bluuebunny/crossref_metadata_2025 huggingface dataset:
Proneural genes define ground state rules to regulate neurogenic patterning and cortical folding
Authors: Han Sisu , Wilkinson Grey A , Okawa Satoshi , Adnani Lata , Dixit Rajiv , Faisal Imrul , Brooks Matthew , Cortay Veronique , Chinchalongporn Vorapin , Zinyk Dawn , Li Saiqun , Gao Jinghua , Malik Faizan , Touahri Yacine , Angarica Vladimir Espinosa , Oproescu Ana-Maria , Raharjo Eko , Ilnytskyy Yaroslav , Kim Jung-Woong , Wu Wei , Rahmani Waleed , Kovalchuk Igor , Chan Jennifer Ai-wen , Kurrasch Deborah , Castro Diogo S. , Dehay Colette , Swaroop Anand , Biernaskie Jeff , del Sol Antonio , Schuurmans Carol
Published: September 2020

Transition from smooth, lissencephalic brains to highly-folded, gyrencephalic structures is associated with neuronal expansion and breaks in neurogenic symmetry. Here we show thatNeurog2andAscl1proneural genes regulate cortical progenitor cell differentiation through cross-repressive interactions to sustain neurogenic continuity in a lissencephalic rodent brain. Usingin vivolineage tracing, we found thatNeurog2andAscl1expression defines a lineage continuum of four progenitor pools, with ‘double+progenitors’ displaying several unique features (least lineage-restricted, complex gene regulatory network, G2pausing). Strikingly, selective killing of double+progenitors using split-Cre;Rosa-DTAtransgenics breaks neurogenic symmetry by locally disrupting Notch signaling, leading to cortical folding. Finally, consistent withNEUROG2andASCL1driving discontinuous neurogenesis and folding in gyrencephalic species, their transcripts are modular in folded macaque cortices and pseudo-folded human cerebral organoids.Neurog2/Ascl1double+progenitors are thus Notch-ligand expressing ‘niche’ cells that control neurogenic periodicity to determine cortical gyrification.

HIGHLIGHTS

Neurog2 and Ascl1 expression defines four distinct transitional progenitor states

Double+NPCs are transcriptionally complex and mark a lineage branch point

Double+NPCs control neurogenic patterning and cortical folding via Notch signaling

Neurog2 and Ascl1 expression is modular in folded and not lissencephalic cortices

eTOC BLURB

Emergence of a gyrencephalic cortex is associated with a break in neurogenic continuity across the cortical germinal zone. Han et al. identify a pool of unbiased neural progenitors at a lineage bifurcation point that co-express Neurog2 and Ascl1 and produce Notch ligands to control neurogenic periodicity and cortical folding.
Mouse Single Islet β Cell Transcriptomics Reveal Sexually Dimorphic Transcriptomes and Type 2 Diabetes Genes
Authors: Liu Gang , Li Yana , Zhang Tengjiao , Li Mushan , Li Sheng , He Qing , Liu Shuxin , Xu Minglu , Xiao Tinghui , Shao Zhen , Shi Weiyang , Li Weida
Published: September 2020

Type 2 diabetes (T2D), characterized by malfunction of pancreatic β cells, is affected by multiple cues including sex differences. Nevertheless, mechanisms of sex differences in type 2 diabetes susceptibility and pathogenesis remain unclear. Using single-cell RNA sequencing (scRNA-seq) technology, we showed that sexual dimorphism of transcriptome exists in mouse β cells. Our analysis further revealed the existence of sex-dependent type 2 diabetes altered genes in high fat diet induced T2D model, suggesting divergences in pathological mechanisms of type 2 diabetes between sexes. Our results indicated that sex should be taken into consideration when treating diabetes, which was further validated by the sex-matched and sex-mismatched islet transplantation in mice. Compared to sex-matched transplants, sex-mismatched transplants showed downregulation of genes involved in the longevity regulating pathway in β cells and led to impaired glucose tolerance in diabetic mice. Taken together, our findings could advance current understanding of type 2 diabetes pathogenesis with sexually dimorphic perspectives and provide new insights to the development of precision medicine.
MarkerCapsule: Explainable Single Cell Typing using Capsule Networks
Authors: Ray Sumanta , Schönhuth Alexander
Published: September 2020

Many single cell typing methods require manual annotation which casts problems with respect to resolution of (sub-)types, manpower resources and bias towards existing human knowledge. The integration of heterogeneous data and biologically meaningful interpretation of results are further current key challenges. We introduceMarkerCapsule, which leverages the landmark advantages of capsule networks achieved in their original applications in single cell typing. Thereby, the small amount of labeled data required and the naturally arising, biologically meaningful interpretation of cell types in terms of characteristic gene activity patterns are exemplary strengths, beyond outperforming the state of the art in terms of basic typing accuracy. MarkerCapsule is available at:https://github.com/sumantaray/MarkerCapsule.
Programming effects of peripubertal stress on spatial learning
Authors: Tzanoulinou S. , Gantelet E. , Sandi C. , Marquez C.
Published: September 2020

