title: Stress generation, relaxation and size control in confined tumor growth

abstract:
Experiments on tumor spheroids have shown that compressive stress from their environment can reversibly decrease tumor expansion rates and final sizes. Stress release experiments show that nonuniform anisotropic elastic stresses can be distributed throughout. The elastic stresses are maintained by structural proteins and adhesive molecules, and can be actively relaxed by a variety of biophysical processes. In this paper, we present a new continuum model to investigate how the growth-induced elastic stresses and active stress relaxation, in conjunction with cell size control feedback machinery, regulate the cell density and stress distributions within growing tumors as well as the tumor sizes in the presence of external physical confinement and gradients of growth-promoting chemical fields. We introduce an adaptive reference map that relates the current position with the reference position but adapts to the current position in the Eulerian frame (lab coordinates) via relaxation. This type of stress relaxation is similar to but simpler than the classical Maxwell model of viscoelasticity in its formulation. By fitting the model to experimental data from two independent studies of tumor spheroid growth and their cell density distributions, treating the tumors as incompressible, neo-Hookean elastic materials, we find that the rates of stress relaxation of tumor tissues can be comparable to volumetric growth rates. Our study provides insight on how the biophysical properties of the tumor and host microenvironment, mechanical feedback control and diffusion-limited differential growth act in concert to regulate spatial patterns of stress and growth. When the tumor is stiffer than the host, our model predicts tumors are more able to change their size and mechanical state autonomously, which may help to explain why increased tumor stiffness is an established hallmark of malignant tumors.

Author summaryThe mechanical state of cells can modulate their growth and division dynamics via mechanotransduction, which affects both the cell size distribution and the tissue size as a whole. Experiments on tumor spheroids have shown that compressive stress from their environment can reversibly decrease tumor expansion rates and final sizes. Besides external confinement and compression on the tumor border, a heterogeneous stress field can be generated inside the tumor by nutrient-driven differential growth. Such growth-induced mechanical stresses can be relaxed by tissue rearrangement, which happens during cell neighbor exchanges, cell divisions, and extracellular matrix renewal. In this study, we have developed a continuum model that describes the above mechanical interactions and the dynamics of tissue rearrangement explicitly. Motivated by published experimental data, we consider mechanotransduction where the local compressive stress slows down cell growth and cell size reduction limits cell division. We have analyzed how external mechanical stimuli and internal processes influence the outcome of cell-and-tissue sizes and spatial patterns of cell density and mechanical stress in growing tumors.


title: Antidepressant drugs act by directly binding to TRKB neurotrophin receptors

abstract: It is unclear how binding of antidepressant drugs to their targets gives rise to the clinical antidepressant effect. We discovered that the transmembrane domain of TRKB, the brain-derived neurotrophic factor (BDNF) receptor that promotes neuronal plasticity and antidepressant responses, has a cholesterol-sensing function that mediates synaptic effects of cholesterol. We then found that both typical and fast-acting antidepressants directly bind to TRKB, thereby facilitating synaptic localization of TRKB and its activation by BDNF. Extensive computational approaches including atomistic molecular dynamics simulations revealed a binding site at the transmembrane region of TRKB dimers. Mutation of the TRKB antidepressant-binding motif impaired cellular, behavioral and plasticity-promoting responses to antidepressants in vitro and in vivo. We suggest that binding to TRKB and the allosteric facilitation of BDNF signaling is the common mechanism for antidepressant action, which proposes a framework for how molecular effects of antidepressants are translated into clinical mood recovery.

category: neuroscience


title: LAB-AID (Laboratory Automated Interrogation of Data): an interactive web application for visualization of multi-level data from biological experiments

abstract: A key step in understanding the results of biological experiments is visualization of the data. Many laboratory experiments contain a range of measurements that exist within a hierarchy of interdependence. An automated way to visualise and interrogate experimental data would: 1) lead to improved understanding of the results, 2) help to determine which statistical tests should be performed, and 3) easily identify outliers and sources of batch effects. Unfortunately, existing graphing solutions often demand expertise in programming, require considerable effort to import and examine such multi-level data, or are unnecessarily complex for the task at hand. Here we present LAB-AID (Laboratory Automated Interrogation of Data), an interactive tool specifically designed to automatically visualize and query hierarchical data resulting from biological experiments.

category: bioinformatics


title: High-level cognition during story listening is reflected in high-order dynamic correlations in neural activity patterns

abstract: Our thoughts arise from coordinated patterns of interactions between brain structures that change with our ongoing experiences. High-order dynamic correlations in neural activity patterns reflect different subgraphs of the brains functional connectome that display homologous lower-level dynamic correlations. We tested the hypothesis that high-level cognition is reflected in high-order dynamic correlations in brain activity patterns. We developed an approach to estimating high-order dynamic correlations in timeseries data, and we applied the approach to neuroimaging data collected as human participants either listened to a ten-minute story or listened to a temporally scrambled version of the story. We trained across-participant pattern classifiers to decode (in held-out data) when in the session each neural activity snapshot was collected. We found that classifiers trained to decode from high-order dynamic correlations yielded the best performance on data collected as participants listened to the (unscrambled) story. By contrast, classifiers trained to decode data from scrambled versions of the story yielded the best performance when they were trained using first-order dynamic correlations or non-correlational activity patterns. We suggest that as our thoughts become more complex, they are reflected in higher-order patterns of dynamic network interactions throughout the brain.


title: MRI of Capn15 knockout mice and analysis of Capn15 distribution reveal possible roles in brain development and plasticity

abstract: The Small Optic Lobe (SOL) family of calpains are intracellular cysteine proteases that are expressed in the nervous system and play an important role in neuronal development in both Drosophila, where loss of this calpain leads to the eponymous small optic lobes, and in mouse and human, where loss of this calpain leads to eye anomalies. Some human individuals with biallelic variants in CAPN15 also have developmental delay and autism. However, neither the specific effect of the loss of the Capn15 protein on brain development nor the brain regions where this calpain is expressed in the adult is known. Here we show using small animal MRI that mice with the complete loss of Capn15 have smaller brains overall with larger decreases in the thalamus and subregions of the hippocampus. These losses are not seen in Capn15 conditional KO mice where Capn15 is knocked out only in excitatory neurons in the adult. Based on {beta}-galactosidase expression in an insert strain where lacZ is expressed under the control of the Capn15 promoter, we show that Capn15 is expressed in adult mice, particularly in neurons involved in plasticity such as the hippocampus, lateral amygdala and Purkinje neurons, and partially in other non-characterized cell types. The regions of the brain in the adult where Capn15 is expressed do not correspond well to the regions of the brain most affected by the complete knockout suggesting distinct roles of Capn15 in brain development and adult brain function.


title: Pulling the strings of cell cycle: a non-coding RNA, CcnA, modulates the master regulators CtrA and GcrA in Caulobacter crescentus

abstract: Bacteria are powerful models for understanding how cells divide and accomplish global regulatory programs. In Caulobacter crescentus, a cascade of essential master regulators supervises the correct and sequential activation of DNA replication, cell division and development of different cell types. Among them, the response regulator CtrA plays a crucial role coordinating all those functions. Here, for the first time we describe the role of a novel factor named CcnA, a cell cycle regulated ncRNA located at the origin of replication, presumably activated by CtrA and responsible for the accumulation of CtrA itself. In addition, CcnA may be also involved in the inhibition of translation of the S-phase regulator, GcrA, by interacting with its 5 untranslated region (5-UTR). Performing in vitro experiments and mutagenesis, we propose a mechanism of action of CcnA based on liberation (ctrA) or sequestration (gcrA) of their ribosome-binding site (RBS). Finally, its role may be conserved in other alphaproteobacterial species, such as Sinorhizobium meliloti, representing indeed a potentially conserved process modulating cell cycle in Caulobacterales and Rhizobiales.

category: microbiology


title: Spatial and phylogenetic structure of Alpine stonefly community assemblages across seven habitats using DNA-species

abstract:
O_LIStream ecosystems are spatially heterogeneous, with many different habitat patches distributed within a small area. The influence of this heterogeneity on the biodiversity of benthic insect communities is well documented; however, studies of the role of habitat heterogeneity in species coexistence and community assembly remain limited. Here, we investigated how habitat heterogeneity influences spatial structure (beta biodiversity) and phylogenetic structure (evolutionary processes) of benthic stonefly (Plecoptera, Insecta) communities.
C_LIO_LIWe sampled 20 sites along two Alpine rivers, including seven habitats in four different reaches (headwaters, meandering, bar-braided floodplain, and lowland spring-fed). We identified 21 morphological species and delineated 52 DNA-species based on sequences from mitochondrial cox1 and nuclear ITS markers. Using DNA-species, we first analysed the patterns of variation in richness, diversity, and community composition by quantifing the contribution of each of the four reaches and seven habitats to the overall DNA-species diversity using an additive partition of species diversity analysis and distance-based redundancy analysis. Using gene-tree phylogenies, we assessed whether environmental filtering led to the co-occurrence of DNA-species using a two-step analysis to find a phylogenetic signal.
C_LIO_LIThe four reaches significantly contributed to DNA-species richness; with the meandering section having the highest contribution. However, we found that habitats had an effect on DNA-species diversity, where glide, riffle and, pool influenced the spatial structure of stonefly communities possibly due to a high species turnover.
C_LIO_LIAmong the habitats, the pool showed significant phylogenetic clustering, suggesting high levels of evolutionary adaptation and strong habitat filtering. This community structure may be caused by long-term stability of the habitat and the similar requirements for co-occurring species.
C_LIO_LIOur study shows the importance of different habitats on the spatial and phylogenetic structure of stonefly community assemblies and sheds light on the habitat-specific diversity that may help improve conservation practices.
C_LI

category: evolutionary biology


title: Single-trial dynamics of competing reach plans in the human motor periphery

abstract:
Contemporary theories of motor control propose that multiple motor plans compete for selection before the winning command is executed. While most competitions are completed prior to movement onset, movements are often initiated before the competition has been resolved. An example of this is saccadic averaging, wherein the eyes land at an intermediate location between two visual targets. Behavioral and neurophysiological signatures of competing motor commands have been reported for reaching movements, but debate remains about whether such signatures attest to an unresolved competition, arise from averaging across many trials, or reflect a strategy to optimize behavior given task constraints. Here, we recorded electromyographic (EMG) activity from an upper limb muscle while human participants performed a reach analogue of a task that elicits saccadic averaging, freely choosing to reach to one of two identical and suddenly presented visual targets. On each trial, muscle recruitment showed two distinct phases of directionally-tuned activity. In the first wave, time-locked ~100 ms of target presentation, EMG activity was clearly influenced by the non-chosen target, reflecting a competition between two reach commands that was biased in favor of the ultimately chosen target. This resulted in an initial movement direction intermediate between the two targets. In contrast, the second wave of EMG activity, time-locked to voluntary reach onset, was not biased toward the non-chosen target, showing that the competition between targets was resolved by the time of movement initiation. Instead, this second wave of activity was already compensating for the averaging induced by the first wave. Thus, single-trial analysis reveals an evolution in how the non-chosen target differentially influences the first and second wave of EMG activity. Ongoing debates about the interaction between competing reach commands may arise, at least in part, from the use of behavioural tasks that mute the magnitude of the earliest wave of EMG activity.

