bluuebunny/crossref_metadata_2025 huggingface dataset:
HIV-infected patients on combined antiretroviral treatment had similar level of arterial stiffness to the patients with ST-segment elevation myocardial infarction
Authors: Mikuła Tomasz , Suchacz Magdalena M. , Peller Michał , Balsam Paweł , Kołtowski Łukasz , Główczyńska Renata , Filipiak Krzysztof J. , Opolski Grzegorz , Wiercińska-Drapało Alicja
Published: January 2021

Purpose

The cardiovascular disease has become very common among HIV-infected patients. The aim was to compare the arterial stiffness and the endothelial dysfunction in HIV-infected patients to non-HIV-infected patients in week 4 after ST-segment elevation myocardial infarction (STEMI).

Methods

The arterial stiffness was calculated by Endo-PAT 2000(ITAMAR®) and the endothelial function by Peripheral Arterial Tonometry(PAT®). The correct endothelial function was defined for natural logarithm of reactive hyperaemia index (lnRHI)>0.51. Arterial stiffness was assessed as the AI and corrected for heart rate of 75 bpm (AI@75).

Results

Sixty-three patients were recruited to this study, n=34 patients with HIV infection (n=18 on cART) and n=29 HIV-negative patients after recent STEMI. No statistically significant differences for AI and AI@75 were found in STEMI and in HIV on cART group. We observed p<0.05 for AI and AI@75 for patients without cART compared to STEMI and on cART patients. The observed lnRHI results were significantly different p<0.05 in STEMI and on cART patients. We get similar endothelial dysfunction p>0.05 for patients without cART compared to STEMI and on cART patients.

Conclusions

Assessing cardiovascular risk also with non-invasive methods among HIV-infected patients is very important especially in HIV-patients on cART. Endothelial dysfunction is connected with HIV infection and can be similar for STEMI and HIV-infected without cART.
Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition
Authors: Yosaatmadja Yuliana , Baddock Hannah T , Newman Joseph A , Bielinski Marcin , Gavard Angeline E , Mukhopadhyay Shubhashish M M , Dannerfjord Adam A , Schofield Christopher J , McHugh Peter J , Gileadi Opher
Published: January 2021

Artemis (DCLRE1C) is an endonuclease that plays a key role in development of B- and T-lymphocytes and in DNA double-strand break repair by non-homologous end-joining (NHEJ). Artemis is phosphorylated by DNA-PKcs and acts to open DNA hairpin intermediates generated during V(D)J and class-switch recombination. Consistently, Artemis deficiency leads to radiosensitive congenital severe immune deficiency (RS-SCID). Artemis belongs to a structural superfamily of nucleases that contain conserved metallo-β-lactamase (MBL) and β-CASP (CPSF-Artemis-SNM1-Pso2) domains. Here, we present crystal structures of the catalytic domain of wild type and variant forms of Artemis that cause RS-SCID Omenn syndrome. The truncated catalytic domain of the Artemis is a constitutively active enzyme that with similar activity to a phosphorylated full-length protein. Our structures help explain the basis of the predominantly endonucleolytic activity of Artemis, which contrast with the predominantly exonuclease activity of the closely related SNM1A and SNM1B nucleases. The structures also reveal a second metal binding site in its β-CASP domain that is unique to Artemis. By combining our structural data that from a recently reported structure we were able model the interaction of Artemis with DNA substrates. Moreover, co-crystal structures with inhibitors indicate the potential for structure-guided development of inhibitors.
Shear-Mediated Platelet Activation is Accompanied by Unique Alterations of Platelet Lipid Profile
Authors: Sweedo Alice , Wise Lisa M. , Roka-Moiia Yana , Arce Fernando Teran , Saavedra S. Scott , Sheriff Jawaad , Bluestein Danny , Slepian Marvin J. , Purdy John G.
Published: January 2021

Platelet activation by mechanical means such as shear stress, is a vital driver of thrombotic risk in implantable blood-contacting devices used in treatment of heart failure. Lipids are essential in platelets activation and have been studied following biochemical activation. However, little is known regarding lipid alterations occurring with mechanical – shear mediated platelet activation. Here, we determined if shear-activation of platelets induced lipidome changes that differ from those associated with biochemically-mediated platelet activation. We performed high-resolution lipidomic analysis on purified platelets from four healthy human donors. For each donor, we compared the lipidome of platelets that were non-activated or activated by shear, ADP, or thrombin treatment. We found that shear activation altered cell-associated lipids and led to the release of lipids into the extracellular environment. Shear-activated platelets released 21 phospholipids and sphingomyelins at levels statistically higher than platelets activated by biochemical stimulation. Many of the released phospholipids contained an arachidonic acid tail or were phosphatidylserine lipids, which have procoagulant properties. We conclude that shear-mediated activation of platelets alters the basal platelet lipidome. Further, these alterations differ and are unique in comparison to the lipidome of biochemically activated platelets. Our findings suggest that lipids released by shear-activated platelets may contribute to altered thrombosis in patients with implanted cardiovascular therapeutic devices.
Tracking the stochastic growth of bacterial populations in microfluidic droplets
Authors: Taylor Daniel , Verdon Nia , Lomax Peter , Allen Rosalind J. , Titmuss Simon
Published: January 2021

