title: Kinesin-6 Klp9 orchestrates spindle elongation by regulating microtubule sliding and growth

abstract: Mitotic spindle function depends on the precise regulation of microtubule dynamics and microtubule sliding. Throughout mitosis, both processes have to be orchestrated to establish and maintain spindle stability. We show that during anaphase B spindle elongation in S. pombe, the sliding motor Klp9 (kinesin-6) also promotes microtubule growth in vivo. In vitro, Klp9 can enhance and dampen microtubule growth, depending on the tubulin concentration. This indicates that the motor is able to promote and block tubulin subunit incorporation into the microtubule lattice in order to set a well-defined microtubule growth velocity. Moreover, Klp9 recruitment to spindle microtubules is dependent on its dephosphorylation mediated by XMAP215/Dis1, a microtubule polymerase, to link the regulation of spindle length and spindle elongation velocity. Collectively, we unravel the mechanism of anaphase B, from Klp9 recruitment to the motors dual-function in regulating microtubule sliding and microtubule growth, allowing an inherent coordination of both processes.


title: Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data

abstract: The creation of scalable single-cell and highly-multiplexed imaging technologies that profile the protein expression and phosphorylation status of heterogeneous cellular populations has led to multiple insights into disease processes including cancer initiation and progression. A major analytical challenge in interpreting the resulting data is the assignment of cells to a priori known cell types in a robust and interpretable manner. Existing approaches typically solve this by clustering cells followed by manual annotation of individual clusters or by strategies that gate protein expression at predefined thresholds. However, these often require several subjective analysis choices such as selecting the number of clusters and do not automatically assign cell types in line with prior biological knowledge. They further lack the ability to explicitly assign cells to an unknown or uncharacterized type, which exist in most highly multiplexed imaging experiments due to the limited number of markers quantified. To address these issues we present Astir, a probabilistic model to assign cells to cell types by integrating prior knowledge of marker proteins. Astir uses deep recognition neural networks for fast Bayesian inference, allowing for cell type annotations at the million-cell scale and in the absence of previously annotated reference data across multiple experimental modalities and antibody panels. We demonstrate that Astir outperforms existing approaches in terms of accuracy and robustness by applying it to over 2.1 million single cells from several suspension and imaging mass cytometry and microscopy datasets in multiple tissue contexts. We further showcase that Astir can be used for the fast analysis of the spatial architecture of the tumour microenvironment, automatically quantifying the immune influx and spatial heterogeneity of patient samples. Astir is freely available as an open source Python package at https://www.github.com/camlab-bioml/astir.

category: bioinformatics


title: On the sensitivity analysis of porous finite element models for cerebral perfusion estimation

abstract:
Computational physiological models are promising tools to enhance the design of clinical trials and to assist in decision making. Organ-scale haemodynamic models are gaining popularity to evaluate perfusion in a virtual environment both in healthy and diseased patients. Recently, the principles of verification, validation, and uncertainty quantification of such physiological models have been laid down to ensure safe applications of engineering software in the medical device industry. The present study sets out to establish guidelines for the usage of a three-dimensional steady state porous cerebral perfusion model of the human brain following principles detailed in the verification and validation (V&V 40) standard of the American Society of Mechanical Engineers. The model relies on the finite element method and has been developed specifically to estimate how brain perfusion is altered in ischaemic stroke patients before, during, and after treatments. Simulations are compared with exact analytical solutions and a thorough sensitivity analysis is presented covering every numerical and physiological model parameter.

The results suggest that such porous models can approximate blood pressure and perfusion distributions reliably even on a coarse grid with first order elements. On the other hand, higher order elements are essential to mitigate errors in volumetric blood flow rate estimation through cortical surface regions. Matching the volumetric flow rate corresponding to major cerebral arteries is identified as a validation milestone. It is found that inlet velocity boundary conditions are hard to obtain and that constant pressure inlet boundary conditions are feasible alternatives. A one-dimensional model is presented which can serve as a computationally inexpensive replacement of the three-dimensional brain model to ease parameter optimisation, sensitivity analyses and uncertainty quantification.

The findings of the present study can be generalised to organ-scale porous perfusion models. The results increase the applicability of computational tools regarding treatment development for stroke and other cerebrovascular conditions.

category: biophysics


title: Twitches emerge postnatally during quiet sleep in human infants and are synchronized with sleep spindles

abstract: SO_SCPLOWUMMARYC_SCPLOWIn humans and other mammals, the stillness of sleep is punctuated by bursts of rapid eye movements (REMs) and myoclonic twitches of the limbs [1]. Contrary to the notion that twitches are mere by-products of dreams, sensory feedback arising from twitching limbs provides a rich and unique source of activation to the developing sensorimotor system [2]. In fact, it is partly because of the behavioral activation of REM sleep that this state is also called active sleep (AS), in contrast with the behavioral quiescence that gives quiet sleep (QS)--the second major stage of sleep--its name. In human infants, for which AS occupies eight or more hours of each day [3], limb twitching is one among several components that help to identify the state [4-7]; nonetheless, we know relatively little about the structure and functions of twitching across development. Recently, in sleeping infants over the first seven postnatal months [8], we documented a pronounced shift in the temporal expression of twitching beginning around three months of age that suggested a qualitative shift in how twitches are produced. Here, we combine behavioral assessments of twitching with high-density electroencephalography (EEG) and demonstrate that this shift reflects the developmental emergence of limb twitches during QS. Twitches during QS are not only unaccompanied by REMs, but they also occur synchronously with sleep spindles, a hallmark of QS. As QS-related twitching increases with age, sleep spindle rate also increases along the sensorimotor strip. The emerging synchrony between subcortically generated twitches and cortical oscillations suggests the development of functional connectivity among distant sensorimotor structures, with potential implications for detecting and explaining atypical developmental trajectories.

category: neuroscience


title: Reduced inhibition in depression impairs stimulus processing in human cortical microcircuits

abstract: Cortical processing depends on finely-tuned excitatory and inhibitory connections in neuronal microcircuits. Reduced inhibition by somatostatin-expressing interneurons is a key component of altered inhibition associated with treatment-resistant major depressive disorder (depression), which is implicated in cognitive deficits and rumination, but the link remains to be better established mechanistically in humans. Here, we tested the impact of reduced somatostatin interneuron mediated inhibition on cortical processing in human neuronal microcircuits using a data-driven computational approach. We integrated human cellular, circuit and gene-expression data to generate detailed models of human cortical microcircuits in health and depression. We simulated microcircuit baseline and response activity and found reduced signal-to-noise ratio and increased false/failed detection of stimuli due to a higher baseline activity in depression. Our results thus applied novel models of human cortical microcircuits to demonstrate mechanistically how reduced inhibition impairs cortical processing in depression, providing quantitative links between altered inhibition and cognitive deficits.


title: Selective auditory attention detection using dynamic learning systems: The study of RNN and reinforcement learning

abstract: The cocktail party phenomenon describes the ability of the human brain to focus auditory attention on a particular stimulus while ignoring other acoustic events. Selective auditory attention detection (SAAD) is an important issue in the development of brain-computer interface systems and cocktail party processors. This paper proposes a new dynamic attention detection system to process the temporal evolution of the input signal. The proposed dynamic SAAD is modeled as a sequential decision-making problem, which is solved by recurrent neural network (RNN) and reinforcement learning methods of Q-learning and deep Q-learning. Among different dynamic learning approaches, the evaluation results show that the deep Q-learning approach with RNN as agent provides the highest classification accuracy (94.2%) with the least detection delay. The proposed SAAD system is advantageous, in the sense that the detection of attention is performed dynamically for the sequential inputs. Also, the system has the potential to be used in scenarios, where the attention of the listener might be switched in time in the presence of various acoustic events.


title: Dynamic selective auditory attention detection using RNN and reinforcement learning


title: Perceptual restoration fails to recover unconscious processing for smooth eye movements after occipital stroke

abstract: The visual pathways that guide actions do not necessarily mediate conscious perception. Patients with primary visual cortex (V1) damage lose conscious perception but often retain unconscious abilities (e.g. blindsight). Here, we asked if saccade accuracy and post-saccadic following responses (PFRs) that automatically track target motion upon saccade landing are retained when conscious perception is lost. We contrasted these behaviors in the blind and intact-fields of 11 chronic V1-stroke patients, and in 8 visually-intact controls. Saccade accuracy was relatively normal in all cases. Stroke patients also had normal PFR in their intact-fields, but no PFR in their blind-fields. Thus, V1 damage did not spare the unconscious visual processing necessary for automatic, post-saccadic smooth eye movements. Importantly, visual training that recovered motion perception in the blind-field did not restore the PFR, suggesting a clear dissociation between pathways mediating perceptual restoration and automatic actions in the V1-damaged visual system.


title: Altered cortical phase- and amplitude-coupling in Multiple Sclerosis

abstract: Multiple Sclerosis is a demyelinating disease of the central nervous system that can result in cognitive decline and physical disability. However, related functional changes in large-scale brain interactions remain poorly understood and corresponding non-invasive biomarkers are sparse. Here, we measured magnetoencephalography in 17 relapsing-remitting Multiple Sclerosis patients at an early disease stage (median EDSS = 1.5, range 0 to 3.5) and 17 healthy controls to investigate brain-wide phase- and amplitude-coupling of frequency specific neuronal activity. We developed a new analysis approach that combines dimensionality reduction, bootstrap aggregating and multivariate classification to identify changes of brain-wide coupling in Multiple Sclerosis. We identified systematic and non-redundant changes of both phase- and amplitude-coupling. Changes included both, increased and decreased neuronal coupling in wide-spread, bilateral neuronal networks across a broad range of frequencies. These changes allowed to successfully classify patients and controls with an accuracy of 84%. Furthermore, classification confidence predicted behavioral scores of disease severity. Our results unravel systematic changes of large-scale neuronal coupling in Multiple Sclerosis and suggest non-invasive electrophysiological coupling measures as powerful biomarkers of Multiple Sclerosis.


