bluuebunny/crossref_metadata_2025_split huggingface dataset:
Depolarizing GABA Transmission Restrains Activity-Dependent Glutamatergic Synapse Formation in the Developing Hippocampal Circuit
Authors: Salmon Christopher K. , Pribiag Horia , Farmer W. Todd , Cameron Scott , Jones Emma V. , Mahadevan Vivek , Stellwagen David , Woodin Melanie A. , Murai Keith K. 
Published: August 2019

ABSTRACTGABA is the main inhibitory neurotransmitter in the mature brain but has the paradoxical property of depolarizing neurons during early development. Depolarization provided by GABAA transmission during this early phase regulates neural stem cell proliferation, neural migration, neurite outgrowth, synapse formation, and circuit refinement, making GABA a key factor in neural circuit development. Importantly, depending on the context, depolarizing GABAA transmission can either drive neural activity, or inhibit it through shunting inhibition. The varying roles of depolarizing GABAA transmission during development, and its ability to both drive and inhibit neural activity, makes it a difficult developmental cue to study. This is particularly true in the later stages of development, when the majority of synapses form and GABAA transmission switches from depolarizing to hyperpolarizing. Here we addressed the importance of depolarizing but inhibitory (or shunting) GABAA transmission in glutamatergic synapse formation in hippocampal CA1 pyramidal neurons. We first showed that the developmental depolarizing-to-hyperpolarizing switch in GABAA transmission is recapitulated in organotypic hippocampal slice cultures. Based on the expression profile of K+-Cl- co-transporter 2 (KCC2) and changes in the GABA reversal potential, we pinpointed the timing of the switch from depolarizing to hyperpolarizing GABAA transmission in CA1 neurons. We found that blocking depolarizing but shunting GABAA transmission increased excitatory synapse number and strength, indicating that depolarizing GABAA transmission can restrain glutamatergic synapse formation. The increase in glutamatergic synapses was activity-dependent, but independent of BDNF signalling. Importantly, the elevated number of synapses was stable for more than a week after GABAA inhibitors were washed out. Together these findings point to the ability of immature GABAergic transmission to restrain glutamatergic synapse formation and suggest an unexpected role for depolarizing GABAA transmission in shaping excitatory connectivity during neural circuit development.
Benchmarking tomographic acquisition schemes for high-resolution structural biology
Authors: Turoňová Beata , Hagen Wim J. H. , Obr Martin , Kräusslich Hans-Georg , Beck Martin 
Published: August 2019

AbstractCryo electron tomography with subsequent subtomogram averaging is a powerful technique to structurally analyze macromolecular complexes in their native context. Although close to atomic resolution, in principle, can be obtained, it is not clear how individual experimental parameters contribute to the attainable resolution. Here, we have used immature HIV-1 lattice as a benchmarking sample to optimize the attainable resolution for subtomogram averaging. We systematically tested various experimental parameters such as the order of projections, different angular increments and the use of the Volta phase plate. We find that although any of the prominently used acquisition schemes is sufficient to obtain subnanometer resolution, dose-symmetric acquisition provides considerably better outcome. We discuss our findings in order to provide guidance for data acquisition. Our data is publicly available at EMPIAR-10277 as well as EMD-10207 and might be used to further develop processing routines.
Privatization of biofilm matrix in structurally heterogeneous biofilms
Authors: Otto Simon B. , Martin Marivic , Schäfer Daniel , Hartmann Raimo , Drescher Knut , Brix Susanne , Dragoš Anna , Kovács Ákos T. 
Published: August 2019