Bacterial growth in microfluidic droplets is relevant in biotechnology, in microbial ecology, and in understanding stochastic population dynamics in small populations. However, it has proved challenging to automate measurement of absolute bacterial numbers within droplets, forcing the use of proxy measures for population size. Here we present a microfluidic device and imaging protocol that allows high-resolution imaging of thousands of droplets, such that individual bacteria stay in the focal plane and can be counted automatically. Using this approach, we track the stochastic growth of hundreds of replicateEscherichia colipopulations within droplets. We find that, for early times, the statistics of the growth trajectories obey the predictions of the Bellman-Harris model, in which there is no inheritance of division time. Our approach should allow further testing of models for stochastic growth dynamics, as well as contributing to broader applications of droplet-based bacterial culture.
Wide distribution of alternatively coded Lak megaphages in animal microbiomes
Authors: Crisci Marco A. , Chen Lin-Xing , Devoto Audra E. , Borges Adair L. , Bordin Nicola , Sachdeva Rohan , Tett Adrian , Sharrar Allison M. , Segata Nicola , Debenedetti Francesco , Bailey Mick , Burt Rachel , Wood Rhiannon M. , Rowden Lewis J. , Corsini Paula M. , Holmes Mark A. , Lei Shufei , Banfield Jillian F. , Santini Joanne M.
Published: January 2021

Lak phages with alternatively coded ~540 kbp genomes were recently reported to replicate in Prevotella in the gut microbiomes of humans that consume a non-western diet, baboons and some pigs. Here, we investigate the diversity and broader distribution of Lak phages in human and animal microbiomes using diagnostic PCR and genome-resolved metagenomics. Lak phages were detected in 13 different animal types and are particularly prevalent in pigs, with significant enrichment in the hindgut compared to foregut. We reconstructed 34 new Lak genomes, including six curated complete genomes, all of which are alternatively coded. The most deeply branched Lak is from a horse faecal sample and is the largest phage genome from an animal microbiome (~660 kbp). From the Lak genomes, we identified families of hypothetical proteins associated with specific animal types. Overall, we substantially expanded Lak phage diversity and demonstrate their occurrence in a variety of human and animal microbiomes.
Moving patronin foci and growing microtubule plus ends direct the spatiotemporal dynamics of Rho signaling and myosin during apical constriction
Authors: Guru Anwesha , Saravanan Surat , Sharma Deepanshu , Narasimha Maithreyi
Published: January 2021

The contraction of the amnioserosa by apical constriction provides the major force for Drosophila dorsal closure. The nucleation, movement and dispersal of apicomedial actomyosin complexes generate pulsed constrictions during early dorsal closure whereas persistent apicomedial and circumapical actomyosin complexes drive the unpulsed constrictions that follow. What governs the spatiotemporal assembly of these distinct complexes, endows them with their pulsatile dynamics, and directs their motility remains unresolved. Here we identify an essential role for microtubule growth in regulating the timely contraction of the amnioserosa. We show that a symmetric cage of apical microtubules forms around the coalescing apicomedial myosin complex. An asymmetric tail of microtubules then trails the moving myosin complex and disperses as the myosin complex dissolves. Perturbing microtubule growth reduced the coalescence and movement of apicomedial myosin complexes and redistributed myosin and its activator, Rho kinase to the circumapical pool and altered the cell constriction and tissue contraction dynamics of the amnioserosa. We show that RhoGEF2, the activator of the Rho1 GTPase, is transiently associated with microtubule plus end binding protein EB1 and the apicomedial actomyosin complex. Our results suggest that microtubule growth from moving patronin platforms modulates actomyosin contractility through the spatiotemporal regulation of Rho1 activity. We propose that microtubule reorganisation enables a self-organising, mechanosensitive feedback loop that buffers the tissue against mechanical stresses by modulating actomyosin contractility.
Monitoring the promoter activity of long noncoding RNAs and stem cell differentiation through knock-in of sgRNA flanked by tRNA in an intron
Authors: Zhao Yu-Ting , Wang Yangming
Published: January 2021

Mammalian genomes encode thousands of long noncoding RNAs (lncRNAs) that are often expressed in a tissue and cell specific manner. Therefore, a reporter that can faithfully reflect the expression or activity of lncRNAs can provide tools useful not only for uncovering the regulators of lncRNAs, but also for tracking cell fate and disease status. Here, we design a sgRNA precursor in anintron (GRIT) strategy that can monitor the promoter activity of lncRNAs. We used this strategy to report the expression of Lncenc1 and Neat1 in mouse embryonic stem cells (ESCs). Furthermore, we show that GRIT may be used to track differentiation status of stem cells. We anticipate that GRIT will be applicable in dissecting regulatory mechanisms underlying the transcription of lncRNAs, tracking cell fate switch during differentiation or disease progression and integrating the promoter activity of various RNAs for synthetic biology applications.
Prime editing enables precise genome editing in mouse liver and retina
Authors: Jang Hyewon , Shin Jeong Hong , Jo Dong Hyun , Seo Jung Hwa , Yu Goosang , Gopalappa Ramu , Cho Sung-Rae , Kim Jeong Hun , Kim Hyongbum Henry
Published: January 2021

Prime editing can induce any small-sized genetic change without donor DNA or double strand breaks. However, it has not been investigated whether prime editing is possible in postnatal animals. Here we delivered prime editors 2 and 3 into a mouse model of hereditary tyrosinemia, a genetic liver disease, using hydrodynamic injection, which corrected the disease-causing mutation and rescued the phenotype. We also achieved prime editing in the retina and retina pigment epithelium in wild-type mice by delivering prime editor 3 using trans-splicing adeno-associated virus. Deep sequencing showed that unintended edits at or near the target site or off-target effects were not detectable except for low levels (0% to 1.2%) of indels when PE3, but not PE2, was used. Our study suggests that precise, prime editor-mediated genome editing is possible in somatic cells of adult animals.
Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing inDrosophila
Authors: Eastwood Evelyn L. , Jara Kayla A. , Bornelöv Susanne , Munafò Marzia , Frantzis Vasileios , Kneuss Emma , Barbar Elisar J. , Czech Benjamin , Hannon Gregory J.
Published: January 2021

