bluuebunny/crossref_metadata_2025_split huggingface dataset:
Universal brain signature of emerging reading in two contrasting languages
Authors: Chyl Katarzyna , Kossowski Bartosz , Wang Shuai , Dębska Agnieszka , Łuniewska Magdalena , Marchewka Artur , Wypych Marek , van den Bunt Mark , Mencl William , Pugh Kenneth , Jednoróg Katarzyna 
Published: December 2019

AbstractDespite dissimilarities among scripts, a universal hallmark of literacy in adults is the convergent brain activity for print and speech. Little is known, however, how early it emerges. Here we compare speech and orthographic processing systems in two contrasting languages, Polish and English, in 100 7-year-old children performing identical fMRI tasks. Results show limited language variation, with speech-print convergence evident mostly in left fronto-temporal perisylvian regions. Correlational and intersect analyses revealed subtle differences in the strength of this coupling in several regions of interest. Specifically, speech-print convergence was higher for transparent Polish than opaque English in right temporal area, associated with phonological processing. Conversely, speech-print convergence was higher for English than Polish in left fusiform, associated with visual reading. We conclude that speech-print convergence is a universal marker of reading even at the beginning of reading acquisition while minor variations can be explained by the differences in the orthographic transparency.
Mismatch responses mediated by adaptation and deviance detection have complementary functional profiles that point to different auditory short-term memory systems
Authors: Teichert Tobias , Jedema Hank , Shen Zhijun , Gurnsey Kate 
Published: December 2019

AbstractMismatch negativity (MMN) is a macroscopic EEG deflection in response to rare or unexpected sounds. It has provided important insights into auditory short-term memory, pre-attentive guidance of attention, and their alteration in conditions such as schizophrenia. It remains unclear if MMN is caused by passive adaptation, active memory-comparison processes (deviance detection; DD), or a mix of both. To answer this question, macaque monkeys listened to a new paradigm that quantified both components of MMN. Micro- and macroscopic mismatch responses in the rhesus were dominated by adaptation at short latencies but included a smaller contribution of deviance detection at longer latencies. Most importantly, we show that mismatch responses mediated by adaptation have a short temporal scope and narrow frequency tuning while mismatch responses mediated by deviance detection have a longer temporal scope but broader frequency tuning. The different functional profiles point to the involvement of two distinct auditory short-term memory systems and complementary roles in the pre-attentive guidance of attention.
Visual experience instructs dendrite orientation but is not required for asymmetric wiring of the retinal direction selective circuit
Authors: El-Quessny Malak , Maanum Kayla , Feller Marla B. 
Published: December 2019

ABSTRACTChanges in dendritic morphology in response to activity have long been thought to be a critical component of how neural circuits develop to properly encode sensory information. Here we report the impact of dark-rearing on the dendritic morphology and function of a retinal ganglion cell type, a ventral-preferring direction-selective ganglion cell (vDSGC). vDSGCs have asymmetric dendrites oriented along their preferred direction. We found that, at eye opening, vDSGC dendrites are not yet ventrally oriented, and that, surprisingly, dark-rearing prevents ventral orientation of vDSGC dendrites. Despite their dramatic change in dendritic morphology, vDSGCs in dark-reared mice maintain ventral directional preference. Direction selective tuning in dark-reared mice is mediated by asymmetric inhibition, as observed in vDSGCs of normally reared animals. Hence, we postulate that dendritic form follows proper circuit function, where dendritic orientation is refined over the course of development and is dependent on structured visual experience following eye opening.
Enhanced canonical Wnt signaling during early zebrafish development perturbs the interaction of cardiac mesoderm and pharyngeal endoderm and causes thyroid specification defects
Authors: Vandernoot Isabelle , Haerlingen Benoît , Trubiroha Achim , Gillotay Pierre , Janssens Véronique , Opitz Robert , Costagliola Sabine 
Published: December 2019

