title: The endemic plant species of Bali Ngemba Forest Reserve, Bamenda Highlands Cameroon, with a new Endangered cloud-forest tree species Vepris onanae (Rutaceae).

abstract:
We revise and update the records of strict and near-endemic species of the Bali Ngemba Forest Reserve, the largest known surviving patch (c. 8 km2 in area) of submontane or cloud forest in the Bamenda Highlands, Cameroon which have lost >96 % of their original forest due to human activities. Nine strict endemics, and 11 near endemics are now documented, a drop from the number recorded after the first survey in 2004, since when five of the provisionally named species have been formally published.

We test the hypothesis that a further one of the provisionally named putative Bali Ngemba new species, Vepris sp. A, an 8 - 20 m tall tree from cloud forest in the 1310 - 1600 m altitudinal band, is indeed new to science. We compare it morphologically with other multicarpellate, apocarpous, trifoliolate Cameroon tree species formerly placed in the genus Oricia Pierre until they were subsumed into Vepris by Mziray (1992). These are Vepris trifoliolata (Engl.) Mziray and V. gabonensis (Pierre) Mziray. We conclude that Vepris sp. A is a new undescribed species here named as Vepris onanae. The new species is illustrated, mapped and its conservation status assessed as Endangered using the 2012 IUCN standard due to the threats of habitat clearance from agricultural pressures at its three locations all of which remain formally unprotected.

Vepris onanae appears unique among the Guineo-Congolian African oricioid species of Vepris in occurring in cloud forest, the other species, apart from V. renierii of the Albertine Rift, occurring in lowland forest. It also differs in the very broad, (7.8 -) 11.3 - 18 cm wide leaflets of the flowering stems which have a 6-18(-30) mm long, narrowly triangular acumen (vs leaflets <12 cm wide, acumen absent or short) and in having both subsessile and pedicellate (pedicels 0.25 - 0.3 mm long and 1(- 2) mm long) male flowers (vs male flower pedicels all sessile, or all c. 3 mm long).

We report for the first time on stage-dependent leaf heteromorphy in Vepris and characterise a level of sexual dimorphism more advanced than usual in the genus.

We highlight the importance of protecting Bali Ngemba and other forest patches in the Bamenda Highlands if species such as Vepris onanae are not soon to become extinct.


title: Development of a Freeze-Dried CRISPR-Cas12 Sensor for Detecting Wolbachia in the Secondary Science Classroom

abstract: Training the future synthetic biology workforce requires opportunity and exposure to biotechnology concepts and activities in secondary education. Detecting Wolbachia bacteria in arthropods using PCR has become a common way for secondary students to investigate and apply DNA technology in the science classroom. Despite this framework, cutting-edge biotechnologies like CRISPR-based diagnostics have yet to be widely implemented in the classroom. To address this gap, we present a freeze-dried CRISPR-Cas12 sensing reaction to complement traditional DNA technology education and teach synthetic biology concepts. The reactions accurately detect Wolbachia from arthropod-derived PCR samples in under 2 hours and can be stored at room temperature for over a month without appreciable degradation. The reactions are easy-to-use and cost less than $40 to implement for a classroom of 22 students including the cost of reusable equipment. We see this technology as an accessible way to incorporate synthetic biology education into existing biology curriculum, which will expand biology educational opportunities in science, technology, engineering, and mathematics (STEM) education.

category: synthetic biology


title: Interplay of positive and negative feedback loops governs robustness in multistable biological networks

abstract:
Epithelial-Mesenchymal plasticity (EMP) is a key arm of cancer metastasis and is observed across many contexts. Cells undergoing EMP can reversibly switch between three classes of phenotypes: Epithelial (E), Mesenchymal (M), and Hybrid E/M. While a large number of multistable regulatory networks have been identified to be driving EMP in various contexts, the exact mechanisms and design principles that enable robustness in driving EMP across contexts are not yet fully understood. Here we investigated dynamic and structural robustness in EMP networks with regards to phenotypic distribution and plasticity. We use two different approaches to simulate these networks: a computationally inexpensive, parameter-independent continuous state space boolean model, and an ODE-based parameter-agnostic framework (RACIPE), both of which yield similar phenotypic distributions. Using perturbations to network topology and by varying network parameters, we show that multistable EMP networks are structurally and dynamically more robust as compared to their randomized counterparts, thereby highlighting their topological hallmarks. These features of robustness are governed by a balance of positive and negative feedback loops embedded in these networks. Using a combination of the number of negative and positive feedback loops weighted by their lengths and sign, we identified a metric that can explain the structural and dynamical robustness of these networks. This metric enabled us to compare networks across multiple sizes, and the network principles thus obtained can be used to identify fragilities in large networks without simulating their dynamics. Our analysis highlights a network topology-based approach to quantify robustness in multistable EMP networks.

Significance StatementEpithelial-Mesenchymal plasticity (EMP) is a key arm of cancer metastasis. Despite extensive intra- and inter-tumor heterogeneity, the characteristics of EMP have been observed to be robust across multiple contexts. We hypothesize that topology of EMP regulatory networks contributes towards this robustness. Here, we measure the robustness of EMP in the form of its phenotypic heterogeneity and multistability and show that EMP networks are more robust to dynamical (change in kinetic parameters) and structural (change in network topology) perturbations as compared to their random network counterparts. Furthermore, we propose a network topology-based metric using the nature and length of feedback loops that explains the observed robustness. Our metric hence serves to quantify robustness in multistable EMP networks without simulating their dynamics.

category: systems biology


title: Robustness in regulatory networks of Epithelial Mesenchymal Plasticity as a function of positive and negative feedback loops


title: AI-assisted Biology: Predict the Conditional Probability Distributions from Noisy Measurements

abstract: The relationship between the genotype, defined as the set of genetic information encoded in the DNA, and the phenotype, defined as the macroscopic realization of that information, is still unclear. The emergence of a specific phenotype may be linked not only to gene expression, but also to environmental perturbations and experimental conditions. Moreover, even genetically identical cells in identical environments may display a variety of phenotypes. This imposes a big challenge in building traditional supervised machine learning models that can only predict determined phenotypic parameters or categories per specific genetic and/or environmental conditions as inputs. Furthermore, biological noise has been proven to play a crucial role in gene regulation mechanisms. The prediction of the average value of a given phenotype is not always sufficient to fully characterize a given biological system. In this study, we develop a deep learning algorithm that can predict the conditional probability distribution of a phenotype of interest with a small number of observations per input condition. The key innovation of this study is that the deep neural network automatically generates the probability distributions based on only few (10 or less) noisy measurements for each input condition, with no prior knowledge or assumption of the probability distributions. This is extremely useful for exploring unknown biological systems with limited measurements for each input condition, which is linked not only to a better quantitative understanding of biological systems, but also to the design of new ones, as it is in the case of synthetic biology and cellular engineering.


title: Comparison between Lotka-Volterra and Multivariate Autoregressive models of ecological interaction systems

abstract:
O_LILotka-Volterra (LV) and Multivariate Autoregressive (MAR) models are computational frameworks with different mathematical structures that have both been proposed for the same purpose of extracting governing features of dynamic interactions among coexisting populations of different species from observed time series data.
C_LIO_LIWe systematically compare the feasibility of the two modeling approaches, using four synthetically generated datasets and seven ecological datasets from the literature.
C_LIO_LIThe overarching result is that LV models outperform MAR models in most cases and are generally superior for representing cases where the dependent variables deviate greatly from their steady states. A large dynamic range is particularly prevalent when the populations are highly abundant, change considerably over time, and exhibit a large signal-to-noise ratio. By contrast, MAR models are better suited for analyses of populations with low abundances and for investigations where the quantification of noise is important.
C_LIO_LIWe conclude that the choice of either one or the other modeling framework should be guided by the specific goals of the analysis and the dynamic features of the data.
C_LI

Availability of algorithms usedhttps://github.com/LBSA-VoitLab/Comparison-Between-LV-and-MAR-Models-of-Ecological-Interaction-Systems


title: Amplification and attenuation of noisy expression by export processes

abstract: Inside mammalian cells, single genes are known to be transcribed in stochastic bursts leading to the synthesis of nuclear RNAs that are subsequently exported to the cytoplasm to create mRNAs. We systematically characterize the role of export processes in shaping the extent of random fluctuations (i.e. noise) in the mRNA level of a given gene. Using the method of Partitioning of Poisson arrivals, we derive an exact analytical expression for the noise in mRNA level assuming that the nuclear retention time of each RNA is an independent and identically distributed random variable following an arbitrary distribution. These results confirm recent experimental/theoretical findings that decreasing the nuclear export rate buffers the noise in mRNA level, and counterintuitively, decreasing the noise in the nuclear retention time enhances the noise in the mRNA level. Next, we further generalize the model to consider a dynamic extrinsic disturbance that affects the nuclear-to-cytoplasm export. Our results show that noise in the mRNA level varies non-monotonically with the disturbance timescale. More specifically, high- and low-frequency external disturbances have little impact on the mRNA noise level, while noise is amplified at intermediate frequencies. In summary, our results systematically uncover how the coupling of bursty transcription with nuclear export can both attenuate or amplify noise in mRNA levels depending on the nuclear retention time distribution and the presence of extrinsic fluctuations.


title: Disrupted intrinsic connectivity links to language and social deficits in toddlers with autism

abstract: Social and language abilities are closely intertwined during early development. Yet, it is still unknown how neural features underlying early social and language deficits are linked in toddlers with autism spectrum disorders (ASD). We examined functional connectivity of left and right temporal language regions and its correlations with language and social abilities in a cohort of 1- 4 years old toddlers (52 ASD/34 non-ASD). Further, ASD toddlers were stratified into those who strongly prefer social visual stimuli (ASDSoc) vs. those who do not (ASDnonSoc) based on performance on an eye-tracking paradigm. In non-ASD toddlers, connectivity between temporal regions and other language- and social-related cortical regions was significantly correlated with language, communication, and social scores. Conversely, ASD toddlers showed atypical correlations between temporal-visual cortex (cuneus) connectivity and communication ability. This temporal-visual connectivity was also correlated with social visual attention in ASDnonSoc but not in ASDSoc toddlers. These findings suggest language- and social-related functional connectivity was not correlated with language and social functions in ASD toddlers. Abnormal engagement of temporal-visual cortex connectivity may be an early-age signature of ASD and may help explain why interventions targeting social skills and language are so challenging, particularly in those with poor social engagement.