Exposure to adversity during early life can have profound influences on brain function and behavior later in life. The peripubertal period is emerging as an important time-window of susceptibility to stress, with substantial evidence documenting long-term consequences in the emotional and social domains. However, little is known about how stress during this period impacts subsequent cognitive functioning. Here, we assessed potential long-term effects of peripubertal stress on spatial learning and memory using the water maze task. In addition, we interrogated whether individual differences in stress-induced behavioral and endocrine changes are related to the degree of adaptation of the corticosterone response to repeated stressor exposure during the peripubertal period. We found that, when tested at adulthood, peripubertally stressed animals displayed a slower learning rate. Strikingly, the level of spatial orientation in the water maze completed on the last training day was predicted by the degree of adaptation of the recovery -and not the peak-of the corticosterone response to stressor exposure (i.e., plasma levels at 60 min post-stressor) across the peripubertal stress period. In addition, peripubertal stress led to changes in emotional and glucocorticoid reactivity to novelty exposure, as well as in the expression levels of the plasticity molecule PSA-NCAM in the hippocampus. Importantly, by assessing the same endpoints in another peripubertally stressed cohort tested during adolescence, we show that the observed effects at adulthood are the result of a delayed programming manifested at adulthood and not protracted effects of stress. Altogether, our results support the view that the degree of stress-induced adaptation of the hypothalamus-pituitary-adrenal axis responsiveness at the important transitional period of puberty relates to the long-term programming of cognition, behavior and endocrine reactivity.
Antibiotics increase aggression behavior and aggression-related pheromones and receptors inDrosophila melanogaster
Authors: Grinberg Michal , Neuman Hadar , Ziv Oren , Turjeman Sondra , Nosenko Rita , Koren Omry
Published: September 2020

Aggression is a behavior common in most species; it is controlled by internal and external drivers, including hormones, environmental cues, and social interactions, and underlying pathways are understood in a broad range of species. To date, though, effects of gut microbiota on aggression in the context of gut-brain communication and social behavior have not been elucidated. We examine how manipulation ofDrosophila melanogastermicrobiota affect aggression as well as the pathways that underly the behavior in this species. Flies treated with antibiotics exhibited significantly more aggressive behaviors. Furthermore, they had higher levels of vCA and (Z)-9 Tricosene, pheromones associated with aggression in flies, as well as higher expression of the relevant pheromone receptors and transporters OR67d, OR83b, GR32a, and LUSH. These findings suggest that aggressive behavior is, at least in part, mediated by bacterial species in flies.
Neurocognitive Heterogeneity in Social Anxiety Disorder: The Role of Self-Referential Processing and Childhood Maltreatment
Authors: Talmon Anat , Dixon Matthew Luke , Goldin Philippe R. , Heimberg Richard G. , Gross James J.
Published: September 2020

Social anxiety disorder (SAD) is characterized by negative self-beliefs and altered brain activation in the default mode network (DMN). However, the extent to which there is neurocognitive heterogeneity in SAD remains unclear. We had two independent samples of patients perform a self-referential encoding task, and complete self-reports of childhood maltreatment, subjective well-being, and emotion regulation. In the replication sample, we also measured DMN activation using functional magnetic resonance imaging. K-means clustering revealed two distinct sub-groups of SAD patients in the discovery sample. Cluster 1 demonstrated higher levels of negative and lower levels of positive self-referential trait endorsement, and significantly higher levels of childhood emotional maltreatment, lower subjective well-being, and altered emotion regulation strategy use. A similar pattern was observed in the replication sample, which further demonstrated higher DMN activation during negative trait judgments in cluster 1. These findings reveal neurocognitive heterogeneity in SAD and its relationship to emotional maltreatment.
A tale of two tails - efficient profiling of protein degraders by specific functional and target engagement readouts
Authors: Chernobrovkin Alexey L. , Cázares-Körner Cindy , Friman Tomas , Caballero Isabel Martin , Amadio Daniele , Molina Daniel Martinez
Published: September 2020

Targeted protein degradation represents an area of great interest, potentially offering improvements with respect to dosing, side effects, drug resistance and reaching ‘undruggable’ proteins compared to traditional small molecule therapeutics. A major challenge in the design and characterization of degraders acting as molecular glues is that binding of the molecule to the protein of interest (PoI) is not needed for efficient and selective protein degradation, instead one needs to understand the interaction with the responsible ligase. Similarly, for proteasome targeting chimeras (PROTACs) understanding the binding characteristics of the PoI alone is not sufficient. Therefore, simultaneously assessing the binding to both PoI and the E3 ligase as well as the resulting degradation profile is of great value. The Cellular Thermal Shift Assay (CETSA) is an unbiased cell-based method, designed to investigate the interaction of compounds with their cellular protein targets by measuring compound-induced changes in protein thermal stability. In combination with mass spectrometry (MS) CETSA can simultaneously evaluate compound induced changes in the stability of thousands of proteins. We have used CETSA MS to profile a number of protein degraders, including molecular glues (e.g. IMiDs) and PROTACs to understand mode of action and to deconvolute off-target effects in intact cells. Within the same experiment we were able to monitor both target engagement by observing changes in protein thermal stability as well as efficacy by simultaneous assessment of protein abundances. This allowed us to correlate target engagement (i.e. binding to the PoI and ligases) and functional readout (i.e. degrader induced protein degradation).
A cell-autonomous PD-1/PD-L1 circuit promotes tumorigenicity of thyroid cancer cells by activating a SHP2/Ras/MAPK signalling cascade
Authors: Liotti Federica , Kumar Narender , Prevete Nella , Marotta Maria , Sorriento Daniela , Ieranò Caterina , Ronchi Andrea , Marino Federica Zito , Moretti Sonia , Colella Renato , Puxeddu Efiso , Paladino Simona , Kano Yoshihito , Ohh Michael , Scala Stefania , Melillo Rosa Marina
Published: September 2020