AbstractBackgroundCongenital hypothyroidism (CH) due to thyroid dysgenesis is a frequent congenital endocrine disorder for which the molecular mechanisms remain unresolved in the far majority of cases. This situation reflects in part our still limited knowledge about the mechanisms involved in the early steps of thyroid specification from the endoderm, in particular the extrinsic signaling cues that regulate foregut endoderm patterning. In this study, we used small molecules and genetic zebrafish models to characterize the role of various signaling pathways in thyroid specification.MethodsWe treated zebrafish embryos during different developmental periods with small molecule compounds known to modulate the activity of Wnt signaling pathway and observed effects in thyroid, endoderm and cardiovascular development using whole mountin situhybridization and transgenic fluorescent reporter models. We used an antisense morpholino to create a zebrafish acardiac model. For thyroid rescue experiments, BMP pathway induction in zebrafish embryos was obtained by using heatshock inducible transgenic lines.ResultsInterestingly, combined analyses of thyroid and cardiovascular development revealed that overactivation of Wnt signaling during early development leads to impaired thyroid specification concurrent with severe defects in the cardiac specification. When using a model of morpholino-induced blockage of cardiomyocyte differentiation, a similar correlation was observed, suggesting that defective signaling between cardiac mesoderm and endodermal thyroid precursors contributes to thyroid specification impairment. Rescue experiments through transient overactivation of BMP signaling could partially restore thyroid specification in models with defective cardiac development.ConclusionCollectively, our results indicate that BMP signaling is critically required for thyroid cell specification and identify cardiac mesoderm as a likely source of BMP signals.
Mechanism underlying autoinducer recognition in theVibrio choleraeDPO-VqmA quorum-sensing pathway
Authors: Huang Xiuliang , Duddy Olivia P. , Silpe Justin E. , Paczkowski Jon E. , Cong Jianping , Henke Brad R. , Bassler Bonnie L. 
Published: December 2019

ABSTRACTQuorum sensing is a bacterial communication process whereby bacteria produce, release and detect the accumulation of extracellular signaling molecules called autoinducers to coordinate collective behaviors. InVibrio cholerae, the quorum-sensing autoinducer, DPO (3,5-dimethyl-pyrazin-2-ol), binds the receptor-transcription factor, VqmA. In response, the DPO-VqmA complex activates transcription of thevqmRgene encoding the VqmR small RNA. VqmR represses genes required for biofilm formation and virulence factor production. Here, we show that VqmA has DPO-dependent and DPO-independent activity. We solved the DPO-VqmA crystal structure and compared it to existing structures to understand the conformational changes the protein undergoes upon DNA binding. Analysis of DPO analogs reveals that a hydroxyl or carbonyl group at the 2’ position is critical for binding. The proposed DPO precursor, a linear molecule, Ala-AA (N-alanyl-aminoacetone), also binds and activates VqmA. DPO and Ala-AA occupy the same binding site as judged by site-directed mutagenesis and competitive ligand binding analyses.
Transient CRISPR immunity leads to coexistence with phages
Authors: Meaden Sean , Capria Loris , Alseth Ellinor , Biswas Ambarish , Lenzi Luca , Buckling Angus , van Houte Stineke , Westra Edze R 
Published: December 2019

AbstractPhages play a major role in shaping the composition, evolution and function of bacterial communities. While bacteria and phages coexist in many natural environments, their coexistence is often short-lived in the lab due to the evolution of phage resistance. However, fitness costs associated with resistance and mutational loss of resistance alleles may limit the durability of acquired resistances, potentially allowing phages to re-invade the population. Here, we explore this idea in the context of bacteria that evolve CRISPR-based immunity against their phages. Consistent with previous studies, we found that the bacterium Pseudomonas aeruginosa PA14 evolved high levels of CRISPR-based immunity and low levels of surface-based resistance following infection with phage DMS3vir, which led to rapid phage extinction. However, when these pre-immunized bacterial populations were subsequently challenged with the same phage, they failed to clear the infection and instead stably coexisted with the phage. Analysis of bacterial genotypes and phenotypes over time explained why CRISPR-Cas immunity provides only a transient advantage: in the absence of phage (i.e. following the initial phage extinction) formerly CRISPR-immune bacteria regain sensitivity due to evolutionary loss of spacers, whereas in the presence of phage (i.e. upon reinfection) selection favours surface-based resistance over CRISPR immunity. The latter results from an infection-induced fitness cost of CRISPR-immunity that is due to phage gene expression prior to target DNA cleavage by the immune system. Together, these results show that CRISPR-Cas immune systems provide only a transient benefit to bacteria upon phage infection and help to explain why bacteria and phages can coexist in natural environments even when bacteria carry CRISPR-Cas adaptive immune systems that allow for rapid acquisition of immunity against phages.
Robust Stability of Multicomponent Membranes: the Role of Glycolipids
Authors: Chen Yuan , Doelman Arjen , Promislow Keith , Veerman Frits 
Published: December 2019