category: neuroscience


title: Heterogeneity and developmental dynamics of LYVE-1 perivascular macrophages distribution in the mouse brain

abstract: Brain perivascular macrophages (PVMs) belong to border-associated macrophages. PVMs are situated along blood vessels in the Virchow-Robin space and are thus found at a unique anatomical position between the endothelium and the parenchyma. Owing to their location and phagocytic capabilities, PVMs are regarded as important components that regulate various aspects of brain physiology in health and pathophysiological states. Here, used LYVE-1 to identify PVMs in the mouse brain. We used brain-tissue sections and cleared whole-brains to learn how they are distributed within the brain and across different developmental postnatal stages. We find that LYVE-1+ PVMs associate with the vasculature in a brain-region-dependent manner, where the hippocampus shows the highest density of LYVE-1+ PVMs. We show that their postnatal distribution is developmentally dynamic and peaks at P10-P20 depending on the brain region. We further demonstrate that their density is reduced in the APP/PS1 mouse model of Alzheimers Disease. In conclusion, our results show an unexpected heterogeneity and dynamics of LYVE-1+ PVMs, and support an important role for this population of PVMs during development and in regulating brain functions in steady-state and disease conditions.


title: Metformin-mediated mitochondrial protection post-cardiac arrest improves EEG activity and confers neuroprotection and survival benefit

abstract:
Cardiac arrest (CA) produces global ischemia/reperfusion injury resulting in substantial multiorgan damage. There are limited efficacious therapies to save lives despite CA being such a lethal disease process. Surviving patients suffer extensive brain damage with mitochondrial dysfunction implicated as a major source of injury. Metformin, a first-line treatment for diabetes, has also shown promising results in other diseases and is known to interact with mitochondria. In the present study, we evaluated the therapeutic benefits of metformin administration immediately after resuscitation using a 10 min asphxyial-CA rat model. This is the first study to show that metformin treatment post-CA a) improves survival and neurologic function, b) potentiates early normalization of brain electrophysiologic activity, and c) protects mitochondrial function with a reduction in apoptotic brain injury. Overall, as an effective and safe drug, metformin has the potential to be an easily translatable intervention for improving survival and preventing brain damage after CA.

SummaryBrain damage post-cardiac arrest is a major cause of death; metformin protects brain mitochondria and improved survival and brain function.


title: A bias generating temporal distortions in serial perception

abstract:
A precise estimation of event timing is essential for survival.1 Yet, temporal distortions are ubiquitous in our daily sensory experience.2 A specific type of temporal distortion is the time order error (TOE), which occurs when estimating the duration of events organized in a series.3 TOEs shrink or dilate objective event duration. Understanding the mechanics of subjective time distortions is fundamental since we perceive events in a series, not in isolation. In previous work,4 we showed that TOEs appear when discriminating small duration differences (20 or 60 ms) between two short events (Standard, S and Comparison, C), but only if the interval between events is shorter than 1 second. TOEs have been variously attributed to sensory desensitization,5,6 reduced temporal attention,7,4 poor sensory weighting of C relative to S,8 or idiosyncratic response bias.6

Surprisingly, the serial dynamics of relative event duration were never considered as a factor generating TOEs. In two experiments we tested them by swapping the order of presentation of S and C. Bayesian hierarchical modelling showed that TOEs emerge when the first event in a series is shorter than the second event, independently of event type (S or C), sensory precision or individual response bias. Participants disproportionately expanded first-position shorter events. Significantly fewer errors were made when the first event was objectively longer, confirming the inference of a strong bias in perceiving ordered event durations. Our finding identifies a hitherto unknown duration-dependent encoding inefficiency in human serial perception.


title: Age-related change in task-evoked amygdala-prefrontal circuitry: a multiverse approach with an accelerated longitudinal cohort aged 4-22 years

abstract:
The amygdala and its connections with medial prefrontal cortex (mPFC) play central roles in the development of emotional processes. While several studies have suggested that this circuitry exhibits functional changes across the first two decades of life, findings have been mixed - perhaps resulting from differences in analytic choices across studies. Here we used multiverse analyses to examine the robustness of task-based amygdala-mPFC function findings to analytic choices within the context of an accelerated longitudinal design (4-22 years- old; N=98; 183 scans; 1-3 scans/participant). Participants, recruited from the greater Los Angeles area, completed an event-related emotional face (fear, neutral) task. Parallel analyses varying in preprocessing and modeling choices found that age-related change estimates for amygdala reactivity were more robust than task-evoked amygdala-mPFC functional connectivity to varied analytical choices. Specification curves indicated evidence for age-related decreases in amygdala reactivity to faces, though within-participant changes in amygdala reactivity could not be differentiated from between-participant differences. In contrast, amygdala--mPFC functional connectivity results varied across methods much more, and evidence for age-related change in amygdala-mPFC connectivity was not consistent. Generalized psychophysiological interaction (gPPI) measurements of connectivity were especially sensitive to whether a deconvolution step was applied. Our findings demonstrate the importance of assessing the robustness of findings to analysis choices, although the age-related changes in our current work cannot be overinterpreted given low test-retest reliability. Together, these findings highlight both the challenges in estimating developmental change in longitudinal cohorts and the value of multiverse approaches in developmental neuroimaging for assessing robustness of results. (Preprint: https://www.biorxiv.org/content/10.1101/2021.10.08.463601v1).

Key PointsO_LIMultiverse analyses applied to fMRI data are valuable for determining the robustness of findings to varied analytical choices
C_LIO_LIIn the current study, age-related change estimates for amygdala reactivity were relatively robust to analytical decisions, though gPPI functional connectivity analyses were much more sensitive, leading some estimates to flip sign
C_LIO_LIBoth test-retest reliability and robustness to analytical choices are important considerations for developmental research
C_LI


title: Learning from the physical consequences of our actions improves motor memory

abstract: Actions have consequences. Motor learning involves correcting actions that lead to movement errors and remembering these actions for future behavior. In most laboratory situations, movement errors have no physical consequences and simply indicate the progress of learning. Here we asked how experiencing a physical consequence when making a movement error affects motor learning. Two groups of participants adapted to a new, prism-induced mapping between visual input and motor output while performing a precision walking task. Importantly, one group experienced an unexpected slip perturbation when making foot-placement errors during adaptation. Because of our innate drive for safety, and the fact that balance is fundamental to movement, we hypothesized that this experience would enhance motor memory. Learning generalized to different walking tasks to a greater extent in the group who experienced the adverse physical consequence. This group also showed faster relearning one week later despite exposure to a competing mapping during initial learning--evidence of greater memory consolidation. The group differences in generalization and consolidation occurred even though they both experienced similar magnitude foot-placement errors and adapted at similar rates. Our results suggest the brain considers the potential physical consequences of movement error when learning and that balance-threatening consequences serve to enhance this process.


title: Developmental neuroanatomy of the Rosy Bitterling Rhodeus ocellatus (Teleostei: Cypriniformes)--A microCT study

abstract: Bitterlings are a group of teleost fish (Cyprinifromes: Acheilanathidae) notable for their brood parasitic lifestyle. Bitterling embryos develop as parasites inside the gill chamber of their freshwater mussel hosts. However, little is known about brain development in this species. Here, we have imaged the development of the brain of the Rosy Bitterling (Rhodeus ocellatus) at four embryonic stages (165, 185, 210, 235 hours post-fertilization) using micro-computed tomography (microCT) with special emphasis on developmental regionalization and brain ventricular organization. We provide a detailed neuroanatomical account of the development of the brain divisions with reference to The Atlas of Early zebrafish Brain Development and the updated prosomeric model. Segmentation and three-dimensional visualization of the ventricular system were performed in order to clarify changes in the longitudinal brain axis as a result of cephalic flexure during development. During early embryonic and larval development, we find that histological differentiation, tissue boundaries, periventricular proliferation zones, and ventricular spaces are all recognizable using microCT. Importantly, our approach is validated by the fact that the profile of CT values displayed here in the bitterling brain are consistent with genoarchitecture identified in previous studies. We also find developmental heterochrony of the inferior lobe in the Rosy Bitterling compared to the zebrafish. Our study provides a foundation for future studies of the brain development in the Rosy Bitterling, a valuable model species for studying the evolutionary adaptations associated with brood parasitism.


title: Sunk cost sensitivity in mice, rats, and humans on the Restaurant Row and WebSurf tasks cannot be explained by attrition biases alone

abstract: In a recent bioRxiv preprint, Ott et al. argue that sensitivities to sunk costs that have been reported in two serial foraging tasks (the Restaurant Row task in mice and rats, and the Web-Surf task in humans) may be due to simple consequences of the way that subjects perform these tasks and not due to an actual sensitivity to sunk costs. However, several variants of these tasks have been studied, in which the sensitivity to sunk costs changes. In order to test the Ott et al. model against these experimental observations, we simulated the model under these additional experimental conditions. We find that it is incompatible with the actual data. While we applaud the simplicity of the Ott et al. model, we must reject it as an explanation for the observed sensitivity to sunk costs seen in these tasks. We thus conclude that the alternative explanation - that mice, rats, and humans are sensitive to actual sunk costs in these tasks - is a better explanation for the data.