ABSTRACTThe self-produced biofilm provides beneficial protection for the enclosed cells, but the costly production of matrix components makes producer cells susceptible to cheating by non-producing individuals. Despite detrimental effects of non-producers, biofilms can be heterogeneous, with isogenic non-producers being a natural consequence of phenotypic differentiation processes. For instance, inBacillus subtilisbiofilm cells differ in the two major matrix components production, the amyloid fiber protein TasA and exopolysaccharides (EPS), demonstrating different expression levels of corresponding matrix genes. This raises questions regarding matrix gene expression dynamics during biofilm development and the impact of phenotypic non-producers on biofilm robustness. Here, we show that biofilms are structurally heterogeneous and can be separated into strongly and weakly associated clusters. We reveal that spatiotemporal changes in structural heterogeneity correlate with matrix gene expression, with TasA playing a key role in biofilm integrity and timing of development. We show that the matrix remains partially privatized by the producer subpopulation, where cells tightly stick together even when exposed to shear stress. Our results support previous findings on the existence of ‘weak points’ in seemingly robust biofilms as well as on the key role of linkage proteins in biofilm formation. Furthermore, we provide a starting point for investigating the privatization of common goods within isogenic populations.IMPORTANCEBiofilms are communities of bacteria protected by a self-produced extracellular matrix. The detrimental effects of non-producing individuals on biofilm development raises questions about the dynamics between community members, especially when isogenic non-producers exist within wild-type populations. We asked ourselves whether phenotypic non-producers impact biofilm robustness, and where and when this heterogeneity of matrix gene expression occurs. Based on our results we propose that the matrix remains partly privatized by the producing subpopulation, since producing cells stick together when exposed to shear stress. The important role of linkage proteins in robustness and development of the structurally heterogeneous biofilm provides an entry into studying the privatization of common goods within isogenic populations.
RNA-seq analysis of a zebrafish tlr2 mutant shows a broad function of this Toll-like receptor in transcriptional and metabolic control and defense to Mycobacterium marinum infection
Authors: Yang Shuxin , Hu Wanbin , Shimada Yasuhito , Münch Magnus , Marín-Juez Rubén , Meijer Annemarie H. , Spaink Herman P. 
Published: August 2019

AbstractBackgroundThe function of Toll-like receptor 2 (TLR2) in host defense against pathogens, especially Mycobacterium tuberculosis (Mtb) is poorly understood. To investigate the role of TLR2 during mycobacterial infection, we analyzed the response of tlr2 zebrafish mutant larvae to infection with Mycobacterium marinum (Mm), a close relative to Mtb, as a model for tuberculosis. We measured infection burdens and transcriptome responses using RNA deep sequencing in mutant and control larvae.Resultstlr2 mutant embryos at 2 dpf do not show morphological alterations or differences in the number of macrophages and neutrophils when compared to control embryos. However, we found substantial changes in gene expression in these mutants, particularly in developmental and metabolic pathways, when compared with the heterozygote tlr2+/− control. After Mm infection, bacterial burden was six to ten fold higher in tlr2−/− larvae than in tlr2+/−, or tlr2+/+ larvae, indicating that Tlr2 acts as a protective factor in zebrafish host defense. RNAseq analysis of infected tlr2−/− versus tlr2+/− shows that the number of up-regulated and down-regulated genes in response to infection was greatly diminished in tlr2 mutants by at least 2 fold and 10 fold, respectively. Analysis of the transcriptome data and qPCR validation shows that Mm infection of tlr2 mutants leads to decreased mRNA levels of genes involved in inflammation and immune responses, including il1b, tnfb, cxcl11aa/ac, fosl1a, and cebpb. Furthermore, RNAseq analyses revealed that the expression of genes for Maf family transcription factors, vitamin D receptors, and Dicps proteins is significantly altered in tlr2 mutants with or without infection. In addition, the data indicate a function of Tlr2 in the control of induction of cytokines and chemokines, such as the CXCR3-CXCL11 signaling axis.ConclusionThe transcriptome and infection burden analyses give support for a function of TLR2 in host defense against mycobacteria. Transcriptome analysis revealed tlr2-specific pathways involved in Mm infection, which are related to responses to Mtb infection in human macrophages. Considering its dominant function in control of transcriptional processes that govern defense responses and metabolism, the TLR2 protein can be expected to be also of importance for other infectious diseases and interactions with the microbiome.
Health behaviors among male and female university students in Cambodia: a cross-sectional survey
Authors: Sok Say , Pal Khuondyla , Tuot Sovannary , Yi Rosa , Chhoun Pheak , Yi Siyan 
Published: August 2019

