Miracle-dz/UniFAR-FTUs huggingface dataset:
Kainate-type of glutamate receptors regulate wiring of intrinsic glutamatergic connectivity in the amygdala

Perturbed information processing in the amygdala has been implicated in developmentally originating neuropsychiatric disorders. However, little is known on the mechanisms that guide formation and refinement of intrinsic connections between amygdaloid nuclei. We demonstrate that the glutamatergic connection from basolateral to central amygdala (BLA-CeA) develops rapidly during the first ten postnatal days, before external inputs underlying amygdala dependent behaviors emerge. During this restricted period of synaptic development, kainate-type of ionotropic glutamate receptors (KARs) are highly expressed in the BLA and tonically activated to regulate glutamate release via a G-protein dependent mechanism. Genetic manipulation of this endogenous KAR activity locally in the newborn LA perturbed development of glutamatergic input to CeA, identifying KARs as a physiological mechanism regulating wiring of the intrinsic glutamatergic circuitry in the amygdala.
Autophagy mediates temporary reprogramming and dedifferentiation in plant somatic cells

Somatic cells acclimate to changes in the environment by temporary reprogramming. Much has been learned about transcription factors that induce these cell-state switches in both plants and animals, but how cells rapidly modulate their proteome remains elusive. Here, we show rapid induction of autophagy during temporary reprogramming in plants triggered by phytohormones, immune and danger signals. Quantitative proteomics following sequential reprogramming revealed that autophagy is required for timely decay of previous cellular states and for tweaking the proteome to acclimate to the new conditions. Signatures of previous cellular programs thus persist in autophagy deficient cells, affecting cellular decision-making. Concordantly, autophagy deficient cells fail to acclimatize to dynamic climate changes. Similarly, they have defects in dedifferentiating into pluripotent stem cells, and redifferentiation during organogenesis. These observations indicate that autophagy mediates cell state switches that underlie somatic cell reprogramming in plants and possibly other organisms, and thereby promotes phenotypic plasticity.
Immunological microenvironment in the testis

The testis is specific in that it produces haploid germ cells of which autoantigens newly appear long after the neonatal immune tolerance. Under normal condition, these autoantigens are protected by the blood‐testis barrier formed by Sertoli cells. Thus, the testis is an immunologically privileged site where haploid cells are protected from autoimmune attack.
Loss of AUXIN RESPONSE FACTOR 4 function alters plant growth, stomatal functions and improves tomato tolerance to salinity and water deficit

Understanding physiological and molecular basis of plant response and tolerance to environmental stresses is important to improve plant survival, crop yield and quality. Auxin controls many aspects of plant growth and development. However, its role in stress responses remains so far poorly studied. Auxin acts on the transcriptional regulation of target genes, mainly through Auxin Response Factors (ARF). The current study aims to study the involvement of SlARF4 in tomato tolerance to salinity and water deficit. Using a reverse genetic approach, we found that the down-regulation of SlARF4 improves tomato tolerance to salt and drought stress by promoting root development and density, increasing soluble sugars content and maintaining chlorophyll content at high levels in stress conditions. Besides that, ARF4-as plants displayed a leaf curl phenotype, a low stomatal conductance coupled with an increase in leaf relative water content and ABA content under normal and stressful conditions. This increase in ABA content was correlated with the activation of ABA biosynthesis genes and the repression of ABA catabolism genes. cat1, Cu/ZnSOD and mdhar genes were up-regulated in ARF4-as plants suggesting that ARF4-as mutant is more tolerant to salt and water stress.The data presented in this work strongly support the involvement of ARF4 as a key actor in tomato tolerance to salt and drought stresses. Significance statement Down regulation of Auxin Response Factor 4 modify leaf structure, alters stomatal responses under normal conditions, and improves tomato tolerance to salt and drought stress.
Population dynamics of insect-pests of paddy and its correlation with weather parameters

