title: Time Trend, Social Vulnerability, and Identification of Risk Areas for Tuberculosis in Brazil: an Ecological Study

abstract:
INTRODUCTIONTuberculosis is one of the ten leading causes of death and the leading infectious cause worldwide. The disease represents a challenge to health systems around the world. In 2018, it is estimated that 10 million people were affected by tuberculosis, and approximately 1.5 million people died due to the disease worldwide, including 251,000 patients coinfected with HIV. In Brazil, the disease caused 4,490 deaths, with rate of 2.2 deaths per 100,000 inhabitants. The objective of this study was to analyze the time behavior, spatial distribution, and the effects of social vulnerability on the incidence of TB in Brazil during the period from 2001 to 2017.

METHODSA spatial-temporal ecological study was conducted, including all new cases of tuberculosis registered in Brazil during the period from 2001 to 2017. The following variables were analyzed: incidence rate of tuberculosis, the Social Vulnerability Index, its subindices, its 16 indicators, and an additional 14 variables available on the Atlas of Social Vulnerability. The statistical treatment of the data consisted of the following three stages: a) time trend analysis with a joinpoint regression model; b) spatial analysis and identification of risk areas based on smoothing of the incidence rate by local empirical Bayesian model, application of global and local Moran statistics, and, finally, spatial-temporal scan statistics; and c) analysis of association between the incidence rate and the indicators of social vulnerability.

RESULTSBrazil reduced the incidence of tuberculosis from 42.8 per 100,000 to 35.2 per 100,000 between 2001 and 2017. Only the state of Minas Gerais showed an increasing trend, whereas nine other states showed a stationary trend. A total of 326 Brazilian municipalities were classified as high priority, and 22 high-risk spatial clusters were identified. The overall Social Vulnerability Index and the subindices of Human Capital and Income and Work were associated with the incidence of tuberculosis. It was also observed that the incidence rates were greater in municipalities with greater social vulnerability.

CONCLUSIONSThis study identified spatial clusters with high risk of TB in Brazil. A significant association was observed between the incidence rate of TB and the indices of social vulnerability.

category: pathology


title: Visual perception of texture regularity: conjoint measurements and a wavelet response-distribution model

abstract:
Texture regularity, such as the repeating pattern in a carpet, brickwork or tree bark, is a ubiquitous feature of the visual world. The perception of regularity has generally been studied using multi-element textures in which the degree of regularity has been manipulated by adding random jitter to the elements positions. Here we used three-factor Maximum Likelihood Conjoint Measurement (MLCM) to investigate the encoding of regularity information under more complex conditions in which element spacing and size, in addition to positional jitter, were manipulated. Human observers were presented with large numbers of pairs of multi-element stimuli with varying levels of the three factors, and indicated on each trial which stimulus appeared more regular. All three factors contributed to regularity perception. Jitter, as expected, strongly affected regularity perception. This effect of jitter on regularity perception is strongest at small element spacing and large texture element size, suggesting that the visual system utilizes the edge-to-edge distance between elements as the basis for regularity judgments. We then examined how the responses of a bank of Gabor wavelet spatial filters might account for our results. Our analysis indicates that SF-peakedness, a previously favored proposal, is insufficient for regularity encoding since it varied more with element spacing and size than with jitter. Instead, our results support the idea that the visual system may extract texture regularity information from the moments of the SF-distribution across orientation. In our best-performing model, the variance of SF-distribution skew across orientations can explain 70% of the variance of estimated texture regularity from our data, suggesting that it could provide a candidate readout for perceived regularity.

Author SummaryWe investigated human perception of texture regularity, in which subjects made comparative judgements of regularity in pairs of texture stimuli with differing levels of three parameters of texture construction - spacing and size of texture elements, and their positional jitter. We analyzed the data using a novel approach involving three-factor Maximum Likelihood Conjoint Measurement (MLCM). We utilized a novel analysis-of-variance approach in MLCM to evaluate the effect size and significance of the three factors as well as their interactions. We found that all three factors contributed to perceived regularity, with significant main effects and interactions between factors, in a manner suggesting edge-to-edge distances between elements might contribute importantly to regularity judgments. Using a bank of Gabor wavelet spatial filters to model the response of the human visual system to our textures, we compared four types of ways that the distribution of wavelet responses could account for our measured data on perceived regularity. Our results suggest that the orientation as well as spatial frequency information from the wavelet filters also contributes importantly - in particular, the skew of the variance of the SF-distribution across orientation provides a candidate basis for perceived texture regularity.

category: neuroscience


title: Cell-type specific arousal-dependent modulation of thalamic activity in the lateral geniculate nucleus

abstract: State dependent thalamocortical activity is important for sensory coding, oscillations and cognition. The lateral geniculate nucleus (LGN) relays visual information to the cortex, but the state dependent spontaneous and visually evoked activity of LGN neurons in awake behaving animals remains controversial. Using a combination of pupillometry, extracellular and intracellular recordings from identified LGN neurons we show that thalamocortical neurons and interneurons are distinctly correlated to arousal forming two complementary coalitions. Intracellular recordings indicated that the membrane potential of LGN TC neurons was tightly correlated to fluctuations in pupil size. Inactivating the corticothalamic feedback to the LGN suppressed the arousal dependency of LGN neurons. Taken together our results show that LGN neuronal membrane potential and action potential output are dynamically linked to arousal dependent brain states in awake mice and this might have important functional implications.


title: Shared functional connections within and between cortical networks predict individual cognitive abilities in males and females

abstract: A thorough understanding of sex-independent and sex-specific neurobiological features that underlie cognitive abilities in healthy individuals is essential for the study of neurological illnesses in which males and females differentially experience and exhibit cognitive impairment. Here, we evaluate sex-independent and sex-specific relationships between functional connectivity and individual cognitive abilities in 392 healthy young adults (196 males) from the Human Connectome Project. First, we establish that sex-independent models comparably predict crystallised abilities in males and females, but more accurately predict fluid abilities in males. Second, we demonstrate sex-specific models comparably predict crystallised abilities within and between sexes, and generally fail to predict fluid abilities in either sex. Third, we reveal that largely overlapping connections between visual, dorsal attention, ventral attention, and temporal parietal networks are associated with better performance on crystallised and fluid cognitive tests in males and females, while connections within visual, somatomotor, and temporal parietal networks are associated with poorer performance. Together, our findings suggest that shared neurobiological features of the functional connectome underlie crystallised and fluid abilities across the sexes.


title: A transient postnatal quiescent period precedes emergence of mature cortical dynamics

abstract: Mature neural networks synchronize and integrate spatiotemporal activity patterns to support cognition. Emergence of these activity patterns and functions is believed to be developmentally regulated, but the postnatal time course for neural networks to perform complex computations remains unknown. We investigate the progression of large-scale synaptic and cellular activity patterns across development using high spatiotemporal resolution in vivo electrophysiology in immature mice. We reveal that mature cortical processes emerge rapidly and simultaneously after a discrete but volatile transition period at the beginning of the second postnatal week of rodent development. The transition is characterized by relative neural quiescence, after which spatially distributed, temporally precise, and internally organized activity occurs. We demonstrate a similar developmental trajectory in humans, suggesting an evolutionarily conserved mechanism to transition network operation. We hypothesize that this transient quiescent period is a requisite for the subsequent emergence of coordinated cortical networks.


title: 3D stochastic simulation of chemoattractant-mediated excitability in cells

abstract:
During the last decade, a consensus has emerged that the stochastic triggering of an excitable system drives pseudopod formation and subsequent migration of amoeboid cells. The presence of chemoattractant stimuli alters the threshold for triggering this activity and can bias the direction of migration. Though noise plays an important role in these behaviors, mathematical models have typically ignored its origin and merely introduced it as an external signal into a series of reaction-diffusion equations. Here we consider a more realistic description based on a reaction-diffusion master equation formalism to implement these networks. In this scheme, noise arises naturally from a stochastic description of the various reaction and diffusion terms. Working on a three-dimensional geometry in which separate compartments are divided into a tetrahedral mesh, we implement a modular description of the system, consisting of G-protein coupled receptor signaling (GPCR), a local excitation-global inhibition mechanism (LEGI), and signal transduction excitable network (STEN). Our models implement detailed biochemical descriptions whenever this information is available, such as in the GPCR and G-protein interactions. In contrast, where the biochemical entities are less certain, such as the LEGI mechanism, we consider various possible schemes and highlight the differences between them. Our stimulations show that even when the LEGI mechanism displays perfect adaptation in terms of the mean level of proteins, the variance shows a dose-dependence. This differs between the various models considered, suggesting a possible means for determining experimentally among the various potential networks. Overall, our simulations recreate temporal and spatial patterns observed experimentally in both wild-type and perturbed cells, providing further evidence for the excitable system paradigm. Moreover, because of the overall importance and ubiquity of the modules we consider, including GPCR signaling and adaptation, our results will be of interest beyond the field of directed migration.