AbstractWe present the multicomponent functionalized free energies that characterize the low-energy packings of amphiphilic molecules within a membrane through a correspondence to connecting orbits within a reduced dynamical system. To each connecting orbits we associate a manifold of low energy membrane-type configurations parameterized by a large class of admissible interfaces. The normal coercivity of the manifolds is established through criteria depending solely on the structure of the associated connecting orbit. We present a class of examples that arise naturally from geometric singular perturbation techniques, focusing on a model that characterizes the stabilizing role of cholesterol-like glycolipids within phospholipid membranes.
Mycorrhiza Co-Association withAspilia prulisetaSchweif and Phosphorus Uptake Effects on Growth Attributes of Gadam Sorghum in Selected Sites in Kenya
Authors: Muchoka J.P. , Mugendi D.N , Njiruh P.N , Onyari C.N. , Mbugua P.K. , Njeru E.M. 
Published: December 2019

ABSTRACTMycorrhiza fungi are important components of soil microbiota in the rhizosphere and greatly influence uptake of mineral elements to plants. A green house experiment was conducted at the University of Embu. The experiment involved use of sterilized polythene potting material sized 30 cm by 40 cm. The pots were filled two thirds the height of the potting material with soil from a predetermined source in Gakurungu, Tunyai and Kanyuombora in the upper eastern region in Kenya. The soil used in the pots was collected from the rhizosphere ofAspilia prulisetaSchweif vegetation as well as adjacent areas without this vegetation as a control at 0-20 cm, 21-40 cm and 41-60 cm for each of the soil types (silty clay, silt loam and sandy loam) used in the experiment. Two sorghum seeds inoculated with mycorrhiza fungi were planted in each pot and a similar number of pots planted with un inoculated sorghum seeds as a control. Each of the 4 treatments mentioned above, was replicated four times giving n=144. Each pot was watered after every two days using a two-litre watering can for the first one week. Thereafter, watering regime was reduced to once a week but ensuring the pots remained moist. Watering was done uniformly to all the pots. This was maintained for a period of thirty five days. Data was analysed using SAS edition 8.2. Seed emergence, hypocotyl development and stand count were enhanced at P≤0.05 in both mycorrhiza fungi inoculated gadam sorghum seeds and in pots whose soils were taken from the rhizosphere ofAspilia prulisetaplants. The growth attributes had a positive correlation to yield at 95% confidence. Soil phosphate level was enhanced in both cases of gadam seed inoculation with mycorrhiza and in soils previously grownAspilia prulisetavegetation.
Cohesin-dockerin code in cellulosomal dual binding modes and its allosteric regulation by proline isomerization
Authors: Vera Andrés Manuel , Galera-Prat Albert , Wojciechowski Michał , Różycki Bartosz , Laurents Douglas Vinson , Carrión-Vázquez Mariano , Cieplak Marek , Tinnefeld Philip 
Published: December 2019

