bluuebunny/crossref_metadata_2025 huggingface dataset:
Acquisition of Innate Odor Preference Depends on Spontaneous and Experiential Activities During Critical Period
Authors: Qiu Qiang , Wu Yunming , Ma Limei , Ramalingam Vivekanandan , Yu C. Ron
Published: January 2020

Animals possess inborn ability to recognize certain odors, which enables them to seek food, avoid predators and find mates even in the absence of prior experiences. The establishment of innate odor preference has been thought to be genetically hardwired. Here we report that the acquisition of innate odor recognition requires spontaneous neural activity and is influenced by sensory experience during early postnatal development. Genetic silencing of mouse olfactory sensory neurons during the developmental critical period has little impact on odor sensitivity, odor discrimination and recognition later in life. However, it abolishes innate odor preference and alters the patterns of activation in brain centers. Moreover, exposure to an innately aversive odor during the critical period abolishes aversion in adulthood in an odor specific manner. The loss of innate aversion is associated with broadened projection of OSNs expressing the cognate receptor such that they innervate ectopic glomeruli in the olfactory bulb. These results indicate that a delicate balance of neural activity is required during critical period in establishing innate odor preference and that ectopic projection is a convergent mechanism to alter innate odor valence.
Synchronized genetic activities in Alzheimer’s brains revealed by heterogeneity-capturing network analysis
Authors: Climer Sharlee , Templeton Alan R. , Garvin Michael , Jacobson Daniel , Lane Matthew , Hulver Scott , Scheid Brittany , Chen Zheng , Cruchaga Carlos , Zhang Weixiong
Published: January 2020

It is becoming increasingly evident that the efficacy of single-gene computational analyses for complex traits is nearly exhausted and future advances hinge on unraveling the intricate combinatorial interactions among multiple genes. However, the discovery of modules of genes working in concert to manifest a complex trait has been crippled by combinatorial complexity, genetic heterogeneity, and validation biases. We introduce Maestro, a novel network approach that employs a multifaceted correlation measure, which captures heterogeneity, and a rigorous validation method. Maestro’s utilization for Alzheimer’s disease (AD) reveals an expression pattern that has virtually zero probability of simultaneous expression by an individual, assuming independence. Yet this pattern is exhibited by 19.0% of AD cases and 7.3% of controls, establishing an unprecedented pattern of synchronized genetic activities in the human brain. This pattern is significantly associated with AD, with an odds ratio of 3.0. This study substantiates Maestro’s power for discovery of orchestrated genetic activities underlying complex traits. More generally, Maestro can be applied in diverse domains in which heterogeneity exists.

Highlights

Synchronized genetic activities associated with Alzheimer’s disease

Novel vector-based correlation measure that captures genetic heterogeneity

Enhanced network model for revealing combinatorial genetic interactions

Pro-survival genetic activities associated with Alzheimer’s disease

General approach for revealing patterns in data subject to heterogeneity
Exome-wide age-of-onset analysis reveals exonic variants inERN1, TACR3andSPPL2Cassociated with Alzheimer’s disease
Authors: He Liang , Loika Yury , Park Yongjin ,   Genotype Tissue Expression (GTEx) consortium, Bennett David A. , Kellis Manolis , Kulminski Alexander M. ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: January 2020

Despite recent discovery in GWAS of genomic variants associated with Alzheimer’s disease (AD), its underlying biological mechanisms are still elusive. Discovery of novel AD-associated genetic variants, particularly in coding regions and from APOE ε4 non-carriers, is critical for understanding the pathology of AD. In this study, we carried out an exome-wide association analysis of age-of-onset of AD with ~20,000 subjects and placed more emphasis on APOE ε4 non-carriers. Using Cox mixed-effects models, we find that age-of-onset shows a stronger genetic signal than AD case-control status, capturing many known variants with stronger significance, and also revealing new variants. We identified two novel rare variants, rs56201815, a synonymous variant in ERN1, from the analysis of APOE ε4 non-carriers, and a missense variant rs144292455 in TACR3. In addition, we detected rs12373123, a common missense variant in SPPL2C in the MAPT region in APOE ε4 non-carriers. In an attempt to unravel their regulatory and biological functions, we found that the minor allele of rs56201815 was associated with lower average FDG uptake across five brain regions in ADNI. Our eQTL analyses based on 6198 gene expression samples from ROSMAP and GTEx revealed that the minor allele of rs56201815 was associated with elevated expression of ERN1, a key gene triggering unfolded protein response (UPR), in multiple brain regions, including posterior cingulate cortex and nucleus accumbens. Our cell-type-specific eQTL analysis of based on ~80,000 single nuclei in the prefrontal cortex revealed that the protective minor allele of rs12373123 significantly increased expression of GRN in microglia, and was associated with MAPT expression in astrocytes. These findings provide novel evidence supporting the hypothesis of the potential involvement of the UPR to ER stress in the pathological pathway of AD, and also give more insights into underlying regulatory mechanisms behind the pleiotropic effects of rs12373123 in multiple degenerative diseases including AD and Parkinson’s disease.
Expert programmers have fine-tuned cortical representations of source code
Authors: Ikutani Yoshiharu , Kubo Takatomi , Nishida Satoshi , Hata Hideaki , Matsumoto Kenichi , Ikeda Kazushi , Nishimoto Shinji
Published: January 2020