SIGNIFICANCE STATEMENTContemporary theories of motor control suggest that multiple motor plans compete for selection before the winning command is executed. Evidence for this is found in intermediate reach movements towards two potential target locations, but recent findings have challenged this notion by arguing that they attest to an optimal response strategy. By examining upper limb muscle recruitment during a free-choice reach task, we show early recruitment of a sub-optimal averaged motor command to the two targets that subsequently transitions to a single motor command that compensates for the initially averaged motor command. Thus, recording limb muscle activity permits single-trial resolution of the dynamic influence of the non-chosen target through time


title: Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice

abstract: Genes with multiple co-active promoters appear common in brain, yet little is known about functional requirements for these potentially redundant genomic regulatory elements. SCN1A, which encodes the NaV1.1 sodium channel alpha subunit, is one such gene with two co-active promoters. Mutations in SCN1A are associated with epilepsy, including Dravet Syndrome (DS). The majority of DS patients harbor coding mutations causing SCN1A haploinsufficiency, however putative causal non-coding promoter mutations have been identified. To determine the functional role of one of these potentially redundant Scn1a promoters, we focused on the non-coding Scn1a 1b regulatory region, previously described as a non-canonical alternative transcriptional start site. Mice harboring a deletion of the extended evolutionarily-conserved 1b non-coding interval exhibited surprisingly severe reductions of Scn1a and NaV1.1 expression in brain with accompanying electroencephalographic seizures and behavioral deficits. This work identified the 1b region as a critical disease-relevant regulatory element and provides evidence that non-canonical and seemingly redundant promoters can have essential function.


title: Representations of complex contexts: A role for hippocampus

abstract: The hippocampus plays a critical role in supporting episodic memory, in large part by binding together experiences and items with surrounding contextual information. At present, however, little is known about the roles of different hippocampal subfields in supporting this item-context binding. To address this question, we constructed a task in which items were affiliated with differing types of context - cognitive associations that vary at the local, item level and membership in temporally organized lists that linked items together at a global level. Participants made item recognition judgments while undergoing high-resolution fMRI imaging. We performed voxel pattern similarity analyses to answer the question of how human hippocampal subfields represent retrieved information about cognitive states and the time at which a past event took place. As participants recollected previously presented items, activity patterns in the CA23DG subregion carried information about prior cognitive states associated with these items. We found no evidence to suggest reinstatement of information about temporal context at the level of list membership, but exploratory analyses revealed representations of temporal context at a coarse level in conjunction with representations of cognitive contexts. Results are consistent with characterizations of CA23DG as a critical site for binding together items and contexts in the service of memory retrieval.


title: No effect of monetary reward in a visual working memory task

abstract: Previous work has shown that humans distribute their visual working memory (VWM) resources flexibly across items: the higher the importance of an item, the better it is remembered. A related, but much less studied question is whether people also have control over the total amount of VWM resource allocated to a task. Here, we approach this question by testing whether increasing monetary incentives results in better overall VWM performance. In three experiments, subjects performed a delayed-estimation task on the Amazon Turk platform. In the first two experiments, four groups of subjects received a bonus payment based on their performance, with the maximum bonus ranging from $0 to $10 between groups. We found no effect of the amount of bonus on intrinsic motivation or on VWM performance in either experiment. In the third experiment, reward was manipulated on a trial-by-trial basis using a within-subjects design. Again, no evidence was found that VWM performance depended on the magnitude of potential reward. These results suggest that encoding quality in visual working memory is insensitive to monetary reward, which has implications for resource-rational theories of VWM.

category: animal behavior and cognition


title: Learning Divisive Normalization in Primary Visual Cortex

abstract:
Divisive normalization (DN) is a prominent computational building block in the brain that has been proposed as a canonical cortical operation. Numerous experimental studies have verified its importance for capturing nonlinear neural response properties to simple, artificial stimuli, and computational studies suggest that DN is also an important component for processing natural stimuli. However, we lack quantitative models of DN that are directly informed by measurements of spiking responses in the brain and applicable to arbitrary stimuli. Here, we propose a DN model that is applicable to arbitrary input images. We test its ability to predict how neurons in macaque primary visual cortex (V1) respond to natural images, with a focus on nonlinear response properties within the classical receptive field. Our model consists of one layer of subunits followed by learned orientation-specific DN. It outperforms linear-nonlinear and wavelet-based feature representations and makes a significant step towards the performance of state-of-the-art convolutional neural network (CNN) models. Unlike deep CNNs, our compact DN model offers a direct interpretation of the nature of normalization. By inspecting the learned normalization pool of our model, we gained insights into a long-standing question about the tuning properties of DN that update the current textbook description: we found that within the receptive field oriented features were normalized preferentially by features with similar orientation rather than non-specifically as currently assumed.

Author summaryDivisive normalization (DN) is a computational building block throughout sensory processing in the brain. We currently lack an understanding of what role this normalization mechanism plays when processing complex stimuli like natural images. Here, we use modern machine learning methods to build a general DN model that is directly informed by data from primary visual cortex (V1). Contrary to high-predictive deep learning models, our DN-based models parameters offer a straightforward interpretation of the nature of normalization. Within the receptive field, we found that neurons responding strongly to a specific orientation are preferentially normalized by other neurons that are highly active for similar orientations, rather than being normalized by all neurons as it is currently assumed by textbook models.


title: An Erwinia amylovora inducible promoter for intragenic improvement of apple fire blight resistance

abstract:
Intragenesis is an important alternative to transgenesis to produce modified plants containing native DNA only. A key point to develop such a strategy is the availability of regulatory sequences controlling the expression of the gene of interest. With the aim of finding apple gene promoters either inducible by the fire blight pathogen Erwinia amylovora (Ea) or moderately constitutive, we focused on polyphenoloxidase genes (PPO). These genes encode oxidative enzymes involved in many physiological processes and have been previously shown to be up-regulated during the Ea infection process. We found ten PPO and two PPO-like sequences in the apple genome and characterized the promoters of MdPPO16 (pPPO16) and MdKFDV02 PPO-like (pKFDV02) for their potential as Ea-inducible and low-constitutive regulatory sequences respectively. Expression levels of reporter genes fused to these promoters and transiently or stably expressed in apple were quantified after various treatments. Unlike pKFDV02 which displayed a variable activity, pPPO16 allowed a fast and strong expression of transgenes in apple following Ea infection in a Type 3 Secretion System dependent manner. Altogether our results indicate that pKFDV02 did not keep its promises as a constitutive and weak promoter whereas pPPO16, the first Ea-inducible promoter cloned from apple, can be a useful component of intragenic strategies to create fire blight resistant apple genotypes.

Key messagepPPO16, the first Ea-inducible promoter cloned from apple, can be a useful component of intragenic strategies to create fire blight resistant apple genotypes.

category: bioengineering


title: An Erwinia amylovora inducible promoter for improvement of apple fire blight resistance


title: Most cancers carry a substantial deleterious load due to Hill-Robertson interference

abstract: Cancer genomes exhibit surprisingly weak signatures of negative selection1,2. This may be because selective pressures are relaxed or because genome-wide linkage prevents deleterious mutations from being removed (Hill-Robertson interference)3. By stratifying tumors by their genome-wide mutational burden, we observe negative selection (dN/dS ~ 0.47) in low mutational burden tumors, while remaining cancers exhibit dN/dS ratios ~1. This suggests that most tumors do not remove deleterious passengers. To buffer against deleterious passengers, tumors upregulate heat shock pathways as their mutational burden increases. Finally, evolutionary modeling finds that Hill-Robertson interference alone can reproduce patterns of attenuated selection and estimates the total fitness cost of passengers to be 40% per cell on average. Collectively, our findings suggest that the lack of observed negative selection in most tumors is not due to relaxed selective pressures, but rather the inability of selection to remove deleterious mutations in the presence of genome-wide linkage.


title: More than Two Populations of Microtubules Comprise the Dynamic Mitotic Spindle

abstract: The microtubules of the mitotic spindle mediate chromosome alignment to the metaphase plate, then sister chromatid segregation to the spindle poles in anaphase. Previous analyses of spindle microtubule kinetics utilizing fluorescence dissipation after photoactivation described two main populations, a slow and a fast turnover population, and these were ascribed to reflect kinetochore versus non-kinetochore microtubules, respectively. Here, we test this categorization by disrupting kinetochores through depletion of the Ndc80 complex. In the absence of functional kinetochores, microtubule dynamics still exhibit slow and fast turnover populations, though the proportion of each population and the timings of turnover are altered. Importantly, the data obtained following Hec1/Ndc80 depletion suggests other sub-populations, in addition to kinetochore microtubules, contribute to the slow turnover population. Further manipulation of spindle microtubules revealed a complex landscape. Dissection of the dynamics of microtubule populations provides a greater understanding of mitotic spindle kinetics and insight into roles in facilitating chromosome attachment, movement, and segregation during mitosis.

