bluuebunny/crossref_metadata_2025 huggingface dataset:
Highly efficient and specific genome editing in human cells with paired CRISPR-Cas9 nickase ribonucleoproteins
Authors: Lamberth Jacob , Daley Laura , Natarajan Pachai , Khoruzhenko Stanislav , Becker Nurit , Taglicht Daniel , Davis Gregory D. , Ji Qingzhou
Published: September 2019

CRISPR technology has opened up many diverse genome editing possibilities in human somatic cells, but has been limited in the therapeutic realm by both potential off-target effects and low genome modification efficiencies. Recent advancements to combat these limitations include delivering Cas9 nucleases directly to cells as highly purified ribonucleoproteins (RNPs) instead of the conventional plasmid DNA and RNA-based approaches. Here, we extend RNP-based delivery in cell culture to a less characterized CRISPR format which implements paired Cas9 nickases. The use of paired nickase Cas9 RNP system, combined with a GMP-compliant non-viral delivery technology, enables editing in human cells with high specificity and high efficiency, a development that opens up the technology for further exploration into a more therapeutic role.
fCite: a fractional citation tool to quantify an individual’s scientific research output
Authors: Kozlowski Lukasz Pawel
Published: September 2019

Here, I present the fCite web service (fcite.org) a tool for the in-depth analysis of an individual’s scientific research output. While multiple existing tools (e.g., Google Scholar, iCite, Microsoft Academic) focus on the total number of citations and the H-index, I propose the analysis of the research output by considering multiple metrics to provide greater insight into a scientist’s multifaceted profile. The most distinguishing feature of fCite is its ability to calculate fractional scores for most of the metrics currently in use. Thanks to the division of citations (and RCR scores) by the number of authors, the tool provides a more detailed analysis of a scholar’s portfolio. fCite is based on PUBMED data (~18 million publications), and the statistics are calculated with respect to ORCID data (~600,000 user profiles).
Bird Song Learning is Mutually Beneficial for Tutee and Tutor
Authors: Beecher Michael D. , Akçay Çağlar , Campbell S. Elizabeth
Published: September 2019

Song learning is generally assumed to be beneficial for a young songbird, but merely incidental, without costs or benefits, for the older song ‘tutors’. In the present study we contrast two mutually exclusive hypotheses about the tutor/tutee relationship: (1) that it is cooperative, or at least mutually tolerant, with tutor and tutee mutually benefiting from their relationship,vs.(2) that it is competitive, with tutor and tutee competing over territory, so that one or the other suffers negative fitness consequences of their relationship. In a field study of three consecutive cohorts of song sparrows (Melospiza melodia) we determined the older bird (primary tutor) from whom the young bird (tutee) learned most of his songs, and how long tutee and primary tutor survived subsequently. We found that the more songs a tutee learns from his primary tutor, the longer their mutual survival on their respective territories. This study provides the first evidence of a mutual benefit of bird song learning and teaching in nature.
Exaiptasia diaphanafrom the Great Barrier Reef: a valuable resource for coral symbiosis research
Authors: Dungan Ashley M. , Hartman Leon , Tortorelli Giada , Belderok Roy , Lamb Annika M. , Pisan Lynn , McFadden Geoffrey I. , Blackall Linda L. , van Oppen Madeleine J. H.
Published: September 2019

The sea anemone,Exaiptasia diaphana, commonly known asExaiptasia pallidaorAiptasia pallida, has become increasingly popular as a model for cnidarian-microbiome symbiosis studies due to its relatively rapid growth, ability to reproduce sexually and asexually, and symbiosis with diverse prokaryotes and the same microalgal symbionts (family Symbiodiniaceae) as its coral relatives. ClonalE. diaphanastrains from Hawaii, the Atlantic Ocean, and Red Sea are now established for use in research. Here, we introduce Great Barrier Reef (GBR)-sourcedE. diaphanastrains as additions to the model repertoire. Sequencing of the 18S rRNA gene confirmed the anemones to beE. diaphanawhile genome-wide single nucleotide polymorphism analysis revealed four distinct genotypes. Based onExaiptasia-specific inter-simple sequence repeat (ISSR)-derived sequence characterized amplified region (SCAR) marker and gene loci data, these fourE. diaphanagenotypes are distributed across several divergent phylogenetic clades with no clear phylogeographical pattern. The GBRE. diaphanagenotypes comprised three females and one male, which all hostBreviolum minutumas their homologous Symbiodiniaceae endosymbiont. When acclimating to an increase in light levels from 12 to 28 μmol photons m-2s-1, the genotypes exhibited significant variation in maximum quantum yield of Symbiodiniaceae photosystem II and Symbiodiniaceae cell density. The comparatively high levels of physiological and genetic variability among GBR anemone genotypes makes these animals representative of globalE. diaphanadiversity and thus excellent model organisms. The addition of these GBR strains to the worldwideE. diaphanacollection will contribute to cnidarian symbiosis research, particularly in relation to the climate resilience of coral reefs.
B cells rapidly target antigen and surface-derived MHCII into peripheral degradative compartments
Authors: Hernández-Pérez S , Vainio M , Kuokkanen E , Sustar V , Petrov P , Fórsten S , Paavola V , Rajala J , Awoniyi LO , Sarapulov AV , Vihinen H , Jokitalo E , Bruckbauer A , Mattila PK
Published: September 2019

