bluuebunny/crossref_metadata_2025 huggingface dataset:
Small, modular and economically attractive fusion enabled by high temperature superconductors
Authors: Whyte Dennis
Published: February 2019

The advantages of high magnetic fields in tokamaks are reviewed, and why they are important in leading to more compact tokamaks. A brief explanation is given of what limits the magnetic field in a tokamak, and why high temperature superconductors (HTSs) are a game changer, not just because of their higher magnetic fields but also for reasons of higher current density and higher operating temperatures. An accelerated pathway to fusion energy is described, defined by the SPARC and ARC tokamak designs.

This article is part of a discussion meeting issue ‘Fusion energy using tokamaks: can development be accelerated?’.
Multi-omics profiling of CHO parental hosts reveals cell line-specific variations in bioprocessing traits
Authors: Lakshmanan Meiyappan , Kok Yee Jiun , Lee Alison P. , Kyriakopoulos Sarantos , Lim Hsueh Lee , Teo Gavin , Poh Swan Li , Tang Wen Qin , Hong Jongkwang , Tan Andy Hee-Meng , Bi Xuezhi , Ho Ying Swan , Zhang Peiqing , Ng Say Kong , Lee Dong-Yup
Published: January 2019

Chinese hamster ovary (CHO) cells are the most prevalent mammalian cell factories for producing recombinant therapeutic proteins due to their ability to synthesize human-like post-translational modifications and ease of maintenance in suspension cultures. Currently, a wide variety of CHO host cell lines have been developed; substantial differences exist in their phenotypes even when transfected with the same target vector. However, relatively less is known about the influence of their inherited genetic heterogeneity on phenotypic traits and production potential from the bioprocessing point of view. Herein, we present a global transcriptome and proteome profiling of three commonly used parental cell lines (CHO-K1, CHO-DXB11 and CHO-DG44) in suspension cultures and further report their growth-related characteristics, and N- and O-glycosylation patterns of host cell proteins (HCPs). The comparative multi-omics analysis indicated that some physiological variations of CHO cells grown in the same media are possibly originated from the genetic deficits, particularly in the cell cycle progression. Moreover, the dihydrofolate reductase deficient DG44 and DXB11 possess relatively less active metabolism when compared to K1 cells. The protein processing abilities and the N- and O-glycosylation profiles also differ significantly across the host cell lines, suggesting the need to select host cells in a rational manner for the cell line development on the basis of recombinant protein being produced.
A 7-channel high-Tc SQUID-based on-scalp MEG system
Authors: Pfeiffer Christoph , Ruffieux Silvia , Jönsson Lars , Chukharkin Maxim L. , Kalaboukhov Alexei , Xie Minshu , Winkler Dag , Schneiderman Justin F.
Published: January 2019

Due to their higher operating temperature, high-Tc superconducting quantum interference devices (SQUIDs) require less thermal insulation than the low-Tc sensors that are utilized in commercial magnetoen-cephalography (MEG) systems. As a result, they can be placed closer to the head, where neuromagnetic fields are higher and more focal, potentially leading to higher spatial resolution. The first such on-scalp MEG measurements using high-Tc SQUIDs have shown the potential of the technology. In order to be useful for neuroscience and clinical applications, however, multi-channel systems are required. Herein, we present a 7-channel on-scalp MEG system based on high-Tc SQUIDs. The YBCO SQUID magnetometers are arranged in a dense, head-aligned hexagonal array inside a single, liquid nitrogen-cooled cryostat. The spacing between the magnetometers and the head is adjustable down to 1 mm. The sensors are side-mounted on the cryostat that is mounted on an articulated armature for recordings on arbitrary head locations of a seated subject. We demonstrate white noise levels of 50-130 fT/Hz1/2 at 10 Hz, sensor-to-sensor crosstalk values of <0.6%, and single-fill operation times of 16 hours. We validate the system with MEG recordings of visual alpha modulation and auditory evoked fields. The system is thus useful for densely and sensitively sampling neuromagnetic fields over any ∼ 10 cm2 patch of the scalp surface over the course of a day.
Porthole and Stormcloud: Tools for visualisation of spatiotemporal M/EEG statistics
Authors: Taylor Jeremy A , Garrido Marta I
Published: January 2019

Electro- and magneto-encephalography are functional neuroimaging modalities characterised by their ability to quantify dynamic spatiotemporal activity within the brain. However, the visualisation techniques currently used to illustrate these effects are currently limited to single- or multi-channel time series plots, topographic scalp maps and orthographic cross-sections of the spatiotemporal data structure. Whilst these methods each have their own strength and weaknesses, they are only able to show a subset of the data and are suboptimal at articulating one or both of the space-time components.

Here, we proposePortholeandStormcloud, a set of data visualisation tools which can automatically generate context appropriate graphics for both print and screen with the following graphical capabilities:

Animated two-dimensional scalp maps with dynamic timeline annotation and optional user interaction;

Three-dimensional construction of discrete clusters within sparse spatiotemporal volumes, rendered with ‘cloud-like’ appearance and augmented by cross-sectional scalp maps indicating local maxima.