Author summaryThough the term noise usually carries negative connotations, it can also contribute positively to the characteristic dynamics of a system. In biological systems, where noise arises from the stochastic interactions between molecules, its study is usually confined to genetic regulatory systems in which copy numbers are small and fluctuations large. However, noise can have important roles when the number of signaling molecules is large. The extension of pseudopods and the subsequent motion of amoeboid cells arises from the noise-induced trigger of an excitable system. Chemoattractant signals bias this triggering thereby directing cell motion. To date, this paradigm has not been tested by mathematical models that account accurately for the noise that arises in the corresponding reactions. In this study, we employ a reaction-diffusion master equation approach to investigate the effects of noise. Using a modular approach and a three-dimensional cell model with specific subdomains attributed to the cell membrane and cortex, we explore the spatiotemporal dynamics of the system. Our simulations recreate many experimentally-observed cell behaviors thereby supporting the biased-excitable hypothesis.

category: cell biology


title: Invariant Differential Expression Analysis Reveals Mechanism of Cancer Resistance to Cell Cycle Inhibitors

abstract: Retinoblastoma (RB) is a good model to study drug resistance to cell-cycle inhibitors because it is driven by mutations in the core components of cell-cycle, i.e, Rb gene. However, there is limited gene expression dataset in RB which has major reproducibility issues. We have developed invariant differential expression analysis (iDEA) that improves the state of the art in differential expression analysis (DEA). iDEA uses strong Boolean implication relationships in a large diverse human dataset GSE119087 (n = 25,955) to filter the noisy differentially expressed genes (DEGs). iDEA was applied to RB datasets and a gene signature was computed that led to prediction and mechanism of drug sensitivity. The prediction was confirmed using drugs-sensitive/resistant RB cell-lines and mouse xenograft models using CDC25 inhibitor NSC663284. iDEA improved reproducibility of differential expression across diverse retina/RB cohorts and RB cell-lines with different drug sensitivity (Y79/Weri vs NCC). Pathway analysis revealed WNT/{beta}-catenin involved in distinguishing drug sensitivity to CDC25 inhibitor NSC663284. NSC663284 inhibited tumour cell proliferation in mouse xenograft model containing Y79 cells indicating novel therapeutic option in RB. Invariant differentially expressed genes (iDEGs) are robustly associated with outcome in diverse cancer datasets and supports for a fundamental mechanism of drug resistance.

category: systems biology


title: The IL-10GFP (VeRT-X) mouse strain is not suitable for the detection of IL-10 production by granulocytes during lung inflammation

abstract: The clear and unequivocal identification of immune effector functions is essential to understand immune responses. The cytokine IL-10 is a critical immune regulator and was shown, for example, to limit pathology during various lung diseases. However, the clear identification of IL-10-producing cells is challenging and, therefore, reporter mouse lines were developed to facilitate their detection. Several such reporter lines utilize GFP, including the IL-10GFP (VeRT-X) reporter strain studied here. In line with previous reports, we found that this IL-10GFP line faithfully reports on the IL-10 production of lymphoid cells. However, we show that the IL-10GFP reporter is not suitable to analyse IL-10 production of myeloid cells during inflammations. During inflammation, the autofluorescence of myeloid cells increased to an extent that entirely masked the IL-10-specific GFP-signal. Our data illustrate a general and important technical caveat using GFP-reporter lines for the analysis of myeloid cells and suggest that previous reports on effector functions of myeloid cells using such GFP-based reporters might require re-evaluation.

category: immunology


title: Soil respiration variation along an altitudinal gradient in Italian Alps: Disentangling forest structure and temperature effects

abstract: To understand the main determinants of soil respiration (SR), we investigated the changes of soil respiration and soil physicochemical properties, including soil carbon (C) and nitrogen (N), root C and N, litter C and N, soil bulk densities and soil pH at five forest sites, along an elevation/temperature gradient (404 to 2101 m a.s.l) in Northern Italy, where confounding factors such as aspect and soil parent material are minimized, but an ample variation in forest structure and composition is present. Our result indicated that SR rates increased with temperature in all sites, and about 55% - 76% of SR was explained by temperature. Annual cumulative SR, ranging between 0.65 and 1.40 kg C m-2 yr-1, declined along the elevation gradient, while temperature sensitivity (Q10) of SR increased with elevation. However, a high SR rate (1.27 kg C m-2 yr-1) and low Q10 were recorded in the old conifer forest stand at 1731 m a.s.l., characterized by a complex structure and high productivity, introducing nonlinearity in the relations with elevation and temperature. Reference SR at the temperature of 10{degrees}C (SRref) was not related to elevation. A significant linear negative relationship was found for bulk density with elevation. On the contrary, soil C, soil N, root C, root N, pH and litter mass were better fitted by nonlinear relations with elevation. However, it was not possible to confirm a significant correlation of SR with these parameters once the effect of temperature has been removed (SRref). These results show how the main factor affecting SR in forest ecosystems along this Alpine elevation gradient is temperature, but its regulating role can be strongly influenced by site biological characteristics, particularly vegetation type and structure. This study also confirms that high elevation sites are rich in C stored in the soil and also more sensitive to climate change, being prone to high carbon losses as CO2. Conversely, forest ecosystems with a complex structure, with high SRref and moderate Q10, can be more resilient.

category: ecology


title: Goal-Driven Recurrent Neural Network Models of the Ventral Visual Stream

abstract: The computational role of the abundant feedback connections in the ventral visual stream (VVS) is unclear, enabling humans and non-human primates to effortlessly recognize objects across a multitude of viewing conditions. Prior studies have augmented feedforward convolutional neural networks (CNNs) with recurrent connections to study their role in visual processing; however, often these recurrent networks are optimized directly on neural data or the comparative metrics used are undefined for standard feedforward networks that lack these connections. In this work, we develop task-optimized convolutional recurrent (ConvRNN) network models that more correctly mimic the timing and gross neuroanatomy of the ventral pathway. Properly chosen intermediate-depth ConvRNN circuit architectures, which incorporate mechanisms of feedforward bypassing and recurrent gating, can achieve high performance on a core recognition task, comparable to that of much deeper feedforward networks. We then develop methods that allow us to compare both CNNs and ConvRNNs to fine-grained measurements of primate categorization behavior and neural response trajectories across thousands of stimuli. We find that high performing ConvRNNs provide a better match to this data than feedforward networks of any depth, predicting the precise timings at which each stimulus is behaviorally decoded from neural activation patterns. Moreover, these ConvRNN circuits consistently produce quantitatively accurate predictions of neural dynamics from V4 and IT across the entire stimulus presentation. In fact, we find that the highest performing ConvRNNs, which best match neural and behavioral data, also achieve a strong Pareto-tradeoff between task performance and overall network size. Taken together, our results suggest the functional purpose of recurrence in the ventral pathway is to fit a high performing network in cortex, attaining computational power through temporal rather than spatial complexity.


title: Recurrent Connections in the Primate Ventral Visual Stream Mediate a Tradeoff Between Task Performance and Network Size During Core Object Recognition


title: Human breast milk enhances intestinal mucosal barrier function and innate immunity in a pediatric human enteroid model

abstract: Breastfeeding has been associated with long lasting health benefits. Nutrients and bioactive components of human breast milk promote cell growth, immune development, and shield the infant gut from insults and microbial threats. The molecular and cellular events involved in these processes are ill defined. We have established human pediatric enteroids and interrogated maternal milks impact on epithelial cell maturation and function in comparison with commercial infant formula. Colostrum applied apically to pediatric enteroid monolayers reduced ion permeability, stimulated epithelial cell differentiation, and enhanced tight junction function by upregulating occludin expression. Breast milk heightened the production of antimicrobial peptide -defensin 5 by goblet and Paneth cells, and modulated cytokine production, which abolished apical release of pro-inflammatory GM-CSF. These attributes were not found in commercial infant formula. Epithelial cells exposed to breast milk elevated apical and intracellular pIgR expression and enabled maternal IgA translocation. Proteomic data revealed a breast milk-induced molecular pattern associated with tissue remodeling and homeostasis. Using a novel ex vivo pediatric enteroid model, we have identified cellular and molecular pathways involved in human milk-mediated improvement of human intestinal physiology and immunity.


title: Humans hastened the range collapse and extinction of woolly mammoth

abstract: Pathways to extinction start long before the death of the last individual. However, causes of early-stage population declines and the susceptibility of small residual populations to extirpation are typically studied in isolation. Using validated process-explicit models, we disentangle the ecological mechanisms and threats that were integral in the initial decline and later extinction of the woolly mammoth. We show that reconciling ancient DNA data on woolly mammoth population decline with fossil evidence of location and timing of extinction requires process-explicit models with specific demographic and niche constraints, and a constrained synergy of climatic change and human impacts. Validated models needed humans to hasten climate-driven population declines by many millennia, and to allow woolly mammoths to persist in mainland Arctic refugia until the mid-Holocene. Our results show that the role of humans in the extinction dynamics of woolly mammoth began well before the Holocene, exerting lasting effects on the spatial pattern and timing of its range-wide extinction.


title: Skillful prediction of tropical Pacific fisheries provided by Atlantic Ninos

abstract: Tropical Pacific upwelling-dependent ecosystems are the most productive and variable worldwide, mainly due to the influence of El Nino Southern Oscillation (ENSO). ENSO can be forecasted seasons ahead thanks to assorted climate precursors (local-Pacific processes, pantropical interactions). However, owing to observational data scarcity and bias-related issues in earth system models, little is known about the importance of these precursors for marine ecosystem prediction. With recently released reanalysis-nudged global marine ecosystem simulations, these constraints can be sidestepped, allowing full examination of tropical Pacific ecosystem predictability. By complementing historical fishing records with marine ecosystem model data, we show herein that equatorial Atlantic Sea Surface Temperatures (SSTs) constitute a superlative predictability source for tropical Pacific marine yields, which can be forecasted over large-scale areas up to 2 years in advance. A detailed physical-biological mechanism is proposed whereby Atlantic SSTs modulate upwelling of nutrient-rich waters in the tropical Pacific, leading to a bottom-up propagation of the climate-related signal across the marine food web. Our results represent historical and near-future climate conditions and provide a useful springboard for implementing a marine ecosystem prediction system in the tropical Pacific.


title: Climate change shifts abiotic niche of temperate skates towards deeper zones in the Southwestern Atlantic Ocean

abstract: Climatic changes are disrupting distribution patterns of populations through shifts in species abiotic niches and habitat loss. The abiotic niche of marine benthic taxa such as skates, however, may be more climatically stable compared to upper layers of the water column, in which aquatic organisms are more exposed to immediate impacts of warming. Here, we estimate climate change impacts in Riorajini, a tribe of four skates, as a proxy to (1) evaluate the vulnerability of a temperate coastal zone in the Atlantic Southwest, and (2) study niche dynamics in a scenario of environmental changes on this group of threatened species. We modelled each species abiotic niche under present (2000-2014) and future (2100, Representative Concentration Pathway 8.5) climatic scenarios, then measured niche overlap, stability, expansion, and unfilling. Our results reveal an expansion of suitable environment for the occurrence of the tribe in up to 20% towards deeper areas (longitudinal shift), although still within the limits of the continental shelf. We discussed the downfalls of such shift to the species and to the local biota in newly invaded areas, and suggest that even deeper layers of marine temperate zones are vulnerable to dramatic environmental changes as a consequence of global warming.