In order to mount high-affinity antibody responses, B cells internalise specific antigens and process them into peptides loaded onto MHCII for presentation to Thcells. While the biochemical principles of antigen processing and MHCII loading have been well dissected, how the endosomal vesicle system is wired to enable these specific functions remains much less studied. Here, we performed a systematic microscopy-based analysis of antigen trafficking in B cells to reveal its route to the MHCII peptide-loading compartment (MIIC). Surprisingly, we detected fast targeting of internalised antigen into peripheral acidic compartments that possessed the hallmarks of MIIC and also showed degradative capacity. In these vesicles, internalised antigen converged rapidly with membrane-derived MHCII and partially overlapped with Cathepsin-S and H2-M, both required for peptide loading. These early compartments appeared heterogenous and atypical as they contained a mixture of both early and late markers, indicating specialized endosomal route. Together, our data suggests that, in addition to previously-reported perinuclear late endosomal MIICs, antigen processing and peptide loading could start already in these specialized early peripheral acidic vesicles (eMIIC) to support fast peptide-MHCII presentation.
Fibroblast-specific genome-scale modelling predicts an imbalance in amino acid metabolism in Refsum disease
Authors: Wegrzyn Agnieszka B. , Herzog Katharina , Gerding Albert , Kwiatkowski Marcel , Wolters Justina C. , Dolga Amalia M. , van Lint Alida E. M. , Wanders Ronald J. A. , Waterham Hans R. , Bakker Barbara M.
Published: September 2019

Refsum disease is an inborn error of metabolism that is characterised by a defect in peroxisomal α-oxidation of the branched-chain fatty acid phytanic acid. The disorder presents with late-onset progressive retinitis pigmentosa and polyneuropathy and can be diagnosed biochemically by elevated levels of phytanic acid in plasma and tissues of patients. To date, no cure exists for Refsum disease, but phytanic acid levels in patients can be reduced by plasmapheresis and a strict diet.

In this study, we reconstructed a fibroblast-specific genome-scale model based on the recently published, FAD-curated model, based on Recon3D reconstruction. We used transcriptomics (available via GEO database with identifier GSE138379), metabolomics, and proteomics data (available via ProteomeXchange with identifier PXD015518), which we obtained from healthy controls and Refsum disease patient fibroblasts incubated with phytol, a precursor of phytanic acid.

Our model correctly represents the metabolism of phytanic acid and displays fibroblast-specific metabolic functions. Using this model, we investigated the metabolic phenotype of Refsum disease at the genome-scale, and we studied the effect of phytanic acid on cell metabolism. We identified 53 metabolites that were predicted to discriminate between Healthy and Refsum disease patients, several of which with a link to amino acid metabolism. Ultimately, these insights in metabolic changes may provide leads for pathophysiology and therapy.
BrainNET: Inference of brain network topology using Machine Learning
Authors: Murugesan Gowtham Krishnan , Ganesh Chandan , Nalawade Sahil , Davenport Elizabeth M , Wagner Ben , Hwa Kim Won , Maldjian Joseph A.
Published: September 2019

Objective

To develop a new fMRI network inference method, BrainNET, that utilizes an efficient machine learning algorithm to quantify contributions of various regions of interests (ROIs) in the brain to a specific ROI.

Methods

BrainNET is based on Extremely Randomized Trees (ERT) to estimate network topology from fMRI data and modified to generate an adjacency matrix representing brain network topology, without reliance on arbitrary thresholds. Open source simulated fMRI data of fifty subjects in twenty-eight different simulations under various confounding conditions with known ground truth was used to validate the method. Performance was compared with correlation and partial correlation (PC). The real-world performance was then evaluated in a publicly available Attention-deficit/hyperactivity disorder (ADHD) dataset including 134 Typically Developing Children (mean age: 12.03, males: 83), 75 ADHD Inattentive (mean age: 11.46, males: 56) and 93 ADHD Combined (mean age: 11.86, males: 77) subjects. Network topologies in ADHD were inferred using BrainNET, correlation, and PC. Graph metrics were extracted to determine differences between the ADHD groups.

Results

BrainNET demonstrated excellent performance across all simulations and varying confounders in identifying true presence of connections. In the ADHD dataset, BrainNET was able to identify significant changes (p< 0.05) in graph metrics between groups. No significant changes in graph metrics between ADHD groups was identified using correlation and PC.
Commensal-derived succinate enhances tuft cell specification and suppresses ileal inflammation
Authors: Banerjee Amrita , Herring Charles A. , Kim Hyeyon , Chen Bob , Simmons Alan J. , Southard-Smith Austin N. , White James R. , Ramirez Solano Marisol A. , Scoville Elizabeth A. , Liu Qi , Washington Mary Kay , Lau Ken S.
Published: September 2019

