bluuebunny/crossref_metadata_2025 huggingface dataset:
Increased qualities and in vitro anticancer effects
of ‘Doenjang’ fermented in ‘Onggi’
Authors: Lee Jong-Hyun , Lim Yaung-Iee , Lee So-Young , Kim Jong-Hee , Park Kun-Young
Published: July 2020

The quality and in vitro anticancer effects of
‘Doenjang’ that was fermented in ‘Onggi’ and other
ordinary containers were studied. The containers employed herein for the
fermentation were non-glazed ‘Onggi’ (OWOG), glazed
‘Onggi’, ceramic and stainless steel containers, in addition to
glass bottles. Grain-type was fermented in each container with salt and water in
a ratio of 33:12:45 at 37°C for 40 day. During the fermentation of
‘Doenjang’ in ‘Onggi’, the pH decreased and the
acidity increased. In addition, the amino-type nitrogen content increased,
although the ammonium nitrogen content decreased. The levels of yeast, mold, and
lactic acid bacteria increased, while the total bacteria content decreased for
the doenjang fermented in ‘Onggi’ compared to the values obtained
when other types of container were employed. Overall, the obtained results
indicated that ‘Onggi’, and especially OWOG, was the optimal
container for the fermentation of ‘Doenjang’ to ensure a high
quality and in vitro anticancer effect.
Qualitative and quantitative evaluation of residual microplastics
in ark shell
Authors: Lee Han-Cheol , Jo Ah-Hyeon , Kang Ju-Yeong , Park Eun-Ji , Park Min-Ji , Kim Jung-Beom
Published: July 2020

The characteristics and particle numbers of residual microplastics were
investigated in ark shell to establish a food safety management method. The ark
shell employed herein was purchased in Jeonnam province. The experimental method
involved disassembly of the organic matter present in the ark shell using
10% KOH, followed by qualitative and quantitative analysis of the
microplastics using Fourier transform infrared (FT-IR) spectroscopy. The mean
value of residual microplastics was 0.8 microplastic (MP)/individual in ark
shell A, and were found to consist of one polypropylene (PP), two polyethylenes
(PE), and one epoxy. The mean value of residual microplastics was 1.2
MP/individual in ark shell B, and were found to consist of two PP, two PE, and
two polyesters. In ark shell C, the mean value of residual microplastics was 1.6
MP/individual, consisting of two PP, two PE, two polyesters, and two acrylates.
These results indicated that the residual microplastics in the ark shell are
present in relatively lower quantitative levels compared to the results
presented in previous reports. However, due to the ability of microplastics to
contaminate marine life by absorbing harmful chemicals, thereby adversely
affecting marine food product safety, regular monitoring of the residual
microplastics present in marine products is necessary to ensure food safety.
The Trans-omics Landscape of COVID-19
Authors: Wu Peng , Chen Dongsheng , Ding Wencheng , Wu Ping , Hou Hongyan , Bai Yong , Zhou Yuwen , Li Kezhen , Xiang Shunian , Liu Panhong , Ju Jia , Guo Ensong , Liu Jia , Yang Bin , Fan Junpeng , He Liang , Sun Ziyong , Feng Ling , Wang Jian , Wu Tangchun , Wang Hao , Cheng Jin , Xing Hui , Meng Yifan , Li Yongsheng , Zhang Yuanliang , Luo Hongbo , Xie Gang , Lan Xianmei , Tao Ye , Yuan Hao , Huang Kang , Sun Wan , Qian Xiaobo , Li Zhichao , Huang Mingxi , Ding Peiwen , Wang Haoyu , Qiu Jiaying , Wang Feiyue , Wang Shiyou , Zhu Jiacheng , Ding Xiangning , Chai Chaochao , Liang Langchao , Wang Xiaoling , Luo Lihua , Sun Yuzhe , Yang Ying , Zhuang Zhenkun , Li Tao , Tian Lei , Zhang Shaoqiao , Zhu Linnan , Chen Lei , Wu Yiquan , Ma Xiaoyan , Chen Fang , Ren Yan , Xu Xun , Liu Siqi , Wang Jian , Yang Huanming , Wang Lin , Sun Chaoyang , Ma Ding , Jin Xin , Chen Gang
Published: July 2020

System-wide molecular characteristics of COVID-19, especially in those patients without comorbidities, have not been fully investigated. We compared extensive molecular profiles of blood samples from 231 COVID-19 patients, ranging from asymptomatic to critically ill, importantly excluding those with any comorbidities. Amongst the major findings, asymptomatic patients were characterized by highly activated anti-virus interferon, T/natural killer (NK) cell activation, and transcriptional upregulation of inflammatory cytokine mRNAs. However, given very abundant RNA binding proteins (RBPs), these cytokine mRNAs could be effectively destabilized hence preserving normal cytokine levels. In contrast, in critically ill patients, cytokine storm due to RBPs inhibition and tryptophan metabolites accumulation contributed to T/NK cell dysfunction. A machine-learning model was constructed which accurately stratified the COVID-19 severities based on their multi-omics features. Overall, our analysis provides insights into COVID-19 pathogenesis and identifies targets for intervening in treatment.
Quantifying Evolutionary Importance of Protein Sites: A Tale of Two Measures
Authors: Sharir-Ivry Avital , Xia Yu
Published: July 2020