category: cell biology


title: Two faces of perceptual awareness during the attentional blink: Gradual and discrete

abstract: In a series of experiments, the nature of perceptual awareness during the attentional blink was investigated. Previous work has considered the attentional blink as a discrete, all-or-none phenomenon, indicative of general access to conscious awareness. Using continuous report measures in combination with mixture modeling, the outcomes showed that perceptual awareness during the attentional blink can be a gradual phenomenon. Awareness was not exclusively discrete, but also exhibited a gradual characteristic whenever the spatial extent of attention induced by the first target spanned more than a single location. Under these circumstances, mental representations of blinked targets were impoverished, but did approach the actual identities of the targets. Conversely, when the focus of attention covered only a single location, there was no evidence for any partial knowledge of blinked targets. These two different faces of awareness during the attentional blink challenge current theories of both awareness and temporal attention, which cannot explain the existence of gradual awareness of targets during the attentional blink. To account for the current outcomes, an adaptive gating model is proposed that casts awareness on a continuum between gradual and discrete, rather than as being of either single kind.


title: Mechanotransduction of strain regulates an invasive phenotype in newly transformed epithelial cells

abstract:
Our organs and tissues are in constant motion, exposing epithelial cells to mechanical stretch. However, how these external forces impact cellular morphology, organization and dynamics in healthy and diseased tissues is still being elucidated. In several studies, we and others have shown how mechanical stresses and strains in the epithelium can modulate the dynamics and invasiveness of transformed cells. Carcinoma, the most common type of cancer, develops in the sheets of cells forming the epithelium and lining our organs and cavities. It usually begins with the transformation of a single cell via the activation of oncogenes such as Ras. Here, we show in a model system how mechanical stretch in epithelial sheets results in a more invasive phenotype in transformed cells.

Cyclic strain prevents the formation of strong circumferential belts of actin in RasV12 cells and greatly promoting the formation of RasV12 protrusions, typical of a more invasive phenotype. We also show that RasV12 and wild type MDCK cells possess distinct sensitivity to strain. External forces remodel their actin cytoskeletons and adhesion complexes differently, resulting in a more invasive system dynamic. Our work demonstrates that the Rho-ROCK mechanotransduction pathway is involved in regulating a mechanically-induced switch to a more invasive phenotype. In a mechanically dynamic microenvironment, transformed cells exhibit drastically different cellular dynamics and movements when compared to static conditions. They grow larger invasive protrusions, potentially making them harder to be eliminated from healthy tissues. The insights gained in this study reveal the complex dynamics at play in healthy and transformed epithelial cells which are found in a mechanically active microenvironment.

category: biophysics


title: Evolutionary genetic integration of behavioural and endocrine components of the stress response

abstract: The vertebrate stress response comprises a suite of behavioural and physiological traits that must be functionally integrated to ensure organisms cope adaptively with acute stressors. Natural selection should favour functional integration, leading to a prediction of genetic integration of these traits. Despite the implications of such genetic integration for our understanding of human and animal health, as well as evolutionary responses to natural and anthropogenic stressors, formal quantitative genetic tests of this prediction are lacking. Here we demonstrate that acute stress response components in Trinidadian guppies are both heritable and integrated on the major axis of genetic covariation. This integration could either facilitate or constrain evolutionary responses to selection, depending upon the alignment of selection with this axis. Such integration also suggests artificial selection on the genetically correlated behavioural responses to stress could offer a viable non-invasive route to the improvement of health and welfare in captive animal populations.


title: Genetic integration of behavioural and endocrine components of the stress response


title: Discovery of a small molecule having both potent anti-fibrotic and anti-inflammatory capabilities

abstract:
AbstractsIdiopathy pulmonary fibrosis (IPF) is an intractable and fatal human disorder. Our previous study showed that eupatilin exerted a potent anti-fibrotic effect on both in vitro fibrogenesis and bleomycin-induced lung fibrosis model (BLM). Subsequently, an analog called ONG41008 had been identified as a more potent anti-fibrotic than eupatilin and also showed a potent anti-inflammatory capability. Orally administered ONG41008 significantly improved onset of BLM in both prophylactic and therapeutic model and its therapeutic efficacy was similarly compared to or better than pirfenidone by measuring production of collagen and hydroxyproline. Staining collagen or SMA corroborated these results.

As in vitro fibrogenesis models, DHLF (Diseased Human Lung Fibroblasts from IPF patients) and HSC (hepatic stellate cells) were used for direct effects of ONG41008 on pivotal cellular and molecular functions associated with pathogenic myofibroblasts; ONG41008 dismantled latent TGFb complex (LTC), generating inactive forms of TGF{beta}, likely limiting TGF{beta} to TGF{beta} receptor via depolymerization of F-actin and this blunted SMAD2/SMAD3 phosphorylation, thereby reprogramming EMT. A set of cell imaging studies and transcriptomic analysis were conducted to explore how ONG41008 elicited both anti-fibrotic and anti-inflammatory capabilities. Elastin (ELN) seemed to be a pioneering pharmacodynamic marker. It was also found that NOX4 played an important role in anti- fibrosis because it was functionally connected to major central nod proteins such as lysyl- oxidase (LOX) and numerous collagen family members in an ONG41008-specific fibrogenic interactome. Human NOX4 was significantly induced by TGF{beta} and completely knocked down by ONG41008. It has been shown that production of reactive oxygen species (ROS) led to activation of inflammasome. ONG41008 may be likely related to anti-inflammation, leading to a key protective effect on fibrogenesis. Concomitant with downregulation of NOX4, expression of macrophages homing chemokines, CCL2 and CCL7 were significantly attenuated by ONG41008. In vitro anti-inflammatory activities of ONG41008 were investigated in RAW264.7 cells, a mouse monocytic cell line stimulated with LPS. ONG41008 substantially attenuated TNF, CXCL10, CCL2 and CCL7, which are proinflammatory cytokine and important chemokines influencing T cells or macrophages. TNF was situated at the central nod in LPS-treated macrophages via an ONG41008-specific interactome analysis.

Taken together, ONG41008 is a TGF{beta} biogenesis inhibitor, being a potent drug for a broad range of fibrotic diseases and could antagonize inflammatory diseases as well.


title: A noble TGF beta biogenesis inhibitor exhibits both potent anti-fibrotic and anti-inflammatory capabilities


title: B-SOiD: An Open Source Unsupervised Algorithm for Discovery of Spontaneous Behaviors

abstract: Studying naturalistic behavior remains a prohibitively difficult objective. Recent machine learning advances have enabled limb localization. Extracting behaviors, however, requires ascertaining the spatiotemporal patterns of these positions. To provide the missing bridge from poses to actions and their kinematics, we developed B-SOiD - an open-source, unsupervised algorithm that identifies behavior without user bias. By training a machine classifier on pose pattern statistics clustered using new methods, our approach achieves greatly improved processing speed and the ability to generalize across subjects or labs. Using a frameshift alignment paradigm, B-SOiD overcomes previous temporal resolution barriers that prevent the use of other algorithms with electrophysiological recordings. Using only a single, off-the-shelf camera, B-SOiD provides categories of sub-action for trained behaviors and kinematic measures of individual limb trajectories in an animal model. These behavioral and kinematic measures are difficult but critical to obtain, particularly in the study of pain, OCD, and movement disorders.


title: Accounting for RNA polymerase heterogeneity reveals state switching and two distinct long-lived backtrack states escaping through cleavage

abstract: Pausing by bacterial RNA polymerase (RNAp) is vital in the recruitment of regulatory factors, RNA folding, and coupled translation. While backtracking and intra-structural isomerization have been proposed to trigger pausing, our understanding of backtrack-associated pauses and catalytic recovery remains incomplete. Using high-throughput magnetic tweezers, we examined the E. coli RNAp transcription dynamics over a wide range of forces and NTP concentrations. Dwell-time analysis and stochastic modeling identified, in addition to a short-lived elemental pause, two distinct long-lived backtrack pause states differing in recovery rates. We further identified two stochastic sources of transcription heterogeneity: alterations in short-pause frequency that underlie elongation-rate switching, and RNA cleavage deficiency that underpins different long-lived backtrack states. Together with effects of force and Gre factors, we demonstrate that recovery from deep backtracks is governed by intrinsic RNA cleavage rather than diffusional Brownian dynamics. We introduce a consensus mechanistic model that unifies our findings with prior models.


title: Cysteine crosslinking in native membranes establishes the transmembrane architecture of Ire1

abstract:
The endoplasmic reticulum (ER) is a key organelle of membrane biogenesis and crucial for the folding of both membrane and secretory proteins. Sensors of the unfolded protein response (UPR) monitor the unfolded protein load in the ER and convey effector functions for maintaining ER homeostasis. Aberrant compositions of the ER membrane, referred to as lipid bilayer stress, are equally potent activators of the UPR. How the distinct signals from lipid bilayer stress and unfolded proteins are processed by the conserved UPR transducer Ire1 remains unknown. Here, we have generated a functional, cysteine-less variant of Ire1 and performed systematic cysteine crosslinking experiments in native membranes to establish its transmembrane architecture in signaling-active clusters. We show that the transmembrane helices of two neighboring Ire1 molecules adopt an X-shaped configuration independent of the primary cause for ER stress. This suggests that different forms of stress converge in a common, signaling-active transmembrane architecture of Ire1.