Expertise enables humans to achieve outstanding performance on domain-specific tasks, and programming is no exception. Many have shown that expert programmers exhibit remarkable differences from novices in behavioral performance, knowledge structure, and selective attention. However, the underlying differences in the brain are still unclear. We here address this issue by associating the cortical representation of source code with individual programming expertise using a data-driven decoding approach. This approach enabled us to identify seven brain regions, widely distributed in the frontal, parietal, and temporal cortices, that have a tight relationship with programming expertise. In these brain regions, functional categories of source code could be decoded from brain activity and the decoding accuracies were significantly correlated with individual behavioral performances on source-code categorization. Our results suggest that programming expertise is built up on fine-tuned cortical representations specialized for the domain of programming.
Genome-wide analyses of chromatin interactions after the loss of Pol I, Pol II and Pol III
Authors: Jiang Yongpeng , Huang Jie , Lun Kehuan , Li Boyuan , Zheng Haonan , Li Yuanjun , Zhou Rong , Duan Wenjia , Feng Yuanqing , Yao Hong , Li Cheng , Ji Xiong
Published: January 2020

Background

The relationship between transcription and the 3D genome organization is one of the most important questions in molecular biology, but the roles of transcription in 3D chromatin remain controversial. Multiple groups showed that transcription affects global Cohesin binding and genome 3D structures. At the same time, several studies have indicated that transcription inhibition does not affect global chromatin interactions.

Results

Here, we provide the most comprehensive evidence to date to demonstrate that transcription plays a marginal role in organizing the 3D genome in mammalian cells: 1) degraded Pol I, Pol II and Pol III proteins in mESCs, and showed their loss results in little or no changes of global 3D chromatin structures for the first time; 2) selected RNA polymerases high abundance binding sites-associated interactions and found they still persist after the degradation; 3) generated higher resolution chromatin interaction maps and revealed that transcription inhibition mildly alters small loop domains; 4) identified Pol II bound but CTCF and Cohesin unbound loops and disclosed that they are largely resistant to transcription inhibition. Interestingly, Pol II depletion for a longer time significantly affects the chromatin accessibility and Cohesin occupancy, suggesting RNA polymerases are capable of affecting the 3D genome indirectly. So, the direct and indirect effects of transcription inhibition explain the previous confusing effects on the 3D genome.

Conclusions

We conclude that Pol I, Pol II, and Pol III loss only mildly alter chromatin interactions in mammalian cells, suggesting the 3D chromatin structures are pre-established and relatively stable.
DASC, a sensitive classifier for measuring discrete early stages in clathrin-mediated endocytosis
Authors: Wang Xinxin , Chen Zhiming , Mettlen Marcel , Noh Jungsik , Schmid Sandra L. , Danuser Gaudenz
Published: January 2020

Clathrin-mediated endocytosis (CME) in mammalian cells is driven by resilient machinery that includes >70 endocytic accessory proteins (EAP). Accordingly, perturbation of individual EAPs often results in minor effects on biochemical measurements of CME, thus providing inconclusive/misleading information regarding EAP function. Live-cell imaging can detect earlier roles of EAPs preceding cargo internalization; however, this approach has been limited because unambiguously distinguishing abortive-clathrin coats (ACs) frombona fideclathrin-coated pits (CCPs) is required but unaccomplished. Here, we develop a thermodynamics-inspired method, “disassembly asymmetry score classification (DASC)”, that unambiguously separates ACs from CCPs without an additional marker. After extensive verification, we use DASC-resolved ACs and CCPs to quantify CME progression in 11 EAP knockdown conditions. We show that DASC is a sensitive detector of phenotypic variation in CCP dynamics that is orthogonal to the variation in biochemical measurements of CME. Thus, DASC is an essential tool for uncovering the function of individual EAPs.
Testing a convolutional neural network-based hippocampal segmentation method in a stroke population
Authors: Zavaliangos-Petropulu Artemis , Tubi Meral A. , Haddad Elizabeth , Zhu Alyssa , Braskie Meredith N. , Jahanshad Neda , Thompson Paul M. , Liew Sook-Lei
Published: January 2020

As stroke mortality rates decrease, there has been a surge of effort to study post-stroke dementia (PSD) to improve long-term quality of life for stroke survivors. Hippocampal volume may be an important neuroimaging biomarker in post-stroke dementia, as it has been associated with many other forms of dementia. However, studying hippocampal volume using MRI requires hippocampal segmentation. Advances in automated segmentation methods have allowed for studying the hippocampus on a large scale, which is important for robust results in the heterogeneous stroke population. However, most of these automated methods use a single atlas-based approach and may fail in the presence of severe structural abnormalities common in stroke. Hippodeep, a new convolutional neural network-based hippocampal segmentation method, does not rely solely on a single atlas-based approach and thus may be better suited for stroke populations. Here, we compared quality control and the accuracy of segmentations generated by Hippodeep and two well-accepted hippocampal segmentation methods on stroke MRIs (FreeSurfer 6.0 whole hippocampus and FreeSurfer 6.0 sum of hippocampal subfields). Quality control was performed using a stringent protocol for visual inspection of the segmentations, and accuracy was measured as volumetric and spatial comparisons to the manual segmentations. Hippodeep performed significantly better than both FreeSurfer methods in terms of quality control and spatial accuracy. Overall, this study suggests that both Hippodeep and FreeSurfer may be useful for hippocampal segmentation in stroke rehabilitation research, but Hippodeep may be more robust to stroke lesion anatomy.
Phytophthora infestansAgo1-bound miRNA promotes potato late blight disease
Authors: Hu Xinyi , Persson Hodén Kristian , Liao Zhen , Dölfors Fredrik , Åsman Anna , Dixelius Christina
Published: January 2020