Longitudinal analysis of Crohn's disease (CD) incidence has identified an inverse correlation with helminth infestation and recent studies have revealed that intestinal tuft cell hyperplasia is critical for helminth response. Tuft cell frequency was decreased in the inflamed ilea of CD patients and a mouse model of TNFα-induced Crohn's-like ileitis (TNFΔARE). Single-cell RNA sequencing paired with unbiased differential trajectory analysis of the tuft cell lineage in a genetic model of tuft cell hyperplasia (AtohKO) demonstrated that the tuft cell lineage had increased tricarboxylic acid (TCA) cycle gene signatures. Commensal microbiome-derived succinate was detected in the ileal lumen of these animals while microbiome depletion suppressed tuft cell hyperplasia. Therapeutic succinate treatment in TNFΔARE animals reduced pathology in correlation with induced tuft cell specification. We provide evidence implicating the modulatory role of intestinal tuft cells in chronic intestinal inflammation, which could facilitate leveraging this rare and elusive cell type for CD treatment.
Do Walking Muscle Synergies Influence Propensity of Severe Slipping?
Authors: Nazifi Mohammad Moein , Beschorner Kurt , Hur Pilwon
Published: September 2019

Slipping is frequently responsible for falling injuries. Preventing slips, and more importantly severe slips, is of importance in fall prevention. Our previous study characterized mild slipping and severe slipping by the analysis of muscle synergies. Significant discrepancies in motor control of slipping have been observed between mild and severe slippers. We are further interested in whether differences exist in baseline motor control patterns between persons who experience mild and severe slips when exposed to a slippery contaminant. This study investigated walking with a muscle synergy approach to detect if walking muscle synergies differ between groups experiencing different slip severities. Twenty healthy young adults (8 mild slippers and 12 severe slippers) participated in this study and their muscle synergies of walking were extracted. Muscle synergy analysis showed that mild slippers had a higher contribution of hamstring and quadriceps during walking while severe slippers had increased contribution of tibialis group. This study provides novel information that may contribute to identifying diagnostic techniques for identifying persons or populations with a high risk of fall based on their walking patterns.
Secondary Motor Cortex Transforms Spatial Information into Planned Action During Navigation
Authors: Olson Jacob M. , Li Jamie , Montgomery Sarah E. , Nitz Douglas A.
Published: September 2019

Fluid navigation requires constant updating of planned movements to adapt to evolving obstacles and goals. A neural substrate for navigation demands spatial and environmental information and the ability to effect actions through efferents. Secondary motor cortex is a prime candidate for this role given its interconnectivity with association cortices that encode spatial relationships and its projection to primary motor cortex. Here we report that secondary motor cortex neurons robustly encode both planned and current left/right turning actions across multiple turn locations in a multi-route navigational task. Comparisons within a common statistical framework reveal that secondary motor cortex neurons differentiate contextual factors including environmental position, route, action sequence, orientation, and choice availability. Despite significant modulation by context, action planning and execution are the dominant output signals of secondary motor cortex neurons. These results identify secondary motor cortex as a structure integrating environmental context toward the updating of planned movements.
Analysing plasma membrane asymmetry of lipid organisation by fluorescence lifetime and correlation spectroscopy
Authors: Gupta Anjali , Korte Thomas , Herrmann Andreas , Wohland Thorsten
Published: September 2019

A fundamental feature of a eukaryotic cell membrane is the asymmetric arrangement of lipids in the two leaflets. A cell invests significant energy to maintain this asymmetry and utilizes it to regulate important biological processes such as apoptosis and vesiculation. Here, we employ fluorescence lifetime imaging microscopy (FLIM) and imaging total internal reflection fluorescence correlation spectroscopy (ITIR-FCS) to differentiate the dynamics and organization of the exofacial and cytoplasmic leaflet of live mammalian cells. We characterize the biophysical properties of fluorescent analogues of phosphatidylcholine (PC), sphingomyelin (SM) and phosphatidylserine (PS) in two mammalian cell membranes. Due to their specific transverse membrane distribution, these probes allow leaflet specific investigation of the plasma membrane. We compare the results with regard to the different temporal and spatial resolution of the methods. Fluorescence lifetimes of fluorescent lipid analogues were found to be in a characteristic range for the liquid ordered phase in the outer leaflet and liquid disordered phase in the inner leaflet. The observation of a more fluid inner leaflet is supported by free diffusion in the inner leaflet with high average diffusion coefficients. The liquid ordered phase in the outer leaflet is accompanied by slower diffusion and diffusion with intermittent transient trapping. Our results show that the combination of FLIM and ITIR-FCS with specific fluorescent lipid analogues provides a powerful tool to investigate lateral and trans-bilayer characteristics of plasma membrane in live cells.

Abstract Figure
The signal and the noise - characteristics of antisense RNA in complex microbial communities
Authors: Michaelsen Thomas Yssing , Brandt Jakob , Singleton Caitlin , Kirkegaard Rasmus Hansen , Segata Nicola , Albertsen Mads
Published: September 2019

High-throughput sequencing has allowed unprecedented insight into the composition and function of complex microbial communities. With the onset of metatranscriptomics, it is now possible to interrogate the transcriptome of multiple organisms simultaneously to get an overview of the gene expression of the entire community. Studies have successfully used metatranscriptomics to identify and describe relationships between gene expression levels and community characteristics. However, metatranscriptomic datasets contain a rich suite of additional information which is just beginning to be explored. In this minireview we discuss the different computational strategies for handling antisense expression in metatranscriptomic samples and highlight their potentially detrimental effects on downstream analysis and interpretation. We also surveyed the antisense transcriptome of multiple genomes and metagenome-assembled genomes (MAGs) from five different datasets and found high variability in the level of antisense transcription for individual species which were consistent across samples. Importantly, we tested the hypothesis that antisense transcription is primarily the product of transcriptional noise and found mixed support, suggesting that the total observed antisense RNA in complex communities arises from a compounded effect of both random, biological and technical factors. Antisense transcription can provide a rich set of information, from technical details about data quality to novel insight into the biology of complex microbial communities.