A key challenge in evolutionary biology is the accurate quantification of selective pressure on proteins and other biological macromolecules at single-site resolution. The evolutionary importance of a protein site under purifying selection is typically measured by the degree of conservation of the protein site itself. A possible alternative measure is the strength of the site-induced conservation gradient in the rest of the protein structure. However, the quantitative relationship between these two measures remains unknown. Here, we show that despite major differences, there is a strong linear relationship between the two measures such that more conserved protein sites also induce stronger conservation gradient in the rest of the protein. This linear relationship is universal as it holds for different types of proteins and functional sites in proteins. Our results show that the strong selective pressure acting on the functional site in general percolates through the rest of the protein via residue-residue contacts. Surprisingly however, catalytic sites in enzymes are the principal exception to this rule. Catalytic sites induce significantly stronger conservation gradients in the rest of the protein than expected from the degree of conservation of the site alone. The unique requirement for the active site to selectively stabilize the transition state of the catalyzed chemical reaction imposes additional selective constraints on the rest of the enzyme.
A disynaptic circuit in the globus pallidus controls locomotion inhibition
Authors: Aristieta Asier , Barresi Massimo , Lindi Shiva A. , Barriere Gregory , Courtand Gilles , de la Crompe Brice , Guilhemsang Lise , Gauthier Sophie , Fioramonti Stéphanie , Baufreton Jérôme , Mallet Nicolas P.
Published: July 2020

Basal ganglia (BG) inhibit movement through two independent pathways, the indirect- and the hyperdirect-pathways. The globus pallidus (GP) has always been viewed as a simple relay within these two pathways, but its importance has changed drastically with the discovery of two functionally-distinct cell types, namely the prototypic and the arkypallidal neurons. Classic BG models suggest that all GP neurons receive GABAergic inputs from striato-pallidal indirect spiny projection neurons and glutamatergic inputs from subthalamic neurons. However, whether this synaptic connectivity scheme applies to both GP cell-types is currently unknown. Here, we optogenetically dissect the input organization of prototypic and arkypallidal neurons and further define the circuit mechanism underlying action inhibition in BG. Our results highlight that an increased activity of arkypallidal neurons is required to inhibit locomotion. Finally, this work supports the view that arkypallidal neurons are part of a novel disynaptic feedback loop that broadcast inhibitory control on movement execution.
Rapid quantitative screening assay for SARS-CoV-2 neutralizing antibodies using HiBiT-tagged virus-like particles
Authors: Miyakawa Kei , Jeremiah Sundararaj Stanleyraj , Ohtake Norihisa , Matsunaga Satoko , Yamaoka Yutaro , Nishi Mayuko , Morita Takeshi , Saji Ryo , Nishii Mototsugu , Kimura Hirokazu , Hasegawa Hideki , Takeuchi Ichiro , Ryo Akihide
Published: July 2020

SARS-CoV-2 neutralizing antibodies confer protective immunity against reinfection. We have developed a rapid test for screening SARS-CoV-2 neutralization antibodies using genome-free virus-like particles incorporated with a small luciferase peptide, HiBiT. Their entry into LgBiT-expressing target cells reconstitutes NanoLuc luciferase readily detected by a luminometer. This newly developed HiBiT-tagged Virus-like particle-based Neutralization Test (hiVNT) can readily quantify SARS-CoV-2 neutralizing antibodies within three hours with a high-throughput in a low biosafety setting. Moreover, the neutralizing activity obtained from hiVNT was highly consistent with that measured by the conventional neutralization test using authentic SARS-CoV-2. Furthermore, antibody responses to both viral spike and nucleocapsid proteins correlated with the neutralization activity assessed by hiVNT. Our newly-developed hiVNT could be instrumental to survey individuals for the presence of functional neutralizing antibody against SARS-CoV-2.
Importation of SARS-CoV-2 following the“semaine de relâche”and Québec’s COVID-19 burden - a mathematical modeling study
Authors: Godin A , Xia Y , Buckeridge DL , Mishra S , Douwes-Schultz D , Shen Y , Lavigne M , Drolet M , Schmidt AM , Brisson M , Maheu-Giroux M
Published: July 2020

Background

The Canadian epidemics of COVID-19 exhibit distinct early trajectories, with Québec bearing a very high initial burden. Thesemaine de relâche, or March break, took place two weeks earlier in Québec as compared to the rest of Canada. This event may have played a role in the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We aimed to examine the role of case importation in the early transmission dynamics of SARS-CoV-2 in Québec.

Methods

Using detailed surveillance data, we developed and calibrated a deterministic SEIR-type compartmental model of SARS-CoV-2 transmission. We explored the impact of altering the number of imported cases on hospitalizations. Specifically, we investigated scenarios without case importation after March break, and as scenarios where cases were imported with the same frequency/timing as neighboring Ontario.

Results

A total of 1,544 and 1,150 returning travelers were laboratory-confirmed in Québec and Ontario, respectively (with symptoms onset before 2020-03-25). The cumulative number of hospitalizations could have been reduced by 55% (95%CrI: 51-59%) had no cases been imported after Québec’s March break. However, had Québec experienced Ontario’s number of imported cases, cumulative hospitalizations would have only been reduced by 12% (95%CrI: 8-16%).

