bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flexibility of the neck-linker during docking is pivotal for function of bi-directional kinesin
Authors: Goldstein-Levitin Alina , Allhuzaeel Kanary , Pandey Himanshu , Gheber Larisa 
Published: May 2020

AbstractThe role of the neck-linker (NL) element in regulating the functions of bi-directional kinesins is unknown. We report that replacing the NL of the bi-directional kinesin-5 Cin8 with sequences from plus-end directed kinesins produces non-functional Cin8 with defective spindle localization and abolished minus-end directionality and microtubule-crosslinking in vitro. Mutation of a single glycine in the NL of Cin8 to asparagine (proposed to serve as an N-latch that stabilizes the docked conformation of the NL in the plus-end directed kinesins) causes defects in the functions of Cin8. Strikingly, in a non-functional Cin8 containing the NL of the plus-end directed kinesin-5 Eg5, a single mutation of the N-latch asparagine back to glycine rescues the in vivo and in vitro defects. Since such replacement eliminates stabilizing interactions between the docked NL and the motor domain, we conclude that flexibility of NL during docking is pivotal for the function of bi-directional kinesin motors.
A giant leap in sequence space reveals the intracellular complexities of evolving a new function
Authors: Hall Kelsi R. , Robins Katherine J. , Rich Michelle H. , Calcott Mark J. , Copp Janine N. , Williams Elsie M. , Little Rory F. , Schwörer Ralf , Evans Gary B. , Patrick Wayne M. , Ackerley David F. 
Published: May 2020

AbstractSelection for a promiscuous enzyme activity provides substantial opportunity for competition between endogenous and new substrates to influence the evolutionary trajectory, an aspect that has generally been overlooked in laboratory directed evolution studies. We evolved theEscherichia colinitro/quinone reductase NfsA to detoxify chloramphenicol by randomising eight active site residues simultaneously and interrogating ∼250,000,000 reconfigured NfsA variants. Analysis of every possible evolutionary intermediate of the two best chloramphenicol reductases revealed complex epistatic interactions that restrict each hypothetical trajectory. In both cases, improved chloramphenicol detoxification was only possible after one essential substitution had eliminated activity with endogenous quinone substrates. Unlike the predominantly weak trade-offs seen in previous experimental studies, this substrate incompatibility suggests endogenous metabolites have considerable potential to shape evolutionary outcomes. Unselected prodrug-converting activities were mostly unaffected, which emphasises the importance of negative selection to effect enzyme specialisation, and offers an application for the evolved genes as dual-purpose selectable/counter-selectable markers.
The orchestrated cellular and molecular responses of the kidney to endotoxin define the sepsis timeline
Authors: Janosevic Danielle , Myslinski Jered , McCarthy Thomas , Zollman Amy , Syed Farooq , Xuei Xiaoling , Gao Hongyu , Liu Yunlong , Collins Kimberly S. , Cheng Ying-Hua , Winfree Seth , El-Achkar Tarek M. , Maier Bernhard , Ferreira Ricardo Melo , Eadon Michael T. , Hato Takashi , Dagher Pierre C. 
Published: May 2020

AbstractClinical sepsis is a highly dynamic state that progresses at variable rates and has life-threatening consequences. Staging patients along the sepsis timeline requires a thorough knowledge of the evolution of cellular and molecular events at the tissue level. Here, we investigated the kidney, an organ central to the pathophysiology of sepsis. Single cell RNA sequencing revealed the involvement of various cell populations in injury and repair to be temporally organized and highly orchestrated. We identified key changes in gene expression that altered cellular functions and can explain features of clinical sepsis. These changes converged towards a remarkable global cell-cell communication failure and organ shutdown at a well-defined point in the sepsis timeline. Importantly, this time point was also a transition towards the emergence of recovery pathways. This rigorous spatial and temporal definition of murine sepsis will uncover precise biomarkers and targets that can help stage and treat human sepsis.
Diploid male gametes circumvent hybrid sterility between Asian and African rice species
Authors: Kuniyoshi Daichi , Masuda Itaru , Kanaoka Yoshitaka , Shimazaki-Kishi Yuki , Okamoto Yoshihiro , Yasui Hideshi , Yamamoto Toshio , Nagaki Kiyotaka , Hoshino Yoichiro , Koide Yohei , Takamure Itsuro , Kishima Yuji 
Published: May 2020