Phytophthoraspp. incite serious plant damages by exploiting a large number of effector proteins and small RNAs (sRNAs). Several reports are describing modulation of host RNA biogenesis and defence gene expression. Here, we analysedP. infestansArgonaute (Ago) 1 associated small RNAs during potato leaf infection.

sRNAs were co-immunoprecipitated, deep sequenced and analysed against theP. infestansand potato genomes, followed by transgenic and biochemical analyses on a predicted host target.

Extensive targeting of potato and pathogen-derived sRNAs to a large number of mRNAs was observed, including 206 sequences coding for resistance (R) proteins in the host genome. The single miRNA encoded byP. infestans(miR8788) was found to target a potato lipase-like membrane protein-encoding gene (StLL1) localized to the tonoplast. Analyses of stable transgenic potato lines harbouring overexpressedStLL1or artificial miRNA gene constructs demonstrated the importance of StLL1 during infection byP. infestans. Similarly, a miR8788 knock-down strain showed reduced growth on potato compared to the wild-type strain 88069.

The data suggest that sRNA encoded byP. infestanscan affect potato mRNA and thereby promote disease. Knowledge of the impact of pathogen small RNAs in plant defence mechanisms is of major significance to succeed in improved disease control management.
Neural stem cells traffic functional mitochondria via extracellular vesicles to correct mitochondrial dysfunction in target cells
Authors: Peruzzotti-Jametti Luca , Bernstock Joshua D. , Manferrari Giulia , Rogall Rebecca , Fernandez-Vizarra Erika , Williamson James C , Braga Alice , van den Bosch Aletta , Leonardi Tommaso , Kittel Ágnes , Benincá Cristiane , Vicario Nunzio , Tan Sisareuth , Bastos Carlos , Bicci Iacopo , Iraci Nunzio , Smith Jayden A. , Lehner Paul J , Buzas Edit Iren , Faria Nuno , Zeviani Massimo , Frezza Christian , Brisson Alain , Matheson Nicholas J , Viscomi Carlo , Pluchino Stefano
Published: January 2020

Neural stem cell (NSC) transplantation induces recovery in animal models of central nervous system (CNS) diseases. Although the replacement of lost endogenous cells was originally proposed as the primary healing mechanism of NSC grafts, it is now clear that transplanted NSCs operate via multiple mechanisms, including the horizontal exchange of therapeutic cargoes to host cells via extracellular vesicles (EVs).

EVs are membrane particles trafficking nucleic acids, proteins, metabolites and metabolic enzymes, lipids and entire organelles. However, the function and the contribution of these cargoes to the broad therapeutic effects of NSCs is yet to be fully understood. Mitochondrial dysfunction is an established feature of several inflammatory and degenerative CNS disorders, most of which are potentially treatable with exogenous stem cell therapeutics.

Herein we investigated the hypothesis that NSCs release and traffic functional mitochondria via EVs to restore mitochondrial function in target cells.

Untargeted proteomics revealed a significant enrichment of mitochondrial proteins spontaneously released by NSCs in EVs. Morphological and functional analyses confirmed the presence of ultrastructurally intact mitochondria within EVs (Mito-EVs) with conserved membrane potential and respiration. We found that the transfer of Mito-EVs to mtDNA-deficient L929 Rho0cells rescued mitochondrial function and increased Rho0cell survival. Furthermore, the incorporation of Mito-EVs into inflammatory professional phagocytes restored normal mitochondrial dynamics and cellular metabolism and reduced the expression of pro-inflammatory markers in target cells. When transplanted in an animal model of multiple sclerosis, exogenous NSCs actively transferred mitochondria to mononuclear phagocytes and induced a significant amelioration of clinical deficits.

Our data provide the first evidence that NSCs deliver functional mitochondria to target cells via Mito-EVs, paving the way for the development of novel (a)cellular approaches aimed at restoring mitochondrial dysfunction not only in multiple sclerosis, but also in degenerative neurological diseases.
FCHSD2 Controls Oncogenic ERK1/2 Signaling Outcome by Regulating Endocytic Trafficking
Authors: Xiao Guan-Yu , Schmid Sandra L.
Published: January 2020

Cancer progression is driven, in part, by altered signaling downstream of receptor tyrosine kinases (RTKs). Surface expression and RTK activity are regulated by clathrin-mediated endocytosis (CME), endosomal recycling or degradation. In turn, oncogenic signaling downstream of RTKs can reciprocally regulate endocytic trafficking, creating feedback loops that enhance tumor progression. We previously reported a cancer-cell specific function of FCHSD2 (FCH/F-BAR and double SH3 domain-containing protein) in regulating CME in non-small-cell lung cancer (NSCLC) cells. Here, we report that FCHSD2 loss impacts recycling of EGFR and MET, diverting their trafficking toward late endosomes and lysosomes. FCHSD2 depletion results in the nuclear translocation of active ERK1/2, leading to enhanced transcription and upregulation of EGFR and MET. The small GTPase, Rab7, is essential for the FCHSD2 depletion-induced effects. Correspondingly, FCHSD2 loss correlates with higher tumor grades of NSCLC. Clinically, NSCLC patients expressing high FCHSD2 exhibit elevated survival, whereas patients with high Rab7 expression display decreased survival rates. Our study provides new insight into the molecular nexus for crosstalk between oncogenic signaling and RTK trafficking that controls cancer progression.
A mathematical model of flagellar gene regulation and construction inSalmonella enterica
Authors: Utsey Kiersten , Keener James P.
Published: January 2020