The research experiment discusses the population dynamics of paddy and its correlation with weather parameters in Zonal Agricultural Research Station, Sindewahi, Chandrapur district of Maharashtra. Occurrence and abundance of insect pests of paddy was monitored on rice variety PKV HMT during the season Kharif, 2014 with the spacing of 20 cm x 15 cm following the recommended package of practices. this investigation revealed that, the pest activity commenced from 29 Standard Meteorological Week and continued to 44 SMW. Highest dead hearts (6.77%) of yellow stem borer, Scirpophaga incertulas was found in the 44 SMW. The maximum population of armyworm (3.43 hill) was recorded in the 36 SMW, the peak population of cutworm (1.71 hill) was estimated in the 36 SMW. The highest per cent leaf damage due to leaf folder (15.63%) was found in the 40 SMW. The maximum population of Brown plant hopper (7.43 hill), WBPH (9.14 hill) were found in 44 SMW while green leaf hopper (3.86 hill ) in 43 SMW. The incidence of gall midge was not noticed. Yellow stem borer, BPH, WBPH, GLH and leaf folder positively correlated with maximum and minimum temperature, morning relative humidity while armyworm and cutworm positively correlated with rainy days, rainfall, Morning and evening relative humidity. Evening relative humidity, rainfall and rainy days discourages the population of yellow stem borer, brown plant hopper, WBPH, green leaf hopper and leaf folder but encourage armyworm and cutworm.
Chemical variations in Quercus pollen as a tool for taxonomic identification: implications for long-term ecological and biogeographic research

Aim Fossil pollen is an important tool for understanding biogeographic patterns in the past, but the taxonomic resolution of the fossil-pollen record may be limited to genus or even family level. Chemical analysis of pollen grains has the potential to increase the taxonomic resolution of pollen, but present-day chemical variability is poorly understood. This study aims to investigate whether a phylogenetic signal is present in the chemical variations of Quercus L. pollen, to determine the prospects of chemical techniques as for identification in biogeographic research. Location Portugal Taxon Six species of Quercus L. , Q. faginea, Q. robur, Q. robur estremadurensis, Q. coccifera, Q. rotundifolia and Q. suber belonging to three sections: Cerris, Ilex, and Quercus (Denk, Grimm, Manos, Deng, & Hipp, 2017) Methods We collected pollen samples from 297 individual Quercus trees across a 4° (∼450 km) latitudinal gradient and determined chemical differences using Fourier-transform infrared spectroscopy (FTIR). We used canonical powered partial least-squares regression (CPPLS) and discriminant analysis to describe within- and between-species chemical variability. Chemical functional groups associated with variation in the FTIR spectra between different Quercus species were determined. Results We find clear differences in the FTIR spectra from Quercus pollen at the section level (Cerris: ∼98%; Ilex: ∼100%; Quercus: ∼97%). Successful discrimination is based on lipids and sporopollenins. However, discrimination of species within individual Quercus sections is more difficult: overall, species recall is ∼76% and species misidentifications within sections lie between 22% and 31% of the test-set. Main Conclusions Our results demonstrate that sub-genus level differentiation of Quercus pollen is possible using FTIR methods, with successful classification at the section level. This indicates that operator-independent FTIR approaches can perform equally to traditional morphological techniques. However, although sporopollenins are identified as important functional groups for discrimination between some Quercus taxa, the importance of lipids to resolve phylogenetic signatures presents challenges for future biogeographic research because lipids may be less likely to be preserved in sediment sequences. We suggest that future work on further discrimination of isolated sporopollenin components is required before FTIR-based chemical discrimination can be used in long-term ecology and biogeography studies.
Growth performance, carcass characteristics, meat and egg quality, and intestinal microbiota in Beijing-you chicken on diets with inclusion of fresh chicory forage