title: Targeted Memory Reactivation of Face-Name LearningDepends on Ample and Undisturbed Slow-Wave Sleep

abstract: Face memory, including the ability to recall the name of a familiar person, is often crucial in social interactions, and like many other memory functions, it may rely on sleep. We investigated whether targeted memory reactivation during sleep could improve associative and perceptual aspects of face memory. Participants studied 80 face-name pairs, and then a subset of spoken names was presented unobtrusively during a daytime nap. This reactivation preferentially improved recall for those face-name pairs, as modulated by two factors related to sleep quality. That is, the memory benefit was positively correlated with the duration of stage N3 sleep (slow-wave sleep) and with the extent to which cues presented during SWS did not produce a sleep disruption indexed by increased alpha-band electroencephalographic activity in the 5 seconds after a cue. Follow-up analyses showed that a memory benefit from presenting spoken names during sleep was evident in participants with high amounts of SWS or with low amounts of sleep disruption. We conclude that sleep reactivation can strengthen memory for specific face-name associations and that the effectiveness of reactivation depends on uninterrupted N3 sleep.


title: Harmonised segmentation of neonatal brain MRI

abstract: Deep learning based medical image segmentation has shown great potential in becoming a key part of the clinical analysis pipeline. However, many of these models rely on the assumption that the train and test data come from the same distribution. This means that such methods cannot guarantee high quality predictions when the source and target domains are dissimilar due to different acquisition protocols, or biases in patient cohorts. Recently, unsupervised domain adaptation (DA) techniques have shown great potential in alleviating this problem by minimizing the shift between the source and target distributions, without requiring the use of labelled data in the target domain. In this work, we aim to predict tissue segmentation maps on T2-weighted (T2w) magnetic resonance imaging (MRI) data of an unseen preterm-born neonatal population, which has both different acquisition parameters and population bias when compared to our training data. We achieve this by investigating two unsupervised DA techniques with the objective of finding the best solution for our problem. We compare the two methods with a baseline fully-supervised segmentation network and report our results in terms of Dice scores obtained on our ground truth test dataset. Moreover, we analyse tissue volumes and cortical thickness (CT) measures of the harmonised data on a subset of the population matched for gestational age (GA) at birth and postmenstrual age (PMA) at scan. Finally, we demonstrate the applicability of the harmonised cortical gray matter maps with an analysis comparing term and preterm-born neonates and a proof-of-principle investigation of the association between CT and a language outcome measure.


title: Broadly Reactive H2 Hemagglutinin Vaccines Elicit Cross-Reactive Antibodies in Ferrets Pre-Immune to Seasonal Influenza A Viruses

abstract:
Influenza vaccines have traditionally been tested in naive mice and ferrets. However, humans are first exposed to influenza viruses within the first few years of their lives. Therefore, there is a pressing need to test influenza virus vaccines in animal models that have been previously exposed to influenza viruses before being vaccinated. In this manuscript, previously described H2 computationally optimized broadly reactive antigen (COBRA) HA vaccines (Z1, Z5) were tested in influenza virus  pre-immune ferret models. Ferrets were infected with historical, seasonal influenza viruses to establish pre-immunity. These pre-immune ferrets were then vaccinated with either COBRA H2 HA recombinant proteins or WT H2 HA recombinant proteins in a prime-boost regimen. A set of naive pre-immune or non pre-immune ferrets were also vaccinated to control of the effects of the multiple different pre-immunities. All of the ferrets were then challenged with a swine H2N3 influenza virus. Ferrets with pre-existing immune responses influenced recombinant H2 HA elicited antibodies following vaccination as measured by HAI and classical neutralization assays. Having both H3N2 and H1N1 immunological memory regardless of the order of exposure significantly decreased viral nasal wash titers and completely protected all ferrets from both morbidity and mortality, including the mock vaccinated ferrets in the group. While the vast majority of the pre-immune ferrets were protected from both morbidity and mortality across all of the different pre-immunities, the Z1 COBRA HA vaccinated ferrets had significantly higher antibody titers and recognized the highest number H2 influenza viruses in a classical neutralization assay compared to the other H2 HA vaccines.

ImportanceH1N1 and H3N2 influenza viruses have co-circulated in the human population since 1977. Nearly every human alive today has antibodies and memory B and T cells against these two subtypes of influenza viruses. H2N2 influenza viruses caused the 1957 global pandemic and people born after 1968 have never been exposed to H2 influenza viruses. It is quite likely that a future H2 influenza virus could transmit within the human population and start a new global pandemic, since the majority of people alive today are immunologically naive to viruses of this subtype. Therefore, an effective vaccine for H2 influenza viruses should be tested in an animal model with previous exposure to influenza viruses that have circulated in humans. Ferrets were infected with historical influenza A viruses to more accurately mimic the immune responses in people who have pre-existing immune responses to seasonal influenza viruses. In this study, pre-immune ferrets were vaccinated with WT and COBRA H2 recombinant HA proteins in order to examine the effects of pre-existing immunity to seasonal human influenza viruses have on the elicitation of broadly cross-reactive antibodies from heterologous vaccination.

category: immunology


title: Accelerated vaccine induction of IgM neutralising antibody enables same day vaccine protection against a lethal influenza virus challenge

abstract:
Novel influenza strains to which humans have no pre-existing immunity can trigger global pandemics without warning. Current pandemic vaccines typically require two doses and up to 6 weeks to induce protective immunity. In addition, to their role in increasing vaccine-induced immune response, adjuvants may also play a part in reducing the time between immunization and vaccine protection, although this role has seldom been previously explored in literature. This study assessed the speed of protection achievable with a standard inactivated influenza vaccine when formulated with or without a novel delta-inulin adjuvant (Advax). When formulated with Advax adjuvant mice were protected even when the vaccine was administered intramuscularly contemporaneously with a lethal intranasal virus challenge. The protection was found to be B-cell dependent and transfer of day 6 immune serum from mice immunised with Advax-adjuvanted influenza vaccine conferred protection to naive animals. This protection was shown to be mediated by vaccine induced IgM rather than IgG neutralising antibodies. The results show that influenza vaccine can be formulated to provide immediate protection following immunization with this novel concept warranting testing in human trials.

IMPORTANCEIn the past 100 years there have been several major influenza pandemics that resulted in significant loss of life. The time taken for individuals to develop vaccine protection is an important factor in curbing the spread of infection and reducing pandemic mortality rates. Current influenza vaccines can take up to 5-6 weeks to generate full protection leaving front-line heath care workers and others, at risk for an extended period of time. Our novel accelerated vaccine protection approach provides effectively immediate vaccine protection against lethal virus challenge. This would assist front-line workers to continue to provide essential services and maintain critical infrastructure during pandemic. The study also highlights the often-overlooked role that antigen-specific IgM plays in virus protection and provides a novel adjuvanted strategy for enlisting IgM to provide accelerated vaccine protection.

category: microbiology


title: Modeling land use impacts on spatial distribution of floating plastic litter in surface water of Southeast Asian archipelago

abstract: Plastics are present in many ecosystems including floating in surface water of remote archipelago and this can lead to the increase in plastic litter density. Whereas the spatial model of plastic litter density related to the population inhabits isolated archipelago is still limited. And what are the underlying factors driving the presence of plastic litter is also poorly understood. This study is trying to find the answers of those questions. The study was implemented in Thousand Island archipelago located in North of Java Island, one of populated islands in Southeast Asia. The studied surface water covers an area of 10000 Ha and consists of 10 islands with 3 islands are occupied by settlements and the remaining islands are occupied by vegetation. This study has recorded 3 types of floating macro-litter from water that consist of PET, HDPE, and LDPE litter. The plastic litter was observed concentrated in the east sides of archipelago where the populated islands were located. The spatial models show LDPE litter was distributed in the vast areas in comparison to PET and HDPE litter. Beside land use variables, the model has confirmed that the population density was the main underlying factors contribute to the plastic litter density in Thousand Island archipelago. The model can be applied to estimate PET (AIC = -0.53060) and HDPE (AIC = 18.28828) litter density. While LDPE litter density was influenced by population (AIC = 22.60201) rather than population density factors.

category: ecology


title: Genome-wide insights into population structure and host specificity of Campylobacter jejuni

abstract:
The zoonotic pathogen Campylobacter jejuni is among the leading causes of foodborne diseases worldwide. While C. jejuni colonises many wild animals and livestock, persistence mechanisms enabling the bacterium to adapt to host species guts are not fully understood. In order to identify putative determinants influencing host preferences of distinct lineages, bootstrapping based on stratified random sampling combined with a k-mer-based genome-wide association was conducted on 490 genomes from diverse origins in Germany and Canada.

We show a strong association of both the core and the accessory genome characteristics with distinct host animal species, indicating multiple adaptive trajectories defining the evolution of C. jejuni lifestyle preferences in different ecosystems. Here, we demonstrate that adaptation towards a specific host niche ecology is most likely a long evolutionary and multifactorial process, expressed by gene absence or presence and allele variations of core genes. Several host-specific allelic variants from different phylogenetic backgrounds, including dnaE, rpoB, ftsX or pycB play important roles for genome maintenance and metabolic pathways. Thus, variants of genes important for C. jejuni to cope with specific ecological niches or hosts may be useful markers for both surveillance and future pathogen intervention strategies.

category: genomics


title: Sharing happy stories increases interpersonal closeness mediated by enhancing interpersonal brain synchronization

abstract:
Our lives revolve around sharing stories with others. Expressing emotion (i.e., happy and sad) is an essential characteristic of sharing stories and could enhance the similarity of story comprehension across speaker-listener pairs. The Emotions as Social Information Model (EASI) suggests that emotional communication may influence interpersonal closeness, but the effect of sharing emotional (happy/sad) stories on interpersonal closeness remains poorly understood. Here, one speaker watched emotional videos and communicated the content of the videos to thirty-two listeners (happy/sad/neutral group). Both speaker and listeners neural activities were recorded using EEG. After listening, we assessed the interpersonal closeness between the speaker and listeners. Compared to the sad group, sharing happy stories showed a better recall quality and a higher rating of interpersonal closeness.

