title: Wilson Statistics: Derivation, Generalization, and Applications to Electron Cryomicroscopy

abstract: The power spectrum of proteins at high frequencies is remarkably well described by the flat Wilson statistics. Wilson statistics therefore plays a significant role in X-ray crystallography and more recently in electron cryomicroscopy (cryo-EM). Specifically, modern computational methods for three-dimensional map sharpening and atomic modelling of macromolecules by single particle cryo-EM are based on Wilson statistics. Here we provide the first rigorous mathematical derivation of Wilson statistics. The derivation pinpoints the regime of validity of Wilson statistics in terms of the size of the macromolecule. Moreover, the analysis naturally leads to generalizations of the statistics to covariance and higher order spectra. These in turn provide theoretical foundation for assumptions underlying the widespread Bayesian inference framework for three-dimensional refinement and for explaining the limitations of autocorrelation based methods in cryo-EM.


title: Membrane phase separation drives organization at B cell receptor clusters

abstract: Heterogeneity in intact cell plasma membranes has been explained by analogy to coexisting liquid-ordered and liquid-disordered phases, although models based on this idea fall short of describing the rich structure within cell membranes. Here, a new framework of lipid-driven plasma membrane heterogeneity is presented, drawing on quantitative measurements of protein partitioning and dynamics within B cell receptor clusters in live B lymphocyte plasma membranes, compared to coexisting phases in isolated plasma membranes. We propose that membrane domains in cells integrate the thermodynamic state of the membrane and the magnitude of the applied stimulus to give rise to a tunable response. This framework is supported through functional observations of B cell receptor phosphorylation in perturbed systems.

category: biophysics


title: The autophagy initiating kinase ULK1 is required for pancreatic cancer cell growth and survival

abstract: Amongst cancer subtypes, pancreatic ductal adenocarcinoma (PDA) has been demonstrated to be most sensitive to autophagy inhibition, which may be due to unique metabolic rewiring in these cells. The serine/threonine kinase ULK1 forms the catalytic center of a complex mediating the first biochemical step of autophagy. ULK1 directly recieves signals from mTORC1 and AMPK to trigger autophagy under stress and nutrient poor conditions. Studies in genetic engineered mouse models of cancer have revealed that deletion of core downstream autophagy genes (ATG5, ATG7) at the time of tumor iniation leads to a profound block in tumor progression leading to the development of autophagy inhibitors as cancer therapeutics. However, most preclinical studies and all clinical studies have relied on non-specific lysomotropic agents such as chloroquine and its derivatives, whose toxicity and off-target issues preclude further clinical development and which do not represent the impact of solely biochemically disrupting the autophagy pathway. Furthermore, druggable targets in the core autophagy pathway are quite limited, with ULK1 and ULK2 representing the only protein kinases in the pathway. Here we explore the genetic requirement for ULK1 and ULK2 in human PDA cancer cell lines and xenografts, and take advantage of new small molecule ULK1 inhibitors to demonstrate that ULK inhibition can overcome autophagy induction triggered by PDA therapeutics including chemotherapy and MEK inhibition. Finally we show that ULK inhibitors increase MHC Class I in PDA cells, suggestion a potential therapeutic avenue for such agents in combination with checkpoint immunotherapy.

category: cancer biology


title: BK polyomavirus (BKPyV) is a risk factor for bladder cancer through induction of APOBEC3-mediated genomic damage

abstract: Limited understanding of bladder cancer aetiopathology hampers progress in reducing incidence. BK polyomavirus (BKPyV) is a common childhood infection that can be reactivated in the adult kidney leading to viruria. Here we used a mitotically-quiescent, differentiated, normal human urothelial in vitro model to study BKPyV infection. BKPyV infection led to significantly elevated APOBEC3A and APOBEC3B protein, increased deaminase activity and greater numbers of apurinic/apyrimidinic sites in the host urothelial genome. BKPyV Large T antigen (LT-Ag) stimulated re-entry into the cell cycle via inhibition of Retinoblastoma protein and activation of EZH2, E2F1 and FOXM1, which combined to push urothelial cells from G0 into an arrested G2 cell cycle state. The single-stranded DNA displacement loops formed during BKPyV-infection, provide a substrate for APOBEC3 enzymes where they interacted with LT-Ag. These results support reactivated BKPyV infections in adults as a risk factor for bladder cancer in immune-insufficient populations, including transplant patients and the elderly.


title: Monolayer graphene-on-polymer dressings promote healing and stabilize skin temperature on acute and chronic wound models.

abstract:
O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

Monolayer graphene presented on the wound bed is assessed for its healing properties using both in vitro and in vivo models. For in vivo study, a cutaneous excisional wound is created on the dorsal surface of healthy and type-1 diabetic mice to mimic acute and delayed wound healing, respectively. A pig model is also chosen for its resemblance to human skin. Photographic and histological assessment of the wound are coupled with thermographic data recorded with an infrared camera. Graphene monolayer accelerates early phases of wound healing in vivo in every tested model. Upon removal of the bandage, wounds coated with graphene are less prone to temperature drop compared to the control samples. We hypothesize that graphene may directly shorten the inflammatory phase and/or enhance angiogenesis and cell migration in proliferative phase as demonstrated in vitro. Thermographic assessment of wounds could be of particular interest to follow both phenomena in an objective, rapid and non-invasive manner.

category: pharmacology and toxicology


title: Modular origins of high-amplitude co-fluctuations in fine-scale functional connectivity dynamics

abstract:
The topology of structural brain networks shapes brain dynamics, including the correlation structure of brain activity (functional connectivity) as estimated from functional neuroimaging data. Empirical studies have shown that functional connectivity fluctuates over time, exhibiting patterns that vary in the spatial arrangement of correlations among segregated functional systems. Recently, an exact decomposition of functional connectivity into frame-wise contributions has revealed fine-scale dynamics that are punctuated by brief and intermittent episodes (events) of high-amplitude co-fluctuations involving large sets of brain regions. Their origin is currently unclear. Here, we demonstrate that similar episodes readily appear in silico using computational simulations of whole-brain dynamics. As in empirical data, simulated events contribute disproportionately to long-time functional connectivity, involve recurrence of patterned co-fluctuations, and can be clustered into distinct families. Importantly, comparison of event-related patterns of co-fluctuations to underlying patterns of structural connectivity reveals that modular organization present in the coupling matrix shape patterns of event-related co-fluctuations. Our work suggests that brief, intermittent events in functional dynamics are partly shaped by modular organization of structural connectivity.

Significance StatementBrain regions engage in complex patterns of activation and co-activation over time. Relating these patterns to rest or task-related neural processing is a central challenge in cognitive neuroscience. Recent work has identified brief intermittent bursts of brain-wide signal co-fluctuations, called events, and shown that events drive functional connectivity. The origins of events are still unclear. Here, we address this gap in knowledge by implementing computational models of neural oscillators coupled by anatomical connections derived from maps of the human cerebral cortex. Analysis of the emerging large-scale brain dynamics reveals brief episodes with high system-wide signal amplitudes. Simulated events closely correspond to those seen recently in empirical recordings. Notably, simulated events are significantly aligned with underlying structural modules, thus suggesting an important role of modular network organization.

category: neuroscience


title: Processing of Pain by the Developing Brain: Evidence of Differences Between Adolescent and Adult Females

abstract: Adolescence is a sensitive period for both brain development and the emergence of chronic pain particularly in females. However, the brain mechanisms supporting pain perception during adolescence remain unclear. This study compares perceptual and brain responses to pain in female adolescents and adults to characterize pain processing in the developing brain. Thirty adolescent (ages 13-17) and thirty adult (ages 35-55) females underwent a functional MRI scan involving acute experimental pain. Participants received 12 ten-second noxious pressure stimuli which were applied to the left thumbnail at 2.5 and 4 kg/cm2, and rated pain intensity and unpleasantness on a visual analogue scale. We found a significant group-by-stimulus intensity interaction on pain ratings. Compared to adults, adolescents reported greater pain intensity and unpleasantness in response to 2.5 kg/cm2, but not 4 kg/cm2. Adolescents showed greater medial-lateral prefrontal cortex (PFC) and supramarginal gyrus activation in response to 2.5 kg/cm2, and greater medial PFC and rostral anterior cingulate responses to 4 kg/cm2. Adolescents showed augmented pain-evoked responses in the Neurologic Pain Signature and greater activation in the default mode (DMN) and ventral attention (VAN) networks. Also, the amygdala and associated regions played a stronger role in predicting pain intensity in adolescents, and activity in DMN and VAN regions more strongly mediated the relationship between stimulus intensity and pain ratings. This study provides the first evidence of augmented pain-evoked brain responses in healthy female adolescents involving regions important for nociceptive, affective and cognitive processing, in line with their augmented sensitivity to low-intensity noxious stimuli.


title: Gymnasts' ability for general motor imagery evaluated by bioelectric sensorimotor rhythms

abstract:
Previous psychological studies using questionnaires have consistently reported that athletes have superior motor imagery ability, both for sports-specific and sports non-specific movements. However, regarding motor imagery of sports non-specific movements, no physiological studies have demonstrated differences in neural activity between athletes and non-athletes. The purpose of the present study was to examine differences in bioelectric sensorimotor rhythms during kinesthetic motor imagery (KMI) of sports non-specific movements between gymnasts and non-gymnasts. We selected gymnasts as an example population because they are likely to have particularly superior motor imagery ability due to frequent usage of motor imagery including KMI as part of daily practice. Healthy young participants (16 gymnasts and 16 non-gymnasts) performed repeated motor execution and KMI of sports non-specific movements (wrist dorsiflexion and shoulder abduction of the dominant hand). Scalp electroencephalogram (EEG) was recorded over the contralateral sensorimotor cortex. During motor execution and KMI, sensorimotor EEG power is known to decrease in the - (8-15 Hz) and {beta}-bands (16-35 Hz), referred to as event-related desynchronization (ERD). We calculated the maximal peak of ERD both in the - (ERDmax) and {beta}-bands ({beta}ERDmax) as a measure of changes in corticospinal excitability. ERDmax was significantly greater in gymnasts, who subjectively evaluated their KMI as being more vivid, for both KMI tasks. On the other hand, {beta}ERDmax was greater in gymnasts only for shoulder abduction KMI. These findings suggest gymnasts signature of flexibly modulating sensorimotor rhythm with no movements, which may be the basis of their superior ability of KMI for sports non-specific movements.

