bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid selection of a human monoclonal antibody that potently neutralizes SARS-CoV-2 in two animal models
Authors: Li Wei , Drelich Aleksandra , Martinez David R. , Gralinski Lisa , Chen Chuan , Sun Zehua , Schäfer Alexandra , Leist Sarah R. , Liu Xianglei , Zhelev Doncho , Zhang Liyong , Peterson Eric C. , Conard Alex , Mellors John W. , Tseng Chien-Te , Baric Ralph S. , Dimitrov Dimiter S.
Published: May 2020

Effective therapies are urgently needed for the SARS-CoV-2/COVID19 pandemic. We identified panels of fully human monoclonal antibodies (mAbs) from eight large phage-displayed Fab, scFv and VH libraries by panning against the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) glycoprotein. One high affinity mAb, IgG1 ab1, specifically neutralized replication competent SARS-CoV-2 with exceptional potency as measured by two different assays. There was no enhancement of pseudovirus infection in cells expressing Fcγ receptors at any concentration. It competed with human angiotensin-converting enzyme 2 (hACE2) for binding to RBD suggesting a competitive mechanism of virus neutralization. IgG1 ab1 potently neutralized mouse ACE2 adapted SARS-CoV-2 in wild type BALB/c mice and native virus in hACE2 expressing transgenic mice. The ab1 sequence has relatively low number of somatic mutations indicating that ab1-like antibodies could be quickly elicited during natural SARS-CoV-2 infection or by RBD-based vaccines. IgG1 ab1 does not have developability liabilities, and thus has potential for therapy and prophylaxis of SARS-CoV-2 infections. The rapid identification (within 6 days) of potent mAbs shows the value of large antibody libraries for response to public health threats from emerging microbes.
Polymer Stiffness Regulates Multivalent Binding and Liquid-Liquid Phase Separation
Authors: Zumbro E. , Alexander-Katz A.
Published: May 2020

Multivalent binding is essential to many biological processes because it builds high affinity bonds by using several weak binding interactions simultaneously. Multivalent polymers have shown promise as inhibitors of toxins and other pathogens, and they are important components in the formation of biocondensates. Explaining how structural features of these polymers change their binding and subsequent control of phase separation is critical to designing better pathogen inhibitors and also to understanding diseases associated with membraneless organelles. In this work, we will examine the binding of a multivalent polymer to a small target. This scenario could represent a polymeric inhibitor binding to a toxic protein or RNA binding to an RNA-binding protein in the case of liquid-liquid phase separation. We use simulation and theory to show that flexible random-coil polymers bind more strongly than stiff rod-like polymers and that flexible polymers nucleate condensed phases at lower energies than their rigid analogues. We hope these results will provide insight into the rational design of polymeric inhibitors and improve understanding of membraneless organelles.

Statement of Significance

Multivalent polymers are essential for many biological systems, including targeting pathogens and controlling the formation of liquid-liquid phase separated biocondensates. Here, we explain how increasing polymer stiffness can reduce multivalent binding affinity to a small target such as a toxic protein and how modulating polymer stiffness can change the phase boundary for liquid-liquid phase separation. These results have implications for designing stronger pathogen inhibitors and provide insights on neurodegenerative diseases associated with abnormal biocondensate formation.
ERH as a component of the Microprocessor facilitates the maturation of suboptimal microRNAs
Authors: Kwon S. Chul , Jang Harim , Yang Jihye , Kim Jeesoo , Baek S. Chan , Kim Jong-Seo , Kim V. Narry
Published: May 2020

The Microprocessor complex cleaves the primary transcript of microRNA (pri-miRNA) to initiate miRNA maturation. Microprocessor is known to consist of RNase III DROSHA and dsRNA-binding DGCR8. Here we identify Enhancer of Rudimentary Homolog (ERH) as a new component of the Microprocessor. ERH binds to a conserved region in the N-terminus of DGCR8. Knockdown of ERH or deletion of the DGCR8 N-terminus results in a decrease of processing of primary miRNAs with suboptimal hairpin structures that reside in polycistronic miRNA clusters. ERH increases the processing of suboptimal pri-miR-451 in a manner dependent on its neighboring pri-miR-144. Thus, the ERH dimer may mediate “cluster assistance” in which the Microprocessor is loaded onto a poor substrate with help from a high-affinity substrate in the same cluster. Our study reveals a role of ERH in the miRNA pathway.
Surface display of designer protein scaffolds on genome-reduced strains ofPseudomonas putida
Authors: Dvořák Pavel , Bayer Edward A. , de Lorenzo Víctor
Published: May 2020

The bacteriumPseudomonas putidaKT2440 is gaining considerable interest as a microbial platform for biotechnological valorization of polymeric organic materials, such as waste lignocellulose or plastics. However,P. putidaon its own cannot make much use of such complex substrates, mainly because it lacks an efficient extracellular depolymerizing apparatus. We seek to meet this challenge by adopting a recombinant cellulosome strategy for this attractive host. Here, we report an essential step in this endeavor – a display of designer enzyme-anchoring protein “scaffoldins”, encompassing cohesin binding domains from divergent cellulolytic bacterial species on theP. putidasurface. TwoP. putidachassis strains, EM42 and EM371, with streamlined genomes and substantial differences in the composition of the outer membrane were employed in this study. Scaffoldin variants were delivered to their surface with one of four tested autotransporter systems (Ag43 fromEscherichia coli), and the efficient display was confirmed by extracellular attachment of chimeric β-glucosidase and fluorescent proteins. Our results highlight the importance of cell surface engineering for display of recombinant proteins in Gram-negative bacteria and pave the way towards designer cellulosome strategies, tailored forP. putida.
Transcriptomic profiling of human effector and regulatory T cell subsets identifies predictive population signatures
Authors: Höllbacher Barbara , Duhen Thomas , Motley Samantha , Klicznik Maria M. , Gratz Iris K. , Campbell Daniel J.
Published: May 2020