AbstractCellulose is the most abundant organic molecule on Earth and represents a renewable and practically everlasting feedstock for the production of biofuels and chemicals. Self-assembled owing to the high-affinity cohesin-dockerin interaction, cellulosomes are huge multi-enzyme complexes with unmatched efficiency in the degradation of recalcitrant lignocellulosic substrates. The recruitment of diverse dockerin-borne enzymes into a multicohesin protein scaffold dictates the three-dimensional layout of the complex, and interestingly two alternative binding modes have been proposed. Using single-molecule Fluorescence Resonance Energy Transfer, molecular dynamics simulations and NMR measurements on a range of cohesin-dockerin pairs, we directly detect varying distributions between these binding modes that follow a built-in cohesin-dockerin code. Surprisingly, we uncover a prolyl isomerase-modulated allosteric control mechanism, mediated by the isomerization state of a single proline residue, which regulates the distribution and kinetics of binding modes. Overall, our data provide a novel mechanistic understanding of the structural plasticity and dynamics of cellulosomes.
Filamentation of the bacterial bi-functional alcohol/aldehyde dehydrogenase AdhE is essential for substrate channeling and enzymatic regulation
Authors: Pony Pauline , Rapisarda Chiara , Terradot Laurent , Marza Esther , Fronzes Rémi 
Published: December 2019

AbstractAcetaldehyde – alcohol dehydrogenase (AdhE) enzymes are a key metabolic enzyme in bacterial physiology and pathogenicity. They convert acetyl-CoA to ethanolviaan acetaldehyde intermediate during ethanol fermentation in anaerobic environment. This two-step reaction is associated to NAD+regeneration, essential for glycolysis. The bifunctional AdhE enzyme is conserved in all bacterial kingdoms but also in more phylogenetically distant microorganisms such as green microalgae. In synthetic biology and biotechnology, because of its central role in bacterial alcoholic fermentation, AdhE raised a lot of attention as a key enzyme to produce ethanol from bacterial cultures.AdhE is commonly found as an oligomeric form called spirosomes. While these helical macromolecular assemblies are conserved, their function remains elusive. We used cryo-electron microscopy to obtain structures ofEscherichia colispirosomes in different conformational states. We confirm that spirosomes contain active AdhE monomers and show that AdhE filamentation is essential for its activityin vitroand functionin vivo. The detailed analysis of these structures provides insight showing that AdhE filamentation is essential for substrate channeling within the filament and for the regulation of enzyme activity. These new data will help to design molecules or mutations that control AdhE activity to fight bacterial pathogens or to optimize ethanol production in biotechnology.
Modelling the role of LHCII-LHCII, PSII-LHCII and PSI-LHCII interactions in state transitions
Authors: Wood W. H. J. , Johnson M. P. 
Published: December 2019

AbstractThe light-dependent reactions of photosynthesis take place in the plant chloroplast thylakoid membrane, a complex three-dimensional structure divided into the stacked grana and unstacked stromal lamellae domains. Plants regulate the macro-organization of photosynthetic complexes within the thylakoid membrane to adapt to changing environmental conditions and avoid oxidative stress. One such mechanism is the state transition which regulates photosynthetic light harvesting and electron transfer. State transitions are driven by changes in the phosphorylation of light harvesting antenna complex II (LHCII), which cause a decrease in grana diameter and stacking, a decreased energetic connectivity between photosystem II (PSII) reaction centres and an increase in the relative LHCII antenna size of photosystem I (PSI) compared to PSII. Phosphorylation is believed to drive these changes by weakening the intra-membrane lateral PSII-LHCII and LHCII-LHCII interactions and the inter-membrane stacking interactions between these complexes, while simultaneously increasing the affinity of LHCII for PSI. We investigated the relative roles and contributions of these three types of interaction to state transitions using a lattice-based model of the thylakoid membrane based on existing structural data, developing a novel algorithm to simulate protein complex dynamics. Monte Carlo simulations revealed that state transitions are unlikely to lead to a large-scale migration of LHCII from the grana to the stromal lamellae. Instead, the increased light harvesting capacity of PSI is largely due to the more efficient recruitment of LHCII already residing in the stromal lamellae into PSI-LHCII supercomplexes upon its phosphorylation. Likewise, the increased light harvesting capacity of PSII upon dephosphorylation was found to be driven by a more efficient recruitment of LHCII already residing in the grana into functional PSII-LHCII clusters, primarily driven by lateral interactions.Statement of significanceFor photosynthesis to operate at maximum efficiency the activity of the light-driven chlorophyll-protein complexes, photosystems I and II (PSI and PSII) must be fine-tuned to environmental conditions. Plants achieve this balance through a regulatory mechanism known as the state transition, which modulates the relative light-harvesting antenna size and therefore excitation rate of each photosystem. State transitions are driven by changes in the extent of the phosphorylation of light harvesting complex II (LHCII), which modulate the interactions between PSI, PSII and LHCII. Here we developed a novel algorithm to simulate protein complex dynamics and then ran Monte Carlo simulations to understand how these interactions cooperate to affect the organization of the photosynthetic membrane and bring about state transitions.
Calcium channel-dependent induction of long-term synaptic plasticity at excitatory Golgi cell synapses of cerebellum
Authors: Locatelli F. , Soda T. , Montagna I. , Tritto S. , Botta L. , Prestori F. , D’Angelo E. 
Published: December 2019