title: iLQR-VAE : control-based learning of input-driven dynamics with applications to neural data

abstract: AO_SCPLOWBSTRACTC_SCPLOWUnderstanding how neural dynamics give rise to behaviour is one of the most fundamental questions in systems neuroscience. To achieve this, a common approach is to record neural populations in behaving animals, and model these data as emanating from a latent dynamical system whose state trajectories can then be related back to behavioural observations via some form of decoding. As recordings are typically performed in localized circuits that form only a part of the wider implicated network, it is important to simultaneously learn the local dynamics and infer any unobserved external input that might drive them. Here, we introduce iLQR-VAE, a control-based approach to variational inference in nonlinear dynamical systems, capable of learning both latent dynamics, initial conditions, and ongoing external inputs. As in recent deep learning approaches, our method is based on an input-driven sequential variational autoencoder (VAE). The main novelty lies in the use of the powerful iterative linear quadratic regulator algorithm (iLQR) in the recognition model. Optimization of the standard evidence lower-bound requires differentiating through iLQR solutions, which is made possible by recent advances in differentiable control. Importantly, the recognition model is naturally tied to the generative model, greatly reducing the number of free parameters and ensuring high-quality inference throughout the course of learning. Moreover, iLQR can be used to perform inference flexibly on heterogeneous trials of varying lengths. This allows for instance to evaluate the model on a single long trial after training on smaller chunks. We demonstrate the effectiveness of iLQR-VAE on a range of synthetic systems, with autonomous as well as input-driven dynamics. We further apply it to neural and behavioural recordings in non-human primates performing two different reaching tasks, and show that iLQR-VAE yields high-quality kinematic reconstructions from the neural data.


title: Light-induced asymmetries in the embryonic retina are mediated by the vascular system and extracellular matrix

abstract: Left-right asymmetries in the nervous system (lateralisation) influence a broad range of behaviours, from social responses to navigation and language. The role and pathways of endogenous and environmental mechanisms in the ontogeny of lateralisation remains to be established. The domestic chick is a model of both endogenous and experience-induced lateralisation driven by light exposure. Following the endogenous rightward rotation of the embryo, the asymmetrical position in the egg results in a greater exposure of the right eye to environmental light. To identify the genetic pathways activated by asymmetric light stimulation, and their time course, we exposed embryos to different light regimes: darkness, 6 hours of light and 24 hours of light. We used RNA-seq to compare gene expression in the right and left retinas and telencephalon. As expected, no differential expression between left and right was present in darkness. We detected differential gene expression in right vs left retina after 6 hours of light exposure. This difference disappeared before 24 hours of light exposure, suggesting that light-induced activation is a self-terminating phenomenon. This transient effect of light exposure was associated with a downregulation of the sensitive-period mediator gene DIO2 (iodothyronine deiodinase 2) in the right retina. No differences between genes expressed in the right vs. left telencephalon were detected. Gene networks associated with lateralisation were connected to vascularisation, cell motility, and the extracellular matrix. Interestingly, we know that the extracellular matrix- including the differentially expressed PDGFRB (platelet-derived growth factor receptor {beta}) gene - is involved in both sensitive periods and in the endogenous chiral mechanism of primary cilia, that drives lateralisation. Our data show a similarity between endogenous and experience-driven lateralisation, identifying functional gene networks that affect lateralisation in a specific time window.


title: Low-dimensional encoding of decisions in parietal cortex reflects long-term training history

abstract: Neurons in parietal cortex exhibit task-related activity during decision-making tasks. However, it remains unclear how long-term training to perform different tasks over months or even years shapes neural computations and representations. We examine lateral intraparietal area (LIP) responses during a visual motion delayed-match-to-category (DMC) task. We consider two pairs of monkeys with different training histories: one trained only on the DMC task, and another first trained to perform fine motion-direction discrimination. We introduce generalized multilinear models to quantify low-dimensional, task-relevant components in population activity. During the DMC task, we found stronger cosine-like motion-direction tuning in the pretrained monkeys than in the DMC-only monkeys, and that the pretrained monkeys performance depended more heavily on sample-test stimulus similarity. These results suggest that sensory representations in LIP depend on the sequence of tasks that the animals have learned, underscoring the importance of training history in studies with complex behavioral tasks.


title: CCR5 closes the temporal window for memory linking

abstract: Real world memories are formed in a particular context and are not acquired or recalled in isolation 1-5. Time is a key variable in the organization of memories, since events experienced close in time are more likely to be meaningfully associated, while those experienced with a longer interval are not1-4. How does the brain segregate events that are temporally distinct? Here, we report that a delayed (12-24h) increase in the expression of the C-C chemokine receptor type 5 (CCR5), an immune receptor well known as a co-receptor for HIV infection6,7, following the formation of a contextual memory, determines the duration of the temporal window for associating or linking that memory with subsequent memories. This delayed CCR5 expression in mouse dorsal CA1 (dCA1) neurons results in a decrease in neuronal excitability, which in turn negatively regulates neuronal memory allocation, thus reducing the overlap between dCA1 memory ensembles. Lowering this overlap affects the ability of one memory to trigger the recall of the other, thus closing the temporal window for memory linking. Remarkably, our findings also show that an age-related increase in CCL5/CCR5 expression leads to impairments in memory linking in aged mice, which could be reversed with a CCR5 knockout and an FDA approved drug that inhibits this receptor, a result with significant clinical implications. All together the findings reported here provide the first insights into the molecular and cellular mechanisms that shape the temporal window for memory linking.


title: Multimodal Magnetic Resonance Histology and Light Sheet Imaging for Quantitative Neurogenetics of the Mouse

abstract:
Paul Lauterbur closed his seminal paper on MRI with the statement that "zeugmatographic (imaging) techniques should find many useful applications in studies of the internal structures, states and composition of microscopic objects" [1]. Magnetic resonance microscopy was subsequently demonstrated in 1986 by three groups [2] [3] [4]. The application of MRI to the study of tissue structure, i.e. magnetic resonance histology (MRH) was suggested in 1993 [5]. MRH, while based on the same physical principals as MRI is something fundamentally different than the clinical exams which are typically limited to voxel dimensions of ~ 1 mm3. Preclinical imaging systems can acquire images with voxels ~ 1000 times smaller. The MR histology images presented here have been acquired at yet another factor of 1000 increase in spatial resolution. Figure S1 in the supplement shows a comparison of a state-of-the-art fractional anisotropy images of a C57 mouse brain in vivo @ 150 m resolution (voxel volume of 3.3 x10-3 mm3) with the atlas we have generated for this work at 15 m spatial resolution (voxel volume of 3.3 x 10-6 mm3). In previous work, we have demonstrated the utility of MR histology in neurogenetics at spatial/angular resolution of 45 m /46 angles [6]. At this spatial/angular resolution it is possible to map whole brain connectivity with high correspondence to retroviral tracers [7]. But the MRH derived connectomes can be derived in less than a day where the retroviral tracer studies require months/years [8]. The resolution index (angular samples/voxel volume) for this previous work was >500,000 [9]. Figure S2 shows a comparison between that previous work and the new atlas presented in this paper with a resolution index of 32 million.

Light sheet microscopy (LSM) has undergone similar rapid evolution over the last 20 years. The invention of tissue clearing, advances in immunohistochemistry and development of selective plane illumination microscopy (SPIM) now make it possible to acquire whole mouse brain images at submicron spatial resolution with a vast array of cell specific markers [10] [11] [12] [13]. And these advantages can be realized in scan times of < 6hrs. The major limitation from these studies is the distortion in the tissue from dissection from the cranium, swelling from clearing and staining, and tissue damage from handling.

We report here the merger of these two methods: O_LIMRH with the brain in the skull to provide accurate geometry, cytoarchitectural measures using scalar imaging metrics and whole brain connectivity at 15 m isotropic spatial resolution with super resolution track density images @ 5 m isotropic resolution;
C_LIO_LIwhole brain multichannel LSM @ 1.8x1.8x4.0 m;
C_LIO_LIa big image data infrastructure that enables label mapping from the atlas to the MR image, geometric correction to the light sheet data, label mapping to the light sheet volumes and quantitative extraction of regional cell density. These methods make it possible to generate a comprehensive collection of image derived phenotypes (IDP) of cells and circuits covering the whole mouse brain with throughput that can be scaled for quantitative neurogenetics.
C_LI


title: Vagus nerve stimulation increases stomach-brain coupling via a vagal afferent pathway

abstract:
Maintaining energy homeostasis is vital and supported by vagal signaling between digestive organs and the brain. Previous research has established a gastric network in the brain that is phase synchronized with the rhythm of the stomach, but tools to perturb its function were lacking. Here, we investigated the effect of acute right-sided transcutaneous auricular vagus nerve stimulation (taVNS) versus sham stimulation (randomized crossover-design) on stomach-brain coupling. In line with preclinical research, taVNS increased stomach-brain coupling in the nucleus of the solitary tract (NTS) and the midbrain while boosting coupling across the brain. Crucially, in the cortex, taVNS-induced changes in coupling occurred primarily in transmodal regions and were associated with changes in hunger ratings as indicators of the subjective metabolic state. Hence, taVNS alters stomach-brain coupling via an NTS-midbrain pathway that signals gut-induced reward, potentially paving the way for novel treatments in disorders such as Parkinsons disease or depression.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/463517v1_ufig1.gif" ALT="Figure 1">
View larger version (53K):
org.highwire.dtl.DTLVardef@39c673org.highwire.dtl.DTLVardef@113b785org.highwire.dtl.DTLVardef@175af94org.highwire.dtl.DTLVardef@15a2fbc_HPS_FORMAT_FIGEXP  M_FIG C_FIG HighlightsO_LITranscutaneous vagus nerve stimulation (taVNS) can emulate interoceptive signals
C_LIO_LItaVNS boosts stomach-brain coupling in the brainstem, midbrain, and transmodal cortex
C_LIO_LItaVNS-induced changes in stomach-brain coupling mirror subjective hunger ratings
C_LI


title: Impact of stimulation location relative to grey and white matter on single pulse electrical stimulation responses in the human brain

abstract:
BackgroundElectrical neuromodulation is an increasingly common therapy for a wide variety of neuropsychiatric diseases. Unfortunately, therapeutic efficacy is inconsistent, possibly a result of our limited understanding of the mechanisms and the massive stimulation parameter space.

Objective/HypothesisTo better understand the role different parameters play in inducing a response, we systematically examined single pulse-induced cortico-cortico evoked potentials (CCEP) as a function of stimulation amplitude, duration and location in the brain and relative to grey and white matter.

MethodsWe measured voltage peak amplitudes and area under the curve of intracranially recorded stimulation responses as a function of distance from the stimulation site, pulse width, current injected, location relative to grey and white matter, and brain region stimulated (N=52, n=719 stimulation sites).