The programmed cell death-1 (PD-1) and its ligands PD-L1 and PD-L2 are immune checkpoints. Typically, cancer cells express the PD-Ls that bind PD-1 on immune cells, inhibiting their anti-cancer activity. Recently, PD-1 expression has been found in cancer cells. We analysed expression and functions of PD-1 in thyroid cancer (TC). Human TC specimens (47%), but not normal thyroids, displayed PD-1 expression in epithelial cells, which significantly correlated with tumour stage and lymph-node metastasis. PD-1 overexpression/stimulation promoted TC cell proliferation and migration in culture. PD-1 recruited the SHP2 phosphatase, potentiated its phosphatase activity thus enhancing Ras activation by dephosphorylation of inhibitory tyrosine 32 and triggering the MAPK cascade. PD-1 inhibition decreased, while PD-1 overexpression facilitated, TC cell xenograft growth by affecting cell proliferation. PD-1 circuit blockade in TC, besides restoring anti-cancer immunity, could also directly impair TC cell growth by inhibiting the Ras/MAPK pathway.
Structural Analysis of Simultaneous Activation and Inhibition of γ-Secretase Activity in Development of Drugs for Alzheimer’s disease
Authors: Svedružić Željko M. , Vrbnjak Katarina , Martinović Manuel , Miletić Vedran
Published: September 2020

Significance

The majority of drugs that target membrane-embedded protease γ-secretase show unusual biphasic activation-inhibition dose-response in cells, model animals, and humans. Semagacestat and avagacestat are two biphasic-drugs that can facilitate cognitive decline in patients with Alzheimer’s disease. Initial mechanistic studies showed that the biphasic-drugs, and pathogenic mutations, can produce the same type of changes in γ-secretase activity.

Results

DAPT, semagacestat LY-411,575, and avagacestat are four drugs that show different binding constants, and biphasic activation-inhibition dose-response curves, for amyloid-β-40 products in SHSY-5 cells. Multiscale molecular dynamics studies showed that all four drugs bind to the most mobile parts in presenilin structure, at different ends of the 29 Å long active site tunnel. Combined results from structure-activity studies, showed that the biphasic dose-response curves are a result of modulation of γ-secretase activity by concurrent binding of multiple drug molecules at each end of the active site tunnel. The drugs activate γ-secretase by forcing the active site tunnel to open, when the rate-limiting step is the tunnel opening, and formation of the enzyme-substrate complex. The drugs inhibit γ-secretase as uncompetitive inhibitors, by binding next to the substrate to dynamic enzyme structures that regulate processive catalysis. The drugs can modulate the production of different amyloid-β catalytic intermediates, by penetrating into the active site tunnel to different depth with different binding affinity. The drugs and pathogenic mutations affect the same dynamic processes in γ-secretase structure.

Conclusions

Biphasic-drugs like disease-causing mutations can reduce the catalytic capacity of γ-secretase and facilitate pathogenic changes in amyloid metabolism.
Amyloid plaque deposition accelerates tau propagation via activation of microglia in a humanized APP mouse model
Authors: Clayton Kevin A. , Delpech Jean Christophe , Herron Shawn , Iwahara Naotoshi , Saito Takashi , Saido Takaomi C. , Ikezu Seiko , Ikezu Tsuneya
Published: September 2020

Microglia have an emerging role in development of tau pathology after amyloid plaque deposition in Alzheimer’s disease, although it has not been definitively shown. We hypothesize that plaque-associated activated microglia accelerate tau propagation via enhanced phagocytosis and secretion of tau. Here we show that the injection of adeno-associated virus expressing P301L tau mutant into the medial entorhinal cortex (MEC) in humanized APPNL-G-Fknock-in mice induces exacerbated tau propagation in the dentate gyrus compared to wild type mice. Depletion of microglia dramatically reduces accumulation of phosphorylated tau (pTau) in the dentate gyrus as well as an extracellular vesicle (EV) marker, Tumor susceptibility gene 101, co-localized in microglia. Mac2+activated microglia secrete significantly more EVs compared to Mac2−microglia in APPNL-G-Fmicein vivowhen injected with lentivirus expressing EV reporter gene mEmerald-CD9, suggesting enhanced EV secretion by microglial activation. Our findings indicate that amyloid plaque-mediated acceleration of tau propagation is dependent on activated microglia, which show enhanced EV secretionin vivo.
NeutrobodyPlex - Nanobodies to monitor a SARS-CoV-2 neutralizing immune response
Authors: Wagner Teresa R. , Kaiser Philipp D. , Gramlich Marius , Ostertag Elena , Ruetalo Natalia , Junker Daniel , Haering Julia , Traenkle Bjoern , Becker Matthias , Dulovic Alex , Schweizer Helen , Nueske Stefan , Scholz Armin , Zeck Anne , Schenke-Layland Katja , Nelde Annika , Strengert Monika , Walz Juliane S. , Zocher Georg , Stehle Thilo , Schindler Michael , Schneiderhan-Marra Nicole , Rothbauer Ulrich
Published: September 2020