SummaryThe endoplasmic reticulum (ER) is a hotspot of lipid biosynthesis and crucial for the folding of membrane and secretory proteins. The unfolded protein response (UPR) controls the size and folding capacity of the ER. The conserved UPR transducer Ire1 senses both unfolded proteins and aberrant lipid compositions to mount adaptive responses. Using a biochemical assay to study Ire1 in signaling-active clusters, Vath et al. provide evidence that the neighboring transmembrane helices of clustered Ire1 form an  X irrespectively of the primary cause of ER stress. Hence, different forms of ER stress converge in a common, signaling-active transmembrane architecture of Ire1.

category: biochemistry


title: Descending neocortical output critical for skilled forelimb movements is distributed across projection cell classes

abstract:
The interaction of descending neocortical outputs and subcortical premotor circuits is critical for shaping the skilled movements. Two broad classes of motor cortical output projection neurons provide input to many subcortical motor areas: pyramidal tract neurons (PT), which project throughout the neuraxis; and intratelencephalic neurons (IT), which project within cortex and subcortical striatum. It is unclear whether these classes are functionally in series or whether separable components of descending motor control signals are distributed across these distinct classes of projection neurons. Here we combine large-scale neural recordings across all layers of motor cortex with cell-type specific perturbations to study cortically-dependent mouse motor behaviors: kinematically-variable manipulation of a joystick and a kinematically-precise reach-to-grasp. We find that striatum-projecting IT neuron activity preferentially represents amplitude whereas pons-projecting PT neurons preferentially represent the variable direction of forelimb movements. Thus, separable components of descending motor cortical commands are distributed across motor cortical projection cell classes.

One-sentence summarySeparable components of cortical motor commands are distributed across distinct glutamatergic projection neuron cell-types.


title: Motor cortical output for skilled forelimb movement is selectively distributed across projection neuron classes


title: Characterizing the Network Architecture of Emotion Regulation Neurodevelopment

abstract: The ability to regulate emotions is key to goal attainment and wellbeing. Although much has been discovered about how the human brain develops to support the acquisition of emotion regulation, very little of this work has leveraged information encoded in whole-brain networks. Here we employed a network neuroscience framework to parse the neural underpinnings of emotion regulation skill acquisition while accounting for age in a sample of youth (N = 70, 34 female). Focusing on three key network metrics--network differentiation, modularity, and community structure differences between active regulation and a passive emotional baseline--we found that the control network, the default mode network, and limbic network were each related to emotion regulation ability while controlling for chronological age. Greater network differentiation in the control and limbic networks was related to better emotion regulation ability. With regards to network community structure, more communities and more crosstalk between modules (i.e., less modularity) in the control network were associated with better regulatory ability. By contrast, less crosstalk (i.e., more modularity) between modules in the default mode network was associated with better regulatory ability. Together, these findings highlight possible whole-brain connectome features that support the acquisition of emotion regulation in youth.


title: In silico stress fibre content affects peak strain in cytoplasm and nucleus but not in membrane for uniaxial substrate stretch

abstract: Existing in silico models for single cell mechanics feature limited representations of cytoskeletal structures that contribute substantially to the mechanics of a cell. We propose a micromechanical hierarchical approach to capture the mechanical contribution of actin stress fibres. For a cell-specific fibroblast geometry with membrane, cytoplasm and nucleus, the Mori-Tanaka homogenization method was employed to describe cytoplasmic inhomogeneities and constitutive contribution of actin stress fibres. The homogenization was implemented in a finite element model of the fibroblast attached to a substrate through focal adhesions. Strain in cell membrane, cytoplasm and nucleus due to uniaxial substrate stretch was assessed for different stress fibre volume fractions and different elastic modulus of the substrate. A considerable decrease of the peak strain with increasing stress fibre content was observed in cytoplasm and nucleus but not the membrane, whereas the peak strain in cytoplasm, nucleus and membrane increased for increasing elastic modulus of the substrate.


title: Astrovirus in Reunion Free-tailed Bat (Mormopterus francoismoutoui)

abstract: Astroviruses (AstVs) are RNA viruses infecting of a large diversity of avian and mammalian species, including bats, livestock, and humans. We investigated AstV infection in a free-tailed bat species, Mormopterus francoismoutoui, endemic to Reunion Island. A total of 380 guano samples were collected in a maternity colony during 38 different sampling sessions, from June 21st 2016 to September 4th 2018. Each sample was tested for the presence of the AstV RNA-dependent RNA-polymerase (RdRp) gene using a pan-AstV semi-nested polymerase chain reaction assay. In total, 27 guano samples (7.1%) tested positive, with high genetic diversity of the partial RdRp gene sequences among positive samples. A phylogenetic analysis further revealed that the detected viruses were genetically related to AstVs reported in rats, reptiles, dogs, and pigs, but did not cluster with AstVs commonly found in bats. Although more investigations need to be conducted to assess the prevalence of infected bats in the studied population, our findings show that Reunion free-tailed bats are exposed to AstVs, and suggest that cross-species transmission may occur with other hosts sharing the same habitat.

category: ecology


title: Mesoamerica is a cradle and the Atlantic Forest is a museum of Neotropical butterfly diversity: Insights from the evolution and biogeography of Brassolini (Lepidoptera: Nymphalidae)

abstract: Regional species diversity is ultimately explained by speciation, extinction, and dispersal. Here we estimate dispersal and speciation rates of Neotropical butterflies to propose an explanation for their distribution and diversity of extant species. We focus on the tribe Brassolini (owl butterflies and allies): a Neotropical group that comprises 17 genera and 108 species, most of them endemic to rainforest biomes. We infer a robust species tree using the multispecies coalescent framework and a dataset including molecular and morphological characters. This formed the basis for three changes in Brassolini classification: 1) Naropina, SYN. NOV. is subsumed within Brassolina; 2) Aponarope, SYN. NOV. is subsumed within Narope; 3) Selenophanes orgetorix, COMB. NOV. is reassigned from Catoblepia to Selenophanes. By applying biogeographical stochastic mapping, we found contrasting species diversification and dispersal dynamics across rainforest biomes, which might be partly explained by the geological and environmental history of each bioregion. Our results reveal a mosaic of biome-specific evolutionary histories within the Neotropics, where butterfly species have diversified rapidly (cradles: Mesoamerica), have accumulated gradually (museums: Atlantic Forest), or have alternately diversified and accumulated (Amazonia). Our study contributes evidence from a major butterfly lineage that the Neotropics are a museum and cradle of species diversity.


title: Size matters, so does condition: the use of a body condition index reveals the costs and benefits of structural body size in an insect.

abstract:
O_LIInsects are core actors for the balance of many earth ecosystems, as well as an alternative source of food and feed with a low ecological footprint. A comprehensive understanding of their life history requires reliable tools. Body condition constitutes the amount of energy reserves available to a fitness trait after maintenance costs have been accounted for. Body condition is standardly estimated using Body Condition Indexes (BCIs) in vertebrates. In insects the relevance of BCIs is frequently questioned on the basis that they might not accurately reflect neither energy reserves nor fitness.. However, to date no study has tested whether the very concept of body condition is relevant in insects, i.e. whether BCIs accurately reflect the relative energy reserves allocated to fitness traits.
C_LIO_LIWe propose that the relevance of using BCIs in insects depends on whether their structural size has a fitness cost. If on the contrary insects only benefit from a larger body size, a simple measurement of body size or mass will predict fitness, but not a BCI. We experimentally manipulated food availability at the larval and adult stage and used total fecundity of females as a fitness proxy of Tenebrio molitor, an important model in physiology, ecology and evolution, and one of the first insects to be considered as a source of food and feed.
C_LIO_LIOur results support three key assumptions of the relevance of BCIs in insects: (i) a valid BCI correlated with energy reserves corrected for a given size (i.e. relative energy reserves) and not with absolute measures of energy reserves; (ii) both structural size and body condition positively predict different components of fitness; and, (iii) the effect of body condition was dependent on resource availability, whereby its effect was only apparent and large when food was unrestricted at the larval stage and restricted at the adult stage.
C_LIO_LIOverall we demonstrate the relevance of using BCIs in insects. Their use should be generalized to improve fitness readouts in evolution, ecological and physiological studies, as well as improve their husbandry for commercial purposes.
C_LI


title: Spatio-temporal control of DNA replication by the pneumococcal cell cycle regulator CcrZ

abstract: Most bacteria replicate and segregate their DNA concomitantly while growing, before cell division takes place. How bacteria synchronize these different cell cycle events to ensure faithful chromosome inheritance is poorly understood. Here, we identified a conserved and essential protein in pneumococci and related Firmicutes named CcrZ (for Cell Cycle Regulator protein interacting with FtsZ) that couples cell division with DNA replication by controlling the activity of the master initiator of DNA replication, DnaA. The absence of CcrZ causes mis-timed and reduced initiation of DNA replication, which subsequently results in aberrant cell division. We show that CcrZ from Streptococcus pneumoniae directly interacts with the cytoskeleton protein FtsZ to place it in the middle of the newborn cell where the DnaA-bound origin is positioned. Together, this work uncovers a new mechanism for the control of the bacterial cell cycle in which CcrZ controls DnaA activity to ensure that the chromosome is replicated at the right time during the cell cycle.


title: A unique mode of nucleic acid immunity performed by a single multifunctional enzyme

abstract:
The perpetual arms race between bacteria and their viruses (phages) has given rise to diverse immune systems, including restriction-modification and CRISPR-Cas, which sense and degrade phage-derived nucleic acids. These complex systems rely upon production and maintenance of multiple components to achieve anti-phage defense. However, the prevalence and effectiveness of much simpler, single-component systems that cleave DNA remain unknown. Here, we describe a novel mode of nucleic acid immunity performed by a single enzyme with nuclease and helicase activities, herein referred to as Nhi. This enzyme provides robust protection against diverse staphylococcal phages and prevents phage DNA accumulation in cells stripped of all other known defenses. Our observations support a model in which Nhi acts as both the sensor and effector to degrade phage-specific replication intermediates.