Interpretation

Our results suggest that case importation played an important role in the early spread of COVID-19 in Québec. Yet, heavy importation of SARS-CoV-2 in early March could be insufficient to resolve interprovincial heterogeneities in cumulative hospitalisations. The importance of other factors-public health preparedness, responses, and capacity-should be investigated.
Examining COVID19 Positivity-Ratio Trends in US States from April-July: Are Rising Caseloads Attributable to ‘More Testing’ and Do State Political-Affiliations Play a Role?
Authors: Sen Bisakha P. , Padalabalanarayanan Sangeetha
Published: July 2020

Importance

Rising Covid19 cases in the US are attributed by some political leaders to more testing. Positivity-ratios (cases to tests ratio) in conjunction with cases and tests provide a better overview. However, comprehensive overviews of positivity-ratio patterns are scarce.

Objective

To examine trends in positivity-ratios, tests and cases by state from mid-April-mid-July. Further, to examine whether positivity-ratio patters are associated with state political-affiliations.

Methods

State-level publicly available data on Covid19 is used. Seven-day moving averages (MA7) of positivity-ratio are computed for April 21-July 15. States are assigned to four groups based on patterns of change in positivity-ratio – higher at end of study period than beginning (Group 1), initial decline but subsequent increase starting Memorial Day weekend (Group 2), initial decrease but an upturn in last 14 days (Group 3), and consistent downward trend (Group 4). ‘Political-affiliation’ is categorized as ‘Republican-leaning’ if President Trump won the state and the governor is Republican. Additionally, a proxy measure is used to indicate intensity of Black Lives Matter (BLM) protests in the state. Associations are tested using chi-square analysis.

Results

Fourteen states are in Group 1, fifteen states in Group 2, fifteen states in Group 3, and six states and DC in Group 4. 78.57% of Group 1, 33.33% of Group 2, 40% of group 3, and none in Group 4 were Republican-leaning. The difference in distribution was statistically significant (p<0.01). Distribution of ‘high’ intensity BLM protests across the four groups was not statistically different (p>0.10).

Conclusion

Increased Covid19 cases cannot be attributed to more testing. Indeed, the high positivity-ratios in most states indicate current testing is failing to capture actual infection rates. The association between state political-affiliation and positivity-ratios suggests Republican voters may be somewhat more skeptical of the gravity of the disease and emphasizes the importance of messaging by political leaders.
Tractography-Pathology Correlations in Traumatic Brain Injury: A TRACK-TBI Study
Authors: Nolan Amber L. , Petersen Cathrine , Iacono Diego , Mac Donald Christine L. , Mukherjee Pratik , van der Kouwe Andre , Jain Sonia , Stevens Allison , Diamond Bram R. , Wang Ruopeng , Markowitz Amy J. , Fischl Bruce , Perl Daniel P. , Manley Geoffrey T. , Keene C. Dirk , Diaz-Arrastia Ramon , Edlow Brian L. ,   the TRACK-TBI Investigators
Published: July 2020

Diffusion tractography MRI can infer changes in network connectivity in patients with traumatic brain injury (TBI), but pathological substrates of disconnected tracts have not been well-defined due to a lack of high-resolution imaging with histopathological validation. We developed anex vivoMRI protocol to analyze tract terminations at 750 μm resolution, followed by histopathologic evaluation of white matter pathology, and applied these methods to a 60-year-old man who died 26 days after TBI. Analysis of 74 cerebral hemispheric white matter regions revealed a heterogeneous distribution of tract disruptions. Associated histopathology identified variable white matter injury with patchy deposition of amyloid precursor protein and loss of neurofilament-positive axonal processes, myelin dissolution, astrogliosis, microgliosis, and perivascular hemosiderin-laden macrophages. Multiple linear regression revealed that tract disruption strongly correlated with neurofilament loss.Ex vivodiffusion MRI can detect tract disruptions in the human brain that reflect axonal injury.
A Visuomotor Model Enhances Human Position Sense
Authors: Omprakash Charitha , Razavizadeh Seyedsina , Stenner Max-Philipp
Published: July 2020

Integrating information from multiple sources reduces uncertainty. Besides sensory input, animals have access to another source of information about their body and the environment, i.e., their own motor commands, which alter the body and environment in a predictable way. Does this predictability reduce perceptual uncertainty, i.e., variance? Participants moved their unseen arm and reported movement endpoint locations. In two conditions, a predictive model of visuomotor contingencies could either be fully formed, and used for this estimation, or remained incomplete. This was achieved through context trials that provided visual endpoint feedback at a predictable vs. unpredictable latency, while carrying identical spatial information. In two experiments, we found that endpoint estimation was less variable when a full, spatiotemporal, model could be formed. Higher perceptual precision was paralleled by enhanced movement accuracy. We conclude that a visuomotor model provides a separate source of information, additional to sensory input, which enhances human position sense.
An aberrant cytoplasmic intron retention programme is a blueprint for ALS-related RBP mislocalization
Authors: Tyzack Giulia E. , Neeves Jacob , Klein Pierre , Crerar Hamish , Ziff Oliver , Taha Doaa M. , Luisier Raphaëlle , Luscombe Nicholas M , Patani Rickie
Published: July 2020