AbstractBackgroundStudents go through a transition when they enter university, which involves major individual and contextual changes in every domain of life that may lead to several behavioral and health problems. This paper describes a wide range of health behaviors among male and female university students in Cambodia.MethodsA cross-sectional survey was conducted in 2015 among students randomly selected from the Royal University of Phnom Penh and University of Battambang. Health-related behaviors in different domains were collected using a structured questionnaire. Chi-square test, Fisher’s exact test, or independent Student’s t-test was used as appropriate to describe and compare the variables among male and female students.ResultsThis study included 1359 students, of whom 50.8% were male, and the mean age was 21.3 years (SD= 2.3). Of the total, 79.5% reported not having any vigorous-intensity activities, 25.9% not having moderate-intensity activities, and 33.5% not having walked continuously for 10 minutes during the past seven days. The prevalence of substance use was low with 38.3% currently drinking alcohol, 1.1% smoking tobacco, and 0.4% using an illicit drug during the past 12 months. About one in ten (10.6%) reported having sexual intercourse, with a mean number of partners of 2.1 (SD= 2.4) during the past 12 months, and 42.4% not using a condom in the last intercourse. Only 7.1% reported having been diagnosed with a sexually transmitted infection in the past 12 months; of whom, 60% sought for treatment. About one-third (33.6%) reported eating fast food once or twice, and 5.3% having it three times or more over the last week. More than half (55.6%) had one to two servings of fruits and vegetables daily, and 9.9% did not eat any fruits and vegetables over the last week.ConclusionsWe found that the prevalence of sexual risk behaviors and substance use was plausibly low among university students in this study. However, the rates of inactive lifestyle and unhealthy food consumption were concerning. Public policy and universities should promote healthy behaviors among the students. The interventions may take advantage of and expend upon the good health behaviors and consider gender differences.
Adaptational lags during periods of environmental change
Authors: Van Dooren Tom J. M. 
Published: August 2019

AbstractEffects of climate change can be handled by means of mitigation and adaptation. In the biological sciences, adaptations are solutions which evolved when organisms needed to match an ecological challenge. Based on Adaptive Dynamics theory, a definition is proposed of adapted states and adaptational lags applicable during periods with environmental change of any speed. Adaptation can thus be studied when it emerges from complex eco-evolutionary processes or when targets for adaptation are not defined a priori. The approach is exemplified with a model for delayed germination in an annual plant. Plasticity and maternal effects are often presumed to be adaptive and added to the model to investigate lags in these modes of trait determination. Adaptational lags can change sign and to understand their dynamics, effects of trait space boundaries and characteristics of years with large numbers of recruits had to be considered. Adaptational lags can be crucial elements of adaptive control strategies for managed ecosystems. To demonstrate their practical relevance, examples from pest management show that evolutionary adaptation has been used to infer targets of control. Adaptational lags then serve as measures of the distance to the control target and become integral elements of strategies for adaptive pest population management.
Mesoscale computational protocols for the design of highly cooperative bivalent macromolecules
Authors: Saurabh S. , Piazza F. 
Published: August 2019

ABSTRACTThe last decade has witnessed a swiftly increasing interest in the design and production of novel multivalent molecules as powerful alternatives for conventional antibodies in the fight against cancer and infectious diseases. However, while it is widely accepted that large-scale flexibility (10 − 100 nm) and free/constrained dynamics (100 ns −µs) control the activity of such novel molecules, computational strategies at the mesoscale still lag behind experiments in optimizing the design of crucial features, such as the binding cooperativity (a.k.a. avidity).In this study, we introduced different coarse-grained models of a polymer-linked, two-nanobody composite molecule, with the aim of laying down the physical bases of a thorough computational drug design protocol at the mesoscale. We show that the calculation of suitable potentials of mean force allows one to apprehend the nature, range and strength of the thermodynamic forces that govern the motion of free and wall-tethered molecules. Furthermore, we develop a simple computational strategy to quantify the encounter/dissociation dynamics between the free end of a wall-tethered molecule and the surface, at the roots of binding cooperativity. This procedure allows one to pinpoint the role of internal flexibility and weak non-specific interactions on the kinetic constants of the NB-wall encounter and dissociation. Finally, we quantify the role and weight of rare events, which are expected to play a major role in real-life situations, such as in the immune synapse, where the binding kinetics is likely dominated by fluctuations.SIGNIFICANCEMultivalent and multispecific molecules composed of polymer-linked nanobodies have gained interest as engineered alternatives to conventional antibodies. These therapeutic molecules have a larger reach due to their smaller size and promise substantial and tunable gains in avidity. This paper studies a model diabody to lay the bases of a multi-scale computational design of the structural and dynamical determinants of binding cooperativity, rooted in a blend of atomistic and coarse-grained MD simulations and concepts from statistical mechanics.
Pdm3 directs sleep circuit development to control sleep maturation
Authors: Dilley Leela Chakravarti , Szuperak Milan , Williams Charlette E. , Saldana Ricardo Linares , Gong Naihua N. , Garbe David S. , Syed Mubarak H. , Jain Rajan , Kayser Matthew S. 
Published: August 2019

