bluuebunny/crossref_metadata_2025_split huggingface dataset:
Highly efficient genome modification of cultured primordial germ cells with lentiviral vectors to generate transgenic songbirds
Authors: Gessara Ivana , Dittrich Falk , Hertel Moritz , Hildebrand Staffan , Pfeifer Alexander , Frankl-Vilches Carolina , McGrew Mike , Gahr Manfred 
Published: August 2020

SUMARYThe ability to genetically manipulate organisms has led to significant insights in functional genomics in many species. In birds, manipulation of the genome is hindered by the inaccessibility of the one-cell embryo. During embryonic development, avian primordial germ cells (PGCs) migrate through the blood stream and reach the gonadalanlage; where they develop into mature germ cells. Here, we explored the use of PGCs to produce transgenic offspring in the zebra finch, which is a major animal model for sexual brain differentiation, vocal learning and vocal communication. Zebra finch PGCs (zfPGCs) obtained from embryonic blood significantly proliferated when cultured in an optimized culture medium and conserved the expression of germ and stem cell markers. Transduction of cultured zfPGCs with lentiviral vectors was highly efficient leading to strong expression of the enhanced green fluorescent protein (eGFP). Transduced zfPGCs were injected into the host embryo and transgenic songbirds were successfully generated.
The effect of stimulus intensity on neural envelope tracking
Authors: Verschueren Eline , Vanthornhout Jonas , Francart Tom 
Published: August 2020

ABSTRACTObjectivesThe last years there has been significant interest in attempting to recover the temporal envelope of a speech signal from the neural response to investigate neural speech processing. The research focus is now broadening from neural speech processing in normal-hearing listeners towards hearing-impaired listeners. When testing hearing-impaired listeners speech has to be amplified to resemble the effect of a hearing aid and compensate peripheral hearing loss. Until today, it is not known with certainty how or if neural speech tracking is influenced by sound amplification. As these higher intensities could influence the outcome, we investigated the influence of stimulus intensity on neural speech tracking.DesignWe recorded the electroencephalogram (EEG) of 20 normal-hearing participants while they listened to a narrated story. The story was presented at intensities from 10 to 80 dB A. To investigate the brain responses, we analyzed neural tracking of the speech envelope by reconstructing the envelope from EEG using a linear decoder and by correlating the reconstructed with the actual envelope. We investigated the delta (0.5-4 Hz) and the theta (4-8 Hz) band for each intensity. We also investigated the latencies and amplitudes of the responses in more detail using temporal response functions which are the estimated linear response functions between the stimulus envelope and the EEG.ResultsNeural envelope tracking is dependent on stimulus intensity in both the TRF and envelope reconstruction analysis. However, provided that the decoder is applied on data of the same stimulus intensity as it was trained on, envelope reconstruction is robust to stimulus intensity. In addition, neural envelope tracking in the delta (but not theta) band seems to relate to speech intelligibility. Similar to the linear decoder analysis, TRF amplitudes and latencies are dependent on stimulus intensity: The amplitude of peak 1 (30-50 ms) increases and the latency of peak 2 (140-160 ms) decreases with increasing stimulus intensity.ConclusionAlthough brain responses are influenced by stimulus intensity, neural envelope tracking is robust to stimulus intensity when using the same intensity to test and train the decoder. Therefore we can assume that intensity is not a confound when testing hearing-impaired participants with amplified speech using the linear decoder approach. In addition, neural envelope tracking in the delta band appears to be correlated with speech intelligibility, showing the potential of neural envelope tracking as an objective measure of speech intelligibility.
DIAPH3 deficiency links microtubules to mitotic errors, defective neurogenesis, and brain dysfunction
Authors: Lau Eva On-Chai , Damiani Devid , Jossin Yves , Chehade Georges , Schakman Olivier , Tajeddine Nicolas , Gailly Philippe , Tissir Fadel 
Published: August 2020