We recently described aberrant cytoplasmic SFPQ intron-retaining transcripts (IRTs) and concurrent SFPQ protein mislocalization as a new hallmark of amyotrophic lateral sclerosis (ALS). However the generalizability and potential roles of cytoplasmic IRTs in health and disease remain unclear. Here, using time-resolved deep-sequencing of nuclear and cytoplasmic fractions of hiPSCs undergoing motor neurogenesis, we reveal that ALS-causing VCP gene mutations lead to compartment-specific aberrant accumulation of IRTs. Specifically, we identify >100 IRTs with increased cytoplasmic (but not nuclear) abundance in ALS samples. Furthermore, these aberrant cytoplasmic IRTs possess sequence-specific attributes and differential predicted binding affinity to RNA binding proteins (RBPs). Remarkably, TDP-43, SFPQ and FUS – RBPs known for nuclear-to-cytoplasmic mislocalization in ALS – avidly and specifically bind to this aberrant cytoplasmic pool of IRTs, as opposed to any individual IRT. Our data are therefore consistent with a novel role for cytoplasmic IRTs in regulating compartment-specific protein abundance. This study provides new molecular insight into potential pathomechanisms underlying ALS and highlights aberrant cytoplasmic IRTs as potential therapeutic targets.

Abstract Figure
V-ATPase controls tumor growth and autophagy in aDrosophilamodel of gliomagenesis
Authors: Formica Miriam , Storaci Alessandra , Bertolini Irene , Vaira Valentina , Vaccari Thomas
Published: July 2020

Glioblastoma (GBM), a very aggressive and incurable tumor, often results from constitutive activation of EGFR (epidermal growth factor receptor) and of PI3K (phosphoinositide 3-kinase). To understand the role of autophagy in the pathogenesis of glial tumorsin vivo, we used an establishedDrosophila melanogastermodel of glioma based on overexpression in larval glial cells of an active humanEGFRand of the PI3K homologDp110. Interestingly, the resulting hyperplastic glia expresses high levels of ref(2)P (refractory to Sigma P), theDrosophilahomolog of p62/SQSTM1. However, cellular clearance of autophagic cargoes appears inhibited upstream of autophagosome formation. Remarkably, downregulation of subunits of the vacuolar-H+-ATPase (V-ATPase) prevents overgrowth, reduces PI3K signaling and restores clearance. Consistent with evidence in flies, neurospheres from patients with high V-ATPase subunit expression show inhibition of autophagy. Altogether, our data suggest that autophagy is repressed during glial tumorigenesis and that V-ATPase could represent a therapeutic target against GBM.
Identifying loci under selection via explicit demographic models
Authors: Luqman Hirzi , Widmer Alex , Fior Simone , Wegmann Daniel
Published: July 2020

Adaptive genetic variation is a function of both selective and neutral forces. To accurately identify adaptive loci, it is thus critical to account for demographic history. Theory suggests that signatures of selection can be inferred using the coalescent, following the premise that genealogies of selected loci deviate from neutral expectations. Here, we build on this theory to develop an analytical framework to identify Loci under Selection via explicit Demographic models (LSD). Under this framework, signatures of selection are inferred through deviations in demographic parameters, rather than through summary statistics directly, and demographic history is accounted for explicitly. Leveraging on the property of demographic models to incorporate directionality, we show that LSD can provide information on the environment in which selection acts on a population. This can prove useful in elucidating the selective processes underlying local adaptation, by characterising genetic trade-offs and extending the concepts of antagonistic pleiotropy and conditional neutrality from ecological theory to practical application in genomic data. We implement LSD via Approximate Bayesian Computation and demonstrate, via simulations, that LSD has i) high power to identify selected loci across a large range of demographic-selection regimes, ii) outperforms commonly applied genome-scan methods under complex demographies, and iii) accurately infers the directionality of selection for identified candidates. Using the same simulations, we further characterise the behaviour of isolation-with-migration models conducive to the study of local adaptation under regimes of selection. Finally, we demonstrate an application of LSD by detecting loci and characterising genetic trade-offs underlying flower colour inAntirrhinum majus.
Dentate spikes and external control of hippocampal function
Authors: Dvorak D. , Chung A. , Park E. H. , Fenton A. A.
Published: July 2020

Mouse hippocampus CA1 place-cell discharge typically encodes current location but during slow gamma dominance (SGdom), when slow gamma oscillations (30-50 Hz) dominate mid-frequency gamma oscillations (70-90 Hz) in CA1 local field potentials, CA1 discharge switches to represent distant recollected locations. We report that dentate spike type 2 (DSM) events initiated by MECII→DG inputs promote SGdomand change excitation-inhibition coordinated discharge in DG, CA3, and CA1, whereas type 1 (DSL) events initiated by LECII→DG inputs do not. Just before SGdom, LECII-originating slow gamma oscillations in dentate gyrus and CA3-originating slow gamma oscillations in CA1 phase and frequency synchronize at the DSMpeak when discharge within DG and CA3 increases to promote excitation-inhibition cofiring within and across the DG→CA3→CA1 pathway. This optimizes discharge for the 5-10 ms DG-to-CA1 neuro-transmission that coincides with SGdom. DSMproperties identify extrahippocampal control of SGdom, and a cortico-hippocampal mechanism that switches between memory-related modes of information processing.
Optical measurement of physiological sodium currents in the axon initial segment
Authors: Filipis Luiza , Canepari Marco
Published: July 2020