title: Association between land use and composition of amphibian species in temperate Brazilian forest remnants

abstract: We evaluated the influence of landscape configuration on the diversity of anurans in Atlantic Forest remnants in southern Brazil. As natural habits provide better conditions for the survival of amphibians, we expected to find more diverse communities in areas with more forest cover. We sampled tadpoles in 28 breeding sites distributed in seven forest remnants. We recorded 22 anuran species and richness varied from 6 to 12 species between sites. Most of the recorded species were not forest specialists, except for Boana curupi and Crossodactylus schmidti. There was a significant overlap in the species composition between all remnants, and the Generalized Linear Mixed Model indicated that landscape use did not affect species richness. The PERMANOVA showed that forest and livestock farming explained the dissimilarity in the composition of the communities. One possible explanation for this is that the remnants are surrounded by a relatively well-preserved landscape, which offers favorable conditions for the maintenance of local populations and homogenizes species composition across the sampling sites. The lack of any strong association between tadpole species richness and land use suggests that anurans are primally affected by habitat characteristics that are detected only on a fine-scale analysis.


title: The frequency and topology of pseudoorthologs

abstract:
Phylogenetics has long relied on the use of orthologs, or genes related through speciation events, to infer species relationships. However, identifying orthologs is difficult because gene duplication can obscure relationships among genes. Researchers have been particularly concerned with the insidious effects of pseudoorthologs--duplicated genes that are mistaken for orthologs because they are present in a single copy in each sampled species. Because gene tree topologies of pseudoorthologs may differ from the species tree topology, they have often been invoked as the cause of counterintuitive results in phylogenetics. Despite these perceived problems, no previous work has calculated the probabilities of pseudoortholog topologies, or has been able to circumscribe the regions of parameter space in which pseudoorthologs are most likely to occur. Here, we introduce a model for calculating the probabilities and branch lengths of orthologs and pseudoorthologs, including concordant and discordant pseudoortholog topologies, on a rooted three-taxon species tree. We show that the probability of orthologs is high relative to the probability of pseudoorthologs across reasonable regions of parameter space. Furthermore, the probabilities of the two discordant topologies are equal and never exceed that of the concordant topology, generally being much lower. We describe the species tree topologies most prone to generating pseudoorthologs, finding that they are likely to present problems to phylogenetic inference irrespective of the presence of pseudoorthologs. Overall, our results suggest that pseudoorthologs are less of a problem for phylogenetics than currently believed, which should allow researchers to greatly increase the number of genes used in phylogenetic inference.

Significance StatementPhylogenetics has long relied on the use of orthologs, or genes related through speciation events, to infer species relationships. However, filtering datasets to include only orthologs is both difficult and restrictive, drastically limiting the amount of data available for phylogenetic inference. Here, we introduce a model to study the probability and topologies of pseudoorthologs--duplicated genes that are mistaken for orthologs because they are present in a single copy in each sampled species. We show that pseudoorthologs are rare and that, even when they are present, they should not mislead phylogenetic inference. Our results suggest that strict filtering to remove pseudoorthologs unnecessarily limits the amount of data used in phylogenetic inference.

category: evolutionary biology


title: Dopamine receptor DOP-1 engages a sleep pathway to modulate swimming in C. elegans

abstract:
Animals require robust yet flexible programs to support locomotion. While it is clear that a variety of processes must be engaged to ensure rhythmic actions, the exact mechanisms remain largely unknown. Here we report a novel pathway that connects the D1-like dopamine receptor DOP-1 with a sleep mechanism to modulate swimming in C. elegans. We show that DOP-1 plays a negative role in sustaining swimming behavior. By contrast, a pathway through the D2-like dopamine receptor DOP-3 negatively regulates the initiation of swimming, but its impact fades quickly over a few minutes. We find that DOP-1 and the GPCR kinase GRK-2 function in the sleep interneuron RIS, where DOP-1 modulates the secretion of a sleep neuropeptide FLP-11. Our genetic studies further show that DOP-1 and FLP-11 act in the same pathway to modulate swimming. Together, these results delineate a functional connection between a dopamine receptor and a sleep program to regulate swimming in C. elegans. The temporal transition between DOP-3 and DOP-1 pathways highlights the dynamic nature of neuromodulation for rhythmic movements that persist over time.

HIGHLIGHTSO_LIThe D1-like dopamine receptor DOP-1 regulates swimming at 10 minutes
C_LIO_LIAn integrated function of DOP-1 and DOP-3 is required for the continuity of swimming
C_LIO_LIDOP-1 and GRK-2 act in the sleep neuron RIS
C_LIO_LIFLP-11, a neuropeptide that promotes sleep, negatively regulates swimming
C_LI

IN BRIEFXu et al. investigated genetic programs that modulate swimming behavior in the nematode C. elegans. They identified a functional link that couples a D1-like dopamine receptor to a sleep program that modulates the sustained phase rather than the initial phase of swimming.

category: genetics


title: Third Backcross Generation Indonesian Indigenous Chicken Kampong Broiler-Type (Kambro) SOX5 Gene Polymorphism

abstract: The comb is an accessory organ on the head of chicken which is influenced by testosterone hormone and can be used as an indicator of chickens fertility. Comb shape is related to climate adaptation and associated with a dominant mutation in chicken chromosome 1. Therefore this research was aimed to study the association between Pea-comb shape and SOX5 gene polymorphism in the population of progenies (BC-III Kambro) derived from a crossbreed between females Pelung and males second backcross generation Kampong Broiler-Type (BC-II Kambro). Chicken (Gallus gallus) SOX5 gene was acquired from NCBI GenBank with the Ref. Seq. 418195. Primers used to amplify the SOX5 gene are (F):5-AGGTAGCCATGGTGACAAGC-3,(R):5-GATCTGTGAGGCAGCCAGTT-3. Progenies showed 100% Pea-comb shape, while parental generation composed of Pea-comb shape and Single-comb shape. PCR-RFLP and endonuclease restriction enzyme HindIII were unable to determine the genotype of the female parent with Pea-comb. The result of SOX5 gene polymorphism showed the comb shape uniformity between progenies and parental of Kambro backcross generation. This study concluded that the genotype of Pea-comb shape female Pelung was undetermined and there was no polymorphism of the SOX5 gene between pea and single comb. PCR-RFLP using endonuclease restriction enzyme HindIII produced both target products and non-target/artifact products. The sequencing procedure was required to provide nucleotide sequences.


title: Compression for population genetic datathrough finite-state entropy

abstract: We improve the efficiency of population genetic file formats and GWAS computation by leveraging the distribution of sample ordering in population-level genetic data. We identify conditional exchangeability of these data, recommending finite state entropy algorithms as an arithmetic code naturally suited to population genetic data. We show between 10% and 40% speed and size improvements over dictionary compression methods for population genetic data such as Zstd and Zlib in computation and and decompression tasks. We provide a prototype for genome-wide association study with finite state entropy compression demonstrating significant space saving and speed comparable to the state-of-the-art.


title: Compression for population genetic data through finite-state entropy


title: Non-destructive extraction of DNA from preserved tissues in medical collections

abstract:
Museum and medically fixed material are valuable samples for the study of historical soft tissues and represent a pathogen-specific source for retrospective molecular investigations. However, current methods for the molecular analysis are inherently destructive, posing a dilemma between performing a study with the available technology thus damaging the sample - or conserving the material for future investigations. Here we present an unprecedented non-destructive alternative that facilitates the genetic analysis of fixed wet tissues while avoiding tissue damage. We extracted DNA from the fixed tissues as well as their embedding fixative solution, to quantify the DNA that was transferred to the liquid component. Our results prove that human ancient DNA can be retrieved from the fixative material of stored medical specimens and provide new options for the sampling of valuable curated collections.

Method summaryWe compared the metagenomic content of historical tissues and their embedding liquid to retrieve DNA from the host and specified pathogens based on the diagnosis of the sample. We applied ancient DNA research techniques, including in-solution hybridization capture with DNA baits for human mitochondrial DNA, Mycobacterium tuberculosis, Mycobacterium leprae, and Treponema pallidum.


title: ATLASx: a computational map for the exploration of biochemical space

abstract: Metabolic "dark matter" describes currently unknown metabolic processes, which form a blind spot in our general understanding of metabolism and slow down the development of biosynthetic cell factories and naturally derived pharmaceuticals. Mapping the dark matter of metabolism remains an open challenge that can be addressed globally and systematically by existing computational solutions. In this work, we use 490 generalized enzymatic reaction rules to map both known and unknown metabolic processes around a biochemical database of 1.5 million biological compounds. We predict over 5 million reactions and integrate nearly 2 million naturally and synthetically-derived compounds into the global network of biochemical knowledge, named ATLASx. ATLASx is available to researchers as a powerful online platform that supports the prediction and analysis of novel biochemical pathways and evaluates the biochemical vicinity of molecule classes (https://lcsbdatabases.epfl.ch/Atlas2).

category: biochemistry


title: Doublecortin engages the microtubule lattice through a cooperative binding mode involving its C- terminal domain

abstract: Doublecortin (DCX) is a microtubule (MT) associated protein that regulates MT structure and function during neuronal development and mutations in DCX lead to a spectrum of neurological disorders. The structural properties of MT-bound DCX remain poorly resolved. Here, we describe the molecular architecture of the DCX-MT complex through an integrative modeling approach that combines data from X-ray crystallography, cryo-EM and a high-fidelity chemical crosslinking method. We demonstrate that DCX interacts with MTs through its N-terminal domain and induces a lattice-dependent self-association involving both the C-terminal structured domain and the C-tails, in a conformation that favors an open, domain-swapped state. The networked state can accommodate multiple different attachment points on the MT lattice, all of which orient the C-tails away from the lattice. As numerous disease mutations cluster in the C-terminus, and regulatory phosphorylations cluster in the C-tail, our study shows that lattice-driven self-assembly is an important property of DCX.


