Miracle-dz/UniFAR-FTUs huggingface dataset:
Asymmetric localization of the cell division machinery during Bacillus subtilis sporulation

The mechanistic details of bacterial cell division are poorly understood. The Gram-positive bacterium Bacillus subtilis can divide via two modes. During vegetative growth, the division septum is formed at the mid cell to produce two equal daughter cells. However, during sporulation, the division septum is formed closer to one pole to yield a smaller forespore and a larger mother cell. We use cryo-electron tomography to visualize the architectural differences in the organization of FtsAZ filaments, the major orchestrators of bacterial cell division during these conditions. We demonstrate that during vegetative growth, FtsAZ filaments are present uniformly around the leading edge of the invaginating septum but during sporulation, they are only present on the mother cell side. Our data show that the sporulation septum is thinner than the vegetative septum during constriction, and that this correlates with half as many FtsZ filaments tracking the division plane during sporulation as compared to vegetative growth. We further find that a sporulation-specific protein, SpoIIE, regulates divisome localization and septal thickness during sporulation. Our data provide first evidence of asymmetric localization of the cell division machinery, and not just septum formation, to produce different cell types with diverse fates in bacteria.
Degenerate circuits use distinct mechanisms to respond similarly to the same perturbation

There is considerable flexibility embedded within neural circuits. For example, separate modulatory inputs can differently configure the same underlying circuit but these different configurations generate comparable, or degenerate, activity patterns. However, little is known about whether these mechanistically different circuits in turn exhibit degenerate responses to the same inputs. We examined this issue using the crab (Cancer borealis) stomatogastric nervous system, in which stimulating the modulatory projection neuron MCN1 and bath applying the neuropeptide CabPK II elicit similar gastric mill (chewing) rhythms in the stomatogastric ganglion, despite differentially configuring the same neural circuit. We showed previously that bath applying the peptide hormone CCAP or stimulating the muscle stretch-sensitive sensory neuron GPR during the MCN1-elicited gastric mill rhythm selectively prolongs the protraction or retraction phase, respectively. Here, we found that these two influences on the CabPK-rhythm elicited some unique and unexpected consequences compared to their actions on the MCN1-rhythm. For example, in contrast to its effect on the MCN1-rhythm, CCAP selectively decreased the CabPK-rhythm retraction phase and thus increased the rhythm speed, whereas the CabPK-rhythm response to stimulating GPR during the retraction phase was similar its effect on the MCN1-rhythm (i.e. prolonging retraction). Interestingly, despite the comparable GPR actions on these degenerate rhythms, the underlying synaptic mechanism was distinct. Thus, degenerate circuits do not necessarily exhibit degenerate responses to the same influence, but when they do, it can occur via different underlying mechanisms. Significance Statement Circuits generating seemingly identical behaviors are often thought to arise from identical circuit states, as that is the most parsimonious explanation. Here we take advantage of an alternate scenario wherein a well-defined circuit with known connectivity generates similar activity patterns using distinct circuit states, via known mechanisms. The same peptide hormone modulation of these distinct circuit states produced divergent activity patterns, whereas the same sensory feedback altered these circuit outputs similarly but via different synaptic pathways. The latter observation limits the insights available from comparable studies in systems lacking detailed access to the underlying circuit.
Neurovascular-modulation

Neurovascular-modulation is based on two principles that derive directly from brain vascular ultra-structure, namely an exceptionally dense capillary bed (BBB length density: 972 mm/mm3) and a blood-brain-barrier (BBB) resistivity (ρ ~ 1×105 Ω.m) much higher than brain parenchyma/interstitial space (ρ ~ 4 Ω.m) or blood (ρ ~ 1 Ω.m). Principle 1: Electrical current crosses between the brain parenchyma (interstitial space) and vasculature, producing BBB electric fields (EBBB) that are > 400x of the average parenchyma electric field (ĒBRAIN), which in turn modulates transport across the BBB. Specifically, for a BBB space constant (λBBB) and wall thickness (dth-BBB): analytical solution for maximum BBB electric field (EABBB) is given as: (ĒBRAIN × λBBB) / dth-BBB. Direct vascular stimulation suggests novel therapeutic strategies such as boosting metabolic capacity or interstitial fluid clearance. Boosting metabolic capacity impacts all forms of neuromodulation, including those applying intensive stimulation or driving neuroplasticity. Boosting interstitial fluid clearance has broad implications as a treatment for neurodegenerative disease including Alzheimer’s disease. Principle 2: Electrical current in the brain parenchyma is distorted around brain vasculature, amplifying neuronal polarization. Specifically, vascular ultra-structure produces ~50% modulation of the average parenchyma electric field (ĒBRAIN) over the ~40 μm inter-capillary distance. The divergence of EBRAIN (activating function) is thus ~100 kV/m2 per unit average parenchyma electric field (ĒBRAIN). This impacts all forms of neuromodulation, including Deep Brain Stimulation (DBS), Spinal Cord Stimulation (SCS), Transcranial Magnetic Stimulation (TMS), Electroconvulsive Therapy (ECT), and transcranial electrical stimulation (tES) techniques such a transcranial Direct Current Stimulation (tDCS). Specifically, whereas spatial profile of EBRAIN along neurons is traditionally assumed to depend on macroscopic anatomy, it instead depends on local vascular ultra-structure.
A comparison of dopaminergic and cholinergic populations reveals unique contributions of VTA dopamine neurons to short-term memory