Abstract The aim of this study was to evaluate the effects of fresh chicory forage in chicken diets on growth performance, carcass characteristics, meat and egg quality, as well as intestinal microbiota. A total of 600 healthy 16 weeks female Beijing-you chickens were randomly assigned to four dietary treatments containing 0%, 5%, 8% and 10% chicory forage with six replicate pens and 25 chickens in each replicate. Chickens were raised in a free-range system for 13 weeks after seven days of adaptation. High-throughput sequencing was used to characterise the microbiota in three different intestinal sections (duodenum, ileum and caecum). The results showed that dietary supplementation of chicory forage increased (p < .05) egg weight, yolk colour, total amino acids and delicious amino acids in muscles, and decreased (p < .05) abdominal fat yield compared to the control. However, increased (p < .05) average daily feed intake, increased (p < .05) feed conversion ratio, increased (p < .05) mortality and decreased (p < .05) eggshell strength were observed in chickens fed chicory forage than in those fed a basal diet. Dietary supplementation of chicory forage stimulated the proliferation of the Lactobacillus in ileum and the Bacteroides in caecum, and depressed pathogenic microbes including the Rikenella, thereby further improved intestinal health and nutrient utilisation. It was concluded that 8% chicory forage could be considered as a beneficial feed additive in Beijing-you chicken diets. In addition to the good nutritional profile, medicinal properties were associated with the beneficial effects of chicory forage on chickens. Highlights Dietary supplementation of chicory forage improved muscle nutritional value and flavour. Dietary supplementation of chicory forage affected egg quality. Dietary supplementation of chicory forage regulated the intestinal microbiota.
Neural Circuit Mechanism Underlying the Feeding Controlled by Insula-Central Amygdala Pathway

Central nucleus of amygdala (CeA) contains distinct populations of neurons that play opposing roles in feeding. The circuit mechanism of how CeA neurons process information sent from their upstream inputs to regulate feeding is still unclear. Here we show that activation of the neural pathway projecting from insular cortex neurons to CeA suppresses food intake. Surprisingly, we find that the inputs from insular cortex form excitatory connections with similar strength to all types of CeA neurons. To reconcile this puzzling result, and previous findings, we developed a conductance-based dynamical systems model for the CeA neuronal network. Computer simulations showed that both the intrinsic electrophysiological properties of individual CeA neurons and the overall synaptic organization of the CeA circuit play a functionally significant role in shaping the CeA neural dynamics. We successfully identified a specific CeA circuit structure that reproduces the desired circuit output consistent with existing experimentally observed feeding behaviors.
Effect of the β-amyloid peptide on microglia activation: ATP release

Previous studies have shown a key role of microglial cells in the neuroinflammatory processes associated with some neurodegenerative diseases, such as Alzheimer’s disease (AD). Microglia sense several types of diffusible molecules that regulate the multiple repertoire of microglial functions. Among them, extracellular nucleotides, acting on microglial P2 receptors, have central roles. In this sense, the ionotropic P2X7 receptor has gained recognition as a key regulator of microglial-mediated inflammatory responses. It is known that microglia releases ATP and other nucleotides to the extracellular medium. Although several mechanisms, such as release trough conexins or panexins, has been proposed, a vesicular origin for this released nucleotides, relying on the activity of the vesicular nucleotide transporter (VNUT), cannot be ruled out. In this work we evaluated whether the expression of VNUT and the P2X7 receptor, as well as the ATP release, could be modified in the reactive microglia. To achieve microglia activation we stimulated the cells with the lipopolysaccharide (LPS). Moreover, we analyzed the effect of the b-amyloid peptide b 1-42 , which is also able to activate the microglial cells, on the expression of VNUT and the ATP release in the microglia.
Introduce the Siberian Sturgeon (Acipenser baerii) to Turkish aquaculture industry: Duoculture possibility with Rainbow Trout

Duo culture response of Siberian sturgeon (Acipenser baeri) and rainbow trout (Oncorhynchus mykiss) was evaluated in culture tank conditions. Triplicated culture groups were planned as: mono-culture sturgeon (M, n=10), duo-culture sturgeon (DM, n=10) and duo-culture trout (DA, n=10), and mono-culture trout (A, n=10). Examination of mono and duo culture of each species, showed neither sturgeon nor trout, was indicated any significance on specific growth rate (SGR) and condition factor (CF). As for final biomasses among groups, no significant differences were recorded (p<0.05).
A mathematical multi-organ model for bidirectional epithelial-mesenchymal transitions in the metastatic spread of cancer