Meanwhile, the happy group showed higher interpersonal brain synchronization (IBS) in the prefrontal cortex (PFC) and temporal cortex (specifically TPJ) than the sad group. Moreover, such IBS mediated the relationship between the quality of sharing stories and interpersonal closeness, and happy emotion moderated this mediation model. The magnitude of IBS differentiated high interpersonal closeness from low interpersonal closeness. Exploratory analysis using support vector regression showed that the IBS could also predict the ratings of interpersonal closeness in left-out subjects. These results suggest that IBS could serve as an indicator of whether sharing emotional stories facilitate interpersonal closeness. These findings improve our understanding of sharing emotional information among individuals that guide behaviors during interpersonal interactions.


title: The P3b differentiates parallel physical and rule-based updating of a sensory model

abstract: The capacity to form and update mental representations of the type and timing of sensory events is a central tenet of adaptive behavior in a dynamically changing environment. An internal model of stimulus contingencies provides a means to optimize behavior through predictive adjustments based on past to future events. To this end, neural and cognitive processes rely on systematic relations between events and use these rules to optimize information processing. The P3 complex of the event-related potential of the electroencephalogram (ERP/EEG) is a well-established and extensively tested index of such mechanisms. Here we investigated the P3b sensitivity to auditory stimulus deviations associated with two updating operations: physical change (switching stimulus pitches) and rule change (switching additive and subtractive target stimulus counting). Participants listened to a variant of the classical oddball sequence consisting of frequent standard (600 Hz) and two equally probable less frequent deviant tones (660 Hz, 540 Hz), keeping count of the deviant tones and switching between addition and subtraction with a pitch change. The results indicate specific amplitude modulations, confirming the P3b as a context-sensitive marker of physical and cognitive components of an internal model. This suggests that the P3b can be used as a differential marker of predictive coding mechanisms.


title: Feature-based attention induces surround suppression during the perception of visual motion

abstract: Feature-based attention prioritizes the processing of the attended feature while strongly suppressing the processing of nearby ones. This creates a non-linearity or attentional suppressive surround predicted by the Selective Tuning model of visual attention. However, previously reported effects of feature-based attention on neuronal responses are linear, e.g., feature-similarity gain. Here, we investigated this apparent contradiction by neurophysiological and psychophysical approaches. Responses of motion direction-selective neurons in area MT/MST of monkeys were recorded during a motion task. When attention was allocated to a stimulus moving in the neurons preferred direction response tuning curves showed its minimum for directions 60-90 degrees away from the preferred direction, an attentional suppressive surround. This effect was modeled via the interaction of two Gaussian fields representing excitatory narrowly-tuned and inhibitory widely-tuned inputs into a neuron, with feature-based attention predominantly increasing the gain of inhibitory inputs. We further showed using a motion repulsion paradigm in humans that feature-based attention produces a similar non-linearity on motion discrimination performance. Our results link the gain modulation of neuronal inputs and tuning curves examined through the feature-similarity gain lens to the attentional impact on neural population responses predicted by the Selective Tuning model, providing a unified framework for the documented effects of feature-based attention on neuronal responses and behavior.


title: Feature-based attention induces non-linearities in neuronal tuning and behavior during visual motion perception


title: A D-2-hydroxyglutarate biosensor based on specific transcriptional regulator DhdR

abstract: D-2-Hydroxyglutarate (D-2-HG) is a metabolite in many physiological metabolic processes. When D-2-HG is aberrantly accumulated due to mutations in isocitrate dehydrogenases or D-2-HG dehydrogenase, it functions in a pro-oncogenic manner and is thus considered a therapeutic target and biomarker in many cancers. In this study, DhdR from Achromobacter denitrificans NBRC 15125 was identified as an allosteric transcription factor that negatively regulates D-2-HG dehydrogenase expression and responds to presence of D-2-HG. It is the first known transcription regulator specifically responding to D-2-HG across all domains of life. Based on the allosteric effect of DhdR, a D-2-HG biosensor was developed by combining DhdR with amplified luminescent proximity homogeneous assay technology. The biosensor was able to detect D-2-HG in serum, urine, and cell culture with high specificity and sensitivity. Additionally, this biosensor was also successfully used to identify the role of D-2-HG metabolism in lipopolysaccharide biosynthesis of Pseudomonas aeruginosa, demonstrating its broad usages.


title: Aspergillus fumigatus In-Host HOG pathway mutation for Cystic Fibrosis Lung Microenvironment Persistence

abstract:
The prevalence of Aspergillus fumigatus colonization in individuals with Cystic Fibrosis (CF) and subsequent fungal persistence in the lung is increasingly recognized. However, there is no consensus for clinical management of A. fumigatus in CF individuals, due largely to uncertainty surrounding A. fumigatus CF pathogenesis and virulence mechanisms. To address this gap in knowledge, a longitudinal series of A. fumigatus isolates from an individual with CF were collected over 4.5 years. Isolate genotypes were defined with whole genome sequencing that revealed both transitory and persistent A. fumigatus in the lung. Persistent lineage isolates grew most readily in a low oxygen culture environment and conidia were more sensitive to oxidative stress inducing conditions compared to non-persistent isolates. Closely related persistent isolates harbor a unique allele of the high osmolarity glycerol (HOG) pathway mitogen activated protein kinase kinase, Pbs2 (pbs2C2). Data suggest this novel pbs2C2 allele arose in vivo and is necessary for the fungal response to osmotic stress in a low oxygen environment through hyperactivation of the HOG (SakA) signaling pathway. Hyperactivation of the HOG pathway through pbs2C2 comes at the cost of decreased conidia stress resistance in the presence of atmospheric oxygen levels. These novel findings shed light on pathoadaptive mechanisms of A. fumigatus in CF, lay the foundation for identifying persistent A. fumigatus isolates that may require antifungal therapy, and highlight considerations for successful culture of persistent fungal CF isolates.

ImportanceAspergillus fumigatus infection causes a spectrum of clinical manifestations. For individuals with Cystic Fibrosis (CF), Allergic Bronchopulmonary Aspergillosis (ABPA) is an established complication, but there is a growing appreciation for A. fumigatus airway persistence in CF disease progression. There currently is little consensus for clinical management of A. fumigatus long-term culture positivity in CF. A better understanding of A. fumigatus pathogenesis mechanisms in CF is expected to yield insights into when antifungal therapies are warranted. Here, a 4.5-year longitudinal collection of A. fumigatus isolates identified a persistent lineage that harbors a unique allele of the Pbs2 MAPKK necessary for unique CF-relevant stress phenotypes. Importantly for A. fumigatus CF patient diagnostics, this allele provides increased CF lung fitness at a cost of reduced in vitro growth in standard laboratory conditions. These data illustrate a molecular mechanism for A. fumigatus CF lung persistence with implications for diagnostics and antifungal therapy.


title: Fluorescence Imaging-Based Discovery of Membrane Domain-Associated Proteins in Mycobacterium smegmatis

abstract:
Mycobacteria spatially organize their plasma membrane, and many enzymes involved in envelope biosynthesis associate with a membrane compartment termed the intracellular membrane domain (IMD). The IMD is concentrated in the polar regions of growing cells and becomes less polarized under non-growing conditions. Because mycobacteria elongate from the poles, the observed polar localization of the IMD during growth likely supports the localized envelope biosynthesis. While we have identified more than 300 IMD-associated proteins by proteomic analyses, only a handful of these have been verified by other experimental methods. Furthermore, we speculate that some IMD-associated proteins may have escaped proteomic identification and remain to be identified. Here, we visually screened an arrayed library of 523 Mycobacterium smegmatis strains each expressing a Dendra2-FLAG-tagged recombinant protein. We identified 29 fusion proteins that showed fluorescence patterns similar to those of IMD proteins and, consistent with this co-localization, we had previously identified 20 of these using a proteomics approach. Of the nine remaining IMD candidate proteins, three were confirmed to be associated with the IMD while some others appear to be lipid droplet-associated. Taken together, our newly devised strategy is effective in verifying the IMD association of proteins found by proteomic analyses, while facilitating the discovery of additional IMD-associated proteins.

ImportanceThe intracellular membrane domain (IMD) is a membrane subcompartment found in Mycobacterium smegmatis cells. Proteomic analysis of purified IMD identified more than 300 proteins, including enzymes involved in cell envelope biosynthesis, that likely contribute to the function of the IMD. How can we find more IMD-associated proteins that escaped proteomic detection? Here, as an alternative approach, fluorescence microscope images of 523 proteins were screened to identify IMD-associated proteins. We confirmed the IMD association of previously identified proteins and discovered three additional proteins associated with the IMD. Together, subcellular fractionation, proteomics, and fluorescence microscopy form a robust combination to more rigorously define IMD proteins, which will aid future investigations to decipher the synthesis, maintenance and functions of this membrane domain.


title: Competence-associated peptide BriC alters fatty acid biosynthesis in Streptococcus pneumoniae

abstract:
Membrane lipid homeostasis is required for bacteria to survive in a spectrum of host environments. This homeostasis is achieved by regulation of fatty acid chain length and of the ratio of saturated to unsaturated fatty acids. In the pathogen Streptococcus pneumoniae, fatty acid biosynthesis is encoded by a cluster of fatty acid biosynthesis (fab) genes (FASII locus) whose expression is controlled by the FabT repressor. Encoded immediately downstream of the FASII locus is BriC, a competence-induced, cell-cell communication peptide that promotes biofilm development as well as nasopharyngeal colonization in a murine model of pneumococcal carriage. Here, we demonstrate that briC is co-transcribed with genes of the fab gene cluster and that a reduction of briC levels, caused by decoupling its transcription from fab gene cluster, negatively impacts biofilm development. BriC elevates fabT transcription, which is predicted to alter the balance of saturated and unsaturated fatty acids produced by the pathway. We find that briC inactivation results in a decreased production of unsaturated fatty acids that impact the membrane properties by decreasing the abundance of di-unsaturated phosphatidylglycerol molecular species. We propose that the link between BriC, FabT and phospholipid composition contributes to the ability of S. pneumoniae to alter membrane homeostasis in response to the production of a quorum-sensing peptide.