New & NoteworthyKinesthetic motor imagery of sports non-specific movements was compared between gymnasts and non-gymnasts (i.e., healthy controls) from both physiological and psychological approaches. The EEG sensorimotor rhythms during kinesthetic motor imagery were more desynchronized in gymnasts who subjectively imaged their own movements as being more vivid. The work reveals novel ability in gymnasts to flexibly control their sensorimotor rhythms with no actual movements, which would be the basis of their superior ability of motor imagery.


title: Gymnasts' ability to modulate bioelectric sensorimotor rhythms during kinesthetic motor imagery of sports non-specific movements


title: Alcohol Use Disrupts Age-Appropriate Cortical Thinning in Adolescence: A Data Driven Approach

abstract:
ObjectiveCortical thickness changes dramatically during development and is influenced by adolescent drinking. However, previous findings have been inconsistent and limited by region-of-interest approaches that are underpowered because they do not conform to the underlying heterogeneity from the effects of alcohol.

MethodsAdolescents (n=657; 12-22 years at baseline) from the National Consortium on Alcohol and Neurodevelopment in Adolescence (NCANDA) who endorsed little to no alcohol use at baseline were assessed with structural MRI and followed longitudinally at four yearly intervals. Seven unique spatially covarying patterns of cortical thickness were obtained from the baseline scans by applying a novel data-driven method called non-negative matrix factorization (NMF). The cortical thickness maps of all participants longitudinal scans were projected onto vertex-level cortical patterns to obtain participant-specific coefficients for each pattern. Linear mixed-effects models were fit to each pattern to investigate longitudinal effects of alcohol consumption on cortical thickness.

ResultsIn most NMF-derived cortical thickness patterns, the longitudinal rate of decline in no/low drinkers was similar for all age cohorts, among moderate drinkers the decline was faster in the younger cohort and slower in the older cohort, among heavy drinkers the decline was fastest in the younger cohort and slowest in the older cohort (FDR corrected p-values < 0.01).

ConclusionsThe NMF method can delineate spatially coordinated patterns of cortical thickness at the vertex level that are unconstrained by anatomical features. Age-appropriate cortical thinning is more rapid in younger adolescent drinkers and slower in older adolescent drinkers.


title: Megalencephalic leukoencephalopathy with subcortical cysts is a developmental disorder of the gliovascular unit

abstract: Absence of the astrocyte-specific membrane protein MLC1 is responsible for megalencephalic leukoencephalopathy with subcortical cysts (MLC); this rare type of leukodystrophy is characterized by early-onset macrocephaly and progressive white matter vacuolation that lead to ataxia, spasticity, and cognitive decline. During postnatal development (from P5 to P15 in the mouse), MLC1 forms a membrane complex with GlialCAM (another astrocytic transmembrane protein) at the junctions between perivascular astrocytic processes (PvAPs, which along with blood vessels form the gliovascular unit (GVU)). We analyzed the GVU in the Mlc1 knock-out mouse model of MLC. The absence of MLC1 led to an accumulation of fluid in the brain but did not modify the endothelial organization or the integrity of the blood-brain barrier. From P10 onward, the postnatal acquisition of vascular smooth muscle cell contractility was altered, resulting in a marked reduction in arterial perfusion and neurovascular coupling. These anomalies were correlated with alterations in astrocyte morphology, astrocyte polarity and the structural organization of the PvAPs perivascular coverage, and poor intraparenchymal circulation of the cerebrospinal fluid (CSF). Hence, MLC1 is required for the postnatal development and organization of PvAPs and controls vessel contractility and intraparenchymal interstitial fluid clearance. Our data suggest that (i) MLC is a developmental disorder of the GVU, and (ii) PvAP and VSMC maturation defects are primary events in the pathogenesis of MLC and therapeutic targets for this disease.


title: Impaired α-tubulin re-tyrosination leads to synaptic dysfunction and is a feature of Alzheimer's disease

abstract: In neurons, dynamic microtubules play regulatory roles in neurotransmission and synaptic plasticity. While stable microtubules contain detyrosinated tubulin, dynamic microtubules are composed of tyrosinated tubulin, suggesting that the tubulin tyrosination/detyrosination (Tyr/deTyr) cycle modulates microtubule dynamics and synaptic function. In the Tyr/deTyr cycle, the C-terminal tyrosine of -tubulin is re-added by tubulin-tyrosine-ligase (TTL). Here we show that TTL+/- mice exhibit decreased tyrosinated microtubules, synaptic plasticity and memory deficits, and that reduced TTL expression is a feature of sporadic and familial Alzheimers disease (AD), with human APPV717I neurons having less dynamic microtubules. We find that spines visited by dynamic microtubules are more resistant to Amyloid{beta}1-42 and that TTL, by promoting microtubule entry into spines, prevents A{beta}1-42-induced spine pruning. Our results demonstrate that the Tyr/deTyr cycle regulates synaptic plasticity, is protective against spine injury, and that tubulin re-tyrosination is lost in AD, providing evidence that a defective Tyr/deTyr cycle may contribute to neurodegeneration.


title: Differentiation of cortical brain organoids and optic nerve-like structures from retinal confluent cultures of pluripotent stem cells

abstract: Advances in the study of neurological conditions have been possible due to induced pluripotent stem cell technologies and the generation of neural cell types and organoids. Numerous studies have described the generation of neural ectoderm-derived retinal and brain structures from pluripotent stem cells. However, the field is still troubled by technical challenges, including high culture costs and organoid-to-organoid variability. Here, we describe a simple and economical protocol that reproducibly gives rise to the neural retina and cortical brain regions from confluent cultures of stem cells. The spontaneously generated cortical organoids were isolated and cultured in suspension conditions for maturation and are transcriptionally comparable to organoids generated by other methods and to human foetal cortex. Furthermore, these organoids show spontaneous functional network activity with proteomic analysis and electron microscopy demonstrating the presence of synaptic components and maturity. The generation of retinal and brain organoids in close proximity also enabled their mutual isolation. Further culture of this complex organoid system demonstrated the formation of optic nerve-like structures connecting retinal and brain organoids, which might facilitate the investigation of the mechanisms of neurological diseases of the eye and brain.


title: High-throughput mapping of single-cell molecular and projection architecture of neurons by retrograde barcoded labelling

abstract:
Deciphering mesoscopic connectivity of the mammalian brain is a pivotal step in neuroscience. Most imaging-based conventional neuroanatomical tracing methods identify area-to-area or sparse single neuronal labeling information. Although recently developed barcode-based connectomics has been able to map a large number of single-neuron projections efficiently, there is a missing link in single-cell connectome and transcriptome. Here, combining single-cell RNA sequencing technology, we established a retro-AAV barcode-based multiplexed tracing method called MEGRE-seq (Multiplexed projEction neuRons retroGrade barcodE), which can resolve projectome and transcriptome of source neurons simultaneously. Using the ventromedial prefrontal cortex (vmPFC) as a proof- of-concept neocortical region, we investigated projection patterns of its excitatory neurons targeting five canonical brain regions, as well as corresponding transcriptional profiles. Dedicated, bifurcated or collateral projection patterns were inferred by digital projectome. In combination with simultaneously recovered transcriptome, we find that certain projection pattern has a preferential layer or neuron subtype bias. Further, we fitted single-neuron two-modal data into a machine learning-based model and delineated gene importance by each projection target. In summary, we anticipate that the new multiplexed digital connectome technique is potential to understand the organizing principle of the neural circuit by linking projectome and transcriptome.

HighlightsO_LIMERGE-seq recovers single-neuron transcriptome and projectome simultaneously
C_LIO_LIMERGE-seq partitions projection pattern into neuronal layer and subtype
C_LIO_LIMERGE-seq bridges projection pattern to differentially expressed genes
C_LIO_LIMachine learning models interpret relationship between digital projectome and gene expression
C_LI


title: Impact of α-synuclein fibrillar strains and β-amyloid assemblies on mouse cortical neurons endo-lysosomal logistics

abstract:
Endosomal transport and positioning are involved in establishing neuronal compartment architecture, dynamics and function, contributing to neuronal intracellular logistics. Furthermore, endo-lysosomal dysfunction has been identified as a common mechanism in neurodegenerative diseases. Here, we analyzed endolysosomal transport following the external application of -synuclein (-syn) fibrillar polymorphs, {beta}-amyloid (A{beta}) fibrils and oligomers on primary cultures of mouse cortical neurons. We used a simple readout to measure this transport: the spontaneous endocytosis of fluorescent nanodiamonds -- a perfectly stable nano-emitter -- in cultured neurons. We then performed a high-throughput automatic extraction and quantification of the directed motions of these nanodiamonds. -syn fibrillar polymorphs, A{beta} fibrils and oligomers halved the proportion of nanodiamonds transported along microtubules, but only slightly decreased their interactions with cortical neurons. This large decrease in endosomal transport would be expected to have a huge impact on neuronal homeostasis. We then assessed lysosomal dynamics with Lysotracker. The exposure of neurons to A{beta} oligomers led to an increase in the number of lysosomes, a decrease in the fraction of moving lysosomes and an increase in their size, reminiscent of findings for the APP transgenic model of Alzheimers disease. We then analyzed the effect of -syn fibrillar polymorphs, A{beta} fibrils and oligomers on endosomal and lysosomal transport and quantified the directed transport of these assemblies within cortical neurons. We report different impacts on endosomal and lysosomal transport parameters and differences in trajectory length for cargoes loaded with pathogenic protein assemblies. Our results suggest that the internalization and transport of intraneuronal pathogenic protein aggregates are potential targets for novel neuroprotective treatment strategies.

