bluuebunny/crossref_metadata_2025 huggingface dataset:
Revealing the information contents of memory within the stimulus information representation framework
Authors: Schyns Philippe G. , Zhan Jiayu , Jack Rachael E. , Ince Robin A. A.
Published: April 2020

The information contents of memory are the cornerstone of the most influential models in cognition. To illustrate, consider that in predictive coding, a prediction implies that specific information is propagated down from memory through the visual hierarchy. Likewise, recognizing the input implies that sequentially accrued sensory evidence is successfully matched with memorized information (categorical knowledge). Although the existing models of prediction, memory, sensory representation and categorical decision are all implicitly cast within an information processing framework, it remains a challenge to precisely specify
what
this information is, and therefore
where
,
when
and
how
the architecture of the brain dynamically processes it to produce behaviour. Here, we review a framework that addresses these challenges for the studies of perception and categorization–stimulus information representation (SIR). We illustrate how SIR can reverse engineer the information contents of memory from behavioural and brain measures in the context of specific cognitive tasks that involve memory. We discuss two specific lessons from this approach that generally apply to memory studies: the importance of task, to constrain what the brain does, and of stimulus variations, to identify the specific information contents that are memorized, predicted, recalled and replayed.

This article is part of the Theo Murphy meeting issue ‘Memory reactivation: replaying events past, present and future’.
A consensus statement: defining terms for reactivation analysis
Authors: Genzel Lisa , Dragoi George , Frank Loren , Ganguly Karunesh , de la Prida Liset , Pfeiffer Brad , Robertson Edwin
Published: April 2020

During a two-day Royal Society meeting entitled ‘
Memory reactivation: replaying events past, present and future
’ held at Chicheley Hall in May, 2019, we discussed and defined a set of terms for investigating and reporting in memory reactivations to facilitate a common language and thus simplifying comparison of results. Here, we present the results of the discussion and supply a set of terms such as reactivation and replay, for which the authors have reached a common consensus.

This article is part of the Theo Murphy meeting issue ‘Memory reactivation: replaying events past, present and future’.
Profiles and clinical significance of immune cell infiltration in pancreatic adenocarcinoma
Authors: Mei Jie , Xu Rui , Xia Dandan , Yang Xuejing , Wang Huiyu , Liu Chaoying
Published: April 2020

Background

It has been well defined that tumor-infiltrating immune cells (TIICs) play critical roles in pancreatic cancer (PAAD) progression. The aim of this research was to comprehensively explore the composition of TIICs in PAAD and their potential clinical significance.

Methods

178 samples from TCGA and 63 samples from GSE57495 dataset were enrolled into our study. ImmuCellAI was applied to calculate the infiltrating abundance of 24 immune cell types in PAAD and further survival analysis revealed the prognostic values of TIICs in PAAD. Moreover, Gene ontology (GO) enticement analysis of differentially expressed genes (DEGs) between low- and high-risk groups was performed as well.

Results

Different kinds of TIICs had distinct infiltrating features. Besides, Specific TIICs subsets had notable prognostic values in PAAD. We further established a 6-TIICs signature to assess the prognosis of PAAD patients. Kaplan-Meier and Cox regression analyses both suggested the significant prognostic value of the signature in PAAD. We next extracted 1,334 DEGs based on the risk model, and the hub modules in the protein-protein interaction (PPI) network of DEGs were involved in regulating immune-related biological processes.

Conclusions

Overall, the current study illuminated the immune cells infiltrating landscape in PAAD and developed a TIICs-dependent prognostic signature, which could be used as an effective prognostic classifier for PAAD patients.
In-silicoanalysis of SARS-CoV-2 genomes: Insights from SARS encoded non-coding RNAs
Authors: Periwal Neha , Sarma Sankritya , Arora Pooja , Sood Vikas
Published: April 2020

Recently a novel coronavirus (SARS-CoV-2) emerged from Wuhan, China and has infected more than 571000 people leading to more than 26000 deaths. Since SARS-CoV-2 genome sequences show similarity with those of SARS, we sought to analyze all the available SARS-CoV-2 genomes based on the insights obtained from SARS genome specifically focusing on non-coding RNAs. Here, results are presented from the dual approach i.e identifying host encoded miRNAs that might regulate viral pathogenesis as well as identifying viral encoded miRNAs that might regulate host cell signaling pathways and aid in viral pathogenesis. Analysis utilizing first approach resulted in the identification of 10 host encoded miRNAs that could target the genome of both the viruses (SARS-CoV-2 and SARS reference genome). Interestingly our analysis revealed that there is significantly higher number of host miRNAs that could target SARS-CoV-2 genome as compared to the SARS reference genome. Results from second approach involving SARS-CoV-2 and SARS reference genome identified a set of virus encoded miRNAs which might regulate host signaling pathways. Our analysis further identified a similar “GA” rich motif in SARS-CoV-2 genome that was shown to play a vital role in lung pathogenesis during severe SARS infections. Hence, we successfully identified human and virus encoded miRNAs that might regulate pathogenesis of both these coronaviruses and the fact that more number of host miRNAs could target SARS-CoV-2 genomes possibly reveal as to why this virus follows mild pathogenesis in healthy individuals. We identified non-coding sequences in SARS-CoV-2 genomes that were earlier reported to contribute towards SARS pathology. The study provides insights into the overlapping sequences among these viruses for their effective inhibition as well as identifying new drug targets that could be used for development of new antivirals.
Fatal toxicity of chloroquine or hydroxychloroquine with metformin in mice
Authors: Rajeshkumar N.V , Yabuuchi Shinichi , Pai Shweta G. , Maitra Anirban , Hidalgo Manuel , Dang Chi V.
Published: April 2020