After activation, CD4+T helper (Th) cells differentiate into functionally specialized populations that coordinate distinct immune responses and protect against different types of pathogens. In humans, these effector and memory Th cell subsets can be readily identified in peripheral blood based on their differential expression of chemokine receptors that govern their homeostatic and inflammatory trafficking. Foxp3+regulatory T (Treg) cells can also be divided into subsets that phenotypically mirror each of these effector populations, and share expression of key transcription factors and effector cytokines. In this study, we performed comprehensive transcriptional profiling of 11 phenotypically distinct Th and Treg cell subsets sorted from peripheral blood of healthy individuals. Despite their shared phenotypes, we found that mirror Th and Treg subsets were transcriptionally dissimilar, and that Treg cell populations showed limited transcriptional diversity compared to Th cells. We identified core transcriptional signatures shared across all Th and Treg cell populations, and unique signatures that define each of the Th or Treg populations. Finally, we applied these signatures to bulk Th and Treg RNA-seq data and found enrichment of specific Th and Treg cell populations in different human tissues. These results further define the molecular basis for the functional specialization and differentiation of Th and Treg cell populations, and provide a new resource for examining Th and Treg specialization in RNA-seq data.
Combined knockout ofLrrk2andRab29does not result in behavioral abnormalitiesin vivo
Authors: Mazza Melissa Conti , Nguyen Victoria , Beilina Alexandra , Ding Jinhui , Cookson Mark R.
Published: May 2020

Coding mutations in theLRRK2gene, encoding for a large protein kinase, have been shown to cause familial Parkinson’s disease (PD). The immediate biological consequence of LRRK2 mutations is to increase kinase activity, leading to the suggestion that inhibition of this enzyme might be useful therapeutically to slow disease progression. Genome-wide association studies have identified the chromosomal loci aroundLRRK2and one of its proposed substrates,RAB29, as contributors towards the lifetime risk of sporadic PD. Considering the evidence for interactions between LRRK2 and RAB29 on the genetic and protein levels, here we generated a double knockout mouse model and determined whether there are any consequences on brain function with aging. From a battery of motor and non-motor behavioral tests, we noted only that 18-24 monthRab29-/-and double (Lrrk2-/-/Rab29-/-) knockout mice had diminished locomotor behavior in open field compared to wildtype mice. However, no genotype differences were seen in number of substantia nigra pars compacta (SNc) dopamine neurons or in tyrosine hydroxylase levels in the SNc and striatum, which might reflect a PD-like pathology. These results suggest that depletion of both Lrrk2 and Rab29 is tolerated, at least in mice, and support that this pathway might be able to be safely targeted for therapeutics in humans.

Significance statement

Genetic variation in LRRK2 that result in elevated kinase activity can cause Parkinson’s disease (PD), suggesting LRRK2 inhibition as a therapeutic strategy. RAB29, a substrate of LRRK2, has also been associated with increased PD risk. Evidence exists for an interactive relationship between LRRK2 and RAB29. Mouse models lacking either LRRK2 or RAB29 do not show brain pathologies. We hypothesized that the loss of both targets would result in additive effects acrossin vivoand post-mortem assessments in aging mice. We found that loss of both LRRK2 and RAB29 did not result in significant behavioral deficits or dopamine neuron loss. This evidence suggests that chronic inhibition of this pathway should be tolerated clinically.
Expansion Sequencing: Spatially PreciseIn SituTranscriptomics in Intact Biological Systems
Authors: Alon Shahar , Goodwin Daniel R , Sinha Anubhav , Wassie Asmamaw T , Chen Fei , Daugharthy Evan R , Bando Yosuke , Kajita Atsushi , Xue Andrew G , Marrett Karl , Prior Robert , Cui Yi , Payne Andrew C , Yao Chun-Chen , Suk Ho-Jun , Wang Ru , Yu Chih-Chieh (Jay) , Tillberg Paul , Reginato Paul , Pak Nikita , Liu Songlei , Punthambaker Sukanya , Iyer Eswar P. R. , Kohman Richie E , Miller Jeremy A , Lein Ed S , Lako Ana , Cullen Nicole , Rodig Scott , Helvie Karla , Abravanel Daniel L , Wagle Nikhil , Johnson Bruce E , Klughammer Johanna , Slyper Michal , Waldman Julia , Jané-Valbuena Judit , Rozenblatt-Rosen Orit , Regev Aviv ,   IMAXT Consortium, Church George M , Marblestone Adam H , Boyden Edward S
Published: May 2020

Methods for highly multiplexed RNA imaging are limited in spatial resolution, and thus in their ability to localize transcripts to nanoscale and subcellular compartments. We adapt expansion microscopy, which physically expands biological specimens, for long-read untargeted and targetedin situRNA sequencing. We applied untargeted expansion sequencing (ExSeq) to mouse brain, yielding readout of thousands of genes, including splice variants and novel transcripts. Targeted ExSeq yielded nanoscale-resolution maps of RNAs throughout dendrites and spines in neurons of the mouse hippocampus, revealing patterns across multiple cell types; layer-specific cell types across mouse visual cortex; and the organization and position-dependent states of tumor and immune cells in a human metastatic breast cancer biopsy. Thus ExSeq enables highly multiplexed mapping of RNAs, from nanoscale to system scale.