SummaryAcross species, sleep in young animals is critical for normal brain maturation. In contrast to mature adult sleep, the molecular determinants of early life sleep remain unknown. Through an RNAi-based screen, we identified a gene, pdm3, required for sleep maturation in Drosophila. Pdm3, a transcription factor, acts during nervous system development to coordinate the ingrowth of wake-promoting dopaminergic neurites to a sleep-promoting region. Loss of PDM3 prematurely increases dopaminergic inhibition of the sleep center, abolishing the juvenile sleep state. RNA-Seq/ChIP-Seq and a subsequent modifier screen reveal that pdm3 regulates expression of the synaptogenesis gene Msp300 to control sleep ontogeny. These studies define the molecular cues governing sleep behavioral and circuit development, and suggest sleep disorders may be of neurodevelopmental origin.
A transient amphipathic helix in PCSK9’s prodomain facilitates low-density lipoprotein binding
Authors: Sarkar Samantha K. , Foo Alexander C.Y. , Matyas Angela , Kosenko Tanja , Goto Natalie K. , Vergara-Jaque Ariela , Lagace Thomas A. 
Published: August 2019

SUMMARYProprotein convertase subtilisin/kexin type-9 (PCSK9) is a ligand of low-density lipoprotein receptor (LDLR) that promotes LDLR degradation in late endosomes/lysosomes. In human plasma, 30-40% of PCSK9 is bound to LDL particles; however, the physiological significance of this interaction remains unknown. LDL bindingin vitrorequires a disordered N-terminal region in PCSK9’s prodomain. Here we report that peptides corresponding to a predicted amphipathic α-helix in the prodomain N-terminus adopted helical structure in a membrane-mimetic environment; this effect was greatly enhanced by an R46L substitution representing an athero-protectivePCSK9loss-of-function mutation. A helix-disrupting proline substitution within the putative α-helical motif in full-length PCSK9 lowered LDL binding affinity >5-fold. Modeling studies suggested the transient α-helix aligns multiple polar residues to interact with positive-charged residues in the C-terminal domain. Gain-of-functionPCSK9mutations associated with familial hypercholesterolemia (FH) and clustered at the predicted interdomain interface (R469W, R496W, F515L) inhibited LDL binding, which was abolished for the R496W variant. These studies inform on allosteric conformational changes in PCSK9 required for high-affinity binding to LDL particles. Moreover, we report the initial identification of FH-associated mutations that diminish the ability of PCSK9 to bind LDL, supporting that LDL association in the circulation inhibits PCSK9 activity.
Paclitaxel-induced peripheral neuropathy is caused by epidermal ROS and mitochondrial damage through conserved MMP-13 activation
Authors: Cirrincione Anthony M. , Pellegrini Adriana D. , Dominy Jessica R. , Benjamin Marisa E. , Utkina-Sosunova Irina , Lotti Francesco , Jergova Stanislava , Sagen Jacqueline , Rieger Sandra 
Published: August 2019