Guided by the principle ofprimum non nocere(first do no harm), we report a cautionary note on the potential fatal toxicity of chloroquine (CQ) or hydroxychloroquine (HCQ) in combination with anti-diabetic drug metformin. We observed that the combination of CQ or HCQ and metformin, which were used in our studies as potential anti-cancer drugs, killed 30-40% of mice. While our observations in mice may not translate to toxicity in humans, the reports that CQ or HCQ has anti-COVID-19 activity, the use of CQ resulting in toxicity and at least one death, and the recent Emergency Use Authorization (EUA) for CQ and HCQ by the US Food and Drug Administration (FDA) prompted our report. Here we report the lethality of CQ or HCQ in combination with metformin as a warning of its potential serious clinical toxicity. We hope that our report will be helpful to stimulate pharmacovigilance and monitoring of adverse drug reactions with the use of CQ or HCQ, particularly in combination with metformin.
Decrease inACE2mRNA expression in aged mouse lung
Authors: Booeshaghi A. Sina , Pachter Lior
Published: April 2020

Angiotensin-converting enzyme 2 (ACE2) has been identified as a critical receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This has led to extensive speculation on the role ofACE2in disease severity, and in particular, whether variation in its expression can explain higher mortality in older individuals. We examine this question in mouse lung and show that 24-month old mice have significantly reducedACE2mRNA expression relative to 3-month old mice. The differences appear to be localized to ciliated cells.
Functional maturation of the gut microbiota at weaning is influenced by maternal environment in piglets
Authors: Beaumont Martin , Cauquil Laurent , Bertide Allan , Ahn Ingrid , Barilly Céline , Gil Lisa , Canlet Cécile , Zemb Olivier , Pascal Géraldine , Samson Arnaud , Combes Sylvie
Published: April 2020

The objective of this study was to analyze in piglets the impact of weaning on the production of metabolites by gut bacteria and to determine whether early life environment influences the functional maturation of the gut microbiota. Fecal metabolome and microbiome were analyzed in piglets raised in two separate maternity farms and mixed at weaning. In piglets from both maternity farms, the relative abundance ofLactobacillusand of the predicted function “Fucose degradation” decreased after weaning while the relative abundance ofRuminococcus 2and of the predicted function “Starch degradation” increased. In piglets from the first maternity farm, the relative concentration of biogenic amines and the relative abundance ofEscherichi-Shigelladecreased after weaning while the relative concentration of short chain fatty acids and the relative abundance ofChristensenellaceae R-7 groupandRuminococcaceae UCG-002increased. These changes were not observed at weaning in piglets from the second maternity farm probably because they already had high relative concentration of short chain fatty acids and higher relative abundance ofChristensenellaceae R-7 groupandRuminococcaceae UCG-002during the suckling period. In conclusion, the functional maturation of the microbiota at weaning is highly dependent on the maternal environment in piglets.

ORIGINALITY - SIGNIFICANCE STATEMENT

Bacterial metabolites are key molecular intermediates between the gut microbiota and host cells. Our study in piglets reveals that the metabolic activity of the gut microbiota shifts at weaning, a key developmental period for intestinal and immune health. We also show that this functional maturation of the gut microbiota is strongly influenced by maternal environment. Thus, targeting early life environmental factors is a promising strategy to program health trough the production of beneficial bacterial metabolites at the suckling-to-weaning transition.
Detecting genetic variation and base modifications together in the same single molecules of DNA and RNA at base pair resolution using a magnetic tweezer platform
Authors: Wang Zhen , Maluenda Jérôme , Giraut Laurène , Vieille Thibault , Lefevre Andréas , Salthouse David , Radou Gaël , Moulinas Rémi , Astete-Morales Sandra , d’Avezac Pol , Smith Geoff , André Charles , Allemand Jean-François , Bensimon David , Croquette Vincent , Ouellet Jimmy , Hamilton Gordon
Published: April 2020

Accurate decoding of nucleic acid variation is important to understand the complexity and regulation of genome function. Here we introduce a single-molecule platform based on magnetic tweezer (MT) technology that can identify and map the positions of sequence variation and multiple base modifications together in the same single molecules of DNA or RNA at single base resolution. Using synthetic templates, we demonstrate that our method can distinguish the most common epigenetic marks on DNA and RNA with high sensitivity, specificity and precision. We also developed a highly specific CRISPR-Cas enrichment strategy to target genomic regions in native DNA without amplification. We then used this method to enrich native DNA from E. coli and characterized the differential levels of adenine and cytosine base modifications together in molecules of up to 5 kb in length. Finally, we enriched the 5‘UTR of FMR1 from cells derived from a Fragile X carrier and precisely measured the repeat expansion length and methylation status of each molecule. These results demonstrate that our platform can detect a variety of genetic, epigenetic and base modification changes concomitantly within the same single molecules.
Non-Canonical Targets of HIF1a Drive Cell-Type-Specific Dysfunction
Authors: Allan Kevin C. , Hu Lucille R. , Morton Andrew R. , Scavuzzo Marissa A. , Gevorgyan Artur S. , Clayton Benjamin L.L. , Bederman Ilya R. , Hung Stevephen , Bartels Cynthia F. , Madhavan Mayur , Tesar Paul J.
Published: April 2020

