bluuebunny/crossref_metadata_2025 huggingface dataset:
Chalcones, stilbenes and ketones have anti-infective properties via inhibition of bacterial drug-efflux and consequential synergism with antimicrobial agents
Authors: Hellewell Lauren , Bhakta Sanjib
Published: February 2020

With antimicrobial resistance creating a major public health crisis, the designing of novel antimicrobial compounds that effectively combat bacterial infection is becoming increasingly critical. Interdisciplinary approaches integrate the best features of whole-cell phenotypic evaluation to validate novel therapeutic targets and discover new leads to combat antimicrobial resistance. In this project, whole-cell phenotypic evaluation such as testing inhibitors on bacterial growth, viability, efflux pump, biofilm formation and their interaction with other drugs were performed on a panel of Gram-positive, Gram-negative and acid-fast group of bacterial species. This enabled additional antimicrobial activities of compounds belonging to the flavonoid family including ketones, chalcones and stilbenes, to be identified. Flavonoids have received renewed attention in literature over the past decade, and a variety of beneficial effects of these compounds have been illuminated, including anti-cancer, anti-inflammatory, anti-tumour as well as anti-fungal and anti-bacterial. However, their mechanisms of action are yet to be identified. In this paper, we found that the compounds belonging to the flavonoid family exerted a range of anti-infective properties being identified as novel efflux pump inhibitors, whilst offering the opportunity to be used in combination therapy. The compound 2-phenylacetophenone displayed broad-spectrum efflux pump inhibition activity, whilst trans-chalcone, displayed potent activity against Gram-negative and mycobacterial efflux pumps causing inhibition higher than known potent efflux pump inhibitors, verapamil and chlorpromazine. Drug-drug interaction studies also highlighted that 2-phenylacetophenone not only has the potential to work additively with known antibacterial agents that affect the cell-wall and DNA replication but also trans-chalcone has the potential to work synergistically with anti-tubercular agents. Overall, this paper shows how whole-cell phenotypic analysis allows for the discovery of new antimicrobial agents and their consequent mode of action whilst offering the opportunity for compounds to be repurposed, in order to contribute in the fight against antimicrobial resistance.
Cryo-EM Structure of the 2019-nCoV Spike in the Prefusion Conformation
Authors: Wrapp Daniel , Wang Nianshuang , Corbett Kizzmekia S. , Goldsmith Jory A. , Hsieh Ching-Lin , Abiona Olubukola , Graham Barney S. , McLellan Jason S.
Published: February 2020

The outbreak of a novel betacoronavirus (2019-nCov) represents a pandemic threat that has been declared a public health emergency of international concern. The CoV spike (S) glycoprotein is a key target for urgently needed vaccines, therapeutic antibodies, and diagnostics. To facilitate medical countermeasure (MCM) development we determined a 3.5 Å-resolution cryo-EM structure of the 2019-nCoV S trimer in the prefusion conformation. The predominant state of the trimer has one of the three receptor-binding domains (RBDs) rotated up in a receptor-accessible conformation. We also show biophysical and structural evidence that the 2019-nCoV S binds ACE2 with higher affinity than SARS-CoV S. Additionally we tested several published SARS-CoV RBD-specific monoclonal antibodies and found that they do not have appreciable binding to nCoV-2019 S, suggesting antibody cross-reactivity may be limited between the two virus RBDs. The atomic-resolution structure of 2019-nCoV S should enable rapid development and evaluation of MCMs to address the ongoing public health crisis.
Glycation and Serum Albumin Infiltration Contribute to the Structural Degeneration of Bioprosthetic Heart Valves
Authors: Frasca Antonio , Xue Yingfei , Kossar Alexander P. , Keeney Samuel , Rock Christopher , Zakharchenko Andrey , Streeter Matthew , Gorman Robert C. , Grau Juan B. , George Isaac , Bavaria Joseph E. , Krieger Abba , Spiegel David A. , Levy Robert J. , Ferrari Giovanni
Published: February 2020

Background

Bioprosthetic heart valves (BHV) are widely used to treat heart valve disease but are fundamentally limited by structural valve degeneration (SVD). Non-calcific mechanisms of SVD entirely account for approximately 30% of SVD cases and contribute to calcific SVD but remain understudied. Glycation mechanisms have not been previously associated with SVD, despite being established as degenerative in collagenous native tissues.

Objectives

To determine whether blood component infiltration-based glycation and concomitant human serum albumin (HSA) deposition contribute mechanistically to SVD.

Methods

Immunohistochemistry (IHC) was used to identify advanced glycation end-products (AGEs) and serum albumin accumulation in 45 aortic valve BHV explanted due to SVD, glutaraldehyde-treated bovine pericardium (BP) incubatedin vitroin glyoxal and HSA, and rat subcutaneous BP implants. Structural impacts of glycation-related mechanisms were evaluated by second harmonic generation (SHG) collagen imaging. Hydrodynamic effects of valve glycation and concomitant HSA exposure were studied with an ISO-5840-compliant pulse duplicator system using surgical grade BHV.

Results

All 45 clinical explants and in vitro-incubated BP demonstrated accumulated AGE and HSA compared to un-implanted, un-exposed BHV. SHG revealed instigation of collagen malalignment similar to that in SVD explants by glycation and HSA infiltration. Rat subdermal explants also showed AGE and serum albumin accumulation. Pulse duplication demonstrated significantly reduced orifice area and increased pressure gradient and peak fluid velocity following glyoxal and HSA incubations.