Key points

Several fundamentally different approaches are used to handle antisense RNA

Prevalence of antisense RNA is highly variable between communities, genomes, and genes.

Antisense RNA is likely an opaque mixture of technical, biological and random effects
Effects of low temperature and cold-acclimation on photoinhibition and singlet oxygen production in four natural accessions ofArabidopsis
Authors: Mattila Heta , Mishra Kumud B. , Kuusisto Iiris , Mishra Anamika , Novotná Kateřina , Šebela David , Tyystjärvi Esa
Published: September 2019

To understand the effects of low temperature and cold-acclimation on reactive oxygen species and photoinhibition of photosystem II (PSII), light-induced inactivation of PSII was measured at 22 and 4 °C from fourArabidopsis thalianaaccessions (Rschew, Tenela, Columbia-0 and Coimbra) grown under optimal conditions. Photoinhibition was also measured at 4 °C from plants cold-acclimated at 4 °C for two weeks. Measurements were done in the absence and presence of lincomycin that blocks PSII repair, and PSII activity was assayed with the ratio of variable to maximum chlorophyllafluorescence (FV/FM) and with light-saturated rate of oxygen evolution using a quinone acceptor. Of the non-acclimated accessions, Rschew was the most tolerant to photoinhibition and Coimbra the least; the rate constants of photoinhibition of the most sensitive accession were 1.3-1.9 times as high as those of the tolerant ones. The damaging reaction of photoinhibition in non-acclimated plants was slower or equal at 4 °C than at 22 °C. The rate constants of photoinhibition of cold-acclimated plants, at 4 °C, were 0.55 to 1.25 times as high as those of non-acclimated plants; the protective effect of cold-acclimation on photoinhibition was consistent in Columbia-0 and Coimbra whereas Rschew and Tenela were either slightly more tolerant or susceptible, depending on the method used to assay photoinhibition. Production of singlet oxygen, measured from thylakoid membranes isolated from non-acclimated and cold-acclimated plants, did not decrease due to cold-acclimation, nor did singlet oxygen production correlate with the rate of photoinhibition or with flavonol contents of the leaves.
Intraflagellar transport complex B proteins regulate the Hippo effector Yap1 during cardiogenesis
Authors: Peralta Marina , Jerabkova Katerina , Lucchesi Tommaso , Lopez Laia Ortiz , Vitre Benjamin , Han Dong , Guillemot Laurent , Dingare Chaitanya , Sumara Izabela , Mercader Nadia , Lecaudey Virginie , Delaval Benedicte , Meilhac Sigolène M. , Vermot Julien
Published: September 2019

Cilia and the intraflagellar transport (IFT) proteins involved in ciliogenesis are associated with congenital heart diseases (CHD). However, the molecular links between cilia, IFT proteins and cardiogenesis are yet to be established. Using a combination of biochemistry, genetics, and live imaging methods, we show that IFT complex B proteins (Ift88, Ift54 and Ift20) modulate the Hippo pathway effector YAP1 in zebrafish and mouse. We demonstrate that this interaction is key to restrict the formation of the proepicardium and the myocardium.In celluloexperiments suggest that IFT88 and IFT20 interact with YAP1 in the cytoplasm and functionally modulates its activity, identifying a molecular link between cilia related proteins and the Hippo pathway. Taken together, our results highlight a novel role for IFT complex B proteins during cardiogenesis and shed light on an unexpected mechanism of action for ciliary proteins in YAP1 regulation. These findings provide mechanistic insights into a non-canonical role for cilia related proteins during cardiogenesis.
Gonadotropes in medaka grow long extensions with varicosity-like swellings, projecting towards each other and blood vessels
Authors: Grønlien Heidi Kristine , Fontaine Romain , Hodne Kjetil , Tysseng Isabelle , Ager-Wick Eirill , Weltzien Finn-Arne , Haug Trude Marie
Published: September 2019

Accumulating evidence in the scientific literature indicates that some pituitary cell types are organized in complex networks. Previous observations have indicated that this may also be the case in medaka (Oryzias latipes), where long cellular extensions with varicosity-like swellings are formed by luteinizing hormone (Lh)-producing gonadotropes expressing green fluorescent protein. In this study, immunofluorescence of intact pituitaries reveal that Lh beta polypeptides are mainly located in the varicosity-like swellings and at the extremity of the extensions. Some extensions approach nearby Lh-producing cells, and other extensions are in close contact with blood vessels. To investigate whether these extensions may contribute to network formation, we followed their development using confocal and fluorescent microscopy on primary cultures. During the first two days in culture, the extensions initiated the formation of homotypic cellular networks and clustering. The extensions were classified as either major or minor. Major extensions were several cell diameters long, dependent on microtubules, and displaying varicosity-like swellings at regular intervals. Minor extensions typically protruded from the major, were significantly shorter and thinner, and dependent on actin. The swellings were dependent on both microtubules and actin. Flash photolysis of caged Ca2+showed that the signal was propagated along the major extensions, intensifying in each swelling, indicating a continuous structure. However, the Ca2+signal did not transfer to the next cell in the network, but was transferred between cells merged at their somas. In summary, Lh-producing gonadotropes in medaka display a complex cellular structure of extensions, possibly linked to communication with blood vessels and/or other gonadotrope cells.
Cytoprotective effects of (E)-N-(2-(3, 5-dimethoxystyryl) phenyl) furan-2-carboxamide (BK3C231) against 4-nitroquinoline 1-oxide-induced damage in CCD-18Co human colon fibroblast cells
Authors: Tan Huan Huan , Thomas Noel F. , Inayat-Hussain Salmaan H. , Chan Kok Meng
Published: September 2019