These publicly available tools were designed specifically for visualisation of M/EEG spatiotemporal statistical maps, however, we also demonstrate alternate use cases of posterior probability maps and weight maps produced by machine learning classifiers. In principle, the methods employed here are transferrable to visualisation of any spatiotemporal image.
Design and Synthesis of Pleated DNA Origami Nanotubes with Adjustable Diameters
Authors: Berengut Jonathan F. , Ruan Juanfang , Kawamoto Akihiro , Lee Lawrence K.
Published: January 2019

DNA origami allows for the synthesis of nanoscale structures and machines with nanometre precision and high yields. Tubular DNA origami nanostructures are particularly useful because their geometry facilitates a variety of applications including nanoparticle encapsulation, the construction of artificial membrane pores and as structural scaffolds that can spatially arrange nanoparticles in circular, linear and helical arrays. Here we report a simple computational approach that determines minimally-strained DNA staple crossover locations for arbitrary nanotube internal angles. We apply the method in the design and synthesis of radially symmetric DNA origami nanotubes with arbitrary diameters and DNA helix stoichiometries. These include regular nanotubes where the wall of the structure is composed of a single layer of DNA helices, as well as those with a thicker pleated wall structure that have a greater rigidity and allow for continuously adjustable diameters and distances between parallel helices. We also introduce a DNA origami staple strand routing that incorporates both antiparallel and parallel crossovers and demonstrate its application to further rigidify pleated DNA nanotubes.
Localizing the chaperone activity of erythroid spectrin
Authors: Bose Dipayan , Chakrabarti Abhijit
Published: January 2019

Spectrin, the major protein of the RBC membrane skeleton has canonically been thought to only serve a structural function. We have described a novel chaperone-like property of spectrin and have shown that it is able to prevent the aggregation of other proteins such as alcohol dehydrogenase, insulin and free globin chains. We have tried to localize the molecular origin of chaperone-like activity in multi-domain spectrin by using recombinant spectrin fragments and investigating individual domains. We have characterized the recombinant domains using intrinsic tryptophan fluorescence and CD spectroscopy to show their identity to native spectrin. Hydrophobic ligands Prodan (6-propionyl-2[dimethylamino]-naphthalene) and ANS (1-anilinonaphthalene-8-sulfonic acid) binding has been used to probe the hydrophobicity of the recombinant domains and it is seen that all domains have surface exposed hydrophobic patches; and in accordance with our previous hypothesis only the reconstituted self-association domain binds Prodan. Recombinant domains display comparable chaperone potential in preventing protein aggregation; and substrate selectivity of α-over β-globin is seen. Enzyme refolding studies show alternate pathways of chaperone action. Our current study points to the presence of hydrophobic patches on the surface of these domains as the source of the chaperone activity of spectrin, as notably seen in the self-association domain. There is no one domain largely responsible for the chaperone activity of spectrin; rather all domains appear to contribute equally, such that the chaperone activity of spectrin seems to be a linear sum of the individual activities of the domains.
Monkey EEG links neuronal color and motion information across species and scales
Authors: Sandhaeger Florian , von Nicolai Constantin , Miller Earl K , Siegel Markus
Published: January 2019

It remains challenging to relate EEG and MEG to underlying circuit processes and comparable experiments on both spatial scales are rare. To close this gap between invasive and non-invasive electrophysiology we developed and recorded human-comparable EEG in macaque monkeys during visual stimulation with colored dynamic random dot patterns. Furthermore, we performed simultaneous microelectrode recordings from 6 areas of macaque cortex and human MEG. Motion direction and color information were accessible in all signal types. Tuning of the non-invasive signals was similar to V4 and IT, but not to dorsal and frontal areas. Thus, MEG and EEG were dominated by early visual and ventral stream sources. Source level analysis revealed corresponding information and latency gradients across the cortex. We show how information-based methods and monkey EEG can identify analogous properties of visual processing in signals spanning spatial scales from single units to MEG – a valuable framework for relating human and animal studies.
The Atypical Cyclin-Like Protein Spy1 Overrides p53-Mediated Tumour Suppression and Promotes Susceptibility to Breast Tumorigenesis
Authors: Fifield Bre-Anne , Qemo Ingrid , Kirou Evie , Cardiff Robert D. , Porter Lisa Ann
Published: January 2019

Breast cancer is the most common cancer to affect women and one of the leading causes of cancer related deaths. Maintenance of genomic stability and proper regulation of cell cycle checkpoints play a critical role in preventing the accumulation of deleterious mutations. Perturbations in the expression or activity of mediators of cell cycle progression or checkpoint activation represent important events that may increase susceptibility to the onset of carcinogenesis. The atypical cyclin-like protein Spy1 was isolated in a screen for novel genes that could bypass the DNA damage response. Clinical data demonstrates that protein levels of Spy1 are significantly elevated in ductal and lobular carcinoma of the breast. Using a transgenic mouse driving expression of Spy1 in the mammary epithelium we demonstrate that sustained elevation of Spy1 leads to enhanced proliferation and an increased susceptibility to mammary tumour formation. We find that Spy1 is targeted for degradation by the tumour suppressor p53 to protect checkpoint control. When crossed with p53 deficient mice, elevation of Spy1 leads to an increase in hyperplastic alveolar nodules. Targeting cyclin-like protein activity may therefore represent a mechanism of re-sensitizing cells to important cell cycle checkpoints in a therapeutic setting.
Perfect adaptation of CD8+ T cell responses to constant antigen input over a wide range of affinity is overcome by costimulation
Authors: Trendel Nicola , Kruger Philipp , Gaglione Stephanie , Nguyen John , Pettmann Johannes , Sontag Eduardo D , Dushek Omer
Published: January 2019