In most neurons of the mammalian central nervous system, the action potential (AP) is triggered in the axon initial segment (AIS) by a fast Na+current mediated by voltage-gated Na+channels. The intracellular Na+increase associated with the AP has been measured using fluorescent Na+indicators, but with insufficient resolution to resolve the Na+current in the AIS. In this article, we report the critical improvement in temporal resolution of the Na+imaging technique allowing the direct experimental measurement of Na+currents in the AIS. We determined the AIS Na+current, from fluorescence measurements at temporal resolution of 100µs and pixel resolution of half a micron, in pyramidal neurons of the layer-5 of the somatosensory cortex from brain slices of the mouse. We identified a subthreshold current before the AP, a fast inactivating current peaking during the rise of the AP and a persistent current during the AP repolarisation. We correlated the kinetics of the current at different distances from the soma with the kinetics of the somatic AP. We quantitatively compared the experimentally measured Na+current with the current obtained by computer simulation of published NEURON models and we show how the present approach can lead to the correct estimate of the native behaviour of Na+channels. Thus, it is expected that the present method will be adopted to investigate the function of different channel types under physiological or pathological conditions.
Plant DNA polymerases alpha and delta mediate replication of geminiviruses
Authors: Wu Mengshi , Wei Hua , Tan Huang , Pan Shaojun , Liu Qi , Bejarano Eduardo R , Lozano-Durán Rosa
Published: July 2020

Geminiviruses are causal agents of devastating diseases in crops. Geminiviruses have circular single-stranded (ss)DNA genomes that are replicated in the nucleus of the infected plant cell through double-stranded (ds)DNA intermediates by the plant’s DNA replication machinery; which host DNA polymerase mediates geminiviral multiplication, however, has so far remained elusive. Here, we show that subunits of the nuclear replicative DNA polymerases α and δ physically interact with the geminivirus-encoded replication enhancer protein, C3, and are required for viral replication. Our results suggest that while DNA polymerase α is essential to generate the viral dsDNA intermediate, DNA polymerase δ mediates the synthesis of new copies of the geminiviral ssDNA genome, and that the virus-encoded C3 acts selectively recruiting DNA polymerase δ over ε to favour a productive replication.
Ivermectin inhibits extracellular vesicle secretion from parasitic nematodes
Authors: Loghry Hannah J. , Yuan Wang , Zamanian Mostafa , Wheeler Nicolas J. , Day Timothy A. , Kimber Michael J.
Published: July 2020

Lymphatic filariasis (LF) is a disease caused by parasitic filarial nematodes that is endemic in 49 countries and affects or threatens over 890 million people. Strategies to control LF rely heavily on mass administration of anthelmintic drugs including ivermectin (IVM), a macrocyclic lactone drug considered an Essential Medicine by the WHO. However, despite its widespread use the therapeutic mode of action of IVM against filarial nematodes is not clear. We have previously reported that filarial nematodes secrete extracellular vesicles (EVs) and that their cargo has immunomodulatory properties. Here we investigate the effects of IVM and other anti-filarial drugs on parasitic nematode EV secretion, motility, and protein secretion. We show that inhibition of EV secretion was a specific property of IVM, which had consistent and significant inhibitory effects across nematode life stages and species (with the exception of male parasites). IVM inhibited EV secretion, but not parasite motility, at therapeutically relevant concentrations. Protein secretion was inhibited by IVM in the microfilariae stage, but not in any other stage tested. Our data provides evidence that inhibiting the secretion of immunomodulatory EVs by parasitic nematodes could explain, at least in part, IVM mode of action and provides a phenotype for novel drug discovery.
Discordant transcriptional signatures of mitochondrial genes in Parkinson’s disease human myeloid cells
Authors: Navarro Elisa , Udine Evan , de Paiva Lopes Katia , Parks Madison , Riboldi Giulietta , Schilder Brian M. , Humphrey Jack , Snijders Gijsje J. L. , Vialle Ricardo A. , Zhuang Maojuan , Sikder Tamjeed , Argyrou Charalambos , Allan Amanda , Chao Michael , Farrell Kurt , Henderson Brooklyn , Simon Sarah , Raymond Deborah , Elango Sonya , Ortega Roberto A. , Shanker Vicki , Swan Matthew , Zhu Carolyn W. , Ramdhani Ritesh , Walker Ruth H. , Tse Winona , Sano Mary , Pereira Ana C. , Ahfeldt Tim , Goate Alison M. , Bressman Susan , Crary John F. , de Witte Lotje , Frucht Steven , Saunders-Pullman Rachel , Raj Towfique
Published: July 2020

An increasing number of identified Parkinson’s disease (PD) risk loci contain genes highly expressed in innate immune cells, yet their potential role in pathological mechanisms is not obvious. We have generated transcriptomic profiles of CD14+monocytes from 230 individuals with sporadic PD and age-matched healthy subjects. We identified dysregulation of genes involved in mitochondrial and proteasomal function. We also generated transcriptomic profiles of primary microglia from autopsied brains of 55 PD and control subjects and observed discordant transcriptomic signatures of mitochondrial genes in PD monocytes and microglia. We further identified PD susceptibility genes, whose expression, relative to each risk allele, is altered in monocytes. These findings reveal that transcriptomic mitochondrial alterations are detectable in PD monocytes and are distinct from brain microglia, and facilitates efforts to understand the roles of myeloid cells in PD.
Voluntary wheel running improves outcomes in an early life stress-induced model of urologic chronic pelvic pain syndrome in male mice
Authors: Fuentes Isabella M. , Jones Brittni M. , Brake Aaron D. , Pierce Angela N. , Eller Olivia C. , Supple Rachel M. , Wright Douglas E. , Christianson Julie A.
Published: July 2020