Stilbenes are a group of chemicals characterized with the presence of 1,2-diphenylethylene. Previously, our group has demonstrated that synthesized (E)-N-(2-(3, 5-dimethoxystyryl) phenyl) furan-2-carboxamide (BK3C231) possesses potential chemopreventive activity specifically inducing NAD(P)H:quinone oxidoreductase 1 (NQO1) protein expression and activity. In this study, the cytoprotective effects of BK3C231 on cellular DNA and mitochondria were investigated in normal human colon fibroblast, CCD-18Co cells. The cells were pretreated with BK3C231 prior to exposure to the carcinogen 4-nitroquinoline 1-oxide (4NQO). BK3C231 was able to inhibit 4NQO-induced cytotoxicity. Cells treated with 4NQO alone caused high level of DNA and mitochondrial damages. However, pretreatment with BK3C231 protected against these damages by reducing DNA strand breaks and micronucleus formation as well as decreasing losses of mitochondrial membrane potential (ΔΨm) and cardiolipin. Interestingly, our study has demonstrated that nitrosative stress instead of oxidative stress was involved in 4NQO-induced DNA and mitochondrial damages. Inhibition of 4NQO-induced nitrosative stress by BK3C231 was observed through a decrease in nitric oxide (NO) level and an increase in glutathione (GSH) level. These new findings elucidate the chemopreventive potential of BK3C231 specifically its cytoprotective effects in human colon fibroblast CCD-18Co cell model.
How do dairy farmers wish their future farm?
Authors: Dalcq Anne-Catherine , Dogot Thomas , Beckers Yves , Brostaux Yves , Froidmont Eric , Vanwindekens Frédéric , Soyeurt Hélène
Published: September 2019

Dairy farming systems are evolving. This study presents dairy producers’ perceptions of their ideal future farm (IFF) to ensure revenue and attempts to determine the reasons for this choice, the environmental aspects related to this choice, the proximity between the current farm and the IFF and the requirements for reaching this IFF. Just before the end of the European milk quota, a total of 245 dairy producers answered a survey about the characteristics of their IFF and other socio-environmental-economic information. A multiple correspondence analysis (MCA) was carried out using seven characteristics of IFF (intensive vs. extensive, specialised vs. diversified, strongly vs. weakly based on new technologies, managed by a group of managers vs. an independent farmer, employed vs. familial workforce, local vs. global market, standard vs. quality-differentiated production). Based on the main contributors to the second dimension of MCA, this axis was defined as an IFF gradient between the local-based extensive (LBE) producers (26%) and the global-based intensive (GBI) producers (46%). The differences of IFF gradient between modalities of qualitative variables were estimated using generalised linear models. Pearson correlations were calculated between the scores on the IFF gradient and quantitative variables. Finally, frequencies for IFF characteristic and the corresponding characteristic for the current situation were calculated to determine the percentages of “unhappy” producers. Some reasons for the choice of IFF by the producers have been highlighted in this study. Environmental initiatives were more valued by LBE than GBI producers. Low similarity was observed between the current farm situation of the respondents and their IFF choice. LBE and GBI producers differed significantly regarding domains of formation (technical and bureaucratic vs transformation and diversification respectively) and paths of formation (non-market vs. market respectively). Two kinds of farming systems were considered by dairy producers and some socioeconomic and environmental components differed between them.
Genome wide DNA methylation profiling identifies specific epigenetic features in high-risk cutaneous squamous cell carcinoma
Authors: Hervás-Marín David , Higgins Faatiemah , Sanmartín Onofre , López-Guerrero Jose Antonio , Bañó M. Carmen , Igual J. Carlos , Quilis Inma , Sandoval Juan
Published: September 2019

Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer. Although most cSCCs have good prognosis, a subgroup of high-risk cSCC has a higher frequency of recurrence and mortality. Therefore, the identification of molecular risk factors associated with this aggressive subtype is of major interest. In this work we carried out a global-scale approach to investigate the DNA-methylation profile in patients at different stages, from premalignant actinic keratosis to low-risk invasive and high-risk non-metastatic and metastatic cSCC. The results showed massive non-sequential changes in DNA-methylome and identified a minimal methylation signature that discriminates between stages. Importantly, a direct comparison of low-risk and high-risk stages revealed epigenetic traits characteristic of high-risk tumours. Finally, a prognostic prediction model in cSCC patients identified a methylation signature able to predict the overall survival of patients. Thus, the analysis of DNA-methylation in cSCC revealed changes during the evolution of the disease through the different stages that can be of great value not only in the diagnosis but also in the prognosis of the disease.
A Human Accelerated Region participates in early human forebrain patterning and expansion
Authors: Acosta Sandra , Sidhaye Jaydeep , Fiore Luciano , Rollan Isabel , Iacono Giovanni , Misharin Alexander V. , Takata Nozomu , Sikora Martin , Joshi Nikita , Xu Beisi , Willerslev Eske , Heyn Holger , Manzanares Miguel , Knoblich Juergen A. , Oliver Guillermo
Published: September 2019