ResultsIncreasing stimulation pulse width increased response values near the stimulation location. Increasing stimulation amplitude (current) increased responses nonlinearly. Locally (<15 mm from the stimulation site), stimulation closer to the grey matter-white matter boundary induced larger responses. In contrast, for distant sites (>15 mm), white matter stimulation consistently produced larger responses than stimulation in or near grey matter. These relationships were different between cingulate, lateral prefrontal, and lateral temporal cortical stimulation.

ConclusionThese results demonstrate the importance of location and stimulation parameters in inducing a specific output and indicate that a stronger local response may require stimulation in the grey-white boundary while stimulation in the white matter may be needed for network activation, suggesting that stimulation location can be tailored for a specific outcome, key to informed neuromodulatory therapy.

HighlightsO_LIIntracranial single pulse electrical stimulation (SPES) response increases with increased pulse duration mostly near the stimulation site
C_LIO_LISPES response varies nonlinearly with injected current with an effect of distance from the stimulation site.
C_LIO_LISPES near the grey-white boundary and 90{degrees} to the nearest cortical axis induces larger local responses, but white matter stimulation produces larger distant responses.
C_LIO_LIThe relationship between SPES location and responses depends on brain region stimulated
C_LI


title: Defining the Characteristics of Type I Interferon Stimulated Genes: Insight from Expression Data and Machine Learning

abstract:
A virus-infected cell triggers a signalling cascade resulting in the secretion of interferons (IFNs), which in turn induce the up-regulation of IFN-stimulated genes (ISGs) that play an important role in the inhibition of the viral infection and the return to cellular homeostasis. Here, we conduct detailed analyses on 7443 features relating to evolutionary conservation, nucleotide composition, gene expression, amino acid composition, and network properties to elucidate factors associated with the stimulation of genes in response to type I IFNs. Our results show that ISGs are less evolutionary conserved than genes that are not significantly stimulated in IFN experiments (non-ISGs). ISGs show significant depletion of GC-content in the coding region of their canonical transcripts, which leads to under-representation in the nucleotide compositions. Differences between ISGs and non-ISGs are also reflected in the properties of their coded amino acid sequence compositions. Network analyses show that ISG products tend to be involved in key paths but are away from hubs or bottlenecks of the human protein-protein interaction (PPI) network. Our analyses also show that interferon-repressed human genes (IRGs), which are down-regulated in the presence of IFNs, can have similar properties to ISGs, thus leading to false positives in ISG predictions. Based on these analyses, we design a machine learning framework integrating the usage of support vector machine (SVM) and feature selection algorithms. The ISG prediction achieves an area under the receiver operating characteristic curve (AUC) of 0.7455 and demonstrates the similarity between ISGs triggered by type I and III IFNs. Our machine learning model predicts a number of genes as potential ISGs that so far have shown no significant differential expression when stimulated with IFN in the cell types and tissue types compiled in the available IFN-related databases. A webserver implementing our method is accessible at http://isgpre.cvr.gla.ac.uk/.

Author summaryInterferons (IFNs) are signalling proteins secreted from host cells. IFN-triggered signalling activates the host immune system in response to intra-cellular infection. It results in the stimulation of many genes that have anti-pathogen roles in host defenses. Interferon-stimulated genes (ISGs) have unique properties that make them different from those not significantly up-regulated in response to IFNs (non-ISGs). We find the down-regulated interferon-repressed genes (IRGs) have some shared properties with ISGs. This increases the difficulty of distinguishing ISGs from non-ISGs. The use of machine learning is a sensible strategy to provide high throughput classifications of putative ISGs, for investigation with in vivo or in vitro experiments. Machine learning can also be applied to human genes for which there are insufficient expression levels before and after IFN treatment in various experiments. Additionally, the interferon type has some impact on ISG predictability. We expect that our study will provide new insight into better understanding the inherent characteristics of human genes that are related to response in the presence of IFNs.

category: immunology


title: Immune cell multi-omics analysis reveals contribution of oxidative phosphorylation to B cell functions and organ damage of lupus

abstract:
ObjectiveSystemic lupus erythematosus (SLE) is the prototypical systemic autoimmune disease, with a poor long-term prognosis. The type I interferon (IFN) signature, a prominent feature of SLE, is not an ideal therapeutic target or outcome predictor. To explore immunological pathways in SLE more precisely, we performed integrative analysis of transcriptomics, epigenomics, and genomics using each immune cell subset from peripheral blood.

MethodsWe sorted 18 immune cell subsets and identified the mRNA expression profiles and genetic polymorphisms in 107 SLE patients and 92 healthy controls. Open chromatin information was also taken by ATAC-seq analysis. Combined differentially expressed genes (DEGs) and expression quantitative trait loci (eQTL) analysis was conducted to find key driver genes in SLE pathogenesis.

ResultsWe found transcriptomic, epigenetic, and genetic importance of oxidative phosphorylation (OXPHOS)/mitochondrial dysfunction in SLE memory B cells. Particularly, we identified an OXPHOS-regulating gene, PRDX6, as a key driver in SLE B cells. Prdx6-deficient B cells showed upregulated mitochondrial respiration as well as antibody production. We revealed OXPHOS signature was associated with type I IFN signaling-related genes (ISRGs) signature in SLE memory B cells. Furthermore, the gene sets related to innate immune signaling among ISRGs presented correlation with OXPHOS and these two signatures showed associations with SLE organ damage as well as specific clinical phenotypes.

ConclusionThis work elucidated the potential prognostic marker for SLE. Since OXPHOS consists of the electron transport chain, a functional unit in mitochondria, these findings suggest the importance of mitochondrial dysfunction as a key immunological pathway involved in SLE.


title: Persistent Immunogenicity of Integrase Defective Lentiviral Vectors delivering membrane tethered Native-Like HIV-1 Envelope Trimers

abstract: Integrase Defective Lentiviral Vectors (IDLVs) represent an attractive vaccine platform for delivering HIV-1 antigens, given their ability to induce specific and persistent immune responses in both mice and non-human primates (NHPs). Recent advances in HIV-1 immunogen design demonstrated that native-like HIV-1 Envelope (Env) trimers that mimic the structure of virion-associated Env induce neutralization breadth in rabbits and macaques. Here, we describe the development of an IDLV-based HIV-1 vaccine expressing either soluble ConSOSL.UFO.664 or membrane-tethered ConSOSL.UFO.750 native-like Env immunogens with enhanced bNAb epitopes exposure. We show that IDLV can be pseudotyped with properly folded membrane-tethered native-like UFO.750 trimers. After a single IDLV injection in BALB/c mice, IDLV-UFO.750 induced a faster humoral kinetic as well as higher levels of anti-Env IgG compared to IDLV-UFO.664. IDLV-UFO.750 vaccinated cynomolgus macaques developed unusually long-lasting anti-Env IgG antibodies, as underlined by their remarkable half-life both after priming and boost with IDLV. After boosting with recombinant ConM SOSIP.v7 protein, two animals developed neutralization activity against the autologous tier 1B ConS virus mediated by V1/V2 and V3 glycan sites responses. By combining the possibility to display stabilized trimeric Env on the vector particles with the ability to induce sustained humoral responses, IDLVs represent an appropriate strategy for delivering rationally designed antigens to progress towards an effective HIV-1 vaccine.


title: Glutamine metabolism enables NKT cell homeostasis and function through the AMPK-mTORC1 signaling axis

abstract:
Cellular metabolism is essential in dictating conventional T cell development and function, but its role in natural killer T (NKT) cells has not been well studied. We have previously shown that NKT cells operate distinctly different metabolic programming from CD4 T cells, including a strict requirement for glutamine metabolism to regulate NKT cell homeostasis. However, the mechanisms by which NKT cells regulate glutamine metabolism for their homeostasis and effector functions remain unknown. In this study, we report that steady state NKT cells have higher glutamine levels than CD4 T cells and NKT cells increase glutaminolysis upon activation. Among its many metabolic fates, NKT cells use glutamine to fuel the tricarboxylic acid cycle and glutathione synthesis, and glutamine-derived nitrogen enables protein glycosylation via the hexosamine biosynthesis pathway (HBP). Each of these functions of glutamine metabolism was found to be critical for NKT cell survival and proliferation. Furthermore, we demonstrate that glutaminolysis and the HBP differentially regulate IL-4 and IFN{gamma} production. Finally, glutamine metabolism appears to be controlled by AMP-activated protein kinase (AMPK)-mTORC1 signaling. These findings highlight a unique metabolic requirement of NKT cells which can be potentially serve as an effective immunotherapeutic agent against certain nutrient restricted tumors.

SignificanceNKT cells get activated very early during an immune response and produce cytokines and chemokines, which further activate other immune cell types. Although metabolism regulates these functions in other T cell subsets, little is understood about how metabolic pathways are controlled in NKT cells. The present study shows that NKT cells metabolize the amino acid glutamine through two different branches of metabolism, which control NKT cell homeostasis and expansion in a similar manner but control cytokine production differently. This glutamine dependency seems to be regulated by AMP-activated protein kinase (AMPK), which is a central regulator of energy homeostasis. Together, our study demonstrates a unique metabolic profile of glutamine metabolism in NKT cells which could be harnessed for NKT cell-based immunotherapy.


title: In vivo emergence of high-level resistance during treatment reveals the first identified mechanism of amphotericin B resistance in Candida auris

abstract: Candida auris has emerged as a healthcare-associated and multidrug-resistant fungal pathogen of great clinical concern. While as much as 50% of C. auris clinical isolates are reported to be resistant to amphotericin B, to date, no mechanisms contributing to this resistance have been identified. We report here mutations in the C. auris sterol-methyltransferase gene, ERG6, as the first identified mechanism of amphotericin B resistance in this emerging pathogen and describe the clinical case in which this high-level amphotericin B resistance was acquired in vivo during therapy. Whole genome sequencing revealed the four C. auris isolates obtained from this single patient case to be genetically related and identified a mutation in ERG6 as being associated with amphotericin B resistance. Cas9-mediated genetic manipulations confirmed this mutation alone to confer a >32-fold increase in amphotericin B resistance, and comprehensive sterol profiling revealed an abrogation of ergosterol biosynthesis and a corresponding accumulation of cholesta-type sterols in isolates and strains harboring the clinically derived ERG6 mutation. Together these findings represent the first significant step forward in the understanding of clinical amphotericin B resistance in C. auris.