All mammalian cells sense and respond to insufficient oxygen, or hypoxia, through the activity of hypoxia-inducible factors (HIFs), an evolutionarily conserved family of transcriptional regulators that promote oxygen-independent energy metabolism and angiogenesis. While HIF activation is transiently protective for all cells, prolonged HIF activity drives distinct pathological responses in different tissues. How HIF achieves this pleiotropic effect is largely unknown. Here, we demonstrate that non-canonical targets of HIF1a impair the function of oligodendrocyte progenitor cells (OPCs) to generate oligodendrocytes. Beyond the canonical gene targets shared between all cell types, HIF1a also bound to and activated a unique set of targets in OPCs includingAscl2andDlx3. Each of these targets, when ectopically expressed, was sufficient to block oligodendrocyte development through suppression of the key oligodendrocyte regulatorSox10. Chemical screening revealed that inhibition of MEK/ERK signaling overcame the HIF1a-mediated block in oligodendrocyte generation by restoringSox10expression without impacting canonical HIF1a activity. Collectively this work defines the mechanism by which chronic HIF1a suppresses oligodendrocyte formation. More broadly, we establish that cell-type-specific HIF1a targets, independent of the canonical hypoxia response, perturb cell function and drive disease in chronic hypoxia.
Revealing Cellular Heterogeneity andIn VitroDifferentiation Trajectory of Cultured Human Endometrial Mesenchymal-like Stem Cells Using Single-cell RNA Sequencing
Authors: Cao Dandan , Chan Rachel W.S. , Ng Ernest H.Y. , Gemzell-Danielsson Kristina , Yeung William S.B.
Published: April 2020

Endometrial mesenchymal-like stem cells (eMSCs) are adult stem cells contributing to endometrial regeneration. One set of perivascular markers (CD140b+CD146+) have been widely used to enrich eMSCs. Although eMSCs are easily accessible for regenerative medicine and have long been studied, their cellular heterogeneity and molecular program controlling their expansion and differentiation in vitro remains largely unclear. In this study, we applied 10X genomics single-cell RNA sequencing to eMSCs cultured in vitro after microbeading from 7 donors to investigate cellular heterogeneity in an unbiased manner. Corresponding clonogenic progenies of eMSCs after culture for 14 days were also sequenced to construct the in vitro differentiation trajectory of eMSCs. Transcriptomic expression based clustering revealed several subpopulations in eMSCs. Each subpopulation manifested distinct functional characteristics associated with immunomodulation, proliferation, extracellular matrix organization and cell differentiation. Pseudotime trajectory analysis on eMSCs and their differentiated progenies identifiedin vitrodifferentiation hierarchy of eMSCs. Further ligand-receptor pair analysis found that WNT signaling, NOTCH signaling, TGF-beta signaling and FGF signaling were important regulatory pathways for eMSC self-renewal and differentiation. By comparing eMSCs to Wharton’s Jelly MSCs and adipose-derived MSCs, we found these 3 kinds of MSCs expressed largely overlapping differentiation (CD) genes and highly variable genes. In summary, we reveal for the first time high molecular and cellular heterogeneity in cultured eMSCs, and identify the key signaling pathways that may be important for eMSC differentiation.
Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis
Authors: Kelly Jenna N. , Laloli Laura , V’kovski Philip , Holwerda Melle , Portmann Jasmine , Thiel Volker , Dijkman Ronald
Published: April 2020

Respiratory viruses, such as the 2009 pandemic strain of influenza A virus (IAV, H1N1pdm09), target cells found in the human respiratory epithelium. These cells, which form a pseudostratified epithelial layer along the airways, constitute the first line of defence against respiratory pathogens and play a crucial role in the host antiviral response. However, despite their key role in host defence, it remains unknown how distinct cell types in the respiratory epithelium respond to IAV infection and how these responses may contribute to IAV-induced pathogenesis and overall disease outcome. Here, we used single cell RNA-sequencing (scRNA-seq) to dissect the host response to IAV infection in its natural target cells. scRNA-seq was performed on human airway epithelial cell (hAEC) cultures infected with either wild-type pandemic IAV (WT) or with a mutant version of IAV (NS1R38A) that induced a robust innate immune response. We then characterized both the host and viral transcriptomes of more than 19,000 single cells across the 5 major cell types populating the human respiratory epithelium. For all cell types, we observed a wide spectrum of viral burden among single infected cells and a disparate host response between infected and bystander populations. Interestingly, we also identified multiple key differences in the host response to IAV among individual cell types, including high levels of pro-inflammatory cytokines and chemokines in secretory and basal cells and an important role for luminal cells in sensing and restricting incoming virus. Multiple infected cell types were shown to upregulate interferons (IFN), with type III IFNs clearly dominating the antiviral response. Transcriptional changes in genes related to cell differentiation, cell migration, and tissue repair were also identified. Strikingly, we also detected a shift in viral host cell tropism from non-ciliated cells to ciliated cells at later stages of infection and observed major changes in the cellular composition. Microscopic analysis of both WT and NS1R38Avirus-infected hAECs at various stages of IAV infection revealed that the transcriptional changes we observed at 18 hpi were likely driving the downstream histopathological alterations in the airway epithelium. To our knowledge, this is the first study to provide a comprehensive analysis of the cell type-specific host antiviral response to a respiratory virus infection in its natural target cells – namely, the human respiratory epithelium.
Melatonin alters fluid phase co-existence in POPC/DPPC/cholesterol membranes
Authors: Mei Nanqin , Robinson Morgan , Davis James H. , Leonenko Zoya
Published: April 2020