Maintaining and limiting T cell responses to constant antigen stimulation is critical to control pathogens and maintain self-tolerance, respectively. Antigen recognition by T cell receptors (TCRs) induces signalling that activates T cells to produce cytokines and also leads to the downregulation of surface TCRs. In other systems, receptor downregulation can induce perfect adaptation to constant stimulation by a mechanism known as state-dependent inactivation that requires complete downregulation of the receptor or the ligand. However, this is not the case for the TCR, and therefore, precisely how TCR downregulation maintains or limits T cell responses is controversial. Here, we observed that in vitro expanded primary human T cells exhibit perfect adaptation in cytokine production to constant antigen stimulation across a 100,000-fold variation in affinity with partial TCR downregulation. By directly fitting a mechanistic model to the data, we show that TCR downregulation produces imperfect adaptation, but when coupled to a switch produces perfect adaptation in cytokine production. A pre-diction of the model is that pMHC-induced TCR signalling continues after adaptation and this is confirmed by showing that, while costimulation cannot prevent adaptation, CD28 and 4-1BB signalling reactivated adapted T cells to produce cytokines in a pMHC-dependent manner. We show that adaptation also applied to 1st generation chimeric antigen receptor (CAR)-T cells but is partially avoided in 2nd generation CARs. These findings high-light that even partial TCR downregulation can limit T cell responses by producing perfect adaptation rendering T cells dependent on costimulation for sustained responses.
Hepatotoxicity during 6-thioguanine treatment in inflammatory bowel disease and childhood acute lymphoblastic leukaemia: a systematic review
Authors: Toksvang Linea Natalie , Schmidt Magnus Strøh , Arup Sofie , Larsen Rikke Hebo , Frandsen Thomas Leth , Schmiegelow Kjeld , Rank Cecilie Utke
Published: January 2019

Background

The recently established association between higher levels of DNA-incorporated thioguanine nucleotides and lower relapse risk in childhood acute lymphoblastic leukaemia (ALL) calls for reassessment of prolonged 6-thioguanine (6TG) treatment, while avoiding the risk of hepatotoxicity.

Objectives

To assess the incidence of hepatotoxicity in patients treated with 6TG, and to explore if a safe dose of continuous 6TG can be established.

Data sources

Databases, conference proceedings, and reference lists of included studies were systematically searched for 6TG and synonyms from 1998–2018.

Methods

We included studies of patients with ALL or inflammatory bowel disorder (IBD) treated with 6TG, excluding studies with 6TG as part of an intensive chemotherapy regimen. We uploaded a protocol to PROSPERO (registration number CRD42018089424). Database and manual searches yielded 1823 unique records. Of these, 395 full-texts were screened for eligibility. Finally, 134 reports representing 42 studies were included.

Results and conclusions

We included data from 42 studies of ALL and IBD patients; four randomised controlled trials (RCTs) including 3,993 patients, 20 observational studies including 796 patients, and 18 case reports including 60 patients. Hepatotoxicity in the form of sinusoidal obstruction syndrome (SOS) occurred in 9–25% of the ALL patients in two of the four included RCTs using 6TG doses of 40–60 mg/m2/day, and long-term hepatotoxicity in the form of nodular regenerative hyperplasia (NRH) was reported in 2.5%. In IBD patients treated with 6TG doses of approximately 23 mg/m2/day, NRH occurred in 14% of patients; SOS has not been reported. At a 6TG dose of approximately 12 mg/m2/day, NRH was reported in 6% of IBD patients, which is similar to the background incidence. According to this review, doses at or below 12 mg/m2/day are rarely associated with notable hepatotoxicity and can probably be considered safe.
Interspecies bacterial competition determines community assembly in theC. elegansintestine
Authors: Lopez Anthony Ortiz , Vega Nicole M. , Gore Jeff
Published: January 2019

From insects to mammals, a large variety of animals hold in their intestines complex bacterial communities that play an important role in health and disease. However, the complexity of these gut microbiomes and their hosts often constrains our ability to understand how these bacterial communities assemble and function. In order to elucidate basic principles of community assembly in a host intestine, we study the assembly of the microbiome ofCaenorhabditis eleganswith a bottom-up approach. We colonize the gut of the wormC. eleganswith 11 bacterial species individually, in all possible pairs, and in selected trios, and we find an organized mixture of coexistence and competitive exclusion that indicates a hierarchical structure in the bacterial interactions. The capacity of a bacterial species fed in monoculture to colonize theC. elegansintestine correlates with its average fraction in co-culture experiments, yet fails to predict its abundance in many two- and three-species microbiomes. Hence, the bacterial fractional abundances in co-culture experiments—pairwise outcomes—are influenced by interspecies interactions. These pairwise outcomes accurately predict the trio outcomes in the worm intestine, further highlighting the importance of pairwise interactions in determining community composition. We also find that theC. elegansgut environment influences the outcome of co-culture experiments, and demonstrate that the low intestinal pH is one of the causes. These results highlight that a bottom-up approach to microbiome community assembly may provide valuable insight into the structure and composition of complex microbial communities.
Chk1 Phosphorylates Cdh1 to Promote SCFβTRCP-Dependent Degradation of Cdh1 During S-Phase
Authors: Pal Debjani , Torres Adrian E. , Messina Abbey L. , Dickson Andrew , De Kuntal , Willard Belinda , Venere Monica , Summers Matthew K.
Published: January 2019