Importantly, Nhi homologs are distributed in diverse bacteria and exhibit functional conservation, highlighting the versatility of such compact weapons as major players in anti-phage defense.


title: Voluntary motor commands are preferentially released during restricted sensorimotor beta rhythm phases

abstract: Voluntary movement requires motor commands to be released from motor cortex (M1) and transmitted to spinal motoneurons and effector muscles. M1 activity oscillates between brief excitatory and inhibitory states that correlate with single neuron spiking rates. Here, we asked if the motor commands needed to produce voluntary, self-paced finger movements are preferentially released from M1 during restricted phases of this ongoing sensorimotor oscillatory activity. 21 healthy adults performed a self-paced finger movement task while EEG and EMG signals were recorded. For each finger movement, we identified the individual sensorimotor mu (8-12 Hz) and beta (13-35 Hz) oscillatory phase at the estimated time of motor command release from M1 by subtracting individually-defined MEP latencies from EMG-determined movement onset times. We report that motor commands were preferentially released at ~120{degrees} along the beta cycle but were released uniformly across the mu cycle. These results suggest that motor commands are preferentially released from M1 near optimal peak phases of endogenous beta rhythms.


title: Neuronal population dynamics during motor plan cancellation in non-human primates

abstract:
To understand the cortical neuronal dynamics behind movement generation and control most studies focused on tasks where actions were planned and then executed, using different instances of visuomotor transformations. However, to fully understand the dynamics related to movement control one must also study how movements are actively inhibited. Inhibition, indeed, represents the first level of control both when different alternatives are available and only one solution could be adopted, and when it is necessary to maintain the current position.

We recorded neuronal activity from a multielectrode array in the dorsal premotor (PMd) cortex of monkeys performing a countermanding reaching task that requires, in a subset of trials, to cancel a planned movement before its onset. In the analysis of the neuronal state-space of PMd we found a subspace in which activities conveying temporal information were confined during active inhibition and position holding. Movement execution required activities to escape from this subspace toward an orthogonal subspace and, furthermore, surpass a threshold associated with the maturation of the motor plan. These results revealed further details in the neuronal dynamics underlying movement control, extending the hypothesis that neuronal computation confined in an  output-null subspace does not produce movements.

Significance StatementA core question in neuroscience is how the brain generates arm movements. Most studies have approached this issue by investigating the neuronal dynamics that accompany movement production, leaving unanswered the question of which aspects of this dynamics are logically necessary to make the movement. Here we explored this topic by characterizing the neuronal correlates of movement decisions between active inhibition and release of movements. We found that active inhibition and stillness require neuronal signals to be confined in a functional sub-space while actions depend on the transit of activities in an orthogonal space. This dynamics is characterized by a threshold mechanism finally allowing the translation of the motor plan into overt action.


title: Robust effects of corticothalamic feedback during naturalistic visual stimulation

abstract: Neurons in the dorsolateral geniculate nucleus (dLGN) of the thalamus receive a substantial proportion of modulatory inputs from corticothalamic (CT) feedback and brain stem nuclei. Hypothesizing that these modulatory influences might be differentially engaged depending on the visual stimulus and behavioral state, we performed in vivo extracellular recordings from mouse dLGN while optogenetically suppressing CT feedback and monitoring behavioral state by locomotion and pupil dilation. For naturalistic movie clips, we found CT feedback to consistently increase dLGN response gain and promote tonic firing. In contrast, for gratings, CT feedback effects on firing rates were mixed. For both stimulus types, the neural signatures of CT feedback closely resembled those of behavioral state, yet effects of behavioral state on responses to movies persisted even when CT feedback was suppressed. We conclude that CT feedback modulates visual information on its way to cortex in a stimulus-dependent manner, but largely independently of behavioral state.


title: Robust effects of corticothalamic feedback and behavioral state on movie responses in mouse dLGN


title: Influencing factors of telephone-cardiopulmonary resuscitation in China: a qualitative exploration based on managerial perspectives

abstract:
BackgroundTelephone-cardiopulmonary resuscitation(T-CPR) has been proven to systematically improve bystander CPR implementation and thus improve the survival rate of out-of-hospital cardiac arrest (OHCA) patients on a large scale. However, China has a lower proportion of cities that provide T-CPR than other countries.This study aimed to explore the factors affecting the providing of T-CPR based on managerial perspectives and promote the implementation of T-CPR in China to Protect human health.

MethodsThis study adopted a descriptive qualitative method.The managers from health bureau and first-aid Center were recruited to participate through purposive sampling. Data were collected using semi-structured interviews and Colaizzi 7-step analysis method was adopted to summarize and conclude the theme.

ResultsA total of 10 managers were interviewed.Five main themes were identified: (a) bystander factors, (b) dispatching factors, (c) legal factors, (d) guiding factors, and (e) financial factors.

ConclusionIt is urgent to promote the implementation of T-CPR in China.We can promote it by strengthening the training of bystanders in CPR knowledge and skills, developing T-CPR guidance process suitable for Chines national conditions, building an intelligent prehospital emergency system, promoting the legislation of first aid exemption, and providing financial support from various channels.

category: systems biology


title: Nuclear bundle/cable containing actin during yeast meiosis

abstract: Actin polymerizes to form filaments/cables for motility, transport, and structural framework in a cell. Recent studies show that actin polymers are present not only in cytoplasm, but also in nuclei of vertebrate cells, and their formation is induced in response to stress. Here, by electron microscopic observation with rapid freezing and high-pressure freezing, we found a unique bundled structure containing actin in nuclei of budding yeast cells undergoing meiosis. The nuclear bundle/cable during meiosis consists of multiple filaments with a rectangular lattice arrangement often showing "feather-like" appearance. The bundle is immuno-labeled with anti-actin antibody and sensitive to an actin-depolymerizing drug. Like cytoplasmic bundles, nuclear bundles with actin are rarely seen in pre-meiotic cells and spores, and are induced during meiotic prophase-I. The formation of the nuclear bundles/cables is independent of meiotic DNA double-stranded breaks. We speculate that nuclear bundles/cables containing actin play a role in nuclear events during meiotic prophase I.


title: Environmentally sensitive hotspots in the methylome of the early human embryo

abstract: In humans, DNA methylation marks inherited from gametes are largely erased following fertilisation, prior to construction of the embryonic methylome. Exploiting a natural experiment of seasonal variation including changes in diet and nutritional status in rural Gambia, we analysed two independent child cohorts and identified 259 CpGs showing consistent associations between season of conception (SoC) and DNA methylation. SoC effects were most apparent in early infancy, with evidence of attenuation by mid-childhood. SoC-associated CpGs were enriched for metastable epialleles, parent-of-origin specific methylation and germline DMRs, supporting a periconceptional environmental influence. Many SoC-sensitive CpGs overlapped enhancers or sites of active transcription in H1 ESCs and fetal tissues. Half were influenced but not determined by measured genetic variants that were independent of SoC. Environmental  hotspots providing a record of environmental influence at periconception constitute a valuable resource for investigating epigenetic mechanisms linking early exposures to lifelong health and disease.

category: genomics


title: Overcoming coarse coding in visual cortex via multiplexing: neural correlations differ dramatically when stimulus bundles are presented

abstract:
Sensory receptive fields are large enough that they can contain more than one perceptible stimulus. How, then, can the brain encode information about each of the stimuli that may be present at a given moment? We recently showed that when more than one stimulus is present, single neurons can fluctuate between coding one vs. the other(s) across some time period, suggesting a form of neural multiplexing of different stimuli (Caruso et al., 2018). Here we investigate (a) whether such coding fluctuations occur in early visual cortical areas; (b) how coding fluctuations are coordinated across the neural population; and (c) how coordinated coding fluctuations depend on the parsing of stimuli into separate vs. fused objects. We found coding fluctuations do occur in V1 but only when the two stimuli form separate objects. Such separate objects evoked a novel pattern of V1 spike count ("noise") correlations involving distinct distributions of positive and negative values. This bimodal correlation pattern was most pronounced among pairs of neurons showing the strongest evidence for coding fluctuations or multiplexing. Whether a given pair of neurons exhibited positive or negative correlations depended on whether the two neurons both responded better to the same object or had different object preferences. Distinct distributions of spike count correlations based on stimulus preferences were also seen in V4 for separate objects but not when two stimuli fused to form one object. These findings suggest multiple objects evoke different response dynamics than those evoked by single stimuli, lending support to the multiplexing hypothesis and suggesting a means by which information about multiple objects can be preserved despite the apparent coarseness of sensory coding.