The structure and biophysical properties of lipid biomembranes are important for normal function of plasma and organelle membranes, which is essential for proper functioning of living cells. In Alzheimer’s disease (AD) the structure of neuronal membranes becomes compromised by the toxic effect of amyloid-β(Aβ) protein which accumulates at neuron synapses, resulting in membrane perforation and dysfunction, oxidative stress and cell death. Melatonin is an important pineal gland hormone that has been shown to be protective against Aβtoxicity in cellular and animal studies, but the molecular mechanism of this protection is not well understood. It has been shown that melatonin can interact with model lipid membranes and alter the membrane biophysical properties, such as membrane molecular order and dynamics. This effect of melatonin has been previously studied in simple model bilayers with one or two lipid components, we consider a more complex ternary lipid mixture as our membrane model. In this study, we used2H-NMR to investigate the effect of melatonin on lipid phase behaviour of a three-component model lipid membranes composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and cholesterol. We used deuterium labelled palmitoyl-d31in POPC-d31and DPPC-d62separately, to probe the changes in hydrocarbon chain order as a function of temperature and varying concentrations of melatonin. We found that melatonin concentration influences phase separation in these ternary mixtures somewhat differently depending on whether POPC-d31or DPPC-d62was used. At 5 mol% melatonin we observed phase separation in samples with POPC-d31, but not with DPPC-d62. However, at 10 mol% melatonin phase separation was observed in both samples with either POPC-d31or DPPC-d62. These results indicate that melatonin can have a strong effect on membrane structure and physical properties, which may provide some clues to understanding how melatonin protects against Aβ.

SIGNIFICANCE

Melatonin has been shown to be protective against Aβpathology in animal and cellular studies. Although the mechanism of this protection is not well-understood, melatonin’s membrane-active properties may be important in this regard. In this work solid-state deuterium nuclear magnetic resonance was used to study the effect of melatonin on the POPC/DPPC/cholesterol model membranes. Specifically, we showed that melatonin modifies lipid hydrocarbon chain order to promote phase separation. This knowledge helps to explain the role of melatonin in lipid domain formation and may provide a deeper understanding of the mechanism of melatonin neuroprotection in AD.
Mice carrying paternal knockout of imprintedGrb10do not show compulsive behaviour
Authors: Rienecker Kira DA , Chavasse Alexander T , Moorwood Kim , Ward Andrew , Humby Trevor , Isles Anthony R
Published: April 2020

Mice lacking paternal expression of imprintedGrb10show a number of social behaviour deficits, including an enhanced allogrooming phenotype. However, this could also index compulsive behaviour, and the increased whisker barbering seen inGrb10+/pmice has been suggested to be indicative of a trichotillomania-type behaviour. Here we test whether compulsive behaviour is a more general phenotype inGrb10+/pmice by examining marble burying. We also examined the mice for potentially confounding anxiety phenotypes using the elevated plus maze (EPM).Grb10+/pmice showed no difference from wild-type littermate controls on any measure in the marble burying test at any age. However,Grb10+/pmice were more willing to enter, spend time on, and head-dip on the open arm of the EPM than wild-type mice. These data suggest thatGrb10+/pmice are not generally more compulsive, and that the enhanced allogrooming is probably indicative of altered social behaviour. Furthermore, the altered behaviours seen on the EPM adds to other published findings suggesting thatGrb10has a role in mediating risk-taking.
Stroma transcriptomic and proteomic profile of prostate cancer metastasis xenograft models reveals conservation of bone microenvironment signatures
Authors: Karkampouna S. , De Filippo M.R. , Ng C.Y. , Klima I. , Zoni E. , Spahn M. , Stein F. , Haberkant P. , Thalmann G.N. , de Julio M.Kruithof
Published: April 2020