As the COVID-19 pandemic escalates, the need for effective vaccination programs, therapeutic intervention, and diagnostic tools increases. Here, we identified 11 unique nanobodies (Nbs) specific for the SARS-CoV-2 spike receptor-binding domain (RBD) of which 8 Nbs potently inhibit the interaction of RBD with angiotensin-converting enzyme 2 (ACE2) as the major viral docking site. Following a detailed epitope determination and characterization of the binding mode by structural analysis, we constructed a hetero-bivalent Nb targeting two different epitopes within the RBD:ACE2 interface. This resulted in a high-affinity binder with a viral neutralization efficacy in the picomolar range. Using the bivalent Nb as a surrogate, we established a competitive multiplex binding assay (“NeutrobodyPlex”) for detailed analysis of the presence and performance of neutralizing RBD-binding antibodies in the serum of convalescent or vaccinated patients. As demonstrated, the NeutrobodyPlex enables high-throughput screening and detailed analysis of neutralizing immune responses in infected or vaccinated individuals, helping to monitor immune status or guide vaccine design. This approach is easily transferrable to diagnostic laboratories worldwide.
CREB is Required in Excitatory Neurons in the Forebrain to Sustain Wakefulness
Authors: Wimmer Mathieu E. , Rosa Cui , Blackwell Jennifer M. , Abel Ted
Published: September 2020

The molecular and intracellular signaling processes that control sleep and wake states remain largely unknown. A consistent observation is that the cyclic-AMP response element binding protein (CREB), an activity-dependent transcription factor, is differentially activated during sleep and wakefulness. CREB is phosphorylated by the cyclic AMP/protein kinase A (cAMP/PKA) signaling pathway as well as other kinases, and phosphorylated CREB (pCREB) promotes transcription of target genes. Genetic studies in flies and mice suggest that CREB signaling influences sleep/wake states by promoting and stabilizing wakefulness. However, it remains unclear where in the brain CREB is required to drive wakefulness. In rats, CREB phosphorylation increases in the cerebral cortex during wakefulness and decreases during sleep, but it is not known if this change is functionally relevant to the maintenance of wakefulness. Here, we used the cre/lox system to conditionally delete CREB in the forebrain and in the locus coereleus (LC), two regions known to be important for the production of arousal and wakefulness. We used polysomnography to measure sleep/wake levels and sleep architecture in conditional CREB mutant mice and control littermates. We found that forebrain-specific deletion of CREB decreased wakefulness and increased non-rapid eye movement (NREM) sleep. Mice lacking CREB in the forebrain were unable sustain normal periods of wakefulness. On the other hand, deletion of CREB from LC neurons did not change sleep/wake levels or sleep/wake architecture. Taken together, these results suggest that CREB is required in neurons within the forebrain but not in the LC to promote and stabilize wakefulness.
Microfluidic Isolation of Aptamers with Affinity towards Multiple Myeloma Monoclonal Immunoglobulins (M-Ig)
Authors: Olsen Timothy R. , Tapia-Alveal Claudia , Stojanovic Milan N. , Worgall Tilla S. , Lin Qiao
Published: September 2020

Multiple myeloma (MM) is a bone marrow cancer of resident plasma cells that affects 125,000 patients in the U.S. with ∼ 30,000 new cases per year. Its signature is the clonal over-proliferation of a single plasma cell that secretes a patient specific monoclonal immunoglobulin (M-Ig). Detecting this patient specific M-Ig could allow sensitive detection of minimal residual disease in multiple myeloma from patient serum. Aptamers, single-stranded oligonucleotides with affinity and specificity to a target molecule, have recently been introduced as affinity reagents able to detect MM M-Igs. Here we adapt these benchtop M-Ig systematic evolution of ligands through exponential enrichment (SELEX) techniques to our bead integrated microfluidic SELEX (BIMS) device to rapidly generate patient specific aptamers. Using MM patient serum, we isolate patient M-Ig specific aptamers rapidly (runtime < 12 hours) with high affinity (KD< 20 nM) while consuming limited quantities of patient M-Ig (< 100 μg).
Targeting Allostery in the Dynein Motor Domain with Small Molecule Inhibitors
Authors: Santarossa Cristina C. , Mickolajczyk Keith J. , Steinman Jonathan B. , Urnavicius Linas , Chen Nan , Hirata Yasuhiro , Fukase Yoshiyuki , Coudray Nicolas , Ekiert Damian C. , Bhabha Gira , Kapoor Tarun M.
Published: September 2020

Cytoplasmic dyneins are AAA (ATPase associated with diverse cellular activities) motor proteins responsible for microtubule minus-end-directed intracellular transport. Dynein’s unusually large size, four distinct nucleotide-binding sites, and the existence of closely-related isoforms with different functions, pose challenges for the design of potent and selective chemical inhibitors. Here we use structural approaches to develop a model for the inhibition of a well-characterizedS. cerevisiaedynein construct by pyrazolo-pyrimidinone-based compounds. These data, along with single molecule experiments and mutagenesis studies, indicate that the compounds likely inhibit dynein by engaging the regulatory ATPase sites in the AAA3 and AAA4 domains, and not by interacting with dynein’s main catalytic site in the AAA1 domain. A double Walker B mutant in AAA3 and AAA4 is an inactive enzyme, suggesting that inhibiting these regulatory sites can have a similar effect to inhibiting AAA1. Our findings reveal how chemical inhibitors can be designed to disrupt allosteric communication across dynein’s AAA domains.
Transplanted pluripotent stem cell-derived photoreceptor precursors elicit conventional and unusual light responses in mice with advanced retinal degeneration
Authors: Zerti Darin , Hilgen Gerrit , Dorgau Birthe , Collin Joseph , Ader Marius , Armstrong Lyle , Sernagor Evelyne , Lako Majlinda
Published: September 2020