AbstractIn F1hybrids ofOryza sativa(Asian rice) andO. glaberrima(African rice), heterozygosity leads to a complete gamete abortion because of allelic conflict at each of the 13hybrid sterility(HS) loci. We systematically produced 19 plants from the F1hybrids of both the rice species by the anther culture (AC) method. Five of the 19 interspecific hybrid plants were fertile and able to produce seeds. Unlike ordinal doubled haploid plants resulting from AC, these regenerated plants showed various ploidy levels (diploid to pentaploid) and different zygosities (completely homozygous, completely heterozygous, and a combination). These properties were attributable to meiotic anomalies in the interspecific hybrid F1plants. Examination of the genetic structures of the regenerated plants suggested meiotic non-reduction took place in the interspecific hybrid F1plants. The centromeric regions in the regenerated plants revealed that the abnormal first and/or second divisions of meiosis, namely the first division restitution (FDR) and/or second division restitution (SDR), had occurred in the interspecific hybrid. Immunohistochemical observations also verified these phenomena. FDR and SDR occurrences at meiosis might strongly lead to the formation of diploid microspores. The results demonstrated that meiotic anomalies functioned as a reproductive barrier occurred before theHSgenes acted in gamete of the interspecific hybrid. Although such meiotic anomalies are detrimental to pollen development, the early rescue of microspores carrying the diploid gamete resulted in the fertile regenerated plants. The five fertile plants carrying tetraploid genomes with heterozygous alleles of theHSloci produced fertile diploid pollens, implying that the diploid gametes circumvented the allelic conflicts at theHSloci. We also proposed how diploid male gametes avoid HS with the killer-protector model.
CAR T cell entry into tumor islets is a two-step process dependent on IFNγ and ICAM-1
Authors: Kantari-Mimoun Chahrazade , Barrin Sarah , Haghiri Sandrine , Gervais Claire , Mittelstaet Joerg , Mockel-Tenbrinck Nadine , Kinkhabwala Ali , Damotte Diane , Lupo Audrey , Sibony Mathilde , Alifano Marco , Vimeux Lene , Dondi Elisabetta , Bercovici Nadège , Trautmann Alain , Kaiser Andrew , Donnadieu Emmanuel 
Published: May 2020

ABSTRACTAdoptive transfer of T cells expressing chimeric antigen receptors (CARs) has shown remarkable clinical efficacy against advanced B cell malignancies but not yet against solid tumors. Here, we used fluorescent imaging microscopy andex vivoassays to compare the early functional responses (migration, Ca2+and cytotoxicity) of CD20 and EGFR CAR T cells upon contact with malignant B and carcinoma cells. Our results indicate that CD20 CAR T cells rapidly form productive ICAM-1-dependent conjugates with their targets. By comparison, EGFR CAR T cells only interact at first with a subset of carcinoma cells located at the periphery of tumor islets. After this initial peripheral activation, EGFR CAR T cells progressively infiltrate the center of tumor cell regions. The analysis of this two-step entry process shows that activated CAR T cells trigger the upregulation of ICAM-1 on tumor cells in an IFNγ-dependent pathway. The blockade of ICAM-1/LFA-1 interactions prevents CAR T cell recruitment into tumor islets. The requirement for IFNγ and ICAM-1 to enable CAR T cell entry into tumor islets is of significance for improving CAR T strategy in solid tumors.
R-type voltage-gated Ca2+channels mediate A-type K+current regulation of synaptic input in hippocampal dendrites
Authors: Murphy Jonathan G. , Gutzmann Jakob J. , Lin Lin , Hu Jiahua , Petralia Ronald S. , Wang Ya-Xian , Hoffman Dax A. 
Published: May 2020

SUMMARYThe transient K+current (IA) carried by pore forming Kv4.2 subunits regulates the propagation of synaptic input, dendritic excitability, and synaptic plasticity in CA1 pyramidal neuron dendrites of the hippocampus. We report that the Ca2+channel subunit Cav2.3 regulates IAin this cell type. We first identified Cav2.3 as a Kv4.2 interacting protein in a proteomic screen and we confirmed Cav2.3-Kv4.2 complex association using multiple techniques. Functionally, Cav2.3 Ca2+-entry increases Kv4.2-mediated whole-cell current due to an increase in Kv4.2 surface expression. Using pharmacology and Cav2.3 knockout mice, Cav2.3 was found to promote whole-cell IAand the increasing gradient of IAin the apical dendrite distal to the neuronal soma. Furthermore, the loss of Cav2.3 function leads to enhancement of synaptic currents and spine Ca2+influx. These results present Cav2.3 and Kv4.2 as integral constituents of an ion channel complex that impacts synaptic function in the hippocampus.
Ir56d-dependent fatty acid responses inDrosophilauncovers taste discrimination between different classes of fatty acids
Authors: Brown Elizabeth B. , Shah Kreesha D. , Palermo Justin , Dey Manali , Dahanukar Anupama , Keene Alex C. 
Published: May 2020