One Sentence Summary

In situsequencing of physically expanded specimens enables multiplexed mapping of RNAs at nanoscale, subcellular resolution.
Mushroom bodies are required for accurate visual navigation in ants
Authors: Buehlmann Cornelia , Wozniak Beata , Goulard Roman , Webb Barbara , Graham Paul , Niven Jeremy
Published: May 2020

Visual navigation in ants has long been a focus of experimental study [1-3], but only recently have explicit hypotheses about the underlying neural circuitry been proposed [4]. Indirect evidence suggests the mushroom bodies (MB), a known site of olfactory learning [5-10], may also be the substrate for visual memory in navigation tasks [11-14]. Computational modelling shows that MB neural architecture could support this function [15, 16], though there is no direct evidence that ants require MBs for visual navigation. Here we show that lesions of MB calyces impair ants' visual navigation to a remembered food location whilst leaving their innate responses to visual cues unaffected. Ants are innately attracted to a large visual cue but we trained them to locate a food source at a specific angle to this visual cue. Subsequent bilateral or unilateral lesioning (through procaine hydrochloride injection) of the MB calyces, caused ants to revert to their innate cue attraction whilst control (saline) injected ants still approached the feeder. The ants' path straightness and walking speed were unaffected by lesions. Reversion towards the cue direction occurred irrespective of whether it was ipsi- or contralateral to the lesion site, showing this is not due simply to an induced motor bias. Monocular occlusion did not diminish ants' ability to locate the feeder, suggesting the lesion is not merely interrupting visual input to the calyx. The demonstrated dissociation between innate and learnt visual responses provides direct evidence for a specific role of the MB in navigational memory.
Detection of Viral RNA Fragments in Human iPSC-Cardiomyocytes following Treatment with Extracellular Vesicles from SARS-CoV-2 Coding-Sequence-Overexpressing Lung Epithelial Cells
Authors: Kwon Youjeong , Nukala Sarath Babu , Srivastava Shubhi , Miyamoto Hiroe , Ismail Nur Izzah , Rehman Jalees , Ong Sang-Bing , Lee Won Hee , Ong Sang-Ging
Published: May 2020

The novel coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into a worldwide pandemic. Early data suggest that the prevalence and severity of COVID-19 appear to be higher among patients with underlying cardiovascular risk factors. Despite the expression of angiotensin-converting enzyme 2 (ACE2), a functional receptor for SARS-CoV-2 infection, in cardiomyocytes, there has been no conclusive evidence of direct viral infection although the presence of inflammation and viral genome within the hearts of COVID-19 patients have been reported. Here we transduced A549 lung epithelial cells with lentivirus overexpressing selected genes of the SARS-CoV-2. We then isolated extracellular vesicles (EVs) from the supernatant of A549 cells and detected the presence of viral RNA within the purified EVs. Importantly, we observed that human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) were able to actively uptake these EVs and viral genes were subsequently detected in the cardiomyocytes. Accordingly, uptake of EVs containing viral genes led to an upregulation of inflammation-related genes in hiPSC-CMs. Thus, our findings indicate that SARS-CoV-2 RNA-containing EVs represent an indirect route of viral RNA entry into cardiomyocytes.
Unveiling diffusion pattern and structural impact of the most invasive SARS-CoV-2 spike mutation
Authors: Trucchi Emiliano , Gratton Paolo , Mafessoni Fabrizio , Motta Stefano , Cicconardi Francesco , Bertorelle Giorgio , D’Annessa Ilda , Di Marino Daniele
Published: May 2020

Starting in Wuhan, China, SARS-CoV-2 epidemics quickly propagated worldwide in less than three months, geographically sorting genomic variants in newly established propagules of infections. Stochasticity in transmission within and between countries and/or actual advantage in virus transmissibility could explain the high frequency reached by some genomic variants during the course of the outbreak.

Using a suite of statistical, population genetics, and theoretical approaches, we show that the globally most represented spike protein variant (i.e., the G clade, A → G nucleotide change at genomic position 23,403; D → G amino acid change at spike protein position 614)i)underwent a significant demographic expansion in most countries not explained by stochastic effects or enhanced pathogenicity;ii)affects the spike S1/S2 furin-like site increasing its conformational plasticity (short range effect), andiii)modifies the internal motion of the receptor-binding domain affecting its cross-connection with other functional domains (long-range effect).