Prostate cancer (PCa) is the second leading cause of cancer-associated death in men with therapy resistance acquisition to androgen deprivation treatment and metastasis progression. Understanding the mechanisms of tumor progression to metastatic stage is necessary for the design of therapeutic and prognostic schemes. The main objective of the current study is to determine, using transcriptomic and proteomic analyses on patient derived-xenograft models, whether differentially aggressive PCa tumors predispose their microenvironment (stroma) to a metastatic gene expression pattern, and how this information could be applied in prognostics. Transcriptomic profiling (RNA Sequencing) was performed on PCa PDX models representing different disease stages; BM18 (androgen dependent bone metastasis) and LAPC9 (androgen independent bone metastasis). Using organism-specific reference databases, the human-specific transcriptome, representing the tumor, was identified and separated from the mouse-specific transcriptome (representing the contributing stroma counterpart) from the same PDX tumor samples. To identify proteome changes in the tumor (human) versus the stroma (mouse), we performed human and mouse cell separation using the MACS mouse depletion sorting kit, and subjected protein lysates to quantitative TMT labeling and mass spectrometry. We show that tenascin C is one of the most abundant stromal genes in bone metastasis PCa PDXs, is modulated by androgen levelsin vivoand is highly expressed in castration resistant LAPC9 PDX compared to castration sensitive BM18 PDX. Tissue microarray of primary PCa samples (N=210) was used to evaluate the potential of TNC to act as a metastasis prognosis marker. Low number of TNC-positive cells were associated with statistically significant clinical progression to local recurrence or metastasis, compared to high TNC-positive group. Our data showed that metastatic PCa PDXs that differ in androgen sensitivity trigger a differential stroma response suggesting that stroma was influenced by tumor cues. Selected stromal markers of osteoblastic PCa induced bone metastases, were induced in the microenvironment of the host organism in metastatic xenografts, although implanted in a non-bone site, indicating a conserved mechanism of tumor cells to induce a stromal pre-metastatic signature with high potential prognostic or diagnostic value.
Membrane Elastic Properties During Neural Progenitor/Neural Stem Cell Differentiation
Authors: Soares Juliana , de S. Araujo Glauber R. , Santana Cintia , Matias Diana , Moura-Neto Vivaldo , Farina Marcos , Frases Susana , Viana Nathan B. , Romão Luciana , Nussenzveig H. Moysés , Pontes Bruno
Published: April 2020

Neural stem cells differentiate into several cell types that display distinct functions. However, little is known about how cell surface mechanics vary during the differentiation process. Here, by precisely measuring membrane tension and bending modulus, we map their variations and correlate them with changes in cell morphology along differentiation into neurons, astrocytes and oligodendrocytes. Both neurons and undifferentiated cells reveal a decrease in membrane tension over the first hours of differentiation followed by stabilization, with no change in bending modulus. Astrocytes membrane tension initially decreases and then increases after 72h, accompanied by consolidation of GFAP expression and striking actin reorganization, while bending modulus increases following observed alterations. For oligodendrocytes, the changes in membrane tension are less abrupt over the first hours but their values subsequently decrease, correlating with a shift from O4 to MBP expressions and a remarkable actin reorganization, while bending modulus remains constant. Oligodendrocytes at later differentiation stages show membrane vesicles with similar membrane tension but higher bending modulus as compared to the cell surface. Altogether, our results display an entire spectrum of how membrane elastic properties are varying, contributing to a better understanding of neural stem cell differentiation from a mechanobiological perspective.
Real-time biomedical knowledge synthesis of the exponentially growing world wide web using unsupervised neural networks
Authors: Wagner Tyler , Awasthi Samir , Wittenberg Gayle , Venkatakrishnan AJ , Tarjan Dan , Anyanwu-Ofili Anuli , Badley Andrew , Halamka John , Flores Christopher , Khan Najat , Barve Rakesh , Soundararajan Venky
Published: April 2020

Decoding disease mechanisms for addressing unmet clinical need demands the rapid assimilation of the exponentially growing biomedical knowledge. These are either inherently unstructured and non-conducive to current computing paradigms or siloed into structured databases requiring specialized bioinformatics. Despite the recent renaissance in unsupervised neural networks for deciphering unstructured natural languages and the availability of numerous bioinformatics resources, a holistic platform for real-timesynthesisof the scientific literature and seamless triangulation with deep omic insights and real-world evidence has not been advanced. Here, we introduce the nferX platform that makes the highly unstructured biomedical knowledge computable and supports the seamless visualtriangulationwith statistical inference from diverse structured databases. The nferX platform will accelerate and amplify the research potential of subject-matter experts as well as non-experts across the life science ecosystem (https://academia.nferx.com/).
The primary donor of far-red Photosystem II: ChlD1or PD2?
Authors: Judd Martyna , Morton Jennifer , Nürnberg Dennis , Fantuzzi Andrea , Rutherford A. William , Purchase Robin , Cox Nicholas , Krausz Elmars
Published: April 2020

Far-red light (FRL) Photosystem II (PSII) isolated fromChroococcidiopsis thermalisis studied using parallel analyses of low-temperature absorption, circular dichroism (CD) and magnetic circular dichroism (MCD) spectroscopies in conjunction with fluorescence measurements. This extends earlier studies (Nurnberget al2018 Science 360 (2018) 1210-1213). We confirm that the chlorophyll absorbing at 726 nm is the primary electron donor. At 1.8 K efficient photochemistry occurs when exciting at 726 nm and shorter wavelengths; but not at wavelengths longer than 726 nm. The 726 nm absorption peak exhibits a 21 ± 4 cm−1electrochromic shift due to formation of the semiquinone anion, QA•-. Modelling indicates that no other FRL pigment is located among the 6 central reaction center chlorins: PD1, PD2ChlD1, ChlD2, PheoD1and PheoD2. Two of these chlorins, ChlD1and PD2, are located at a distance and orientation relative to QA•-so as to account for the observed electrochromic shift. Previously, ChlD1was taken as the most likely candidate for the primary donor based on spectroscopy, sequence analysis and mechanistic arguments. Here, a more detailed comparison of the spectroscopic data with exciton modelling of the electrochromic pattern indicates that PD2is at least as likely as ChlD1to be responsible for the 726 nm absorption. The correspondence in sign and magnitude of the CD observed at 726 nm with that predicted from modelling favors PD2as the primary donor. The pros and cons of PD2vs ChlD1as the location of the FRL-primary donor are discussed.