Significance StatementNeurodegenerative diseases (NDs) are characterized by the deposition of protein aggregates with broad-range neuronal toxicity. Defects of endolysosomal trafficking are increasingly being seen as key pathological features of NDs, probably contributing to synaptic dysfunction and ultimate neuronal death. We used fast fluorescence videomicroscopy to investigate endosomal and lysosomal dynamics in the branches of mouse cortical neurons in primary cultures following the application of -syn fibrillar polymorphs (fibrils and ribbons) and A{beta} assemblies (oligomers and fibrils). We provide new insight into the differential effects of these pathogenic protein assemblies on endosomal and lysosomal transport, and reveal differences in the transport characteristics of the compartments loaded with these protein assemblies relative to endosomes.


title: Mind the gap: performance metric evaluation in brain-age prediction

abstract: Estimating age based on neuroimaging-derived data has become a popular approach to developing markers for brain integrity and health. While a variety of machine-learning algorithms can provide accurate predictions of age based on brain characteristics, there is significant variation in model accuracy reported across studies. We predicted age based on neuroimaging data in two population-based datasets, and assessed the effects of age range, sample size, and age-bias correction on the model performance metrics r, R2, Root Mean Squared Error (RMSE), and Mean Absolute Error (MAE). The results showed that these metrics vary considerably depending on cohort age range; r and R2 values are lower when measured in samples with a narrower age range. RMSE and MAE are also lower in samples with a narrower age range due to smaller errors/brain age delta values when predictions are closer to the mean age of the group. Across subsets with different age ranges, performance metrics improve with increasing sample size. Performance metrics further vary depending on prediction variance as well as mean age difference between training and test sets, and age-bias corrected metrics indicate high accuracy - also for models showing poor initial performance. In conclusion, performance metrics used for evaluating age prediction models depend on cohort and study-specific data characteristics, and cannot be directly compared across different studies. Since age-bias corrected metrics in general indicate high accuracy, even for poorly performing models, inspection of uncorrected model results provides important information about underlying model attributes such as prediction variance.


title: Slow Cortical Waves via Cyclicity

abstract:
Fine-grained understanding of dynamics in cortical networks is crucial in unpacking brain function. Here, we introduce a novel analytical method to characterize the dynamic interaction between distant brain regions, and apply it to data from the Human Connectome Project.

Resting-state fMRI results in time series recordings of the activity of different brain regions, which are aperiodic and lacking a base frequency. Cyclicity Analysis, a novel technique robust with respect to time-reparametrizations, is effective in recovering temporal ordering of such time series along a circular trajectory without assuming any time-scale. Our analysis detected slow cortical waves of activity propagating across the brain with consistent lead-lag relationships between specific brain regions. We also observed short bursts of task-modulated strong temporal ordering that dominate overall lead-lag relationships between pairs of regions in the brain. Our results suggest the possible role played by slow waves of information transmission between brain regions that underlie emergent cognitive function.


title: Slow Cortical Waves through Cyclicity Analysis


title: Large-scale digital traces of university students show that morning classes are bad for attendance, sleep, and academic performance

abstract:
Attending classes and sleeping well are important for students academic success. However, early classes might impede learning by contributing to absenteeism and insufficient sleep. We used big datasets collected passively from university students to test the hypothesis that morning classes are associated with poorer attendance, shorter sleep, and lower grades. Wi-Fi connection data were used to estimate attendance rates of 24,678 students enrolled in lecture courses with start times ranging from 08:00 to 16:00. Students interactions with the universitys Learning Management System (LMS) were used to estimate nocturnal sleep opportunities by compiling 17.4 million logins from 39,458 students with data sorted by students first class of the day. Objective sleep behavior was assessed in 181 students who took part in a 6-week actigraphy study. We found that Wi-Fi confirmed attendance was about 15 percentage points lower in students taking classes at 08:00 compared with later start times. Actigraphy data revealed that students frequently slept past the start of morning classes. LMS and actigraphy data showed that nocturnal sleep opportunities and total sleep time decreased with earlier class start times due to students waking up earlier. Analyses of grades in 27,281 students showed that having morning classes on more days of the week resulted in a lower grade point average. These findings suggest cumulative negative effects of morning classes on learning. Early morning classes force many students to decide to either sleep more and skip class, or sleep less to attend class. Therefore, universities should avoid scheduling early morning classes.

Significance StatementWe show that morning classes are associated with lower attendance, shorter nocturnal sleep, and lower grade point average in university students. Scalable methods for measuring attendance and sleep were developed using students Wi-Fi connection data and interactions with the Learning Management System. Students had lower attendance rates and frequently slept past the start of early morning classes. However, students still lost about an hour of sleep on average when they had early morning classes due to waking up earlier than usual. Students who had morning classes on more days of the week had a lower grade point average. Our results suggest cumulative negative effects of morning classes on students academic performance. Universities should avoid scheduling early morning classes.


title: Reduced cortico-muscular beta coupling in Parkinsons disease predicts motor impairment

abstract: Long-range communication through the motor system is thought to be facilitated by phase coupling between neural activity in the 15-30 Hz beta range. During periods of sustained muscle contraction (grip), such coupling is manifest between motor cortex and the contralateral forearm muscles - measured as the cortico-muscular coherence (CMC). We examined alterations in CMC in individuals with Parkinsons disease (PD), while equating grip strength between individuals with PD (off their medication) and healthy control participants. We show a marked reduction in beta CMC in the PD group, even though the grip strength was comparable between the two groups. Moreover, the reduced CMC was related to motor symptoms, so that individuals with lower CMC also displayed worse motor symptoms. These findings highlight the CMC as a simple, effective, and clinically relevant neural marker of PD pathology, with the potential to aid monitoring of disease progression and the efficacy of novel treatments for PD.


title: Corpus callosal microstructure predicts bimanual motor performance in chronic stroke survivors

abstract:
AO_SCPLOWBSTRACTC_SCPLOWMicrostructural changes in the corpus callosum are associated with more severe motor impairment in the paretic hand, poor recovery, and general disability. Considering its role in bimanual coordination, we suspected that these microstructural changes across the callosum may also be reflected in the performance of ecologically valid routine bimanual tasks. Thus, the purpose of this study was to determine if callosal microstructure predicts bimanual motor performance in chronic stroke survivors by examining the regions of the corpus callosum connecting both the sensorimotor and non-sensorimotor cortices. We examined the relationship between the fractional anisotropy across the CC and movement times for two self-initiated and self-paced bimanual tasks in 41 chronic stroke survivors. Using publicly available control datasets (n = 52), matched closely for acquisition parameters, we also explored the effect of stroke and age on callosal microstructure. There were two main findings: First, callosal microstructure was significantly associated with bimanual performance in chronic stroke survivors. Notably, a significant relationship was observed not only with the primary sensorimotor regions, but also regions of the premotor/supplementary motor and prefrontal regions. Second, chronic stroke survivors presented with significantly lower mean FA, compared to neurologically intact adults. We conclude that in mild-to-moderate chronic stroke survivors with relatively localized lesions to the motor areas, callosal microstructure can be expected to change in not only the primary sensorimotor region, but also more anteriorly in the secondary motor regions and the genu and is associated with performance on cooperative bimanual tasks.

SignificanceA goal of rehabilitation after stroke is to promote the return to pre-stroke levels of upper limb function and use, predominantly characterized by coordinated bimanual activities. In this study, we find that in the chronic phase of stroke, microstructural disorganization within the corpus callosum predicts motor performance on real-world bimanual tasks and lends important insight into the indirect, remote effects of stroke.

HO_SCPLOWIGHLIGHTSC_SCPLOWO_LIWe provide initial evidence that corpus callosal microstructure predicts performance on two self-initiated and self-paced bimanual tasks.
C_LIO_LIAssociations were strongest for fibers connecting the primary sensorimotor cortices followed by the pre- and supplementary motor, and prefrontal cortices.
C_LIO_LISignificant reductions in fractional anisotropy were observed in stroke survivors for all regions of the corpus callosum.
C_LI


title: Corpus callosal microstructure predicts bimanual motor performance in chronic stroke survivors: A preliminary cross-sectional study


title: BpOmpW Antigen Stimulates the Necessary Immune Correlates of Protection Against Melioidosis

abstract: SUMMMARYMelioidosis is a fatal disease caused by Burkholderia pseudomallei Gram-negative bacteria. It is the causative of 89,000 deaths per year in endemic areas of Southeast Asia and Northern Australia. Diabetes mellitus is the most risk factor, increasing 12-fold the susceptibility for severe disease. IFN-{gamma} responses from CD4 and CD8 T cells, but also from NK and NKT cells are necessary to eliminate the pathogen. Elucidating the immune correlates of protection of our previously described protective BpOmpW vaccine is an essential step of any vaccine before clinical trials. Thus, we immunized non-insulin resistant C57BL/6j mice and an insulin resistant C57BL/6j mouse model of Type 2 Diabetes (T2D) with BpOmpW using Sigma Adjuvant System (SAS) (treatment) or SAS only (control). Two weeks later bloods and spleens were collected and serological analysis & in vitro exposure of splenocytes to the antigen for 60 hours were performed in both controls and treatment groups to finally analyze the stained splenocytes by flow cytometry. BpOmpW induced strong antibody response, stimulated effector CD4+ and CD8+ T cells and CD4+ CD25+ Foxp3+regulatory T cells and produced higher IFN-{gamma} responses in CD4+, CD8+, NK and NKT cells relative to the control group in non-insulin resistant mice. T cell responses of insulin resistant mice to BpOmpW were comparable to those in non-insulin resistant mice. In addition, as a precursor to its evaluation in human studies, humanised HLA-DR and HLA-DQ transgenic mice elicited IFN-{gamma} recall responses in an ELISPoT-based study and PBMCs from donors that were in contact to BpOmpW for seven days experienced T cell proliferation. Finally, plasma from melioidosis survivors with diabetes recognized our BpOmpW vaccine antigen. Overall, these range of approaches used strongly indicate that BpOmpW elicits the required immune correlates of protection to combat melioidosis and bring the vaccine closer to clinical trials.

category: immunology


title: Detection of Campylobacter in air samples from poultry houses using shot-gun metagenomics - a pilot study

abstract:
BackgroundFoodborne pathogens such as Campylobacter jejuni are responsible for a large fraction of the gastrointestinal infections worldwide associated with poultry meat. Campylobacter spp. can be found in the chicken fecal microbiome and can contaminate poultry meat during the slaughter process. The current standard methods to detect these pathogens at poultry farms use fecal dropping or boot swaps in combination with cultivation / PCR. In this study, we have used air filters in combination with shotgun metagenomics for the detection of Campylobacter in poultry houses and MOCK communities to test the applicability of this approach for the detection of foodborne pathogens.