Cancer invasion and metastatic spread to secondary sites in the body are facilitated by a complex interplay between cancer cells of different phenotypes and their microenvironment. A trade-off between the cancer cells’ ability to invade the tissue and to metastasise, and their ability to proliferate has been observed. This gives rise to the classification of cancer cells into those of mesenchymal and epithelial phenotype, respectively. Additionally, mixed phenotypic states between these two extremes exist. Cancer cells can transit between these states via epithelial-mesenchymal transition (EMT) and the reverse process, mesenchymal-epithelial transition (MET). These processes are crucial both for the local tissue invasion and the metastatic spread of cancer cells. To shed light on the role of these phenotypic states and the transitions between them in the invasive and metastatic process, we extend our recently published multi-grid, hybrid, individual-based mathematical metastasis framework (Franssen et al., 2019a). In addition to cancer cells of epithelial and of mesenchymal phenotype, we now also include those of an intermediate partial-EMT phenotype. Furthermore, we allow for the switching between these phenotypic states via EMT and MET at the biologically appropriate steps of the invasion-metastasis cascade. We also account for the likelihood of spread of cancer cells to the various secondary sites and differentiate between the tissues of the organs involved in our simulations. Finally, we consider the maladaptation of metastasised cancer cells to the new tumour microenvironment at secondary sites as well as the immune response at these sites by accounting for cancer cell dormancy and death. This way, we create a first mathematical multi-organ model that explicitly accounts for EMT-processes in individual cancer cells in the context of the invasion-metastasis cascade.
Does higher sampling rate (Multiband + SENSE) benefit the detection of task correlated BOLD for cognitive neuroscience applications at 3T?

Multiband (MB) or Simultaneous multi-slice (SMS) acquisition schemes allow the acquisition of MRI signals from more than one spatial coordinate at a time. Commercial availability has brought this technique within the reach of many neuroscientists and psychologists. Most early evaluation of the performance of MB acquisition employed resting state fMRI or the most basic tasks. In this study, we tested whether the advantages of using MB acquisition schemes generalize to group analyses using a cognitive task more representative of typical cognitive neuroscience applications. Twenty-three subjects were scanned on a Philips 3T scanner using five sequences up to eight-fold acceleration with MB-factors 1 to 4, SENSE factors up to 2 and corresponding TRs of 2.45s down to 0.63s, while they viewed (i) movies showing complex actions with hand object interactions and (ii) control movies without hand object interaction. Using random effects group-level, voxel-wise analysis we found that all sequences were able to detect the basic action observation network known to be recruited by our task. The highest t-values were found for sequences with MB4 acceleration. For the MB1 sequence, a 50% bigger voxel volume was needed to reach comparable t-statistics. The group-level t-values for resting state networks (RSNs) were also highest for MB4 sequences. Here the MB1 sequence with larger voxel size did not perform comparable to the MB4 sequence. Altogether, we can thus recommend the use of MB4 (and SENSE 1.5 or 2) on a Philips scanner when aiming to perform group-level analyses using cognitive block design fMRI tasks and voxel sizes in the range of cortical thickness (e.g. 2.7mm isotropic). While results will not be dramatically changed by the use of multiband, our results suggest that MB will bring a moderate but significant benefit.
Cariogenic Streptococcus mutans produces strain-specific antibiotics that impair commensal colonization

Streptococcus mutans is a common constituent of dental plaque and an etiologic agent of dental caries (tooth decay). Here we elucidate a biosynthetic pathway, encoded by globally distributed strains of S. mutans, which produces a series of bioactive small molecules including reutericyclin and two N-acyl tetramic acid analogues active against oral commensal bacteria. This pathway may provide S. mutans with a competitive advantage, promoting dysbiosis and caries pathogenesis.
Expression and Function of 1 and av3 Integrins in Ovarian Cancer

