and ovarian cancer risk, and effects of risk disclosure to biobank participants
Authors: Leitsalu Liis , Palover Marili , Tõnis Sikka Timo , Reigo Anu , Kals Mart , Pärn Kalle , Nikopensius Tiit , Esko Tõnu , Metspalu Andres , Padrik Peeter , Tõnisson Neeme 
Published: June 2020

ABSTRACTGenotype-first approach allows to systematically identify carriers of pathogenic variants in BRCA1/2 genes conferring a high risk of familial breast and ovarian cancer. Participants of the Estonian biobank have expressed support for the disclosure of clinically significant findings. With an Estonian biobank cohort, we applied a genotype-first approach, contacted carriers and offered return of results with genetic counseling. We evaluated participants’ responses to and the clinical utility of the reporting of actionable genetic findings. Twenty-two of 40 contacted carriers of 17 pathogenic BRCA1/2 variants responded and chose to receive results. Eight of these 22 participants qualified for high-risk assessment based on National Comprehensive Cancer Network criteria. Twenty of 21 counseled participants appreciated being contacted. Relatives of 10 participants underwent cascade screening. Five of 16 eligible female BRCA1/2 variant carriers chose to undergo risk-reducing surgery, and 10 adhered to surveillance recommendations over the 30-month follow-up period. We recommend the return of results to population-based biobank participants; this approach could be viewed as a model for population-wide genetic testing. The genotype-first approach permits the identification of individuals at high risk who would not be identified by application of an approach based on personal and family histories only.
Dairy-free imitation cheese: is further development required?
Authors: Nicolás Saraco Maximiliano , Blaxland James 
Published: June 2020

PurposeThe aim of this study was to compare the organoleptic attributes and meltability of selected, commercial dairy-free imitation cheeses (DFICs) with those of their dairy counterparts to thus determine whether commercial DFIC needs to be further developed.Design/methodology/approachMarket research was conducted to determine the availability of DFICs in the United Kingdom (UK) and thus select the varieties to assess. Mild cheddar was chosen for its popularity wide availability in the United Kingdom and Italian-style hard cheese for its complex organoleptic profile. The organoleptic attributes and melting properties of the chosen DFIC products were assessed by using descriptive sensory evaluation and their meltability was assessed using the Arnott test, respectively.Findings109 different DFICs were found; most of them (74%) presented coconut oil as their primary ingredient. None of the assessed DFICs assessed could mimic the organoleptic attributes of their dairy counterparts accurately; however, one of the non-dairy mild cheddar samples was regarded as potentially acceptable by the assessors of the sensory evaluation assessors. Nonetheless, the meltability of this sample was significantly lower than that of mild cheddar cheese.Practical implicationsThe findings indicate that, to obtain products that can mimic the organoleptic attributes and meltability of cheese more accurately, further development is required for the DFIC varieties assessed.Originality/valueNo academic publications have explored and investigated commercial DFICs with similar ingredients to those found in commercial DFICs; the commercial importance of these products may augment in the short term owing to the reported growth in the number of vegan individuals in the UK and in Europe.
A simple model of time zone differences, virtual trade and informality
Authors: Mandal Biswajit , Prasad Alaka Shree 
Published: June 2020

Purpose
This paper aims to strive to model virtual trade resulting from time zone differences in an otherwise Heckscher–Ohlin set up which is absent in the literature. So, the paper adds some value to the existing literature on time zones (TZ) and trade.

Design/methodology/approach
A competitive general equilibrium model is developed first to capture the effect of TZ differences on virtual trade. Then the authors examine, in brief, if distance can be accommodated in such framework. Finally, the authors extend the model to incorporate informality.

Findings
It is seen that exploitation of time zone difference benefits skilled labor and hurts capital under reasonable assumption. In what follows, time zone difference exploiting sector expands, whereas the other sector contracts. Then, the model has been extended to examine how distance may also lead to similar outcomes. In addition, the model is further modified to explore the effect of virtual trade in an informality and associated extortion ridden economy. Interestingly, virtual trade turns out to be beneficial to unskilled workers as well, and leads to a fall in the number of extortionists, though informal production is augmented.