Retinal dystrophies often lead to blindness. Developing therapeutic interventions to restore vision is therefore of paramount importance. Here we demonstrate the ability of pluripotent stem cell-derived cone precursors to engraft and restore light responses in thePde6brd1mouse, an end-stage photoreceptor degeneration model. Up to 1.5% of precursors integrated into the host retina, differentiated into cones and formed synapses with bipolar cells. Half of the transplanted mice exhibited visual behaviour and 33% showed binocular light sensitivity. The majority of ganglion cells exhibited contrast-sensitive ON, OFF or ON-OFF light responses and even motion sensitivity. Many cells also exhibited unusual responses (e.g. light-induced suppression), presumably reflecting remodelling of the neural retina. Our data indicate that despite relatively low engraftment yield, engrafted pluripotent stem cell-derived cone precursors can elicit light responsiveness even at advanced degeneration stages. Further work is needed to improve engraftment yield and counteract retinal remodelling to achieve useful clinical applications.
Spatial population genetics in heavily managed species: Separating patterns of historical translocation from contemporary gene flow in white-tailed deer
Authors: Chafin Tyler K. , Zbinden Zachery D. , Douglas Marlis R. , Martin Bradley T. , Middaugh Christopher R. , Gray M. Cory , Ballard Jennifer R. , Douglas Michael E.
Published: September 2020

Approximately 100 years ago, unregulated harvest nearly eliminated white-tailed deer (Odocoileus virginianus) from eastern North America, which subsequently served to catalyze wildlife management as a national priority. An extensive stock-replenishment effort soon followed, with deer broadly translocated among states as a means of re-establishment. However, an unintended consequence was that natural patterns of gene flow became obscured and pre-translocation signatures of population structure were replaced. We applied cutting-edge molecular and biogeographic tools to disentangle genetic signatures of historical management from those reflecting spatially heterogeneous dispersal by evaluating 35,099 single nucleotide polymorphisms (SNPs) derived via reduced-representation genomic sequencing from 1,143 deer sampled state-wide in Arkansas. We then employed Simpson’s diversity index to summarize ancestry assignments and visualize spatial genetic transitions. Using sub-sampled transects across these transitions, we tested clinal patterns across loci against theoretical expectations of their response under scenarios of recolonization and restricted dispersal. Two salient results emerged: (A) Genetic signatures from historic translocations are demonstrably apparent; and (B) Geographic filters (major rivers; urban centers; highways) now act as inflection points for the distribution of this contemporary ancestry. These results yielded a state-wide assessment of contemporary population structure in deer as driven by historic translocations as well as ongoing processes. In addition, the analytical framework employed herein to effectively decipher extant/historic drivers of deer distribution in Arkansas are also applicable for other biodiversity elements with similarly complex demographic histories.
Epigenetic clock and methylation studies in elephants
Authors: Prado Natalia A. , Brown Janine L. , Zoller Joseph A. , Haghani Amin , Yao Mingjia , Bagryanova Lora R. , Campana Michael G. , Maldonado Jesús E. , Raj Ken , Schmitt Dennis , Robeck Todd R. , Horvath Steve
Published: September 2020

Age-associated DNA-methylation profiles have been used successfully to develop highly accurate biomarkers of age (“epigenetic clocks”) in humans, mice, dogs, and other species. Here we present epigenetic clocks for African and Asian elephants. These clocks were developed using novel DNA methylation profiles of 140 elephant blood samples of known age, at loci that are highly conserved between mammalian species, using a custom Infinium array (HorvathMammalMethylChip40). We present epigenetic clocks for Asian elephants (Elephas maximus), African elephants (Loxodonta africana), and both elephant species combined. Two additional human-elephant clocks were constructed by combing human and elephant samples. Epigenome-wide association studies identified elephant age-related CpGs and their proximal genes. The products of these genes play important roles in cellular differentiation, organismal development, metabolism, and circadian rhythms. Intracellular events observed to change with age included the methylation of bivalent chromatin domains, targets of polycomb repressive complexes, and TFAP2C binding sites. These readily available epigenetic clocks can be used for elephant conservation efforts where accurate estimates of age are needed to predict demographic trends.
Secretome characterization of the lignocellulose-degrading fungiPycnoporus sanguineusandGanoderma applanatum
Authors: Gauna Albertina , Larran Alvaro S. , Feldman Susana R. , Permingeat Hugo R. , Perotti Valeria E.
Published: September 2020

C4 grasses are common species in rangelands around the world and represent an attractive option for second-generation biofuels production. Although they display a high polysaccharide content and reach great levels of biomass accumulation, there is a major technical issue to be solved before they can be considered as biofuels feedstock: lignin removal. Concerning this,PycnoporusandGanodermafungal genera have been highlighted due to their ability to hydrolyze lignocellulose. The goals here were to evaluate the pretreatment efficiency usingP. sanguineusandG. applanatumsecretomes harvested from a glucose-free inductive medium and to identify the fungal enzymatic activities responsible for the lignin degradation and glucose release. The findings show thatP. sanguineussecretome exhibits a higher activity of lignocellulolytic enzymes compared to the one fromG. applanatum. Interestingly, zymograms in presence of glucose suggest that a β-glucosidase isoform fromP. sanguineuscould be glucose-tolerant. The proteomic approach carried out allowed to identify 73 and 180 different proteins forG. applanatumandP. sanguineussecretomes, respectively, which were functionally classified in five main categories, and a miscellaneous group. Many uncharacterized proteins were found in both secretomes, reflecting that greater research is still needed for a better comprehension of lignocellulose degradation.
SFPQ intron retention, reduced expression and aggregate formation in central nervous system tissue are pathological features of amyotrophic lateral sclerosis
Authors: Hogan Alison L. , Grima Natalie , Fifita Jennifer A. , McCann Emily P. , Heng Benjamin , Fat Sandrine Chan Moi , Maharjan Ram , Cain Amy K , Henden Lyndal , Tarr Ingrid , Zang Katharine Y. , Zhao Qiongyi , Zhang Zong-Hong , Wright Amanda , Wu Sharlynn , Morsch Marco , Yang Shu , Williams Kelly L. , Blair Ian P.
Published: September 2020