AbstractDiaphanous (DIAPH) 3 is a member of the formin proteins that have the capacity to nucleate and elongate actin filaments and therefore, to remodel the cytoskeleton. DIAPH3 is essential for cytokinesis as its dysfunction impairs the contractile ring and produces multinucleated cells. Here, we report that DIAPH3 localizes at the centrosome during mitosis and regulates the assembly and polarity of the mitotic spindle. DIAPH3-deficient cells display disorganized cytoskeleton, multipolar spindles, and supernumerary centrosomes. DIAPH3-deficiency disrupts the expression and/or stability of microtubule-associated proteins SPAG5 and KNSTRN. SPAG5 and DIAPH3 have similar expression patterns in the developing brain and overlapping subcellular localization during mitosis. Knockdown of SPAG5 phenocopies the DIAPH3 deficiency, whereas its overexpression rescues the DIAH3 phenotype. Conditional inactivation ofDiaph3in the cerebral cortex profoundly disrupts neurogenesis depleting cortical progenitors and neurons; and leading to cortical malformation and autistic-like behavior. Our data uncover uncharacterized functions of DIAPH3 and provide evidence that this protein belongs to a molecular toolbox that links microtubule dynamics during mitosis to aneuploidy, cell death, fate determination defects, and cortical malformation.
The historical range and drivers of decline of the Tapanuli orangutan
Authors: Meijaard Erik , Ni’matullah Safwanah , Dennis Rona , Sherman Julie , Onrizal  , Wich Serge A. 
Published: August 2020

AbstractThe Tapanuli Orangutan (Pongo tapanuliensis) is the most threatened great ape species in the world. It is restricted to an area of about 1,000 km2of upland forest where fewer than 800 animals survive in three declining subpopulations. Through a historical ecology approach involving analysis of newspaper, journals, books and museum records from the early 1800s to 2009, we demonstrate that historicallyPongo tapanuliensisinhabited a much larger area, and across a much wider range of habitat types than now. Its current Extent of Occurrence is between 2.5% and 5.0% of the historical range in the 1890s and 1940s respectively. A combination of historical fragmentation of forest habitats, mostly for small-scale agriculture, and unsustainable hunting likely drove various populations to the south, east and west of the current population to extinction. This happened prior to the industrial-scale forest conversion that started in the 1970s. Our findings indicate how sensitiveP. tapanuliensisis to the combined effects of habitat fragmentation and unsustainable take-off rates. Saving this species will require prevention of any further fragmentation and killings or other removal of animals from the remaining population. Without concerted action to achieve this, the remaining populations ofP. tapanuliensisare doomed to become extinct within several orangutan generations.
Sonlicromanol improves neuronal network dysfunction and transcriptome changes linked to m.3243A>G heteroplasmy in iPSC-derived neurons
Authors: Gunnewiek T.M. Klein , Verboven A. H. A. , Hogeweg M. , Schoenmaker C. , Renkema H. , Beyrath J. , Smeitink J. , de Vries B. B. A. , ’t Hoen P.A.C. , Kozicz T. , Kasri N. Nadif 
Published: August 2020

SummaryMitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS) is often caused by an adenine to guanine mutation at m.3243 (m.3243A>G) of theMT-TL1gene (tRNAleu(UUR)). To understand how this mutation affects the nervous system, we differentiated human induced-pluripotent stem cells (iPSCs) into excitatory neurons with normal (low heteroplasmy) and impaired (high heteroplasmy) mitochondrial function from MELAS patients with the m.3243A>G mutation. We combined micro-electrode array (MEA) measurements with RNA sequencing (MEA-seq) and found that the m.3243A>G mutation affects expression of genes involved in mitochondrial respiration- and presynaptic function, as well as non-cell autonomous processes in co-cultured astrocytes. Finally, we show that the clinical II stage drug sonlicromanol (KH176) improved neuronal network activity in a patient-specific manner when treatment is initiated early in development. This was intricately linked with changes in the neural transcriptome. Overall, MEA-seq is a powerful approach to identify mechanisms underlying the m.3243A>G mutation and to study the effect of pharmacological interventions in iPSC-derived neurons.Highlights- High m.3243A>G heteroplasmy leads to lower neuronal network activity and synchronicity- High heteroplasmy affects expression of genes involved in mitochondrial ATP production and the synaptic function / the presynaptic vesicle cycle- High neuronal heteroplasmy non cell autonomously affects gene expression in healthy co-cultured astrocytes- Sonlicromanol partially rescues neuronal network activity and transcriptome changes induced by high heteroplasmyeTOC BlurbUsing human inducible pluripotent stem cell-derived neurons with high levels of m.3243A>G heteroplasmy, Klein Gunnewiek et al. show transcriptome changes underlying the functional neuronal network phenotype, and how sonlicromanol can partially improve both this neuronal network phenotype, and the transcriptome changes, in a patient-specific manner.
Dissociating harmonic and non-harmonic phase-amplitude coupling in the human brain
Authors: Giehl Janet , Noury Nima , Siegel Markus 
Published: August 2020