Significance StatementHow the brain separates information about multiple objects despite overlap in the neurons responsive to each item is not well understood. Here we show that some neurons in V1 exhibit coding fluctuations in response to two objects, and that these coding fluctuations are coordinated at the population level in ways that are not observed for single objects. Broadly similar results were obtained in V4. These response dynamics lend support to the hypothesis that information about individual objects may be multiplexed across the neural population, preserving information about each item despite the coarseness of sensory coding.


title: Coordinated multiplexing of information about separate objects in visual cortex


title: Hackflex: low cost Illumina Nextera Flex sequencing library construction

abstract: We developed a low-cost method for the production of Illumina-compatible sequencing libraries that allows up to 14 times more libraries for high-throughput Illumina sequencing to be generated for the same cost. We call this new method Hackflex. Quality of library preparation was tested by constructing libraries from E. coli MG1655 genomic DNA using either Hackflex, standard Nextera Flex or a variation of standard Nextera Flex in which the bead-linked transposase is diluted prior to use. In order to test the library quality for genomes with a higher and a lower GC content, library construction methods were also tested on P. aeruginosa PAO1 and S. aureus ATCC25923, respectively. We demonstrated that Hackflex can produce high quality libraries and yields a highly uniform coverage, equivalent to the standard Nextera Flex kit. We show that strongly size selected libraries produce sufficient yield and complexity to support de novo microbial genome assembly, and that assemblies of the large insert libraries can be much more contiguous than standard libraries without strong size selection. We introduce a new set of sample barcodes that are distinct from standard Illumina barcodes, enabling Hackflex samples to be multiplexed with samples barcoded using standard Illumina kits. Using Hackflex, we were able to achieve a per sample reagent cost for library prep of A$7.22 (USD$5.60), which is 9.87 times lower than the Standard Nextera Flex protocol at advertised retail price. An additional simple modification and further simplification of the protocol by omitting the wash step enables a further price reduction to reach an overall 14-fold cost saving. This method will allow researchers to construct more libraries within a given budget, thereby yielding more data and facilitating research programs where sequencing large numbers of libraries is beneficial.


title: Mechanism of Interaction of BMP and Insulin Signaling in C. elegans Development and Homeostasis

abstract: A small number of peptide growth factor ligands are used repeatedly in development and homeostasis to drive programs of cell differentiation and function. Cells and tissues must integrate inputs from these diverse signals correctly, while failure to do so leads to pathology, reduced fitness, or death. Previous work using the nematode C. elegans identified an interaction between the bone morphogenetic protein (BMP) and insulin/IGF-1-like signaling (IIS) pathways in the regulation of lipid homeostasis. The molecular components required for this interaction, however, were not known. Here we report that INS-4, one of 40 insulin-like peptides (ILPs), is regulated by BMP signaling to modulate fat accumulation. Furthermore, we find that the IIS transcription factor DAF-16/FoxO, but not SKN-1/Nrf, acts downstream of BMP signaling in lipid homeostasis. Interestingly, BMP activity alters sensitivity of these two transcription factors to IIS-promoted cytoplasmic retention in opposite ways. Finally, we probe the extent of BMP and IIS interactions by testing two additional IIS functions, dauer formation and autophagy induction. Coupled with our previous work and that of other groups, we conclude that BMP and IIS pathways have at least three modes of interaction: independent, epistatic, and antagonistic. The molecular interactions we identify provide new insight into mechanisms of signaling crosstalk and potential therapeutic targets for IIS-related pathologies such as diabetes and metabolic syndrome.


title: The lipid kinase PI3Kα is required for the cohesion and survival of cancer cells disseminated in serous cavities.

abstract:
AO_SCPLOWBSTRACTC_SCPLOWBreast, ovarian, digestive and lung adenocarcinomas are often associated with the accumulation of malignant cells in serous cavities. As PI3K is one of the most mutated pathways in cancer, we investigated the importance of oncogenic PI3K in this process. We analyzed tumor cell organization in ascites from carcinomas at diagnosis. In some malignant ascites, tumor cells grew as adhesive coherent masses. Ex-vivo patient-derived cell cultures with the addition of mesenchymal stem cells, as a model of tumoral stroma, favored the compaction of tumorospheres. Ascites-derived ovarian cancer cell lines frequently harbored PIK3CA mutations coexisting with other mutations. PI3K promoted the formation and maintenance of multicellular adhesive PIK3CA-mutant spheroids, promoting cell survival. Cultures in 3D conditions as opposed to cultures in cell monolayers increased chemotherapy resistance, which was overcome by PI3K inhibition. We identified a signaling pathway of interest for the treatment of cancer cells disseminated in serous cavities, limiting cancer progression.

Graphical abstractSchematic representation of PI3K involvement in tumor cell aggregates from ascites. 1) Known involvement of PI3K in primary ovarian tumors. 2) PI3K participates in tumorosphere formation within the peritoneum (treatment with PI3K inhibitors causes a delay in the formation of clusters). 3) PI3K participates in the maintenance of tumorospheres and in resistance to conventional treatment for peritoneal carcinomatosis. PI3K is a target to prevent transcoelomic dissemination and maintenance of tumorospheres in patients with ovarian cancer.

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category: cancer biology


title: HYPK scaffolds the Nedd8 and LC3 proteins to initiate formation of autophagosome around polyneddylated huntingtin exon1 aggregates

abstract: Selective degradation of protein aggregates by autophagy is an essential homeostatic process of safeguarding cells from the effects of proteotoxicity. Among the ubiquitin-like modifier proteins, Nedd8 conjugation to misfolded proteins is prominent in stress-induced protein aggregates, albeit the function of neddylation in autophagy is unclear. Here, we report that polyneddylation functions as a post-translational modification for autophagic degradation of proteotoxic-stress induced protein aggregates. We also show that HYPK functions as an autophagy receptor in the polyneddylation-dependent aggrephagy. The scaffolding function of HYPK is facilitated by its C-terminal ubiquitin-associated domain and N-terminal tyrosine-type LC3 interacting region which bind to Nedd8 and LC3 respectively. Both Nedd8 and HYPK are positive modulators of basal and induced-autophagy, leading to desensitizing cells from protein aggregates, such as aggregates of mutant huntingtin-exon1. Thus, we propose an additive role of neddylation and HYPK in clearance of protein aggregates by autophagy, resulting in cytoprotective effect during proteotoxic stress.


title: KIAA0319 influences cilia length, cell migration and mechanical cell-substrate interaction

abstract:
Following its association with dyslexia in multiple genetic studies, the KIAA0319 gene has been extensively investigated in different animal models but its function in neurodevelopment remains poorly understood.

We developed the first cellular knockout model for KIAA0319 via CRISPR-Cas9n to investigate its role in processes suggested but not confirmed in previous studies, including cilia formation and cell migration. We found that KIAA0319 knockout increased cilia length and accelerated cell migration. Using Elastic Resonator Interference Stress Microscopy (ERISM), we detected an increase in cellular force for the knockout cells that was restored by a rescue experiment. Combining ERISM and immunostaining we show that KIAA0319 depletion reduces the number of podosomes formed by the cells.

Our results suggest an involvement of KIAA0319 in cilia biology and force regulation and show for the first time that podosomes exert highly dynamic, piconewton vertical forces in epithelial cells.


title: Hue tuning curves in V4 change with visual context

abstract:
Neurons are often probed by presenting a set of stimuli that vary along one dimension (e.g. color) and quantifying how this stimulus property affect neural activity. An open question, in particular where higher-level areas are involved, is how much tuning measured with one stimulus set reveals about tuning to a new set. Here we ask this question by estimating tuning to hue in macaque V4 from a set of natural scenes and a set of simple color stimuli. We found that hue tuning was strong in each dataset but was not correlated across the datasets, a finding expected if neurons have strong mixed selectivity. We also show how such mixed selectivity may be useful for transmitting information about multiple dimensions of the world. Our finding suggest that tuning in higher visual areas measured with simple stimuli may thus not generalize to naturalistic stimuli.

New & NoteworthyVisual cortex is often investigated by mapping neural tuning to variables selected by the researcher such as color. How much does this approach tell us a neurons general  role in vision? Here we show that for strongly hue-tuned neurons in V4, estimating hue tuning from artificial stimuli does not reveal the hue tuning in the context of natural scenes. We show how models of optimal information processing suggest that such mixed selectivity maximizes information transmission.


title: A conserved expression signature predicts growth rate and reveals cell & lineage-specific differences

abstract:
Isogenic cells cultured together show heterogeneity in their proliferation rate. To determine the differences between fast and slow-proliferating cells, we developed a method to sort cells by proliferation rate, and performed RNA-seq on slow and fast proliferating subpopulations of pluripotent mouse embryonic stem cells (mESCs) and mouse fibroblasts. We found that slowly proliferating mESCs have a more naive pluripotent character. We identified an evolutionarily conserved proliferation-correlated transcriptomic signature that is common to all eukaryotes: fast cells have higher expression of genes for protein synthesis and protein degradation. This signature accurately predicted growth rate in yeast and cancer cells, and identified lineage-specific proliferation dynamics during development, using C. elegans scRNA-seq data. In contrast, sorting by mitochondria membrane potential revealed a highly cell-type specific mitochondria-state related transcriptome. mESCs with hyperpolarized mitochondria are fast proliferating, while the opposite is true for fibroblasts. The mitochondrial electron transport chain inhibitor antimycin affected slow and fast subpopulations differently. While a major transcriptional-signature associated with cell-to-cell heterogeneity in proliferation is conserved, the metabolic and energetic dependency of cell proliferation is cell-type specific.

SynopsisBy performing RNA-seq on cells FACS sorted by their proliferation rate, this study identifies a gene expression signature capable of predicting proliferation rates in diverse eukaryotic cell types and species. This signature, applied to scRNAseq data from C.elegans, reveals lineage-specific differences in proliferation during development. In contrast to the universality of the proliferation signature, mitochondria and metabolism related genes show a high degree of cell-type specificity; mouse pluripotent stem cells (mESCs) and differentiated cells (fibroblasts) exhibit opposite relations between mitochondria state and proliferation. Furthermore, we identified a slow proliferating subpopulation of mESCs with higher expression of pluripotency genes. Finally, we show that fast and slow proliferating subpopulations are differentially sensitive to mitochondria inhibitory drugs in different cell types.