Background

Splicing factor proline and glutamine rich (SFPQ, also known as polypyrimidine tract-binding protein-associated-splicing factor, PSF) is a RNA-DNA binding protein with roles in key cellular pathways such as DNA transcription and repair, RNA processing and paraspeckle formation. Dysregulation of SFPQ is emerging as a common pathological feature of multiple neurodegenerative diseases including amyotrophic lateral sclerosis (ALS). Increased retention ofSFPQintron nine and nuclear loss of the protein have been linked to multiple genetic subtypes of ALS. Consequently, SFPQ dysregulation has been hypothesised to be a common pathological feature of this highly heterogeneous disease.

Methods

This study provides a comprehensive assessment of SFPQ pathology in large ALS patient cohorts.SFPQgene expression and intron nine retention were examined in multiple neuroanatomical regions and blood from ALS patients and control individuals using RNA sequencing (RNA-Seq) and quantitative PCR (RT-qPCR). SFPQ protein levels were assessed by immunoblotting of patient and control motor cortex and SFPQ expression pattern was examined by immunofluorescent staining of patient and control spinal cord sections. Finally, whole-genome sequencing data from a large cohort of sporadic ALS patients was analysed for genetic variation inSFPQ.

Results

SFPQintron nine retention was significantly increased in ALS patient motor cortex. TotalSFPQmRNA expression was significantly downregulated in ALS patient motor cortex but not ALS patient blood, indicating tissue specificSFPQdysregulation. At the protein level, nuclear expression of SFPQ in both control and patient spinal motor neurons was highly variable and nuclear depletion of SFPQ was not a consistent feature in our ALS cohort. However, we did observe SFPQ-positive cytoplasmic ubiquitinated protein aggregates in ALS spinal motor neurons. In addition, our genetic screen of ALS patients identified two novel, and two rare sequence variants inSFPQnot previously reported in ALS.

Conclusions

This study shows that dysregulation of SFPQ is a feature of ALS patient central nervous system tissue. These findings confirm SFPQ pathology as a feature of ALS and indicate that investigations into the functional consequences of this pathology will provide insight into the biology of ALS.
Calaxin is essential for the transmission of Ca2+-dependent asymmetric waves in sperm flagella
Authors: Shiba Kogiku , Baba Shoji A , Fujiwara Eiji , Inaba Kazuo
Published: September 2020

Regulation of waveform asymmetry in sperm flagella is critical for changes in sperm swimming trajectory as seen during sperm chemotaxis towards eggs. Ca2+is known as an important regulator of asymmetry in flagellar waveforms. A calcium sensor protein, calaxin, which is associated with the outer arm dynein, plays a key role in the sperm waveform regulation in a Ca2+-dependent manner. However, the molecular mechanism underlying the regulation of asymmetric waves by Ca2+and calaxin remains unclear. We performed experiments using caged ATP to elucidate the formation and propagation of asymmetric flagellar waves in the sperm of the ascidianCiona intestinalis. Demembranated sperm cells were suspended in a solution containing caged ATP and reactivated using UV flash photolysis. Initial bends were formed at the base and propagated towards the tip of flagella; however, the bend direction was different between asymmetric and symmetric waves. A calaxin inhibitor, repaglinide, had no effect on initial bend formation, but significantly inhibited the generation of the second flagellar bend in the reverse direction, resulting in the failure of asymmetric wave formation and propagation. These results suggest that calaxin plays a critical role in Ca2+-dependent transmission of flagellar asymmetric waveforms.
Structural Connectivity in Children Treated with Therapeutic Hypothermia for Neonatal Encephalopathy
Authors: Spencer Arthur P.C. , Brooks Jonathan C.W. , Masuda Naoki , Byrne Hollie , Lee-Kelland Richard , Jary Sally , Thoresen Marianne , Tonks James , Goodfellow Marc , Cowan Frances M. , Chakkarapani Ela
Published: September 2020

Neonatal encephalopathy leads to high risk of death and neurodevelopmental impairment, including cerebral palsy. Treatment with therapeutic hypothermia offers improved outcome. However, recent studies have shown that school-age children treated with therapeutic hypothermia for neonatal encephalopathy have reduced performance on cognitive and motor tests, attention difficulties, slower reaction times and reduced visuo-spatial processing abilities compared to typically developing controls, despite ruling out a diagnosis of cerebral palsy and having developmental scores around the normative mean at 18 months. We hypothesised that alterations in white matter microstructure and disruption to brain connectivity might underlie these symptoms. In this case-control study, we used diffusion-weighted imaging to investigate white matter microstructure and whole-brain structural connectivity in school-age children without cerebral palsy treated with therapeutic hypothermia for neonatal encephalopathy at birth, compared to controls matched for age, sex and socio-economic status.