In animal gonads, the PIWI-interacting RNA (piRNA) pathway guards genome integrity in part through the co-transcriptional gene silencing of transposon insertions. InDrosophilaovaries, piRNA-loaded Piwi detects nascent transposon transcripts and instructs heterochromatin formation through thePanoramix-inducedco-transcriptionalsilencing (PICTS) complex, containing Panoramix, Nxf2 and Nxt1. Here, we report that the highly conserved dynein light chain LC8/Cut-up (Ctp) is an essential component of the PICTS complex. Loss of Ctp results in transposon de-repression and a reduction in repressive chromatin marks specifically at transposon loci. In turn, Ctp can enforce transcriptional silencing when artificially recruited to RNA and DNA reporters. We show that Ctp drives dimerisation of the PICTS complex through its interaction with conserved motifs within Panoramix. Artificial dimerisation of Panoramix bypasses the necessity for its interaction with Ctp, demonstrating that conscription of a protein from a ubiquitous cellular machinery has fulfilled a fundamental requirement for a transposon silencing complex.
Sex and origin-specific inbreeding effects on flower attractiveness to specialised pollinators
Authors: Schrieber Karin , Paul Sarah Catherine , Höche Levke Valena , Salas Andrea Cecilia , Didszun Rabi , Mößnang Jakob , Müller Caroline , Erfmeier Alexandra , Eilers Elisabeth Johanna
Published: January 2021

We investigate whether inbreeding has particularly fatal consequences for dioecious plants by diminishing their floral attractiveness and the associated pollinator visitation rates disproportionally in females. We also test whether the magnitude of such effects depends on the evolutionary histories of plant populations. We recorded spatial, olfactory, colour and rewarding flower attractiveness traits as well as pollinator visitation rates in experimentally inbred and outbred, male and femaleSilene latifoliaplants from European and North American populations differing in their evolutionary histories. We found that inbreeding specifically impairs spatial and olfactory attractiveness. Our results support that sex-specific selection and gene expression partially magnified these inbreeding costs for females, and that divergent evolutionary histories altered the genetic architecture underlying inbreeding effects across population origins. Moreover, they highlight that inbreeding effects on olfactory attractiveness have a huge potential to disrupt interactions among plants and specialist moth pollinators, which are mediated by elaborate chemical communication.
Somatic mutations in CTCF zinc fingers produce cellular phenotypes explained by structure-function relationships
Authors: Bailey Charles G , Gupta Shailendra , Metierre Cynthia , Amarasekera Punkaja MS , O’Young Patrick , Kyaw Wunna , Laletin Tatyana , Francis Habib , Semaan Crystal , Singh Krishna P , Mullighan Charles G , Wolkenhauer Olaf , Schmitz Ulf , Rasko John EJ
Published: January 2021

Background

Human cancers commonly contain mutations in transcription factors that lead to aberrant DNA binding or altered effector function at target sites. One such factor significantly mutated in cancer is the evolutionarily-conserved CCCTC-binding factor (CTCF), which has fundamental roles in maintaining chromatin architecture and transcriptional regulation. Numerous cancer genome sequencing and functional studies have revealed CTCF’s role as a haploinsufficient tumour suppressor gene. However, to date, structure-function relationships of somatic CTCF mutations have not been examined.

Methods

We collated somatic CTCF mutations from cancer genome portals and published studies to determine their nature, frequency, distribution and potential functional impact. We undertook an in-depth examination of 5 CTCF missense zinc finger (ZF) mutations occurring within key intra- and inter-ZF residues. We performed functional analyses including cell growth, colony-formation, chromatin immunoprecipitation and transcriptional reporter assays. Based on their homology, each ZF mutation was then modelled on CTCF’s ZF domain crystal structure and its structural impact analysed using molecular dynamics simulations.

Results

We observed an enrichment of somatic missense mutations occurring in the ZF region of CTCF, compared to the unstructured N- and C-termini. Functional characterisation of CTCF ZF mutations revealed a complete (L309P, R339W, R377H) or intermediate (R339Q) abrogation as well as an enhancement (G420D) of the anti-proliferative effects of CTCF. DNA binding at select sites was disrupted and transcriptional regulatory activities abrogated.In silicomutagenesis revealed that L309P had the highest mutation energy and thus most severe impact on protein stability. Molecular docking and molecular dynamics simulations confirmed that mutations in residues specifically contacting DNA bases or backbone exhibited loss of DNA binding (R339Q, R339W, R377H). Remarkably, R339Q and G420D were stabilised by the formation of new primary DNA bonds. All mutations exhibited some loss or gain of bonds at neighbouring residues, often in adjacent zinc fingers.