AbstractPhase-amplitude coupling (PAC) has been hypothesized to coordinate cross-frequency interactions of neuronal activity in the brain. However, little is known about the distribution of PAC across the human brain and the frequencies involved. Furthermore, it remains unclear to what extend PAC may reflect spurious cross-frequency coupling induced by physiological artifacts or rhythmic non-sinusoidal signals with higher harmonics. Here, we combined MEG, source-reconstruction and different measures of cross-frequency coupling to systematically characterize PAC across the resting human brain. We show that cross-frequency measures of phase-amplitude, phase-phase, and amplitude-amplitude coupling are all sensitive to signals with higher harmonics. In conjunction, these measures allow to distinguish harmonic and non-harmonic PAC. Based on these insights, we found no evidence for non-harmonic PAC in resting-state MEG. Instead, we found cortically and spectrally wide-spread PAC driven by harmonic signals. Furthermore, we show how physiological artifacts and spectral leakage cause spurious PAC across wide frequency ranges. Our result clarify how different measures of cross-frequency interactions can be combined to characterize PAC and cast doubt on the presence of prominent non-harmonic phase-amplitude coupling in human resting-state MEG.
K18-hACE2 mice develop respiratory disease resembling severe COVID-19
Authors: Yinda Claude Kwe , Port Julia R. , Bushmaker Trenton , Owusu Irene Offei , Avanzato Victoria A. , Fischer Robert J. , Schulz Jonathan E. , Holbrook Myndi G. , Hebner Madison J. , Rosenke Rebecca , Thomas Tina , Marzi Andrea , Best Sonja M. , de Wit Emmie , Shaia Carl , van Doremalen Neeltje , Munster Vincent J. 
Published: August 2020

AbstractSARS-CoV-2 emerged in late 2019 and resulted in the ongoing COVID-19 pandemic. Several animal models have been rapidly developed that recapitulate the asymptomatic to moderate disease spectrum. Now, there is a direct need for additional small animal models to study the pathogenesis of severe COVID-19 and for fast-tracked medical countermeasure development. Here, we show that transgenic mice expressing the human SARS-CoV-2 receptor (angiotensin-converting enzyme 2 [hACE2]) under a cytokeratin 18 promoter (K18) are susceptible to SARS-CoV-2 and that infection resulted in a dose-dependent lethal disease course. After inoculation with either 104TCID50or 105TCID50, the SARS-CoV-2 infection resulted in rapid weight loss in both groups and uniform lethality in the 105TCID50group. High levels of viral RNA shedding were observed from the upper and lower respiratory tract and intermittent shedding was observed from the intestinal tract. Inoculation with SARS-CoV-2 resulted in upper and lower respiratory tract infection with high infectious virus titers in nasal turbinates, trachea and lungs. The observed interstitial pneumonia and pulmonary pathology, with SARS-CoV-2 replication evident in pneumocytes, were similar to that reported in severe cases of COVID-19. SARS-CoV-2 infection resulted in macrophage and lymphocyte infiltration in the lungs and upregulation of Th1 and proinflammatory cytokines/chemokines. Extrapulmonary replication of SARS-CoV-2 was observed in the cerebral cortex and hippocampus of several animals at 7 DPI but not at 3 DPI. The rapid inflammatory response and observed pathology bears resemblance to COVID-19. Taken together, this suggests that this mouse model can be useful for studies of pathogenesis and medical countermeasure development.Authors SummaryThe disease manifestation of COVID-19 in humans range from asymptomatic to severe. While several mild to moderate disease models have been developed, there is still a need for animal models that recapitulate the severe and fatal progression observed in a subset of patients. Here, we show that humanized transgenic mice developed dose-dependent disease when inoculated with SARS-CoV-2, the etiological agent of COVID-19. The mice developed upper and lower respiratory tract infection, with virus replication also in the brain after day 3 post inoculation. The pathological and immunological diseases manifestation observed in these mice bears resemblance to human COVID-19, suggesting increased usefulness of this model for elucidating COVID-19 pathogenesis further and testing of countermeasures, both of which are urgently needed.
Whole genome CRISPR screens identify a LRRK2-regulated pathway for extracellular tau uptake by human neurons
Authors: Evans Lewis D. , Strano Alessio , Tuck Eleanor , Campbell Ashley , Smith James , Hung Christy , Behr Tiana S. , Ghetti Bernardino , Ryskeldi-Falcon Benjamin , Karakoc Emre , Iorio Francesco , Reith Alastair , Bassett Andrew R. , Livesey Frederick J. 
Published: August 2020