category: microbiology


title: Proximity interactome of LC3B in normal growth conditions

abstract: LC3 (Light Chain 3) is a key player of autophagy, a major stress-responsive proteolysis pathway promoting cellular homeostasis. It coordinates the formation and maturation of autophagosomes and recruits cargo to be further degraded upon autophagosome-lysosome fusion. To orchestrate its functions, LC3 binds to multiple proteins from the autophagosomes inner and outer membranes, but the full extent of these interactions is not known. Moreover, LC3 has been increasingly reported in other cellular locations than the autophagosome, with cellular outcome not fully understood and not all related to autophagy. Furthermore, novel functions of LC3 as well as autophagy can occur in cells growing in a normal medium thus in non-stressed conditions. A better knowledge of the molecule in proximity to LC3 in normal growth conditions will improve the understanding of LC3 function in autophagy and in other cell biology function. Using an APEX2 based proteomic approach, we have detected 407 proteins in proximity to the well-characterised LC3B isoform in non-stress conditions. These include known and novel LC3B proximity proteins, associated with various cell localisation and biological functions. Sixty-nine of these proteins contain a putative LIR (LC3 Interacting Region) including 41 not reported associated to autophagy. Several APEX2 hits were validated by co-immunoprecipitation and co-immunofluorescence. This study uncovers the LC3B global interactome and reveals novel LC3B interactors, irrespective of LC3B localisation and function. This knowledge could be exploited to better understand the role of LC3B in autophagy and non-autophagy cellular processes.

category: cell biology


title: Kidney pathological changes alter cell clustering features in single-cell RNA sequencing

abstract: Single cell RNA sequencing (scRNA-Seq) is useful to classify cell-specific gene expression profiles in kidney tissue. As viable cells are required, we report an optimized cell dissociation methodology and the necessity of screening tissue histology prior to scRNA-Seq. We demonstrate that glomerular injury can selectively reduce the appearance of groups of cells during analysis of cell clustering and we confirmed reductions in cell-specific markers among injured cells on kidney sections with fluorescence microscopy. Interpretation of scRNA-Seq results may be refined based upon these considerations.


title: The  prion and HSP104 modulate cytochrome c oxidase deficiency caused by deletion of COX12

abstract: Cytochrome c oxidase is a pivotal enzyme of the mitochondrial respiratory chain, which sustains bioenergetics of eukaryotic cells. Cox12, a peripheral subunit of cytochrome c oxidase, is required for full activity of the enzyme, but its exact function is unknown. Here, experimental evolution of a Saccharomyces cerevisiae {Delta}cox12 strain for ~300 generations allowed to restore the activity of cytochrome c oxidase. In one population, the enhanced bioenergetics was caused by a A375V mutation in the AAA+ disaggregase Hsp104. Deletion or overexpression of Hsp104 also increased respiration of the {Delta}cox12 ancestor strain. This beneficial effect of Hsp104 was related to the loss of the [PSI+] prion, which forms cytosolic amyloid aggregates of the Sup35 protein. Overall, our data demonstrate that cytosolic aggregation of a prion impairs the mitochondrial metabolism of cells defective for Cox12. These findings identify a new functional connection between cytosolic proteostasis and biogenesis of the mitochondrial respiratory chain.


title: Self-organized tissue mechanics underlie embryonic regulation

abstract: Early amniote development is a highly regulative and self-organized process, capable to adapt to interference through cell-cell interactions, which are widely believed to be mediated by molecules. Analyzing intact and mechanically perturbed avian embryos, we show that the mechanical forces that drive embryogenesis self-organize in an analog of Turings molecular reaction-diffusion model, with contractility locally self-activating and the ensuing tension acting as a long-range inhibitor. This mechanical feedback governs the persistent pattern of tissue flows that shape the embryo and steers the concomitant emergence of embryonic territories by modulating gene expression, ensuring the formation of a single embryo under normal conditions, yet allowing the emergence of multiple, well-proportioned embryos upon perturbations. Thus, mechanical forces are a central signal in embryonic self-organization, feeding back onto gene expression to canalize both patterning and morphogenesis.

category: developmental biology


title: Endoglin deficiency elicits hypoxia-driven congestive heart failure in zebrafish.

abstract:
Hereditary hemorrhagic Telangiectasia (HHT) is a rare genetic disease relying on mutations affecting components of Bone Morphogenetic Protein and Transforming Growth Factor-{beta} (BMP/TGF-{beta}) signaling pathway in endothelial cells. This disorder is characterized by arterio-venous malformations prone to rupture. and ensuing hemorrhages are responsible for iron deficiency anemia. Along with Activin receptor-like kinase ALK1, Endoglin is involved in the vast majority of HHT cases. In this report, we characterized zebrafish endoglin locus and demonstrated that it produces two phylogenetically conserved protein isoforms using a distinctive alternative splicing mechanism. Functional analysis of a Crispr/Cas9 zebrafish Endoglin mutant revealed that Endoglin deficiency results in massive death during the course from juvenile stage to adulthood. Endoglin deficient fish develop a cardiomegaly resulting in heart failure and hypochromic anemia which both stem from chronic hypoxia. Histological analysis and confocal imaging evidenced structural alterations of the developing gill and its underlying vascular network that tally with hypoxia. Finally, phenylhydrazine treatment demonstrated that lowering hematocrit/blood viscosity alleviates heart failure and enhances survival of Endoglin deficient fish. Altogether, our data indicate that Endoglin is crucial for gill vascular development and that further studies using zebrafish in general and this endoglin mutant in particular will provide crucial hints regarding the molecular and cellular events altered in HHT for the development of new therapeutic strategies.

Summary StatementEndoglin deficiency in zebrafish recapitulates critical aspects of Hereditary Hemorrhagic Telangiectasia (HHT) and will thus constitute a valuable model in large scale screens for HHT-active drugs.


title: Development and retinal remodeling in the brown anole lizard (Anolis sagrei)

abstract:
BackgroundThe fovea, a pit in the retina, is believed to be important for high-acuity vision and is a feature found in the eyes of humans and a limited number of vertebrate species that include certain primates, birds, lizards, and fish. At present, model systems currently used for ocular research lack a foveated retina and studies investigating fovea development have largely been limited to histological and molecular studies in primates. As a result, progress towards understanding the mechanisms involved in regulating fovea development in humans is limited and is completely lacking in other, non-primate, vertebrates. To address this knowledge gap, we provide here a detailed histological atlas of retina and fovea development in the bifoveated Anolis sagrei lizard, a novel reptile model for fovea research. We also further test the hypothesis that retinal remodeling, which leads to fovea formation and photoreceptor cell packing, is related to asymmetric changes in eye shape.

ResultsAnole retina development follows the conventional spatiotemporal patterning observed in most vertebrates, where retina neurogenesis begins within the central retina, progresses throughout the temporal retina, and concludes in the nasal retina. One exception to this general rule is that areas that give rise to the fovea undergo retina differentiation prior to the rest of the retina. We find that retina thickness changes dynamically during periods of ocular elongation and retraction. During periods of ocular elongation, the retina thins, while during retraction it becomes thicker. Ganglion cell layer mounding is also observed in the temporal fovea region just prior to pit formation.

ConclusionsAnole retina development parallels that of humans, including the onset and progression of retinal neurogenesis followed by changes in ocular shape and retinal remodeling that leads to pit formation in the retina. We propose that anoles are an excellent model system for fovea development research.

Key FindingsO_LIRetina mounding that occurs in foveal areas prior to retinal differentiation progressively disappear as foveal regions of the eye elongate.
C_LIO_LIThe central and temporal foveal areas undergo retina differentiation before the rest of the retina.
C_LIO_LIGCL mounding prior to pit formation occurs in the area of the temporal fovea but not the central fovea.
C_LIO_LIWhen the eye is experiencing ocular retraction, photoreceptor cell packing, and pit formation are observed within foveal regions.
C_LI


title: RUSBoost: A suitable species distribution method for imbalanced records of presence and absence. A case study of twenty-five species of Iberian bats

abstract:
O_LITraditional Species Distribution Models (SDMs) may not be appropriate when examples of one class (e.g. absence or pseudo-absences) greatly outnumber examples of the other class (e.g. presences or observations), because they tend to favor the learning of observations more frequently.
C_LIO_LIWe present an ensemble method called Random UnderSampling and Boosting (RUSBoost), which was designed to address the case where the number of presence and absence records are imbalanced, and we opened the "black-box" of the algorithm to interpret its results and applicability in ecology.
C_LIO_LIWe applied our methodology to a case study of twenty-five species of bats from the Iberian Peninsula and we build a RUSBoost model for each species. Furthermore, in order to improve to build tighter models, we optimized their hyperparameters using Bayesian Optimization. In particular, we implemented a objective function that represents the cross-validation loss: [Formula], with [Formula] representing the hyper-parameters Maximum Number of Splits, Number of Learners and Learning Rate.
C_LIO_LIThe models reached average values for Area Under the ROC Curve (AUC), specificity, sensitivity, and overall accuracy of 0.84 {+/-} 0.05%, 79.5 {+/-} 4.87%, 74.9 {+/-} 6.05%, and 78.8 {+/-} 5.0%, respectively. We also obtained values of variable importance and we analyzed the relationships between explanatory variables and bat presence probability.
C_LIO_LIThe results of our study showed that RUSBoost could be a useful tool to develop SDMs with good performance when the presence/absence databases are imbalanced. The application of this algorithm could improve the prediction of SDMs and help in conservation biology and management.
C_LI

category: ecology


title: Plastic biodegradation: do Galleria mellonella larvae - bio-assimilate polyethylene? A spectral histology approach using isotopic labelling and infrared microspectroscopy.

abstract: Environmental pollution by non-biodegradable polyethylene (PE) plastics is of major concern, thus, organisms capable of bio-degrading PE are required. The larvae of the Greater Wax Moth, Galleria mellonella (Gm), were identified as a potential candidate to digest PE. In this study, we tested whether PE was metabolized by Gm larvae and could found in their tissues. We examined the implication of the larval gut microbiota by using conventional and axenic reared insects. First, our study showed that neither beeswax nor PE alone favour the growth of young larvae. We then used Fourier-Transform Infrared Microspectroscopy ({micro}FTIR) to detect deuterium in larvae fed with isotopically labelled food. Perdeuterated molecules were found in most tissues of larvae fed with deuterium labelled oil for 72 hours proving that {micro}FTIR can detect metabolization of 1-2 mg of deuterated food. No bio-assimilation was detected in the tissues of larvae fed with 1-5 mg of perdeuterated PED4 for 72 hours and 19-21 days, but micron sized PE particles were found in the larval digestive tract cavities. We evidenced weak bio-degradation of PE films in contact for 24 hours with the dissected gut of conventional larvae; and in the PED4 particles from excreted larval frass. Our study confirms that Gm larvae can bio-degrade PE but can not necessarily metabolize it.


title: Social information use for spatial decision in Zootoca vivipara

abstract:
Movements of individuals are conditioned by information acquisition coming from either personal or social sources. Yet, little is known about the processes used by individuals to make movement decisions when facing multiple sources of social information simultaneously. This study aimed to test experimentally how social information from multiple sources is used to make movement decisions, and whether a contrast in this information allows individuals to orientate in space. We used common lizards (Zootoca vivipara) in a replicated experimental setting: one focal individual received information from two other individuals coming from peripheral environments, before being given the opportunity to relocate in one or another of the peripheral environments.