title: Capturing actively produced microbial volatile organic compounds from human associated samples with vacuum assisted sorbent extraction

abstract:
Volatile organic compounds (VOC) from biological samples have unknown origins. VOCs may originate from the host or different microbial organisms from a microbial community. In order to disentangle the origin of microbial VOCs, we performed volatile headspace analysis of bacterial mono- and co-cultures of Staphylococcus aureus, Pseudomonas aeruginosa, and Acinetobacter baumannii, and stable isotope probing in biological samples of feces, saliva, sewage, and sputum. We utilized mono- and co-cultures to identify volatile production from individual bacterial species or in combination with stable isotope probing to identify the active metabolism of microbes from the biological samples. To extract the VOCs, we employed vacuum assisted sorbent extraction (VASE). VASE is an easy-to-use commercialized solvent-free headspace extraction method for semi-volatile and volatile compounds. The lack of solvents and the near vacuum conditions used make developing a method relatively easy and fast when compared to other extraction options like tert-butylation and solid phase microextraction. However, VASE does not work on nonvolatile compounds, thus excluding many protein analyses and heavy stable isotope labelling experiments. Using the workflow described here, we identified volatile signatures from mono- and co-cultures indicating there were volatiles specific to certain microbes or co-cultures. Furthermore, analysis of the stable isotope probing of biological samples identified VOCs that were either commonly or uniquely produced from the different human derived biological samples. Here we present the general workflow and experimental considerations of VASE.

SUMMARYFrom this protocol, readers will be able to extract volatile organic compounds from a biological sample with the vacuum assisted sorbent extraction method, run samples on a GC-MS with the use of the Entech autosampler, and analyze data.


title: Quantifying Viscous Damping and Stiffness in Parkinsonism Using Data-Driven Model Estimation

abstract: Rigidity of upper and lower limbs in Parkinsons disease (PD) is typically assessed via a clinical rating scale that is subject to biases inherent to human perception. Methodologies and systems to systematically quantify changes in rigidity associated with angular position (stiffness) or velocity (viscous damping) are needed to enhance our understanding of PD pathophysiology and objectively assess therapies. We developed a robotic system and a model-based approach to estimate viscous damping and stiffness of the elbow. Our methodology enables the subject to freely rotate the elbow, while torque perturbations tailored to identify the arm dynamics are delivered. The viscosity and stiffness are calculated based on the experimental data using least-squares optimization. We validated our technique using computer simulations of the arm dynamics and experiments with a nonhuman animal model of PD in the presence and absence of deep brain stimulation (DBS) therapy. Computer simulations of the arm demonstrate that the proposed approach can accurately estimate viscous damping and stiffness. The experimental data show that both viscosity and stiffness significantly decreased when DBS was delivered. Computer simulations and experiments showed that stiffness and viscosity measurements obtained with the proposed methodology could better differentiate changes in rigidity than scores previously used for research, including the work score, impulse score, and modified Unified Parkinsons Disease Rating Scale (mUPDRS). The proposed estimation method is suitable to quantify the effect of therapies on viscous damping and stiffness and study the pathophysiological mechanisms underlying rigidity in PD.

category: bioengineering


title: Bioengineering of genetically encoded gene promoter repressed by flavonoids for constructing intracellular sensor for molecular events

abstract: In recent years, Synthetic Biology has emerged as a new discipline where functions that were traditionally performed by electronic devices are replaced by "cellular devices". Those are genetically encoded circuits, constructed of DNA that are built from biological parts (aka bio-parts). The cellular devices can be used for sensing and responding to natural and artificial signals. However, a major challenge in the field is that the crosstalk between many cellular signaling pathways use the same signaling endogenous molecules that can result in undesired activation. To overcome this problem, we utilized a specific promoter that can activate genes with a natural, non-toxic ligand at a highly-induced transcription level with low background or undesirable off-target expression. Here we used the orphan aryl hydrocarbon receptor (AHR), a ligand-activated transcription factor that upon activation binds to specific AHR response elements (AHRE) of the Cytochrome P450, family 1, subfamily A, polypeptide 1 (CYP1A1) promoter. Flavonoids have been identified as AHR ligands. Data presented here shows successful creation of a synthetic gene "off" switch that can be monitored directly using an optical reporter gene. This is the first step towards bioengineering of a synthetic, nanoscale bio-part for constructing a sensor for molecular events.


title: A Programmable Toolkit to Dynamically Signal Cells using Peptide Strand Displacement

abstract: The native extracellular matrix communicates and interacts with cells by dynamically displaying signals to control their behavior. Mimicking this dynamic environment in vitro is essential in order to unravel how cell-matrix interactions guide cell fate. Here, we present a synthetic platform for the temporal display of cell adhesive signals using coiled-coil peptides. By designing an integrin-engaging coiled-coil pair to have a toehold (unpaired domain), we were able to use a peptide strand displacement reaction to remove the cell cue from the surface. This allowed us to test how the on-demand display of RGDS ligands at variable duration and periodicity of ligand exposure influence cell spreading degree and kinetics. Transient display of V{beta}3 selective ligands instructed fibroblast cells to reversibly spread and contract in response to changes in ligand exposure over multiple cycles, exhibiting a universal kinetic response. Also, cells that were triggered to spread and contract repeatedly exhibited greater enrichment of integrins in focal adhesions versus cells cultured on persistent RGDS-displaying surfaces. This dynamic platform will allow us to uncover the molecular code by which cells sense and respond to changes in their environment and will provide insights into ways to program cellular behavior.


title: coupleCoC+: an information-theoretic co-clustering-basedtransfer learning framework for the integrative analysis of single-cell genomic data

abstract: Technological advances have enabled us to profile multiple molecular layers at unprecedented single-cell resolution and the available datasets from multiple samples or domains are growing. These datasets, including scRNA-seq data, scATAC-seq data and sc-methylation data, usually have different powers in identifying the unknown cell types through clustering. So, methods that integrate multiple datasets can potentially lead to a better clustering performance. Here we propose coupleCoC+ for the integrative analysis of single-cell genomic data. coupleCoC+ is a transfer learning method based on the information-theoretic co-clustering framework. In coupleCoC+, we utilize the information in one dataset, the source data, to facilitate the analysis of another dataset, the target data. coupleCoC+ uses the linked features in the two datasets for effective knowledge transfer, and it also uses the information of the features in the target data that are unlinked with the source data. In addition, coupleCoC+ matches similar cell types across the source data and the target data. By applying coupleCoC+ to the integrative clustering of mouse cortex scATAC-seq data and scRNA-seq data, mouse and human scRNA-seq data, mouse cortex sc-methylation and scRNA-seq data, and human blood dendritic cells scRNA-seq data from two batches, we demonstrate that coupleCoC+ improves the overall clustering performance and matches the cell subpopulations across multimodal single-cell genomic datasets. coupleCoC+ has fast convergence and it is computationally efficient. The software is available at https://github.com/cuhklinlab/coupleCoC_plus.

category: bioinformatics


title: Evidences for functional trans-acting eRNA-promoter R-loops at Alu sequences

abstract: Enhancers modulate gene expression by interacting with promoters. Models of enhancer-promoter interactions (EPIs) in the literature involve the activity of many components, including transcription factors and nucleic acid. However, the role that sequence similarity plays in EPIs, remains largely unexplored. Herein, we report that Alu-derived sequences dominate sequence similarity between enhancers and promoters. After rejecting the alternative DNA:DNA and DNA:RNA triplex models, we proposed that enhancer-associated RNAs, or eRNAs, may directly contact their targeted promoters by forming trans-acting R-loops at those Alu sequences. We showed how the characteristic distribution of functional genomic data, such as RNA-DNA proximate ligation reads, binding of transcription factors, and RNA-binding proteins, align with the Alu sequences of EPIs. We also showed that these aligned Alu sequences may be subject to the constraint of coevolution, further implying the functional significance of these R-loop hybrids. Finally, our results showed that eRNA and Alu elements associate in a manner previously unrecognized in the EPIs and the evolution of gene regulation networks in mammals.


title: Structural effects driven by rare point mutations in amylin hormone, the type II diabetes associated peptide

abstract:
BackgroundAmylin is a 37-amino-acid peptide hormone co-secreted with insulin, which participates in glucose homeostasis. This hormone is able to aggregate in a {beta}-sheet conformation and deposit in islet amyloids, a hallmark in type II diabetes. Since amylin is a gene-encoded hormone, this peptide has variants caused by point mutations that can impact its functions.

MethodsHere, we analyzed the structural effects caused by S20G and G33R point mutations which, according to the 1000 Genomes Project, have frequency in East Asian and European populations, respectively. The analyses were performed by means of aggrescan server, SNP functional effect predictors, and molecular dynamics.

ResultsWe found that both mutations have aggregation potential and cause changes in the monomeric forms when compared with wild-type amylin. Furthermore, comparative analyses with pramlintide, an amylin drug analogue, allowed us to infer that second -helix maintenance may be related to the aggregation potential.

ConclusionsThe S20G mutation has been described as pathologically related, which is in agreement with our findings. In addition, our data suggest that the G33R mutation might have a deleterious effect. The data presented here also provide new therapy opportunities, whether for creating more effective drugs for diabetes or implementing specific treatment for patients with these mutations.