AbstractChemosensory systems are critical for evaluating the caloric value and potential toxicity of food prior to ingestion. While animals can discriminate between 1000’s of odors, much less is known about the discriminative capabilities of taste systems. Fats and sugars represent calorically potent and innately attractive food sources that contribute to hedonic feeding. Despite the differences in nutritional value between fats and sugars, the ability of the taste system to discriminate between different rewarding tastants is thought to be limited. InDrosophila, sweet taste neurons expressing the Ionotropic Receptor 56d (IR56d) are required for reflexive behavioral responses to the medium-chain fatty acid, hexanoic acid. Further, we have found that flies can discriminate between a fatty acid and a sugar in aversive memory assays, establishing a foundation to investigate the capacity of theDrosophilagustatory system to differentiate between various appetitive tastants. Here, we tested whether flies can discriminate between different classes of fatty acids using an aversive memory assay. Our results indicate that flies are able to discriminate medium-chain fatty acids from both short- and long-chain fatty acids, but not from other medium-chain fatty acids. Characterization of hexanoic acid-sensitiveIonotropic receptor 56d(Ir56d) neurons reveals broad responsive to short-, medium-, and long-chain fatty acids, suggesting selectivity is unlikely to occur through activation of distinct sensory neuron populations. However, genetic deletion ofIR56dselectively disrupts response to medium chain fatty acids, but not short and long chain fatty acids. These findings reveal Ir56d is selectively required for fatty acid taste, and discrimination of fatty acids occurs through differential receptor activation within shared populations of neurons. These findings uncover a capacity for the taste system to encode tastant identity within a taste category.
Observations of the Effect of Scopolamine on Hippocampal CA1 Place Cell and Network Properties in Freely Moving Mice Using Miniscope Imaging
Authors: Sun Dechuan , Unnithan Ranjith Rajasekharan , French Chris 
Published: May 2020

AbstractThe hippocampus and associated cholinergic inputs regulate spatial memory in rodents. Muscarinic blockade with scopolamine results in cognition deficits usually attributed to impaired memory encoding, but effects on memory retrieval are controversial. Here, we simultaneously recorded hundreds of neurons in mouse hippocampal CA1 using calcium imaging with a miniatured fluorescent microscope to study place cell and ensemble neuronal properties in a linear track environment. We found decoding accuracy and ensemble stability were significantly reduced after the administration of scopolamine. Several other parameters including theCa2+event rate, number of total cells and place cells observed, spatial information content were affected including a small increase in running speed. This study enhances the understanding of cholinergic blockade on spatial memory impairment.
Expansion of SARS-CoV-2-specific Antibody-secreting Cells and Generation of Neutralizing Antibodies in Hospitalized COVID-19 Patients
Authors: Varnaitė Renata , García Marina , Glans Hedvig , Maleki Kimia T. , Sandberg John Tyler , Tynell Janne , Christ Wanda , Lagerqvist Nina , Asgeirsson Hilmir , Ljunggren Hans-Gustaf , Ahlén Gustaf , Frelin Lars , Sällberg Matti , Blom Kim , Klingström Jonas , Gredmark-Russ Sara 
Published: May 2020

AbstractCoronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in late 2019 and has since become a global pandemic. Pathogen-specific antibodies are typically a major predictor of protective immunity, yet B cell and antibody responses during COVID-19 are not fully understood. Here, we analyzed antibody-secreting cell (ASC) and antibody responses in twenty hospitalized COVID-19 patients. The patients exhibited typical symptoms of COVID-19, and presented with reduced lymphocyte numbers and increased T cell and B cell activation. Importantly, we detected an expansion of SARS-CoV-2 nucleocapsid protein-specific ASCs in all twenty COVID-19 patients using a multicolor FluoroSpot assay. Out of the 20 patients, 16 had developed SARS-CoV-2-neutralizing antibodies by the time of inclusion in the study. SARS-CoV-2-specific IgA, IgG and IgM antibody levels positively correlated with SARS-CoV-2-neutralizing antibody titers, suggesting that SARS-CoV-2-specific antibody levels may reflect the titers of neutralizing antibodies in COVID-19 patients during the acute phase of infection. Lastly, we showed that interleukin 6 (IL-6) and C-reactive protein (CRP) concentrations were higher in serum of patients who were hospitalized for longer, supporting the recent observations that IL-6 and CRP could be used to predict COVID-19 severity. Altogether, this study constitutes a detailed description of clinical and immunological parameters in twenty COVID-19 patients, with a focus on B cell and antibody responses, and provides tools to study immune responses to SARS-CoV-2 infection and vaccination.
Robust estimates of cuticle conductance on stomatous leaf surfaces during the light induction of photosynthesis
Authors: Tominaga Jun , Stinziano Joseph R. , Hanson David T. 
Published: May 2020