The interplay of the Anaphase-Promoting Complex/Cyclosome (APC/C) and Skp1-Cul1-F-box (SCF) E3 ubiquitin ligases is necessary for controlling cell cycle transitions and checkpoint responses, which are critical for maintaining genomic stability. Yet, the mechanisms underlying the coordinated activity of these enzymes are not completely understood. Recently, Cyclin A- and Plk1- mediated phosphorylation of Cdh1 was demonstrated to trigger its ubiquitination by SCFβTRCPat the G1/S transition. However, Cyclin A-Cdk and Plk1 activities peak in G2 so it is unclear why Cdh1 is targeted at G1/S but not in G2. Here, we show that phosphorylation of Cdh1 by Chk1 contributes to its recognition by SCFβTRCP, promotes efficient S-phase entry, and is important for cellular proliferation. Conversely, Chk1 activity in G2 inhibits Cdh1 accumulation. Overall, these data suggest a model whereby the rise and fall of Chk1 activity is a key factor in the feedback loop between APC/CCdh1and the replication machinery that enhances the G1/S and S/G2 transitions, respectively.
Species abundance distributions should underpin ordinal cover-abundance transformations
Authors: McNellie Megan J , Dorrough Josh , Oliver Ian
Published: January 2019

The cover and abundance of individual plant species have been recorded on ordinal scales for millions of plots world-wide. Many ecological questions can be addressed using these data. However ordinal cover data may need to be transformed to a quantitative form (0 to 100%), especially when scrutinising summed cover of multiple species. Traditional approaches to transforming ordinal data often assume that data are symmetrically distributed. However, skewed abundance patterns are ubiquitous in plant community ecology. A failure to account for this skew will bias plant cover estimates, especially when cover of multiple species are summed. The questions this paper addresses are (i) how can we estimate transformation values for ordinal data that accounts for the underlying right-skewed distribution of plant cover; (ii) do different plant groups require different transformations and (iii) how do our transformations compare to other commonly used transformations within the context of exploring the aggregate properties of vegetation? Using a continuous cover dataset, each occurrence record was mapped to its commensurate ordinal value, in this case, the ubiquitous Braun-Blanquet cover-abundance (BBCA) scale. We fitted a Bayesian hierarchical beta regression to estimate the predicted mean (PM) cover of each of six plant growth forms within different ordinal classes. We illustrate our method using a case study of 2 809 plots containing 95 812 occurrence records with visual estimates of cover for 3 967 species. We compare the model derived estimates to other commonly used transformations. Our model found that PM estimates differed by growth form and that previous methods overestimated cover, especially of smaller growth forms such as forbs and grasses. Our approach reduced the cumulative compounding of errors when transformed cover data were used to explore the aggregate properties of vegetation and was robust when validated against an independent dataset. By accounting for the right-skewed distribution of cover data, our alternate approach for estimating transformation values can be extended to other ordinal scales. A more robust approach to transforming floristic data and aggregating cover estimates can strengthen ecological analyses to support biodiversity conservation and management.
Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data
Authors: Amin Sara A. , Chavez Elizabeth , Nair Nikhil U. , Hassoun Soha
Published: January 2019

Background

Metabolic models are indispensable in guiding cellular engineering and in advancing our understanding of systems biology. As not all enzymatic activities are fully known and/or annotated, metabolic models remain incomplete, resulting in suboptimal computational analysis and leading to unexpected experimental results. We posit that one major source of unaccounted metabolism is promiscuous enzymatic activity. It is now well-accepted that most, if not all, enzymes are promiscuous – i.e., they transform substrates other than their primary substrate. However, there have been no systematic analyses of genome-scale metabolic models to predict putative reactions and/or metabolites that arise from enzyme promiscuity.

Results

Our workflow utilizes PROXIMAL – a tool that uses reactant-product transformation patterns from the KEGG database – to predict putative structural modifications due to promiscuous enzymes. Using iML1515 as a model system, we first utilized a computational workflow, referred to as Extended Metabolite Model Annotation (EMMA), to predict promiscuous reactions catalyzed, and metabolites produced, by natively encoded enzymes in E. coli. We predict hundreds of new metabolites that can be used to augment iML1515. We then validated our method by comparing predicted metabolites with the Escherichia coli Metabolome Database (ECMDB).