Conclusions

Glycation and concomitant HSA infiltration occur in clinical BHV and contribute to structural and functional degeneration of leaflet tissue, thus representing novel, interacting mechanisms of BHV SVD.
Radiosynthesis,in vitroand preliminaryin vivoevaluation of the novel glutamine derived PET tracers [18F]fluorophenylglutamine and [18F]fluorobiphenylglutamine
Authors: Baguet Tristan , Verhoeven Jeroen , Pauwelyn Glenn , Hu Jiyun , Lambe Patricia , De Lombaerde Stef , Piron Sarah , Donche Sam , Descamps Benedicte , Goethals Ingeborg , Vanhove Christian , De Vos Filip , Beyzavi M. Hassan
Published: February 2020

Introduction

Glucose has been deemed the driving force of tumor growth for decades. However, research has shown that several tumors metabolically shift towards glutaminolysis. The development of radiolabeled glutamine derivatives could be a useful molecular imaging tool for visualizing these tumors. We elaborated on the glutamine-derived PET tracers by developing two novel probes, namely [18F]fluorophenylglutamine and [18F]fluorobiphenylglutamine

Materials and methods

Both tracers were labelled with fluorine-18 using our recently reported ruthenium-based direct aromatic fluorination method. Their affinity was evaluated with a [3H]glutamine inhibition experiment in a human PC-3 and a rat F98 cell line. The imaging potential of [18F]fluorophenylglutamine and [18F]fluorobiphenylglutamine was tested using a mouse PC-3 and a rat F98 tumor model.

Results

The radiosynthesis of both tracers was successful with overall non-decay corrected yields of 18.46 ± 4.18 % (n=10) ([18F]fluorophenylglutamine) and 8.05 ± 3.25 % (n=5) ([18F]fluorobiphenylglutamine).In vitroinhibition experiments showed a moderate and low affinity of fluorophenylglutamine and fluorobiphenylglutamine, respectively, towards the human ASCT-2 transporter. Both compounds had a low affinity towards the rat ASCT-2 transporter. These results were endorsed by thein vivoexperiments with low uptake of both tracers in the F98 rat xenograft, low uptake of [18F]FBPG in the mice PC-3 xenograft and a moderate uptake of [18F]FPG in the PC-3 tumors.

Conclusion

We investigated the imaging potential of two novel PET radiotracers [18F]FPG and [18F]FBPG. [18F]FPG is the first example of a glutamine radiotracer derivatized with a phenyl group which enables the exploration of further derivatization of the phenyl group to increase the affinity and imaging qualities. We hypothesize that increasing the affinity of [18F]FPG by optimizing the substituents of the arene ring can result in a high-quality glutamine-based PET radiotracer.

Advances in Knowledge and Implications for patient care

We hereby report novel glutamine-based PET-tracers. These tracers are tagged on the arene group with fluorine-18, hereby preventingin vivodefluorination, which can occur with alkyl labelled tracers (e.g. (2S,4R)4-[18F]fluoroglutamine). [18F]FPG shows clear tumor uptakein vivo, has noin vivodefluorination and has a straightforward production. We believe this tracer is a good starting point for the development of a high-quality tracer which is useful for the clinical visualization of the glutamine transport.
Voltage-gated ion channels mediate the electrotaxis of glioblastoma cells in a hybrid PMMA/PDMS microdevice
Authors: Tsai Hsieh-Fu , IJspeert Camilo , Shen Amy Q.
Published: February 2020

Transformed astrocytes in the most aggressive form cause glioblastoma, the most common cancer in central nervous system with high mortality. The physiological electric field by neuronal local field potentials and tissue polarity may guide the infiltration of glioblastoma cells through the electrotaxis process. However, microenvironments with multiplex gradients are difficult to create. In this work, we have developed a hybrid microfluidic platform to study glioblastoma electrotaxis in controlled microenvironments with high through-put quantitative analysis by a machine learning-powered single cell tracking software. By equalizing the hydrostatic pressure difference between inlets and outlets of the microchannel, uniform single cells can be seeded reliably inside the microdevice. The electrotaxis of two glioblastoma models, T98G and U-251MG, require optimal laminin-containing extracellular matrix and exhibits opposite directional and electro-alignment tendencies. Calcium signaling is a key contributor in glioblastoma pathophysiology but its role in glioblastoma electrotaxis is still an open question. Anodal T98G electrotaxis and cathodal U-251MG electrotaxis require the presence of extracellular calcium cations. U-251MG electrotaxis is dependent on the P/Q-type voltage-gated calcium channel (VGCC) and T98G is dependent on the R-type VGCC. U-251MG and T98G electrotaxis are also mediated by A-type (rapidly inactivating) voltage-gated potassium channels and acid-sensing sodium channels. The involvement of multiple ion channels suggests that the glioblastoma electrotaxis is complex and patient-specific ion channel expression can be critical to develop personalized therapeutics to fight against cancer metastasis. The hybrid microfluidic design and machine learning-powered single cell analysis provide a simple and flexible platform for quantitative investigation of complicated biological systems.
Cell-cell communication through FGF4 generates and maintains robust proportions of differentiated cell types in embryonic stem cells
Authors: Raina Dhruv , Bahadori Azra , Stanoev Angel , Protzek Michelle , Koseska Aneta , Schröter Christian
Published: February 2020