The expansion of the mammalian brain is associated with specific developmental processes; however, not much is known about how evolutionary changes participated in the acquisition of human brain traits during early developmental stages. Here we investigated whether enhancers active during the phylotypic stage show human-specific genomic divergence which could contribute to the evolutionary expansion of the forebrain. Notably, we identified an active enhancer containing a human accelerated region (HAR) located in the Chromosome 14q12, a region enriched with neurodevelopmental genes, such as Foxg1, Nkx2.1 and Nova1. Reporter analysis revealed that the human variant is active in the forebrain in transgenic mice and that it has stronger enhancer activity than the mouse or chimpanzee versions. Humanization of the mouse enhancer variant in transgenic mice and in mouse organoids resulted in an expansion of Foxg1 expressing domains in the forebrain early neural progenitors with a bias towards dorsal identities. Overall, our results suggest that human-specific mutations in critical regulatory elements controlling early brain development impact the expansion and patterning of the forebrain.
Generalized differential equation compartmental models of infectious disease transmission
Authors: Greenhalgh Scott , Rozins Carly
Published: September 2019

For decades, mathematical models of disease transmission have provided researchers and public health officials with critical insights into the progression, control, and prevention of disease spread. Of these models, one of most fundamental is the SIR differential equation model. However, this ubiquitous model has one significant and rarely acknowledged shortcoming: it is unable to account for a disease’s true infectious period distribution. As the misspecification of such a biological characteristic is known to significantly affect model behavior, there is a need to develop new modeling approaches that capture such information. Therefore, we illustrate an innovative take on compartmental models, derived from their general formulation as systems of nonlinear Volterra integral equations, to capture a broader range of infectious period distributions, yet maintain the desirable formulation as systems of differential equations. Our work illustrates a compartmental model that captures any Erlang distributed duration of infection with only 3 differential equations, instead of the typical inflated model sizes required by differential equation compartmental models, and a compartmental model that capture any mean, standard deviation, skewness, and kurtosis of an infectious period distribution with merely 4 differential equations. The significance of our work is that it opens up a new class of easy-to-use compartmental models to predict disease outbreaks that does not require a complete overhaul of existing theory, and thus provides a starting point for multiple research avenues of investigation under the contexts of mathematics, public health, and evolutionary biology.
Monocyte reconstitution and gut microbiota composition after hematopoietic stem cell transplantation
Authors: Morjaria Sejal , Zhang Allen W. , Kim Sohn , Peled Jonathan U. , Becattini Simone , Littmann Eric R. , Pamer Eric. G. , Perales Miguel-Angel , Abt Michael C.
Published: September 2019

Background

Monocytes are an essential cellular component of the innate immune system that support the host’s effectivenss to combat a range of infectious pathogens. Hemopoietic cell transplantation (HCT) results in transient monocyte depletion, but the factors that regulate recovery of monocyte populations are not fully understood. In this study, we investigated whether the composition of the gastrointestinal microbiota is associated with the recovery of monocyte homeostasis after HCT.

Methods

We performed a single-center, prospective, pilot study of 18 recipients of either autologous or allogeneic HCT. Serial blood and stool samples were collected from each patient during their HCT hospitalization. Analysis of the gut microbiota was done using 16S rRNA gene sequencing and flow cytometric analysis was used to characterize the phenotypic composition of monocyte populations.

Results

Dynamic fluctuations in monocyte reconstitution occurred after HCT and large differences were observed in monocyte frequency among patients over time. Recovery of absolute monocyte counts and monocyte subsets showed significant variability across the heterogeneous transplant types and conditioning intensities; no relationship to the microbiota composition was observed in this small cohort.

Conclusion

A relationship between the microbiota composition and monocyte homeostasis could not be firmly established in this pilot study.
Anatomical tool in the identification of ploids in maize seedlings and potential use in initial stage of double haploides obtainment process
Authors: Pires Raquel M. O. , Souza Genaina A. , Vilela Danielle R. , Santos Heloisa O. , C.Vasconcellos Renato C. , Von Pinho Édila V. R.
Published: September 2019