Patients with a history of early life stress (ELS) exposure have an increased risk of developing chronic pain and mood disorders later in life. The severity of ELS in patients with urologic chronic pelvic pain syndrome (UCPPS) is directly correlated with symptom severity and increased comorbidity, and is inversely related to likelihood of improvement. Voluntary exercise improves chronic pain symptoms and our group and others have shown that voluntary wheel running can improve outcomes in stress-induced UCPPS models, suggesting that exercise may negate some of the outcomes associated with ELS. Here we provide further evidence that voluntary wheel running can attenuate increased perigenital mechanical sensitivity, bladder output, and mast cell degranulation in the bladder and prostate in male mice that underwent neonatal maternal separation (NMS). Sedentary male NMS mice had reduced serum corticosterone, which was not impacted by voluntary wheel running, although stress-related regulatory gene expression in the hypothalamus and hippocampus was significantly increased following exercise. Neurogenesis in the dentate gyrus of the hippocampus was diminished in sedentary NMS mice and significantly increased in both exercised naïve and NMS mice. Sucrose consumption increased in exercised naïve but not NMS mice, and anxiety behaviors measured on an elevated plus maze were increased following exercise. Together these data suggest that voluntary wheel running is sufficient to normalize many of the UCPPS-related outcomes resulting from NMS. Exercise also increased hippocampal neurogenesis and stress-related gene expression within the hypothalamic-pituitary-adrenal axis, further supporting exercise as a non-pharmacological intervention for attenuating outcomes related to ELS exposure.
Dimerization of kringle 1 domain from hepatocyte growth factor/scatter factor provides a potent minimal MET receptor agonist
Authors: de Nola Giovanni , Leclercq Bérénice , Mougel Alexandra , Taront Solenne , Simonneau Claire , Forneris Federico , Adriaenssens Eric , Drobecq Hervé , Iamele Luisa , Dubuquoy Laurent , Melnyk Oleg , Gherardi Ermanno , de Jonge Hugo , Vicogne Jérôme
Published: July 2020

Hepatocyte Growth Factor/Scatter Factor (HGF/SF) and its cognate receptor MET play several essential roles in embryogenesis and regeneration in post-natal life of epithelial organs such as liver, kidney, lung, and pancreas, prompting a strong interest in harnessing HGF/SF-MET signalling for regeneration of epithelial organs after acute or chronic damage. The limited stability and tissue diffusion of native HGF/SF, however, which reflect the tightly controlled, local mechanism of action of the morphogen, have led to a major search for HGF/SF mimics for therapy. In this work, we describe the rational design, production and characterisation of K1K1, a novel minimal MET agonist consisting of two copies of the kringle 1 domain of HGF/SF placed in tandem. K1K1 is highly stable and displays biological activities equivalent or superior to native HGF/SF in a variety ofin vitroassay systems and in a mouse model of liver disease. These data suggest that this engineered ligand may find wide applications in acute and chronic diseases of the liver and other epithelial organs dependent on MET activation.
Integration of Transcriptome and Small RNA Sequencing to Decipher Molecular Interaction ofChenopodium quinoaVarieties with Cucumber Mosaic Virus
Authors: Soltani Nourolah , Staton Margaret , Gwinn Kimberly D.
Published: July 2020

Saponins are secondary metabolites with antiviral properties. Low saponin (sweet) varieties of quinoa (Chenopodium quinoa) have been developed because seeds high in saponins taste bitter. The aim of this study was to elucidate the role of saponin in resistance of quinoa toCucumber mosaic virus(CMV). Differential gene expression was studied in time-series study of CMV infection. High-throughput transcriptome sequence data were obtained from 36 samples (3 varieties × +/- CMV × 1 or 4 days after inoculation × 3 replicates). Translation, lipid, nitrogen, amino acid metabolism, and mono- and sesquiterpenoid biosynthesis genes were upregulated in CMV infections. In ‘Red Head’, (bitter), CMV-induced systemic symptoms were concurrent with downregulation of a key saponin biosynthesis gene, TSARL1, four days after inoculation. In local lesion responses (sweet and semi-sweet), TSARL1 levels remained up-regulated. Known microRNAs (miRNA) (81) from 11 miR families and 876 predicted novel miRNAs were identified. Differentially expressed miRNA and short interfering RNA clusters (24nt) induced by CMV infection are predicted to target genomic and intergenic regions enriched in repetitive elements. This is the first report of integrated RNASeq and sRNASeq data in quinoa-virus interactions and provides comprehensive understanding of involved genes, non-coding regions, and biological pathways in virus resistance.
The hunt for ancient prions: Archaeal prion-like domains form amyloids and substitute for yeast prion domains
Authors: Zajkowski Tomasz , Lee Michael D. , Mondal Shamba S. , Carbajal Amanda , Dec Robert , Brennock Patrick D. , Piast Radoslaw W. , Snyder Jessica E. , Bense Nicholas B. , Dzwolak Wojciech , Jarosz Daniel F. , Rothschild Lynn J.
Published: July 2020