AbstractPaclitaxel is a chemotherapeutic agent that causes peripheral neuropathy (PIPN) as a side effect of cancer treatment. Severely affected patients need to terminate chemotherapy, diminishing their chance of survival. The underlying causes of PIPN are unclear, but epidermal, unmyelinated axons have been shown to be the first to degenerate. We previously utilized a zebrafish in vivo model to show that the epidermal matrix-metalloproteinase 13 (MMP-13) induces degeneration of unmyelinated axons, whereas pharmacological inhibition of MMP-13 prevented axon degeneration. The precise functions by which MMP-13 is regulated and affects axons, however, remained elusive. In this study, we assessed mitochondrial damage and reactive oxygen species (ROS) formation as possible inducers of MMP-13, and we analyzed MMP-13-dependent damage. We show that the small ROS, H2O2, is increased in keratinocytes following treatment with paclitaxel. Epidermal mitochondrial damage appears to be a source of ROS leading to cytoplasmic H2O2 elevation, upregulation of MMP-13, and increased matrix degradation. Intriguingly, although axonal mitochondria also show aberrant morphologies and are vacuolized, as shown in other neuropathies, these axonal mitochondria do not produce increased H2O2 levels. We suggest that mitochondrial vacuolization occurs independently of axonal damage given that MMP-13 inhibition prevents axon degeneration, though vacuoles persist. We further show that MMP-13 dysregulation also underlies PIPN in rodent paclitaxel models, and that this function appears to be DRG neuron-extrinsic. These findings suggest that vacuolization is not a cause of paclitaxel-induced neuropathy, and that epidermal MMP-13 is a strong candidate for therapeutic interventions in cancer patients with neuropathy.
Extradomain-B Fibronectin is a molecular marker of invasive breast cancer cells
Authors: Vaidya Amita M. , Wang Helen , Qian Victoria , Lu Zheng-Rong 
Published: August 2019

AbstractBreast tumor heterogeneity is a major impediment to oncotherapy. Tumor cells undergo rapid clonal evolution, thereby acquiring significant growth and invasive advantages. The absence of specific markers of these high-risk tumors precludes efficient therapeutic and diagnostic management of breast cancer. Given the critical function of tumor microenvironment in the oncogenic circuitry, we sought to determine the role of the extracellular matrix oncoprotein, extradomain-B fibronectin (EDB-FN), as a molecular marker of aggressive cancers. High-risk invasive cell lines generated from relatively less invasive MCF7 and MDA-MB-468 breast cancer cells by long-term TGF-β treatment and chemoresistance demonstrated hybrid epithelial-mesenchymal phenotype, enhanced motility, and significantly elevated EDB-FN levels in 2D- and 3D-cultures. To determine if EDB-FN could serve as a therapy-predictive marker, the invasive cell lines were treated with MK2206-HCl, a pan-AKT inhibitor. Phospho-AKT depletion reduced EMT and invasion of the populations, with a concomitant decrease in EDB-FN expression, partly through the phosphoAKT-SRp55 pathway, demonstrating that EDB-FN expression is strongly associated with high-risk breast cancer. EDB-FN is a promising molecular marker for accurate detection, differential diagnosis, and non-invasive therapeutic surveillance of aggressive breast cancer.Summary StatementDynamic changes in invasive properties of breast cancer cells directly influence extradomain-B fibronectin levels, suggesting its potential role as a molecular marker for active surveillance and therapeutic monitoring of breast cancer.
Cables2 Is a Novel Smad2-Regulatory Factor Essential for Early Embryonic Development in Mice
Authors: Dinh Tra Thi Huong , Iseki Hiroyoshi , Mizuno Seiya , Iijima-Mizuno Saori , Tanimoto Yoko , Daitoku Yoko , Kato Kanako , Hamada Yuko , Hasan Ammar Shaker Hamed , Suzuki Hayate , Murata Kazuya , Muratani Masafumi , Ema Masatsugu , Kim Jun-dal , Ishida Junji , Fukamizu Akiyoshi , Kato Mitsuyasu , Takahashi Satoru , Yagami Ken-ichi , Wilson Valerie , Arkell Ruth M. , Sugiyama Fumihiro 
Published: August 2019

ABSTRACTCDK5 and Abl enzyme substrate 2 (Cables2), a member of the Cables family that has a C-terminal cyclin box-like domain, is widely expressed in adult mouse tissues. However, the physiological role of Cables2in vivois unknown. We show here thatCables2-deficiency causes post-gastrulation embryonic lethality in mice. The mutant embryos progress to gastrulation, but then arrest, and fail to grow. Analysis of gene expression patterns reveals that formation of the anterior visceral endoderm and the primitive streak is impaired inCables2-deficient embryos. Tetraploid complementation analyses support the critical requirement of Cables2 in both the epiblast and visceral endoderm for progression of embryogenesis. In addition, we show that Cables2 physically interacts with a key mediator of the canonical Nodal pathway, Smad2, and augments its transcriptional activity. These findings provide novel insights into the essential role of Cables2 in the early embryonic development in mice.