TOC Graphic

Highlights

Primary Donor confirmed at 726 nm

Determination of far-red chl pigment Qyexcitation positions, widths, CD and MCD amplitudes

Quantification of electrochromic shifts and QA•-photoconversion yield

Electrochromic shift consistent with primary donor at either ChlD1or PD2

The CD amplitude favors the primary donor at PD2
Genomic Epidemiology with Mixed Samples
Authors: Mäklin Tommi , Kallonen Teemu , Alanko Jarno , Samuelsen Ørjan , Hegstad Kristin , Mäkinen Veli , Corander Jukka , Heinz Eva , Honkela Antti
Published: April 2020

Genomic epidemiology is a tool for tracing transmission of pathogens based on whole-genome sequencing. We introduce the mGEMS pipeline for genomic epidemiology with plate sweeps representing mixed samples of a target pathogen, skipping the colony pick step. The pipeline includes the novel mGEMS read binner for probabilistic assignments of sequencing reads, and the scalable pseudoaligner Themisto. We demonstrate the effectiveness of our approach using closely related samples in a nosocomial setting, obtaining results that are comparable to those based on colony picks. Our results lend firm support to more widespread consideration of genomic epidemiology with mixed infection samples.
Multi-dimensional tuning in motor cortical neurons during active behavior
Authors: Yuan Rachel C. , Bottjer Sarah W.
Published: April 2020

A region within songbird cortex, AId (dorsal intermediate arcopallium), is functionally analogous to motor cortex in mammals and has been implicated in vocal learning during development. AId thus serves as a powerful model for investigating motor cortical contributions to developmental skill learning. We made extracellular recordings in AId of freely behaving juvenile zebra finches and evaluated neural activity during diverse motor behaviors throughout entire recording sessions, including song production as well as hopping, pecking, preening, fluff-ups, beak interactions with cage objects, scratching, and stretching. A large population of single neurons showed significant modulation of activity during singing relative to quiescence. In addition, AId neurons demonstrated heterogeneous response patterns that were evoked during multiple movements, with single neurons often demonstrating excitation during one movement type and suppression during another. Lesions of AId do not disrupt vocal motor output or impair generic movements, suggesting that the responses observed during active behavior do not reflect direct motor drive. Consistent with this idea, we found that some AId neurons showed differential activity during pecking movements depending on the context in which pecks occurred, suggesting that AId circuitry encodes diverse inputs beyond generic motor parameters. Moreover, we found evidence of neurons that did not respond during discrete movements but were nonetheless modulated during active behavioral states compared to quiescence. Taken together, our results support the idea that AId neurons are involved in sensorimotor integration of external sensory inputs and/or internal feedback cues to help modulate goal-directed behaviors.

SIGNIFICANCE STATEMENT

Motor cortex across taxa receives highly integrated, multi-modal information and has been implicated in both execution and acquisition of complex motor skills, yet studies of motor cortex typically employ restricted behavioral paradigms that target select movement parameters, preventing wider assessment of the diverse sensorimotor factors that can affect motor cortical activity. Recording in AId of freely behaving juvenile songbirds that are actively engaged in sensorimotor learning offers unique advantages for elucidating the functional role of motor cortical neurons. The results demonstrate that a diverse array of factors modulate motor cortical activity and lay important groundwork for future investigations of how multi-modal information is integrated in motor cortical regions to contribute to learning and execution of complex motor skills.
A Mechanistic Investigation into Ischemia-Driven Distal Recurrence of Glioblastoma
Authors: Curtin Lee , Hawkins-Daarud Andrea , Porter Alyx B. , van der Zee Kristoffer G. , Owen Markus R. , Swanson Kristin R.
Published: April 2020

Glioblastoma (GBM) is the most aggressive primary brain tumor with a short median survival. Tumor recurrence is a clinical expectation of this disease and usually occurs along the resection cavity wall. However, previous clinical observations have suggested that in cases of ischemia following surgery, tumors are more likely to recur distally. Through the use of a previously established mechanistic model of GBM, the Proliferation Invasion Hypoxia Necrosis Angiogenesis (PIHNA) model, we explore the phenotypic drivers of this observed behavior. We have extended the PIHNA model to include a new nutrient-based vascular efficiency term that encodes the ability of local vasculature to provide nutrients to the simulated tumor. The extended model suggests sensitivity to a hypoxic microenvironment and the inherent migration and proliferation rates of the tumor cells are key factors that drive distal recurrence.
Sleep spindles preferentially consolidate weakly encoded memories
Authors: Denis Dan , Mylonas Dimitrios , Poskanzer Craig , Bursal Verda , Payne Jessica D. , Stickgold Robert
Published: April 2020

Sleep has been shown to be critical for memory consolidation, with some research suggesting that certain memories are prioritized for consolidation. Initial strength of a memory appears to be an important boundary condition in determining which memories are consolidated during sleep. However, the role of consolidation-mediating oscillations, such as sleep spindles and slow oscillations, in this preferential consolidation has not been explored. Here, 54 human participants (76% female) studied pairs of words to three distinct encoding strengths, with recall being tested immediately following learning and again six hours later. Thirty-six had a two-hour nap opportunity following learning, whilst the remaining 18 remained awake throughout. Results showed that across six hours awake, weakly encoded memories deteriorated the fastest. In the nap group however, this effect was attenuated, with forgetting rates equivalent across encoding strengths. Within the nap group, consolidation of weakly encoded items was associated with fast sleep spindle density during non-rapid eye movement sleep. Moreover, sleep spindles that were coupled to slow oscillations predicted the consolidation of weak memories independently of uncoupled sleep spindles. These relationships were unique to weakly encoded items, with spindles not correlating with memory for intermediate or strong items. This suggests that sleep spindles facilitate memory consolidation, guided in part by memory strength.