We systematically compared the contribution of two dopaminergic and two cholinergic ascending populations to a spatial short-term memory task in rats. In ventral tegmental area dopamine (VTA-DA) and nucleus basalis cholinergic (NB-ChAT) populations, trial-by-trial fluctuations in activity during the delay period related to performance with an inverted-U, despite the fact that both populations had low activity during that time. Transient manipulations revealed that only VTA-DA neurons, and not the other three populations we examined, contributed causally and selectively to short-term memory. This contribution was most significant during the delay period, when both increases or decreases in VTA-DA activity impaired short-term memory. Our results reveal a surprising dissociation between when VTA-DA neurons are most active and when they have the biggest causal contribution to short-term memory, while also providing new types of support for classic ideas about an inverted-U relationship between neuromodulation and cognition.
Drosophila p53 isoforms have overlapping and distinct functions in germline genome integrity and oocyte quality control

p53 gene family members in humans and other organisms encode a large number of protein isoforms whose functions are largely undefined. Using Drosophila as a model, we find that a p53B isoform is expressed predominantly in the germline where it colocalizes with p53A into subnuclear bodies. It is only p53A, however, that mediates the apoptotic response to ionizing radiation in the germline and soma. In contrast, p53A and p53B both respond to meiotic DNA breaks and are required during oogenesis to prevent persistent germline DNA breaks, an activity that is more crucial when meiotic recombination is defective. We find that in oocytes with persistent DNA breaks p53A is required to activate a meiotic pachytene checkpoint. Our findings indicate that Drosophila p53 isoforms have DNA lesion and cell type-specific functions, with parallels to the functions of mammalian p53 family members in the genotoxic stress response and oocyte quality control.
The LTB4–BLT1 axis regulates actomyosin and β2-integrin dynamics during neutrophil extravasation

Neutrophils arrest and extravasate from the blood vessels in response to infection and injury. Using intravital subcellular microscopy, Subramanian et al. identify a role for extracellular vesicle–based autocrine/paracrine LTB4/BLT1 signaling in promoting the rearrangement of the actomyosin cytoskeleton and β2-integrin during neutrophil extravasation in live animals.
Glycogene Expression Profiling of Hepatic Cells by RNA-Seq Analysis for Glyco-Biomarker Identification

Glycans are primarily generated by “glycogenes,” which consist of more than 200 genes for glycosynthesis, including sugar-nucleotide synthases, sugar-nucleotide transporters, and glycosyltransferases. Measuring the expression level of glycogenes is one of the approaches to analyze the glycomes of particular biological and clinical samples. To develop an effective strategy for identifying the glycosylated biomarkers, we performed transcriptome analyses using quantitative real-time polymerase chain reaction (qRT-PCR) arrays and RNA sequencing (RNA-Seq). First, we measured and analyzed the transcriptome from the primary culture of human liver cells and hepatocarcinoma cells using RNA-Seq. This analysis revealed similar but distinctive expression profiles of glycogenes among hepatic cells as indicated by the qRT-PCR arrays, which determined a copy number of 186 glycogenes. Both data sets indicated that altered expression of glycosyltransferases affect the glycosylation of particular glycoproteins, which is consistent with the mass analysis data. Moreover, RNA-Seq analysis can uncover mutations in glycogenes and search differently expressed genes out of more than 50,000 distinct human gene transcripts including candidate biomarkers that were previously reported for hepatocarcinoma cells. Identification of candidate glyco-biomarkers from the expression profile of the glycogenes and proteins from liver cancer tissues available from public database emphasized the possibility that even though the expression level of biomarkers might not be altered, the expression of the glycogenes modifying biomarkers, generating glyco-biomarkers, might be different. Pathway analysis revealed that ~20% of the glycogenes exhibited different expression levels in normal and cancer cells. Thus, transcriptome analyses using both qRT-PCR array and RNA-Seq in combination with glycome and glycoproteome analyses can be advantageous to identify “glyco-biomarkers” by reinforcing information at the expression levels of both glycogenes and proteins.
Relationships between anatomical and densitometric characteristics of black spruce and summer temperature at tree line in northern Quebec