Conclusions

Our data confirm the significant negative impact haploinsufficient CTCF ZF mutations have on its tumour suppressor function. A spectrum of loss-, change- and gain-of-function impacts in CTCF zinc fingers are observed in cell growth regulation and gene regulatory activities. We have established that diverse cellular phenotypes in CTCF are explained by examining structure-function relationships.
RNA-directed DNA methylation prevents rapid and heritable reversal of transposon silencing under heat stress in Zeamays
Authors: Guo Wei , Wang Dafang , Lisch Damon
Published: January 2021

In large complex plant genomes, RNA-directed DNA methylation (RdDM) ensures that epigenetic silencing is maintained at the boundary between genes and flanking transposable elements. In maize, RdDM is dependent onModifer of Paramutation 1(Mop1), a putative RNA dependent RNA polymerase. Here we show that although RdDM is essential for the maintenance of DNA methylation of a silencedMuDRtransposon in maize, a loss of that methylation does not result in a restoration of activity. Instead, heritable maintenance of silencing is maintained by histone modifications. At one terminal inverted repeat (TIR) of this element, heritable silencing is mediated via H3K9 and H3K27 dimethylation, even in the absence of DNA methylation. At the second TIR, heritable silencing is mediated by H3K27 trimethylation, a mark normally associated with somatically inherited gene silencing. We find that a brief exposure of high temperature in amop1mutant rapidly reverses both of these modifications in conjunction with a loss of transcriptional silencing. These reversals are heritable, even inmop1wild type progeny in which methylation is restored at both TIRs. These observations suggest that DNA methylation is neither necessary to maintain silencing, nor is it sufficient to initiate silencing once has been reversed. However, given that heritable reactivation only occurs in amop1mutant background, these observations suggest that DNA methylation is required to buffer the effects of environmental stress on transposable elements.

Author Summary

Most plant genomes are mostly transposable elements (TEs), most of which are held in check by modifications of both DNA and histones. The bulk of silenced TEs are associated with methylated DNA and histone H3 lysine 9 demethylation (H3K9me2). In contrast, epigenetically silenced genes are often associated with histone lysine 27 trimethylation (H3K27me3). Although stress can affect each of these modifications, plants are generally competent to rapidly reset them following that stress. Here we demonstrate that although DNA methylation is not required to maintain silencing of theMuDRelement, it is essential for preventing heat-induced, stable and heritable changes in both H3K9me2 and H3K27me3 at this element, and for concomitant changes in transcriptional activity. These finding suggest that RdDM acts to buffer the effects of heat on silenced transposable elements, and that a loss of DNA methylation under conditions of stress can have profound and long lasting effects on epigenetic silencing in maize.
Cep55 regulation of PI3K/Akt signaling is required for neocortical development and ciliogenesis
Authors: Rashidieh Behnam , Shohayeb Belal , Bain Amanda Louise , Fortuna Patrick R. J. , Sinha Debottam , Burgess Andrew , Mills Richard , Adams Rachael C. , Lopez J. Alejandro , Blumbergs Peter , Finnie John , Kalimutho Murugan , Piper Michael , Hudson James Edward , Ng Dominic , Khanna Kum Kum
Published: January 2021

Homozygous nonsense mutations in CEP55 are associated with several congenital malformations that lead to perinatal lethality suggesting that it plays a critical role in regulation of embryonic development. CEP55 has previously been studied as a critical regulator of cytokinesis predominantly in transformed cells and its deregulation is linked to carcinogenesis. However, its molecular functions during embryonic development in mammals have not been clearly defined. We have generated a Cep55 knockout (Cep55-/-) mouse model which demonstrated perinatal lethality associated with a wide range of neural defects. Focusing our analysis on the neocortex, we show that Cep55-/- embryos exhibited depleted neural stem/progenitor cells in the ventricular zone as a result of significantly increased cellular apoptosis. Mechanistically, we demonstrated that Cep55-loss downregulates the pGsk3β/β-Catenin/Myc axis in an Akt-dependent manner. The phenotype was recapitulated using human cerebral organoids and we could rescue the phenotype by inhibiting active Gsk3β. Additionally, we show that Cep55-loss leads to a significant reduction of ciliated cells, highlighting its novel role in regulating ciliogenesis. Collectively, our findings demonstrate a critical role of Cep55 during brain development and provide mechanistic insights that may have important implications for genetic syndromes associated with Cep55-loss.
Family cluster comparisons to detect infection byMycobacterium lepraein at-risk populations of six endemic regions in Colombia
Authors: Serrano-Coll Héctor , Osorio-Leal Yuliana , Escobar-Builes María Victoria , Cardona-Castro Nora
Published: January 2021

Introduction

Leprosy is a chronic infectious disease, caused byMycobacterium leprae, which is endemic in some tropical countries. It is necessary to implement strategies for its detection and elimination. We propose a strategy useful could be identifying risk factors associated with a seropositive test in leprosy.

Objective

We aimed to quantify the infection rates and identify risk factors for M. leprae infection using the serological evaluations against NDO-LID in family clusters of leprosy patients, from regions with a high burden of leprosy in Colombia.

Results

We observed that belong to a low socioeconomic condition (OR 5.6 [95% IC 1.1-29]) and living in geographic area of residing such as Chocó and Atlántico (OR 2 [95% IC 1.1-3.7]) could be risk factors related to infection byM. lepraebetween the members of a family cluster.