Our study unambiguously links the spread of the G614 with a non-random process, and we hypothesize that this process is related to the selective advantage produced by a specific structural modification of the spike protein. We conclude that the different conformation of the S1/S2 proteolytic site is at the basis of the higher transmission rate of this invasive SARS-CoV-2 variant, and provide structural information to guide the design of selective and efficient drugs.
Self-organized map: the new aproach for study of genetic divergence in kale
Authors: Brito Orlando Gonçalves , de Andrade Júnior Valter Carvalho , Azevedo Alcinei Mistico , Silva Maria Thereza Netta Lopes , de Sá Ludimila Geiciane , Rodrigues Clóvis Henrique Oliveira , Fernandes Ana Clara Gonçalves
Published: May 2020

The objective of this study was to study the genetic divergence between genotypes of kale, to propose a methodology for the use of neural networks of the SOM type and to test its efficiency through Anderson’s discriminant analysis. We evaluated 33 families of half-siblings of kale and three commercial cultivars. The design was a randomized block with four replications with six plants per plot. A total of 14 plant-level quantitative traits were evaluated. Genetic values were predicted at family level via REML / BLUP. For the study of divergence, neural networks of the SOM type (Self-organizing Map) were adopted. We evaluated different network architectures, whose consistencies of the clusters were identified by the Anderson discriminant analysis and by the number of empty clusters. After selecting the best network configuration, a dissimilarity matrix was obtained, from which a dendrogram was constructed using the UPGMA method. The best network architecture was formed with five rows and one column, totaling five neurons and consequently five clusters. The greatest dissimilarity was established between clusters I and V. The crossing between the genotypes of cluster I and those belonging to clusters III and V are the most recommended, since they aim to recombine families with characteristics of interest to the improvement and high dissimilarity. Anderson’s discriminant analysis showed that the genotype classification was 100% correct, indicating the efficiency of the methodology used.
Differential Effects of RASA3 Mutations on Hematopoiesis are Profoundly Influenced by Genetic Background and Molecular Variant
Authors: Robledo Raymond F. , Ciciotte Steven L. , Graber Joel H. , Zhao Yue , Lambert Amy J. , Gwynn Babette , Maki Nathaniel J. , Blanc Lionel , Peters Luanne L.
Published: May 2020

Studies of the severely pancytopenicscatmouse model first demonstrated the crucial role of RASA3, a dual RAS and RAP GTPase activating protein (GAP), in hematopoiesis. RASA3 is required for survivalin utero; germline deletion is lethal at E12.5-13.5 due to severe hemorrhage and decreased fetal liver erythropoiesis. Conditional deletion in hematopoietic stem and progenitor cells (HSPCs) usingVav-Crerecapitulates the null phenotype demonstrating that RASA3 is required at the stem and progenitor level to maintain blood vessel development and integrity and effective blood production. In adults, bone marrow blood cell production and spleen stress erythropoiesis are suppressed significantly upon induction of RASA3 deficiency, leading to pancytopenia and death within two weeks. Notably, RASA3 missense mutations in mouse modelsscat(G125V) andhlb381(H794L) show dramatically different hematopoietic consequences specific to both genetic background and molecular variant. Global transcriptomic studies inscatsuggest potential targets to ameliorate disease progression.

Author Summary

Hematopoiesis is the process by which blood cells are formed. The individual must have a normal complement of red blood cells to prevent anemia, platelets to control bleeding, and white blood cells to maintain immune functions. All blood cells are derived from hematopoietic stem cells that differentiate into progenitor cells that then develop into mature circulating cells. We studied several mouse strains carrying different mutations in RASA3. We show that RASA3 is required at the earliest stages of blood formation, the stem and progenitor cells, and that the complement of genes other than RASA3, or the genetic background of the mutant strain, profoundly alters the overall effect on blood formation. Further, the molecular nature of the mutation in RASA3 also has a profound and independent effect on overall blood formation. One strain, designatedscat, suffers cyclic anemia characterized by severe anemic crisis episodes interspersed with remissions where the anemia significantly improves. Comparison ofscatcrisis and remission hematopoietic stem and progenitor cells reveals striking differences in gene expression. Analyses of these expression differences provide clues to processes that potentially drive improvement of anemia inscatand provide new avenues to pursue in future studies to identify novel therapeutics for anemia.
IntracellularCryptococcus neoformansdisrupts the transcriptome profile of M1- and M2-polarized host macrophages
Authors: Subramani Aarthi , Griggs Prianca , Frantzen Niah , Mendez James , Tucker Jamila , Murriel Jada , Sircy Linda M. , McClelland Erin E. , Seipelt-Thiemann Rebecca L. , Nelson David E.
Published: May 2020

Macrophages serve as a first line of defense against infection with the facultative intracellular pathogen,Cryptococcus neoformans(Cn). However, the ability of these innate phagocytic cells to destroy ingestedCnis strongly influenced by polarization state with classically (M1) activated macrophages better able to control cryptococcal infections than alternatively (M2) activated cells. While earlier studies have demonstrated that intracellularCnminimally affects the expression of M1 and M2 markers, the impact on the broader transcriptome associated with these states remains unclear. To investigate this, we used anin vitrocell culture model of intracellular infection together with RNA sequencing-based transcriptome profiling to measure the impact ofCninfection on gene expression in both polarization states. The gene expression profile of both M1 and M2 cells was extensively altered to become more like naive (M0) macrophages. Gene ontology analysis suggested that this involved changes in the activity of the Janus kinase-signal transducers and activators of transcription (JAK-STAT), p53, and nuclear factor-κB (NF-κB) pathways. Analyses of the principle polarization markers at the protein-level also revealed discrepancies between the RNA- and protein-level responses. In contrast to earlier studies, intracellularCnwas found to increase protein levels of the M1 marker iNos. In addition, we identified common gene expression changes that occurred post-Cninfection, independent of polarization state. This included upregulation of the transcriptional co-regulatorCited1, which was also apparent at the protein level. These changes constitute a transcriptional signature of macrophageCninfection and provide new insights into howCnimpacts gene expression and the phenotype of host phagocytes.
Prevalence, Placenta Development, and Perinatal Outcomes of Women with Hypertensive Disorders of Pregnancy at Komfo Anokye Teaching Hospital
Authors: Awuah S. P. , Okai I. , Ntim E. A. , Bedu-Addo K.
Published: May 2020

Background

One of the most common medical problems associated with pregnancy is hypertension. Hypertensive disorders of pregnancy (HDP), which has been attributable to abnormal placentation may have adverse effects on both mother and foetus if left unchecked. The objective of this study was to determine the prevalence of Hypertensive Disorders of Pregnancy (HDP), the morphological variations of human placenta in HDP, and maternal and perinatal outcomes in HDP.