Research limitations/implications
This model is a competitive model that may not clearly reflect the realistic world. However, interestingly this may form the basis of looking into some other appealing dimensions of the real world.

Originality/value
TZ and related communication-cost-driven trade arguments are relatively less explored theoretically. Therefore, the work adds some value to the theoretical understanding of outsourcing in service trade that uses day-night differences across the globe.
Las Cruces housing price fluctuations
Authors: Fullerton Steven L. , Holcomb James H. , Fullerton Jr Thomas M. 
Published: June 2020

Purpose
This paper aims to analyze the median price for existing single-family housing units in Las Cruces, New Mexico. The proposed theoretical model accounts for the interplay between supply and demand sides of a metropolitan housing market.

Design/methodology/approach
This study analyzes the median price for existing single-family housing units in Las Cruces, New Mexico. The proposed theoretical model accounts for the interplay between supply and demand sides of a metropolitan housing market. Explanatory variables used in the analysis are real per capita income, the housing stock, real mortgage rates, real apartment rents and the median real price of single-family units in the USA. Annual frequency data are collected for a 1971–2017 sample period. Parameter estimation is completed using two-stage generalized least squares. Empirical results confirm several, but not all, of the hypotheses associated with the underlying analytical model. In particular, Las Cruces housing prices are found to be reliably correlated with local income and national housing prices.

Findings
Empirical results confirm several of the hypotheses associated with the underlying analytical model. In particular, Las Cruces housing prices are found to be reliably correlated with local income and national housing prices.

Research limitations/implications
Results obtained support only a subset of the hypothetical relationships associated with the theoretical model. Additional testing for other small and/or medium sized is required to clarify whether these outcomes are unique to Las Cruces.

Practical implications
Local income fluctuations and national housing price fluctuations appear to be reliably related to housing price fluctuations for this metropolitan economy.

Originality/value
Comparatively little housing market research has been conducted for small and medium size urban economies. There is no guarantee that results obtained for large metropolitan housing markets are representative of smaller regional housing markets. The model developed has fairly moderate data requirements and may be applicable to other small and medium size economies such as Las Cruces.
Mark Johnson: “Future-back” strategizing for beyond-the-core growth
Authors: Leavy Brian 
Published: June 2020

Purpose
Interview with Mark W. Johnson, Innosight co-founder and former consultant at Booz Allen Hamilton,an authority on the application of disruption theory. ]His latest book, Lead From the Future: How to Turn Visionary Thinking into Breakthrough Growth, co-authored with Innosight partner Josh Suskewicz, addresses the challenge of how to strategize for the beyond-the-core breakthrough initiatives which will be key to sustaining future growth.

Design/methodology/approach
His interviewer is Brian Leavy, emeritus professor of strategy at Dublin City University Business School and a Strategy & Leadership contributing editor. The interview focuses on Future-back thinking and a set of allied processes that can help leaders think further out than the three to five years that most set as their planning horizons. Then they can identify the threats and opportunities that await them and envision their best path forward.

Findings
Future-back thinking and planning begins with exploring and envisioning–actively, intensively and imaginatively immersing yourself in your organization’s likely future and then determining what you must do to not only fit into that environment but to actively shape your enterprise to thrive in it.

Practical implications
Future-back thinking is geared to discovery, so it iswhat you use when you need to develop a market-creating innovation or new business model to fill a projected gap–to explore, envision and then chart out a new path.

Originality/value
The lesson for leaders: when programming a breakthrough strategy, you need to formalize the roles and responsibilities of the senior leadership team as its champions and overseers, set up an organizational model that will protect those teams from the countervailing influences of the core and ensure that the initiative is managed with an explore, envision and discover approach.