SummaryCuticle conductance (gcw) can bias calculations of intercellular CO2concentration inside the leaf (Ci) when stomatal conductance (gsw) is small.We examined how the light induction of photosynthesis impacts calculations by directly measuringCialong with standard gas exchange in sunflower and tobacco leaves.When photosynthesis was induced from dark to saturating light (1200 μmol m−2s−1PAR) the calculatedCiwas significantly larger than measuredCiand the difference decreased asgswincreased. This difference could lead to over-estimation of rubisco deactivation by limited CO2supply during early induction of photosynthesis. However, only small differences inCiwere observed during the induction from shade (50 μmol m−2s−1PAR) becausegswwas sufficiently large. The induction from dark also allowed robust estimations ofgcwwhen combined with directCimeasurements. Thesegcwestimates succeeded in correcting the calculation, suggesting that the cuticle was the major source of error.Despite a technical restriction to amphi-stomatous leaves, the presented technique has a potential to provide insights into the cuticle conductance on intact stomatous leaf surfaces.
Lapatinib protects against epileptic seizures via halting glutathione peroxidase 4-dependent ferroptosis
Authors: Jia Jining , Li Qin , Sun Qianyi , Yang Nan , Chen Kangni , Yin Xixi , Zhou Honghao , Mao Xiaoyuan 
Published: May 2020

ABSTRACTBackground and PurposeRepetitive epileptic seizures trigger massive neuronal death. Therefore, neuroprotection plays a role in preventing neuronal death and inversely suppresses seizure generation. Additionally, some studies have shown ferroptosis, featured by lipid peroxidation (a dominant form of oxidative stress in the brain), is of paramount importance in epileptic seizures. Lapatinib can play a first-line anti-tumor role by targeting oxidative stress and a recent work illustrates the improvement of encephalomyelitis in rodent models after lapatinib treatment. We hypothesize whether lapatinib can protect against ferroptosis in epileptic seizures via regulating lipid peroxidation.Experimental ApproachThe epileptic behavior of the mice was recorded after intracranial injection of KA. Western blot and RT-qPCR were used to detect the protein expression of 4-hydroxynonenal (4-HNE) and glutathione peroxidase 4 (GPX4) and the mRNA expression of prostaglandin endoperoxide synthase 2 (PTGS2) in vivo and in vitro. The level of lipid reactive oxygen species (lipid ROS) in cells pretreated with lapatinib was analyzed by flow cytometry.Key ResultsLapatinib remarkably prevented KA-induced epileptic seizures in mice and ferroptosis was involved in the neuroprotection of lapatinib. Compared with the model group, western blot showed that lapatinib significantly upregulated the levels of GPX4. In the ferroptotic cell death model, lapatinib exerted neuroprotection via up-regulating GPX4. Treatment with Ras-selective lethal small molecule 3 (RSL3), a selective GPX4 inhibitor abrogated its anti-ferroptotic potential.Conclusions and ImplicationsThese results illustrated that lapatinib has neuroprotective potential against KA-triggered epileptic seizures via suppressing GPX4-dependent ferroptosis.What is already knownActivation of ferroptosis occurs in epileptic seizures.What this study addsLapatinib protects brain against epileptic seizures via blocking ferroptosis.GPX4-dependent ferroptosis is involved in the neuroprotection of lapatinib.What is the clinical significanceInhibition of ferroptosis by lapatinib represents a potential neuroprotective strategy for epileptic patients.
Interleukin-6 trans-signaling is a candidate mechanism to drive progression of human DCCs during periods of clinical latency
Authors: Werner-Klein Melanie , Grujovic Ana , Irlbeck Christoph , Obradovic Milan , Hoffmann Martin , Koerkel-Qu Huiqin , Lu Xin , Treitschke Steffi , Köstler Cäcilia , Botteron Catherine , Weidele Kathrin , Werno Christian , Polzer Bernhard , Kirsch Stefan , Guzvic Miodrag , Warfsmann Jens , Honarnejad Kamran , Czyz Zbigniew , Blochberger Isabell , Grunewald Sandra , Schneider Elisabeth , Haunschild Gundula , Patwary Nina , Guetter Severin , Huber Sandra , Buchholz Stefan , Rümmele Petra , Heine Norbert , Rose-John Stefan , Klein Christoph A. 
Published: May 2020