IMPORTANCEAdaptation of bacteria to their host environment is a key component of colonization and pathogenesis. As an essential component of bacterial membranes, fatty acid composition contributes to host adaptation. Similarly, so does cell-cell communication, which serves as a mechanism for population levels responses. While much is known about the pathways that control the biosynthesis of fatty acids, many questions remain regarding regulation of these pathways and consequently the factors that impacts the balance between saturated and unsaturated fatty acids. We find that BriC, a cell-cell communication peptide implicated in biofilm regulation and colonization, is both influenced by a fatty acid biosynthesis pathway and impacts this same pathway. This study identified a link between cell-cell communication, fatty acid composition, and biofilms and, in doing so, suggests that these pathways are integrated into the networks that control pneumococcal colonization and host adaptation.


title: Dynamics and nanoscale organization of the postsynaptic endocytic zone at excitatory synapses

abstract: At postsynaptic sites of neurons, a prominent clathrin-coated structure, the endocytic zone (EZ), controls the trafficking of glutamate receptors and is essential for synaptic plasticity. Despite its importance, little is known about how this clathrin structure is organized to mediate endocytosis. We used live-cell and super-resolution microscopy techniques to reveal the dynamic organization of this poorly understood clathrin structure. We found that a subset of endocytic proteins only transiently appeared at postsynaptic sites. In contrast, other proteins, including Eps15, intersectin1L, and {beta}2-adaptin, were persistently enriched and partitioned at the edge of the EZ. We found that uncoupling the EZ from the synapse led to the loss of most of these components, while disrupting the actin cytoskeleton or AP2-membrane interactions did not alter EZ positioning. We conclude that the EZ is a stable, highly organized molecular platform where components are differentially recruited and positioned to orchestrate the endocytosis of synaptic receptors.

category: cell biology


title: TKTDsimulation.jl and tktdjl2r: innovative packages for High Performance Computing of survival predictions in support of environmental risk assessment under time-variable scenarios

abstract:
Predictive environmental risk scenarios are today of major interest for environmental risk assessment as they provide plausible and consistent descriptions of possible effects of chemical in natura. In particular, they can be used for predictions of the future as consistent descriptions of pathways towards desired targets to protect. One single scenario would therefore be meaningless, as it could not capture all the variability and uncertainty involved in natural phenomenon combined with socio-economical events. A set of environmental risk scenarios is then a key asset to address sustainable and collaborative decision making associated with appropriate actions.

Toxicokinetics-Toxicodynamics (TKTD) models are increasingly used for the assessment and the prediction of environmental risk assessment due to chemical products. This mechanistic modelling approach offers many advantages as the possibility to perform simulations under non-observed realistic situations with time-variable exposure profiles embedded in environmental risk scenarios. TKTD simulations can also be linked with other types of models (e.g., Individual Based Model) within a pipeline of computing inference as for example Bayesian inference or Machine Learning. To handle such challenges within the particular framework of TKTD models for survival, we present an innovative simulation tool written in the new programming language Julia, called TKTDsimulations.jl. Given that TKTD models for survival usually require high performance computing due to the numerical integration of differential equations, our tool strongly benefits from Julias facilities, in particular a code that is fast to compile and easy to maintain. In addition, to ease the link with the already developed R-package morse dedicated to the statistical handling of ecotoxicity data, we also developed a new R-package, called tktdjl2r, interfacing morse with our new simulation tool TKTDsimulations.jl that considerably faster predictions with the corresponding ready-to-use morse functions.


title: Collective detection based on visual information in animal groups

abstract: The spatio-temporal distribution of individuals within a group (i.e its internal structure) plays a defining role in how individuals interact with their environment, make decisions, and transmit information via social interactions. Group-living organisms across taxa, including many species of fish, birds, ungulates, and insects, use vision as the predominant modality to coordinate their collective behavior. Despite this importance, there have been few quantitative studies examining visual detection capabilities of individuals within groups. We investigate key principles underlying individual, and collective, visual detection of stimuli (which could include cryptic predators, potential food items, etc.) and how this relates to the internal structure of groups. While the individual and collective detection principles are generally applicable, we employ a model experimental system of schooling golden shiner fish (Notemigonus crysoleucas) to relate theory directly to empirical data, using computational reconstruction of the visual fields of all individuals to do so. Our integrative approach allows us to reveal how the external visual information available to each group member depends on the number of individuals in the group, the position within the group, and the location of the external visually-detectable stimulus. We find that in small groups, individuals have detection capability in nearly all directions, while in large groups, occlusion by neighbors causes detection capability to vary with position within the group. We then formulate a simple, and generally applicable, model that captures how visual detection properties emerge due to geometric scaling of the space occupied by the group and occlusion caused by neighbors. We employ these insights to discuss principles that extend beyond our specific system, such as how collective detection depends on individual body shape, and the size and structure of the group.

category: animal behavior and cognition


title: TransPi - a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

abstract: The use of RNA-Seq data and the generation of de novo transcriptome assemblies have been pivotal for studies in ecology and evolution. This is distinctly true for non-model organisms, where no genome information is available. Nevertheless, studies of differential gene expression, DNA enrichment baits design, and phylogenetics can all be accomplished with the data gathered at the transcriptomic level. Multiple tools are available for transcriptome assembly, however, no single tool can provide the best assembly for all datasets. Therefore, a multi assembler approach, followed by a reduction step, is often sought to generate an improved representation of the assembly. To reduce errors in these complex analyses while at the same time attaining reproducibility and scalability, automated workflows have been essential in the analysis of RNA-Seq data. However, most of these tools are designed for species where genome data is used as reference for the assembly process, limiting their use in non-model organisms. We present TransPi, a comprehensive pipeline for de novo transcriptome assembly, with minimum user input but without losing the ability of a thorough analysis. A combination of different model organisms, k-mer sets, read lengths, and read quantities were used for assessing the tool. Furthermore, a total of 49 non-model organisms, spanning different phyla, were also analyzed. Compared to approaches using single assemblers only, TransPi produces higher BUSCO completeness percentages, and a concurrent significant reduction in duplication rates. TransPi is easy to configure and can be deployed seamlessly using Conda, Docker and Singularity.


title: Relating simulation studies by provenance--Developing a family of Wnt signaling models

abstract:
For many biological systems, a variety of simulation models exist. A new simulation model is rarely developed from scratch, but rather revises and extends an existing one.

A key challenge, however, is to decide which model might be an appropriate starting point for a particular problem and why. To answer this question, we need to identify entities and activities that contributed to the development of a simulation model.

Therefore, we exploit the provenance data model, PROV-DM, of the World Wide Web Consortium and, building on previous work, continue developing a PROV ontology for simulation studies. Based on a case study of 19 Wnt/{beta}-catenin signaling models, we identify crucial entities and activities as well as useful metadata to both capture the provenance information from individual simulation studies and relate these forming a family of models. The approach is implemented in WebProv, a web application for inserting and querying provenance information.

Our specialization of PROV-DM contains the entities Research Question, Assumption, Requirement, Qualitative Model, Simulation Model, Simulation Experiment, Simulation Data, and Wet-lab Data as well as activities referring to building, calibrating, validating, and analyzing a simulation model. We show that most Wnt simulation models are connected to other Wnt models by using (parts of) these models. However, the overlap, especially regarding the Wet-lab Data used for calibration or validation of the models is small.

Making these aspects of developing a model explicit and queryable is an important step for assessing and reusing simulation models more effectively. Exposing this information helps to integrate a new simulation model within a family of existing ones and may lead to the development of more robust and valid simulation models.

We hope that our approach becomes part of a standardization effort and that modelers adopt the benefits of provenance when considering or creating simulation models.

Author summaryWe revise a provenance ontology for simulation studies of cellular biochemical models. Provenance information is useful for understanding the creation of a simulation model because it not only contains information about the entities and activities that have led to a simulation model but also their relations, all of which can be visualized. It provides additional structure by explicitly recording research questions, assumptions, and requirements and relating them along with data, qualitative models, simulation models, and simulation experiments through a small set of predefined but extensible activities.

We have applied our concept to a family of 19 Wnt signaling models and implemented a web-based tool (WebProv) to store the provenance information from these studies. The resulting provenance graph visualizes the story line of simulation studies and demonstrates the creation and calibration of simulation models, the successive attempts of validation and extension, and shows, beyond an individual simulation study, how the Wnt models are related. Thereby, the steps and sources that contributed to a simulation model are made explicit.