Tracheid cell number, cell diameter, and cell-wall thickness of black spruce (Picea mariana (Mill.) BSP) tree rings at the tree line (northern Quebec, Canada) were measured using image analysis. The densitometric data from the same samples were used to evaluate the features of image analysis. The anatomical data were correlated with summer temperature variables, including: means of pentad temperature (five consecutive days), growing season (May- September), sum of degree-days, and number of frost-free days. Our results suggest that the main cause of the pale appearance of light rings is thinner latewood cell-wall thickness. Some latewood variables are strongly correlated with corresponding indices for ring cell number and diameter, and ring cell wall thickness. Anatomical ring cell number and the sum of cell diameters (ring widths) were correlated to tree-ring width parameters derived from densitometry. Ring cell number and annual sum of cell diameter also showed very similar trends with both chronologies.
Discovery and Characterization of an Endo-1,3-Fucanase From Marine Bacterium Wenyingzhuangia fucanilytica: A Novel Glycoside Hydrolase Family

Sulfated fucans are important marine polysaccharides widely distributed in brown algae and echinoderms, which gained increasing research interest for their various biological and biomedical activities. Fucanases could serve as tools in the bioconversion and structural investigation of sulfated fucans. A few gene-defined endo-1,4-fucanases have been characterized, while the sequence of endo-1,3-fucanase remain unstudied. Here, an endo-1,3-fucanase gene funA was screened from the genome of marine bacterium Wenyingzhuangia fucanilytica CZ1127T using transcriptomics. None of the previously reported glycoside hydrolase domains were predicted in the enzyme FunA, which hydrolyzed sulfated fucans in a random endo-acting manner. Ultrahigh performance size exclusion chromatography-mass spectrometry and nuclear magnetic resonance analyses revealed that FunA specifically cleaves α-1,3 glycosidic linkage between 2-O-sulfated and non-sulfated fucose residues. FunA exhibited transglycosylating activity with glycerin, methanol, and L-fucose as acceptors. D206 and E264 were critical for the functioning of FunA as identified by the site-directed mutagenesis. Another five homologs of FunA were confirmed to possess endo-1,3-fucanase activities. This is the first report on the sequence of endo-1,3-fucanase. The novelty of FunA and its homologs in sequences and activity shed light on a novel glycoside hydrolase family, GH168.
Feed efficiency of Nellore cattle selected for postweaning weight

Foram comparados dois rebanhos Nelore, um selecionado para maior peso pos-desmame e outro controle, selecionado para a media de peso pos-desmame, para avaliar os efeitos de 29 anos de selecao sobre a eficiencia alimentar. Sessenta machos Nelore com 205 kg e 267 dias de idade (41 selecionados e 19 controle), foram avaliados em baias individuais durante a prova de ganho de peso. O desempenho e o consumo de materia seca foram utilizados para determinar as seguintes medidas de eficiencia: conversao alimentar; consumo alimentar residual; ganho residual; eficiencia parcial de crescimento; taxa de crescimento relativo; e taxa de Kleiber. Apos o periodo experimental de 112 dias, os animais controle apresentaram menor peso vivo final em comparacao aos selecionados, contudo, nao diferiram quanto ao consumo de materia seca (% do peso vivo), a area de olho-de-lombo e as espessuras de gordura subcutânea na altura da 12a costela e na regiao da picanha. O consumo de materia seca (kg/dia) e o ganho medio diario dos animais selecionados foram, respectivamente, 19,4 e 26,4% superiores aos dos controle. O maior ganho medio diario dos animais selecionados promoveu melhora significativa, em torno de 6%, na conversao alimentar; 70 g/dia no ganho residual; e de 17% na taxa de Kleiber. As demais medidas de eficiencia (consumo alimentar residual, eficiencia parcial de crescimento e taxa de crescimento relativo) nao diferiram entre os rebanhos. Os 29 anos de selecao para peso pos-desmame nao afetaram a eficiencia alimentar de bovinos Nelore.
Mating system and reproductive success in the Siberian flying squirrel

Abstract Mating systems and factors affecting reproductive success are much studied especially for mammals that are large bodied, have marked sexual size dimorphisms, and have a female-defense mating system. For species that deviate from these patterns, we need more information on mating systems and reproductive success. Here, we study mating system and factors related to reproductive success in a solitary rodent, the Siberian flying squirrel (Pteromys volans). In contrast to most other mammals, males are not larger than females in flying squirrels. Similarly to most mammalian species, we observed multimale paternity within litters and reproductive success of males being positively related to body mass. Variation in reproductive success was clearly higher for males than for females, although remained lower than observed in species with highly male-biased sexual size dimorphism. Female flying squirrels lived in nonoverlapping home ranges and reproductive success was positively related to body mass, in line with earlier predictions for large female size in mammals.
Frequency-Dependent Changes in Interhemispheric Functional Connectivity Measured by Resting-State fMRI in Children With Idiopathic Generalized Epilepsy