Conclusions

We utilized EMMA to augment the iML1515 metabolic model to more fully reflect cellular metabolic activity. This workflow uses enzyme promiscuity as basis to predict hundreds of reactions and metabolites that may exist in E. coli but have not been documented in iML1515 or other databases. Among these, we found that 17 metabolites have previously been documented in E. coli metabolomics studies. Further, 6 of these metabolites are not documented for any other E. coli metabolic model (e.g. KEGG, EcoCyc). The corresponding reactions should be added to iML1515 to create an Extended Metabolic Model (EMM). Other predicted metabolites and reactions can guide future experimental metabolomics studies. Further, our workflow can easily be applied to other organisms for which comprehensive genome-scale metabolic models are desirable.
Characterization of Sex Differences in Ocular HSV-1 Infection and Herpes Stromal Keratitis Pathogenesis of Wild Type and Herpesvirus Entry Mediator Knockout Mice
Authors: Riccio Rachel E , Park Seo J , Longnecker Richard M , Kopp Sarah J
Published: January 2019

Sex differences related to immune response and inflammation play a role in the susceptibility and pathogenesis of a variety of viral infections and disease (S. L. Klein, Bioessays 34:1050-9, 2012). Herpes simplex virus type 1 (HSV-1) causes chronic inflammatory disease in the cornea, an immune privileged tissue, resulting in irreversible damage and blindness in affected individuals (A. Rowe, A. St Leger, S. Jeon, D. K. Dhaliwal, J. E. Knickelbein, and E. Vilain, Prog Retin Eye Res 32:88-101, 2013). Our research focuses on the role of Herpes Viral Entry Mediator (HVEM) as an immune regulator during ocular HSV-1 infection. Mice lacking HVEM (HVEM KO) exhibit lower immune cell infiltrates and less severe ocular disease in the cornea compared to wild type (WT) mice. As sex differences contribute to pathogenesis in many inflammatory diseases, we tested sex as a biological variable in the immune response to HSV-1 infection and Herpes Stromal Keratitis pathogenesis (HSK). Adult male and female WT and HVEM KO mice were inoculated with HSV-1 via corneal scarification and monitored daily for disease course. Viral titers and immune cell infiltrates were collected and analyzed. Our results indicate no significant difference in viral titers in tear film or affected tissues; immune cell infiltration; or clinical symptoms between males and females of either genotype. These results suggest that sex is not a significant biological variable in this experimental model, and that male and female mice can similarly be used in studies of ocular HSV-1 pathogenesis.

IMPORTANCE

Sex hormones have only recently been considered as an important factor for the development of certain diseases and as such should continue to be considered as a biological variable. Ocular Herpesvirus Type 1 (HSV-1), and the resulting Herpes Stromal Keratitis, is the leading cause of infectious blindness worldwide. We compared ocular HSV-1 infection and pathogenesis between sexes and found no significance difference between male and female wild type mice or herpesvirus entry mediator knockout mice. Therefore, male and female mice can be used interchangeably in studying ocular HSV-1 pathogenesis.
DypFISH: Dynamic Patterned FISH to Interrogate RNA and Protein Spatial and Temporal Subcellular Distribution
Authors: Savulescu Anca F. , Brackin Robyn , Bouilhol Emmanuel , Dartigues Benjamin , Warrell Jonathan H. , Pimentel Mafalda R. , Dallongeville Stephane , Schmoranzer Jan , Olivo-Marin Jean-Christophe , Gomes Edgar R. , Nikolski Macha , Mhlanga Musa M.
Published: January 2019

Advances in single cell RNA sequencing have allowed for the identification and characterization of cellular subtypes based on quantification of the number of transcripts in each cell. However, cells may differ not only in the number of mRNA transcripts that they exhibit, but also in their spatial and temporal distribution, intrinsic to the definition of their cellular state. Here we describe DypFISH, an approach to quantitatively investigate the spatial and temporal subcellular localization of RNA and protein, by combining micropatterning of cells with fluorescence microscopy at high resolution. We introduce a range of analytical techniques for quantitatively interrogating single molecule RNA FISH data in combination with protein immunolabeling over time. Strikingly, our results show that constraining cellular architecture reduces variation in subcellular mRNA and protein distributions, allowing the characterization of their localization and dynamics with high reproducibility. Many tissues contain cells that exist in similar constrained architectures. Thus DypFISH reveals reproducible patterns of clustering, strong correlative influences of mRNA-protein localization on MTOC orientation when they are present and interdependent dynamics globally and at specific subcellular locations which can be extended to physiological systems.
Tissue shape determines actin-dependent nuclear migration mechanisms in neuroepithelia
Authors: Yanakieva Iskra , Erzberger Anna , Matejčić Marija , Modes Carl D. , Norden Caren
Published: January 2019

Correct nuclear position is crucial for cellular function. Depending on cell context however, cytoskeletal elements and force generation mechanisms vary. While these mechanisms have been intensely studied in single cells, how nuclear positioning is linked to tissue morphology is less clear. Here, we compare apical nuclear positioning in developing straight and curved neuroepithelia of zebrafish.

Interestingly, in differently shaped neuroepithelia the kinetics of nuclear positioning differ and we find that distinct actin-dependent mechanisms are employed. In straight neuroepithelia nuclear positioning is controlled by Rho-ROCK-dependent myosin contractility. Curved neuroepithelia use a formin-dependent pushing mechanism for which we propose a force generation theory.