Our approach complements other approaches aimed at facilitating the reuse and assessment of simulation products in systems biology such as model repositories as well as annotation and documentation guidelines.


title: Sensitive, reliable, and robust circRNA detection from RNA-seq with CirComPara2

abstract: Circular RNAs (circRNAs) are a large class of covalently closed RNA molecules that originate by a process called back-splicing. CircRNAs are emerging as functional RNAs involved in the regulation of biological processes as well as in disease and cancer mechanisms. Current computational methods for circRNA identification from RNA-seq experiments are characterised by low discovery rates and performance dependent on the analysed data set. We developed a new automated computational pipeline, CirComPara2 (https://github.com/egaffo/CirComPara2), that consistently achieves high recall rates without losing precision by combining multiple circRNA detection methods. In our benchmark analysis, CirComPara2 outperformed state-of-the-art circRNA discovery tools and proved to be a reliable and robust method for comprehensive transcriptomics characterisation.


title: Structural basis of drug recognition by the multidrug transporter ABCG2

abstract: ABCG2 is an ATP-binding cassette (ABC) transporter whose function affects the pharmacokinetics of drugs and contributes to multidrug resistance of cancer cells. While its interaction with the endogenous substrate estrone-3-sulfate (E1S) has been elucidated at a structural level, the recognition and recruitment of exogenous compounds is not understood at sufficiently high resolution. Here we present three cryo-EM structures of nanodisc-reconstituted, human ABCG2 bound to anticancer drugs tariquidar, topotecan and mitoxantrone. To enable structural insight at high resolution, we used Fab fragments of the ABCG2-specific monoclonal antibody 5D3, which binds to the external side of the transporter but does not interfere with drug-induced stimulation of ATPase activity. We observed that the binding pocket of ABCG2 can accommodate a single tariquidar molecule in a C-shaped conformation, similar to one of the two tariquidar molecules bound to ABCB1, where tariquidar acts as an inhibitor. We also found single copies of topotecan and mitoxantrone bound between key phenylalanine residues. Mutagenesis experiments confirmed the functional importance of two residues in the binding pocket, F439 and N436. Using 3D variability analyses, we found a correlation between substrate binding and reduced dynamics of the nucleotide binding domains (NBDs), suggesting a structural explanation for drug-induced ATPase stimulation. Our findings provide insight into how ABCG2 differentiates between inhibitors and substrates and may guide a rational design of new modulators and substrates.


title: Integrating genomics and multi-platform metabolomics enables metabolite QTL detection in breeding-relevant apple germplasm

abstract:
Research ConductedApple (Malus x domestica) has commercial and nutritional value, but breeding constraints of tree crops limit varietal improvement. Marker-assisted selection minimizes these drawbacks, but breeders lack applications for targeting fruit phytochemicals. To understand genotype-phytochemical associations in apples, we have developed a high-throughput integration strategy for genomic and multi-platform metabolomics data.

Methods124 apple genotypes, including members of three pedigree-connected breeding families alongside diverse cultivars and wild selections, were genotyped and phenotyped. Metabolite genome-wide association studies (mGWAS) were conducted with 10,000 single nucleotide polymorphisms and phenotypic data acquired via LC-MS and 1H NMR untargeted metabolomics. Putative metabolite quantitative trait loci (mQTL) were then validated via pedigree-based analyses (PBA).

Key ResultsUsing our developed method, 519, 726, and 177 putative mQTL were detected in LC-MS positive and negative ionization modes and NMR, respectively. mQTL were indicated on each chromosome, with hotspots on linkage groups 16 and 17. A chlorogenic acid mQTL was discovered on chromosome 17 via mGWAS and validated with a two-step PBA, enabling discovery of novel candidate gene-metabolite relationships.

Main ConclusionComplementary data from three metabolomics approaches and dual genomics analyses increased confidence in validity of compound annotation and mQTL detection. Our platform demonstrates the utility of multi-omics integration to advance data-driven, phytochemicalbased plant breeding.

category: plant biology


title: Evolving a new efficient mode of fructose utilization for improved bioproduction in Corynebacterium glutamicum

abstract: Fructose utilization in Corynebacterium glutamicum starts with its uptake and concomitant phosphorylation via the phosphotransferase system (PTS) to yield intracellular fructose 1-phosphate, which enters glycolysis upon ATP dependent phosphorylation to fructose 1,6-bisphosphate by 1-phosphofructokinase. This is known to result in a significantly reduced oxidative pentose phosphate pathway (oxPPP) flux on fructose (~10 %) compared to glucose (~60 %). Consequently, the biosynthesis of NADPH demanding products, e.g. L-lysine, by C. glutamicum is largely decreased, when fructose is the only carbon source. Previous works reported that fructose is partially utilized via the glucose specific PTS presumably generating fructose 6-phosphate. This closer proximity to the entry point of the oxPPP might increase oxPPP flux and consequently NADPH availability. Here, we generated deletion strains either lacking in the fructose-specific PTS or 1-phosphofructokinase activity. We used these strains in short-term evolution experiments on fructose minimal medium and isolated mutant strains, which regained the ability of fast growth on fructose as a sole carbon source. In these fructose mutants, the deletion of the glucose specific PTS, as well as the 6-phosphofructokinase gene, abolished growth, unequivocally showing fructose phosphorylation via glucose specific PTS to fructose 6-phosphate. Gene sequencing revealed three independent amino acid substitutions in PtsG (M260V, M260T, P318S). These three PtsG variants mediated faster fructose uptake and utilization compared to native PtsG. In-depth analysis of the effects of fructose utilization via these PtsG variants revealed significantly increased biomass formation, reduced side-product accumulation, and increased L-lysine production by 50 %.

category: synthetic biology


title: Indoleamine 2,3-dioxygenase upregulates PD-1 expression on ovarian tumor infiltrating CD8+ T cells via kynurenine activation of the aryl hydrocarbon receptor

abstract: The immunoregulatory enzyme, indoleamine 2,3-dioxygenase (IDO1) and the PD-1/PD-L1 axis are potent mechanisms that impede effective anti-tumor immunity in ovarian cancer. However, whether the IDO pathway regulates PD-1 expression in T cells is currently unknown. Here we show that tumoral IDO1 expression led to profound changes in tryptophan, nicotinate/nicotinamide, and purine metabolic pathways in the ovarian tumor microenvironment, and to an increased frequency of PD-1+CD8+ tumor infiltrating T cells. We determined that activation of the aryl hydrocarbon receptor (AHR) by kynurenine induced PD-1 expression, and this effect was significantly abrogated by the AHR antagonist CH223191. Mechanistically, kynurenine alters chromatin accessibility in regulatory regions of T cell inhibitory receptors, allowing AHR to bind to consensus XRE motifs in the promoter region of PD-1. These results enable the design of strategies to target the IDO1 and AHR pathways for enhancing anti-tumor immunity in ovarian cancer.


title: Pyrazinamide action is driven by the cell envelope stress response in Mycobacterium tuberculosis

abstract: Pyrazinamide (PZA) plays a crucial role in first-line tuberculosis drug therapy. Unlike other antimicrobial agents, PZA is only active against Mycobacterium tuberculosis at low pH. The basis for this conditional drug susceptibility remains undefined. In this study, we utilized a genome-wide approach to interrogate potentiation of PZA action. We find that mutations in numerous genes involved in central metabolism as well as cell envelope maintenance and stress response are associated with PZA resistance. Further, we demonstrate that constitutive activation of the cell envelope stress response can drive PZA susceptibility independent of environmental pH. Consequently, treatment with peptidoglycan synthesis inhibitors, such as beta-lactams and D-cycloserine, potentiate PZA action through triggering this response. These findings illuminate a regulatory mechanism for conditional PZA susceptibility and reveals new avenues for enhancing potency of this important drug through targeting activation of the cell envelope stress response.


title: Replication-related control over cell division in  Escherichia coli is growth-rate dependent

abstract: How replication and division processes are coordinated in the cell cycle is a fundamental yet poorly understood question in cell biology. In Escherichia coli different data sets and models have supported a range of conclusions from one extreme where these two processes are tightly linked to another extreme where these processes are completely independent of each other. Using high throughput optical microscopy and cell cycle modeling, we show that in slow growth conditions replication and division processes are strongly correlated, indicating a significant coupling between replication and division. This coupling weakens as the growth rate of cells increases. Our data suggest that the underlying control mechanism in slow growth conditions is related to unreplicated chromosome blocking the onset of constriction at the midcell. We show that the nucleoid occlusion protein SlmA does not play a role in this process and neither do other known factors involved in positioning bacterial Z-ring relative to the chromosome. Altogether this work reconciles different ideas from the past and brings out a more nuanced role of replication in controlling the division process in a growth-rate dependent manner.


title: Revisiting the early evolution of Cyanobacteria with a new thylakoid-less and deeply diverged isolate from a hornwort

abstract: Cyanobacteria have played pivotal roles in Earths geological history especially during the rise of atmospheric oxygen. However, our ability to infer the early transitions in Cyanobacteria evolution has been limited by their extremely lopsided tree of life--the vast majority of extant diversity belongs to Phycobacteria (or "crown Cyanobacteria"), while its sister lineage, Gloeobacteria, is depauperate and contains only two closely related species of Gloeobacter and a metagenome-assembled genome. Here we describe a new culturable member of Gloeobacteria, Anthocerobacter panamensis, isolated from a tropical hornwort. Anthocerobacter diverged from Gloeobacter over 1.4 billion years ago and has low 16S identities with environmental samples. Our ultrastructural, physiological, and genomic analyses revealed that this species possesses a unique combination of traits that are exclusively shared with either Gloeobacteria or Phycobacteria. For example, similar to Gloeobacter, it lacks thylakoids and circadian clock genes, but the carotenoid biosynthesis pathway is typical of Phycobacteria. Furthermore, Anthocerobacter has one of the most reduced gene sets for photosystems and phycobilisomes among Cyanobacteria. Despite this, Anthocerobacter is capable of oxygenic photosynthesis under a wide range of light intensities, albeit with much less efficiency. Given its key phylogenetic position, distinct trait combination, and availability as a culture, Anthocerobacter opens a new window to further illuminate the dawn of oxygenic photosynthesis.

category: evolutionary biology


title: MITOCHONDRIAL GENOME REVEALS CONTRASTING PATTERN OF ADAPTIVE SELECTION IN TURTLES AND TORTOISES

abstract:
Testudinoidea represents an evolutionarily unique taxon comprising both turtles and tortoises. The contrasting habitats that turtles and tortoises inhabit are associated with unique physio-ecological challenges hence enable distinct adaptive evolutionary strategies. To comparatively understand the pattern and strength of Darwinian selection and physicochemical evolution in turtle and tortoise mitogenomes, we employed adaptive divergence and selection analyses. We evaluated changes in structural and biochemical properties, and codon models on the mitochondrial protein-coding genes (PCGs) among three turtles and a tortoise lineage. We used mitochondrial PCGs that constitute the crucial oxidative phosphorylation (OXPHOS) respiratory system, a critical metabolic regulator which assumes key significance in energy regulation of ectotherms.