ResultsThe spiked MOCK communities showed that we could detect as little as 200 CFU Campylobacter per sample using our protocols. Since we were interested in detecting Campylobacter, a DNA extraction protocol for Gram negative bacteria was chosen, and as expected, we found that the DNA extraction protocol created a substantial bias affecting the community composition of the MOCK communities. It can be expected that the same bias is present for poultry house samples analyzed. We observed significant amounts of Campylobacter on the air filters using both real-time PCR as well as shotgun metagenomics, irrespective of the amount of spiked in Campylobacter cells, suggesting that the flocks in both houses harboured Campylobacter spp.. Interestingly, in both houses we find diverse microbial communities present in the indoor air. In addition, have we tested the Campylobacter detection rate using shotgun metagenomics by spiking with different levels of C. jejuni cells in both the mock and the house samples. This showed that even with limited sequencing Campylobacter is detectable in samples with low abundance.

ConclusionsThese results show that air sampling of poultry houses in combination with shotgun metagenomics can detect and identify Campylobacter spp. present at low levels. This is important since early detection of Campylobacter in food production can help to decrease the number of food-borne infections.

category: microbiology


title: OmpF Downregulation Mediated by Sigma E or OmpR Activation Confers Cefalexin Resistance in Escherichia coli in the Absence of Acquired β-Lactamases.

abstract: Cefalexin is a widely used 1st generation cephalosporin, and resistance in Escherichia coli is caused by Extended-Spectrum (e.g. CTX-M) and AmpC {beta}-lactamase production and therefore frequently coincides with 3rd generation cephalosporin resistance. However, we have recently identified large numbers of E. coli isolates from human infections, and from cattle, where cefalexin resistance is not {beta}-lactamase mediated. Here we show, by studying laboratory selected mutants, clinical isolates, and isolates from cattle, that OmpF porin disruption or downregulation is a major cause of cefalexin resistance in E. coli. Importantly, we identify multiple regulatory mutations that cause OmpF downregulation. In addition to mutation of ompR, already known to downregulate OmpF and OmpC porin production, we find that rseA mutation, which strongly activates the Sigma E regulon, greatly increasing DegP production, which degrades OmpF, OmpC and OmpA porins. Furthermore, we reveal that mutations affecting lipopolysaccharide structure, exemplified by the loss of GmhB, essential for lipopolysaccharide heptosylation, also modestly activate DegP production, resulting in OmpF degradation. Remarkably, given the critical importance attached to such systems for normal E. coli physiology, we find evidence for DegP-mediated OmpF downregulation, gmhB and rseA loss of function mutation in E. coli isolates derived from human infections. Finally, we show that these regulatory mutations enhance the ability of group 1 CTX-M {beta}-lactamase to confer reduced carbapenem susceptibility, particularly those mutations that cause OmpC in addition to OmpF downregulation.


title: Genetic code degeneracy is established by the decoding center of the ribosome

abstract: The degeneracy of the genetic code confers a wide array of properties to coding sequences. Yet, its origin is still unclear. A structural analysis has shown that the stability of the Watson-Crick base pair at the second position of the anticodon-codon interaction is a critical parameter controlling the extent of non-specific pairings accepted at the third position by the ribosome, a flexibility at the root of degeneracy. Based on recent cryo-EM analyses, the present work shows that residue A1493 of the decoding center provides a significant contribution to the stability of this base pair, revealing that the ribosome is directly involved in the establishment of degeneracy. Building on existing evolutionary models, we show the evidence that the early appearance of A1493 and A1492 established the basis of degeneracy when an elementary kinetic scheme of translation was prevailing. Logical considerations on the expansion of this kinetic scheme indicate that the acquisition of the peptidyl transferase center was the next major evolutionary step, while the induced-fit mechanism, that enables a sharp selection of the tRNAs, necessarily arose later when G530 was acquired by the decoding center.

category: molecular biology


title: Nuclear RNA concentration coordinates RNA production with cell size in human cells

abstract: Unlike its DNA template, RNA abundance and synthesis rates increase with cell size, as part of a mechanism of cellular RNA concentration homeostasis. Here, we study this scaling phenomenon in human cells by combining genome-wide perturbations with quantitative single-cell measurements. Despite relative ease in perturbing RNA synthesis, we find that RNA concentrations remain highly constant. Systems-level analysis indicates that perturbations that would lead to increased nuclear mRNA abundance result in downregulation of mRNA synthesis. This is associated with reduced levels of several transcription-associated proteins and protein states that are normally coordinated with RNA production in single cells, including RNA polymerase II (Pol II) itself. Acute shut-down of nuclear RNA degradation, elevation of nuclear mRNA levels, and mathematical modelling indicate that mammalian cells achieve RNA concentration homeostasis by an mRNA-based negative feedback on transcriptional activity in the nucleus. Ultimately, this acts to robustly scale Pol II abundance with cell volume and coordinate mRNA synthesis and degradation.


title: 3D matrix adhesion composition facilitates nuclear force coupling to drive invasive cell migration

abstract: Cell invasion and metastasis is a multi-step process, initialised through the acquisition of a migratory phenotype and the ability to move through differing and complex 3D extracellular environments. In this study we set out to identify the parameters required for invasive cell migration in 3D environments. Cells interact with the extracellular matrix via transmembrane-spanning integrin adhesion complexes, which are well characterised in cells plated on 2D surfaces, yet much less is known about them in cells embedded in 3D matrices. We establish a technique to determine the composition of cell matrix adhesion complexes of invasive breast cancer cells in 3D matrices and on 2D surfaces and we identify an interaction complex enriched in 3D adhesive sites required for 3D invasive migration. Depletion of {beta}-PIX-Myosin18A (Myo18A) abolishes cancer cell invasion, without negatively affecting matrix degradation, Rho GTPase signalling, or protrusion formation in collagen matrices. Instead, in a mechanism only seen in cells moving through 3D matrix, {beta}-PIX and Myo18A drive the polarised recruitment of non-muscle Myosin 2A (NM2A) to the tips of protrusions. This recruitment of NM2A is required for the creation of an NM2A-NM2B isoform gradient, which ranges from the protrusion to the nucleus. We observe a requirement for active force transmission to the nucleus during invasive migration that is needed to pull the nucleus forward. We postulate that the establishment of the NM2A-NM2B actomyosin gradient facilitates the coupling of cell-matrix interactions at the protrusive cell front with nuclear movement, enabling effective invasive migration and front-rear cell polarity.

category: cell biology


title: Selection-free non-viral method revealed highly efficient CRISPR-Cas9 genome editing of human pluripotent stem cells guided by cellular autophagy

abstract: CRISPR-Cas9 mediated genome editing of human pluripotent stem cells (hPSCs) provides strong avenues for human disease modeling, drug discovery and cell replacement therapy. Genome editing of hPSCs is an extremely inefficient process and requires complex gene delivery and selection methods to improve edit efficiency which are not ideal for clinical applications. Here, we have shown a selection free simple lipofectamine based transfection method where a single plasmid encoding guide RNA (gRNA) and Cas9 selectively transfected hPSCs at the colony edges. Upon dissection and sequencing, the edge cells showed more than 30% edit frequency compared to the reported 3% rate under no selections. Increased cellular health of the edge cells as revealed by reduced autophagy gene-expressions is critical for such transfection pattern. Edge specific transfection was inhibited by blocking lysosomal activity which is essential for autophagy. Hence, our method provides robust scarless genome-editing of hPSCs which is ideal for translational research.


title: Restoration of DNA Integrity and Cell Cycle by Electric Stimulation in Planarian Tissues Damaged by Ionizing Radiation

abstract: Exposure to high levels of ionizing {gamma}-radiation leads to irreversible DNA damage and cell death. Here, we establish that exogenous application of electric stimulation enables cellular plasticity to reestablish stem cell activity in tissues damaged by ionizing radiation. We show that sub-threshold direct current stimulation (DCS) rapidly restores pluripotent stem cell populations previously eliminated by lethally {gamma}-irradiated tissues of the planarian flatworm Schmidtea mediterranea. Our findings reveal that DCS enhances DNA repair, transcriptional activity, and cell cycle entry in post-mitotic cells. These responses involve rapid increases in cytosolic [Ca2+] through the activation of L-type Cav channels and intracellular Ca2+ stores leading to the activation of immediate early genes and ectopic expression of stem cell markers in postmitotic cells. Overall, we show the potential of electric current stimulation to reverse damaging effects of high dose {gamma}-radiation in adult tissues. Furthermore, our results provide mechanistic insights describing how electric stimulation effectively translates into molecular responses capable of regulating fundamental cellular functions without the need for genetic or pharmacological intervention.