General SignificanceOur data could help to better understand the impact of mutations on the wild-type amylin sequence, as a starting point for the evaluation and characterization of other variations. Moreover, these findings could improve the health of patients with type II diabetes.


title: Structural effects driven by rare point mutations in amylin hormone, the type II diabetes-associated peptide


title: Chromatin accessibility regulates intron retention in a cell type-specific manner

abstract: Dynamic intron retention (IR) in vertebrate cells is of widespread biological importance. Aberrant IR is associated with numerous human diseases including cancer. Despite consistent reports demonstrating intrinsic sequence features that predispose introns to become retained, conflicting findings about cell type-specific IR regulation demand a systematic analysis in a controlled experimental setting. We integrated matched transcriptomics and epigenetics data (including DNA methylation, nucleosome occupancy, histone modifications) from primary human myeloid and lymphoid cells. Using machine learning we trained two complementary models to determine the role of epigenetic factors in the regulation of IR. We show that increased chromatin accessibility contributes substantially to the retention of introns in a cell-specific manner. We also confirm that intrinsic characteristics of introns are key for them to evade splicing. With mounting reports linking pathogenic alterations to RNA processing, our findings may have profound implications for the design of therapeutic approaches targeting aberrant splicing.


title: Chromatin accessibility determines cell-type specific intron retention


title: An integral genomic signature approach for tailored cancer targeted therapy using genome-wide sequencing data

abstract: With the advent of low-cost sequencing, transcriptome and genome sequencing is expected to become clinical routine and transform precision oncology within next decade. However, viable genome-wide modeling methods that can facilitate rational selection of patients for tailored intervention while tolerating sequencing biases are far lacking. Here we propose an integral genomic signature (iGenSig) analysis as a new class of transparent, interpretable, and resilient methods for precision oncology based on multiple types of genome-wide sequencing data. We postulate that the redundant high-dimensional genomic features, which are typically eliminated during multi-omics modeling, may help overcome the sequencing biases. We thus conceive a novel method that models the therapeutic response using the high-dimensional transcriptional and mutational features predictive of tumor response, which we termed as an integral genomic signature (iGenSig), and then algorithmically resolve the feature redundancy tailored for each patient subject. Using genomic dataset of chemical perturbations, we developed the iGenSig models for predicting targeted therapy responses, and applied selected models to independent datasets for cancer cell lines, patient-derived xenografts, and patient subjects. iGenSig models exhibit outstanding cross-dataset performance compared to artificial intelligence methods, with exceptional resilience against simulated errors in genomic features. In particular, the iGenSig model for the EGFR inhibitor Erlotinib significantly predicted the responses of patient-derived xenografts and patients from a clinical trial, biological interpretation of which led to new insights into the predictive signature pathways with clinical relevance. Together, iGenSig will provide a computational infrastructure to empower tailored cancer intervention based on genome-wide sequencing data.


title: Predicting Dengue Fever in Brazilian Cities

abstract: Dengue Fever is an increasingly serious public health concern both in Brazil and globally. In the absence of a universal vaccine or specific treatments, prevention relies on vector control and disease surveillance. Accurate and early forecasts can help reduce the spread of the disease. In this study, we develop a model to predict the number of Dengue Fever cases in Brazilian cities one month ahead. We compare different machine learning approaches as well as different sets of input features based on epidemiological and meteorological data. We find that different models work best in different cities, and a random forests model trained on data of historical Dengue cases performs best overall. It produces lower aggregate errors than a seasonal naive baseline model, Gradient Boosting Regression, feed-forward Neural Networks, and Support Vector Regression. Predictions on an unseen test set are on average within 11.5 cases for the median city. Mean absolute errors on the hold-out test set are reduced to 10.8 for the median city when selecting the optimal combination of algorithm and input features for each city individually.


title: Spatiotemporal organization of chromatin domains: role of interaction energy and polymer entropy

abstract: Chromatin is known to be organized into multiple domains of varying sizes and compaction. While these domains are often imagined as static structures, they are highly dynamic and show cell-to-cell variability. Since processes such as gene regulation and DNA replication occur in the context of these domains, it is important to understand their organization, fluctuation and dynamics. To simulate chromatin domains, one requires knowledge of interaction strengths among chromatin segments. Here, we derive interaction strength parameters from experimentally known contact maps and use them to predict chromatin organization and dynamics. Taking two domains on the human chromosome as examples, we investigate its 3D organization, size/shape fluctuations, and dynamics of different segments within a domain, accounting for hydrodynamic effects. Considering different cell types, we quantify changes in interaction strengths and chromatin shape fluctuations in different epigenetic states. Perturbing the interaction strengths systematically, we further investigate how epigenetic-like changes can alter the spatio-temporal nature of the domains. Our results show that heterogeneous weak interactions are crucial in determining the organization of the domains. Computing effective stiffness and relaxation times, we investigate how perturbations in interactions affect the solid-like and liquid-like nature of chromatin domains. Quantifying dynamics of chromatin segments within a domain, we show how the competition between polymer entropy and interaction energy influence the timescales of loop formation and maintenance of stable loops.

category: biophysics


title: Heterogeneous interactions and polymer entropy decide organization and dynamics of chromatin domains


title: Weighted force analysis method for derivation of multidimensional free energy landscapes from adaptively-biased replica simulations

abstract:
A methodology is proposed for the calculation of multidimensional free-energy landscapes of molecular systems, based on analysis of multiple Molecular Dynamics trajectories wherein adaptive biases have been applied to enhance the sampling of different collective variables. In this approach, which we refer to as Force Correction Analysis Method (FCAM), local averages of the total and biasing forces are evaluated post-hoc, and the latter are subtracted from the former to obtain unbiased estimates of the mean force across collective-variable space. Multidimensional free-energy surfaces and minimum free-energy pathways are then derived from integration of the mean force landscape through kinetic Monte Carlo algorithm. To evaluate the proposed method, a series of numerical tests and comparisons with existing approaches were carried out for small molecules, peptides, and proteins, based on all-atom trajectories generated with standard, concurrent and replica-exchange Metadynamics in collective-variable spaces ranging from one- to six-dimensional. The tests confirm the correctness of the FCAM formulation and demonstrate that calculated mean forces and free energies converge rapidly and accurately, outperforming other methods used to unbias this kind of simulation data.

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title: Force correction analysis method for derivation of multidimensional free energy landscapes from adaptively-biased replica simulations


title: Force-correction Analysis Method for Derivation of Multidimensional Free Energy Landscapes from Adaptively Biased Replica Simulations


title: Phospholipid membrane formation templated by coacervatedroplets

abstract: We report formation of coacervate-supported phospholipid membranes by hydrating a dried lipid film in the presence of coacervate droplets. In contrast to traditional giant lipid vesicles formed by gentle hydration in the absence of coacervates, the coacervate-templated membrane vesicles are more uniform in size, shape, and apparent lamellarity. Due to their fully-coacervate model cytoplasm, these simple artificial cells are macromolecularly crowded and can be easily pre-loaded with high concentrations of proteins or nucleic acids. Coacervate-supported membranes were characterized by fluorescence imaging, polarization, fluorescence recovery after photobleaching of labeled lipids, lipid quenching experiments, and solute uptake experiments. Our findings are consistent with the presence of lipid membranes around the coacervates, with many droplets fully coated with what appear to be continuous lipid bilayers. Within the same population, other coacervate droplets are coated with membranes having defects or pores that permit solute entry, and still others are coated with multilayered membranes. These membranes surrounding protein-based coacervate droplets provided protection from a protease added to the external solution. The simplicity of producing artificial cells having a coacervate model cytoplasm surrounded by a model membrane is at the same time interesting as a potential mechanism for prebiotic protocell formation and appealing for biotechnology. We anticipate that such structures could serve as a new type of model system for understanding interactions between intracellular phases and cell- or organelle membranes, which are implicated in a growing number of processes ranging from neurotransmission to signaling.


title: Pharmacological inhibition of PAI-1 alleviates cardiopulmonary pathologies induced by exposure to air pollutants PM2.5

abstract:
OBJECTIVEExposure to air pollutants leads to the development of pulmonary and cardiovascular diseases, and thus air pollution is one of the major global threats to human health. Air pollutant particulate matter 2.5 (PM2.5)-induced cellular dysfunction impairs tissue homeostasis and causes vascular and cardiopulmonary damage. To test a hypothesis that elevated plasminogen activator inhibitor-1 (PAI-1) levels play a pivotal role in air pollutant-induced cardiopulmonary pathologies, we examined the efficacy of a drug-like novel inhibitor of PAI-1, TM5614, in treating PM2.5-induced vascular and cardiopulmonary pathologies.

APPROACH AND RESULTSResults from biochemical, histological, and immunohistochemical studies revealed that PM2.5 increases the circulating levels of PAI-1 and thrombin and that TM5614 treatment completely abrogates these effects in plasma. PM2.5 significantly augments levels of pro-inflammatory cytokine IL-6 in bronchoalveolar lavage fluid, and this also can be reversed by TM5614, indicating its efficacy in amelioration of PM2.5-induced increases in inflammatory and pro-thrombotic factors. TM5614 reduces PM2.5-induced increased levels of inflammatory markers Mac3 and pSTAT3, adhesion molecule VCAM1, and apoptotic marker cleaved caspase 3. Longer exposure to PM2.5 induces pulmonary and cardiac thrombosis, but TM5614 significantly ameliorates PM2.5-induced vascular thrombosis. TM5614 also reduces PM2.5-induced increased blood pressure and heart weight. In vitro cell culture studies revealed that PM2.5 induces the levels of PAI-1, type I collagen, fibronectin, and SREBP-1/2, a transcription factor that mediates profibrogenic signaling, in cardiac fibroblasts. TM5614 abrogated that stimulation, indicating that it may block PM2.5-induced PAI-1 and profibrogenic signaling through suppression of SREBP-1. Furthermore, TM5614 blocked PM2.5-mediated suppression of Nrf2, a major antioxidant regulator in cardiac fibroblasts.

CONCLUSIONSPharmacological inhibition of PAI-1 with TM5614 is a promising therapeutic approach to control air pollutant PM2.5-induced cardiopulmonary and vascular pathologies.