Conclusions

Leprosy is a persistent disease that affects vulnerable and large family clusters, in which the detection of antibodies against NDO-LID can be a useful tool for early detection ofM. lepraein family clusters with high risk for this infection.
Lamina-associated polypeptide 2α is required for intranuclear MRTF-A activity
Authors: Sidorenko Ekaterina , Sokolova Maria , Pennanen Antti , Kyheröinen Salla , Posern Guido , Foisner Roland , Vartiainen Maria K.
Published: January 2021

Myocardin-related transcription factor A (MRTF-A), a coactivator of serum response factor (SRF), regulates the expression of many cytoskeletal genes in response to cytoplasmic and nuclear actin dynamics. Here we describe a novel mechanism to regulate MRTF-A activity within the nucleus by showing that lamina-associated polypeptide 2α (Lap2α), the nucleoplasmic isoform of Lap2, is a direct binding partner of MRTF-A, and required for the efficient expression of MRTF-A/SRF target genes. Mechanistically, Lap2α is not required for MRTF-A nuclear localization, unlike most other MRTF-A regulators, but is required for binding of MRTF-A to its target genes. This regulatory step takes place prior to MRTF-A chromatin binding, because Lap2α neither interacts with, nor specifically influences active histone marks on MRTF-A/SRF target genes. Phenotypically, Lap2α is required for serum-induced cell migration, and deregulated MRTF-A activity may also contribute to muscle and proliferation phenotypes associated with loss of Lap2α. Our studies therefore add another regulatory layer to the control of MRTF-A-SRF-mediated gene expression, and broaden the role of Lap2α in transcriptional regulation.
Pin Electrode Reactor: A novel cold atmospheric plasma device and its potential in glioblastoma treatment
Authors: de Carvalho Andressa Maria Aguiar , Behan Sean , Scally Laurence , Sarangapani Chaitanya , Malone Renee , Cullen Patrick J. , Tiwari Brijesh , Curtin James F.
Published: January 2021

Glioblastoma multiforme (GBM) is the most common and biologically aggressive brain tumour. The current standard therapy for GBM consists in surgical resection, followed by radiotherapy and chemotherapy. Yet, the treatment is limited due to the area for the surgical resection and for the inability of some drugs to cross the brain blood barrier, leading to a general prognostic of no more than a year. Cold atmospheric plasma (CAP) is a new approach in the treatment of this challenging disease. CAP interaction with cells is dependent on physical and chemical factors, with different plasma discharges, cell type, and culture conditions leading to different CAP activity. Considering the plasma self-adaptation that different plasma discharge modes can undergo, which leads to different interaction plasma/cells, the characterization of a new device is essential. In this study we analysed the effect of a novel large pin-to-plate non-thermal atmospheric plasma on U-251 MG cells under different conditions. The analysis of reactive oxygen and nitrogen species (RONS) on plasma, media and cells were also assessed. We were able to demonstrate that the pin-to-plate device is cytotoxic to GBM cells in a dose, time and ROS dependent manner. The measurements of RONS on plasma/media also give us an insight on the chemical effect of this novelty device, and the possibility to better understand the use of this device as a promising GBM therapy.
Caspase inhibition mitigates tau cleavage and neurotoxicity in iPSC-induced neurons with the V337MMAPTmutation
Authors: Theofilas Panos , Wang Chao , Butler David , Morales Dulce O. , Petersen Cathrine , Chin Brian , Yang Teddy , Khan Shireen , Ng Raymond , Kayed Rakez , Karch Celeste M. , Miller Bruce L. , Gestwicki Jason E. , Gan Li , Temple Sally , Arkin Michelle R. , Grinberg Lea T.
Published: January 2021

Tau post-translational modifications (PTMs) are associated with progressive tau accumulation and neuronal loss in tauopathies, including forms of frontotemporal lobar degeneration (FTLD) and Alzheimer’s disease (AD). Proteolytic cleavage of tau by active caspases, including caspase-6, represents an underexplored tau PTM implicated in tau pathology. Caspase-cleaved tau is toxic and prone to self-aggregation in experimental models. To elucidate the presence and temporal course of caspase activation, tau cleavage, and neuronal death, we generated two neoepitope monoclonal antibodies (mAbs) against caspase-6 tau proteolytic sites and cortical neurons from induced pluripotent stem cells (iPSCs) with the frontotemporal dementia (FTD)-causing V337MMAPTmutation. FTLD V337MMAPTand AD postmortem brains showed positivity for both cleaved tau mAbs as well as active caspase-6. Relative to isogenic wild-typeMAPTcontrols, V337MMAPTneurons showed a time-dependent increase in pathogenic tau in the form of tau oligomers, caspase-cleaved tau, and p-tau. Accumulation of toxic tau species in 3-month V337MMAPTneurons also increased vulnerability to stress, which was pharmacologically rescued by caspase inhibition. We propose a model in which time-dependent accumulation of caspase-cleaved tau in V337MMAPTneurons promotes neurotoxicity that is reversed by caspase-6 inhibition. Caspase-cleaved tau may be a biomarker of tauopathy, and caspases could be viable targets for therapeutic intervention against tau pathogenesis in FTLD and other tauopathies.

