bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractMicroglia 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

AbstractAs 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

AbstractThe 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

AbstractMultiple 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).
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

SummaryRetinal 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

ABSTRACTApproximately 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

ABSTRACTAge-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

ABSTRACTC4 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

AbstractBackgroundSplicing 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.MethodsThis 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.ResultsSFPQintron 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.ConclusionsThis 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

ABSTRACTRegulation 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

AbstractNeonatal 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

SummaryModern 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 implementationBigDataProcessor2 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).Contactchristian.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

AbstractThe 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.