Our analyses revealed that the behavior of informants, their mothers morphology, as well as the quality of informants environment, affected movement decisions: the probability to relocate from the focal area increased when informants displayed traits associated with low resources (no food intake, poor maternal condition) or high competition (high activity). The physical condition of individuals also mediated the use of social information about food intake, with a match between resource availability in informants and personal condition. Conversely, spatial orientation was not affected by the contrast of phenotype between informants nor by spatial variability in resource availability.

This study highlights that multiple social information sources can be used for movement decisions, likely because these information sources reflect the quality of the surrounding environment (e.g., competition level or resources availability). It also emphasizes that social information use for movement is conditioned by individual phenotype.


title: Modelling the effects of land use on mangroves in a RAMSAR site of Panama

abstract: The role of mangroves as pivotal providers of ecosystem services has been widely acknowledged. In Latin America, mangroves play an important role in traditional coastal livelihoods, but the growing economy of these nations demands the expansion of land for development, putting pressure in ecosystems such as mangroves. Here we examine the impact of land use activities on mangroves in the Gulf of Montijo, a RAMSAR site located in the Pacific coast of Panama. Spatial information of land use was analysed, ground-truthed and classified into agriculture, aquaculture and coastal development, and subsequently ranked according to estimated level of impact on mangroves based on 27 interviews with local informants. We developed a spatially-referenced cumulative impact model of human activities on mangroves. Results showed that despite the protection status of the Gulf of Montijo, its mangrove forests are affected by localised human activities, dominated by agriculture. Given the importance of fishing for local livelihoods, evaluating the effects of agriculture, rice in particular, on mangroves and their associated fauna will be essential for the sustainable management of this RAMSAR site.


title: Global port survey quantifies commercial shippings effect on biodiversity

abstract: Spread of nonindigenous organisms by shipping is one of the largest threats to coastal ecosystems. Limited monitoring and understanding of this phenomenon currently hinder development of effective prevention policies. Surveying ports in North America, South America, Europe, Southeast Asia, and Australia we explored environmental DNA community profiles evident of ship-born species spread. We found that community similarities between ports increased with the number of ship voyages, particularly if the ports had similar environments, and when indirect stepping-stone connections were considered. We also found 57 known non-indigenous taxa, some in hitherto unreported locations. We demonstrate the usefulness of eDNA-based tools for global biodiversity surveys, and highlight that shipping homogenizes biodiversity in predictable that could inform policy and management.


title: Artificial reefs geographical location matters more than its age and depth for sessile invertebrate colonization in the Gulf of Lion (NorthWestern Mediterranean Sea)

abstract: AO_SCPLOWBSTRACTC_SCPLOWArtificial reefs (ARs) have been used to support fishing activities. Sessile invertebrates are essential components of trophic networks within ARs, supporting fish productivity. However, colonization by sessile invertebrates is possible only after effective larval dispersal from source populations, usually in natural habitat. While most studies focused on short term colonization by pioneer species, we propose to test the relevance of geographic location, shape, age and depth of immersion on the ARs long term colonization by species found in natural stable communities in the Gulf of Lion. We recorded the presence of five sessile invertebrates species, with contrasting life history traits and regional distribution in the natural rocky habitat, on ARs with different shapes deployed during two immersion time periods (1985 and the 2000s) and in two depth ranges (<20m and >20m). At the local level ([~]5kms), neither shape, depth nor immersion duration differentiated ARs assemblages. At the regional scale (>30kms), colonization patterns differed between species, resulting in diverse assemblages. This study highlights the primacy of geographical positioning over shape, immersion duration and depth in ARs colonization, suggesting it should be accounted for in maritime spatial planning.


title: Artificial reefs geographical location matters more than shape, age and depth for sessile invertebrate colonization in the Gulf of Lion (NorthWestern Mediterranean Sea)


title: Evolution of increased early-life fecundity but faster reproductive senescence in Drosophila melanogaster females through adaptation to chronic live-yeast deprivation

abstract: Dietary restriction is a common ecological challenge that limits reproduction. Yet only a few studies have explored adaptation under chronic protein deprivation. We subjected four replicate laboratory-adapted populations (YLB) of Drosophila melanogaster to a complete deprivation of live-yeast to mimic diet restricted ecology. In this insect, live-yeast is a critical source of protein that strongly affect reproductive output, especially in females. Following 24 generations of experimental evolution, compared to their matched controls (BL), females from YLB populations showed increase in reproductive output early in life, both in presence and absence of live-yeast. The observed increase in reproductive output was not associated with any accommodating alteration in average egg size; and development time, pre-adult survivorship, and body mass at eclosion of the progeny. Interestingly, adult lifespan was also found to be unaffected. However, YLB females were found to have a significantly faster rate of reproductive senescence albeit without any change in a measure of lifetime reproductive output. Taken together, adaptation to LYD ecology shows that reproductive output can evolve without affecting lifespan, suggesting that widely observed reproduction-survival trade-off is not universal. Populations can optimize fitness by fine tuning the scheduling of reproduction even when lifetime reproductive output is constrained.

category: evolutionary biology


title: Polygenic sex determination produces modular sex polymorphism in an African cichlid fish

abstract:
For many vertebrates, a single genetic locus initiates a cascade of developmental sex differences in the gonad and throughout the organism, resulting in adults with two, phenotypically distinct sexes. Species with polygenic sex determination (PSD) have multiple interacting sex determination alleles segregating within a single species, allowing for more than two genotypic sexes, and scenarios where sex genotype at a given locus can be decoupled from gonadal sex. Here we investigate the effects of PSD on secondary sexual characteristics in the cichlid fish Metriaclima mbenjii, where one female (W) and one male (Y) sex determination allele interact to produce siblings with four possible sex classes: ZZXX females, ZWXX females, ZWXY females, and ZZXY males. We find that PSD in M. mbenjii produces an interplay of sex-linkage and sex-limitation resulting in modular variation in morphological and behavioral traits. Further, the evolution or introgression of a novel sex determiner creates additional axes of phenotypic variation for varied traits, including genital morphology, craniofacial morphology, gastrointestinal morphology, and home tank behaviors. In contrast to single-locus sex determination, which broadly results in sexual dimorphism, polygenic sex determination can induce higher-order sexual polymorphism. The modularity of secondary sexual characteristics produced by PSD provides novel context for understanding the evolutionary causes and consequences of maintenance, gain, or loss of sex determination alleles in populations.

Significance StatementSex differences in traits can occur when those traits are modified by genetic factors inherited on sex chromosomes. We investigated how sex differences emerge in a species with more than one set of sex chromosomes, measuring a variety of morphological, physiological, and behavioral traits. Rather than exhibiting sexual dimorphism associated with primary sex, the species has higher-order sexual polymorphism in secondary sexual characteristics, or more than two phenotypic sexes. Variation in secondary sexual characteristics is modular, involving the interplay of sex-linked and sex-limited traits. Our findings provide novel implications for how sex determination systems and whole-organism fitness traits co-evolve, including that significant creation or loss of variation in diverse traits can occur during transitions among sex chromosome systems.


title: Connexins evolved after early chordates lost innexin diversity

abstract: Gap junction channels are formed by two unrelated protein families. Non-chordates use the primordial innexins, while chordates use connexins that superseded the gap junction function of innexins. Chordates retained innexin-homologs, but N-glycosylation prevents them from forming gap junctions. It is puzzling why chordates seem to exclusively use the new gap junction protein and why no chordates should exist that use non-glycosylated innexins to form gap junctions. Here, we identified glycosylation sites of 2270 innexins from 152 non-chordate and 274 chordate species. Among all chordates, we found not a single innexin without glycosylation sites. Surprisingly, the glycosylation motif is also widespread among non-chordate innexins indicating that glycosylated innexins are not a novelty of chordates. In addition, we discovered a loss of innexin diversity during the early chordate evolution. Most importantly, the most basal living chordates, which lack connexins, exclusively possess innexins with glycosylation sites. A bottleneck effect might thus explain why connexins have become the only protein used to form chordate gap junctions.


title: Constrained optimisation of divisional load in hierarchically-organised tissues during homeostasis

abstract: It has been hypothesised that the structure of tissues and the hierarchy of differentiation from stem cell to terminally-differentiated cell play a significant role in reducing the incidence of cancer in that tissue. One specific mechanism by which this risk can be reduced is by minimising the number of divisions - and hence the mutational risk - that cells accumulate as they divide to maintain tissue homeostasis. Here we investigate a mathematical model of cell division in a hierarchical tissue, calculating and minimising the divisional load while constraining parameters such that homeostasis is maintained. We show that the minimal divisional load is achieved by binary division tress with progenitor cells incapable of selfrenewal. Contrary to the protection hypothesis, we find that an increased stem cell turnover can lead to lower divisional load. Furthermore, we find that the optimal tissue structure depends on the time horizon of the duration of homeostasis, with faster stem cell division favoured in short-lived organisms and more progenitor compartments favoured in longer-lived organisms.