Significance

The mechanisms leading to tau pathology in frontotemporal dementia (FTD) and Alzheimer’s disease (AD) remain elusive. Experimental studies in AD demonstrate that tau cleavage by active caspase-6 contributes to tau pathology since cleaved tau may be toxic and prone to self-aggregation. Yet, the role of caspase-cleaved tau in promoting toxicity and cell death is unclear. Here, we generated two neoepitope monoclonal antibodies against caspase-6 tau and evaluated tau cleavage in postmortem human brains, iPSC-induced cortical neurons with the FTD-causing V337MMAPTmutation, and isogenic wild-typeMAPTcontrols. Our results demonstrate a time-dependent accumulation of caspase-cleaved tau and increased neurotoxicity in the mutant iNs that is reversed by caspase-6 inhibition. Caspases could be viable therapeutic targets against tau pathology in tauopathies.
Ad26.COV2.S-elicited immunity protects against G614 spike variant SARS-CoV-2 infection in Syrian hamsters and does not enhance respiratory disease in challenged animals with breakthrough infection after sub-optimal vaccine dosing
Authors: van der Lubbe Joan E.M. , Rosendahl Huber Sietske K. , Vijayan Aneesh , Dekking Liesbeth , van Huizen Ella , Vreugdenhil Jessica , Choi Ying , Baert Miranda R.M. , Feddes-de Boer Karin , Gil Ana Izquierdo , van Heerden Marjolein , Dalebout Tim J. , Myeni Sebenzile K. , Kikkert Marjolein , Snijder Eric J. , de Waal Leon , Stittelaar Koert J. , Tolboom Jeroen T.B.M. , Serroyen Jan , Muchene Leacky , van der Fits Leslie , Rutten Lucy , Langedijk Johannes P.M. , Barouch Dan H. , Schuitemaker Hanneke , Zahn Roland C. , Wegmann Frank
Published: January 2021

Previously we have shown that a single dose of recombinant adenovirus serotype 26 (Ad26) vaccine expressing a prefusion stabilized SARS-CoV-2 spike antigen (Ad26.COV2.S) is immunogenic and provides protection in Syrian hamster and non-human primate SARS-CoV-2 infection models. Here, we investigated the immunogenicity, protective efficacy and potential for vaccine-associated enhanced respiratory disease (VAERD) mediated by Ad26.COV2.S in a moderate disease Syrian hamster challenge model, using the currently most prevalent G614 spike SARS-CoV-2 variant. Vaccine doses of 1×109vp and 1×1010vp elicited substantial neutralizing antibodies titers and completely protected over 80% of SARS-CoV-2 inoculated Syrian hamsters from lung infection and pneumonia but not upper respiratory tract infection. A second vaccine dose further increased neutralizing antibody titers which was associated with decreased infectious viral load in the upper respiratory tract after SARS-CoV-2 challenge. Suboptimal non-protective immune responses elicited by low-dose A26.COV2.S vaccination did not exacerbate respiratory disease in SARS-CoV-2-inoculated Syrian hamsters with breakthrough infection. In addition, dosing down the vaccine allowed to establish that binding and neutralizing antibody titers correlate with lower respiratory tract protection probability. Overall, these pre-clinical data confirm efficacy of a 1-dose vaccine regimen with Ad26.COV2.S in this G614 spike SARS-CoV-2 virus variant Syrian hamster model, show the added benefit of a second vaccine dose, and demonstrate that there are no signs of VAERD under conditions of suboptimal immunity.
Clr4SUV39H1ubiquitination and non-coding RNA mediate transcriptional silencing via heterochromatic phase transitions
Authors: Kim Hyun-Soo , Roche Benjamin , Bhattacharjee Sonali , Todeschini Leila , Chang An-Yun , Hammell Christopher , Verdel André , Martienssen Robert A.
Published: January 2021

Transcriptional silencing by RNAi paradoxically relies on transcription, but how the transition from transcription to silencing is achieved has remained unclear. The Cryptic Loci Regulator complex (CLRC) inSchizosaccharomyces pombeis a cullin-ring E3 ligase required for silencing that is recruited by RNAi. We found that the E2 ubiquitin conjugating enzyme Ubc4 interacts with CLRC and mono-ubiquitinates the histone H3K9 methyltransferase Clr4SUV39H1, promoting the transition from co-transcriptional gene silencing (H3K9me2) to transcriptional gene silencing (H3K9me3). Ubiquitination of Clr4 occurs in an intrinsically disordered region (IDR), which undergoes robust liquid-liquid phase separation (LLPS), along with Swi6HP1the effector of transcriptional gene silencing. Phase separation of Clr4 and Swi6 is exquisitely sensitive to non-coding RNA (ncRNA), which promotes dimerization, chromatin association, and di-, but not tri-methylation instead. Ubc4-CLRC also targets the transcriptional co-activator Bdf2BRD4, down-regulating centromeric transcription and small RNA production. The deubiquitinase Ubp3 counteracts both activities.
CYK-1/Formin activation in cortical RhoA signaling centers promotes organismal left-right symmetry breaking
Authors: Middelkoop Teije C. , Garcia-Baucells Júlia , Quintero-Cadena Porfirio , Pimpale Lokesh G. , Yazdi Shahrzad , Sternberg Paul , Gross Peter , Grill Stephan W.
Published: January 2021

1

Proper left-right symmetry breaking is essential for animal development and in many species the actin cytoskeleton plays an instrumental role in this process. Active torque generation in the actomyosin layer promotes left-right symmetry breaking inC. elegansembryos by driving chiral counter-rotating cortical flows. While both Formins and Myosins have been implied in left-right symmetry breaking, and both can rotate actin filamentsin vitro, it remains unclear if active torques in the actomyosin cortex are generated by Formins, Myosins, or both. We combined the strength ofC. elegansgenetics with quantitative imaging and thin film, chiral active fluid theory to show that, while Non-Muscle Myosin II activity drives cortical actomyosin flows, it is permissive for chiral counter-rotation and dispensable for chiral symmetry breaking of cortical flows. Instead, we find that CYK-1/Formin activation in RhoA foci is instructive for chiral counter-rotation and promotes in-plane, active torque generation in the actomyosin cortex. Notably, we observe that artificially generated large active RhoA patches undergo rotations with consistent handedness in a CYK-1/Formin-dependent manner. Altogether, we conclude that, CYK-1/Formin-dependent active torque generation facilitates chiral symmetry breaking of actomyosin flows and drives organismal left-right symmetry breaking in the nematode worm.