At the whole-brain level, tract-based spatial statistics of 33 cases (median age 6.9 years; range 6.0-7.9) and 36 controls confirmed reduced fractional anisotropy in cases in widespread areas of white matter (p < 0.05), particularly in the fornix, corpus callosum, anterior and posterior limbs of the internal capsule bilaterally, and the cingulum bilaterally. By parcellating the brain and performing probabilistic tractography, we then extracted structural brain networks, weighted by fractional anisotropy, for 22 cases (median age 7.0 years; range 6.0-7.8) and 32 controls. Network properties related to network integration and segregation were found to correlate with cognitive scores in cases but not controls. Network-based statistic analysis revealed weakened connectivity in cases (p = 0.0304) for a subnetwork involving the precuneus, thalamus, left superior parietal gyrus and left inferior temporal gyrus. Subnetworks were also found in which the dependence of cognitive outcome on connectivity was higher in cases than in controls, for both full-scale IQ (p = 0.0132) and processing speed (p = 0.0122), possibly reflecting delayed or disrupted white matter maturation. These analyses implicated numerous brain regions involved in visuo-spatial processing and attention, aligning with previous behavioural findings. Additionally, many of these regions have been highlighted as major hubs in the human connectome, which are thought to be vulnerable to damage due to their high metabolic rate.

Our findings demonstrate that, despite the successes of therapeutic hypothermia, there remain aspects of brain structure which are impacted by neonatal encephalopathy. Therefore, these children may benefit from targeted therapeutic intervention.
BigDataProcessor2: A free and open-source Fiji plugin for inspection and processing of TB sized image data
Authors: Tischer Christian , Ravindran Ashis , Reither Sabine , Pepperkok Rainer , Norlin Nils
Published: September 2020

Modern bioimaging and related areas such as sensor technology has seen tremendous development the last years allowing several contemporary imaging techniques, electron microscopy (EM) and light sheet microscopy in particular, to generate datasets frequently reaching the size of several terabytes (TB). As a consequence, even seemingly simple data operations such as cropping, chromatic- and drift-corrections and even visualisation, poses challenges when applied to thousands of time points or tiles. To address this we developed BigDataProcessor2 – a Fiji plugin facilitating processing workflows for TB sized image datasets.

Availability and implementation

BigDataProcessor2 is available as a Fiji plugin via the BigDataProcessor update site. The application is implemented in Java and the code is publicly available on GitHub (https://github.com/bigdataprocessor/bigdataprocessor2).

Contact

christian.tischer@embl.de,nils.norlin@med.lu.se
Mother’s curse is pervasive across a large mito-nuclearDrosophilapanel
Authors: Carnegie Lorcan , Reuter Max , Fowler Kevin , Lane Nick , Camus M. Florencia
Published: September 2020

The maternal inheritance of mitochondrial genomes entails a sex-specific selective sieve, whereby mutations in mitochondrial DNA can only respond to selection acting directly on females. In theory, this enables male-harming mutations to accumulate in mitochondrial genomes if they are neutral, beneficial, or only slightly deleterious to females. Ultimately, this bias could drive the evolution of male-specific mitochondrial mutation loads, an idea known as mother’s curse. Earlier work on this hypothesis has mainly used smallDrosophilapanels, in which naturally-sourced mitochondrial genomes were coupled to an isogenic nuclear background. However, the lack of nuclear genetic variation has precluded robust generalization. Here we test the predictions of mother’s curse using a largeDrosophilamito-nuclear genetic panel, comprising 9 isogenic nuclear genomes coupled to 9 mitochondrial haplotypes, giving a total of 81 different mito-nuclear genotypes. This enables systematic testing of both mito-nuclear interactions and mitochondrial genetic variance. Following a predictive framework, we performed a screen for wing centroid size, as this trait is highly sexually dimorphic and depends on metabolic function. We confirmed that the trait is sexually dimorphic, and show high levels of mito-nuclear epistasis. Importantly, we report that mitochondrial genetic variance has a greater impact on male versus femaleDrosophila, in 8 out of the 9 nuclear genetic backgrounds. These results demonstrate that the maternal inheritance of mitochondrial DNA does indeed modulate male life-history traits in a more generalisable way than previously envisaged.
Multimodal Brain Age Gap as a Mediating Indicator in the Relation between Modifiable Dementia Risk Factors and Cognitive Functioning
Authors: Chen Chang-Le , Chen Pin-Yu , Tung Yu-Hung , Hsu Yung-Chin , Tseng Wen-Yih Isaac
Published: September 2020

Introduction

As a structural proxy for evaluating brain health, neuroimaging-based brain age gap (BAG) is presumed to link the dementia risks to cognitive changes in the premorbid phase, but this remains unclear.

Methods

Brain age prediction models were constructed and applied to a population-based cohort (N=371) to estimate their BAG. Further, structural equation modeling was employed to investigate the mediation effect of BAG between risk levels (assessed by 2 dementia-related risk scores) and cognitive changes (examined by 4 cognitive assessments).

Results

A higher burden of modifiable dementia risk factors was causally associated with a greater cognitive decline, and this was significantly mediated (P=0.017) by a larger multimodal BAG, which indicated an older brain. Moreover, a steeper slope (P=0.020) of association between cognitive decline and multimodal BAG was observed when individuals had higher dementia risks.