AbstractExtracellular release and cellular uptake of pathogenic forms of the microtubule-associated protein tau contribute to the pathogenesis of several neurodegenerative diseases, including Alzheimer’s disease. Defining the cellular mechanisms and pathways for tau entry to human neurons is essential to understanding tauopathy pathogenesis and the rational design of disease-modifying therapeutics. Whole genome CRISPR loss-of-function screens in human iPSC-derived excitatory neurons, the major neuronal cell type affected in these diseases, enabled the delineation of the different cellular pathways for uptake of extracellular monomeric and fibrillar tau. Monomeric and fibrillar tau are both taken up by human neurons by receptor-mediated endocytosis, but involve different routes of entry at the neuronal surface: the low-density lipoprotein LRP1 is the primary receptor for monomeric tau, but contributes less to fibrillar tau entry. Similarly, endocytosis of monomeric tau is dependent on the familial Parkinson’s disease gene LRRK2, but not required for endocytosis of fibrillar tau. These findings implicate LRP1 and LRRK2 in the pathogenesis of tauopathies and Parkinson’s disease and identify LRRK2 as a potential therapeutic target for altering progression of these diseases.
Dynamics of mutation accumulation and adaptation during three years of evolution under long-term stationary phase
Authors: Katz Sophia , Avrani Sarit , Yavneh Meitar , Hilau Sabrin , Gross Jonathan , Hershberg Ruth 
Published: August 2020

AbstractMany bacterial species that cannot sporulate, such as the model bacteriumEscherichia coli, can nevertheless survive for years under resource exhaustion, in a state termed long-term stationary phase (LTSP). Here we describe the dynamics ofE. coliadaptation during the first three years spent under LTSP. We show that during this timeE. colicontinuously adapts genetically, through the accumulation of mutations. For non-mutator clones, the majority of mutations accumulated appear to be adaptive under LTSP, reflected in an extremely convergent pattern of mutation accumulation. Despite the rapid and convergent manner in which populations adapt under LTSP, they continue to harbor extensive genetic variation. The dynamics of evolution of mutation rates under LTSP are particularly interesting. The emergence of mutators, affects overall mutation accumulation rates as well as the mutational spectra and the ultimate spectrum of adaptive alleles acquired under LTSP. With time, mutators can evolve even higher mutation rates, through the acquisition of additional mutation-rate enhancing mutations. Different mutator and non-mutator clones within a single population and time point can display extreme variation in their mutation rates, resulting in differences in both the dynamics of adaptation and their associated deleterious burdens. Despite these differences, clones that vary greatly in their mutation rates tend to co-exist within their populations for many years, under LTSP.
Opposing activities of IFITM proteins in SARS-CoV-2 infection
Authors: Shi Guoli , Kenney Adam D. , Kudryashova Elena , Zhang Lizhi , Hall-Stoodley Luanne , Robinson Richard T. , Kudryashov Dmitri S. , Compton Alex A. , Yount Jacob S. 
Published: August 2020

AbstractInterferon-induced transmembrane proteins (IFITMs) restrict infections by many viruses, but a subset of IFITMs enhance infections by specific coronaviruses through currently unknown mechanisms. Here we show that SARS-CoV-2 Spike-pseudotyped virus and genuine SARS-CoV-2 infections are generally restricted by expression of human IFITM1, IFITM2, and IFITM3, using both gain- and loss-of-function approaches. Mechanistically, restriction of SARS-CoV-2 occurred independently of IFITM3S-palmitoylation sites, indicating a restrictive capacity that is distinct from reported inhibition of other viruses. In contrast, the IFITM3 amphipathic helix and its amphipathic properties were required for virus restriction. Mutation of residues within the human IFITM3 endocytosis-promoting YxxΦ motif converted human IFITM3 into an enhancer of SARS-CoV-2 infection, and cell-to-cell fusion assays confirmed the ability of endocytic mutants to enhance Spike-mediated fusion with the plasma membrane. Overexpression of TMPRSS2, which reportedly increases plasma membrane fusion versus endosome fusion of SARS-CoV-2, attenuated IFITM3 restriction and converted amphipathic helix mutants into strong enhancers of infection. In sum, these data uncover new pro- and anti-viral mechanisms of IFITM3, with clear distinctions drawn between enhancement of viral infection at the plasma membrane and amphipathicity-based mechanisms used for endosomal virus restriction. Indeed, the net effect of IFITM3 on SARS-CoV-2 infections may be a result of these opposing activities, suggesting that shifts in the balance of these activities could be coopted by viruses to escape this important first line innate defense mechanism.
Closely related budding yeast species respond to different ecological signals for spore activation
Authors: Plante Samuel , Landry Christian R 
Published: August 2020