Millions of people worldwide develop foodborne illnesses caused bySalmonella enterica(S. enterica) every year. The pathogenesis ofS. entericadepends on flagella, which are appendages that the bacteria use to move through the environment. Interestingly, populations of genetically identical bacteria exhibit heterogeneity in the number of flagella. To understand this heterogeneity and the regulation of flagella quantity, we propose a mathematical model that connects the flagellar gene regulatory network to flagellar construction. A regulatory network involving more than 60 genes controls flagellar assembly. The most important member of the network is the master operon,flhDC, which encodes the FlhD4C2protein. FlhD4C2controls the construction of flagella by initiating the production of hook basal bodies (HBBs), protein structures that anchor the flagella to the bacterium. By connecting a model of FlhD4C2regulation to a model of HBB construction, we investigate the roles of various feedback mechanisms. Analysis of our model suggests that a combination of regulatory mechanisms at the protein and transcriptional levels induce bistable FlhD4C2levels and heterogeneous numbers of flagella. Also, the balance of regulatory mechanisms that become active following HBB construction is sufficient to provide a counting mechanism for controlling the total number of flagella produced.

Author summary

Salmonellacauses foodborne illnesses in millions of people worldwide each year. Flagella, which are appendages that the bacteria use to move through the environment, are a key factor in the infection process. Populations of genetically identical bacteria have been observed to contain both motile cells, generally with 6–10 flagella, and nonmotile cells, with no flagella. In this paper, we use mathematical models of the gene network that regulates flagellar construction to explore how the bacteria controls the number of flagella produced. We suggest that a bacterium must accumulate a threshold amount of a master regulator protein to initiate flagella production and failure to reach the threshold results in no flagella. Downstream mechanisms that impact the amount of master regulator protein are sufficient to determine how many flagella are produced.
Parental investment and immune dynamics in sex-role reversed pipefishes
Authors: Keller Isabel S. , Roth Olivia
Published: January 2020

Parental care elevates reproductive success by allocating resources into the upbringing of the offspring. However, it also imposes strong costs for the care giving parent and can foster sexual dimorphism. Trade-offs between the reproductive system and the immune system may result in differential immunological capacities between the care-providing and the non-care-providing parent. Usually, providing care is restricted to the female sex making it impossible to study a sex-independent influence of parental investment on sexual immune dimorphism. The decoupling of sex-dependent parental investment and their influences on the parental immunological capacity, however, is possible in syngnathids, which evolved the unique male pregnancy on a gradient ranging from a simple carrying of eggs on the trunk (Nerophinae, low paternal investment) to full internal pregnancy (Syngnathus, high paternal investment). In this study, we compared candidate gene expression between females and males of different gravity stages in three species of syngnathids (Syngnathus typhle,Syngnathus rostellatusandNerophis ophidion) with different male pregnancy intensities to determine how parental investment influences sexual immune dimorphism. While our data failed to detect sexual immune dimorphism in the subset of candidate genes assessed, we show a parental care specific resource-allocation trade-off between investment into pregnancy and immune defense when parental care is provided.
Wing Metric Variation inAedes aegyptiEffect of Altitude on Wing Metric Variation ofAedes aegypti(Diptera: Culicidae) in a Region of the Colombian Central Andes
Authors: Leyton-Ramos Luis M. , Aguirre-Obando Oscar Alexander , Duque Jonny Edward , García-Merchán Víctor Hugo
Published: January 2020

In mosquitoes of medical importance, wing shape and size can vary with altitude, an aspect that can influence dispersion and, consequently, their vector capacity. Using geometric morphometry analysis,Aedes aegyptiwing size and shape variation of males and females was studied in four altitudes in the second-smallest department in Colombia: 1.200 m (Tebaida), 1.400 m (Armenia), 1.500 m (Calarcá), and 1.700 m (Filandia). Wing shape in males (P < 0.001) and females (P < 0.001) was significantly different through the altitudinal gradient; in turn, wing size in males followed the altitudinal gradient (Males R2= 0.04946, P = 0.0002), Females (R2= 0.0011, P = 0.46). Wing allometry for males (P < 0.001) and females (P < 0.001) was significant. Likewise, the shape and size of the wings of males (P < 0.001) and females (P < 0.001) had significant fluctuating asymmetry. It is concluded that, in a small scale with an altitudinal variation of 500 meters, it is detected that the size and shape of the wings varied inA. aegypti, principal vector of dengue, chikungunya, and Zika. The fluctuating asymmetry is present in the individuals studied and could be associated with environmental effects caused by vector control campaigns present in some sampling locations.
Transposon mobilization in the human fungal pathogenCryptococcus deneoformansis mutagenic during infection and promotes drug resistancein vitro
Authors: Gusa Asiya , Williams Jonathan D. , Cho Jang-Eun , Floyd-Averette Anna , Sun Sheng , Shouse Eva Mei , Heitman Joseph , Alspaugh J. Andrew , Jinks-Robertson Sue
Published: January 2020