Studies that optimize the haploid technique in the removal of maize lines are necessary. Between the stages that mostly requires attention and it is directly related to the success of the technology is the correctly separation of induced haploids and diploids. Morphological markers are commonly used but have strong influence of the environment, and laboratory methods have been developed and may be more efficient. Thus, the objective was to study the use of the anatomical analysis tool, through the analysis of young maize leaf for use as the indirect markers in the identification of ploidys. The hybrids were crossed with the KEMS haploid inducer. The seeds crossed, were selected according to the R-navajo marker and submitted to two different protocols of chromosome duplication. Plants that survived to the duplication protocols were acclimated in greenhouse and then transferred to the field. After the self-polinization of the DH0 plants, the DH1 seeds were taken to the field, divided into treatments according to the parentals and duplication protocols. At the vegetative stage V4 of the plants, leaf tissue samples were collected to the evaluation of the amount of DNA and identification of ploidys and anatomical analysis. The nuclear DNA review of each sample was performed for the comparison in histograms of the position of G1 peak to the G1 peak of the internal or external reference standard. A high accuracy came to validate an anatomical tool, through the variables studied in this work, as a marker in the differentiation of ploidis in maize plants, and it can be used in selection programs. The anatomy made in some letters is a non-destructible technique and, together with a flow cytometry technique, can be used as an indirect method in haploid cutting programs at the initial stage of the identification of seedlings.
Allele-specific miRNA-binding analysis identifies candidate target genes for breast cancer risk
Authors: Jacinta-Fernandes Ana , Xavier Joana M. , Magno Ramiro , Lage Joel G. , Maia Ana-Teresa
Published: September 2019

Most breast cancer (BC) risk-associated variants (raSNPs) identified in genome-wide association studies (GWAS) are believed to cis-regulate the expression of genes. We hypothesise that cis-regulatory variants contributing to disease risk may be affecting miRNA genes and/or miRNA-binding. To test this we adapted two miRNA-binding prediction algorithms — TargetScan and miRanda — to perform allele-specific queries, and integrated differential allelic expression (DAE) and expression quantitative trait loci (eQTL) data, to query 150 genome-wide significant (P ≤ 5 × 10−8) raSNPs, plus proxies. We found that no raSNP mapped to a miRNA gene, suggesting that altered miRNA targeting is an unlikely mechanism involved in BC risk. Also, 11.5% (6 out of 52) raSNPs located in 3’UTRs of putative miRNA target genes were predicted to alter miRNA∷mRNA pair binding stability in five candidate target genes. Of these, we propose RNF115, at locus 1q21.1, as a strong novel target gene associated with BC risk, and re-inforce the role of miRNA mediated cis-regulation at locus 19p13.11. We believe that integrating allele-specific querying in miRNA-binding prediction, and data supporting cis-regulation of expression, improves the identification of candidate target genes in BC risk, as well as in other common cancers and complex diseases.
Lamellipodin tunes cell migration by stabilizing protrusions and promoting adhesion formation
Authors: Dimchev Georgi , Amiri Behnam , Humphries Ashley C. , Schaks Matthias , Dimchev Vanessa , Stradal Theresia E.B. , Faix Jan , Krause Matthias , Way Michael , Falcke Martin , Rottner Klemens
Published: September 2019

Efficient migration on adhesive surfaces involves the protrusion of lamellipodial actin networks and their subsequent stabilization by nascent adhesions. The actin binding protein lamellipodin (Lpd) is thought to play a critical role in lamellipodium protrusion, by delivering Ena/VASP proteins onto the growing plus ends of actin filaments and by interacting with the WAVE regulatory complex (WRC), an activator of the Arp2/3 complex, at the leading edge. Using B16-F1 melanoma cell lines, we demonstrate that genetic ablation of Lpd compromises protrusion efficiency and coincident cell migration without altering essential parameters of lamellipodia, including their maximal rate of forward advancement and actin polymerization. We also confirmed lamellipodia and migration phenotypes with CRISPR/Cas9-mediated Lpd knockout Rat2 fibroblasts, excluding cell type-specific effects. Moreover, computer-aided analysis of cell edge morphodynamics on B16-F1 cell lamellipodia revealed that loss of Lpd correlates with reduced temporal protrusion maintenance as a prerequisite of nascent adhesion formation. We conclude that Lpd optimizes protrusion and nascent adhesion formation by counteracting frequent, chaotic retraction and membrane ruffling.

Summary statement

We describe how genetic ablation of the prominent actin- and VASP-binding protein lamellipodin combined with software-aided protrusion analysis uncovers mechanistic insights into its cellular function during cell migration.
Cryo-EM structure of the RNA-rich plant mitochondrial ribosome
Authors: Waltz Florent , Soufari Heddy , Bochler Anthony , Giegé Philippe , Hashem Yaser
Published: September 2019

The vast majority of eukaryotic cells contain mitochondria, essential powerhouses and metabolic hubs1. These organelles have a bacterial origin and were acquired during an early endosymbiosis event2. Mitochondria possess specialized gene expression systems composed of various molecular machines including the mitochondrial ribosomes (mitoribosomes). Mitoribosomes are in charge of translating the few essential mRNAs still encoded by mitochondrial genomes3. While chloroplast ribosomes strongly resemble those of bacteria4,5, mitoribosomes have diverged significantly during evolution and present strikingly different structures across eukaryotic species6–10. In contrast to animals and trypanosomatides, plants mitoribosomes have unusually expanded ribosomal RNAs and conserved the short 5S rRNA, which is usually missing in mitoribosomes11. We have previously characterized the composition of the plant mitoribosome6revealing a dozen plant-specific proteins, in addition to the common conserved mitoribosomal proteins. In spite of the tremendous recent advances in the field, plant mitoribosomes remained elusive to high-resolution structural investigations, and the plant-specific ribosomal features of unknown structures. Here, we present a cryo-electron microscopy study of the plant 78S mitoribosome from cauliflower at near-atomic resolution. We show that most of the plant-specific ribosomal proteins are pentatricopeptide repeat proteins (PPR) that deeply interact with the plant-specific rRNA expansion segments. These additional rRNA segments and proteins reshape the overall structure of the plant mitochondrial ribosome, and we discuss their involvement in the membrane association and mRNA recruitment prior to translation initiation. Finally, our structure unveils an rRNA-constructive phase of mitoribosome evolution across eukaryotes.
Mitochondria define intestinal stem cell differentiation downstream of a FOXO/Notch axis
Authors: Ludikhuize M.C. , Meerlo M. , Gallego M. Pages , Julià M. Burgaya , Nguyen N.T.B. , Brombacher E. C. , Paik J.H. , Burgering B.M. T. , Rodriguez Colman M.J.
Published: September 2019