Discussion

Multimodal BAG is a potential mediating indicator to reflect the changes in the pathophysiological mechanism of cognitive aging.
Comprehensive analysis of epigenetic signatures of human transcription control†
Authors: Devailly Guillaume , Joshi Anagha
Published: September 2020

Advances in sequencing technologies have enabled exploration of epigenetic and transcription profiles at a genome-wide level. The epigenetic and transcriptional landscape is now available in hundreds of mammalian cell and tissue contexts. Many studies have performed multi-omics analyses using these datasets to enhance our understanding of relationships between epigenetic modifications and transcription regulation. Nevertheless, most studies so far have focused on the promoters/enhancers and transcription start sites, and other features of transcription control including exons, introns and transcription termination remain under explored. We investigated interplay between epigenetic modifications and diverse transcription features using the data generated by the Roadmap Epigenomics project. A comprehensive analysis of histone modifications, DNA methylation, and RNA-seq data of about thirty human cell lines and tissue types, allowed us to confirm the generality of previously described relations, as well as to generate new hypotheses about the interplay between epigenetic modifications and transcript features. Importantly, our analysis included previously under-explored features of transcription control namely, transcription termination sites, exon-intron boundaries, middle exons and exon inclusion ratio. We have made the analyses freely available to the scientific community atjoshiapps.cbu.uib.no/perepigenomics_app/for easy exploration, validation and hypotheses generation.
Accelerated dystrophy and decay of oligodendrocyte precursor cells in the APP/PS1 model of Alzheimer’s-like pathology
Authors: Chacon-De-La-Rocha Irene , Fryatt Gemma , Rivera Andrea , Verkhratsky Alex , Raineteau Olivier , Gomez-Nicola Diego , Butt Arthur M.
Published: September 2020

Myelin disruption is a feature of natural aging and of Alzheimer’s disease (AD). In the CNS, myelin is produced by oligodendrocytes, which are generated throughout life by oligodendrocyte progenitor cells (OPCs). Here, we examined age-related changes in OPCs in APP/PS1 mice, a model for AD-like pathology, compared with non-transgenic (Tg) age-matched controls. Analysis was performed in the CA1 area of the hippocampus following immunolabelling for NG2 with the nuclear dye Hoescht, to identify OPC and OPC sister cells, a measure of OPC replication, together with Gpr17 and Olig2 for oligodendrocytes and myelin basic protein (MBP) immunostaining as a measure of myelination. The results indicate a decrease in the number of OPCs between 9 and 14 months in natural ageing and this occurred earlier at 9 months in APP/PS1 mice, without further decline at 14 months. The number of OPC sister cells was unaltered in natural aging, but declined significantly at 14-months in APP/PS1 mice. The number of GPR17+ and Olig2+ oligodendrocytes was not altered in APP/PS1, whereas MBP immunostaining increased between 9 and 14 months in natural ageing, but not in APP/PS1 mice. Notably, OPCs displayed marked morphological changes at 14 months in APP/PS1 mice, characterized by an overall shrinkage of OPC process domains and increased process branching, characteristic of reactive pathological changes. The results indicate that OPC and myelin disruption are pathological signs in the APP/PS1 mouse model of AD.
Synaptic silencing affects the density and complexity of oligodendrocyte precursor cells in the adult mouse hippocampus
Authors: Chacon-De-La-Rocha Irene , Fryatt Gemma L. , Rivera Andrea D. , Restani Laura , Caleo Matteo , Raineteau Olivier , Gomez-Nicola Diego , Butt Arthur M.
Published: September 2020

Oligodendrocyte progenitor cells (OPCs) are responsible for generating oligodendrocytes, the myelinating cells of the CNS. Life-long myelination is promoted by neuronal activity and is essential for neural network plasticity and learning. OPCs are known to contact synapses and it is proposed that neuronal synaptic activity in turn regulates OPC proliferation and differentiation. To examine this in the adult, we performed unilateral injection of the synaptic blocker botulinum neurotoxin A (BoNT/A) into the hippocampus of adult mice. We confirm BoNT/A cleaves SNAP-25 in the CA1 are of the hippocampus, which has been proven to block neurotransmission. Notably, synaptic silencing by BoNT/A significantly decreased OPC density and caused their shrinkage, as determined by immunolabelling for the OPC marker NG2. Inhibition of synaptic activity resulted in an overall decrease in the number of OPC processes, as well as a decrease in their lengths and branching frequency. These data indicate that synaptic activity is important for maintaining adult OPC numbers and cellular integrity, which is relevant to pathological scenarios characterized by decreased synaptic activity.
Frequency domain analysis of fluctuations of mRNA and protein copy numbers within a cell lineage: theory and experimental validation
Authors: Jia Chen , Grima Ramon
Published: September 2020

The stochasticity of gene expression is manifested in the fluctuations of mRNA and protein copy numbers within a cell lineage over time. While data of this type can be obtained for many generations, most mathematical models are unsuitable to interpret such data since they assume non-growing cells. Here we develop a theoretical approach that quantitatively links the frequency content of lineage data to subcellular dynamics. We elucidate how the position, height, and width of the peaks in the power spectrum provide a distinctive fingerprint that encodes a wealth of information about mechanisms controlling transcription, translation, replication, degradation, bursting, promoter switching, cell cycle duration, cell division, and gene dosage compensation. Predictions are confirmed by analysis of single-cellEscherichia colidata obtained using fluorescence microscopy. Furthermore, by matching the experimental and theoretical power spectra, we infer the temperature-dependent gene expression parameters, without the need of measurements relating fluorescence intensities to molecule numbers.