When transitioning from the environment, pathogenic microorganisms must adapt rapidly to survive in hostile host conditions. This is especially true for environmental fungi that cause opportunistic infections in immunocompromised patients since these microbes are not well adapted human pathogens.Cryptococcusspecies are yeast-like fungi that cause lethal infections, especially in HIV-infected patients. UsingCryptococcus deneoformansin a murine model of infection, we examined contributors to drug resistance and demonstrated that transposon mutagenesis drives the development of 5-fluoroorotic acid (5FOA) resistance. Inactivation of target genesURA3orURA5primarily reflected the insertion of two transposable elements (TEs): the T1 DNA transposon and the TCN12 retrotransposon. Consistent within vivoresults, increased rates of mutagenesis and resistance to 5FOA and the antifungal drugs rapamycin/FK506 and 5-fluorocytosine (5FC) were found whenCryptococcuswas incubated at 37° compared to 30°in vitro, a condition that mimics the temperature shift that occurs during the environment-to-host transition. Inactivation of the RNAi pathway, which suppresses TE movement in many organisms, was not sufficient to elevate TE movement at 30° to the level observed at 37°. We propose that temperature-dependent TE mobilization inCryptococcusis an important mechanism that enhances microbial adaptation and promotes pathogenesis and drug resistance in the human host.

SIGNIFICANCE STATEMENT

The incidence of infections due to fungal pathogens has dramatically increased in the past few decades with similar increases in human populations with weakened or suppressed immune systems. Understanding the mechanisms by which organisms rapidly adapt during human infection to enhance virulence and evolve drug resistance is important for developing effective treatments. We find that transposon mobilization in the human pathogenCryptococcuscauses genomic mutations in a murine model of infection and promotes resistance to antifungal drugsin vitro. Thermotolerance is a key virulence determinant for pathogenic fungi during the environment-to-host transition, and we demonstrate that a temperature increase is sufficient to trigger transposon mobilizationin vitro. The link between temperature stress and transposon-associated mutations may significantly impact adaptation to the host during infection, including the acquisition of drug resistance.
Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation
Authors: Barter Matt J. , Cheung Kathleen , Falk Julia , Panagiotopoulos Andreas C. , Cosimini Caitlin , O’Brien Siobhan , Teja-Putri Karina , Neill Graham , Deehan David J. , Young David A.
Published: January 2020

Genome-wide methods for examining chromatin modification provide detailed information on regulatory regions of the genome. Dynamic modifications of chromatin allow rapid access of the gene regulatory machinery to condensed genomic regions facilitating subsequent gene expression. Inflammatory cytokine stimulation of cells can cause rapid gene expression changes through direct signalling pathway-mediated transcription factor activation and regulatory element binding.

Here we used the Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) to assess regions of the genome that are differentially accessible following treatment of cells with interleukin-1 (IL-1). We identified 126,483 open chromatin regions, with 241 regions significantly differentially accessible following stimulation, with 64 and 177 more or less accessible, respectively. These differentially accessible regions predominantly correspond to regions of the genome marked as enhancers. Motif searching identified an overrepresentation of a number of transcription factors, most notably RelA in the regions becoming more accessible, with analysis of ChIP-seq data confirmed RelA binding to these regions. A significant correlation in differential chromatin accessibility and gene expression was also observed.

Functionality in regulating gene expression was confirmed using CRISPR/Cas9 genome-editing to delete regions for that became more accessible following stimulation in the genesMMP13,IKBKEandC1QTNF1. These same regions were also accessible for activation using a dCas9-transcriptional activator and showed enhancer activity in a cellular model.

Together, these data describe and functionally validate a number of dynamically accessible chromatin regions involved in inflammatory signalling.
Evolution from adherent to suspension – systems biology of HEK293 cell line development
Authors: Malm Magdalena , Saghaleyni Rasool , Lundqvist Magnus , Giudici Marco , Chotteau Veronique , Field Raymond , Varley Paul , Hatton Diane , Grassi Luigi , Svensson Thomas , Uhlen Mathias , Nielsen Jens , Rockberg Johan
Published: January 2020

The need for new safe and efficacious therapies has led to an increased focus on biologics produced in mammalian cells. The human cell line HEK293 has bio-synthetic potential for human-like production and is today used for manufacturing of several therapeutic proteins and viral vectors. Despite this increasing popularity there is still limited knowledge of the detailed genetic and composition of derivatives of this strain. Here we present a genomic, transcriptomic and metabolic gene analysis of six of the most widely used HEK293 cell lines. Changes in gene copy and expression between industrial progeny cell lines and the original HEK293 were associated with cellular component organization, cell motility and cell adhesion. Changes in gene expression between adherent and suspension derivatives highlighted switching in cholesterol biosynthesis and expression of five key genes (RARG, ID1, ZIC1, LOX and DHRS3), a pattern validated in 63 human adherent or suspension cell lines of other origin.
Convolutional neural network MRI segmentation for fast and robust optimization of transcranial electrical current stimulation of the human brain
Authors: Sendra-Balcells Carla , Salvador Ricardo , Pedro Juan B. , Biagi M C , Aubinet Charlène , Manor Brad , Thibaut Aurore , Laureys Steven , Lekadir Karim , Ruffini Giulio
Published: January 2020