category: developmental biology


title: The role of Cyp19a1 in female pathway of a freshwater turtle (Mauremys reevesii) with temperature-dependent sex determination

abstract: The molecular mechanism of temperature-dependent sex determination (TSD) in reptiles has been drawn great interest from biologists for several decades. However, which genetic factors are essential for TSD remain elusive, especially for the female sex determination process. Cyp19a1, encodes an enzyme of aromatase catalyzing the conversion of testosterone to estrogen, has been confirmed to modulate steroid hormones involved in the sexual differentiation of many species, but whether it has a critical role in determining the gonadal sexual fate in TSD is still to be elucidated. Here, we identified that Cyp19a1 expression exhibited a temperature-dependent, sexually dimorphic expression pattern, preceding gonadal sex differentiation in a TSD turtle Mauremys reevesii. Cyp19a1 expression in gonads increased dramatically when embryos developed at high female-producing temperatures (FPT), but were extremely low throughout embryogenesis at low male-producing temperatures (MPT). Cyp19a1 expression increased rapidly in response to the temperature shift from MPT to FPT in developing gonads. The sexual phenotype of turtles was successfully reversed by aromatase inhibitor treatment at FPT, and by estrogen treatment at MPT, accompanied with the rapid upregulation of Cyp19a1. These results demonstrate that Cyp19a1 is essential for the female sex determination process in M. reevesii, indicating its vital role in the female pathway of TSD.


title: Diel CO2 fluctuations alter the molecular response of coral reef fishes to ocean acidification conditions

abstract: Environmental CO2 variation can modify the responses of marine organisms to ocean acidification, yet the underlying mechanisms for this effect remain unclear. On coral reefs, environmental CO2 fluctuates on a regular day-night cycle. Effects of future ocean acidification on coral reef fishes might therefore depend on their response to this diel cycle of CO2. To evaluate the effects on the brain molecular response, we exposed two common reef fishes (Acanthochromis polyacanthus and Amphiprion percula) to two projected future CO2 levels (750 and 1,000 atm) under both stable and diel fluctuating conditions. We found a common signature to stable elevated pCO2 for both species, which included the downregulation of immediate early genes, indicating lower brain activity. The transcriptional program was more strongly affected by higher average CO2 in a stable treatment than for fluctuating treatments, however, the largest difference in molecular response was between stable and fluctuating CO2 treatments. This indicates that a response to a change in environmental CO2 conditions is different for organisms living in a fluctuating than in stable environments. The differential regulation was related to steroid hormones and circadian rhythm (CR). Both species exhibited a marked difference in the expression of CR genes among CO2 treatments, possibly accommodating a more flexible adaptive approach to acid-base control, which could explain reduced impairment. Our results suggest that environmental CO2 fluctuations might enable reef fishes to phase shift their clocks and anticipate CO2 changes, thereby avoiding impairments and more successfully adjust to ocean acidification conditions.

category: ecology


title: Species turnover between age groups of horses and positive network of co-occurrences define the structure of horse strongylid communities: a meta-analysis

abstract:
Grazing horses are infected by a wide range of strongylid species mostly located in the large intestine. Despite their impact on equine health and the emergence of drug resistant isolates, the phenology of these nematodes has been poorly characterized and the rules structuring their assembly as a community are not understood. Here, we compiled data on 46 equine strongylid species collected worldwide at the regional or horse scales (upon deworming or after necropsy) to analyse their richness, diversity and associated factors of variation. Worldwide, twelve species from the Cylicocyclus (n = 4), Cylicostephanus (n = 3), Coronocyclus (n = 2) and Cyathostomum (n = 2) genera were found in at least 75% of sites. Geoclimatic conditions had a limited effect on strongylid communities, but reduced species richness was found under the temperate European area. The recovery method did not affect species richness and differences on the temporal and sampling effort scales between studies applying either methods underpinned heterogeneous variances in community diversity.

At the horse level, rarefaction curves correlated poorly to parasite egg excretion, suggesting little contribution of community diversity to this trait. Using a diversity partitioning approach, we found that within-host diversity represented half of overall diversity underscoring the importance of host density and environmental contamination to the diversity of strongylid communities. While this is expected to erase diversity across communities, species turnover between age classes was the second most important contributor to overall diversity (23.9%). This was associated with a network of positive co-occurrences between the four most prevalent genera that we resolved at the anatomical niche level. Altogether this pattern of {beta}-diversity maintenance across age classes combined with positive co-occurrences may be grounded by priority effects between major species. Our findings set the first assembly rules of equine strongylid communities.


title: Key informant perceptions on wildlife hunting in India during the COVID-19 lockdown

abstract: Lockdowns intended to control the COVID-19 pandemic resulted in major socioeconomic upheavals across the world. While there were numerous reports of these lockdowns benefiting wildlife by reducing human movement and habitat disturbance, increased hunting during these lockdowns emerged as a conservation concern, particular in tropical Asia and Africa. We used online interviews with key informants including wildlife researchers, enforcement staff and NGO employees (N=99), and media reports (N=98), to examine the impacts of Indias COVID-19 lockdown (March-May 2020) on wildlife hunting across the country. We asked whether and how hunting patterns changed during the lockdown, and explored socioeconomic and institutional factors underlying these changes. Over half the interviewees spread over 43 administrative districts perceived hunting (mammals, in particular) to have increased during the lockdown relative to a pre-lockdown reference period. Interviewees identified household consumption (53% of respondents) and sport and recreation (34%) as main motivations for hunting during the lockdown, and logistical challenges for enforcement (36%), disruption of food supply (32%), and need for recreational opportunities (32%) as key factors associated with hunting during this period. These insights were corroborated by statements by experts extracted from media articles. Collectively, our findings suggest that the COVID-19 lockdown potentially increased hunting across much of India, and emphasize the role of livelihood and food security in mitigating threats to wildlife during such periods of acute socioeconomic perturbation.


title: Environmental DNA (eDNA) metabarcoding surveys extend the range of invasion for non-indigenous freshwater species in Eastern Europe.

abstract: Active environmental DNA (eDNA) surveillance through species-specific amplification has shown increased sensitivity in the detection of non-indigenous species (NIS) compared to traditional approaches. When many NIS are of interest, however, active surveillance decreases in cost- and time-efficiency. Passive surveillance through eDNA metabarcoding takes advantage of the complex DNA signal in environmental samples and facilitates the simultaneous detection of multiple species. While passive eDNA surveillance has previously detected NIS, comparative studies are essential to determine the ability of eDNA metabarcoding to accurately describe the range of invasion for multiple NIS versus alternative approaches. Here, we surveyed twelve sites, covering nine rivers across Belarus for NIS with three different techniques, i.e., an ichthyological, hydrobiological, and eDNA survey, whereby DNA was extracted from 500 mL surface water samples and amplified with two 16S rRNA primer assays targeting the fish and macro-invertebrate biodiversity. Nine non-indigenous fish and ten non-indigenous sediment-living macro-invertebrates were detected by traditional surveys, while seven NIS eDNA signals were picked up, including four fish, one aquatic and two sediment-living macro-invertebrates. Passive eDNA surveillance extended the range of invasion further north for two invasive fish and identified a new NIS for Belarus, the freshwater jellyfish Craspedacusta sowerbii. False-negative detections for the eDNA survey could be attributed to (i) preferential amplification of aquatic over sediment-living macro-invertebrates from surface water samples and (ii) an incomplete reference database. The evidence provided in this study recommends the implementation of both molecular-based and traditional approaches to maximize the probability of early detection of non-native organisms.


title: Heritability and phenotypic plasticity of biting time behaviors in the major African malaria vector Anopheles arabiensis

abstract: Use of Insecticide Treated Nets for malaria control has been associated with shifts in mosquito vector feeding behavior including earlier and outdoor biting on humans. The relative contribution of phenotypic plasticity and heritability to these behavioural shifts is unknown. Elucidation of the mechanisms behind these shifts is crucial for anticipating impacts on vector control. We used a novel portable semi-field system (PSFS) to experimentally measure heritability of biting time in the malaria vector Anopheles arabiensis in Tanzania. In PSFS assays, the biting time of F2 offspring (early: 18:00-21:00, mid: 22:00-04:00 or late: 05:00-07:00) was significantly associated with that of their wild-caught F0 grandmothers, corresponding to an estimated heritability of 0.30 (95% CI: 0.20, 0.41). F2 from early-biting F0 were more likely to bite early than F2 from mid or late late-biting F0. Similarly, the probability of biting late was higher in F2 derived from mid and late-biting F0 than from early-biting F0. Our results indicate that variation in biting time is attributable to additive genetic variation. Selection can therefore act efficiently on mosquito biting times, highlighting the need for control methods that target early and outdoor biting mosquitoes.

category: evolutionary biology


title: Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

abstract: The teleost medaka (Oryzias latipes) is a well-established vertebrate model system, with a long history of genetic research, and multiple high-quality reference genomes available for several inbred strains (HdrR, HNI and HSOK). Medaka has a high tolerance to inbreeding from the wild, thus allowing one to establish inbred lines from wild founder individuals. We have exploited this feature to create an inbred panel resource: the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. This panel of 80 near-isogenic inbred lines contains a large amount of genetic variation inherited from the original wild population. We used Oxford Nanopore Technologies (ONT) long read data to further investigate the genomic and epigenomic landscapes of a subset of the MIKK panel. Nanopore sequencing allowed us to identify a much greater variety of high-quality structural variants compared with Illumina sequencing. We also present results and methods using a pan-genome graph representation of 12 individual medaka lines from the MIKK panel. This graph-based reference MIKK panel genome revealed novel differences between the MIKK panel lines compared to standard linear reference genomes. We found additional MIKK panel-specific genomic content that would be missing from linear reference alignment approaches. We were also able to identify and quantify the presence of repeat elements in each of the lines. Finally, we investigated line-specific CpG methylation and performed differential DNA methylation analysis across the 12 lines. We thus present a detailed analysis of the MIKK panel genomes using long and short read sequence technologies, creating a MIKK panel specific pan genome reference dataset allowing for the investigation of novel variation types that would be elusive using standard approaches.