2

Significance

Active torque generation in the actin cytoskeleton has been implicated in driving left-right symmetry breaking of developing embryos, but which molecules generate the active torque and how active torque generation is organized subcellularly remains unclear. This study shows that cortical Formin, recruited to cortical regions where RhoA signaling is active, promotes active torque generation in the actomyosin layer. We find that active torque tends to locally rotate the cortex in a clockwise fashion, which drives the emergence of chiral counter-rotating flows with consistent handedness and facilitates left-right symmetry breaking ofC. elegansembryos.
Cysteine is a limiting factor for glioma proliferation and survival
Authors: Ruiz-Rodado Victor , Dowdy Tyrone , Lita Adrian , Kramp Tamalee , Zhang Meili , Jung Jinkyu , Dios-Esponera Ana , Herold-Mende Christel C. , Camphausen Kevin , Gilbert Mark R. , Larion Mioara
Published: January 2021

Nutritional intervention is becoming more prevalent as adjuvant therapy for many cancers in view of the tumor dependence on external sources for some nutrients. We report the dependence of glioma cells on exogenous cysteine/cystine, despite this amino acid being nonessential.13C-tracing and the analysis of cystathionine synthase and cystathioninase levels revealed the metabolic landscape attributable to cysteine deprivation, and the disconnection between the methionine cycle and the transsulfuration pathway. Therefore, we explored the nutritional deprivation in a mouse model of glioma. Animals subjected to a cysteine/cystine-free diet survived longer, with concomitant reductions in glutathione and cysteine plasma levels. At the end point, however, tumors displayed the ability to synthesize glutathione, although higher levels of oxidative stress were detected. We observed a compensation from the nutritional intervention revealed as the recovery of cysteine-related metabolites in plasma. Our study highlights a time window where cysteine deprivation can be exploited for additional therapeutic strategies.
Genetic modulation of initial sensitivity to Δ9-tetrahydrocannabinol (THC) among the BXD family of mice
Authors: Parks C. , Rogers C.M. , Prins J.P. , Williams R.W. , Chen H. , Jones B.C. , Moore B.M. , Mulligan M.K.
Published: January 2021

Cannabinoid receptor 1 activation by the major psychoactive component in cannabis, Δ9-tetrahydrocannabinol (THC), produces motor impairments, hypothermia, and analgesia upon acute exposure. In previous work, we demonstrated significant sex and strain differences in acute responses to THC following administration of a single dose (10 mg/kg,i.p.) in C57BL/6J (B6) and DBA/2J (D2) inbred mice. To determine the extent to which these differences are heritable, we quantified acute responses to a single dose of THC (10 mg/kg,i.p.) in males and females from 20 members of the BXD family of inbred strains derived by crossing and inbreeding B6 and D2 mice. Acute THC responses (initial sensitivity) were quantified as changes from baseline for: 1. spontaneous activity in the open field (mobility), 2. body temperature (hypothermia), and 3. tail withdrawal latency to a thermal stimulus (analgesia/antinociception). Initial sensitivity to the immobilizing, hypothermic, and antinociceptive effects of THC varied substantially across the BXD family. Heritability was highest for mobility and hypothermia traits, indicating that segregating genetic variants modulate initial sensitivity to THC. We identified genomic loci and candidate genes, includingNdufs2, Scp2, Rps6kb1or P70S6K,Pde4d, andPten, that may control variation in THC initial sensitivity. We also detected strong correlations between initial responses to THC and legacy phenotypes related to intake or response to other drugs of abuse (cocaine, ethanol, and morphine). Our study demonstrates the feasibility of mapping genes and variants modulating THC responses in the BXDs to systematically define biological processes and liabilities associated with drug use and abuse.
Decoupling of global brain activity and cerebrospinal fluid flow in Parkinson’s cognitive decline
Authors: Han Feng , Brown Gregory L. , Zhu Yalin , Belkin-Rosen Aaron E. , Lewis Mechelle M. , Du Guangwei , Gu Yameng , Eslinger Paul J. , Mailman Richard B. , Huang Xuemei , Liu Xiao
Published: January 2021

Background

Deposition and spreading of misfolded proteins (α-synuclein and tau) have been linked to Parkinson’s cognitive dysfunction. The glymphatic system may play an important role in the clearance of these toxic proteins via cerebrospinal fluid (CSF) flow through perivascular and interstitial spaces. Recent studies discovered that sleep-dependent global brain activity is coupled to CSF flow that may reflect glymphatic function.

Objective

To determine if the decoupling of brain activity-CSF flow is linked to Parkinson’s cognitive dysfunction.

Methods

Functional and structural MRI data, clinical motor (Unified Parkinson's Disease Rating Scale), and cognitive (Montreal Cognitive Assessment, MoCA) scores were collected from 60 Parkinson’s and 58 control subjects. Parkinson’s patients were subgrouped into those with (MoCA < 26; N = 29) and without (MoCA ≥ 26; N = 31) mild cognitive impairment (MCI).

The coupling strength between the resting-state global blood-oxygen-level-dependent signal (gBOLD) and associated CSF flow was quantified, compared among groups, and associated with clinical and structural measurements.