Materials and Methods

This was a prospective case-control study, conducted at Komfo Anokye Teaching Hospital (KATH), Ghana. The progression of pregnancy in normotensive and hypertensive pregnant women, and the eventual perinatal outcomes were closely followed. Statistical analysis was performed using IMB-SPSS version 23. Associations were considered significant at p values of ≤ 0.05.

Results

From a total of 214 deliveries recorded during the period of study, 84 (39.25%) were hypertensives. Forty four (52%) of the hypertensives had preeclampsia, 28 (33.3%) had gestational hypertension, 6 (7.1%) had eclampsia, 4 (4.8%) had chronic hypertension, and 2 (2.4%) had preeclampsia superimposed on chronic hypertension. The frequency of placental haematoma, placental infarction, and placental calcification in the normotensives were significantly (p=0.001) lower than that of the hypertensives. The mean placental weight (p = 0.01), placental volume (p = 0.001), placental diameter (p = 0.03), and placental thickness (p = 0.001) of the normotensives were significantly higher than those of the hypertensives. The number of normotensives in whom labour was induced, who had their babies delivered by caesarean section, and who were admitted after they had given birth were significantly (p=0.001) lower than that of hypertensives who underwent similar procedures. No stillbirths were recorded in the normotensives compared with four in the hypertensives. The number of babies delivered to the normotensives who were admitted to the NICU was significantly (p=0.001) lower than those delivered by hypertensives.

Conclusion

There was a high prevalence of hypertensive disorders of pregnancy in the study site. The condition adversely affected placental development and perinatal outcomes. These adverse effects can be curtailed by embarking on a vigorous health education drive.
Cerebrospinal fluid endo-lysosomal proteins as potential biomarkers for Huntington’s disease
Authors: Lowe Alexander J. , Sjodin Simon , Rodrigues Filipe B. , Byrne Lauren M. , Blennow Kaj , Tortelli Rosanna , Zetterberg Henrik , Wild Edward J.
Published: May 2020

Molecular markers derived from cerebrospinal fluid (CSF) represent an accessible means of exploring the pathobiology of Huntington’s disease (HD) in vivo. The endo-lysosomal/autophagy system is dysfunctional in HD, potentially contributing to disease pathogenesis and representing a potential target for therapeutic intervention. Several endo-lysosomal proteins have shown promise as biomarkers in other neurodegenerative diseases; however, they have yet to be fully explored in HD. We performed parallel reaction monitoring mass spectrometry analysis (PRM-MS) of multiple endo-lysosomal proteins in the CSF of 60 HD mutation carriers and 20 healthy controls. Using generalised linear models controlling for age and CAG, none of the 18 proteins measured displayed significant differences in concentration between HD patients and controls. This was affirmed by principal component analysis, in which no significant difference across disease stage was found in any of the three components representing lysosomal hydrolases, binding/transfer proteins and innate immune system/peripheral proteins. However, several proteins were associated with measures of disease severity and cognition: most notably amyloid precursor protein, which displayed strong correlations with composite Unified Huntington’s Disease Rating Scale, UHDRS Total Functional Capacity, UHDRS Total Motor Score, Symbol Digit Modalities Test and Stroop Word Reading. We conclude that although endo-lysosomal proteins are unlikely to have value as disease state CSF biomarkers for Huntington’s disease, several proteins demonstrate associations with clinical severity, thus warranting further, targeted exploration and validation in larger, longitudinal samples.
Predicting the Immunogenicity of T cell epitopes: From HIV to SARS-CoV-2
Authors: Gao Ang , Chen Zhilin , Segal Florencia Pereyra , Carrington Mary , Streeck Hendrik , Chakraborty Arup K. , Julg Boris
Published: May 2020

We describe a physics-based learning model for predicting the immunogenicity of Cytotoxic T Lymphocyte (CTL) epitopes derived from diverse pathogens, given a Human Leukocyte Antigen (HLA) genotype. The model was trained and tested on experimental data on the relative immunodominance of CTL epitopes in Human Immunodeficiency Virus infection. The method is more accurate than publicly available models. Our model predicts that only a fraction of SARS-CoV-2 epitopes that have been predicted to bind to HLA molecules is immunogenic. The immunogenic CTL epitopes across all SARS-CoV-2 proteins are predicted to provide broad population coverage, but the immunogenic epitopes in the SARS-CoV-2 spike protein alone are unlikely to do so. Our model predicts that several immunogenic SARS-CoV-2 CTL epitopes are identical to those contained in low-pathogenicity coronaviruses circulating in the population. Thus, we suggest that some level of CTL immunity against COVID-19 may be present in some individuals prior to SARS-CoV-2 infection.
Crystal structures of SARS-CoV-2 ADP-ribose phosphatase (ADRP): from the apo form to ligand complexes
Authors: Michalska Karolina , Kim Youngchang , Jedrzejczak Robert , Maltseva Natalia I. , Stols Lucy , Endres Michael , Joachimiak Andrzej
Published: May 2020