We detected strong evidence of positive selection along the turtle lineages: Geoemydidae, Emydidae, and Platysternidae, but relatively weak signals in tortoises. The Platysternidae turtles revealed the highest gene and site-wise positive selection. In turtles, positively selected sites were prevalent in NAD2 and NAD4 genes in OXPHOS Complex I, and COB gene of Complex III, indicating convergent adaptive evolution. Besides, NAD3 was the only subunit that showed adaptive selection in both turtles and tortoises, expressing its relevance for all Testudinoidea. Structural and functional analysis revealed many sites and physiochemical changes in important conserved as well as biomedically significant regions, suggesting the influence of adaptive pressure on mitogenome functions. Hence, our study furnished novel evidence of contrasting evolutionary selective pressure acting on closely related groups such as turtles and tortoises with unique habitat preferences and associated eco-physiological challenges.


title: Integration of differential gene expression with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues

abstract: Gene expression alterations occur in all mouse tissues during aging, but recent works highlight minor rather than major dysregulation amplitude for most genes, questioning whether differentially expressed genes on their own provide deep insight into aging biology. To clarify this issue, we have combined differential gene expression with weighted gene correlation network analysis (WGCNA) to identify expression signatures accounting for the pairwise relations between gene expression profiles and the cumulative effect of genes with small fold- changes during aging in the brain, heart, liver, skeletal muscle, and pancreas of C57BL/6 mice. Functional enrichment analysis of the overlap of genes identified in both approaches showed that immunity-related responses, mitochondrial energy metabolism, tissue regeneration and detoxification are prominently altered in the brain, heart, muscle, and liver, respectively, reflecting an age-related global loss of tissue function. While data showed little overlap among the age-dysregulated genes between tissues, aging triggered common biological processes in distinct tissues, particularly proteostasis-related pathways, which we highlight as important features of murine tissue physiological aging.

category: genetics


title: Ancient DNA and microfossils reveal dynamics of three harmful dinoflagellate species off Eastern Tasmania, Australia, over the last 9,000 years

abstract:
Harmful algal blooms (HABs) have significantly impacted the seafood industry along the Tasmanian east coast over the past three decades, and are expected to change in frequency and magnitude due to climate change induced changing oceanographic conditions. To investigate the long-term history of regional HABs, a combination of palynological and sedimentary ancient DNA (sedaDNA) analyses was applied to marine sediment cores from inshore (up to 145 years old) and offshore (up to ~9,000 years) sites at Maria Island, southeast Tasmania. Analyses focused Paralytic Shellfish Toxin (PST) producing dinoflagellates Alexandrium catenella and Gymnodinium catenatum, and the red-tide dinoflagellate Noctiluca scintillans, which were specifically targeted using a hybridization capture sedaDNA technique. Identification of primulin-stained A. catenella cysts throughout the inshore sediment core, together with sedaDNA evidence of a bloom-phase of Alexandrium ~15 years ago, indicates recent stimulation of a cryptic endemic population. Morphologically similar but unstained Alexandrium cysts were observed throughout the offshore core, with sedaDNA confirming the presence of A. catenella from ~8,300 years ago to present. Gymnodinium catenatum cysts were detected only in inshore surface sediments from 30 years ago to present, supporting previous evidence of a 1970s introduction via shipping ballast water. sedaDNA confirmed the presence of G. catenatum-related sequences in the inshore and offshore cores, however, unambiguous species identification could not be achieved due to limited reference sequence coverage of Gymnodinium. Our hybridization capture sedaDNA data also confirmed the historically recent dispersal of the non-fossilizing dinoflagellate Noctiluca scintillans, detected inshore from ~30 years ago, matching first observations of this species in Tasmanian waters in 1994. At the offshore site, N. scintillans sedaDNA was detected only in surface sediments, confirming a recent climate-driven range expansion this species. This study provides new insights into the distribution and abundance of three HAB species in the Tasmanian region, including clues to past bloom phases. Further research into paleo-environmental conditions and paleo-community structure are required to identify the factors driving bloom phases through time and predict plankton community responses under different future climate scenarios.

HighlightsO_LIDinocyst and sedaDNA analyses were applied to marine sediments off Tasmania
C_LIO_LIAlexandrium catenella has been endemic to Australia for at least ~9,000 years
C_LIO_LIRecent A. catenella blooms are likely induced by climate and oceanographic change
C_LIO_LIGymnodinium catenatum cysts in recent (~30y) sediments confirm a 1970s introduction
C_LIO_LINoctiluca scintillans sedaDNAin recent (~30y) sediments matches a 1994 introduction
C_LI


title: Identifying gene regulatory networks of senescence in postharvest broccoli (Brassica oleracea)

abstract:
The facts of postharvest food loss and waste and the resulting consequences affect us in many ways, ranging from important economic and social issues to lasting and detrimental environmental problems. We are using genomic tools to understand senescence in postharvest broccoli florets when stored at room temperature or 4 {degrees}C. The RNA-sequencing approaches provide key insights into the gradual changes in transcriptome profiling in broccoli during postharvest storage. Identification of those key factors could lead to a better understanding of gene regulation of postharvest senescence. Those genes could serve as  freshness-indicators that have the potential to mediate senescence and to generate germplasm for breeding new varieties with longer shelf-life in Brassica vegetables. Such a tool would also allow a new level of postharvest logistics based on physiological age, supporting improved availability of high-quality, nutritious, fresh vegetables and fruits.

One sentence summaryA gene regulatory network modulates senescence in postharvest broccoli florets


title: Mosquito Larvae (Culex spp.) Startle Responses to Vibration Stimuli

abstract: We explored startle responses of Culex spp. larvae to varying frequencies and durations of vibrations, before investigating habituation (a behavioural learning phenomenon). The startle response consists of a rapid movement to permit escape from a potentially dangerous stimulus. We used the automated Zantiks MWP_vb unit to analyse larval startle responses through the built-in live video tracking. Set within the units controlled environmental chamber, we recorded distance travelled by the larvae. These results were used to optimise the vibration startle response for use in habituation studies. Repeated vibrations appeared to reduce larvae startle responses, although further analysis is required to confirm habituation. This study not only provides an insight into the learning ability of mosquito larvae, but demonstrates the ease, replicability and control conferred by the automated unit. Furthermore, this method is applicable to many other organisms and shows potential for more sophisticated environmental effect testing, such as behavioural toxicology.


title: Protein and substrate flexibility contribute to enzymatic specificity in human and bacterial methionine adenosyltransferases

abstract: Protein conformational change can facilitate the binding of non-cognate substrates and underlie promiscuous activities. However, the contribution of substrate conformational dynamics to this process is comparatively poorly understood. Here we analyse human (hMAT2A) and Escherichia coli (eMAT) methionine adenosyltransferases that have identical active sites but different substrate specificity. In the promiscuous hMAT2A, non-cognate substrates bind in a stable conformation to allow catalysis. In contrast, non-cognate substrates rarely sample stable productive binding modes in eMAT owing to altered mobility in the enzyme active site. Different cellular concentrations of substrate likely drove the evolutionary divergence of substrate specificity in these orthologs. The observation of catalytic promiscuity in hMAT2A led to the detection of a new human metabolite, methyl thioguanosine, that is produced at elevated level in a cancer cell line. This work establishes that identical active sites can result in different substrate specificity owing to the effects of substrate and enzyme dynamics.

category: biochemistry


title: Substrate dynamics contribute to enzymatic specificity in human and bacterial methionine adenosyltransferases


title: The cryo-EM structure of the neurofibromin dimer reveals the molecular basis for von Recklinghausen disease

abstract: Neurofibromin (NF1) is a tumour suppressor mutated in neurofibromatosis type 1 (von Recklinghausen disease), one of the most common human genetic diseases(1). NF1 regulates cellular growth through suppressing the Rat Sarcoma (RAS) pathway and, accordingly, mutations in this protein drive numerous cancers, including melanoma, ovarian, breast and brain cancer(2, 3). Currently, however, the molecular basis for NF1 function remains to be understood. Here we address this problem and use cryogenic Electron Microscopy (cryo-EM) to determine the structure of fulllength NF1. The 640 kDa NF1 homodimer forms an extraordinary lemniscate ({infty}) shaped molecule that is ~30 nm in length and ~ 10 nm wide. Each NF1 monomer comprises an N-terminal HEAT-repeat domain (N-HEAT), a guanosine triphosphatase activating protein (GAP)-related domain (GRD), a Sec14 homologous and pleckstrin homologous module (SEC-PH), and a C-terminal HEAT domain (C-HEAT). The core NF1 scaffold is formed via a head-to-tail dimer of the N- and C-HEAT domains. This platform, which is responsible for interacting with more than 10 regulatory binding partners, comprises an extraordinary array of over 150 -helices. Analysis of these EM data revealed that the GRD and SEC-PH domain are highly mobile with respect to the core scaffold and could not initially be accurately placed in electron density. Strikingly, however, using 3D variability analysis we were able to identify a significant subpopulation of NF1 particles and determine the complete NF1 structure to 5.6 [A] resolution. These data revealed that the catalytic GRD and lipid binding SEC-PH domain are positioned against the core scaffold in a closed, autoinhibited conformation. We postulate that interaction with the plasma membrane may release the closed conformation in order to promote RAS inactivation. Our structural data further allow us to map the location of disease-associated NF1 variants and provide a long sought-after structural explanation for the extreme susceptibility of the molecule to loss-of-function mutations. Finally, it is suggested that approaches to combat NF1-linked diseases may include release of the autoinhibited state in order to improve NF1 catalytic efficiency.