During embryonic development and tissue homeostasis, reproducible proportions of differentiated cell types are specified from populations of multipotent precursor cells. Molecular mechanisms that enable both robust cell type proportioning despite variable initial conditions in the precursor cells, as well as the re-establishment of these proportions upon perturbations in a developing tissue remain to be characterized. Here we report that the differentiation of robust proportions of epiblast-like and primitive endoderm-like cells in mouse embryonic stem cell cultures emerges at the population level through cell-cell communication via a short-range FGF4 signal. We characterize the molecular and dynamical properties of the communication mechanism, and show how it controls both robust cell type proportioning from a wide range of experimentally controlled initial conditions, as well as the autonomous re-establishment of these proportions following the isolation of one cell type. The generation and maintenance of reproducible proportions of discrete cell types is a new function for FGF signaling that may operate in a range of developing tissues.
Open microfluidic coculture reveals paracrine signaling from human kidney epithelial cells promotes kidney specificity of endothelial cells
Authors: Zhang Tianzi , Lih Daniel , Nagao Ryan J. , Xue Jun , Berthier Erwin , Himmelfarb Jonathan , Zheng Ying , Theberge Ashleigh B.
Published: February 2020

Endothelial cells (ECs) from different human organs possess organ-specific characteristics that support specific tissue regeneration and organ development. EC specificity are identified by both intrinsic and extrinsic cues, among which, parenchyma and organ-specific microenvironment are critical contributors. These extrinsic cues are, however, largely lost duringex vivocultures. Outstanding challenges remain to understand and re-establish EC organ-specificity forin vitrostudies to recapitulate human organ-specific physiology. Here, we designed an open microfluidic platform to study the role of human kidney tubular epithelial cells in supporting EC specificity. The platform consists of two independent cell culture regions segregated with a half wall; culture media is added to connect the two culture regions at a desired timepoint, and signaling molecules can travel across the half wall (paracrine signaling). Specifically, we report that in the microscale coculture device, primary human kidney proximal tubular epithelial cells (HPTECs) rescued primary human kidney peritubular microvascular EC (HKMEC) monolayer integrity and fenestra formation, and HPTECs upregulated key HKMEC kidney-specific genes (HNF1B,AJAP1,KCNJ16) and endothelial activation genes (VCAM1,MMP7,MMP10) in coculture. Co-culturing with HPTECs also promoted kidney-specific genotype expression in human umbilical vein ECs (HUVECs), and human pluripotent stem cell-derived ECs (hPSC-ECs). In comparison to the culture in HPTEC conditioned media, co-culture of ECs with HPTECs showed increased upregulation of kidney specific genes, suggesting potential bidirectional paracrine signaling. Importantly, our device is compatible with standard pipettes, incubators, and imaging readouts, and could also be easily adapted to study cell signaling between other rare or sensitive cells.
Structural basis of substrate recognition and catalysis by fucosyltransferase 8
Authors: Järvå Michael A. , Dramicanin Marija , Lingford James P. , Mao Runyu , John Alan , Jarman Kate , Grinter Rhys W. , Goddard-Borger Ethan D.
Published: February 2020

Fucosylation of the inner-most N-acetyl-glucosamine (GlcNAc) of N-glycans by fucosyltransferase 8 (FUT8) is an important step in the maturation of complex and hybrid N-glycans. This simple modification can have a dramatic impact on the activity and half-life of glycoproteins. These effects are relevant to understanding the invasiveness of some cancers, the development of monoclonal antibody therapeutics, and to a congenital disorder of glycosylation. The acceptor substrate preferences of FUT8 are well characterised and provide a framework for understanding N-glycan maturation in the Golgi, however the structural basis for these substrate preferences and the mechanism through which catalysis is achieved remains unknown. Here, we describe several structures of mouse and human FUT8 in the apo state and in complex with guanosine diphosphate (GDP), a mimic of the donor substrate, and a glycopeptide acceptor substrate. These structures provide insights into: a unique conformational change associated with donor substrate binding; common strategies employed by fucosyltransferases to coordinate GDP; features that define acceptor substrate preferences; and a likely mechanism for enzyme catalysis. Together with molecular dynamics simulations, the structures also reveal how FUT8 dimerisation plays an important role in defining the acceptor substrate binding site. Collectively, this information significantly builds on our understanding of the core-fucosylation process.
In vivomulti-dimensional information-keeping inHalobacterium salinarum
Authors: Davis J. , Bisson-Filho A. , Kadyrov D. , De Kort T. M. , Biamonte M. T. , Thattai M. , Thutupalli S. , Church G. M.
Published: February 2020

Shortage of raw materials needed to manufacture components for silicon-based digital memory storage has led to a search for alternatives, including systems for storing texts, images, movies and other forms of information in DNA. Use of DNA as a medium for storage of 3-D information has also been investigated. However, two problems have yet to be addressed: first, storage of 3-D information in DNA has used objects and coding schemes which require large volumes of data; second, the medium used for DNA information-keeping has been inconsistent with qualities needed for long-term data storage. Here, we address these problems. First, we createdin vivoDNA-encoded digital archives holding precise specifications for 3- and 4-dimensional figures with unprecedented efficiency. Second, we have demonstrated more robust and longer-lasting information-carriers than earlier repositories for DNA-based data archives by inserting digital information into the halophile,Halobacterium salinarum, an extremophilic archaeon. We then embedded Information-keeping halophiles into crystalline mineral salts in which similar organisms have been shown to persistin stasisfor hundreds of millions of years. We propose that digital information archives composed in 3 or more dimensions may be inserted into halophilic organisms and preserved intact for indefinite periods of time.
Integrin Affinity Modulation Critically Regulates Atherogenic Endothelial Activationin vitroandin vivo
Authors: Al-Yafeai Zaki , Peretik Jonette M. , Pearson Brenna H. , Bhattarai Umesh , Wang Dongdong , Petrich Brian G. , Orr A. Wayne
Published: February 2020