Among 15 nonstructural proteins (Nsps), the newly emerging SARS-CoV-2 encodes a large, multidomain Nsp3. One of its units is ADP-ribose phosphatase domain (ADRP, also known as macrodomain) which is believed to interfere with the host immune response. Such a function appears to be linked to the protein’s ability to remove ADP-ribose from ADP-ribosylated proteins and RNA, yet the precise role and molecular targets of the enzyme remains unknown. Here, we have determined five, high resolution (1.07 - 2.01 Å) crystal structures corresponding to the apo form of the protein and complexes with 2-(N-morpholino)ethanesulfonic acid (MES), AMP and ADPr. We show that the protein undergoes conformational changes to adapt to the ligand in a manner previously observed before for in close homologs from other viruses. We also identify a conserved water molecule that may participate in hydrolysis. This work builds foundations for future structure-based research of the ADRP, including search for potential antiviral therapeutics.
A Molecular Mechanism for Probabilistic Bet-hedging and its Role in Viral Latency
Authors: Chaturvedi Sonali , Klein Jonathan , Vardi Noam , Bolovan-Fritts Cynthia , Wolf Marie , Du Kelvin , Mlera Luwanika , Calvert Meredith , Moorman Nathaniel J. , Goodrum Felicia , Huang Bo , Weinberger Leor S.
Published: May 2020

Probabilistic bet hedging, a strategy to maximize fitness in unpredictable environments by matching phenotypic variability to environmental variability, is theorized to account for the evolution of various fate-specification decisions, including viral latency. However, the molecular mechanisms underlying bet-hedging remain unclear. Here, we report that large variability in protein abundance within individual herpesvirus virion particles enables probabilistic bet hedging between viral replication and latency. Super-resolution imaging of individual virions of the human herpesvirus cytomegalovirus (CMV) showed that virion-to-virion levels of pp71 tegument protein—the major viral transactivator protein—exhibit extreme variability. This super-Poissonian tegument variability promoted alternate replicative strategies: high virion pp71 levels enhance viral replicative fitness but, strikingly, impede silencing, whereas low virion pp71 levels reduce fitness but promote silencing. Overall, the results indicate that stochastic tegument packaging provides a mechanism enabling probabilistic bet hedging between viral replication and latency.

SIGNIFICANCE

Probabilistic bet hedging is a generalized diversification strategy to maximize fitness in unpredictable environments, and has been proposed as an evolutionary basis for herpesvirus latency. However, the molecular mechanisms enabling probabilistic bet hedging have remained elusive. Here, we find that the human herpesvirus cytomegalovirus—a major cause of birth defects and transplant failures—utilizes stochastic variability in the abundance of a protein packaged into individual viral particles to enable probabilistic bet hedging between alternate viral states.
Discovery of anti-amoebic inhibitors from screening the MMV Pandemic Response Box onBalamuthia mandrillaris, Naegleria fowleriandAcanthamoeba castellanii
Authors: Rice Christopher A. , Troth Emma V. , Russell A. Cassiopeia , Kyle Dennis E.
Published: May 2020

Pathogenic free-living amoebae,Balamuthia mandrillaris, Naegleria fowleriand severalAcanthamoebaspecies are the etiological agents of severe brain diseases, with case mortality rates >90%. A number of constraints including misdiagnosis and partially effective treatments lead to these high fatality rates. The unmet medical need is for rapidly acting, highly potent new drugs to reduce these alarming mortality rates. Herein, we report the discovery of new drugs as potential anti-amoebic agents. We used the CellTiter-Glo 2.0 high-throughput screening methods to screen the Medicines for Malaria Ventures (MMV) Pandemic Response Box in a search for new active chemical scaffolds. Initially we screened the library as a single-point assay at 10 and 1 µM. From these data, we reconfirmed hits by conducting quantitative dose response assays and identified 12 hits againstB. mandrillaris, 29 againstN. fowleriand 14 againstA. castellaniiranging from nanomolar to low micromolar potency. We further describe 11 novel molecules with activity againstB. mandrillaris, 22 againstN. fowleriand 9 againstA. castellanii.These structures serve as a starting point for medicinal chemistry studies and demonstrate the utility of phenotypic screening for drug discovery to treat diseases caused by free-living amoebae.
ChABC infusions into medial prefrontal cortex, but not posterior parietal cortex, improve the performance of rats tested on a novel, challenging delay in the touchscreen TUNL task
Authors: Anderson Michael D. , Paylor John W. , Scott Gavin A. , Greba Quentin , Winship Ian R. , Howland John G.
Published: May 2020