title: Resolving the Interactions Between Class 3 Semaphorin Receptors in Live Cells

abstract: The plexin/neuropilin/semaphorin family of proteins is involved with tissue patterning in the developing embryo. These proteins play roles in cell migration and adhesion, but are also important in disease, including cancer angiogenesis and metastasis. While some structures of the soluble domains of these proteins have been determined, the conformations of full-length receptor complexes are just beginning to be studied, especially within the context of the cell plasma membrane. Pulsed-interleaved excitation fluorescence cross-correlation spectroscopy (PIE-FCCS) allows direct insight to the formation of protein-protein interactions in the membrane of live cells. Here we investigated the homodimerization of neuropilin-1, Plexin A2, Plexin A4, and Plexin D1. Consistent with previous studies, we found that neuropilin-1, Plexin A2 and Plexin A4 are dimers in the absence of exogenous ligand. Plexin D1, on the other hand, was monomeric under similar conditions, which had not been previously reported. We also found that Plexin A2 and A4 assemble into a heteromeric complex. Stimulation with Semaphorin 3A or Semaphorin 3C ligand neither disrupts nor enhances the dimerization of the receptors when they are expressed alone, suggesting that activation involves a conformational change rather than a shift in the monomer-dimer equilibrium. However, upon stimulation with Semaphorin 3C, Plexin D1 and neuropilin-1 form a heteromeric complex, while Semaphorin 3A does not induce a stable complex with these receptors. This analysis of interactions by PIE-FCCS provides a complementary approach to the existing structural and biochemical data that will aid in the development of new therapeutic strategies to target these receptors during disease.


title: Biological and Transcriptomic Characterization of Pre-haustorial Resistance to Sunflower Broomrape (Orobanche cumana W.)

abstract: Infestations with sunflower broomrape (Orobanche cumana Wallr.), an obligatory root parasite, constitute a major limitation to sunflower production in many regions around the world. Breeding for resistance is the most effective approach to reduce sunflower broomrape infestation, yet resistance mechanisms are often overcome by new races of the pathogen. Elucidating the mechanisms controlling the resistance to broomrape at the molecular level is thus the most desirable pathway to obtaining long-lasting resistance and reducing yield loss in sunflower. In this study, we investigated broomrape resistance in a confectionery sunflower hybrid with a robust and long-lasting resistance to sunflower broomrape. Visual screening and histological examination of sunflower roots revealed that penetration of the intrusive broomrape cells into the host root endodermis is blocked at the host cortex, indicating a pre-haustorial mechanism of resistance. A comparative RNA-Seq experiment conducted between roots obtained from the resistant cultivar, a bulk of five broomrape resistant lines and a bulk of five broomrape susceptible lines allowed the identification of genes that were significantly differentially expressed upon broomrape infestation. Among these differentially expressed genes, {beta}-1,3-endoglucanase, {beta}-glucanase and ethylene-responsive transcription factor4 (ERF4) genes were identified. These genes were previously reported to be pathogenesis-related genes in other plant species. This genetics investigation together with the histological examinations led us to conclude that the resistance mechanism involves the identification of the broomrape and the consequent formation of a physical barrier that prevents the penetration of the broomrape into the sunflower roots.


title: Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii

abstract: Large-scale mutant libraries have been indispensable for genetic studies, and the development of next-generation genome sequencing technologies has greatly advanced efforts to analyze mutants. In this work, we sequenced the genomes of 660 Chlamydomonas reinhardtii acetate-requiring mutants, part of a larger photosynthesis mutant collection previously generated by insertional mutagenesis with a linearized plasmid. We identified 554 insertion events from 509 mutants by mapping the plasmid insertion sites through paired-end sequences, in which one end aligned to the plasmid and the other to a chromosomal location. Nearly all (96%) of the events were associated with deletions, duplications, or more complex rearrangements of genomic DNA at the sites of plasmid insertion, and 1405 genes in total were affected. Functional annotations of these genes were enriched in those related to photosynthesis, signaling, and tetrapyrrole synthesis as would be expected from a library enriched for photosynthesis mutants. Systematic manual analysis of the disrupted genes for each mutant generated a list of 273 higher-confidence candidate photosynthesis genes, and we experimentally validated two genes that are essential for photoautotrophic growth, CrLPA3 and CrPSBP4. The inventory of candidate genes includes 55 genes from a phylogenomically defined set of conserved genes in green algae and plants. Altogether, 68 candidate genes encode proteins with previously characterized functions in photosynthesis in Chlamydomonas, land plants, and/or cyanobacteria, 15 genes encode proteins previously shown to have functions unrelated to photosynthesis, and 190 genes encode proteins without any functional annotation, signifying that our results connect a function related to photosynthesis to these previously unknown proteins. This mutant library, with genome sequences that reveal the molecular extent of the chromosomal lesions and resulting higher-confidence candidate genes, represents a rich resource for gene discovery and protein functional analysis in photosynthesis.


title: Perceptual history acts in world-centred coordinates

abstract: Serial dependence effects have been observed using a variety of stimuli and tasks, revealing that the recent past can bias current percepts, leading to increased similarity between two. The aim of this study is to determine whether this temporal integration occurs in egocentric or allocentric coordinates. We ask participants to perform an orientation reproduction task using grating stimuli while the head is kept at a fixed position throughout the whole session or while alternating position from one trial to the next, from left (-20{degrees}) to right (+20{degrees}), putting the egocentric and allocentric cues in conflict. Under these conditions, allocentric cues prevail.


title: Disrupting short-term memory in premotor but not visual cortex affects serial dependence in visuomotor integration

abstract:
Human behavior is biased by past experience. For example, when intercepting a moving target, the speed of previous targets will bias responses in future trials. Neural mechanisms underlying this so-called serial dependence are still under debate. Here, we tested the hypothesis that the previous trial leaves a neural trace in brain regions associated with encoding task-relevant information in visual and/or motor regions. We reasoned that injecting noise by means of transcranial magnetic stimulation (TMS) over premotor and visual areas would degrade such memory traces and hence reduce serial dependence. To test this hypothesis, we applied bursts of TMS pulses to right visual motion processing region hV5/MT+ and to left dorsal premotor cortex during inter-trial intervals of a coincident timing task performed by twenty healthy human participants (15 female). Without TMS, participants presented a bias towards the speed of the previous trial when intercepting moving targets. TMS over dorsal premotor cortex decreased serial dependence in comparison to the control Vertex stimulation, whereas TMS applied over hV5/MT+ did not. In addition, TMS seems to have specifically affected the memory trace that leads to serial dependence, as we found no evidence that participants behavior worsened after applying TMS. These results provide causal evidence that an implicit short-term memory mechanism in premotor cortex keeps information from one trial to the next, and that this information is blended with current trial information so that it biases behavior in a visuomotor integration task with moving objects.

Significance StatementHuman perception and action are biased by the recent past. The origin of such serial bias is still not fully understood, but a few components seem to be fundamental for its emergence: the brain needs to keep previous trial information in short-term memory and blend it with incoming information. Here, we present evidence that a premotor area has a potential role in storing previous trial information in short-term memory in a visuomotor task, and that this information is responsible for biasing ongoing behavior. These results corroborate the perspective that areas associated with processing information of a stimulus or task also participate in maintaining that information in short-term memory even when this information is no longer relevant for current behavior.


title: Disrupting short-term memory in premotor cortex affects serial dependence in visuomotor integration


title: Functional MRI of native and non-native speech production in sequential German-English bilinguals

abstract: Bilingualism and multilingualism are highly prevalent. Non-invasive brain imaging has been used to study the neural correlates of native (L1) and non-native (L2) speech and language production, mainly on the lexical and syntactic level. Here, we acquired continuous fast event-related FMRI during visually cued overt production of exclusively German and English vowels and syllables. We analyzed data from 13 university students, native speakers of German and sequential English bilinguals. The production of non-native English sounds was associated with increased activity of the left primary sensori-motor cortex, bilateral cerebellar hemispheres (lobule VI), left inferior frontal gyrus, and left anterior insula compared to native German sounds. The contrast German > English sounds was not statistically significant. Our results emphasize that the production of non-native speech requires additional neural resources already on a basic phonological level in sequential bilinguals.


title: MEG, myself, and I: individual identification from neurophysiological brain activity

abstract: Large, openly available datasets and current analytic tools promise the emergence of population neuroscience. The considerable diversity in personality traits and behaviour between individuals is reflected in the statistical variability of neural data collected in such repositories. This amount of variability challenges the sensitivity and specificity of analysis methods to capture the personal characteristics of a putative neural portrait. Recent studies with functional magnetic resonance imaging (fMRI) have concluded that patterns of resting-state functional connectivity can both successfully identify individuals within a cohort and predict some individual traits, yielding the notion of a neural fingerprint. Here, we aimed to clarify the neurophysiological foundations of individual differentiation from features of the rich and complex dynamics of resting-state brain activity using magnetoencephalography (MEG) in 158 participants. Akin to fMRI approaches, neurophysiological functional connectomes enabled the identification of individuals, with identifiability rates similar to fMRIs. We also show that individual identification was equally successful from simpler measures of the spatial distribution of neurophysiological spectral signal power. Our data further indicate that identifiability can be achieved from brain recordings as short as 30 seconds, and that it is robust over time: individuals remain identifiable from recordings performed weeks after their baseline reference data was collected. Based on these results, we can anticipate a vast range of further research and practical applications of individual differentiation from neural electrophysiology in personalized, clinical, and basic neuroscience.


title: Still no evidence for disruption of global patterns of nest predation in shorebirds

abstract:
Many shorebird species are rapidly declining (Piersma et al. 2016; Munro 2017; Studds et al. 2017), but it is not always clear why. Deteriorating and disappearing habitat, e.g. due to intensive agriculture (Donal et al. 2001; Kentie et al. 2013; Kentie et al. 2018), river regulation (Nebel et al. 2008) or mudflat reclamation (Ma et al. 2014; Larson 2017), and hunting (Reed et al. 2018; Gallo-Cajiao et al. 2020) are some of the documented causes. A recent study suggests yet another possible cause of shorebird decline: a global increase in nest predation (Kubelka et al. 2018). The authors compiled an impressive dataset on patterns of nest predation in shorebirds and their analyses suggest that global patterns of nest predation have been disrupted by climate change, particularly in the Arctic. They go as far as to conclude that the Arctic might have become an ecological trap (Kubelka et al. 2018). Because these findings might have far-reaching consequences for conservation and related political decisions, we scrutinized the study and concluded that the main conclusions of Kubelka et al. (2018) are invalid (Bulla et al. 2019a). The authors then responded by reaffirming their conclusions (Kubelka et al. 2019b).