While vital to platelet and leukocyte adhesion, the role of integrin affinity modulation in adherent cells remains controversial. In endothelial cells, atheroprone hemodynamics and oxidized lipoproteins drive an increase in the high affinity conformation of α5β1 integrins in endothelial cellsin vitro, and α5β1 integrin inhibitors reduce proinflammatory endothelial activation to these stimuliin vitroandin vivo. However, the importance of α5β1 integrin affinity modulation to endothelial phenotype remains unknown. We now show that endothelial cells (talin1 L325R) unable to induce high affinity integrins initially adhere and spread, but show significant defects in nascent adhesion formation. In contrast, overall focal adhesion number, area, and composition in stably adherent cells are similar between talin1 wildtype and talin1 L325R endothelial cells. However, talin1 L325R endothelial cells fail to induce high affinity α5β1 integrins, fibronectin deposition, and proinflammatory responses to atheroprone hemodynamics and oxidized lipoproteins. Inducing the high affinity conformation of α5β1 integrins in talin1 L325R cells partially restores fibronectin deposition, whereas NF-κB activation and maximal fibronectin deposition require both integrin activation and other integrin-independent signaling. In endothelial-specific talin1 L325R mice, atheroprone hemodynamics fail to promote inflammation and macrophage recruitment, demonstrating a vital role for integrin activation in regulating endothelial phenotype.
Parvalbumin+and Npas1+Pallidal Neurons Have Distinct Circuit Topology and Function
Authors: Pamukcu Arin , Cui Qiaoling , Xenias Harry S. , Berceau Brianna L. , Augustine Elizabeth C. , Fan Isabel , Chalasani Saivasudha , Hantman Adam W. , Lerner Talia N. , Boca Simina M. , Chan C. Savio
Published: February 2020

The external globus pallidus (GPe) is a critical node within the basal ganglia circuit. Phasic changes in the activity of GPe neurons during movement and their alterations in Parkinson’s disease (PD) argue that the GPe is important in motor control. PV+neurons and Npas1+neurons are the two principal neuron classes in the GPe. The distinct electrophysiological properties and axonal projection patterns argue that these two neuron classes serve different roles in regulating motor output. However, the causal relationship between GPe neuron classes and movement remains to be established. Here, by using optogenetic approaches in mice (both males and females), we showed that PV+neurons and Npas1+neurons promoted and suppressed locomotion, respectively. Moreover, PV+neurons and Npas1+neurons are under different synaptic influences from the subthalamic nucleus (STN). Additionally, we found a selective weakening of STN inputs to PV+neurons in the chronic 6-hydroxydopamine lesion model of PD. This finding reinforces the idea that the reciprocally connected GPe-STN network plays a key role in disease symptomatology and thus provides the basis for future circuit-based therapies.

Significance Statement

The external pallidum is a key, yet an understudied component of the basal ganglia. Neural activity in the pallidum goes awry in neurological diseases, such as Parkinson’s disease. While this strongly argues that the pallidum plays a critical role in motor control, it has been difficult to establish the causal relationship between pallidal activity and motor (dys)function. This was in part due to the cellular complexity of the pallidum. Here, we showed that the two principal neuron types in the pallidum have opposing roles in motor control. In addition, we described the differences in their synaptic influence. Importantly, our research provides new insights into the cellular and circuit mechanisms that explain the hypokinetic features of Parkinson’s disease.
Alterations in the intrinsic properties of striatal cholinergic interneurons after dopamine lesion and chronic L-DOPA
Authors: Choi Se Joon , Ma Thong C. , Ding Yunmin , Cheung Timothy , Joshi Neal , Sulzer David , Mosharov Eugene V. , Kang Un Jung
Published: February 2020

Summary

Changes in striatal cholinergic interneuron (ChI) activity are thought to contribute to Parkinson’s disease pathophysiology and dyskinesia from chronic L-3,4-dihydroxyphenylalanine (L-DOPA) treatment, but the physiological basis of these changes are unknown. We find that dopamine lesion decreases the spontaneous firing rate of ChIs, whereas chronic treatment with L-DOPA of lesioned mice increases baseline ChI firing rates to levels beyond normal activity. The effect of dopamine loss on ChIs was due to decreased currents of both hyperpolarization-activated cyclic nucleotide-gated (HCN) and small conductance calcium-activated potassium (SK) channels. L-DOPA reinstatement of dopamine normalized HCN activity, but SK current remained depressed. Pharmacological blockade of HCN and SK activities mimicked changes in firing, confirming that these channels are responsible for the molecular adaptation of ChIs to dopamine loss and chronic L-DOPA treatment. These findings suggest that targeting ChIs with channel-specific modulators may provide therapeutic approaches for alleviating L-DOPA-induced dyskinesia in PD patients.
Quantitative Proteomics and Phosphoproteomics Supports a Role for Mut9-Like Kinases in Multiple Metabolic and Signaling Pathways inArabidopsis
Authors: Wilson Margaret E. , Tzeng Shin-Cheng , Augustin Megan M. , Meyer Matthew , Jiang Xiaoyue , Choi Jae H. , Rogers John C. , Evans Bradley S. , Kutchan Toni M. , Nusinow Dmitri A.
Published: February 2020