Perineuronal nets (PNNs) are specialized extracellular matrix structures that surround subsets of neurons throughout the central nervous system (CNS). They are made up of chondroitin sulfate proteoglycans (CSPGs), hyaluronan, tenascin-R, and many other link proteins that together make up their rigid and lattice-like structure. Modulation of PNNs can alter synaptic plasticity and thereby affect learning, memory, and cognition. In the present study, we degraded PNNs in the medial prefrontal (mPFC) and posterior parietal (PPC) cortices of Long–Evans rats using the enzyme chondroitinase ABC (ChABC), which cleaves apart CSPGs. We then measured the consequences of PNN degradation on spatial working memory (WM) with a trial-unique, non-matching-to location (TUNL) automated touchscreen task. All rats were trained with a standard 6 sec delay and 20 sec inter-trial interval (ITI) and then tested under four different conditions: a 6 sec delay, a variable 2 or 6 sec delay, a 2 sec delay with a 1 sec ITI (interference condition), and a 20 sec delay. Rats that received mPFC ChABC treatment initially performed TUNL with higher accuracy, more selection trials completed, and fewer correction trials completed compared to controls in the 20 sec delay condition but did not perform differently from controls in any other condition. Rats that received PPC ChABC treatment did not perform significantly differently from controls in any condition. Posthumous immunohistochemistry confirmed an increase in CSPG degradation products (C4S stain) in the mPFC and PPC following ChABC infusions while WFA staining intensity and parvalbumin positive neuron number were decreased following mPFC, but not PPC, ChABC infusions. These findings suggest that PNNs in the mPFC play a subtle role in spatial WM, but PNNs in the PPC do not. Furthermore, it appears that PNNs in the mPFC are involved in adapting to a challenging novel delay, but that they do not play an essential role in spatial WM function.
A new ZnII metallocryptand with unprecedented diflexure helix induced by V-shaped diimidazole building blocks
Authors: Shi Zhi-Qiang , Ji Ning-Ning , Hu Hai-Liang
Published: May 2020

Taking advantage of V-shaped ligands, a ZnII metallocryptand, namely {[Zn2(didp)2(m-bdc)2]}
n
, (1) [didp = 2,8-di(1H-imidazol-1-yl)-dibenzothiophene and m-H2bdc = isophthalic acid], has been hydrothermally synthesized. Single-crystal X-ray diffraction analysis reveals a 26-membered butterfly-type metallomacrocycle [Zn2(didp)2]. One m-bdc2− ligand bridges [Zn2(didp)2] units to form a laterally non-symmetric [Zn2(didp)2(m-bdc)] metallocryptand with an exo–exo conformation. Another crystallographically independent m-bdc2− functions as a secondary synthon to bridge discrete metallocryptands into a 1D zigzag chain architecture. Undoubtedly, the choice of two matched ligands in this work is crucial for metallocryptand construction and structure expansion. Interestingly, a rare helical chain with two flexures in one single L and/or R strand is observed. Another important feature is the C—O...π interactions, by which the dimensionality extension of (1) can be induced. Fluorescence measurements and density functional theory (DFT) calculations illustrate that the emission of (1) can probably be attributed to ligand-to-ligand charge transfer (LLCT).
Intra- and intermolecular interactions in a series of chlorido-tricarbonyl-diazabutadienerhenium(I) complexes: structural and theoretical studies
Authors: Kia Reza , Kalaghchi Azadeh
Published: May 2020

A series of new chlorido-tricarbonylrhenium(I) complexes bearing alkyl-substituted diazabutadiene (DAB) ligands, namely N,N′-bis(2,4-dimethylbenzene)-1,4-diazabutadiene (L1), N,N′-bis(2,4-dimethylbenzene)-2,3-dimethyl-1,4-diazabutadiene (L2), N,N′-bis(2,4,6-trimethylbenzene)-2,3-dimethyl-1,4-diazabutadiene (L3) and N,N′-bis(2,6-diisopropylbenzene)-1,4-diazabutadiene (L4), were synthesized and investigated. The crystal structures have been fully characterized by X-ray diffraction and spectroscopic methods. Density functional theory, natural bond orbital and non-covalent interaction index methods have been used to study the optimized geometry in the gas phase and intra- and intermolecular interactions in the complexes, respectively. The most important studied interactions in these metal carbonyl complexes are n→π*, n→σ* and π→π*. Among complexes 1–4, only 2 shows interesting intermolecular n→π* interactions due to lp(C[triple-bond]O)...π* and lp(Cl)...π* (lp = lone pair) contacts.
Three 4-(4-fluorophenyl)piperazin-1-ium salts containing organic anions: supramolecular assembly in one, two and three dimensions
Authors: Harish Chinthal Chayanna , Yathirajan Hemmige S. , Archana Sreeramapura D. , Foro Sabine , Glidewell Christopher
Published: May 2020

Three salts containing the 4-(4-fluorophenyl)piperazin-1-ium cation have been prepared and structurally characterized. In 4-(4-fluorophenyl)piperazin-1-ium 2-hydroxy-3,5-dinitrobenzoate, C10H14FN2
+·C7H3N2O7
−, (I), the anion contains an intramolecular O—H...O hydrogen bond, and it has a structure similar to that of the picrate ion. The cations and anions are linked into [001] chains of rings by a combination of two three-centre N—H...(O)2 hydrogen bonds. The anion in 4-(4-fluorophenyl)piperazin-1-ium hydrogen oxalate, C10H14FN2
+·C2HO4
−, (II), is planar, and the cations and anions are linked into (100) sheets by multiple hydrogen bonds including two-centre N—H...O, three-centre N—H...(O)2, O—H...O, C—H...O and C—H...π(arene) types. In 4-(4-fluorophenyl)piperazin-1-ium hydrogen (2R,3R)-tartrate monohydrate, C10H14FN2
+·C4H5O6
−·H2O, (III), the anion exhibits an approximate non-crystallographic twofold rotation symmetry with antiperiplanar carboxyl groups. A combination of eight hydrogen bonds, encompassing two- and three-centre N—H...O systems, O—H...O and C—H...π(arene) types, link the independent components into a three-dimensional framework. Comparisons are made with some related structures.
Defining the art product: a network perspective
Authors: Wickham Mark , Lehman Kim , Fillis Ian
Published: May 2020

Purpose

This paper explores the nature of art as a product through a network perspective, accounting for key contributing stakeholders in shaping its essence.