Here, we evaluate some of Kubelka et al.s (2019b) responses, including their recent erratum (2020), and show that the main concerns about the original study still hold. Specifically, (1) we reaffirm that Kubelka et al.s (2018) original findings are confounded by study site. Hence, their conclusions are over-confident because of pseudo-replication. (2) We reiterate that there is no statistical support for the assertion that predation rate has changed in a different way in the Arctic compared to other regions. The relevant test is an interaction between a measure of time (year or period) and a measure of geography (e.g., Arctic vs the rest of the world). The effect of such an interaction is weak, uncertain and statistically non-significant, which undermines Kubelka et al.s (2018) key conclusion. (3) We further confirm that the suggested general increase in predation rates over time is at best a weak and uncertain trend. The most parsimonious hypothesis for the described results is that the temporal changes in predation rate are an artefact of temporal changes in methodology and data quality. Using only high-quality data, i.e. directly calculated predation rates, reveals no overall temporal trend in predation rate. Below we elaborate in detail on each of these points.

We conclude that (i) there is no evidence whatsoever that the pattern in the Arctic is different from that in the rest of the world and (ii) there is no solid evidence for an increase in predation rate over time. While we commend Kubelka et al. for compiling and exploring the data, we posit that the data underlying their study, and perhaps all currently available data, are not sufficient (or of sufficient quality) to test their main hypotheses. We call for standardized and consistent data collection protocols and experimental validation of current methods for estimating nesting success.


title: Peak shifts and extinction under sex-specific selection

abstract: A well-known property of sexual selection combined with a cross sex genetic correlation (rmf), is that it can facilitate a peak shift on the adaptive landscape. How do these diversifying effects of sexual selection + rmf balance with the constraints imposed by such sexual antagonism, to affect macroevolution of sexual dimorphism? Here, I extend existing quantitative genetic models of evolution on complex adaptive landscapes. Beyond recovering classical predictions for the conditions promoting a peak shift, I show that when rmf is moderate to strong, relatively weak sexual selection is required to induce a peak shift in males only. Increasing the strength of sexual selection leads to a sexually-concordant peak shift, suggesting that macroevolutionary rates of sexual dimorphism may be largely decoupled from the strength of within-population sexual selection. Accounting explicitly for demography further reveals that sex-specific peak shifts may be more likely to be successful than concordant shifts in the face of extinction, especially when natural selection is strong. An overarching conclusion is that macroevolutionary patterns of sexual dimorphism are unlikely to be readily explained by within-population estimates of selection or constraint alone.


title: Chromosome-level genome assembly of the horned-gall aphid, Schlechtendalia chinensis (Hemiptera: Aphididae: Erisomatinae)

abstract: The horned gall aphid Schlechtendalia chinensis, is an economically important insect that induces galls valuable for medicinal and chemical industries. S. chinensis manipulates its host plant to form well-organized horned galls during feeding. So far, more than twenty aphid genomes have been reported; however, all of those are derived from free-living aphids. Here we generated a high-quality genome assembly of S. chinensis, representing the first genome sequence of a galling aphid. The final genome assembly was 280.43 Mb, with 97% of the assembled sequences anchored into thirteen chromosomes. S. chinensis presents the smallest aphid genome size among available aphid genomes to date. The contig and scaffold N50 values were 3.39 Mb and 20.58 Mb, respectively. The assembly included 96.4% of conserved arthropod and 97.8% of conserved Hemiptera single-copy orthologous genes based on BUSCO analysis. A total of 13,437 protein-coding genes were predicted. Phylogenomic analysis showed that S. chinensis formed a single clade between the Eriosoma lanigerum clade and the Aphidini+Macrosiphini aphid clades. In addition, salivary proteins were found to be differentially expressed when S. chinensis underwent host alternation, indicating their potential roles in gall formation and plant defense suppression. A total of 36 cytochrome P450 genes were identified in S. chinensis, considerably fewer compared to other aphids, probably due to its small host plant range. The high-quality S. chinensis genome assembly and annotation provide an essential genetic background for future studies to reveal the mechanism of gall formation and to explore the interaction between aphids and their host plants.


title: Rats show a preference for certain unfamiliar strains of rats

abstract: Humans show distinct social behaviours when we recognise social similarity in opponents that are members of the same social group. However, little attention has been paid to the role of social similarity in non-human animals. In Wistar subject rats, the presence of an unfamiliar Wistar rat mitigated stress responses, suggesting the importance of social similarity in this phenomenon. We found that the presence of unfamiliar Sprague-Dawley (SD) or Long-Evans (LE) rats, but not an unfamiliar Fischer 344 (F344) rat, similarly mitigated stress in subject rats. It is therefore possible that the subject rats recognised social similarity to unfamiliar SD and LE rats. In this study, we demonstrated that Wistar subject rats were capable of categorizing unfamiliar rats based on their strain, and that Wistar subjects showed a preference for unfamiliar Wistar, SD, and LE rats over F344 rats. However, the subject rats did not show a preference among Wistar, SD, and LE rats. In addition, the results were not due to an aversion to F344 rats, and preference was not affected when anaesthetised rats were presented to subject rats. The findings suggested that rats recognise social similarity to certain unfamiliar strains of rats.


title: Celecoxib exhibits therapeutic potential in experimental model of hyperlipidaemia

abstract: Hyperlipidaemia is a major risk factor for cardiovascular diseases, the leading cause of death globally. Celecoxib attenuated hypercholesterolemia associated with CCl4-induced hepatic injury in rats without improving liver function in our previous study. This present study investigated the lipid lowering potential of celecoxib in normal rats fed with coconut oil subjected to five deep-frying episodes. Male Sprague Dawley rats were randomly assigned to groups (n=6 rats/group) which received physiological saline (10 mL/kg), unheated coconut oil (UO, 10 mL/kg) or heated coconut oil (HO, 10 ml/kg) for 60 days. Groups that received HO were subsequently treated with either physiological saline, atorvastatin (25 mg/kg), celecoxib (5 mg/kg) or celecoxib (10 mg/kg) in the last fifteen days of the experiment. Rats were sacrificed 24 hours after last treatment and blood and tissue samples collected for analysis. HO consumption produced significant hyperlipidaemia and elevation in marker enzymes of hepatic function. Celecoxib ameliorated the hyperlipidaemia as shown by the significantly (P<0.05) lower total cholesterol, triglycerides, low and very low density lipoprotein in the celecoxib-treated rats when compared with HO-fed rats that received saline. Celecoxib also reduced (P<0.05) alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase and liver weight of hyperlipidaemic rats. Similarly, hepatocellular damage and inflammation of the aorta associated with the hyperlipidaemia was significantly reversed by celecoxib. However, serum TNF- and IL-6 did not change significantly between the various groups. Taken together, data from this study suggest that celecoxib may exert therapeutic benefit in hyperlipidaemia and its attendant consequences.

category: pharmacology and toxicology


title: Chemical characterization; Antimicrobial and Larvicidal activity of essential oil from Callistemon citrinus (Bottle brush) leaves

abstract: Mosquito-borne diseases are prevalent in more than 100 countries across the world. They are the major vectors for transmission of Malaria, dengue, yellow fever, filariasis, schistosomiasis, Japanese encephalitis etc. Many of the formerly employed insecticides in mosquito control have harmful effects on human health and other non-target populations, their non-biodegradable nature, the higher rate of bio-magnification in our ecosystem and increasing insecticide resistance on global scale are raising serious concerns. . Therefore, search for natural, eco-friendly alternatives such as bio-insecticides is imperative. In this study, Larvicidal activity of the essential oil obtained from the leaves of Callistemon citrinus was tested on Dengue vector mosquito Aedes aegypti & Chikungunya vector mosquito Culex sp. Also, the chemical composition of the essential oil was recorded using GC-MS analysis. The anti-microbial activity of the essential oil was checked against a few common bacteria and fungi. Callistemon citrinus comes out to be one of such bio-insecticides with many therapeutic active constituents, showing appreciable anti-microbial activity and 80-100% larvicidal activity.


title: Carotenoid and tocopherol fortification of zucchini fruits using a viral RNA vector

abstract: Carotenoids and tocopherols are health-promoting metabolites in livestock and human diets. Some important crops have been genetically modified to increase their content. Although the usefulness of transgenic plants to alleviate nutritional deficiencies is obvious, their social acceptance has been controversial. Here, we demonstrate an alternative biotechnological strategy for carotenoid and tocopherol fortification of edible fruits in which no transgenic DNA is involved. A viral RNA vector derived from Zucchini yellow mosaic virus (ZYMV) was modified to express a bacterial phytoene synthase (crtB), and inoculated in zucchini (Cucurbita pepo L.) leaves nurturing pollinated flowers. After the viral vector moved to the developing fruit and expressed crtB, the rind and flesh of the fruits developed yellow-orange rather than green color. Metabolite analyses showed a substantial enrichment in health-promoting carotenoids, such as - and {beta}-carotene (pro-vitamin A), lutein and phytoene, in both rind and flesh. Considerably higher accumulation of - and {gamma}-tocopherol was also detected, particularly in fruit rind. Although this strategy is perhaps not free from controversy due to the use of genetically modified viral RNA, our work does demonstrate the possibility of metabolically fortifying edible fruits using an approach in which no transgenes are involved.