Summary/Abstract

Protein phosphorylation is one of the most prevalent post-translational modifications found in eukaryotic systems. It serves as a key molecular mechanism that regulates protein function in response to environmental stimuli. The Mut9-Like Kinases (MLKs) are a plant-specific family of Ser/Thr kinases linked to light, circadian, and abiotic stress signaling. Here we use quantitative phosphoproteomics in conjunction with global proteomic analysis to explore the role of the MLKs in daily protein dynamics. Proteins involved in light, circadian, and hormone signaling, as well as several chromatin-modifying enzymes and DNA damage response factors, were found to have altered phosphorylation profiles in the absence of MLK family kinases. In addition to altered phosphorylation levels,mlkmutant seedlings have an increase in glucosinolate metabolism enzymes. Subsequently, we show that a functional consequence of the changes to the proteome and phosphoproteome inmlkmutant plants is elevated glucosinolate accumulation, and increased sensitivity to DNA damaging agents. Combined with previous reports, this work supports the involvement of MLKs in a diverse set of stress responses and developmental processes, suggesting that the MLKs serve as key regulators linking environmental inputs to developmental outputs.
PDH Mediated Mitochondrial Respiration Controls the Speed of Muscle Stem Cell Activation in Muscle Repair and Aging
Authors: Raval Manmeet H. , Cheng Pin-Chung , Guardino Nicholas , Ahsan Sanjana , Zhou Hao , Tiwari Rajiv Lochan , Wang Lu , Chareunsouk Andrew , Ederer Maxwell , Hwang Ara B. , Ellenberger Matt , Pepin Rob , Raftery Daniel , Promislow Daniel , Shen Keyue , Brack Andrew S. , Rodgers Joseph T.
Published: February 2020

Decline in the skeletal muscle stem cell (MuSC) function is a major contributor to age-associated impairments in muscle regeneration and function. The ability of MuSCs to activate (i.e. exit quiescence, enter the cell cycle, and divide) following injury is a critical step that initiates muscle regeneration. However, the mechanisms that regulate MuSC activation function are poorly understood. Here, we show that the activation function, specifically the speed by which cells progress through G0-G1, declines tremendously with age in mouse MuSCs. Using a number ofin vivomodels andex vivoassays of MuSC activation and muscle regenerative functions, live cell metabolic flux analyses, and metabolomics we present data indicating that changes in MuSC mitochondrial flux underlie age-associated changes in MuSC activation. We show that, in the course of MuSC activation, there is a profound,16-fold, increase in ATP production rates, which is fueled largely by increases in pyruvate flux into mitochondria. We found that MuSCs from aged mice display progressive defects in the ability to increase mitochondrial flux during activation and that this correlates with higher levels of phosphorylated, inactivated, pyruvate dehydrogenase (PDH). Importantly, we demonstrate that pharmacologic and physiologic methods to induce dephosphorylation and activation of PDH in MuSCs are sufficient to rescue the activation and muscle regenerative functions of MuSCs in aged mice. Collectively the data presented show that MuSC mitochondrial function is a central regulator of MuSC activation and muscle regenerative functions. Moreover, our results suggest that approaches to increase MuSC pyruvate oxidation may have therapeutic potential to promote muscle repair and regeneration.
RNAAgeCalc: A multi-tissue transcriptional age calculator
Authors: Ren Xu , Kuan Pei Fen
Published: February 2020

We introduced RNAAgeCalc, a versatile across-tissue and tissue-specific transcriptional age calculator. We utilized GTEx database to identify 1,616 common age-related genes based on meta-analysis of transcriptional age signature across multi-tissues. Additionally, tissue-specific age-related genes were obtained from differential expression analysis on individual tissues. By performing across-tissue transcriptional age prediction, we showed that our 1,616 common age-related genes outperformed other prior age related gene signatures. Furthermore, we utilized TCGA database to demonstrate that the transcriptional age acceleration computed from our within-tissue predictor was significantly correlated with mutation burden, mortality risk and cancer stage. RNAAgeCalc is available athttp://www.ams.sunysb.edu/~pfkuan/softwares.html#RNAAgeCalc.
WDR90 is a centriolar microtubule wall protein important for centriole architecture integrity
Authors: Steib Emmanuelle , Gambarotto Davide , Laporte Marine , Olieric Natacha , Zheng Céline , Borgers Susanne , Olieric Vincent , Le Guennec Maeva , Koll France , Tassin Anne-Marie , Steinmetz Michel O. , Guichard Paul , Hamel Virginie
Published: February 2020

Centrioles are characterized by a nine-fold arrangement of long-lived microtubule triplets that are held together by an inner protein scaffold. These structurally robust organelles experience strenuous cellular processes such as cell division or ciliary beating while performing their function. However, the molecular mechanisms underlying the stability of microtubule triplets, as well as centriole architectural integrity remain poorly understood. Here, using ultrastructure expansion microscopy (U-ExM) for nanoscale protein mapping, we reveal that POC16 and its human homolog WDR90 are components of the centriolar microtubule wall along the central core region of the centriole. We further found that WDR90 is an evolutionary microtubule associated protein with a predicted structurally homology with the ciliary inner junction protein FAP20. Finally, we demonstrate that WDR90 depletion impairs the localization of inner scaffold components, leading to centriole structural abnormalities in both human andChlamydomonascells. Altogether, this work highlights that POC16/WDR90 is a crucial evolutionary conserved molecular player participating in centriole architecture integrity.
2 MV/cm Pulsed Electric Fields Promote Transthyretin Amyloid Disintegration
Authors: Urabe Gen , Sato Takashi , Nakamura Gomaru , Kobashigawa Yoshihiro , Morioka Hiroshi , Katsuki Sunao
Published: February 2020