AbstractThe Golgi cells, together with granule cells and mossy fibers, form a neuronal microcircuit regulating information transfer at the cerebellum input stage. Despite theoretical predictions, little was known about long-term synaptic plasticity at Golgi cell synapses. Here we have used whole-cell patch-clamp recordings and calcium imaging to investigate long-term synaptic plasticity at excitatory synapses impinging on Golgi cells. In acute mouse cerebellar slices, mossy fiber theta-burst stimulation (TBS) could induce either long-term potentiation (LTP) or long-term depression (LTD) at mossy fiber-Golgi cell and granule cell-Golgi cell synapses. This synaptic plasticity showed a peculiar voltage-dependence, with LTD or LTP being favored when TBS induction occurred at depolarized or hyperpolarized potentials, respectively. LTP required, in addition to NMDA channels, activation of T-type Ca2+channels, while LTD required uniquely activation of L-type Ca2+channels. Notably, the voltage-dependence of plasticity at the mossy fiber-Golgi cell synapses was inverted with respect to pure NMDA receptor-dependent plasticity at the neighboring mossy fiber-granule cell synapse, implying that the mossy fiber presynaptic terminal can activate different induction mechanisms depending on the target cell. In aggregate, this result shows that Golgi cells show cell-specific forms of long-term plasticity at their excitatory synapses, that could play a crucial role in sculpting the response patterns of the cerebellar granular layer.Significance statementThis paper shows for the first time a novel form of Ca2+channel-dependent synaptic plasticity at the excitatory synapses impinging on cerebellar Golgi cells. This plasticity isbidirectionalandinvertedwith respect to NMDA receptor-dependent paradigms, with LTD and LTP being favored at depolarized and hyperpolarized potentials, respectively. Furthermore, LTP and LTD induction requires differential involvement ofT-ype and L-type voltage-gated Ca2+channelsrather than the NMDA receptors alone. These results, along with recent computational predictions, support the idea that Golgi cell plasticity could play a crucial role in controlling information flow through the granular layer along with cerebellar learning and memory.
Performance of the k-kL model for aerodynamics applications
Authors: Kalkote Nikhil , Kumar Ashutosh , Assam Ashwani , Eswaran Vinayak 
Published: December 2019

Purpose
The purpose of this paper is to study the predictability of the recently proposed length scale-based two-equation k-kL model for external aerodynamic flows such as those also encountered in the high-lift devices.

Design/methodology/approach
The two-equation k-kL model solves the transport equations of turbulent kinetic energy (TKE) and the product of TKE and the integral length scale to obtain the effect of turbulence on the mean flow field. In theory, the use of governing equation for length scale (kL) along with the TKE promises applicability in a wide range of applications in both free-shear and wall-bounded flows with eddy-resolving capability.

Findings
The model is implemented in the in-house unstructured grid computational fluid dynamics solver to investigate its performance for airfoils in difficult-to-predict situations, including stalling and separation. The numerical findings show the good capability of the model in handling the complex flow physics in the external aerodynamic computations.

Originality/value
The model performance is studied for stationary turbulent external aerodynamic flows, using five different airfoils, including two multi-element airfoils in high-lift configurations which, in the knowledge of the authors, have not been simulated with k-kL model until now.