Prions are proteins capable of acquiring an alternate conformation that can then induce additional copies to adopt this same alternate conformation. Although initially discovered in relation to mammalian disease, subsequent studies have revealed the presence of prions in Bacteria and Viruses, suggesting an ancient evolutionary origin. Here we explore whether prions exist in Archaea - the last domain of life left unexplored with regard to prions. After searching for potential prion-forming protein sequences computationally, we tested candidatesin vitroand in organisms from the two other domains of life:Escherichia coliandSaccharomyces cerevisiae. Out of the 16 candidate prion-forming domains tested, 8 bound to amyloid-specific dye, and six acted as protein-based elements of information transfer, driving non-Mendelian patterns of inheritance. We additionally identified short peptides from archaeal prion candidates that can form amyloid fibrils independently. Candidates that tested positively in our assays had significantly higher tyrosine and phenylalanine content than candidates that tested negatively, suggesting that the presence of these amino acids may help distinguish functional prion domains from nonfunctional ones. Our data establish the presence of amyloid-forming prion-like domains in Archaea. Their discovery in all three domains of life further suggests the possibility that they were present at the time of the last universal common ancestor (LUCA).

Significance Statement

This work establishes that amyloid-forming, prion-like domains exist in Archaea and are capable of vertically transmitting their prion phenotype – allowing them to function as protein-based elements of inheritance. These observations, coupled with prior discoveries in Eukarya and Bacteria, suggest that prion-based self-assembly was likely present in life’s last universal common ancestor (LUCA), and therefore may be one of the most ancient epigenetic mechanisms.
Iterative Epigenomic Analyses in the Same Single Cell
Authors: Ohnuki Hidetaka , Venzon David J. , Lobanov Alexei , Tosato Giovanna
Published: July 2020

Gene expression in individual cells is epigenetically regulated by DNA modifications, histone modifications, transcription factors and other DNA-binding proteins. It has been shown that multiple histone modifications can predict gene expression and reflect future responses of bulk cells to extracellular cues. However, the predictive ability of epigenomic analysis is still limited for mechanistic research at a single cell level. To overcome this limitation, it is useful to acquire reliable signals from multiple epigenetic marks in the same single cell. Here, we propose a new approach for analysis of several components of the epigenome in the same single cell. The new method allows reanalysis of the same single cell. We found that reanalysis of the same single cell is feasible, and provides confirmation of the signals and allows application of statistical analysis to identify reliable signals using data sets generated only from the single cell. Reanalysis of the same single cell is also useful to acquire multiple-epigenetic marks from the same single cells. The method can acquire at least 4 epigenetic marks, H3K27ac, H3K27me3, mediator complex subunit 1 and a DNA modification. We predicted active signaling pathways in K562 single cells using the data. We confirmed that the prediction results showed a strong correlation with actual active signaling pathways shown by RNA-seq results. These results suggest that the new approach provides mechanistic insights for cellular phenotypes through multi-layered epigenome analysis in the same single cells.
DynaMorph: self-supervised learning of morphodynamic states of live cells
Authors: Wu Zhenqin , Chhun Bryant B. , Popova Galina , Guo Syuan-Ming , Kim Chang N. , Yeh Li-Hao , Nowakowski Tomasz , Zou James , Mehta Shalin B.
Published: July 2020

The cell’s shape and motion represent fundamental aspects of the cell identity, and can be highly predictive of the function and pathology. However, automated analysis of the morphodynamic states remains challenging for most cell types, especially primary human cells where genetic labeling may not be feasible. To enable automated and quantitative analysis of morphodynamic states, we developed DynaMorph – a computational framework that combines quantitative live cell imaging with self-supervised learning. To demonstrate the fidelity and robustness of this approach, we used DynaMorph to annotate morphodynamic states observed with label-free measurements of density and anisotropy of live microglia isolated from human brain tissue. These cells show complex behavior and have varied responses to disease-relevant stimuli. DynaMorph generates quantitative morphodynamic representations that can be used to evaluate the effects of disease-relevant perturbations. Using DynaMorph, we identify distinct morphodynamic states of microglia polarization and detect rare transition events between states. The methodologies presented here can facilitate automated discovery of functional states of diverse cellular systems.
The fiber knob protein of human adenovirus type 49 mediates highly efficient and promiscuous infection of cancer cell lines using a novel cell entry mechanism
Authors: Baker Alexander T. , Marlow Gareth , Davies James A. , Moses Elise , Mundy Rosie M. , Cole David K. , Rizkallah Pierre J. , Parker Alan L.
Published: July 2020

The human adenovirus (HAdV) phylogenetic tree is diverse, divided across seven species and comprising over 100 individual types. Species D HAdV are rarely isolated with low rates of pre-existing immunity, making them appealing for therapeutic applications. Several species D vectors have been developed as vaccines against infectious diseases where they induce robust immunity in pre-clinical models and early phase clinical trials. However, many aspects of the basic virology of species D HAdV, including their basic receptor usage and means of cell entry, remain understudied.