Significance statement

Given the countless pieces of information we encode each day, how does the brain select which memories to commit to long-term storage? Sleep is known to aid in memory consolidation, and it appears that certain memories are prioritized to receive this benefit. Here, we found that compared to staying awake, sleep was associated with better memory for weakly encoded information. This suggests that sleep helps attenuate the forgetting of weak memory traces. Fast sleep spindles, a hallmark oscillation of non-rapid eye movement sleep, mediate consolidation processes. We extend this to show that fast spindles were uniquely associated with the consolidation of weakly encoded memories. This provides new evidence for preferential sleep-based consolidation and elucidate a physiological correlate of this benefit.
The lateral entorhinal cortex is a hub for local and global dysfunction in pre-tauopathy states
Authors: Mandino Francesca , Yeow Ling Yun , Bi Renzhe , Sejin Lee , Bae Han Gyu , Baek Seung Hyun , Lee Chun-Yao , Mohammad Hasan , Teoh Chai Lean , Horien Corey , Lee Jasinda H. , Lai Mitchell K. P. , Jung Sangyong , Fu Yu , Olivo Malini , Gigg John , Grandjean Joanes
Published: April 2020

Functional network activity alterations are one of the earliest hallmarks of Alzheimer’s disease (AD), detected prior to amyloidosis and tauopathy. Better understanding the neuronal underpinnings of such network alterations could offer mechanistic insight into AD progression. Here, we examined a mouse model (early-tauopathy 3xTgAD mice) recapitulating this early AD stage. We found resting functional connectivity loss within ventral networks, including the entorhinal cortex, aligning with the spatial distribution of tauopathy reported in humans. Unexpectedly, in contrast to decreased connectivity at rest, 3xTgAD mice show enhanced fMRI signal within several projection areas following optogenetic activation of the entorhinal cortex. We corroborate this finding by demonstrating neuronal facilitation within ventral networks and synaptic hyperexcitability in projection targets. 3xTgAD mice thus reveal a dichotomic hypo-connected resting/hyper-responsive active phenotype. The strong homotopy between the areas affected supports the translatability of this pathophysiological model to tau-related deficits in humans.
Maternal phylogenetic relationships and genetic variation among rare similar phenotype donkey breeds
Authors: Mazzatenta Andrea , Caputo Maurizio , De Sanctis Francesco , Mirò Roig Jordi , Robbe Domenico , Carluccio Augusto
Published: April 2020

Maternal inheritance is an indispensable aspect in donkey rare breed population biodiversity management and breeding programs. It is a challenge to characterize breeds genetic inheritance using morphology and historical records, we study mtDNA, to overcome those limitations. The mitochondrial DNA (mtDNA) sequencing is a highly informative system to investigate maternal lineages and breed linkage such as molecular evolution and phylogenetic relationships. Martina Franca, Ragusano, Pantesco and Catalonian donkey mtDNA sequencing analyses were used to study intraspecific genetic diversity and population structure, and to reconstruct phylogenetic relations among these geographically isolated breeds.

A wide lost in variability among all breeds emerged. In this scenario, the primeval haplotypes, higher haplogroups variability and larger number of maternal lineages are preserved in Martina Franca and Ragusano. Accordingly, a putative pivotal role in the phyletic relationship is likely for such breeds.

Given the level of endangerment undergone by these breeds, some actions are necessary to ensure their longtime survival and conservation. Improving the reproduction and management of existing populations, clarifying their historic interactions by studying the genetic status of their populations, extending and improving monitoring maternal lineages represent valid options.
A single-cell gene regulatory network inference method for identifying complex regulatory dynamics across cell phenotypes
Authors: Peng Jianhao , Serrano Guillermo , Traniello Ian M. , Calleja-Cervantes Maria E. , Chembazhi Ullas V. , Bangru Sushant , Ezponda Teresa , Rodriguez-Madoz Juan Roberto , Kalsotra Auinash , Prosper Felipe , Ochoa Idoia , Hernaez Mikel
Published: April 2020