category: genomics


title: Middle Eastern Genetic Variation Improves Clinical Annotation of the Human Genome

abstract: Genetic variation in populations of Middle Eastern origin remains highly underrepresented in most comprehensive genomic databases. This underrepresentation hampers the functional annotation of the human genome and challenges accurate clinical variant interpretation. To highlight the importance of capturing genetic variation in the Middle East, we aggregated whole exome and genome sequencing data from 2116 individuals in the Middle East and established the Middle East Variation (MEV) database. Of the high-impact coding (missense and loss of function) variants in this database, 53% were absent from the most comprehensive Genome Aggregation Database (gnomAD), thus representing a unique Middle Eastern variation dataset which might directly impact clinical variant interpretation. We highlight 39 variants with minor allele frequency >1% in the MEV database that were previously reported as rare disease variants in ClinVar and the Human Gene Mutation Database (HGMD). Furthermore, the MEV database consisted of 281 putative homozygous loss of function (LoF) variants, or complete knockouts, of which 31.7% (89/281) were absent from gnomAD. This set represents either complete knockouts of 83 unique genes in reportedly healthy individuals, with implications regarding disease penetrance and expressivity, or might affect dispensable exons, thus refining the clinical annotation of those regions. Intriguingly, 24 of those genes have several clinically significant variants reported in ClinVar and/or HGMD. Our study shows that genetic variation in the Middle East improves functional annotation and clinical interpretation of the genome and emphasizes the need for expanding sequencing studies in the Middle East and other underrepresented populations.


title: Functional analysis of Ost3p and Ost6p containing yeast oligosaccharyltransferases

abstract: The oligosaccharyltransferase (OST) is the central enzyme in the N-glycosylation pathway. It transfers a defined oligosaccharide from a lipid-linker onto the asparagine side chain of proteins. The yeast OST consists of eight subunits and exists in two catalytically distinct isoforms that differ in one subunit, Ost3p or Ost6p. The cryo-electron microscopy structure of the Ost6p containing complex was found to be highly similar to the Ost3p containing OST. OST enzymes with altered Ost3p/Ost6p subunits were generated and functionally analysed. The three C-terminal transmembrane helices were responsible for the higher turnover-rate of the Ost3p vs. the Ost6p containing enzyme in vitro and the more severe hypoglycosylation in Ost3p lacking strains in vivo. Glycosylation of specific OST target sites required the N-terminal thioredoxin domain of Ost3p or Ost6p. This Ost3p/Ost6p dependence was glycosylation site but not protein specific. We concluded that the Ost3p/Ost6p subunits modulate the catalytic activity of OST and provide additional specificity for OST substrate recognition.

category: biochemistry


title: A novel MRI-based data fusion methodology for efficient, personalised, compliant simulations of aortic haemodynamics

abstract: We present a novel, cost-efficient methodology to simulate aortic haemo-dynamics in a patient-specific, compliant aorta using an MRI data fusion process. Based on a previously-developed Moving Boundary Method, this technique circumvents the high computational cost and numerous structural modelling assumptions required by traditional Fluid-Structure Interaction techniques. Without the need for Computed Tomography (CT) data, the MRI images required to construct the simulation can be obtained during a single imaging session. Black Blood MR Angiography and 2D Cine-MRI data were used to reconstruct the luminal geometry and calibrate wall movement specifically to each region of the aorta. 4D-Flow MRI and non-invasive pressure measurements informed patient-specific inlet and outlet boundary conditions. Luminal area closely matched 2D Cine-MRI measurements with a mean error of less than 4.6% across the cardiac cycle, while physiological pressure and flow distributions were simulated to within 3.3% of patient-specific targets. Moderate agreement with 4D-Flow MRI velocity data was observed. Despite lower peak velocity, an equivalent rigid-wall simulation predicted a mean Time-Averaged Wall Shear Stress (TAWSS) 13% higher than the compliant simulation. The agreement observed between compliant simulation results and MRI data is testament to the accuracy and efficiency of this MRI-based simulation technique.

category: bioengineering


title: DISCA: high-throughput cryo-ET structural pattern mining by deep unsupervised clustering

abstract:
Cryo-electron tomography directly visualizes heterogeneous macromolecular structures in complex cellular environments, but existing computer-assisted sorting approaches are low-throughput or inherently limited due to their dependency on available templates and manual labels.

We introduce a high-throughput template-and-label-free deep learning approach that automatically discovers subsets of homogeneous structures by learning and modeling 3D structural features and their distributions.

Diverse structures emerging from sorted subsets enable systematic unbiased recognition of macro-molecular complexes in situ.

category: bioinformatics


title: Single nucleotide polymorphism induces divergent dynamic patterns in CYP3A5: a microsecond scale biomolecular simulation of variants identified in Sub-Saharan African populations

abstract: Pharmacogenomics aims to reveal variants associated with drug response phenotypes. Genes whose roles involve the absorption, distribution, metabolism, and excretion of drugs, are highly polymorphic between populations. High coverage whole genome sequencing showed that a large proportion of the variants for these genes are rare in African populations. This study investigates the impact of such variants on protein structure to assess their functional importance. We use genetic data of CYP3A5 from 458 individuals from sub-Saharan Africa to conduct a structural bioinformatics analysis. Five missense variants were modeled and microsecond scale molecular dynamics simulations were conducted for each, as well as for the CYP3A5 wildtype, and the Y53C variant, which has a known deleterious impact on enzyme activity. The binding of ritonavir and artemether to CYP3A5 variant structures was also evaluated. Our results showed different conformational characteristics between all the variants. No significant structural changes were noticed. However, the genetic variability acts on the plasticity of the protein. The impact on drug binding may be drug dependant. We conclude that rare variants hold relevance in determining the pharmacogenomics properties of populations. This could have a significant impact on precision medicine applications in sub-Saharan Africa.


title: Distance-guided protein folding based on generalized descent direction

abstract: Advances in the prediction of the inter-residue distance for a protein sequence have increased the accuracy to predict the correct folds of proteins with distance information. Here, we propose a distance-guided protein folding algorithm based on generalized descent direction, named GDDfold, which achieves effective structural perturbation and potential minimization in two stages. In the global stage, random-based direction is designed using evolutionary knowledge, which guides conformation population to cross potential barriers and explore conformational space rapidly in a large range. In the local stage, locally rugged potential landscape can be explored with the aid of conjugate-based direction integrated into a specific search strategy, which can improve exploitation ability. GDDfold is tested on 347 proteins of a benchmark set, 24 FM targets of CASP13 and 20 FM targets of CASP14. Results show that GDDfold correctly folds (TM-score [≥] 0.5) 316 out of 347 proteins, where 65 proteins have TM-scores that are greater than 0.8, and significantly outperforms Rosetta-dist (distance-assisted fragment assembly method) and L-BFGSfold (distance geometry optimization method). On CASP FM targets, GDDfold is comparable with five state-of-the-art methods, namely, Quark, RaptorX, Rosetta, MULTICOM and trRosetta in the CASP 13 and 14 server groups.


title: Decoding Angiotensin II Type 1 Receptor Allosteric Communication to Gq and β-arrestin

abstract:
The allosteric communication between the agonist binding site and the G protein or {beta}-arrestin coupling sites in G protein-coupled receptors (GPCRs) play an important role in determining ligand efficacy towards these two signaling pathways and hence the ligand bias. Knowledge of the amino acid residue networks involved in the allosteric communication will aid understanding GPCR signaling and the design of biased ligands. Angiotensin II type I receptor (AT1R) is an ideal model GPCR to study the molecular basis of ligand bias as it has multiple {beta}-arrestin2 and Gq protein biased agonists as well as three-dimensional structures. Using Molecular Dynamics simulations, dynamic allostery analysis, and functional BRET assays, we identified a network of residues involved in allosteric communication from the angiotensin II binding site to the putative Gq coupling sites and another network to the {beta}-arrestin2 coupling sites, with 6 residues common to both pathways located in TM3, TM5 and TM6. Our findings unveil unique and common allosteric communication residue hubs for Gq and {beta}-arr2 coupling by AngII ligands and suggests that some of these residues can be targeted to design biased AT1R ligands. Finally, we show through analysis of the inter-residue distance distributions of the activation microswitches involved in class A GPCR activation for ten different agonists, that these microswitches behave like rheostats with different relative strengths of activation, which we speculate could modulate the relative efficacy of these agonists toward the two signaling pathways.

Significance StatementKnowledge of the residues involved in allosteric communication from the ligand binding site to the G protein or {beta}-arrestin ({beta}-arr) coupling sites in GPCRs will aid in understanding their role in mediating ligand bias. Using a combination of molecular dynamics simulations and functional signaling assays we have identified a network of residues involved in allosteric communication from the Angiotensin II (Ang II) binding site to the Gq and {beta}-arr2 coupling sites in the Ang II type I receptor (AT1R). The residues in the allosteric network for {beta}-arr2 coupling are distributed across multiple structural regions of AT1R compared to Gq coupling. The residues in the two networks show conserved chemical properties across class A GPCRs, demonstrating the importance of allosteric communication in modulating ligand bias.


title: Mechanical demands of the two-handed hardstyle kettlebell swing in novice older adults: an exploratory profile

abstract:
BackgroundUnderstanding the force profile of an exercise increases clinical confidence when assessing the benefits and potential risks of a prescribed exercise. This exploratory study presents the force profile of the hardstyle kettlebell swing in novice older adults and compares peak force with kettlebell deadlifts. These data will help inform healthcare providers and coaches who are considering prescribing kettlebell exercises for older adults.

MethodsThirty-five community-dwelling males and females (59-79 years) were recruited, from applicants to participate in the BELL trial. Two-handed hardstyle swings were performed with 8-16 kg. Deadlifts were performed with 8-24 kg and 8-32 kg for females and males, respectively. Ground reaction force was obtained from a floor-mounted force platform. Pairwise comparisons of peak force, forward force, rate of force development, swing cadence, sex, and kettlebell mass, were investigated for the kettlebell swing, with representative force-time curves described. Pairwise comparisons of peak force, sex and kettlebell mass were investigated for the deadlift, with comparisons of peak force, kettlebell mass, and sex, between swings and deadlifts.