title: Expression analysis and single-nucleotide polymorphisms of MLPH and PMEL17 genes associated with melanin deposition in Xuefeng black-bone chickens

abstract: Melanin deposition related genes such as MLPH and PMEL17 play an important role in black-bone chicken. This study was aimed to identify and associate SNPs in the MLPH and PMEL17 genes with melanin content of pectoral muscle (MCPM) in Xuefeng black-bone chicken. A total of 120 Xuefeng black-bone chickens at 120-day-old were randomly selected to measure blackness of pectoral muscle (BPM), according to the degree of BPM selected 22 high blackness (HB) and 22 low blackness (LB) chickens to determine the MCPM, and extract DNA and mRNA. The results indicated that the MCPM in the HB group was higher than in the LB group (P < 0.01), and the L value in the HB group was lower than in the LB group (P < 0.01). And we measured the mRNA expression levels of MLPH and PMEL17 genes in pectoral muscle by quantitative real-time PCR. The results revealed that the mRNA expression levels of MLPH gene (P < 0.05) and PMEL17 gene (P < 0.01) in the HB group was higher than in the LB group, and the mRNA relative expression level of MLPH and PMEL17 genes with MCPM was positive correlation (P < 0.01). And the sequencing results found that a total of 17 SNPs were found in MLPH gene, the C-1411T was associated with MCPM (P < 0.05), there was no difference in MCPM among other locus (P > 0.05). And there were 10 SNPs in PMEL17 gene, the G-1843C, C-2812T, and G-2794A were associated with MCPM (P < 0.05), there was no difference in the MCPM among other locus (P > 0.05). These SNPs could be molecular markers for breeding selection of blackness traits.

category: genetics


title: Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs

abstract:
Cohesin loop extrusion facilitates precise gene expression by continuously driving promoters to sample all enhancers located within the same topologically-associated domain (TAD). However, many TADs contain multiple genes with divergent expression patterns, thereby indicating additional forces further refine how enhancer activities are utilised. Here, we unravel the mechanisms enabling a new gene, Rex1, to emerge with divergent expression within the ancient Fat1 TAD in placental mammals. We show that such divergent expression is not determined by a strict enhancer-promoter compatibility code, intra-TAD position or nuclear envelope-attachment. Instead, TAD-restructuring in embryonic stem cells (ESCs) separates Rex1 and Fat1 with distinct proximal enhancers that independently drive their expression. By contrast, in later embryonic tissues, DNA methylation renders the inactive Rex1 promoter profoundly unresponsive to Fat1 enhancers within the intact TAD. Combined, these features adapted an ancient regulatory landscape during evolution to support two entirely independent Rex1 and Fat1 expression programs. Thus, rather than operating only as rigid blocks of co-regulated genes, TAD-regulatory landscapes can orchestrate complex divergent expression patterns in evolution.

HIGHLIGHTSO_LINew genes can emerge in evolution without taking on the expression pattern of their surrounding pre-existing TAD.
C_LIO_LICompartmentalisation can restructure seemingly evolutionarily stable TADs to control a promoters access to enhancers.
C_LIO_LILamina-associated domains neither prevent transcriptional activation nor enhancer-promoter communication.
C_LIO_LIRepression rather than promoter-specificity refines when genes respond to promiscuous enhancer activities in specific tissues.
C_LI


title: Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives

abstract:
BackgroundAs the major source of sugar in moderate climates, sugar-producing beets (Beta vulgaris subsp. vulgaris) have a high economic value. However, the low genetic diversity within cultivated beets requires introduction of new traits, for example to increase their tolerance and resistance attributes - traits that often reside in the crop wild relatives. For this, genetic information of wild beet relatives and their phylogenetic placements to each other are crucial. To answer this need, we sequenced and assembled the complete plastome sequences from a broad species spectrum across the beet genera Beta and Patellifolia, both embedded in the Betoideae (order Caryophyllales). This pan-plastome dataset was then used to determine the wild beet phylogeny in high-resolution.

ResultsWe sequenced the plastomes of 18 closely related accessions representing 11 species of the Betoideae subfamily and provided high-quality plastome assemblies which represent an important resource for further studies of beet wild relatives and the diverse plant order Caryophyllales. Their assembly sizes range from 149,723 bp (Beta vulgaris subsp. vulgaris) to 152,816 bp (Beta nana), with most variability in the intergenic sequences. Combining plastome-derived phylogenies with read-based treatments based on mitochondrial information, we were able to suggest a unified and highly confident phylogenetic placement of the investigated Betoideae species.

Our results show that the genus Beta can be divided into the two clearly separated sections Beta and Corollinae. Our analysis confirms the affiliation of B. nana with the other Corollinae species, and we argue against a separate placement in the Nanae section. Within the Patellifolia genus, the two diploid species Patellifolia procumbens and Patellifolia webbiana are, regarding the plastome sequences, genetically more similar to each other than to the tetraploid Patellifolia patellaris. Nevertheless, all three Patellifolia species are clearly separated.

ConclusionIn conclusion, our wild beet plastome assemblies represent a new resource to understand the molecular base of the beet germplasm. Despite large differences on the phenotypic level, our pan-plastome dataset is highly conserved. For the first time in beets, our whole plastome sequences overcome the low sequence variation in individual genes and provide the molecular backbone for highly resolved beet phylogenomics. Hence, our plastome sequencing strategy can also guide genomic approaches to unravel other closely related taxa.

category: genomics


title: Electrostatic interaction of loop 1 and backbone of human cardiac myosin regulates the rate of ATP induced actomyosin dissociation

abstract:
Double mutation D208Q:K450L was introduced in the beta isoform of human cardiac myosin to remove the salt bridge D208:K450 connecting loop 1 and the seven-stranded beta sheet within the myosin head. Beta isoform-specific salt bridge D208:K450 was previously discovered in the molecular dynamics simulations. It was proposed that loop 1 modulates nucleotide affinity to actomyosin and we hypothesized that the electrostatic interactions between loop 1 and myosin head backbone regulates ATP binding to and ADP dissociation from actomyosin, and therefore, the time of the strong actomyosin binding. Wild type and the mutant of the myosin head construct (1-843 amino acid residues) were expressed in differentiated C2C12 cells, and the kinetics of ATP induced actomyosin dissociation and ADP release were characterized using transient kinetics spectrophotometry. Both constructs exhibit a fast rate of ATP binding to actomyosin and a slow rate of ADP dissociation, showing that ADP release limits the time of the strongly bound state of actomyosin. We observed a faster rate of ATP-induced actomyosin dissociation with the mutant, compared to the wild type actomyosin. The rate of ADP release from actomyosin remains the same for the mutant and the wild type actomyosin. We conclude that the flexibility of loop 1 is a factor affecting the rate of ATP binding to actomyosin and actomyosin dissociation. We observed no effect of loop 1 flexibility on the rate of ADP release from actomyosin.

HighlightsO_LIHuman cardiac myosin has the isoform-specific salt bridge, electrostatically linking loop 1 and myosin head backbone.
C_LIO_LIAbsence of loop 1 - backbone salt bridge increases rate of ATP-induced actomyosin dissociation
C_LIO_LIThe rate of ADP dissociation from actomyosin is not affected by the isoform-specific salt bridge.
C_LI

category: biochemistry


title: Molecular Dynamics Simulations of hydrophobic peptides that form β-hairpin structures in solution

abstract: Peptides designed with residues that have high propensity to occur in {beta}-turns, form {beta}-hairpin structures in apolar solvents as well in polar organic solvents such as dimethyl sulfoxide (DMSO), methanol and varying percentages of DMSO in chloroform (CHCl3). Presumably due to limited solubility, their conformations have not been investigated by experimental methods in water. We have examined the conformations of such designed peptides that fold into well-defined {beta}-hairpin structures facilitated by {beta}-turns, in the crystalline state and in solution, by Molecular Dynamics Simulations (MDS). The peptides fold into {beta}-hairpin structures in water, starting from extended conformation. In DMSO, folding into {beta}-hairpin structures was not observed, starting from extended conformation. However, when the starting structure is in {beta}-hairpin conformation, unfolding is not observed during MDS in DMSO. Water clearly favours folding of short, hydrophobic peptides into {beta}-turn and {beta}-hairpin conformations from extended structures. DMSO does not have a denaturing effect on short, hydrophobic peptides.


title: HyINDEL - A Hybrid approach for Detection of Insertions and Deletions

abstract: Insertion and deletion (INDELs) mutations, the most common type of structural variation in the human genome, have been implicated in numerous human traits and diseases including rare genetic disorders and cancer. Next generation sequencing (NGS) technologies have drastically reduced the cost of sequencing whole genomes, greatly contributing to genome-wide detection of structural variants. However, due to large variations in INDEL sizes and presence of low complexity and repeat regions, their detection remains a challenge. Here we present a hybrid approach, HyINDEL, which integrates clustering, split-mapping and assembly-based approaches, for the detection of INDELs of all sizes (from small to large) and also identifies the insertion sequences. The method starts with identifying clusters of discordant and soft-clip reads which are validated by depth-of-coverage and alignment of soft-clip reads to identify candidate INDELs, while the assembly -based approach is used in identifying the insertion sequence. Performance of HyINDEL is evaluated on both simulated and real datasets and compared with state-of-the-art tools. A significant improvement in recall and F-score metrics as well as in breakpoint support is observed on using soft-clip alignments. It is freely available at https://github.com/alok123t/HyINDEL.

category: bioinformatics


title: A sense-antisense RNA interaction promotes breast cancer metastasis via regulation of NQO1 expression

abstract: Antisense RNAs are ubiquitous in human cells, yet the role that they play in healthy and diseased states remains largely unexplored. Here, we developed a computational framework to catalog and profile antisense RNAs and applied it to poorly and highly metastatic breast cancer cell lines. We identified one antisense RNA that plays a functional role in driving breast cancer progression by upregulating the redox enzyme NQO1, and hence named NQO1-antisense RNA or NQO1-AS. This upregulation occurs via a stabilizing interaction between NQO1-AS and its complementary region in the 3UTR of NQO1 mRNA. By increasing expression of NQO1 protein, breast cancer cells are able to tolerate higher levels of oxidative stress, enabling them to colonize the lung. During this process the cancer cells become dependent on NQO1 to protect them from ferroptosis. We have shown that this dependence can be exploited therapeutically in xenograft models of metastasis. Together, our findings establish a previously unknown role for NQO1-AS in the progression of breast cancer by serving as a post-transcriptional regulator of RNA processing and decay for its sense mRNA.