We suggest that cytoskeleton adaptability to tissue shape ensures correct nuclear positioning and robust epithelial maturation across different geometries. We further speculate that different mechanisms arise due to differences in actin arrangements during development, a theme highlighting the importance of developmental context for the execution of intracellular processes.
Hydrogen Bond Donors and Acceptors are Generally Depolarized in α-Helices as Revealed by a Molecular Tailoring Approach
Authors: Kondo Hiroko X. , Kusaka Ayumi , Kitakawa Colin K. , Onari Jinta , Yamanaka Shusuke , Nakamura Haruki , Takano Yu
Published: January 2019

Hydrogen-bond (H-bond) interaction energies in α-helices of short alanine peptides were systematically examined by precise DFT calculations, followed by a molecular tailoring approach (MTA). The contribution of each H-bond interaction in α-helices was estimated in detail from the entire conformation energies, and the results were compared with those in the minimal H-bond models, in which only H-bond donors and acceptors exist with the capping methyl groups. Consequently, the former interaction energies were always significantly weaker than the latter energies, when the same geometries of the H-bond donors and acceptors were applied. The chemical origin of this phenomenon was investigated by analyzing the differences among the electronic structures of the local peptide backbones of the α-helices and those of the minimal H-bond models. Consequently, we found that the reduced H-bond energy originated from the depolarizations of both the H-bond donor and acceptor groups, due to the repulsive interactions with the neighboring polar peptide groups in the α-helix backbone. The classical force-fields provide similar H-bond energies to those in the minimal H-bond models, which ignore the current depolarization effect, and thus they overestimate the actual H-bond energies in α-helices.
Multilevel regulation of the glass locus during Drosophila eye development
Authors: Fritsch Cornelia , Bernardo-Garcia F. Javier , Humberg Tim-Henning , Miellet Sara , Almeida Silvia , Huber Armin , Sprecher Simon G.
Published: January 2019

Development of eye tissue is initiated by a conserved set of transcripton factors termed retinal determination network (RDN). In the fruit fly Drosophila melanogaster, the zinc-finger transcription factor Glass acts directly downstream of the RDN to control idendity of photoreceptor as well as non-photoreceptors cells. Tight control of spatial and temporal gene expression is a critical feature during development, cell-fate determination as well as maintainance of differentiated tissues. The molecular mechanisms that control expression of glass, however remain largely unknown. We here identify complex regulatory mechanisms controlling expression of the glass locus. All information to recapitulate glass expression are contained in a compact 5.2 kb cis-acting genomic element by combining different cell-type specific and general enhancers with repressor elements. Moreover, the immature RNA of the locus contains an alterantive small open reading frame (smORF) upstream of the actual glass translation start, resulting in a small peptide instead of the three possible glass protein isoforms. CRISPR/Cas9-based mutagenesis shows that the smORF is not required for the formation of functioning photoreceptors, but to attenuate effects of glass misexpression. Furthermore, editing the genome to generate glass loci eliminating either one or two isoforms shows that only one of the three proteins is critical for formation of functioning photoreceptors, while removing the two other isoforms did not cause defects in developmental or photoreceptor function. Our results show that eye development and function is surprisingly robust and appears buffered to targeted manipulations of critical features of the glass transcript, suggesting a strong selection pressure to allow the formation of a functioning eye.
Mechanism of electroneutral sodium/proton antiporter from transition-path shooting
Authors: Okazaki Kei-ichi , Wöhlert David , Warnau Judith , Jung Hendrik , Yildiz Özkan , Kühlbrandt Werner , Hummer Gerhard
Published: February 2019

Na+/H+ antiporters exchange sodium ions (Na+) and protons (H+) on opposite sides of lipid membranes, using the gradient of one ion to drive the uphill transport of the other. The electroneutral Na+/H+ antiporter NhaP from archaea Pyrococcus abyssi (PaNhaP) is a functional homolog of the human Na+/H+ exchanger NHE1, which is an important drug target. Here we resolve the Na+ and H+ transport cycle of PaNhaP in continuous and unbiased molecular dynamics trajectories that cover the entire transport cycle. We overcome the enormous time-scale gap between seconds-scale ion exchange and microseconds simulations by transition-path shooting. In this way, we selectively capture the rare events in which the six-helix-bundle transporter domain spontaneously moves up and down to shuttle protons and ions across the membrane. The simulations reveal two hydrophobic gates above and below the ion-binding sites that open and close in response to the bundle motion. Weakening the outside gate by mutagenesis makes the transporter faster, suggesting that the gate balances competing demands of fidelity and efficiency. Transition-path sampling and a committor-based reaction coordinate optimization identify the essential motions and interactions that realize conformational alternation between the two access states in transporter function.
Concerted localization-resets precede YAP-dependent transcription
Authors: Ghosh Rajarshi P. , Franklin J. Matthew , Shi Quanming , Reddick Michael P. , Liphardt Jan T.
Published: February 2019

Yes-associated protein 1 (YAP) is a transcriptional regulator with critical roles in mechanotransduction, organ size control, and regeneration. Here, using new tools for real-time visualization of native YAP and target gene transcription dynamics, we show that a cycle of fast exodus of nuclear YAP to the cytoplasm followed by fast reentry to the nucleus (“localization-resets”) activates YAP target genes. These “resets” could be induced by calcium signaling, modulation of actomyosin contractility, or mitosis. Using nascent-transcription reporter knock-ins of YAP target genes, we observed a strict association between these resets and downstream transcription. Oncogenically-transformed transformed cell lines lacked localization-resets and instead showed dramatically elevated rates of nucleocytoplasmic shuttling of YAP, suggesting an escape from compartmentalization-based control. The single-cell localization and transcription traces suggest that YAP activity is not a simple linear function of nuclear enrichment and point to a new model of transcriptional activation based on nucleocytoplasmic exchange properties of YAP.
Divergence-based introgression polarization
Authors: Forsythe Evan S. , Sloan Daniel B. , Beilstein Mark A.
Published: February 2019