AbstractSpore activation is one of the most important developmental decisions in fungi as it initiates the transition from dormant and stress resistant cells to vegetative cells. Because in many species mating follows spore activation and germination, signals that trigger this developmental transition can also contribute to species reproductive barriers. Here we examine the biochemical signals triggering spore activation in a natural species complex of budding yeast,Saccharomyces paradoxus(lineagesSpA, SpB, SpCandSpC*). We first demonstrate that we can quantitatively monitor spore activation in these closely related lineages. Second, we dissect the composition of culture media to identify components necessary and/or sufficient to activate spores in the four lineages. We show that, contrary to expectation, glucose is necessary but not sufficient to trigger spore activation. We also show that two of the North American lineages (SpCandSpC*) diverge from the other North American (SpB) and European (SpA) lineages in terms of germination signal as their spore activation requires inorganic phosphate. Our results show that the way budding yeast interpret environmental conditions during spore activation diverged among closely related and incipient species, which means that it may play a role in their ecological differentiation and reproductive isolation.
Up-Regulation of αCaMKII Impairs Cued Fear Extinction and NMDAR-Dependent LTD in the Lateral Amygdala
Authors: An Shuming , Wang Jiayue , Zhang Xuliang , Duan Yanhong , Lv Junyan , Wang Dasheng , Zhang Huan , Richter-Levin Gal , Caoa Xiaohua 
Published: August 2020

ABSTRACTImpaired fear extinction is one of the hallmark symptoms of post-traumatic stress disorder (PTSD). The roles of αCaMKII have been not extensively studied in fear extinction and LTD. Here, we found PTSD susceptible mice exhibited significant up-regulation of αCaMKII in the lateral amygdala (LA). Consistently, increasing αCaMKII in LA profoundly not only caused PTSD-like symptoms such as impaired fear extinction and anxiety-like behaviors, but also attenuated NMDAR-dependent LTD at thalamo-LA synapses, reduced GluA1-Ser845/Ser831 dephosphorylation and AMPAR internalization. Suppressing the elevated αCaMKII to normal level could completely reverse both PTSD-like symptoms and the impairments in LTD, GluA1-Ser845/Ser831 dephosphorylation and AMPAR internalization. Intriguingly, deficits in AMPAR internalization and GluA1-Ser845/Ser831 dephosphorylation were detected not only after impaired fear extinction, but also after attenuated LTD Our results demonstrate for the first time GluA1-Ser845/Ser831 dephosphorylation and AMPAR internalization are molecular links between LTD and fear extinction, and suggest αCaMKII may be a potential molecular determinant of PTSD.
Targeting KRAS-mutant stomach/colorectal tumours by disrupting the ERK2-p53 complex
Authors: Wang Xiang , Xie Qing , Ji Yan , Shen Jiayan , Zhang Yongfeng , Jiang Feng , Kong Xiangyin , Liu Dandan , Zheng Leizhen , Qing Chen , Lang Jing-Yu 
Published: August 2020

ABSTRACTKRAS is widely mutated in human cancers, resulting in nearly unchecked tumour proliferation and metastasis. No therapies have been developed for targeting KRAS-mutant tumours. Herein, we observed that mutant KRAS specifically promoted the formation of ERK2-p53 complex in stomach/colorectal tumour cells. Disruption of this complex by applying MEK1/2 and ERK2 inhibitors elicits strong apoptotic responses in a p53-dependent manner, validated by genome-wide knockout screening. Mechanistically, p53 physically associates with phosphorylated ERK2 through the hydrophobic interaction in the presence of mutant KRAS, which suppresses p53 activation by preventing the recruitment of p300/CBP; trametinib disrupts the ERK2-p53 complex by reducing ERK2 phosphorylation, allowing the acetylation of p53 protein by recruiting p300/CBP; acetylated p53 activates PUMA transcription and thereby kills KRAS-mutant tumours. Our study unveils an important role of the ERK2-p53 complex and provides a potential therapeutic strategy for treating KRAS-mutant cancer via ERK2 inhibition.