ResultsFor kettlebells up to 16 kg, paired samples T-tests show a large exercise effect ({delta} > 1.4) with peak force higher for swings than deadlifts. Data shows: (i) higher peak force during swings than deadlifts ({delta} = 1.77), reaching 4.5 (1.0) N.kg-1, (ii) peak force during an 8 kg swing was greater than a 32kg deadlift, (iii) negligible difference in normalised peak force between males and females performing kettlebell swings, but a moderately large effect size during deadlifts (males > females, {delta} = 0.69), (iv) mean rate of force development of 19.9 (4.7) N.s-1.kg-1 with a very weak, positive correlation with kettlebell mass (y = 14.4 + 0.32x), and trivial effect of sex, (v) mean forward force equal to 5.5% of vertical force during swings, increasing from 3.8 (1.6) % with 8 kg to 7.1 (2.6) % with 16 kg.

ConclusionDuring kettlebell swings, there is negligible difference in normalised net peak force between novice males and females using the same absolute loads. Where ground reaction force is a therapeutic target, kettlebell swings with an 8 kg kettlebell could have similar effects to much heavier deadlifts (>24 kg). Kettlebell swings performed with lighter loads, could provider similar therapeutic value to much heavier deadlifts, and may be a more appealing, affordable, and convenient option for older adults.

category: physiology


title: Force profile of the two-handed hardstyle kettlebell swing in novice older adults: an exploratory profile


title: Synergism between Chromatin Dynamics and Gene Transcription Enhances Robustness and Stability of Epigenetic Cell Memory

abstract: Apart from carrying hereditary information inherited from their ancestors and being able to pass on the information to their descendants, cells can also inherit and transmit information that is not stored as changes in their genome sequence. Such epigenetic cell memory, which is particularly important in multicellular organisms, involves multiple biochemical modules mainly including chromatin organization, epigenetic modification and gene transcription. The synergetic mechanism among these three modules remains poorly understood and how they collaboratively affect the robustness and stability of epigenetic memory is unclear either. Here we developed a multiscale model to address these questions. We found that the chromatin organization driven by long-range epigenetic modifications can significantly enhance epigenetic cell memory and its stability in contrast to that driven by local interaction and that chromatin topology and gene activity can promptly and simultaneously respond to changes in nucleosome modifications while maintaining the robustness and stability of epigenetic cell memory over several cell cycles. We concluded that the synergism between chromatin dynamics and gene transcription facilitates the faithful inheritance of epigenetic cell memory across generations.

category: systems biology


title: LACTATE IS A MAJOR ENERGY SUBSTRATE FOR CORTICAL NEURONS AND ENHANCES THEIR FIRING ACTIVITY

abstract:
Glucose is the mandatory fuel for the brain, yet the relative contribution of glucose and lactate for neuronal energy metabolism is unclear. We found that increased lactate, but not glucose concentration, enhances the spiking activity of neurons of the cerebral cortex. Enhanced spiking was dependent on ATP-sensitive potassium (KATP) channels formed with Kir6.2 and SUR1 subunits, which we show are functionally expressed in most neocortical neuronal types. We also demonstrate the ability of cortical neurons to take-up and metabolize lactate. We further reveal that ATP is produced by cortical neurons largely via oxidative phosphorylation and only modestly by glycolysis. Our data demonstrate that in active neurons, lactate is preferred to glucose as an energy substrate, and that lactate metabolism shapes neuronal activity in the neocortex through KATP channels. Our results highlight the importance of metabolic crosstalk between neurons and astrocytes for brain function.

HighlightsO_LIMost cortical neurons subtypes express pancreatic beta-cell like KATP channels.
C_LIO_LILactate enhances spiking activity via its uptake and closure of KATP channels.
C_LIO_LICortical neurons take up and oxidize lactate.
C_LIO_LICortical neurons produce ATP mainly by oxidative phosphorylation.
C_LI


title: Lactate is a major energy substrate for cortical neurons and enhances their firing activity.


title: The 3' end of the human norovirus antigenomic sequence is required for its genomic RNA synthesis by RNA-dependent RNA polymerase

abstract: Norovirus genome is a single-stranded positive-strand RNA. To reveal the mechanism underlying the initiation of the norovirus genomic RNA synthesis by its RNA-dependent RNA polymerase (RdRp), we used an in vitro assay to detect the complementary RNA synthesis activity. Results showed that the purified recombinant RdRp synthesized the complementary positive-sense RNA from the 100 nt template corresponding to the 3' end region of the viral antisense genome sequence, but that RdRp did not synthesize the antisense genomic RNA from the 100 nt template, corresponding to the 5' end region of the positive-sense genome sequence. The 31 nt region at the 3' end of the RNA antisense template was then predicted to form the stem-loop structure. Its deletion resulted in the loss of complementary RNA synthesis by RdRp. The connection of the 31 nt to the 3' end of the positive-sense RNA template allowed to be recognized by the RdRp. Similarly, an electrophoretic mobility shift assay further revealed that RdRp bound to the antisense RNA specifically, but the 31 nt deletion at the 3' end lost the binding to RdRp. Therefore, combining this observation with further deletion and mutation analysis, we concluded that the predicted stem-loop structure in the 31 nt and region close to the antisense viral genomic stem sequences are important for initiating the positive-sense human norovirus genomic RNA synthesis by its RdRp.


title: Genomic contacts reveal the control of sister chromosome decatenation in E. coli

abstract: In bacteria, chromosome segregation occurs progressively, from the origin to the terminus, a few minutes after the replication of each locus. In-between replication and segregation, sister loci are maintained in an apparent cohesive state by topological links. Whereas topoisomerase IV (Topo IV), the main bacteria decatenase, controls segregation, little is known regarding the influence of the cohesion step on chromosome folding. In this work, we investigated chromosome folding in cells with altered decatenation activities. Within minutes after Topo IV inactivation, a massive chromosome reorganization takes place, associated with increases in trans-contacts between catenated sister chromatids and in long-range cis-contacts between the terminus and distant loci on the genome. A genetic analysis of these signals allowed us to decipher specific roles for Topo IV and Topo III, an accessory decatenase. Moreover we revealed the role of MatP, the terminus macrodomain organizing system and MukB, the E. coli SMC in organizing sister chromatids tied by persistent catenation links. We propose that large-scale conformation changes observed in these conditions reveal a defective decatenation hub located in the terminus area. Altogether, our findings support a model of spatial and temporal partition of the tasks required for sister chromosome segregation.


title: Assessment of exposure to ionizing radiation in Chernobyl tree frogs (Hyla orientalis)

abstract: Ionizing radiation can damage organic molecules, causing detrimental effects on human and wildlife health. The accident at the Chernobyl nuclear power plant (1986) represents the largest release of radioactive material to the environment. An accurate estimation of the current exposure to radiation in wildlife, often reduced to ambient dose rate assessments, is crucial to understand the long-term impact of radiation on living organisms. Here, we present an evaluation of the sources and variation of current exposure to radiation in breeding Eastern tree frogs (Hyla orientalis) males living in the Chernobyl Exclusion Zone. Total dose rates in H. orientalis were highly variable, although generally below widely used thresholds considered harmful for animal health. Internal exposure was the main source of absorbed dose rate (81% on average), with 90Sr being the main contributor (78% of total dose rate, on average). These results highlight the importance of assessing both internal and external exposure levels in order to perform a robust evaluation of the exposure to radiation in wildlife. Further studies incorporating life-history, ecological, and evolutionary traits are needed to fully evaluate the effects that these exposure levels can have in amphibians and other taxa inhabiting radio-contaminated environments.


title: How to describe and measure phenology? An investigation on the diversity of metrics using phenology of births in large herbivores

abstract: Proposed in 1849 by Charles Morren to depict periodical phenomena governed by seasons, the term "phenology" has spread in many fields of biology. With the wide adoption of the concept of phenology flourished a large number of metrics with different meaning and interpretation. Here, we first a priori classified 52 previously published metrics used to characterise the phenology of births in large herbivores according to four biological characteristics of interest: timing, synchrony, rhythmicity and regularity of births. We then applied each metric retrieved on simulation data, considering normal and non-normal distributions of births, and varying distributions of births in time. We then evaluated the ability of each metric to capture the variation of the four phenology characteristics via a sensitivity analysis. Finally, we scored each metric according to eight criteria we considered important to describe phenology correctly. The high correlation we found among the many metrics we retrieved suggests that such diversity of metrics is unnecessary. We further show that the best metrics are not the most commonly used, and that simpler is often better. Circular statistics with the mean vector orientation and mean vector length seems, respectively, particularly suitable to describe the timing and synchrony of births in a wide range of phenology patterns. Tests designed to compare statistical distributions, like Mood and Kolmogorov-Smirnov tests, allow a first and easy quantification of rhythmicity and regularity of birth phenology respectively. By identifying the most relevant metrics our study should facilitate comparative studies of phenology of births or of any other life-history event. For instance, comparative studies of the phenology of mating or migration dates are particularly important in the context of climate change.


title: Functional or vestigial? The genomics of the pineal gland in Xenarthra

abstract: Vestigial organs are historical echoes of past phenotypes. Determining whether a specific organ constitutes a functional or vestigial structure can be a challenging task, given that distinct levels of atrophy may arise between and within lineages. The mammalian pineal gland, an endocrine organ involved in melatonin biorhythmicity, represents a classic example, often yielding contradicting anatomical observations. In Xenarthra (sloths, anteaters and armadillos), a peculiar mammalian order, the presence of a distinct pineal organ was clearly observed in some species (i.e. Linnaeuss two-toed sloth) but undetected in other closely related species (i.e. brown-throated sloth). In the nine-banded armadillo, contradicting evidence supports either functional or vestigial scenarios. Thus, to untangle the physiological status of the pineal gland in Xenarthra, we used a genomic approach to investigate the evolution of the gene hub responsible for melatonin synthesis and signaling. We show that both synthesis and signaling compartments are eroded and were lost independently. Additionally, by expanding our analysis to 157 mammal genomes we offer a comprehensive view showing that species with very distinctive habitats and lifestyles have convergently evolved a similar phenotype: Cetacea, Pholidota, Dermoptera, Sirenia and Xenarthra. Our findings suggest that the recurrent inactivation of melatonin genes correlates with pineal atrophy, and endorse the use of genomic analyses to ascertain the physiological status of suspected vestigial structures.