Design/methodology/approach

This study adopted a qualitative data collection and analysis design and is centred on a series of face-to-face interviews with established Australian visual artists.

Findings

Results support the notion of an art product shaped by interconnections and interdependencies of actors in the art market. In particular, attention is paid to the roles of actors in conceptual, production and distribution networks.

Research limitations/implications

Although there are idiosyncrasies that (in part) define the Australian art market context, the issues identified here are nonetheless useful in determining the nature of the interconnectedness of the art market in other similar Western contexts. Many Australian artists have achieved similar recognition and status to other established artists elsewhere. Future cross-cultural comparative research should be carried out in order to assess this relationship in the longer term.

Practical implications

Artists at different stages of their careers can transfer the findings of this research into the development of a series of relevant strategies and tactics for developing their art and culture products more effectively.

Originality/value

Although philosophical assessments of art as a product have been carried out elsewhere, there is a lack of evaluation from an art versus marketplace lens in considering the perspectives of interested stakeholders
Correlations between facial emotion recognition and cognitive flexibility in autism spectrum disorder
Authors: Fabio Rosa Angela , Esposito Sonia , Carrozza Cristina , Pino Gaetana , Caprì Tindara
Published: May 2020

Purpose

Various studies have examined the role of executive functions in autism, but there is a lack of research in the current literature on cognitive flexibility in autism spectrum disorders (ASD). The purpose of this study is to investigate whether cognitive flexibility deficits could be related to facial emotion recognition deficits in ASD.

Design/methodology/approach

In total, 20 children with ASD and 20 typically developing children, matched for intelligence quotient and gender, were examined both in facial emotion recognition tasks and in cognitive flexibility tasks through the dimensional change card sorting task.

Findings

Despite cognitive flexibility not being a core deficit in ASD, impaired cognitive flexibility is evident in the present research. Results show that cognitive flexibility is related to facial emotion recognition and support the hypothesis of an executive specific deficit in children with autism.

Research limitations/implications

One of the limit is the use of just one cognitive test to measure cognitive flexibility and facial recognition. This could be important to be taken into account in the new research. By increasing the number of common variables assessing cognitive flexibility, this will allow for a better comparison between studies to characterize impairment in cognitive flexibility in ASD.

Practical implications

Investigating impairment in cognitive flexibility may help to plan training intervention based on the induction of flexibility.

Social implications

If the authors implement cognitive flexibility people with ASD can have also an effect on their social behavior and overcome the typical and repetitive behaviors that are the hallmark of ASD.

Originality/value

The originality is to relate cognitive flexibility deficits to facial emotion.
The complexities of managing historic buildings with BIM
Authors: Charlton James , Kelly Kenneth , Greenwood David , Moreton Leo
Published: May 2020

Purpose

The adoption of building information modelling (BIM) in managing built heritage is an exciting prospect, but one that presents complexities additional to those of modern buildings. If challenges can be identified and overcome, the adoption of historic BIM (HBIM) could offer efficiencies in how heritage buildings are managed.

Design/methodology/approach

Using Durham Cathedral as a case study, we present the workflows applied to create an asset information model to improve the way this unique UNESCO World Heritage Site is managed, and in doing so, set out the challenges and complexities in achieving an HBIM solution.

Findings

This study identifies the need for a better understanding of the distinct needs and context for managing historic assets, and the need for heritage information requirements (HIR) that reflect this.

Originality/value

This study presents first-hand findings based on a unique application of BIM at Durham Cathedral, a UNESCO World Heritage Site. The study provides a better understanding of the challenges and drivers of HBIM adoption across the heritage sector and underlines the need for information requirements that are unique to historical buildings/assets to deliver a coherent and relevant HBIM approach.
Tailoring service recovery messages to consumers’ affective states
Authors: Hill Cummings Krista , Yule Jennifer A.
Published: May 2020

Purpose

This study aims to propose that providers should tailor recovery responses to consumers’ emotional states to improve evaluations and behavioral intentions.

Design/methodology/approach

A multi-study approach comprising field and lab data was used. The field study, conducted on the Boston public transport network during a weather crisis, sought to determine how a provider should deliver their recovery response to match the consumer’s affective state. In the lab studies, the importance of tailoring a recovery message to the consumer’s state is experimentally demonstrated while controlling for factors such as consumer brand involvement.

Findings

This study finds that an emotion-focused recovery emphasizing empathy should be given to those in an avoidance affective state (i.e. focused on the avoidance of negative outcomes) such as worry. A problem-focused recovery, in which the focus is on the process that led to the failure and the steps that will be taken to correct it, should be provided to those in an approach state (i.e. concerned with advancement and accomplishment) such as anger. This study also finds this effect is more salient under low involvement conditions.

Research limitations/implications

Future research should examine how nonverbal behavior during recovery can be tailored to a consumer’s state.

Practical implications

Service providers are encouraged to tailor recovery messages to consumers’ affective states.

Originality/value

To the best of the authors’ knowledge, this study is the first to examine matching recovery messages to affective states, an important contribution as service failures can elicit a wide variety of affective states that influence how consumers react to recovery messages.