category: cancer biology


title: Anti-cancer potential of cannabis terpenes in a taxol-resistant model of breast cancer

abstract: Chemotherapeutic resistance can limit breast cancer outcomes; therefore, the exploration of novel therapeutic options is warranted. Isolated compounds found in cannabis have previously been shown to exhibit anti-cancer effects, but little is known about their effects in resistant breast cancer. Our study aims to evaluate the effects of terpenes found in cannabis in in vitro chemotherapy-resistant model of breast cancer. We aimed to identify whether five terpenes found in cannabis produced anti-cancer effects, and if their effects were improved upon co-treatment with cannabinoids and flavonoids also found in cannabis. Nerolidol and {beta}-caryophyllene produced the greatest cytotoxic effects, activated the apoptotic cascade and reduced cellular invasion. Combinations with the flavonoid kaempferol potentiated the cytotoxic effects of ocimene, terpinolene, and {beta}-myrcene. Combinations of nerolidol and {Delta}9-tetrahydrocannabinol or cannabidiol produced variable responses ranging from antagonism and additivity to synergy, depending on concentrations used. Our results indicate that cannabis terpenes, alone or combined with cannabinoids and flavonoids, produced anti-cancer effects in chemotherapy-resistant breast cancer cell lines. This study is a first step in the identification of compounds that could have therapeutic potential in the treatment of resistant breast cancer.


title: Antibiotic and novel compounds manipulation in vitro collagen matrix cells changes extracellular matrix non-complete cell division of fibroblast cells as new dermology technology

abstract: Fibroblasts are several cells that are essential for human skin function and regulation process, the underfeed cells are a further issue of skin disorder the current study was based on isolated novel antibiotics compounds comparison of (Chloramphenicol IV) with the changes of Extracellular matrix (RC), inflammatory cells (SC) and non-complete cell division (ICD) effects on fibroblasts cell changes with the cell wall in structural and morphological changes. The new antibiotic compounds were measured and characters in (FTIR) methods with their functional groups analysis of bioactive compounds from Adhatoda vasica and Calotropis procera plants and their effective inhibition concentrations (I C50) extracts against tyrosinase conditions with their activity in vitro enzymatic process, both extracts have higher enzymatic inhibition assay was assessed. The fibroblast cells were compared with Chloramphenicol IV antibiotics with extracted compounds the cell wall was indiscretion and complete shape and structural changes were measured. The higher values of Diphenolase (22.5 g/mL) was noted in Adhatoda vasica while an IC50 value of Monophenolase was 19.16 g/mL, which is helpful in the treatment of fibroblast cell disorders, were higher in collagenase inhibition assay, elastase inhibition assay, hyaluronidase inhibition assay, tyrosinase inhibition assay process. It was concluded that novel antibiotics compounds from species could act an as effective role in fibroblast were used in future medicines as sources of locations and creams to control various skin diseases and skin disorder managements processes.

category: pharmacology and toxicology


title: Drought stress delays photosynthetic induction and accelerates photoinhibition of photosystem I under fluctuating light

abstract: Fluctuating light (FL) and drought stress usually occur concomitantly. However, whether drought stress affects photosynthetic performance under FL remains unknown. Here, we measured gas exchange, chlorophyll fluorescence, and P700 redox state under FL in drought-stressed tomato (Solanum lycopersicum) seedlings. Drought stress significantly affected stomatal opening and mesophyll conductance after transition from low to high light and thus delayed photosynthetic induction under FL. Therefore, drought stress exacerbated the loss of carbon gain under FL. Furthermore, restriction of CO2 fixation under drought stress aggravated the over-reduction of photosystem I (PSI) upon transition from low to high light. The resulting stronger FL-induced PSI photoinhibition significantly supressed linear electron flow and PSI photoprotection. These results indicated that drought stress not only affected gas exchange under FL but also accelerated FL-induced photoinhibition of PSI. Furthermore, drought stress enhanced relative cyclic electron flow in FL, which partially compensated for restricted CO2 fixation and thus favored PSI photoprotection under FL. Therefore, drought stress has large effects on photosynthetic dark and light reactions under FL.

category: plant biology


title: Progressive chromatin silencing of ABA biosynthesis gene permits seed germination in Arabidopsis

abstract: Seed germination represents a major developmental switch in plants that is vital to agricultural, but how this process is controlled at the chromatin level remains obscure. Here we demonstrate that successful germination in Arabidopsis requires a chromatin mechanism that progressively silences NCED6, which encodes a rate-limiting enzyme for abscisic acid (ABA) biosynthesis, through the cooperative action of the RNA-binding protein RZ-1 and the polycomb repressive complex 2 (PRC2). Simultaneous inactivation of RZ-1 and PRC2 blocks germination and synergistically derepresses NCEDs and hundreds of genes. At NCED6, by promoting H3 deacetylation and suppressing H3K4me3, RZ-1 facilitates transcriptional silencing and also a H3K27me3 accumulation process that occurs during seed germination and early seedling growth. Genome-wide analysis reveals RZ-1 is preferentially required for transcriptional silencing of many PRC2 targets early during seed germination when H3K27me3 is not yet established. We propose RZ-1 confers a novel silencing mechanism to compensate and coordinate with PRC2. Our work highlights the progressive chromatin silencing of ABA biosynthesis genes via synergized action of the RNA-binding protein RZ1 and PRC2, which is vital for seed germination.


title: Metabolomic and transcriptomic analyses reveal the effects of grafting on anthocyanin synthesis in grapevine

abstract: The grafting has been commonly used in viticulture, which joints the scion from a cultivar with the stem of a rootstock. Grafting has crucial impacts on various phenotypes of the cultivar including berry metabolome and berry coloring, however, the genetics and regulation mechanisms are largely unexplored. In this study, we analyzed the phenotypic, metabolomic and transcriptomic profiles at three stages (45, 75 and105 days after flowering) of the Crimson Seedless (Vitis vinifera, CS) cultivar grafted to four rootstocks (three heterografting: CS/101-14MG, CS/SO4, CS/110R and one self-grafting CS/CS) with an own-rooted grafting-free Crimson Seedless (CS) as a control. All the heterografting plants had a significant influence on berry reddening as early as ~45 days after flowering. The grafting of rootstocks promoted anthocyanin synthesis and accumulation in grape berries. The metabolomic features showed that Cyanidin 3-O-glucoside, Delphinidin 3-O-glucosid, Malvidin 3-O-glucoside, Peonidin 3-O-glucoside and Petunidin 3-O-glucoside were the pigments responsible for the purplish-red color peels. Transcriptomic analyses revealed that the anthocyanins biosynthetic related genes from the upstream (phenylalanine ammonia-lyase) to the downstream (anthocyanidin 3-O-glucosyltransferase and anthocyanidin synthase) were upregulated with the accumulations of anthocyanins in CS/101-14MG, CS/SO4 and CS/110R. At the same time, all these genes were also highly expressed and more anthocyanin was accumulated in CS/CS samples compared to CS samples, suggesting that self-grafting rootstocks might also have promoted berry reddening in grapevine. Our results provide global transcriptomic and metabolomic features in berry coloring regulation under different grafting conditions for improving the berry quality in grapevine production.


title: Chloroplast movement and positioning protein CHUP1 is required for focal immunity against Phytophthora infestans

abstract: When a plant detects a pathogen, chloroplasts terminate photosynthetic activity and uptake vital roles in the immune system to help stave off infection, including the production of defense hormone precursors and antimicrobial reactive oxygen species. Additionally, chloroplasts associate with the nucleus and produce greater numbers of tubular extensions called stromules during immune challenge. We previously showed that during infection by the potato blight pathogen Phytophthora infestans, chloroplasts accumulate at the pathogen haustoria, hyphal extensions that are accommodated within the host cell. However, the extent to which chloroplast positioning around haustoria, or at the nucleus, contributes to immunity during infection remains unknown. Here we show a striking increase in the susceptibility to P. infestans of Nicotiana benthamiana CRISPR knock-out lines lacking the chloroplast movement and anchoring gene, CHLOROPLAST UNUSUAL POSITIONING 1 (CHUP1). However, the positioning of chloroplasts around the haustorium or nucleus is not impaired in the absence of CHUP1. Further, loss of CHUP1 leads to an extreme clustering of chloroplasts around the nucleus in the presence and absence of infection, showing that greater chloroplast-nucleus association does not necessarily equate to more robust immunity. While plants lacking CHUP1 have reduced basal stromules, they are still able to induce stromules following immune stimulation, indicating that multiple populations of stromules exist. Lastly, we found that CHUP1 is required for proper deposition of callose - a cell wall material implicated in pathogen penetration resistance - around P. infestans haustorium, but not for other core immune processes. Our results implicate chloroplasts in plant focal immunity and point to a key role of CHUP1 in facilitating the deposition of defense material at the pathogen interface.


title: An intein-mediated split-nCas9 system for base editing in plants

abstract: Virus-assisted delivery of the clustered regularly interspaced short palindromic (CRISPR)/CRISPR-associated (Cas) system represents a promising approach for editing plant genomes. However, the relatively large size of the CRISPR/Cas9 system is challenging to package into viral vectors with confined packaging capacity. To address this technical challenge, we developed a strategy that splits the required CRISPR-Cas9 components across a dual-vector system in which CRISPR-Cas reassembles into an active form following co-infection to achieve targeted genome editing in plant cells. An intein-mediated split system was adapted and optimized in plant cells by successfully demonstrating split-eYGFPuv expression. Using a plant-based biosensor, we demonstrated for the first time that the split-SpnCas9 is capable of inducing efficient base editing in plant cells and identified several valid split sites for future biodesign strategies. Overall, this strategy provides new opportunities to bridge different CRISPR/Cas9 tools including base editor, prime editor, and CRISPR activation with virus-mediated gene editing.