Epilepsy is associated with abnormal spatiotemporal changes in resting-state brain connectivity, but how these changes are characterized in interhemispheric coupling remains unclear. This study aimed to characterize frequency-dependent alterations in voxel-wise mirrored homotopic connectivity (VMHC) measured by resting-state functional magnetic resonance imaging (rs-fMRI) in children with idiopathic generalized epilepsy (IGE). Rs-fMRI data were collected in 21 children with IGE and 22 demographically matched children with typical development. We used three resting-state frequency bands (full, 0.01–0.08 Hz; slow-4, 0.027–0.073 Hz; slow-5, 0.01–0.027 Hz) to compute VMHC and locate the significant foci. Voxel-wise p <0.001 and cluster-level p <0.05 cluster-level family-wise error correction was applied. In between-group comparisons, we identified that the full and higher frequency (slow-4) bands showed similar reductions in VMHC including Rolandic operculum, putamen, superior frontal, lateral parietal, middle cingulate, and precuneus in children with IGE. In the lower frequency band (slow-5), we identified specific reductions in VMHC in orbitofrontal and middle temporal gyri in children with IGE. Further analyses on main effects and interaction between group and frequency band suggested significant frequency-dependent changes in VMHC, and no significant interaction was found. The results were generally similar with global brain signal regression. Additional association analysis showed that VMHC in the putamen within the full and slow-4 bands was significantly positively correlated with chronological age in children with IGE, and the same analysis was non-significant in the controls; VMHC in the medial prefrontal region in the slow-4 band was significantly positively correlated with IQ performance sub-score. Our findings suggest that IGE children show frequency-dependent changes in interhemispheric integration that spans regions and systems involving cortical-subcortical, language, and visuomotor processing. Decreased functional coupling within the dorsal striatum may reflect atypical development in children with IGE.
THE ANATOMY OF PACHYDERMIA LAEVIS (ARCHAEOGASTROPODA: 'PELTOSPIRIDAE')

The anatomy of Pachydermia laevis Waren & Bouchet, 1989 is investigated. It is a deep-sea gastropod and restricted to hydrothermal vents of the East Pacific Rise. Its anatomy resembles that of Melanodrymia aurantiaca Hickman, 1984 (Melanodrymiidae) in most respects, except that its gonopericardial duct opens into the renopericardial duct, not into the peri-cardial chamber, and that it lacks a copulatory organ. Examination of M. aurantiaca main confirms earlier work. The two species have a cerebral buccal connective fused with the cerebral ganglion (not free from it), a synapomorphy that has not been described for any other archaeogastropod. The investigation suggests that Melanodrymia and Pachydermia are closely related and together with Cyathermiidae and Neomphalidae form a monophyletic group within the Neomphalina. No evidence was found to support earlier speculations about close relations of Neomphalina to Viviparoidea.
Absence of reliable physiological signature of illusory body ownership revealed by fine-grained autonomic measurement during the rubber hand illusion

The neural representation of a ‘biological self’ is linked theoretically to the control of bodily physiology. In an infleuntial model, selfhood relates to internal agency and higher-order interoceptive representation, inferred from the predicted impact of efferent autonomic nerves on afferent viscerosensory feedback. Here we tested if an altered representation of physical self (illusory embodiment of an artificial hand) is accompanied by sustained shifts in autonomic activity. Participants (N=37) underwent procedures for induction of the rubber hand illusion (synchronous stroking of own unseen hand and observed stroking of artificial hand) and a control condition (asychronous stroking). We recorded electrodermal activity, electrocardiography, and non-invasive measurement of multiunit skin sympathetic nerve activity (SKNA) from the chest. We compared measures between task conditions, and between individuals who did and did not experience the illusion. Bayes factors quantified the strength of evidence for and against null hypotheses. Subjective reports and observed proprioceptive drift confirmed the efficacy of synchronous vs asynchronous condition in inducing illusory hand ownership. Stringent discriminant analysis classified 24 /37 individuals as experiencing the rubber hand illusion. Electrodermal activity, heart rate, heart rate variability, and SKNA measures revealed no autonomic differences between synchronous vs asynchronous conditions, nor between individuals who did or did not experience the rubber hand illusion. Bayes factors confirmed there was substantial evidence for no physiological differences. In contrast to earlier reports, our cardiac and electrodermal autonomic data, including fine grained SKNA measurement, provide substantial evidence for the absence of a reliable change in physiological state during induction or experience of the rubber hand illusion. If illusory body ownership is coupled to, or facilitated by, changes in efferent autonomic activity and afferent viscerosensory feedback, our findings suggest that such changes in bodily physiology are not sustained as an obligatory component of the illusion.