Exposing transthyretin amyloid to 1000 sub-nanosecond 2 MV/cm pulsed electric fields (PEFs) promotes both amyloid disassembly and amyloid-derived transthyretin disintegration. The process produced no change in pH, and the resulting temperature increase was less than 1 °C. We conclude that PEFs’ physical effects facilitate amyloid disassembly, rather than thermal or chemical effects, and provoke amyloid-derived transthyretin disintegration, the latter of which is reported here for the first time.
Path integration changes as a cognitive marker for vascular cognitive impairment? – a pilot study
Authors: Lowry Ellen , Puthusseryppady Vaisakh , Coughlan Gillian , Jeffs Stephen , Hornberger Michael
Published: February 2020

Path integration spatial navigation processes are emerging as promising cognitive markers for prodromal and clinical Alzheimer’s disease (AD). However, such path integration changes have been little explored in Vascular Cognitive Impairment (VCI), despite neurovascular change being a major contributing factor to dementia and potentially AD. In particular, the sensitivity and specificity of path integration impairments in VCI compared to AD is unclear. In the current pilot study, we explore path integration performance in AD and VCI patient groups and hypothesise that i) medial parietal mediated egocentric processes will be more affected in VCI and ii) medial temporal mediated allocentric processes will be more affected in AD. This retrospective cross-sectional study included early stage VCI patients (n=9), AD patients (n=10) and healthy age-matched controls (n=20). All participants underwent extensive neuropsychological testing, as well as spatial navigation testing. The spatial navigation tests included the virtual reality ‘Supermarket’ task assessing egocentric (body-based) and allocentric (map-based) navigation as well as the ‘Clock Orientation’ test assessing egocentric and path integration processes. Results showed that egocentric path integration processes are only impaired in VCI, potentially distinguishing it from AD. However, in contrast to our prediction, allocentric path integration was similarly impaired for VCI and AD. These preliminary findings suggest limited specificity of allocentric path integration deficits between VCI and AD. By contrast, egocentric path integration deficits emerge as more specific to VCI, potentially allowing for more specific diagnostic and treatment outcome measures for vascular impairment in dementia.
Nutrient parsimony shapes diversity and functionality in hyper-oligotrophic Antarctic soils
Authors: Van Goethem Marc W. , Vikram Surendra , Hopkins David W. , Hall Grant , Woodborne Stephan , Aspray Thomas J. , Hogg Ian D. , Cowan Don A. , Makhalanyane Thulani P.
Published: February 2020

The balance of nutrients in soil is critical for microbial growth and function, and stoichiometric values below the Redfield ratio for C:N:P can negatively affect microbial ecosystem services. However, few studies have assessed the relationships between nutrient balance and biological productivity in extremely nutrient-poor habitats. The Mackay Glacier region of Eastern Antarctica is a hyper-oligotrophic ice-free desert and is an appropriate landscape to evaluate the effects of nutrient deficiency and imbalance on microbial community ecology. In a survey of multiple, widely dispersed soil samples from this region, we detected only low rates of microbial respiration, and observed that C:N:P ratios were well below those required for optimal activity. In silico metagenomic and soil isotopic ratio (δ15N) analyses indicated that the capacity for nitrogen fixation was low, but that soil microbial communities were enriched for soil nitrate assimilation processes, mostly associated with heterotrophic taxa. δ13C isotope ratio data suggested that carbon dioxide was fixed principally via the Calvin cycle. Genes involved in this pathway were common to all metagenomes and were primarily attributed to members of the dominant soil bacterial phyla: Bacteroidetes and Acidobacteria. The identification of multiple genes encoding non-photoautotrophic RUBISCO and carbon dioxide dehydrogenase enzymes in both the metagenomic sequences and assembled MAGs is suggestive of a trace-gas scavenging physiology in members of these soil communities.
Modeling and Analysis of the Macronutrient Signaling Network in Budding Yeast
Authors: Jalihal Amogh P. , Kraikivski Pavel , Murali T. M. , Tyson John J.
Published: February 2020

In eukaryotes, distinct nutrient signals are relayed by specific plasma membrane receptors to signal transduction pathways that are interconnected in complex information-processing networks. The function of these networks is to govern robust cellular responses to unpredictable changes in the nutritional environment of the cell. In the budding yeast,Saccharomyces cerevisiae, these nutrient signaling pathways and their interconnections have been well characterized. However the complexity of the signaling network confounds the interpretation of the overall regulatory ‘logic’ of the control system. Here, we propose a literature-curated molecular mechanism of the integrated nutrient signaling network in budding yeast, focusing on early temporal responses to carbon and nitrogen signaling. We build a computational model of this network to reconcile literature-curated quantitative experimental data with our proposed molecular mechanism. We evaluate the robustness of our estimates of the model’s kinetic parameter values. We test the model by comparing predictions made in mutant strains with qualitative experimental observations made in the same strains. Finally, we use the model to predict nutrient-responsive transcription factor activities in a number of mutant strains undergoing complex nutrient shifts.
In and outs of Chuviridae endogenous viral elements: origin of a retrovirus and signature of ancient and ongoing arms race in mosquito genomes
Authors: Dezordi Filipe Zimmer , dos Santos Vasconcelos Crhisllane Rafaele , Rezende Antonio Mauro , Wallau Gabriel Luz
Published: February 2020

Background

Endogenous viral elements (EVEs) are sequences of viral origin integrated into the host genome. EVEs have been characterized in various insect genomes, including mosquitoes. A large EVE content has been found inAedes aegyptiandAedes albopictusgenomes among which a recently describedChuviridaeviral family is of particular interest, owing to the abundance of EVEs derived from it, the discrepancy in the endogenized gene regions and the frequent association with retrotransposons from the BEL-Pao superfamily. In order to better understand the endogenization process of chuviruses and the association between chuvirus glycoproteins and BEL-Pao retrotransposons, we performed a comparative genomics and evolutionary analysis of chuvirus-derived EVEs found in 37 mosquito genomes.