Here, we investigated HAdV-D49, which previously has been studied for vaccine and vascular gene transfer applications. We generated a pseudotyped HAdV-C5 presenting the HAdV-D49 fiber knob protein (HAdV-C5/D49K). This pseudotyped vector was efficient at infecting cells devoid of all known HAdV receptors, indicating HAdV-D49 uses an unidentified cellular receptor. Conversely, a pseudotyped vector presenting the fiber knob protein of the closely related HAdV-D30 (HAdV-C5/D30K), differing in four amino acids to HAdV-D49, failed to demonstrate the same tropism. These four amino acid changes resulted in a change in isoelectric point of the knob protein, with HAdV-D49K possessing a basic apical region compared to a more acidic region in HAdV-D30K. Structurally and biologically we demonstrate that HAdV-D49 knob protein is unable to engage CD46, whilst potential interaction with CAR is extremely limited by extension of the DG loop. HAdV-C5/49K efficiently transduced cancer cell lines of pancreatic, breast, lung, oesophageal and ovarian origin, indicating it may have potential for oncolytic virotherapy applications, especially for difficult to transduce tumour types.

Importance

Adenoviruses are powerful tools experimentally and clinically. To maximise efficacy, the development of serotypes with low pre-existing levels of immunity in the population is desirable. Consequently, attention has focussed on those derived from species D, which have proven robust vaccine platforms. This widespread usage is despite limited knowledge in their basic biology and cellular tropism.

We investigated the tropism of HAdV-D49, demonstrating it uses a novel cell entry mechanism that bypasses all known HAdV receptors. We demonstrate, biologically, that a pseudotyped HAdV-C5/D49K vector efficiently transduces a wide range of cell lines, including those presenting no known adenovirus receptor. Structural investigation suggests that this broad tropism is the result of a highly basic electrostatic surface potential, since a homologous pseudotyped vector with a more acidic surface potential, HAdV-C5/D30K, does not display a similar pan-tropism. Therefore, HAdV-C5/D49K may form a powerful vector for therapeutic applications capable of infecting difficult to transduce cells.
Identification of novel mutations contributing to azole tolerance ofAspergillus fumigatus throughin vitroexposure to tebuconazole
Authors: Toyotome Takahito , Onishi Kenji , Sato Mio , Kusuya Yoko , Hagiwara Daisuke , Watanabe Akira , Takahashi Hiroki
Published: July 2020

Azole resistance ofAspergillus fumigatusis a global problem. The major resistant mechanism is acyp51Aalteration such as mutation(s) in the gene and the acquisition of a tandem repeat in the promoter. Although other azole tolerances and resistant mechanisms such ashmg1mutation are known, few reports describe studies elucidating non-cyp51Aresistance mechanisms. This study explored genes contributing to azole tolerance inA. fumigatusbyin vitromutant selection with tebuconazole, an azole fungicide. After three-round selection, we obtained four isolates with low susceptibility to tebuconazole. These isolates also showed low susceptibility to itraconazole and voriconazole. Comparison of the genome sequences of the obtained isolates and the parental strain revealed a non-synonymous mutation in MfsD (Afu1g11820, R337L mutation) in all isolates. Furthermore, non-synonymous mutations in AgcA (Afu7g05220, E535Stop mutation), UbcD (Afu3g06030, T98K mutation), AbcJ (Afu3g12220, G297E mutation), and RttA (Afu7g04740, A83T mutation), a protein responsible for tebuconazole tolerance, were found in at least one isolate. Clarification by constructing the MfsD R337L mutant suggests that the mutation contributes to azole tolerance. Disruption of theagcAgene and reconstruction of the A83T point mutation in RttA led to decreased susceptibility to azoles. The reversion of T98K mutation to wild type in UbcD led to the level of azole susceptibility comparable to the parental strain. These results suggest that these mutations contribute to lowered susceptibility to medical azoles and to agricultural azole fungicides.
How does childhood maltreatment influence cardiovascular disease? A sequential causal mediation analysis
Authors: Soares Ana G , Howe Laura D , Heron Jon , Hammerton Gemma , Rich-Edwards Janet , Magnus Maria C , Halligan Sarah L , Fraser Abigail
Published: July 2020

Background

Childhood maltreatment has been consistently associated with cardiovascular disease (CVD). However, the mechanisms of this relationship are not yet fully understood. We explored the relative contribution of anxiety/depression, smoking, body mass index (BMI) and inflammation (C-reactive protein, CRP) to the association between childhood maltreatment and CVD in men and women aged 40-69 years in the United Kingdom (UK).

Methods

We used data from 40,596 men and 59,511 women from UK Biobank. To estimate the indirect effects of childhood maltreatment (physical, sexual and emotional abuse, and emotional and physical neglect) on incident CVD via each of the mediators, we applied a sequential mediation approach.

Results

All forms of maltreatment were associated with increased CVD risk (hazard ratios (HR) ranging from 1.09 to 1.27). Together anxiety/depression, smoking, BMI and CRP mediated 26%-90% of the association between childhood maltreatment and CVD, and the contribution of these mediators differed by type of maltreatment and sex. Anxiety/depression mediated the largest proportion of the association of sexual abuse, emotional abuse and emotional neglect with CVD (accounting for 16%-43% of the total effect), especially in women. In men, BMI contributed the most to the indirect effect of associations of physical abuse and physical neglect with CVD; in women anxiety/depression and BMI had similar contributions.

Conclusions

These findings add to the understanding of how childhood maltreatment affects CVD risk and identify modifiable mediating factors which could potentially reduce the burden of CVD in people exposed to maltreatment in early life.