HighlightsO_LIA FACS-based method to determine the transcriptomes of fast and slow proliferating subpopulations.
C_LIO_LIA universal proliferation-correlated transcriptional signature indicates high protein synthesis and degradation in fast proliferating cells across cell types and species.
C_LIO_LIApplied to scRNA-seq, the expression signature predicts correctly the global slowdown in proliferation during C. elegans development, with lineage-specific exceptions.
C_LIO_LIMitochondria membrane potential predicts proliferation rate in a cell-type specific manner, with ETC complex III inhibitor having distinct effects on the proliferation of fibroblasts vs mESCs.
C_LI


title: Genetic and epigenetic characteristics associated with. the rapid radiation of Aquilegia species

abstract: Elucidating the genetic and epigenetic bases underlying species diversification is crucial to understanding the evolution and persistence of biodiversity. As a well-known horticultural plant grown worldwide, the genus Aquilegia (columbine) is also a model system in adaptive radiation research. In this study, we surveyed the genomes and DNA methylomes of ten representative Aquilegia species from the Asian, European and North American lineages. Our inferences of the phylogenies and population structure revealed clearly high genetic and DNA methylomic divergence across the three lineages. By multi-levelled genome-wide scanning, we identified candidate genes exhibiting lineage-specific genetic or epigenetic variation patterns that are signatures of inter-specific divergence. We demonstrated that these species diversification-associated genetic variations and epigenetic variabilities were partially independent but were both functionally related to various biological processes vital to adaptation, including stress tolerance, cell reproduction and DNA repair. Our study provides an exploratory overview of how the established genetic and epigenetic signatures are associated with the rapid radiation of Aquilegia species.

category: plant biology


title: Gelsolin and dCryAB act downstream of muscle identity genes and contribute to preventing muscle splitting and branching in Drosophila

abstract: A combinatorial code of identity transcription factors (iTFs) specifies the diversity of muscle types in Drosophila. We previously showed that two iTFs, Lms and Ap, play critical role in the identity of a subset of larval body wall muscles, the lateral transverse (LT) muscles. Intriguingly, a small portion of ap and lms mutants displays an increased number of LT muscles, a phenotype that recalls pathological split muscle fibers in human. However, genes acting downstream of Ap and Lms to prevent these aberrant muscle feature are not known. Here, we applied a cell type specific translational profiling (TRAP) to identify gene expression signatures underlying identity of muscle subsets including the LT muscles. We found that Gelsolin (Gel) and dCryAB, both encoding actin-interacting proteins, displayed LT muscle prevailing expression positively regulated by, the LT iTFs. Loss of dCryAB function resulted in LTs with irregular shape and occasional branched ends also observed in ap and lms mutant contexts. In contrast, enlarged and then split LTs with a greater number of myonuclei formed in Gel mutants while Gel gain of function resulted in unfused myoblasts, collectively indicating that Gel regulates LTs size and prevents splitting by limiting myoblast fusion. Thus, dCryAB and Gel act downstream of Lms and Ap and contribute to preventing LT muscle branching and splitting. Our findings offer first clues to still unknown mechanisms of pathological muscle splitting commonly detected in human dystrophic muscles and causing muscle weakness.

category: developmental biology


title: Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition

abstract: Agricultural soil harbors a diverse microbiome that can form beneficial relationships with plants, including the inhibition of plant pathogens. Pseudomonas spp. are one of the most abundant bacterial genera in the soil and rhizosphere and play important roles in promoting plant health. However, the genetic determinants of this beneficial activity are only partially understood. Here, we genetically and phenotypically characterize the Pseudomonas fluorescens population in a commercial potato field, where we identify strong correlations between specialized metabolite biosynthesis and antagonism of the potato pathogens Streptomyces scabies and Phytophthora infestans. Genetic and chemical analyses identified hydrogen cyanide and cyclic lipopeptides as key specialized metabolites associated with S. scabies inhibition, which was supported by in planta biocontrol experiments. We show that a single potato field contains a hugely diverse and dynamic population of Pseudomonas bacteria, whose capacity to produce specialized metabolites is shaped both by plant colonization and defined environmental inputs.


title: SPF45/RBM17-dependent, but not U2AF-dependent, splicing in a distinct subset of human short introns

abstract: Human pre-mRNA introns vary in size from under fifty to over a million nucleotides. We searched for essential factors involved in the splicing of human short introns by screening siRNAs against 154 human nuclear proteins. The splicing activity was assayed with a model HNRNPH1 pre-mRNA containing short 56-nucleotide intron. We identified a known alternative splicing regulator SPF45 (RBM17) as a constitutive splicing factor that is required to splice out this 56-nt intron. Whole-transcriptome sequencing of SPF45-deficient cells revealed that SPF45 is essential in the efficient splicing of many short introns. To initiate the spliceosome assembly on a short intron with the truncated poly-pyrimidine tract, the U2AF-homology motif (UHM) of SPF45 competes out that of U2AF65 for binding to the UHM-ligand motif (ULM) of the U2 snRNP protein SF3b155 (SF3B1). We propose that splicing in a distinct subset of human short introns depends on SPF45 but not U2AF heterodimer.

category: molecular biology


title: X chromosome inactivation in the human placenta is patchy and distinct from adult tissues

abstract: One of the X chromosomes in genetic females is silenced by a process called X chromosome inactivation (XCI). Variation in XCI across the placenta may contribute to observed sex differences and variability in pregnancy outcomes. However, XCI has predominantly been studied in human adult tissues. Here we sequenced and analyzed DNA and RNA from two locations from 30 full-term pregnancies. Implementing an allele specific approach to examine XCI, we report evidence that XCI in the human placenta is patchy, with large patches of either silenced maternal or paternal X chromosomes. Further, using similar measurements, we show that this is in contrast to adult tissues, which generally exhibit mosaic X-inactivation, where bulk samples exhibit both maternal and paternal X chromosome expression. Further, by comparing skewed samples in placenta and adult tissues, we identify genes that are uniquely silenced or expressed in the placenta compared to adult tissues highlighting the need for tissue-specific maps of XCI.


title: Quantitative characterization of the path of glucose diffusion facilitated by human glucose transporter 1

abstract:
Glucose transporter GLUT1 is ubiquitously expressed in the human body from the red cells to the blood-brain barrier to the skeletal muscles. It is physiologically relevant to understand how GLUT1 facilitates diffusion of glucose across the cell membrane. It is also pathologically relevant because GLUT1 deficiency causes neurological disorders and anemia and because GLUT1 overexpression fuels the abnormal growth of cancer cells. This article presents a quantitative investigation of GLUT1 based on all-atom molecular-dynamics (MD) simulations of the transporter embedded in lipid bilayers of asymmetric inner-and-outer-leaflet lipid compositions, subject to asymmetric intra-and-extra-cellular environments. This is in contrast with the current literature of MD studies that have not considered both of the aforementioned asymmetries of the cell membrane. The equilibrium (unbiased) dynamics of GLUT1 shows that it can facilitate glucose diffusion across the cell membrane without undergoing large-scale conformational motions. The Gibbs free-energy profile, which is still lacking in the current literature of GLUT1, quantitatively characterizes the diffusion path of glucose from the periplasm, through an extracellular gate of GLUT1, on to the binding site, and off to the cytoplasm. This transport mechanism is validated by the experimental data that GLUT1 has low water-permeability, uptake-efflux symmetry, and 10 kcal/mol Arrhenius activation barrier around 37{degrees}C.

GRAPHICAL ABSTRACT (or TABLE OF CONTENTS ENTRY)

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title: Predictive Representations in Hippocampal and Prefrontal Hierarchies

abstract: As we navigate the world, we use learned representations of relational structures to explore and to reach goals. Studies of how relational knowledge enables inference and planning are typically conducted in controlled small-scale settings. It remains unclear, however, how people use stored knowledge in continuously unfolding navigation, e.g., walking long distances in a city. We hypothesized that multiscale predictive representations guide naturalistic navigation, and these scales are organized along posterior-anterior prefrontal and hippocampal hierarchies. We conducted model-based representational similarity analyses of neuroimaging data measured during navigation of realistically long paths in virtual reality. We tested the pattern similarity of each point-along each path-to a weighted sum of its successor points within predictive horizons of different scales. We found that anterior PFC showed the largest predictive horizons, posterior hippocampus the smallest, with the anterior hippocampus and orbitofrontal regions in between. Our findings offer novel insights into how cognitive maps support hierarchical planning at multiple scales.


title: Oxidation shuts down an auto-inhibitory mechanism of von Willebrand factor

abstract: The blood protein von Willebrand factor (VWF) is a key link between inflammation and pathological thrombus formation. In particular, oxidation of methionine residues in specific domains of VWF due to the release of oxidants in inflammatory conditions has been linked to an increased platelet-binding activity. However, the atomistic details how methionine oxidation activates VWF have not been elucidated to date. Yet understanding the activation mechanism of VWF under oxidizing conditions can lead to the development of novel therapeutics that target VWF selectively under inflammatory conditions in order to reduce its thrombotic activity while maintaining its haemostatic function. In this manuscript, we used a combination of a dynamic flow assay and molecular dynamics (MD) simulations to investigate how methionine oxidation removes an auto-inhibitory mechanism of VWF. Results from the dynamic flow assay revealed that oxidation does not directly activate the A1 domain, which is the domain in VWF that contains the binding site to the platelet surface receptor glycoprotein Ib (GpIb), but rather removes the inhibitory function of the neighboring A2 and A3 domains. Furthermore, the MD simulations combined with free energy perturbation calculations suggested that methionine oxidation may destabilize the binding interface between the A1 and A2 domains leading to unmasking of the GpIb-binding site in the A1 domain.


title: Evolution and development of male-specific leg brushes in Drosophilidae

abstract: The origin, diversification, and secondary loss of sexually dimorphic characters are common in animal evolution. In some cases, structurally and functionally similar traits have evolved independently in multiple lineages. Prominent examples of such traits include the male-specific grasping structures that develop on the front legs of many dipteran insects. In this report, we describe the evolution and development of one of these structures, the male-specific "sex brush". The sex brush is composed of densely packed, irregularly arranged modified bristles and is found in several distantly related lineages in the family Drosophilidae. Phylogenetic analysis using 250 genes from over 200 species provides modest support for a single origin of the sex brush followed by many secondary losses; however, independent origins of the sex brush cannot be ruled out completely. We show that sex brushes develop in very similar ways in all brush-bearing lineages. The dense packing of brush hairs is explained by the specification of bristle precursor cells at a near-maximum density permitted by the lateral inhibition mechanism, as well as by the reduced size of the surrounding epithelial cells. In contrast to the female and the ancestral male condition, where bristles are arranged in stereotypical, precisely spaced rows, cell migration does not contribute appreciably to the formation of the sex brush. The complex phylogenetic history of the sex brush can make it a valuable model for investigating coevolution of sex-specific morphology and mating behavior.