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category: pharmacology and toxicology


title: Hot days are associated with short-term adrenocortical responses in a Southern African arid-zone passerine bird.

abstract: Non-invasive methods for investigating the biological effects of environmental variables are invaluable for understanding potential impacts of climate change on behavioural and physiological stress responses of free-ranging animals. Foraging efficiency, body mass maintenance and breeding success are compromised in Southern pied babblers Turdoides bicolor exposed to air temperatures between ~35{degrees}C and ~40{degrees}C. We tested the hypothesis that these very hot days are acute stressors for free-ranging babblers by quantifying the relationship between daily maximum air temperature (Tmax) and faecal glucocorticoid metabolite (fGCM) levels. We collected naturally-excreted droppings from free-ranging pied babblers and analysed fGCM levels. Levels of fGCMs in droppings collected after 3pm were independent of same-day Tmax < 38 {degrees}C and averaged 140.25 ng g-1 Dry Weight {+/-} 56.92 ng g-1 DW (mean {+/-} SD) over this range. Above an inflection Tmax = 38 {degrees}C, however, fGCM levels increased linearly with same-day Tmax and averaged 190.79 ng g-1 DW {+/-} 70.13 ng g-1 DW. There was no relationship between Tmax on the previous day and fGCM levels in droppings collected the following morning. Group size, breeding stage, sex and rank did not predict variation in fGCM levels. These results suggest that very high Tmax may be linked to acute, but not chronic, heat stress responses. The fGCM levels we measured are likely to represent a biologically meaningful response to an environmental stressor (high Tmax), suggesting a physiological mechanism underlying observed changes in behaviour and reproductive success at high temperatures in this species.

category: physiology


title: FRAGMENTED BIODIVERSITY: FERNS AND LYCOPHYTES FROM FOREST FRAGMENTS IN JUIZ DE FORA, MINAS GERAIS, BRAZIL

abstract: The Atlantic Forest is one of the most threatened formations in the world. In this context, the urbanization process stands out as one of the major factors causing environmental degradation, mainly due to the loss of native vegetation and habitat destruction. In order to fill this gap, we carried out the inventory of ferns and lycophytes in the forest remnants of the municipality of Juiz de Fora. We analyzed more than 1,353 samplings recorded throughout approximately 150 years, as result we recorded a total of 174 species distributed in 73 genera and 26 families. The most representative families were Pteridaceae with 32 species, followed by Polypodiaceae with 26 and Thelypteridaceae with 20. In addition, we present the historical data on the sampling of ferns and lycophytes, as well as the history of the fragmentation process of the Atlantic Forest remnants in the municipality. Juiz de Fora becomes an interesting model for broader floristic studies, generating subsequent subsidies for conservation actions and preservation of the natural patrimony.

category: plant biology


title: Heparan Sulfated Glypican-4 is Released from Astrocytes Predominantly by Proteolytic Shedding

abstract:
Astrocytes provide neurons with diffusible factors that promote synapse formation and maturation. In particular, glypican-4/GPC4 released from astrocytes promotes the maturation of excitatory synapses. Unlike other secreted factors, GPC4 contains the C-terminal GPI-anchorage signal. However, the mechanism by which membrane-tethered GPC4 is released from astrocytes is unknown. Using primary astrocyte cultures and a quantitative luciferase-based release assay, we show that GPC4 is expressed on the astrocyte surface exclusively via a GPI-anchorage. Soluble GPC4 is robustly released from the astrocytes predominantly by proteolytic shedding and, to a lesser extent, by GPI-anchor cleavage, but not by vesicular release. Pharmacological, overexpression, and loss of function screens showed that ADAM9 in part mediates the release of GPC4 from astrocytes. The released GPC4 contains the heparan sulfate side chain, suggesting that these release mechanisms provide the active form that promotes synapse maturation and function. Overall, our studies identified the release mechanisms and the major releasing enzyme of GPC4 in astrocytes and will provide insights into understanding how astrocytes regulate synapse formation and maturation.

Significance StatementAstrocyte-derived diffusible factors regulate synapse development and function. However, the regulatory mechanism underlying the release of astrocyte-derived factors is poorly understood. Noting that, unlike many other secreted factors, glypican-4/GPC4 is GPI-anchored, we characterized the release mechanism of GPI-anchored GPC4 from astrocytes and identified the releasing enzyme. Heparan sulfated GPC4 is robustly released from the astrocytes predominantly by proteolytic shedding. In particular, ADAM9 in part mediates the release of GPC4 from astrocytes. Our study provides an enzymatic mechanism for releasing GPC4 from astrocytes and will provide a novel opportunity to understand the regulatory mechanism of neuron-glia communication for synaptogenesis.


title: Remyelination restores myelin content on distinct neuronal subtypes in the cerebral cortex

abstract: Axons in the cerebral cortex exhibit diverse patterns of myelination, with some axons devoid of myelin, some exhibiting discontinuous patches of myelin, and others continuous myelin that is interrupted only by nodes of Ranvier. Oligodendrocytes establish this pattern by sorting through a high density of potential targets to select a small cohort of axons for myelination; however, the myelination patterns established on distinct excitatory and inhibitory neurons within the cortex remain to be fully defined and little is known about the extent to which these patterns are restored after oligodendrocyte regeneration. Here we show that axons in layer I of the somatosensory cortex, a key region for integration of input from local and distant sources, exhibit an extraordinarily diverse range of myelination patterns, even among distinct neuronal subtypes. Although larger axons were more often selected for myelination, neuronal identity profoundly influenced the probability of myelination. The relative differences in myelination among neuron subtypes were preserved between cortical areas with widely varying myelin density, suggesting that regional differences in myelin abundance arises through local control of oligodendrogenesis, rather than selective reduction of myelin on distinct neuron subtypes. By following the loss and regeneration of myelin sheaths along defined neurons in vivo we show that even though the distribution of myelin on individual PV and VM neuron axons was altered following remyelination, the overall myelin content on these neurons was restored. The findings suggest that local changes in myelin can be tolerated, allowing opportunistic selection of available targets by newly formed oligodendrocytes to restore relative differences in myelin content between functionally distinct neurons.


title: Functional cooperativity mediated by rationally selected combinations of human monoclonal antibodies targeting the henipavirus receptor binding protein

abstract: Hendra virus (HeV) and Nipah virus (NiV), the prototypic members of the Henipavirus (HNV) genus, are emerging, zoonotic paramyxoviruses known to cause severe disease across six mammalian orders, including humans (Eaton et al., 2006). While several research groups have made strides in developing candidate vaccines and therapeutics against henipaviruses, such countermeasures have not been licensed for human use, and significant gaps in knowledge about the human immune response to these viruses exist. To address these gaps, we isolated a large panel of human monoclonal antibodies (mAbs) from the B cells of an individual with prior occupation-related exposure to the equine HeV vaccine (Equivac(R) HeV). Competition-binding and hydrogen-deuterium exchange mass spectrometry (HDX-MS) studies identified at least six distinct antigenic sites on the HeV/NiV receptor binding protein (RBP) that are recognized by human mAbs. Antibodies recognizing multiple antigenic sites potently neutralized NiV and/or HeV isolates in vitro. The most potent class of cross-reactive antibodies achieved neutralization by blocking viral attachment to the host cell receptors ephrin-B2 and ephrin-B3. Antibodies from this class mimic receptor binding by inducing a receptor-bound conformation to the HeV-RBP protein tetramer, exposing an epitope that appears to lie hidden in the interface between protomers within the HeV-RBP tetramer. Antibodies that recognize this cryptic epitope potently neutralized HeV and NiV. Flow cytometric studies using cell-surface-displayed HeV-RBP protein showed that cross-reactive, neutralizing mAbs from each of these classes cooperate for binding. In a highly stringent hamster model of NiVB infection, antibodies from both classes reduced morbidity and mortality and achieved synergistic protection in combination and provided therapeutic benefit when combined into two bispecific platforms. These studies identified multiple candidate mAbs that might be suitable for use in a cocktail therapeutic approach to achieve synergistic antiviral potency and reduce the risk of virus escape during treatment.


title: Subventricular zone/white matter microglia reconstitute the empty adult microglial niche in a dynamic wave

abstract: Microglia, the brains resident myeloid cells, play central roles in brain defense, homeostasis, and disease. Using sustained colony-stimulating factor 1 receptor inhibition, we report an unprecedented level of microglial depletion and establish a model system that achieves an empty microglial niche in the adult brain. We identify a myeloid cell that migrates from an important neurogenic niche, the subventricular zone, and associated white matter areas. These cells exhibit tremendous chemotaxis potential, migrating radially and tangentially in a dynamic wave and filling the brain in a distinct pattern, to fully replace the microglial-depleted brain. These repopulating cells are enriched in disease-associated microglia genes and exhibit distinct phenotypic and functional profiles to endogenous microglia. Our findings shed light on the overlapping and distinct functional complexity and diversity of myeloid cells of the CNS and provide new insight into myeloid cell dynamics in an empty microglial niche without contributions from bone marrow-derived cells.


title: Spatial modulation of individual behaviors enables collective decision-making during bacterial group migration

abstract: Coordination of individuals with diversity often requires sophisticated communications and high-order computational abilities. Microbial populations can exhibit diverse individualistic behaviors and yet can engage in collective migratory patterns with a spatially sorted arrangement of phenotypes following a self-generated attractant gradient. However, its unclear how individual bacteria without complex computational abilities can achieve the consistent group performance and determine their positions in the group while facing spatiotemporally dynamic stimuli. Here, we investigate the statistics of bacterial run-and-tumble trajectories during group migration. We discover that, despite of the constant migrating speed as a group, the individual drift velocity exhibits a spatially dependent structure that decreases from the back to the front of the group. The spatial modulation of individual stochastic behaviors constrains cells in the group, ensuring the coherent population movement with ordered patterns of phenotypes. These results reveal a simple computational principle for emergent collective behaviors from heterogeneous individuals.