The segmentation of structural MRI data is an essential step for deriving geometrical information about brain tissues. One important application is in transcranial electrical stimulation (e.g., tDCS), a non-invasive neuromodulatory technique where head modeling is required to determine the electric field (E-field) generated in the cortex to predict and optimize its effects. Here we propose a deep learning-based model (StarNEt) to automatize white matter (WM) and gray matter (GM) segmentation and compare its performance withFreeSurfer, an established tool. Since good definition of sulci and gyri in the cortical surface is an important requirement for E-field calculation,StarNEtis specifically designed to output masks at a higher resolution than that of the original input T1w-MRI.StarNEtuses a residual network as the encoder (ResNet) and a fully convolutional neural network with U-net skip connections as the decoder to segment an MRI slice by slice. Slice vertical location is provided as an extra input. The model was trained on scans from 425 patients in the open-access ADNI+IXI datasets, and usingFreeSurfersegmentation as ground truth. Model performance was evaluated using the Dice Coefficient (DC) in a separate subset (N=105) of ADNI+IXI and in two extra testing sets not involved in training. In addition,FreeSurferandStarNEtwere compared to manual segmentations of the MRBrainS18 dataset, also unseen by the model. To study performance in real use cases, first, we created electrical head models derived from theFreeSurferandStarNEtsegmentations and used them for montage optimization with a common target region using a standard algorithm (Stimweaver) and second, we usedStarNEtto successfully segment the brains of minimally conscious state (MCS) patients having suffered from brain trauma, a scenario whereFreeSurfertypically fails. Our results indicate thatStarNEtmatchesFreeSurferperformance on the trained tasks while reducing computation time from several hours to a few seconds, and with the potential to evolve into an effective technique even when patients present large brain abnormalities.
Characterization ofEscherichia coliExbD protein modificationin vivo
Authors: Kumar Aruna , Postle Kathleen
Published: January 2020

The TonB system ofEscherichia colicouples the protonmotive force of the cytoplasmic membrane to active transport of nutrients across the outer membrane. In the cytoplasmic membrane, this system consists of three known proteins, TonB, ExbB, and ExbD. ExbB and ExbD appear to harvest the protonmotive force and transmit it to TonB, which then makes direct physical contact with TonB-dependent active transport proteins in the outer membrane. Using two-dimensional gel electrophoresis, we found that ExbD exists as two different species with the same apparent molecular mass but with different pIs. The more basic ExbD species was consistently present, while the more acidic species arose when cells were starved for iron by the addition of iron chelators. The cause of the modification was, however, more complex than simple iron starvation. Absence of either TonB or ExbB protein also gave rise to modified ExbD under iron-replete conditions where the wild-type strain exhibited no ExbD modification. The effect of thetonBorexbBmutations were not entirely due to iron limitation since an equally iron-limitedaroBmutation did not replicate the ExbD modification. This constitutes the first report ofin vivomodification for any of the TonB system proteins.
Pervasive promoter hypermethylation of silencedTERTalleles in human cancers
Authors: Esopi D , Graham MK , Brosnan-Cashman J , Meyers J , Vaghasia A , Gupta A , Kumar B , Haffner MC , Heaphy CM , De Marzo AM , Meeker AK , Nelson WG , Wheelan SJ , Yegnasubramanian S
Published: January 2020

In cancers, maintenance of telomeres often occurs through activation of the catalytic subunit of telomerase, encoded byTERT. Yet, most cancers show only modest levels of telomerase gene expression, even in the context of activating hotspot promoter mutations (C228T and C250T). The role of epigenetic mechanisms, including DNA methylation, in regulating telomerase gene expression in cancer cells is not fully understood. Here, we have carried out the most comprehensive characterization to date ofTERTpromoter methylation using ultra-deep bisulfite sequencing spanning the CpG island surrounding the coreTERTpromoter in 96 different human cell lines. In general, we observed that immortalized and cancer cell lines were hypermethylated in a region upstream of the recurrent C228T and C250TTERTpromoter mutations, while non-malignant primary cells were comparatively hypomethylated in this region. However, at the allele-level, we generally observe hypermethylation of promoter sequences in cancer cells is associated with repressed expression, and the remaining unmethylated alleles marked with open chromatin are largely responsible for the observedTERTexpression in cancer cells. Our findings suggest that hypermethylation of theTERTpromoter alleles signals transcriptional repression of those alleles, leading to the attenuation ofTERTactivation in cancer cells.