title: Motor training improves coordination and anxiety in symptomatic Mecp2-null mice despite impaired functional connectivity within the motor circuit

abstract: Rett Syndrome (RTT) is a severe neurodevelopmental disorder caused by loss of function of the X-linked Methyl-CpG-binding protein 2 (MECP2). Several case studies report that gross motor function can be improved in children with RTT through treadmill walking, but whether the MeCP2-deficient motor circuit can support actual motor learning remains unclear. We used two-photon calcium imaging to simultaneously observe layer (L) 2/3 and L5a excitatory neuronal activity in the motor cortex (M1) while mice adapted to changing speeds on a computerized running wheel. Despite circuit hypoactivity and weakened functional connectivity across L2/3 and L5a, the Mecp2-null circuits firing pattern evolved with improved performance over two weeks. Moreover, trained mice became less anxious and lived 20% longer than untrained mice. Since motor deficits and anxiety are core symptoms of Rett, which is not diagnosed until well after symptom onset, these results underscore the benefit of motor learning.


title: Connectome Constrained Graphical Models of MEG Coherence

abstract: Structural connectivity by axonal fiber bundles provides the backbone for communication between neural populations. Since axonal transmission occurs on a millisecond time scale, measures of M/EEG functional connectivity sensitive to phase synchronization in a frequency band, such as coherence, are expected to reflect structural connectivity. We develop a complex-valued Gaussian Graphical Model (cGGM) of MEG coherence whose edges are constrained by the structural connectome. The cGGMs edge strengths are summarized by partial coherence, a measure of conditional dependence. We made use of the adaptive graphical lasso (AGL) to fit the cGGMs which allows us to perform inference on the hypothesis that the structural connectome is reflected in MEG coherence in a frequency band. In simulations, we demonstrate that the structural connectivitys influence on the cGGM can be inferred using the AGL. Further, we show that fitting the cGGM is superior to alternative methods at recovering the structural connectome. Graphical modeling of MEG coherence is robust to the source localization estimates required to map MEG from sensors to the cortex. Finally, we show how cG-GMs can be used to explore how distinct parts of the structural connectome contribute to MEG coherence in different frequency bands. We think the cGGM is a useful tool that can improve interpretation of MEG coherence by making a direct link to the structural connectome.


title: Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor

abstract: The deletion of the third exon of the growth hormone receptor (GHR) is one of the most common genomic structural variants in the human genome. This deletion (GHRd3) has been linked to response to growth hormone, placenta size, birth weight, growth after birth, time of puberty, adult height, and longevity. However, its evolutionary history and the molecular mechanisms through which it affects phenotypes remain unresolved. Here, we analyzed thousands of genomes and provide evidence that this deletion was nearly fixed in the ancestral population of anatomically modern humans and Neanderthals. However, it underwent a paradoxical adaptive reduction in frequency approximately 30 thousand years ago in East Asia that roughly corresponds with the emergence of archaeological evidence for multiple modern human behaviors, dramatic changes in climate, and a concurrent population expansion. Further, we provide evidence that GHRd3 is associated with protection from edematous severe acute malnutrition primarily in males. Using a mouse line engineered to contain the deletion, we found Ghrd3s effect on the liver transcriptome of male mice grown without any calorie restriction mimics response to calorie restriction through regulation of circadian pathways. In contrast, under calorie restriction, Ghrd3 leads to the female-like gene expression in male livers. As a likely consequence, the dramatic weight difference between male and female mice disappears among GHRd3 mice under calorie restriction. Our data provide evidence for sex- and environment-dependent effects of GHRd3 and are consistent with a model in which the allele frequency of GHRd3 varies throughout human evolution as a response to fluctuations in resource availability.


title: Impact of early childhood malnutrition on the adult brain function: an ERP study

abstract:
According to the World Health Organization, 45% of deaths among children under five years of age are caused by malnutrition, which impacts more than 224 million children globally. The Barbados Nutrition Study (BNS) is a 50+ year longitudinal study on a Barbadian cohort with histories of moderate to severe protein-energy malnutrition (PEM) limited to the first year of life and a healthy comparison group. We have previously used quantitative electroencephalography (EEG) to highlight differences in brain function during childhood (lower alpha1 activity and higher theta, alpha2 and beta activity) between participants who suffered from early PEM and controls. In order to determine whether similar differences between the PEM and control groups persisted into adulthood, our current study used recordings obtained during a Go-No-Go task in a subsample of the original BNS cohort (N=53) at ages 45-51 years. We found that previously malnourished adults (n=24) had a higher rate of omission errors on the task relative to controls (n=29). Evoked-Related Potentials (ERP) were significantly different in participants with histories of early PEM, who presented with lower N2 amplitudes (p<0.05). These findings are typically associated with impaired conflict monitoring and/or attention deficits and may therefore be linked to the attentional and executive function deficits that have been previously reported in this cohort in childhood and again in middle-adulthood.

HighlightsO_LIChildhood malnutrition increases risk of brain function alterations.
C_LIO_LIThere is a need to investigate the evolution of those outcomes later in life.
C_LIO_LIAdults who suffered childhood malnutrition undertook a Go-No-Go task during EEG.
C_LIO_LITask performance and N2 amplitude were reduced in malnutrition group (vs control).
C_LIO_LIFirst evidence of adult brain function alteration following childhood malnutrition.
C_LI


title: Cortico-striatal activity driving compulsive reward seeking

abstract: Addicted individuals compulsively seek drugs. Cortico-striatal projections have been implicated in persevering to seek rewards even when punished. The temporo-spatial determinants of the activity underlying the compulsive reward seeking however remains elusive. Here we trained mice in a seek-take chain, rewarded by optogenetic dopamine neuron self-stimulation (oDASS). Mice that persevered when seeking was punished, exhibited an increased AMPA/NMDA ratio selectively at orbitofrontal cortex (OFC) to dorsal striatum (DS) synapses. In addition, an activity peak of spiny projection neurons (SPNs) in the DS at the moment of signalled reward availability was detected. Chemogenetic inhibition of OFC neurons curbed the activity peak and reduced punished reward seeking, as did optogenetic hyperpolarization of SPNs time locked to the cue predicting reward availability, establishing a causal link. Taken together, we conclude that the strengthening of OFC-DS synapses drives SPNs activity when a reward predictive cue is delivered, thus encouraging reward seeking in subsequent trials.


title: Pulmonary acini exhibit complex changes during postnatal rat lung development

abstract: Pulmonary acini represent the functional gas-exchanging units of the lung. Due to technical limitations, individual acini cannot be identified on microscopic lung sections. To overcome these limitations, we imaged the right lower lobes of instillation-fixed rat lungs from postnatal days P4, P10, P21, and P60 at the TOMCAT beamline of the Swiss Light Source synchrotron facility at a voxel size of 1.48 m. Individual acini were segmented from the three-dimensional data by closing the airways at the transition from conducting to gas exchanging airways. For a subset of acini (N=268), we followed the acinar development by stereologically assessing their volume and their number of alveoli. We found that the mean volume of the acini increases 23 times during the observed time-frame. The coeffcients of variation dropped from 1.26 to 0.49 and the difference between the mean volumes of the fraction of the 20 % smallest to the 20 % largest acini decreased from a factor of 27.26 (day 4) to a factor of 4.07 (day 60), i.e. shows a smaller dispersion at later time points. The acinar volumes show a very large variation early in lung development and homogenize during maturation of the lung by reducing their size distribution by a factor of 7 until adulthood. The homogenization of the acinar sizes hints at an optimization of the gas-exchange region in the lungs of adult animals and that acini of different size are not evenly distributed in the lungs. This likely leads to more homogeneous ventilation at later stages in lung development.

category: physiology


title: Visualization and Analysis of Whole Depot Adipose Tissue Neural Innervation

abstract: Little is known about the diversity and function of adipose tissue nerves due, in part, to the inability to effectively visualize the various nerve subtypes residing within these tissues. The tools currently available for researchers to image and quantify adipose tissue innervation are limited and dependent on optical clearing techniques and light sheet microscopy. Here we present a method of tissue processing that uses mechanical force to compress tissue to decrease tissue thickness in the z-axis by expanding it in the x and y-axes whilst leaving cells intact. This has been combined with autofluorescence quenching techniques to permit intact whole tissues to be mounted on slides and imaged on any microscope, with a complementary means to perform whole tissue neurite density quantification. We have included examples of how this technique can be used to further our current knowledge of adipose-nerve communication by characterizing the nerves, nerve-subtypes, and neurovascular interactions within subcutaneous white adipose tissue in mice.

category: neuroscience


title: Spatially-explicit modeling improves empirical characterization of dispersal

abstract:
Dispersal is a key ecological process, but remains difficult to measure. By recording numbers of dispersed individuals at different distances from the source one can acquire a dispersal gradient. Although dispersal gradients contain information on dispersal, they are influenced by the spatial extent of the source. How can we separate the two contributions to extract knowledge on dispersal?

One could use a small, point-like source for which a dispersal gradient represents a dispersal kernel, which quantifies the probability of an individual dispersal event from a source to a destination point. However, the validity of this approximation cannot be established before conducting measurements.

We formulated a theory that incorporates the spatial extent of sources to estimate dispersal kernels from dispersal gradients. We re-analyzed published dispersal gradients for three major plant pathogens. We also demonstrated using simulations that this approach provides more accurate estimates of dispersal kernels across biologically plausible scenarios. We concluded that the three plant pathogens disperse over substantially shorter distances compared to conventional estimates. Using this method, a significant proportion of published dispersal gradients can be re-analyzed to improve our knowledge about spatial scales of dispersal. Thus, our results can boost progress in characterization of dispersal across taxa.


title: Spatially explicit ecological modeling improves empirical characterization of dispersal