Introgressive hybridization results in the transfer of genetic material between species, often with fitness implications for the recipient species. The development of statistical methods for detecting the signatures of historical introgression (IG) in whole-genome data has been a major area of focus. While existing techniques are able to identify the taxa that exchanged genes during IG using a four-taxon system, most methods do not explicitly distinguish which taxon served as donor and which as recipient during IG (i.e. polarization of IG directionality). The existing methods that do polarize IG are only able to do so when there is a fifth taxon available and that taxon is sister to one of the taxa involved in IG. Here, we presentDivergence-based Introgression Polarization(DIP), a method for polarizing IG using patterns of sequence divergence across whole genomes, which operates in a four-taxon context. Thus,DIPcan be applied to infer the directionality of IG when additional taxa are not available. We use simulations to show thatDIPcan polarize IG and identify potential sources of bias in the assignment of directionality, and we applyDIPto a well-described hominin IG event.
A Genome-Wide Association Study of Non-Photochemical Quenching in response to local seasonal climates in Arabidopsis thaliana
Authors: Rungrat Tepsuda , Almonte Andrew A. , Cheng Riyan , Gollan Peter J. , Stuart Tim , Aro Eva-Mari , Borevitz Justin O. , Pogson Barry , Wilson Pip B.
Published: February 2019

Field-grown plants have variable exposure to sunlight as a result of shifting cloud-cover, seasonal changes, canopy shading, and other environmental factors. As a result, they need to have developed a method for dissipating excess energy obtained from periodic excessive sunlight exposure. Non-photochemical quenching (NPQ) dissipates excess energy as heat, however the physical and molecular genetic mechanics of NPQ variation are not understood. In this study, we investigated the genetic loci involved in NPQ by first growing different Arabidopsis thaliana accessions in local and seasonal climate conditions, then measured their NPQ kinetics through development by chlorophyll fluorescence. We used genome-wide association studies (GWAS) to identify 15 significant quantitative trait loci (QTL) for a range of photosynthetic traits, including a QTL co-located with known NPQ gene PSBS (AT1G44575). We found there were large alternative regulatory segments between the PSBS promoter regions of the functional haplotypes and a significant difference in PsbS protein concentration. These findings parallel studies in rice showing recurrent regulatory evolution of this gene. The variation in the PSBS promoter and the changes underlying other QTLs could give insight to allow manipulations of NPQ in crops to improve their photosynthetic efficiency and yield.

B.P. & J.B. conceived the project; B.P., J.B., P.W. and T.R. designed the research plan and analysis; P.W. supervised the experiments; T.R. performed most of the experiments and analysis; P.G., T.S., A.A. & E.A. designed and undertook experimental design, experiments and analysis for Figure 4; R.C. did the GWAS analysis; P.W., T.R. & A.A. wrote the article with contributions of all the authors.
METASPACE: A community-populated knowledge base of spatial metabolomes in health and disease
Authors: Alexandrov Theodore , Ovchinnikova Katja , Palmer Andrew , Kovalev Vitaly , Tarasov Artem , Stuart Lachlan , Nigmetzianov Renat , Fay Dominik ,   Key METASPACE contributors, Gaudin Mathieu , Lopez Cristina Gonzalez , Vetter Marina , Swales John , Bokhart Mark , Kompauer Mario , McKenzie James , Rappez Luca , Velickovic Dusan , Lavigne Regis , Zhang Guanshi , Thinagaran Dinaiz , Ruhland Elisa , Sans Marta , Triana Sergio , Sammour Denis Abu , Aboulmagd Sarah , Bagger Charlotte , Strittmatter Nicole , Rigopoulos Angelos , Gemperline Erin , Joensen Asta Maria , Geier Benedikt , Quiason Christine , Weaver Eric , Prasad Mridula , Balluff Benjamin , Nagornov Konstantin , Li Lingjun , Linscheid Michael , Hopf Carsten , Heintz Dimitri , Liebeke Manuel , Spengler Bernhard , Boughton Berin , Janfelt Christian , Sharma Kumar , Pineau Charles , Anderton Christopher , Ellis Shane , Becker Michael , Pánczél József , Violante Georges Da , Muddiman David , Goodwin Richard , Eberlin Livia , Takats Zoltan , Shahidi-Latham Sheerin
Published: February 2019