SIGNIFICANCE

Hypermethylation of theTERTpromoter alleles to attenuateTERTactivation in cancer cells may account for the modest activation ofTERTexpression in most cancers.
Quantifying influences on intragenomic mutation rate
Authors: Simon Helmut , Huttley Gavin
Published: January 2020

We report work to quantify the impact on the probability of human genome polymorphism both of recombination and of sequence context at different scales. We use population-based analyses of data on human genetic variants obtained from the public Ensembl database. For recombination, we calculate the variance due to recombination and the probability that a recombination event causes a mutation. We employ novel statistical procedures to take account of the spatial auto-correlation of recombination and mutation rates along the genome. Our results support the view that genomic diversity in recombination hotspots arises from a direct effect of recombination on mutation rather than from the effect of selective sweeps. We also use the statistic of variance due to context to compare the effect on the probability of polymorphism of contexts of various sizes. We find that when the 12 point mutations are considered separately, variance due to context increases significantly as we move from 3-mer to 5-mer and from 5-mer to 7-mer contexts. However, when all mutations are considered in aggregate, these differences are outweighed by the effect of interaction between the central base and its immediate neighbors. This interaction is itself dominated by the transition mutations, including, but not limited to, the CpG effect. We also demonstrate strand-asymmetry of contextual influence in intronic regions, which is hypothesized to be a result of transcription coupled DNA repair. We consider the extent to which the measures we have used can be used to meaningfully compare the relative magnitudes of the impact of recombination and context on mutation.
A Systematic Evaluation of Single-cell RNA-sequencing Imputation Methods
Authors: Hou Wenpin , Ji Zhicheng , Ji Hongkai , Hicks Stephanie C.
Published: January 2020

The rapid development of single-cell RNA-sequencing (scRNA-seq) technology, with increased sparsity compared to bulk RNA-sequencing (RNA-seq), has led to the emergence of many methods for preprocessing, including imputation methods. Here, we systematically evaluate the performance of 18 state-of-the-art scRNA-seq imputation methods using cell line and tissue data measured across experimental protocols. Specifically, we assess the similarity of imputed cell profiles to bulk samples as well as investigate whether methods recover relevant biological signals or introduce spurious noise in three downstream analyses: differential expression, unsupervised clustering, and inferring pseudotemporal trajectories. Broadly, we found significant variability in the performance of the methods across evaluation settings. While most scRNA-seq imputation methods recover biological expression observed in bulk RNA-seq data, the majority of the methods do not improve performance in downstream analyses compared to no imputation, in particular for clustering and trajectory analysis, and thus should be used with caution. Furthermore, we find that the performance of scRNA-seq imputation methods depends on many factors including the experimental protocol, the sparsity of the data, the number of cells in the dataset, and the magnitude of the effect sizes. We summarize our results and provide a key set of recommendations for users and investigators to navigate the current space of scRNA-seq imputation methods.
Recurrent SRSF2 mutations in MDS affect both splicing and NMD
Authors: Rahman Mohammad Alinoor , Lin Kuan-Ting , Bradley Robert K. , Abdel-Wahab Omar , Krainer Adrian R.
Published: January 2020

Oncogenic mutations in the RNA splicing factors SRSF2, SF3B1, and U2AF1 are the most frequent class of mutations in myelodysplastic syndromes and are also common in clonal hematopoiesis, acute myeloid leukemia, chronic lymphocytic leukemia, and a variety of solid tumors. They cause genome-wide splicing alterations that affect important regulators of hematopoiesis. Several mRNA isoforms promoted by the various splicing factor mutants comprise a premature termination codon (PTC) and are therefore potential targets of nonsense-mediated mRNA decay (NMD). In light of the mechanistic relationship between splicing and NMD, we sought evidence for a specific role of mutant SRSF2 in NMD. We show that SRSF2 Pro95 hot spot mutations elicit enhanced mRNA decay, which is dependent on sequence-specific RNA binding and splicing. SRSF2 mutants enhance the deposition of exon junction complexes (EJCs) downstream from the PTC through RNA-mediated molecular interactions. This architecture then favors the association of key NMD factors to elicit mRNA decay. Gene-specific blocking of EJC deposition by antisense oligonucleotides circumvents aberrant NMD promoted by mutant SRSF2, restoring the expression of PTC-containing transcript. Our study uncovered critical effects of SRSF2 mutants in hematologic malignancies, reflecting the regulation at multiple levels of RNA metabolism, from splicing to decay.
Noncoding SNPs influence a distinct phase of Polycomb silencing to destabilize long-term epigenetic memory at Arabidopsis FLC
Authors: Qüesta Julia I. , Antoniou-Kourounioti Rea L. , Rosa Stefanie , Li Peijin , Duncan Susan , Whittaker Charles , Howard Martin , Dean Caroline
Published: January 2020

In Arabidopsis thaliana, the cold-induced epigenetic regulation of FLOWERING LOCUS C (FLC) involves distinct phases of Polycomb repressive complex 2 (PRC2) silencing. During cold, a PHD–PRC2 complex metastably and digitally nucleates H3K27me3 within FLC. On return to warm, PHD–PRC2 spreads across the locus delivering H3K27me3 to maintain long-term silencing. Here, we studied natural variation in this process in Arabidopsis accessions, exploring Lov-1, which shows FLC reactivation on return to warm, a feature characteristic of FLC in perennial Brassicaceae. This analysis identifies an additional phase in this Polycomb silencing mechanism downstream from H3K27me3 spreading. In this long-term silencing (perpetuated) phase, the PHD proteins are lost from the nucleation region and silencing is likely maintained by the read-write feedbacks associated with H3K27me3. A combination of noncoding SNPs in the nucleation region mediates instability in this long-term silencing phase with the result that Lov-1 FLC frequently digitally reactivates in individual cells, with a probability that diminishes with increasing cold duration. We propose that this decrease in reactivation probability is due to reduced DNA replication after flowering. Overall, this work defines an additional phase in the Polycomb mechanism instrumental in natural variation of silencing, and provides avenues to dissect broader evolutionary changes at FLC.
Hydrogen bonding and π–π interactions in the cocrystal salt [Fe(bpe)2(H2O)4](TCEP)2·2(bpe) [bpe is trans-1,2-bis(pyridin-4-yl)ethene and TCEP is 1,1,3,3-tetracyano-2-ethoxypropenide]
Authors: Addala Abderrezak , Geiger David K. , Setifi Zouaoui , Setifi Fatima
Published: January 2020