Abstract Ovarian cancer cells disseminate by implanting onto the peritoneal mesothelial cell surface of the abdominal cavity. A common feature of these peritoneal implants is the presence of tumor cell invasion into the submesothelial extracellular matrix (ECM). In view of the important role of integrins in ECM recognition and cell migration, we were interested in defining the pattern of integrin expression and function in ovarian cancer cell lines and primary tissue samples. The β1 integrin chain was expressed by CAOV-3, SKOV-3, OVCAR-3, and SW626 ovarian cancer cell lines, associated with expression of α1, -2, -3, -5, and -6 chains. The α4 chain was also expressed by two of the four lines. In addition to β1 integrins, the αvβ3 integrin was also expressed, although there was no expression of β2, -4, and -7 chains. Immunoprecipitation of surface-labeled CAOV-3 cells with an anti-β2 antibody revealed a band at ≈110-130 kDa consistent with the known molecular mass of the β1 chain, as well as several associated bands consistent with noncovalently linked integrin α chains. A similar pattern of β1 and αvβ3 integrin expression was observed for primary ovarian cancer tissue samples. Ovarian cancer cell lines exhibited significant binding to collagen type I and laminin which was primarily mediated by β1 integrins. In contrast, ovarian cancer cell binding to fibronectin was mediated by both α5β1 and αvβ3 integrins. Even though mesothelial cells were observed to express fibronectin mRNA and protein, binding of ovarian cancer cells to peritoneal mesothelium was not blocked by neutralizing antibodies to β1 or αvβ3 integrins. These data suggest that functional integrins are commonly expressed by ovarian cancer cells, although they do not appear to mediate ovarian cancer cell implantation onto peritoneal mesothelium. The role that integrins play in the invasion of ovarian cancer cells into the submesothelial ECM deserves further investigation.
Electromagnetic mapping of the effects of deep brain stimulation and dopaminergic medication on movement-related cortical activity and corticomuscular coherence in Parkinson’s disease

Background Parkinson’s disease (PD) is a debilitating neurodegenerative disorder. PD can be treated with deep brain stimulation (DBS) when dopaminergic medication is no longer a viable option. Both treatments are effective in improving motor symptoms, however, their underlying mechanisms are not fully elucidated yet. Objectives To study the effects of DBS and dopaminergic medication treatments on cortical processing and corticomuscular drive during movements. Methods Magnetoencephalography (MEG) was recorded in 10 PD patients and 10 healthy controls, performing phasic hand contractions (hand gripping). Measurements were performed in DBS-treated, untreated and dopaminergic-medicated states; healthy controls received no treatment interventions. Participants performed phasic contractions with their right hand, recorded with electromyography (EMG). Our measures of interest were beta (13-30 Hz) corticomuscular coherence (CMC) and low-gamma (31-45 Hz) power. We used Bayesian statistics on summary values from sensor space data, and we localized the sources of the effects of treatments on beta-CMC and low-gamma power using beamforming. Results In PD patients, DBS led to reduced CMC values, whereas dopaminergic medication increased beta-CMC values (localized to contralateral M1) to even higher levels than the controls. DBS, on the other hand, increased low-gamma power (localized to M1) compared to controls and to other conditions. Yet both treatments had similar beneficial effects on the patients’ motor symptoms evaluated by UPDRS-III. Conclusion Despite comparable improvements from both treatments on motor symptoms, DBS and dopaminergic medication seem to have different effects on motor cortical function. This indicates that the treatments undertake different functional strategies to improve PD symptoms.
Bathymetric and geographical trends in growth of golden redfish (Sebastes norvegicus)

Golden redfish (Sebastes norvegicus) are a long-living (>50 years), late maturing (>10 years) species of commercial interest, distributed along the coast, shelves and continental slope of Norway, down to approximately 400 m depth in the water column. In recent years, analyses of size-at-age data have revealed variable growth trajectories for this species. Whilst some individuals appear to grow slowly after sexual maturity (37cm at ~ 15 years), others continue to grow throughout their lifetime up to 100 cm or more. To investigate how depth and latitude affect golden redfish growth patterns, we developed non-linear mixed effects statistical models. Alongside this, small scale experiments were also conducted to assess the quality of age-determination. The results showed that individuals found in deeper, northern waters present a higher growth potential, even when uncertainty in age determination and species identification were considered. The proximal causes for variations in the growth potential of S. norvegicus are still unresolved and the existence of a possible cryptic species remains a fundamental issue that will need to be addressed, in order to understand the causes behind observed growth variations.