Results

We identified 428 EVEs belonging to theChuviridaefamily confirming the wide discrepancy between the number of genomic regions endogenized: 409 glycoproteins, 18 RNA-dependent RNA polymerases and one nucleoprotein region. Most of the glycoproteins (263 out of 409) are associated specifically with retroelements from the Pao family. Focusing only on well assembled Pao retroelement copies, we estimated that 263 out of 379 Pao elements are associated with chuvirus-derived glycoproteins. Seventy-three potentially active Pao copies were found to contain glycoproteins into their LTR boundaries. Thirteen out of these were classified as complete and likely autonomous copies, with a full LTR structure and protein domains. We also found 116 Pao copies with no trace of glycoproteins and 37 solo glycoproteins. All potential autonomous Pao copies, contained highly similar LTRs, suggesting a recent/current activity of these elements in the mosquito genomes.

Conclusion

Evolutionary analysis revealed that most of the glycoproteins found are likely derived from a single or few glycoprotein endogenization events associated with a recombination event with a Pao ancestral element. A potential fully functional Pao-chuvirus hybrid (named Anakin) emerged and the glycoprotein was further replicated through retrotransposition. However, a number of solo glycoproteins, not associated with Pao elements, can still be found in some mosquito genomes 114 million years later, suggesting that these glycoproteins were likely domesticated by the host genome and may participate in an antiviral defense mechanism against both chuvirus and Anakin retrovirus.
Non-photopic and photopic visual cycles differentially regulate immediate, early and late-phases of cone photoreceptor-mediated vision
Authors: Ward Rebecca , Kaylor Joanna J. , Cobice Diego F. , Pepe Dionissia A. , McGarrigle Eoghan M. , Brockerhoff Susan E. , Hurley James B. , Travis Gabriel H. , Kennedy Breandán N.
Published: February 2020

Cone photoreceptors in the retina enable vision over a wide range of light intensities. However, the processes enabling cone vision in bright light (i.e.photopic vision) are not adequately understood. Chromophore regeneration of cone photopigments may require the retinal pigment epithelium (RPE) and/or retinal Müller glia. In the RPE, isomerization of all-trans-retinyl esters (atRE) to 11-cis-retinol (11cROL) is mediated by the retinoid isomerohydrolase Rpe65. An alternative retinoid isomerase, dihydroceramide desaturase-1 (DES1), is expressed in RPE and Müller cells. The retinol-isomerase activities of Rpe65 and Des1 are inhibited by emixustat and fenretinide, respectively. Here, we tested the effects of these visual cycle inhibitors on immediate, early and late phases of cone photopic vision. In zebrafish larvae raised under cyclic light conditions, fenretinide impaired late cone photopic vision, whereas emixustat-treated zebrafish unexpectedly had normal vision. In contrast, emixustat-treated larvae raised under extensive dark-adaption displayed significantly attenuated immediate photopic vision concomitantly with significantly reduced 11-cis-retinaldehyde (11cRAL). Following 30 minutes of light, early photopic vision recovered, despite 11cRAL levels remaining significantly reduced. Defects in immediate cone photopic vision were rescued in emixustat- or fenretinide-treated larvae following exogenous 9-cis-retinaldehyde (9cRAL) supplementation. Genetic knockout ofdegs1or retinaldehyde-binding protein 1b (rlbp1b)revealed that neither are required for photopic vision in zebrafish. Our findings define the molecular and temporal requirements of the non-photopic and photopic visual cycles for mediating vision in bright light.
Dynamic molecular architecture of the synaptonemal complex
Authors: Köhler Simone , Wojcik Michal , Xu Ke , Dernburg Abby F.
Published: February 2020

During meiosis, pairing between homologous chromosomes is stabilized by the assembly of a protein lattice known as the synaptonemal complex (SC). The SC ensures the formation of crossovers between homologous chromosomes and also regulates their distribution. However, how the SC regulates crossover formation remains elusive. We isolated an unusual mutation inC. elegansthat disrupts crossover interference but not the assembly of the SC. This mutation alters the unique C-terminal domain of an essential SC protein, SYP-4, a likely ortholog of the vertebrate SC protein SIX6OS1. To characterize the structure of the SC in wild-type and mutant animals, we use three-dimensional STochastic Optical Reconstruction Microscopy (3D-STORM) to interrogate the molecular architecture of the SC in intact germline tissue fromC. elegans. The approach enabled us to define positions of protein epitopes with respect to the 3D architecture of this complex. Using a probabilistic mapping approach to analyze super-resolution image data, we detect a marked structural transition in wild-type animals that coincides with crossover designation. We also found that oursyp-4mutant subtly perturbs SC architecture. Our findings add to growing evidence that the SC is an active material whose molecular organization contributes to chromosome-wide crossover regulation.
Aberrant astrocyte protein secretion contributes to altered neuronal development in diverse disorders
Authors: Caldwell Alison L.M. , Diedrich Jolene K. , Shokhirev Maxim N. , Allen Nicola J.
Published: February 2020