Differential signalling of the WNT and Notch pathways regulates proliferation and differentiation of Lgr5+crypt-based columnar cells (CBCs) into all cell lineages of the intestine. We have recently shown that high mitochondrial activity in CBCs is key in maintaining stem cell function. Interestingly, while high mitochondrial activity drives CBCs, it is reduced in the adjacent secretory Paneth cells (PCs). This observation implies that during differentiation towards PCs, CBCs undergo a metabolic rewiring involving downregulation of mitochondrial number and activity, through a hitherto unknown mechanism. Here we demonstrate, using intestinal organoids that FoxO transcription factors and Notch signalling functionally interact in determining CBC cell fate. In agreement with the organoid data, combinedFoxo1and3deletion in mice increases PC number in the intestine. Importantly, we show that FOXO and Notch signalling converge onto regulation of mitochondrial fission, which in turn provokes stem cell differentiation into the secretory types; Goblet cells and PCs. Finally, mapping intestinal stem cell differentiation based on pseudotime computation of scRNA-seq data further supports the role of FOXO, Notch and mitochondria in determining secretory differentiation. This shows that mitochondria is not only a discriminatory hallmark of CBCs and PCs, but that its status actively determines lineage commitment during differentiation. Together, our work describes a new signalling-metabolic axis in stem cell differentiation and highlights the importance of mitochondria in determining cell fate.
Quantification of reactive oxygen species production by the red fluorescent proteins KillerRed, SuperNova and mCherry
Authors: Onukwufor John O. , Trewin Adam J. , Baran Timothy M. , Almast Anmol , Foster Thomas H. , Wojtovich Andrew P.
Published: September 2019

Fluorescent proteins can generate reactive oxygen species (ROS) upon absorption of photons via type I and II photosensitization mechanisms. The red fluorescent proteins KillerRed and SuperNova are phototoxic proteins engineered to generate ROS and are used in a variety of biological applications. However, their relative quantum yields and rates of ROS production are unclear, which has limited the interpretation of their effects when used in biological systems. We cloned and purified KillerRed, SuperNova, and mCherry - a related red fluorescent protein not typically considered a photosensitizer - and measured the superoxide (O2•-) and singlet oxygen (1O2) quantum yields with irradiation at 561 nm. The formation of the O2•--specific product 2-hydroxyethidium (2-OHE+) was quantified via HPLC separation with fluorescence detection. Relative to a reference photosensitizer, Rose Bengal, the O2•- quantum yield (ΦO2•-) of SuperNova was determined to be 0.00150, KillerRed was 0.00097, and mCherry 0.00120. At an excitation fluence of 916.5 J/cm2 and matched absorption at 561 nm, SuperNova, KillerRed and mCherry made 3.81, 2.38 and 1.65 μM O2•-/min, respectively. Using the probe Singlet Oxygen Sensor Green (SOSG), we ascertained the 1O2 quantum yield (Φ1O2) for SuperNova to be 0.0220, KillerRed 0.0076, and mCherry 0.0057. These photosensitization characteristics of SuperNova, KillerRed and mCherry improve our understanding of fluorescent proteins and are pertinent for refining their use as tools to advance our knowledge of redox biology.

GRAPHICAL ABSTRACT
Social isolation impacts late-life socio-cognitive decline in APP/PS1 mice
Authors: Rens Eva , D’Hooge Rudi , Van der Jeugd Ann
Published: September 2019

In this study the effects of social isolation (SI) were investigated in APP/PS1 mice. It was found that SI during adolescence has an impact on anxiogenic behaviour, such that isolated animals tend to explore a threatening environment less than non-isolated animals as assessed with the EPM test, and that this holds for both AD and non-AD mice. While no evidence was found for any differences in short-term memory as assessed by the Y-maze, long-term memory seemed to be affected in a context-dependent manner. Object memory as assessed with the NOR test was affected in APP/PS1 mice compared to WT mice, but this deficit was not induced or influenced by SI. When it comes to social recognition memory however, we found that SI exacerbated the social memory deficit in AD mice, and even induced a deficit in WTs. Associative fear memory as assessed with the PA test suggested that WTs perform better when group housed, and APP/PS1 mice better when socially isolated. The link between isolation and AD, or cognition in general, may be more complex than initially thought. The effect of isolation may not be the same for AD versus non-AD subjects.