Single-cell RNA-Sequencing has made it possible to infer high-resolution gene regulatory networks (GRNs), providing deep biological insights by revealing regulatory interactions at single-cell resolution. However, current single-cell GRN analysis methods produce only a single GRN per input dataset, potentially missing relationships between cells from different phenotypes. To address this issue, we present SimiC, a single-cell GRN inference method that produces a GRN per phenotype while imposing a similarity constraint that forces a smooth transition between GRNs, allowing for a direct comparison between different states, treatments, or conditions. We show that jointly inferring GRNs can uncover variation in regulatory relationships across phenotypes that would have otherwise been missed. Moreover, SimiC can recapitulate complex regulatory dynamics across a range of systems, both model and non-model alike. Taken together, we establish a new approach to quantitating regulatory architectures between the GRNs of distinct cellular phenotypes, with far-reaching implications for systems biology.
Addition of Multiple Introns to a Cas9 Gene Results in Dramatic Improvement in Efficiency for Generation of Gene Knockouts in Plants
Authors: Grützner Ramona , Martin Patrick , Horn Claudia , Mortensen Samuel , Cram Erin J. , Lee-Parsons Carolyn W. T. , Stuttmann Johannes , Marillonnet Sylvestre
Published: April 2020

The recent discovery of the mode of action of the CRISPR/Cas9 system has provided biologists with a useful tool for generating site-specific mutations in genes of interest. In plants, site-targeted mutations are usually obtained by stably transforming a Cas9 expression construct into the plant genome. The efficiency with which mutations are obtained in genes of interest can vary considerably depending on specific features of the constructs, including the source and nature of the promoters and terminators used for expression of the Cas9 gene and the guide RNA, and the sequence of the Cas9 nuclease itself. To optimize the efficiency with which mutations could be obtained in target genes inArabidopsis thalianawith the Cas9 nuclease, we have investigated several features of its nucleotide and/or amino acid sequence, including the codon usage, the number of nuclear localization signals (NLS) and the presence or absence of introns. We found that the Cas9 gene codon usage had some effect on Cas9 activity and that two NLSs work better than one. However, the most important impact on the efficiency of the constructs was obtained by addition of 13 introns into the Cas9 coding sequence, which dramatically improved editing efficiencies of the constructs; none of the primary transformants obtained with a Cas9 lacking introns displayed a knockout mutant phenotype, whereas between 70% and 100% of primary transformants generated with intronized Cas9 displayed mutant phenotypes. The intronized Cas9 was also found to be effective in other plants such asNicotiana benthamianaandCatharanthus roseus.
Ratchetaxisin channels: cells move directionally by pushing walls asymmetrically
Authors: Le Maout Emilie , Vecchio Simon Lo , Korla Praveen Kumar , Sheu Jim Jinn-Chyuan , Riveline Daniel
Published: April 2020

Cell motility is essential in a variety of biological phenomena ranging from early development to organ homeostasis and diseases. This phenomenon was so far mainly studied and characterized on flat surfaces in vitro whereas this situation is rarely seen in vivo. Recently, cell motion in 3D microfabricated channels was reported to be possible, and it was shown that confined cells push on walls. However, rules setting cell directions in this context were not characterized yet. Here, we show by using assays that ratchetaxis operates in 3D ratchets on fibroblasts and on epithelial cancerous cells. Open ratchets rectify cell motion, whereas closed ratchets impose a direct cell migration along channels set by the cell orientation at the channel entry point. We also show that nuclei are pressed at constrictions zones through mechanisms involving dynamic asymmetries of focal contacts, stress fibers, and intermediate filaments. Interestingly, cells do not pass these constricting zones when defective in the keratin fusion implicated in squamous cancer. By combining ratchetaxis with chemical gradients, we finally report that cells are sensitive to local asymmetries in confinement and that topological and chemical cues may be encoded differently by cells. Altogether our ratchet channels could mimic small blood vessels where cells are confined: cells would probe local asymmetries which would determine their entry into tissues and direction. Our results could shed light on invasions mechanisms in cancer.
Phenotypic screening using synthetic CRISPR gRNAs reveals pro-regenerative genes in spinal cord injury
Authors: Keatinge Marcus , Tsarouchas Themistoklis M. , Munir Tahimina , Larraz Juan , Gianni Davide , Tsai Hui-Hsin , Becker Catherina G. , Lyons David A. , Becker Thomas
Published: April 2020

Acute CRISPR/Cas9 targeting offers the opportunity for scalable phenotypic genetic screening in zebrafish. However, the unpredictable efficiency of CRISPR gRNA (CrRNA) activity is a limiting factor. Here we describe how to resolve this by prescreening CrRNAs for high activity in vivo, using a simple standardised assay based on restriction fragment length polymorphism analysis (RFLP). We targeted 350 genomic sites with synthetic RNA Oligo guide RNAs (sCrRNAs) in zebrafish embryos and found that almost half exhibited > 90% efficiency in our RFLP assay. Having the ability to preselect highly active sCrRNAs (haCRs), we carried out a focussed phenotypic screen of 30 macrophage-related genes in spinal cord regeneration and found 10 genes whose disruption impaired axonal regeneration. Four (tgfb1a, tgfb3, tnfa, sparc) out of 5 stable mutants subsequently analysed retained the acute haCR phenotype, validating the efficiency of this approach. Mechanistically, lack of tgfb1a leads to a prolonged immune response after injury, which inhibits regeneration. Our rapid and scalable screening approach has identified functional regulators of spinal cord regeneration, and can be applied to study any biological function of interest.

HIGHLIGHTS

- Synthetic CRISPR gRNAs are highly active

- in vivo pre-screening allows rapid assessment of CRISPR gRNA activity

- Phenotypic CRISPR screen reveals crucial genes for spinal cord regeneration

- tgfb1a promotes spinal regeneration by controlling inflammation