Astrocytes negatively impact neuronal development in many neurodevelopmental disorders (NDs), however how they do this, and if mechanisms are shared across disorders, is not known. We developed an in vitro system to ask how astrocyte protein secretion and gene expression change in three genetic NDs. We identified disorder specific changes, and changes common to all disorders. ND astrocytes increase release of Igfbp2, a secreted inhibitor of IGF. IGF rescues neuronal deficits in many NDs, and we found blocking Igfbp2 partially rescues inhibitory effects of Rett Syndrome astrocytes, suggesting increased astrocyte Igfbp2 contributes to decreased IGF signaling in NDs. We identified increased BMP signaling in ND astrocytes is upstream of protein secretion changes, including Igfbp2, and blocking BMP signaling in Fragile X Syndrome astrocytes reverses inhibitory effects on neurite outgrowth. We provide a resource of astrocyte secreted proteins in health and NDs, and identify novel targets for intervention in diverse NDs.
Comprehensive Network Analysis and Experimental Verification of Dedu Safflower’s Influence on Ascites Hepatocarcinoma
Authors: Wang Lu , Li Sha , Bao Lidao
Published: February 2020

Background

Dedu Safflower Powder is a kind of classical prescription of Mongolian Medicine, and its main ingredients are the safflower and the Scabiosa tschiliensis. In the former Mongolian Medicine clinical practice, Dedu Safflower Powder, etc. had obvious effect on curing hepatocarcinoma so as to ease ascites. But the principle of Dedu Safflower Powder’s curing ascites hepatocarcinoma has been not clear.

Aim

H22 mouse hepatocarcinoma ascites models are used for researching the safflower and the Scabiosa tschiliensis’s function of jointly being against hepatocarcinoma ascites, and for verifying their possible combination principle (miR-23a-DAPK1-PVT1 signal axis).

Method

Through simulating an interaction network of the safflower and the Scabiosa tschiliensis with target spots, the function target was predicted. H22 mouse hepatocarcinoma ascites models were randomly divided into a blank contrast group, a model contrast group, a safflower group, a Scabiosa tschiliensis group and a compatibility group of the safflower/the Scabiosa tschiliensis. On the 10thday, mice were killed to measure their weights and abdominal perimeters, also to collect ascites and blood for physical examinations. Kidney tissues were dissected at once and fixed in paraformaldehyde, for a real-time quantitative polymerase chain reaction (qRT-PCR) analysis.

Result

In the network, the DAPK1-PVT1 interaction showed the biggest edge betweenness, so it was predicted that DAPK1 and PVT1 were respectively presumed targets of the safflower and the Scabiosa tschiliensis. Compared with the model contrast group, the safflower group, the Scabiosa tschiliensis group and the safflower/Scabiosa tschiliensis group all had decreasing ascites volumes, body weights, abdominal perimeters. Compared with the model group, the safflower group and the safflower/Scabiosa tschiliensis group had rising DAPK1 expressions (p<0.05), while the safflower group had more obvious increasing DAPK1 (p<0.01); the Scabiosa tschiliensis group and the safflower/Scabiosa tschiliensis group had lowering PVT1 expressions (p<0.05), while the Scabiosa tschiliensis group had more obvious lowering PVT1 (p<0.01); the safflower group, the Scabiosa tschiliensis group and the safflower/Scabiosa tschiliensis group had lowering miR-23a expressions (p<0.05), while the safflower/Scabiosa tschiliensis group had more obvious lowering (p<0.01).

Conclusion

DAPK1 and PVT1 are respectively the presumed targets of the safflower and the Scabiosa tschiliensis. So Dedu Safflower Powder has good effects on ascites hepatocarcinoma, and that function may be partly related to regulation of miR-23a-DAPK1-PVT1 signal axis.
Trans-generational effect of protein restricted diet on adult body and wing size ofDrosophila melanogaster
Authors: Krittika Sudhakar , Yadav Pankaj
Published: February 2020

Dietary Restriction (DR) via protein restriction (PR) has become an inquisitive field and has established feasible trade-offs between various fitness and behavioral traits inDrosophila melanogasterto understand lifespan or aging in a nutritionally challenged environment. However, the phenotypes of body size, weight and wing length respond according to factors such as flies’ genotype, environmental exposure, and parental diet. Hence, understanding the long-term effect of PR on these phenotypes is essential. Here, we demonstrate the effect of PR diet on body size, weight and normal & dry wing length of flies subjected to PR50 and PR70 (50% and 70% protein content present in control food respectively) for 20 generations from pre-adult stage. We found that PR fed flies have lower body weight, relative water content (in males), unaltered (PR50%) and higher (PR70%) relative fat content in males, smaller normal and dry body size as compared to control and generations 1 and 2. Interestingly, wing size and pupal size of PR flies are smaller and showed significant effects of diet and generation. Thus, these traits are sex and generation dependent along with an interaction of diet, which is capable of modulating these results variably. Our study suggests that trans-generational effect is more prominent in influencing these traits and wing length might not be a predictor for body size. Taken together, the trans-generational effect of PR on fitness and fitness-related traits might be helpful to understand the underpinning mechanisms of evolution and aging in fruit fliesD. melanogaster.

Summary statement

Twenty generations of protein restricted diet have a diet and generation dependent effect on adult body size, wing length and body weight.