AbstractAlthough thousands of breast cancer cells disseminate and home to bone marrow until primary surgery, usually less than a handful will succeed in establishing manifest metastases months to years later. To identify signals that support survival or outgrowth in patients, we profiled rare bone marrow-derived disseminated cancer cells (DCCs) long before manifestation of metastasis and identified IL6/PI3K-signaling as candidate pathway for DCC activation. Surprisingly, and similar to mammary epithelial cells, DCCs lacked membranous IL6 receptor expression and mechanistic dissection revealed IL6 trans-signaling to regulate a stem-like state of mammary epithelial cells via gp130. Responsiveness to IL6 trans-signals was found to be niche-dependent as bone marrow stromal and endosteal cells down-regulated gp130 in premalignant mammary epithelial cells as opposed to vascular niche cells.PIK3CAactivation rendered cells independent from IL6 trans-signaling. Consistent with a bottleneck function of microenvironmental DCC control, we foundPIK3CAmutations highly associated with late-stage metastatic cells while being extremely rare in early DCCs. Our data suggest that the initial steps of metastasis formation are often not cancer cell-autonomous, but also depend on microenvironmental signals.
Single-lipid dynamics in phase-separated supported lipid bilayers
Authors: Woodward Xinxin , Kelly Christopher V. 
Published: May 2020

ABSTRACTPhase separation is a fundamental organizing mechanism on cellular membranes. Lipid phases have complex dependencies on the membrane composition, curvature, tension, and temperature. Single-molecule diffusion measures a key characteristic of membrane behavior and relates to the effective membrane viscosity. Lipid diffusion rates vary by up to ten-fold between liquid-disordered (Ld) and liquid-ordered (Lo) phases depending on the membrane composition, measurement technique, and the surrounding environment. This manuscript reports the lipid diffusion on phase-separated supported lipid bilayers (SLBs) with varying temperature, composition, and lipid phase. Lipid diffusion is measured by single-particle tracking (SPT) and fluorescence correlation spectroscopy (FCS) via custom data acquisition and analysis protocols that apply to diverse membranes systems. We demonstrate agreement between FCS and SPT analyses with both the single-step length distribution and the mean squared displacement of lipids with significant immobile diffusers. Traditionally, SPT is sensitive to diffuser aggregation, whereas FCS largely excludes aggregates from the reported data. Protocols are reported for identifying and culling the aggregates prior to calculating diffusion rates via SPT. With aggregate culling, all diffusion measurement methods provide consistent results. With varying membrane composition and temperature, we demonstrate the importance of the tie-line length that separates the coexisting lipid phases in predicting the differences in diffusion between the Ld and Lo phases.HIGHLIGHTSLipid diffusion varies with the lipid phases, temperature, and aggregationAggregate culling yields consistent measurements from single-particle tracking and fluorescence correlation spectroscopyMembrane with higher cholesterol content or at low temperature have more aggregatesA more variation in the diffusion rates occurred between the coexisting lipid phases at low temperatures and low cholesterol content
A systematic analysis of gene-gene interaction in multiple sclerosis
Authors: Slim Lotfi , Chatelain Clément , de Foucauld Hélène , Azencott Chloé-Agathe 
Published: May 2020

AbstractMultiple sclerosis is a complex autoimmune disease which genetic basis has been extensively investigated through genome wide association studies. So far, the conducted studies have detected a number of loci independently associated with the disease but few have investigated the interaction between distant loci, or epistasis. In the present work, we perform a gene level epistasis analysis of multiple sclerosis GWAS from the Wellcome Trust Case Control Consortium 2. We systematically study the epistatic interactions between all pairs of genes within 19 multiple sclerosis disease maps from the MetaCore pathway database. We report 4 gene pairs with epistasis involving missense variants, and 117 gene pairs with epistasis mediated by eQTLs. Our epistasis analysis is able to retrieve known interactions linked to multiple sclerosis: direct binding interaction between GLI-I and SUFU, involved in oligodendrocyte precursor cells differentiation, and regulation of IP10 transcription by NF-κB, thus validating the potential of epistasis analysis to reveal biological interaction with relevance in a disease specific context.