The cocrystal salt tetraaquabis[trans-1,2-bis(pyridin-4-yl)ethene-κN]iron(II) bis(1,1,3,3-tetracyano-2-ethoxypropenide)–trans-1,2-bis(pyridin-4-yl)ethene (1/2), [Fe(C12H10N2)2(H2O)4](C9H5N4O)2·2C12H10N2, is a rare example of a mononuclear FeII compound with trans-1,2-bis(pyridin-4-yl)ethane (bpe) ligands. The complex cation resides on a crystallographically imposed inversion center and exhibits a tetragonally distorted octahedral coordination geometry. Both the symmetry-independent bpe ligand and the cocrystallized bpe molecule are essentially planar. The 1,1,3,3-tetracyano-2-ethoxypropenide counter-ion is nonplanar and the bond lengths are consistant with significant electron delocalization. The extended structure exhibits an extensive O—H...N hydrogen-bonding network with layers of complex cations joined by the cocrystallized bpe. Both the coordinated and the cocrystallized bpe are involved in π–π interactions. Hirshfeld and fingerprint plots reveal the important intermolecular interactions. Density functional theory was used to estimate the strengths of the hydrogen-bonding and π–π interactions, and suggest that the O—H...N hydrogen bonds enhance the strength of the π-interactions by increasing the polarization of the pyridine rings.
Crystal structures of the two domains that constitute the Plasmodium vivax p43 protein
Authors: Gupta Swati , Chhibber-Goel Jyoti , Sharma Manmohan , Parvez Suhel , Harlos Karl , Sharma Amit , Yogavel Manickam
Published: January 2020

Scaffold modules known as aminoacyl-tRNA synthetase (aaRS)-interacting multifunctional proteins (AIMPs), such as AIMP1/p43, AIMP2/p38 and AIMP3/p18, are important in driving the assembly of multi-aaRS (MARS) complexes in eukaryotes. Often, AIMPs contain an N-terminal glutathione S-transferase (GST)-like domain and a C-terminal OB-fold tRNA-binding domain. Recently, the apicomplexan-specific Plasmodium falciparum p43 protein (Pfp43) has been annotated as an AIMP and its tRNA binding, tRNA import and membrane association have been characterized. The crystal structures of both the N- and C-terminal domains of the Plasmodium vivax p43 protein (Pvp43), which is an ortholog of Pfp43, have been resolved. Analyses reveal the overall oligomeric structure of Pvp43 and highlight several notable features that show Pvp43 to be a soluble, cytosolic protein. The dimeric assembly of the N-terminal GST-like domain of Pvp43 differs significantly from canonical GST dimers, and it is tied to the C-terminal tRNA-binding domain via a linker region. This work therefore establishes a framework for dissecting the additional roles of p43 orthologs in eukaryotic multi-protein MARS complexes.
Variance constrained trajectory tracking for tandem-rotor helicopters
Authors: Sal Firat
Published: January 2020

Purpose

This paper aims to present novel results for trajectory tracking of tandem-rotor helicopters via variance-constrained controllers.

Design/methodology/approach

Regarding these purposes, linearized tandem-rotor helicopter models are benefitted.

Findings

Variance-constrained controllers are very beneficial for trajectory tracking of tandem-rotor helicopters while there exists variance bounds on outputs of interest.

Practical implications

Variance-constrained controllers can be used for cheaper tandem-rotor helicopter operations with high trajectory tracking quality.

Originality/value

Applying variance-constrained control strategy for tandem-rotor helicopters during trajectory tracking. This also causes less fuel consumption and green environment, and good trajectory tracking quality.
Craft beer mon amour: an exploration of Italian craft consumers
Authors: Carbone Anna , Quici Luisangela
Published: January 2020

Purpose

The purpose of this paper is to contribute understanding tendencies of the Italian demand for craft beer. More in details, it seeks at exploring consumers’ awareness about craft beer, their attitudes, habits and behaviors. It also aims at assessing the impact of each and all these features on consumers’ choice. At last, the paper frames different consumers’ profiles.

Design/methodology/approach

The analysis is based on an online survey associated with a choice experiment designed for assessing willingness to buy (WTB) and willingness to pay (WTP) for craft vs industrial beer. Factors influencing consumers’ expenditure for craft beer are explored via an OLS estimation of a simple regression model. Afterwards, different consumers’ profiles are depicted via cluster analysis.

Findings

The survey shows that, overall, Italian consumers appreciate craft beers and are interested in this market. Socio-demographic characteristics impact this inclination but have no significant influence on the results of the choice experiment. Market knowledge, preferences and consumption habits influence consumer spending. Five different consumer profiles emerge.

Originality/value

The research proposes a combined original methodology for assessing beer consumers’ features and their impacts on beer WTB and WTP. The complementary perspectives adopted provide new insights on craft beer demand. Results are of interest for craft brewery managers and for the design of policies aimed at promoting and expanding the sector. Enlarging the sample and improving its representativeness would allow for more general results.