Metabolites, lipids, and other small molecules are key constituents of tissues supporting cellular programs in health and disease. Here, we present METASPACE, a community-populated knowledge base of spatial metabolomes from imaging mass spectrometry data. METASPACE is enabled by a high-performance engine for metabolite annotation in a confidence-controlled way that makes results comparable between experiments and laboratories. By sharing their results publicly, engine users continuously populate a knowledge base of annotated spatial metabolomes in tissues currently including over 3000 datasets from human cancer cohorts, whole-body sections of animal models, and various organs. The spatial metabolomes can be visualized, explored and shared using a web app as well as accessed programmatically for large-scale analysis. By using novel computational methods inspired by natural language processing, we illustrate that METASPACE provides molecular coverage beyond the capacity of any individual laboratory and opens avenues towards comprehensive metabolite atlases on the levels of tissues and organs.
Both the inflammatory response and clinical outcome differ markedly between adults with pneumococcal and meningococcal meningitis in a high HIV-1 prevalent setting in sub-Saharan Africa
Authors: Wall Emma C , Guerra-Assunção José Afonso , Denis Brigitte , Scarborough Matthew , Ajdukiewicz Katherine , Cartwright Katharine , Mukaka Mavuto , Mlozowa Veronica S , Venturini Cristina , Allain Theresa J , Lalloo David G , Brown Jeremy S , Gordon Stephen B , Heyderman Robert S
Published: February 2019

Outcomes from pneumococcal meningitis (PM) are worse than meningococcal meningitis (MM), particularly in settings with high HIV-1 prevalence, but the reasons are unknown. We compared inflammatory responses between PM and MM in Malawian adults.

As compared to MM (n=27, 67% HIV-infected, mortality 11%), patients with PM (n=440, 84% HIV-infected, mortality 54%) were older, had strikingly lower CSF WCC, higher pro-inflammatory cytokine concentrations and higher mortality. PM is characterized by significantly lower CSF WCC, but greater inflammation and higher mortality compared to MM. Mechanistic understanding of blunting of the CSF leukocyte response in PM in-vivo is required.
Hybrid genome assembly and annotation of Danionella translucida, a transparent fish with the smallest known vertebrate brain
Authors: Kadobianskyi Mykola , Schulze Lisanne , Schuelke Markus , Judkewitz Benjamin
Published: February 2019

Studying the activity of distributed neuronal circuits at a cellular resolution in vertebrates is very challenging due to the size and optical turbidity of their brains. We recently presented Danionella translucida, a close relative of zebrafish, as a model organism suited for studying large-scale neural network interactions in adult individuals. Danionella remains transparent throughout its life, has the smallest known vertebrate brain and possesses a rich repertoire of complex behaviours. Here we sequenced, assembled and annotated the Danionella translucida genome employing a hybrid Illumina/Nanopore read library as well as RNA-seq of embryonic, larval and adult mRNA. We achieved high assembly continuity using low-coverage long-read data and annotated a large fraction of the transcriptome. This dataset will pave the way for molecular research and targeted genetic manipulation of the smallest known vertebrate brain.
Relating brain connectivity with persistent symptoms in pediatric concussion
Authors: Iyer Kartik K. , Barlow Karen M. , Brooks Brian , Ofoghi Zahra , Zalesky Andrew , Cocchi Luca
Published: February 2019

Persistent post-concussion symptoms (PCS) in children following a mild traumatic brain injury (mTBI) is a growing public health concern. There is a pressing need to understand the neural underpinning of PCS. Here, we examined whole-brain functional connectivity from resting-state fMRI with behavioral assessments in a cohort of 110 children with mTBI. Children with mTBI and controls had similar levels of connectivity. PCS symptoms and behaviors including poor cognition and sleep were associated with connectivity within functional brain networks. The identification of a single “positive-negative” dimension linking connectivity with behaviors enables better prognosis and stratification towards personalized therapeutic interventions.
Polled Digital Cell Sorter (p-DCS): Automatic identification of hematological cell types from single cell RNA-sequencing clusters
Authors: Domanskyi Sergii , Szedlak Anthony , Hawkins Nathaniel T , Wang Jiayin , Paternostro Giovanni , Piermarocchi Carlo
Published: February 2019

Background

Single cell RNA sequencing (scRNA-seq) brings unprecedented opportunities for mapping the heterogeneity of complex cellular environments such as bone marrow, and provides insight into many cellular processes. Single cell RNA-seq, however, has a far larger fraction of missing data reported as zeros (dropouts) than traditional bulk RNA-seq. This makes difficult not only the clustering of cells, but also the assignment of the resulting clusters into predefined cell types based on known molecular signatures, such as the expression of characteristic cell surface markers.

Results

We present a computational tool for processing single cell RNA-seq data that uses a voting algorithm to identify cells based on approval votes received by known molecular markers. Using a stochastic procedure that accounts for biases due to dropout errors and imbalances in the number of known molecular signatures for different cell types, the method computes the statistical significance of the final approval score and automatically assigns a cell type to clusters without an expert curator. We demonstrate the utility of the tool in the analysis of eight samples of bone marrow from the Human Cell Atlas. The tool provides a systematic identification of cell types in bone marrow based on a recently-published manually-curated cell marker database [1], and incorporates a suite of visualization tools that can be overlaid on a t-SNE representation. The software is freely available as a python package at https://github.com/sdomanskyi/DigitalCellSorter

Conclusions

This methodology assures that extensive marker to cell type matching information is taken into account in a systematic way when assigning cell clusters to cell types. Moreover, the method allows for a high throughput processing of multiple scRNA-seq datasets, since it does not involve an expert curator, and it can be applied recursively to obtain cell sub-types. The software is designed to allow the user to substitute the marker to cell type matching information and apply the methodology to different cellular environments.