category: microbiology


title: Frequent intergenotypic recombination between the non-structural and structural genes is a major driver of epidemiological fitness in caliciviruses

abstract: The diversity of lagoviruses (Caliciviridae) in Australia has increased considerably. By the end of 2017, five variants from three viral genotypes were present in populations of Australian rabbits, while prior to 2014 only two variants were known. To understand the interactions between these lagovirus variants we monitored their geographical distribution and relative incidence over time through a landscape-scale competition study, and from this, revealed potential drivers of epidemiological fitness. Within three years of the arrival of GI.1bP-GI.2 (RHDV2) into Australia, we observed the emergence of two novel recombinant lagovirus variants, GI.4eP-GI.2 (4e-recombinant) in New South Wales and GI.4cP-GI.2 (4c-recombinant) in Victoria. Although both novel recombinants contain the non-structural genes from benign, rabbit-specific, enterotropic viruses, these variants were recovered from the livers of both rabbits and hares that had died acutely. This suggests that determinants of host and tissue tropism for lagoviruses are associated with the structural genes, and that tropism is intricately connected with pathogenicity. Phylogenetic analyses demonstrated that the 4c-recombinant emerged independently on multiple occasions, with five distinct lineages observed. Both new recombinant variants replaced the previous dominant parental RHDV2 in their respective geographical areas, despite sharing an identical or near-identical (i.e., single amino acid change) major capsid protein with the parental virus. This suggests that epidemiological fitness of these recombinants was not driven by antigenic variation in the capsid, implicating the non-structural genes as key drivers of epidemiological fitness. Molecular clock estimates place the GI4.e recombination event in early to mid-2015, while the five GI.4c recombination events occurred from late 2015 through to early 2017. The emergence of at least six viable recombinant variants within a two-year period highlights an unprecedented frequency of these events, detectable only due to intensive surveillance, and demonstrates the importance of recombination in lagovirus evolution.


title: Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells

abstract: Cell homeostasis is perturbed when dramatic shifts in the external environment cause the physical-chemical properties inside the cell to change. Methods that dynamically monitor these intracellular effects are currently lacking. Here, we leveraged the environmental sensitivity and structural plasticity of intrinsically disordered regions (IDRs) to develop a FRET biosensor capable of monitoring rapid intracellular changes caused by osmotic stress. The biosensor, named SED1, utilizes the Arabidopsis intrinsically disordered AtLEA4-5 protein expressed in plants under water deficit. Computational modeling and in vitro studies reveal that SED1 is highly sensitive to macromolecular crowding. SED1 exhibits large and near-linear osmolarity-dependent changes in FRET inside living bacteria, yeast, plant, and human cells, demonstrating the broad utility of this tool for studying water-associated stress. This study demonstrates the remarkable ability of IDRs to sense the cellular environment across the tree of life and provides a blueprint for their use in environmentally-responsive molecular tools.


title: Plant responses to multiple antagonists are mediated by order of attack and phytohormone crosstalk

abstract: Plants are often attacked by multiple antagonists, and traits of the attacking organisms, and their order of arrival onto hosts, may affect plant defenses. However, few studies have assessed how multiple antagonists, and varying attack order, affect plant defense or nutrition. To address this, we assessed defensive and nutritional responses of Pisum sativum plants after attack by a vector herbivore (Acrythosiphon pisum), a non-vector herbivore (Sitona lineatus), and a pathogen (Pea enation mosaic virus, PEMV). We show PEMV-infectious A. pisum induced several pathogen-specific plant defense signals, but these defenses were inhibited when S. lineatus was present in peas infected with PEMV. In contrast, feeding by S. lineatus induced anti-herbivore defense signals, but these defenses were enhanced by PEMV. Sitona lineatus also increased abundance of plant amino acids, but only when they attacked after PEMV-infectious A. pisum. Our results suggest that diverse communities of biotic antagonists alter defense and nutritional traits of plants through complex pathways that depend on the identity of attackers and their order of arrival onto hosts. Moreover, we show interactions among a group of biotic stressors can vary along a spectrum from antagonism to enhancement/synergism based on the identity and order of attackers, and these interactions are mediated by a multitude of phytohormone pathways.


title: A method to estimate effective population size from linkage disequilibrium when generations overlap

abstract: Effective population size (Ne) is a key parameter in evolutionary and conservation studies. It represents the number of individuals of an ideal panmictic population that would have the same genetic drift as the observed population and can be used to establish management programmes. Several methods have been developed to estimate this parameter. Currently, for studies with one sample in time, the simplest methods are based on linkage disequilibrium. These methods rely on simple models, and biases have been shown when populations deviate from the assumptions made in those models. This occurs in particular when populations are age-structured or have overlapping generations. Recently, several methods have been developed to correct such biases. Here, we develop analytical equations to predict linkage disequilibrium within age groups, and use such results to infer cohort size from samples of newborn individuals. We can in turn use these equations to estimate Ne accurately for a variety of species. Furthermore, using publicly available data, we apply our method to the white-crowned sparrow (Zonotrichia leucophrys).


title: Singlet oxygen-dependent chloroplast degradation is independent of macroautophagy in the Arabidopsis ferrochelatase two mutant

abstract:
BackgroundChloroplasts respond to stress and changes in the environment by producing reactive oxygen species (ROS) that have specific signaling abilities. The ROS singlet oxygen (1O2) is unique in that it can signal to initiate selective degradation of damaged chloroplasts and then cell death. This chloroplast quality control pathway can be monitored in the Arabidopsis mutant plastid ferrochelatase two (fc2) that conditionally accumulates chloroplast 1O2 under diurnal light cycling conditions leading to rapid chloroplast degradation and eventual cell death. The cellular machinery involved in such degradation, however, remains unknown. Recently it has been demonstrated that whole damaged chloroplasts can be transported to the central vacuole via a process requiring autophagosomes and core components of the autophagy machinery. The relationship between this process, referred to as chlorophagy, and the degradation of 1O2-stressed chloroplasts and cells has remained unexplored.

ResultsTo further understand 1O2-induced cellular degradation and determine what role autophagy may play, the expression of autophagy-related genes were monitored in 1O2-stressed fc2 seedlings and found to be induced. Although autophagosomes were present in fc2 cells, they did not associate with chloroplasts during 1O2 stress. Mutations blocking the core autophagy machinery (atg5, atg7, and atg10) were unable to suppress 1O2-induced chloroplast degradation or cell death in the fc2 mutant, suggesting autophagosome formation and macroautophagy are dispensable for 1O2-mediated cellular degradation. However, both atg5 and atg7 led to specific defects in chloroplast ultrastructure and photosynthetic efficiencies, suggesting macroautophagy may be involved in protecting chloroplasts from photo-oxidative damage. Finally, genes predicted to be involved in microautophagy were shown to be induced in stressed fc2 seedlings, indicating a possible role for an alternate form of autophagy in the dismantling of 1O2-damaged chloroplasts.

ConclusionsOur results support the hypothesis that 1O2-dependent chloroplast degradation is independent from autophagosome formation, canonical macroautophagy, and chlorophagy. Instead, ATG-independent microautophagy may be involved in such degradation. However, canonical macroautophagy may still play a role in protecting chloroplasts from 1O2-induced photo-oxidative stress. Together, this suggests chloroplast function and degradation is a complex process that utilizes multiple autophagy and degradation machineries, possibly depending on the type of stress or damage incurred.


title: A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

abstract: Eukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of multiple biological networks into a single model for cell analysis and engineering. One of the current most accurate models of biological systems include metabolism and expression (ME-models), and Expression and Thermodynamics FLux (ETFL) is one such formulation that efficiently integrates RNA and protein synthesis with traditional genome-scale metabolic models. However, ETFL is so far only applicable for E. coli. To therefore adapt this ME-model for Saccharomyces cerevisiae, we herein developed yETFL. To do this, we augmented the original formulation with additional considerations for biomass composition, the compartmentalized cellular expression system, and the energetic costs of biological processes. We demonstrated the predictive ability of yETFL to capture maximum growth rate, essential genes, and the phenotype of overflow metabolism. We envision that the extended ETFL formulation can be applied to ME-model development for a wide range of eukaryotic organisms. The utility of these ME-models can be extended into academic and industrial research.


title: High-throughput and high-efficiency sample preparation for single-cell proteomics using a nested nanowell chip

abstract: Global quantification of protein abundances in single cells would provide more direct information on cellular function phenotypes and complement transcriptomics measurements. However, single-cell proteomics (scProteomics) is still immature and confronts technical challenges, including limited proteome coverage, poor reproducibility, as well as low throughput. Here we describe a nested nanoPOTS (N2) chip to dramatically improve protein recovery, operation robustness, and processing throughput for isobaric-labeling-based scProteomics workflow. The N2 chip allows reducing cell digestion volume to <30 nL and increasing processing capacity to > 240 single cells in one microchip. In the analysis of [~]100 individual cells from three different cell lines, we demonstrate the N2 chip-based scProteomics platform can robustly quantify [~]1500 proteins and reveal functional differences. Our analysis also reveals low protein abundance variations (median CVs < 16.3%), highlighting the utility of such measurements, and also suggesting the single-cell proteome is highly stable for the cells cultured under identical conditions.


title: The type and source of reactive oxygen species influences the outcome of oxidative stress in cultured cells

abstract: Oxidative stress can be modeled using various different experimental approaches, such as exposing the cells or organisms to oxidative chemicals. However, the actual effects of these chemicals, outside of the immediate measured effect, have attracted relatively little attention. We show here that three commonly used oxidants, menadione, potassium bromate and hydrogen peroxide, while known to function differently, also elicit different types of responses in cultured cells. While cells response to menadione and bromate exposure mainly by an integrated stress response, hydrogen peroxide has more indirect effects. Primary oxidative stress does not induce DNA repair or antioxidant defense mechanisms. However, cells with previous experience of oxidative stress show adaptive changes when the stress is renewed. Our results urge caution when comparing studies using different sources of oxidative stress or generalizing the findings of these studies to different tissue or oxidant types.