Results

gBOLD-CSF coupling decreased significantly (p< 0.006) in Parkinson’s patients showing MCI, compared to those without MCI and controls. Reduced gBOLD-CSF coupling was associated with decreased MoCA scores that was present in Parkinson’s patients (p= 0.005) but not in controls (p= 0.65). Weaker gBOLD-CSF coupling in Parkinson’s patients also was associated with a thinner right entorhinal cortex (Spearman’s correlation = − 0.36;p= 0.012), an early structural change often seen in Alzheimer’s.

Conclusions

The decoupling between global brain activity and associated CSF flow is related to Parkinson’s cognitive impairment.
Differential regulation of progranulin derived granulin peptides
Authors: Zhang Tingting , Du Huan , Santos Mariela Nunez , Wu Xiaochun , Reinheckel Thomas , Hu Fenghua
Published: January 2021

Haploinsufficiency of progranulin (PGRN) is a leading cause of frontotemporal lobar degeneration (FTLD). PGRN is comprised of 7.5 granulin repeats and is processed into individual granulin peptides in the lysosome. However, very little is known about the levels and regulations of individual granulin peptides due to the lack of specific antibodies. Here we report the generation and characterization of antibodies specific to each granulin peptide. We found that the levels of granulins C, E and F are differentially regulated compared to granulins A and B. Furthermore, we demonstrated that granulin B, C and E are heavily glycosylated and the glycosylation pattern of granulin C varies in different physiological and pathological conditions. Deficiency of lysosomal proteases leads to alterations in the levels of a specific subset of granulins. These data support that the levels of individual granulin peptides are differentially regulated under physiological and pathological conditions and provide novel insights into how granulin peptides function in the lysosome.
Super-Resolution Label-free Volumetric Vibrational Imaging
Authors: Qian Chenxi , Miao Kun , Lin Li-En , Chen Xinhong , Du Jiajun , Wei Lu
Published: January 2021

Innovations in high-resolution optical imaging have allowed visualization of nanoscale biological structures and connections. However, super-resolution fluorescence techniques, including both optics-oriented and sample-expansion based, are limited in quantification and throughput especially in tissues from photobleaching or quenching of the fluorophores, and low-efficiency or non-uniform delivery of the probes. Here, we report a general sample-expansion vibrational imaging strategy, termed VISTA, for scalable label-free high-resolution interrogations of protein-rich biological structures with resolution down to 82 nm. VISTA achieves decent three-dimensional image quality through optimal retention of endogenous proteins, isotropic sample expansion, and deprivation of scattering lipids. Free from probe-labeling associated issues, VISTA offers unbiased and high-throughput tissue investigations. With correlative VISTA and immunofluorescence, we further validated the imaging specificity of VISTA and trained an image-segmentation model for label-free multi-component and volumetric prediction of nucleus, blood vessels, neuronal cells and dendrites in complex mouse brain tissues. VISTA could hence open new avenues for versatile biomedical studies.
Endogenous Retroviral Elements Generate Pathologic Neutrophils and Elastase Rich Exosomes in Pulmonary Arterial Hypertension
Authors: Taylor Shalina , Contrepois Kévin , Benayoun Bérénice A. , Jiang Lihua , Isobe Sarasa , Wang Lingli , Melemenidis Stavros , Ozen Mehmet O. , Otsuki Shoichiro , Shinohara Tsutomu , Sweatt Andrew J. , Kaplan Jordan , Cao Aiqin , Moonen Jan-Renier , Marciano David P. , Gu Mingxia , Miyagawa Kazuya , Del Rosario Patricia A. , Hsi Andrew , Thompson A. A. Roger , Ariza Maria-Eugenia , Demirci Utkan , Zamanian Roham T. , Haddad Francois , Nicolls Mark R. , Snyder Michael P. , Rabinovitch Marlene
Published: January 2021

Neutrophil elastase (NE) is implicated in pulmonary arterial hypertension (PAH) but the role of neutrophils in the pathogenesis of PAH is unclear. Here we show that neutrophils from PAH vs. control subjects produce and release increased NE associated with enhanced extracellular trap formation. PAH neutrophils are highly adherent and show decreased migration consistent with increased vinculin, identified on proteomic analysis and previously linked to an antiviral response. This was substantiated by a transcriptomic interferon signature in PAH neutrophils and an increase in human endogenous retrovirus (HERV-K) envelope protein. NE and interferon genes are induced by HERV-K envelope and vinculin is increased by HERV-K dUTPase that is elevated in PAH plasma. Neutrophil exosomes from PAH plasma contain increased NE and HERV-K envelope and induce pulmonary hypertension in mice, that is mitigated by the NE inhibitor and antiviral agent, elafin. Thus, elevated HERVs explain pathological neutrophils linked to PAH induction and progression.
Influence of Fara-darmani Consciousness Field on Bacterial Population Growth
Authors: Taheri Mohammad Ali , Zarrini Gholamreza , Torabi Sara , Nabavi Noushin , Semsarha Farid
Published: January 2021

The treatment of bacterial infections and the rising challenges of antibiotics resistance are global concerns and the primary topics in basic science and clinical microbiology. In the present study, the effectiveness of treatment of selected populations of bacteria using an immaterial and non-energetic method called Fara-darmani Consciousness Field treatment is investigated. Population growth was assessed by turbidimetry, colony counting and tetrazolium chloride reduction assays in non-treated control and Fara-darmani-treated groups. Our results suggest effectiveness of the Fara-darmani Consciousness Field on reducing various types of bacterial strain growth rates (up to 46%). In addition, along with a decrease in bacterial population, evidence of increased survival can be seen in the larger healthy population (up to about 60%). Thus, in this study, we confirm the effects of the Consciousness Field on bacterial population survival. This study also warrants additional research.