title: The PMT-driven p-coumaroylation of poplar lignins impacts lignin structure and improves wood saccharification

abstract:
Transgenic poplars (Populus tremula x Populus alba, clone INRA 717-1B4) were produced by introducing the Brachypodium distachyon Bradi2g36910 (BdPMT1) gene driven by the Arabidopsis (Arabidopsis thaliana) Cinnamate 4-Hydroxylase (AtC4H) promoter in the wild-type (WT) line and in a line overexpressing the Arabidopsis Ferulate 5-Hydroxylase (AtF5H). BdPMT1 encodes a transferase which catalyzes the acylation of monolignols by p-coumaric acid (CA). Several BdPMT1- OE/WT and BdPMT1-OE/AtF5H-OE transgenic lines were grown in the greenhouse and BdPMT1 expression in xylem was confirmed by RT-PCR. The analysis of the cell walls (CW) of poplar stems and of corresponding purified dioxan lignins (DL) revealed that the BdPMT1-OE lignins were as p-coumaroylated as the lignins of C3 grass straws. For some transformants, CA levels even reached about 11 mg/g CW and 66 mg/g DL, which by far exceeds those of Brachypodium or wheat samples. This unprecedentedly high p-coumaroylation of poplar lignins affected neither the poplar growth, nor the stem lignin content. By contrast, the transgenic lignins were structurally modified, with an increase of terminal units with free phenolic groups. Relative to controls, this increase argues for a reduced polymerization degree of BdPMT1-OE lignins and makes them more soluble in cold NaOH solution. The p-coumaroylation of poplar samples, up to the levels of C3 grasses, improved the saccharification yield of alkali-pretreated poplar CW. These results establish that the genetically-driven p-coumaroylation of lignins is a promising strategy to make wood lignins more susceptible to the alkaline treatments that can be used during the industrial processing of lignocellulosics.

One-sentence summaryThe expression of a grass p-coumaroyl-CoA:monolignol transferase induces a high p-coumaroylation of poplar lignins and a better saccharification of alkali-pretreated poplar wood without growth penalty


title: A candidate neuroimaging biomarker for detection of neurotransmission-related functional alterations and prediction of pharmacological analgesic response in chronic pain

abstract:
BackgroundChronic pain is a world-wide clinical challenge. Response to analgesic treatment is limited and difficult to predict. Functional MRI (fMRI) has been suggested as a potential solution. However, while most analgesics target specific neurotransmission pathways, fMRI-based biomarkers are not specific for any neurotransmitter system, limiting our understanding of how they might contribute to predict treatment response.

MethodsHere, we sought to bridge this gap by applying Receptor-Enriched Analysis of Functional Connectivity by Targets (REACT) to investigate whether neurotransmission-enriched functional connectivity (FC) mapping can provide insights into the brain mechanisms underlying chronic pain and inter-individual differences in analgesic response after a placebo or duloxetine. Chronic knee osteoarthritis (OA) pain patients (n=56) underwent pre-treatment brain scans in two clinical trials. Study 1 (n=17) was a 2-week single-blinded placebo pill trial. Study 2 (n=39) was a 3-month double-blinded randomized trial comparing placebo to duloxetine, a dual serotonin-noradrenaline reuptake inhibitor.

ResultsAcross two independent studies, we found that chronic pain OA patients present FC alterations in the FC related to the serotonin (SERT) and noradrenaline (NET) transporters, when compared to age-matched healthy controls. Placebo responders presented with higher pre-treatment dopamine transporter (DAT)-enriched FC than non-responders. Duloxetine responders presented with higher pre-treatment SERT and NET-enriched FC than non-responders. Pre-treatment SERT and NET-enriched FC achieved predictive positive values of duloxetine response up to 85.71%.

ConclusionNeurotransmission-enriched FC mapping might hold promise as a new mechanistic-informed biomarker for functional brain alterations and prediction of response to pharmacological analgesia in chronic pain.


title: Timing of selective basal ganglia white matter loss in Huntington's disease

abstract:
ObjectivesTo investigate the timeframe prior to symptom onset when cortico-basal ganglia white matter (WM) loss begins in premanifest Huntingtons disease (preHD), and which striatal and thalamic sub-region WM tracts are most vulnerable.

MethodsWe performed fixel-based analysis, which allows resolution of crossing WM fibres at the voxel level, on diffusion tractography derived WM tracts of striatal and thalamic sub-regions in two independent cohorts; TrackON-HD, which included 72 preHD (approx. 11 years before disease onset) and 85 controls imaged at three time points over two years; and the HD young adult study (HD-YAS), which included 54 preHD (approx. 25 years before disease onset) and 53 controls, imaged at one time point. Group differences in fibre density and cross section (FDC) were investigated.

ResultsWe found no significant group differences in cortico-basal ganglia sub-region FDC in preHD gene carriers 25 years before onset. In gene carriers 11 years before onset, there were reductions in striatal (limbic and caudal motor) and thalamic (premotor, motor and sensory) FDC at baseline, with no significant change over 2 years. Caudal motor-striatal, pre-motor-thalamic, and primary motor-thalamic FDC at baseline, showed significant correlations with the Unified Huntingtons disease rating scale (UHDRS) total motor score (TMS). Limbic cortico-striatal FDC and apathy were also significantly correlated.

ConclusionsOur findings suggest that the initiation of disease modifying therapies 25 years before onset could protect these important brain networks from undergoing neurodegeneration and highlight selectively vulnerable sub-regions of the striatum and thalamus that may be important targets for future therapies.


title: MK-801-induced behavioral and dopaminergic responses in the shell part of the nucleus accumbens in adult rats are disrupted after neonatal blockade of the ventral subiculum.

abstract:
The present study was conducted in the context of animal modeling of schizophrenia. It investigated in adult rats, after transient neonatal blockade of the ventral subiculum (VSub), the impact of a very specific non-competitive antagonist of NMDA receptors (MK-801) on locomotor activity and dopaminergic (DAergic) responses in the dorsomedial shell part of the nucleus accumbens (Nacc), a striatal subregion described as the common target region for antipsychotics.

The functional neonatal inactivation of the VSub was achieved by local microinjection of tetrodotoxin (TTX) at postnatal day 8 (PND8). Control pups were microinjected with the solvent phosphate buffered saline (PBS). Locomotor responses and DAergic variations in the dorsomedial shell part of the Nacc were measured simultaneously using in vivo voltammetry in awake, freely moving animals after sc administration of MK-801. The following results were obtained: 1) a dose-dependent increase in locomotor activity in PBS and TTX animals, greater in TTX rats/PBS rats; and 2) divergent DAergic responses for PBS and TTX animals. A decrease in DA levels with a return to around basal values was observed in PBS animals. An increase in DA levels was obtained in TTX animals. The present data suggest that neonatal blockade of the VSub results in disruption in NMDA glutamatergic transmission, causing a disturbance in DA release in the dorsomedial shell in adults rats. In the context of animal modeling of schizophrenia using the same approach it would be interesting to investigate possible changes in postsynaptic NMDA receptors-related proteins in the dorsomedial shell region in the Nacc.


title: Temporal enhancement of cross-adaptation between density and size perception based on the theory of magnitude

abstract: The estimation of spatial distances is one of the most important perceptual outputs of vision and can easily be deduced even with detached objects. However, how the visual system encodes distances between objects and object sizes is unclear. Hisakata, Nishida, and Johnston (2016) reported a new adaptation effect, in which the perceived distance between objects and the size of an object shrink after adaptation to a dense texture. They proposed that the internal representation of density plays a role in a spatial metric system that measures distance and size. According to the theory of magnitude (Walsh, 2003), the estimation of spatial extent (distance and size) shares common metrics with the estimation of temporal length and numerosity magnitudes and is processed at the same stage. Here, we show the existence of temporal enhancement in cross-adaptation between density and size perception. We used the staircase method to measure the temporal property. The test stimuli were two circles, and the adapting stimulus had a dotted texture. The adapting texture refreshed every 100 or 300 ms, or not at all (static), during the adaptation. The results showed that the aftereffects from a refreshing stimulus were larger than those under the static condition. On the other hand, density adaptation lacked such enhancement. This result indicates that repetitive presentation of an adapting texture enhanced the density-size cross-aftereffect. According to the theory of magnitude, a common mechanism encodes spatial and temporal magnitude estimation and the adaptation to temporal density explains this cross-adaptation enhancement.


title: Phase-based cortical synchrony is affected by prematurity

abstract: Inter-areal synchronization by phase-phase correlations (PPC) of cortical oscillations mediates many higher neurocognitive functions, which are often affected by prematurity, a globally prominent neurodevelopmental risk factor. Here, we used electroencephalography (EEG) to examine brain-wide cortical PPC networks at term-equivalent age, comparing human infants after early prematurity to a cohort of healthy controls. We found that prematurity affected these networks in a sleep state-specific manner, and the differences between groups were also frequency-selective, involving brain-wide connections. The strength of synchronization in these networks was predictive of clinical outcomes in the preterm infants. These findings show that prematurity affects PPC networks in a clinically significant manner suggesting early functional biomarkers of later neurodevelopmental compromise to be used in clinical and translational studies after early neonatal adversity.


title: Intra-ocular dendritic cells are increased in HLA-B27 associated acute anterior uveitis

abstract:
Uveitis describes a heterogeneous group of inflammatory eye diseases characterized by infiltration of leukocytes into the uveal tissues. HLA-B27-associated uveitis is a common subtype of uveitis and a prototypical ocular autoimmune disease. Local immune mechanisms driving human uveitis are poorly characterized mainly due to the limited available biomaterial and subsequent technical limitations.

Here, we provide the first high-resolution characterization of intraocular leukocytes in HLA-B27 positive and negative anterior uveitis and an infectious endophthalmitis control by combining single cell RNA-sequencing (scRNA-seq) with flow cytometry and low-input proteomics. Ocular cell infiltrates consisted primarily of lymphocytes in uveitis and of myeloid cells in infectious endophthalmitis. HLA-B27 positive uveitis exclusively featured an plasmacytoid and classical dendritic cells (cDC) infiltrate, and of plasma cells. Moreover, cDCs were central in predicted local cell-cell communication.

The data suggests a unique pattern of ocular leukocyte infiltration in HLA-B27 positive uveitis with relevance of particular dendritic cells.