title: A tandem segmentation-classification approach for the localization of morphological predictors of C. elegans lifespan and motility

abstract: C. elegans is an established model organism for studying genetic and drug effects on ageing, many of which are conserved in humans. It is also an important model for basic research, and C. elegans pathologies is a new emerging field. Here we develop a proof-of-principal convolutional neural network-based platform to segment C. elegans and extract features that might be useful for lifespan prediction. We use a dataset of 734 worms tracked throughout their lifespan and classify worms into long-lived and short-lived. We designed WormNet - a convolutional neural network (CNN) to predict the worm lifespan class based on young adult images (day 1 - day 3 old adults) and showed that WormNet, as well as, InceptionV3 CNN can successfully classify lifespan. Based on U-Net architecture we develop HydraNet CNNs which allow segmenting worms accurately into anterior, mid-body and posterior parts. We combine HydraNet segmentation, WormNet prediction and the class activation map approach to determine the segments most important for lifespan classification. Such a tandem segmentation-classification approach shows posterior part of the worm might be more important for classifying long-lived worms. Our approach can be useful for the acceleration of anti-ageing drug discovery and for studying C. elegans pathologies.


title: Deep Learning Assisted Mechanotyping of Individual Cells Through Repeated Deformations and Relaxations in Undulating Channels

abstract: Mechanical properties of cells are important features that are tightly regulated, and are dictated by various pathologies. Deformability cytometry allows for the characterization of mechanical properties of hundreds of cells per second, opening the way to differentiating cells via mechanotyping. A remaining challenge for detecting and classifying rare sub-populations is the creation of a combined experimental and analysis protocol that would assure classification accuracy approaching 100%. In order to maximize the accuracy, we designed a microfluidic channel that subjects each cell to repeated deformations and relaxations. We also track the shape dynamics of individual cells with high time resolution, and apply sequence-based deep learning models for feature extraction. HL60 cells with and without treatment with cytochalasin D (cytoD), a reagent previously shown to perturb the actin network, were used as a model system to understand the classification potential of our approach. Multiple recurrent and convolutional neural network architectures were trained using time sequences of cell shapes, and shown to achieve high classification accuracy based on cytoskeletal properties alone. The best model classified the two sub-populations of HL60 cells with an accuracy of 95%. This work establishes the application of sequence-based deep learning models to dynamic deformability cytometry.

category: biophysics


title: Three new species of nematodes from the syconia of Ficus racemosa in southern India

abstract: SummaryFicus racemosa with an Indo-Australasian distribution, has so far been recorded to harbour in its fruits, nematode species of the aphelenchoid genera Schistonchus, Ficophagus and Martininema, and species of diplogastrid genera Teratodiplogaster and Pristionchus. The Indian species reported so far from Ficus racemosa lack comprehensive details on morphology and molecular characterization. In this paper, we describe three new species of nematodes obtained from syconia (enclosed globular infructescence or fruit) of Ficus racemosa found in southern India. Ficophagus glomerata n. sp. is characterised by small body having b=5.2-9.6, c= 18-23; slightly set-off lip region having well developed cephalic framework; secretory-excretory pore opens near the head; slender stylet with small, rounded/ sloping knobs; ovoid median bulb with relatively posteriorly-placed valve plates; males with sickle-shaped spicules having spatulate or hammer-shaped capitulum, represented by an elongate-ovoid condylus and long digitate rostrum and tail conoid with fine, hair-like terminal spike. Teratodiplogaster glomerata n. sp. is characterised by long tubular and narrow stoma with fractal pieces in prostegostom; long rectangular metacorpus; female reproductive system with conspicuous spermatheca and amoeboid sperms; males having short, arcuate spicules and keeled gubernaculum; genital papillae in the configuration of P1, P2, C, P3, P4, P5d, (P6d, P7), P8d, Ph and tail conoid with a terminal or subterminal mucro. Pristionchus glomerata n. sp. is characterised by four morphotypes mainly with variations in lip region, stoma, spicules, gubernaculum, and the position of genital papillae. Phylogenetic analyses based upon near-full-length small subunit (SSU) and D2-D3 expansion segments of large subunit (LSU) rRNA genes confirmed affinities with sister species of corresponding genera.

category: zoology


title: Probabilistically Weighted Multilayer Networks disclose the link between default mode network instability and psychosis-like experiences in healthy adults

abstract: The brain is a complex system in which the functional interactions among its subunits vary over time. The trajectories of this dynamic variation contribute to inter-individual behavioral differences and psychopathologic phenotypes. Despite many methodological advancements, the study of dynamic brain networks still relies on biased assumptions in the temporal domain. The current paper has two goals. First, we present a novel method to study multilayer networks: by modelling intra-nodal connections in a probabilistic, biologically driven way, we introduce a temporal resolution of the multilayer network based on signal similarity across time series. This new method is tested on synthetic networks by varying the number of modules and the sources of noise in the simulation. Secondly, we implement these probabilistically weighted (PW) multilayer networks to study the association between network dynamics and subclinical, psychosis-relevant personality traits in healthy adults. We show that the PW method for multilayer networks outperforms the standard procedure in modular detection and is less affected by increasing noise levels. Additionally, the PW method highlighted associations between the temporal instability of default mode network connections and psychosis-like experiences in healthy adults. PW multilayer networks allow an unbiased study of dynamic brain functioning and its behavioral correlates.


title: Schema representations in distinct brain networks support narrative memory during encoding and retrieval

abstract: Schematic prior knowledge can scaffold the construction of event memories during perception and also provide structured cues to guide memory search during retrieval. We measured the activation of story-specific and schematic representations using fMRI while participants were presented with 16 stories and then recalled each of the narratives, and related these activations to memory for specific story details. We predicted that schema representations in mPFC would be correlated with successful recall of story details. In keeping with this prediction, an anterior mPFC region showed a significant correlation between activation of schema representations at encoding and subsequent behavioral recall performance; however, this mPFC region was not implicated in schema representation during retrieval. More generally, our analyses revealed largely distinct brain networks at encoding and retrieval in which schema activation was related to successful recall. These results provide new insight into when and where event knowledge can support narrative memory.


title: A Meta-Analysis of fMRI Studies of Semantic Cognition in Children

abstract: Our capacity to derive meaning from things that we see and words that we hear is unparalleled in other animal species and current AI systems. Despite a wealth of functional magnetic resonance imaging (fMRI) studies on where different semantic features are processed in the adult brain, the development of these systems in children is poorly understood. Here we conducted an extensive database search and identified 50 fMRI experiments investigating semantic world knowledge, semantic relatedness judgments, and the differentiation of visual semantic object categories in children (total N = 1,018, mean age = 10.1 years, range 4-15 years). Synthesizing the results of these experiments, we found consistent activation in the bilateral inferior frontal gyri (IFG), fusiform gyri (FG), and supplementary motor areas (SMA), as well as in the left middle and superior temporal gyri (MTG/STG). Within this system, we found little evidence for age-related changes across childhood and high overlap with the adult semantic system. In sum, the identification of these cortical areas provides the starting point for further research on the mechanisms by which the developing brain learns to make sense of its environment.


title: Compensatory changes in contralesional node strength, brain wide modularity and cross-modular functional interactions in a rat model of traumatic brain injury

abstract: Penetrating cortical impact injuries alter neuronal communication beyond the injury epicenter, across regions involved in affective, sensorimotor, and cognitive processing. Understanding how traumatic brain injury (TBI) reorganizes local and brain wide nodal functional interactions may provide valuable quantitative parameters for monitoring pathological progression and functional recovery. To this end, we investigated spontaneous fluctuations in the functional magnetic resonance imaging (fMRI) signal obtained at 11.1 Tesla in rats sustaining controlled cortical impact (CCI) and imaged at 2- and 30-days post-injury. Graph theory-based calculations were applied to weighted undirected matrices constructed from 12,879 pairwise correlations between fMRI signals from 162 regions. Our data indicate that on days 2 and 30 post-CCI there is a significant increase in connectivity strength in nodes located in contralesional cortical, thalamic, and basal forebrain areas. Rats imaged on day 2 post-injury had significantly greater network modularity than controls, with influential nodes (with high eigenvector centrality) contained within the contralesional module and participating less in cross-modular interactions. By day 30, modularity and cross-modular interactions recover, although a cluster of nodes with low strength and low eigenvector centrality remain in the ipsilateral cortex. Our results suggest that changes in node strength, modularity, eigenvector centrality, and participation coefficient track early and late TBI effects on brain functional connectivity. We propose that the observed compensatory functional connectivity reorganization in response to CCI may be unfavorable to brain wide communication in the early post-injury period.


title: Compensatory functional connectome changes in a rat model of traumatic brain injury


title: Pathogen clonal expansion underlies multiorgan dissemination and organ-specific outcomes during systemic infection

abstract: The dissemination of pathogens through blood and their establishment within organs lead to severe clinical outcomes. However, the within-host dynamics that underly pathogen spread to and clearance from systemic organs remain largely uncharacterized. Here, we investigate the population dynamics of extraintestinal pathogenic E. coli, a common cause of bacteremia, during systemic infection. We show that while bacteria are largely cleared by most organs, organ-specific clearance failures are pervasive and result from dramatic expansions of clones representing less than 0.0001% of the inoculum. Clonal expansion underlies the variability in bacterial burden between animals, and stochastic dissemination of clones profoundly alters the pathogen population structure within organs. Despite variable pathogen expansion events, host bottlenecks are consistent yet highly sensitive to infection variables, including inoculum size and macrophage depletion. Finally, we identify organ-specific bacterial genetic factors that distinguish between establishment of within-organ pathogen populations and subsequent survival or expansion.


title: Biochar alters soil properties, microbial community diversity, and enzyme activities, while decreasing conifer performance

abstract: Biochars are porous charcoal-like materials that can enhance soil health and plant growth, but its use has not been adequately evaluated in woody cropping systems. We set up an experimental Christmas tree plantation on a Marlette series soil amended with two types of biochar and conducted two studies on the impacts of biochar on the agroecosystem over three years following establishment. The first study investigated the effects of biochar on plant performance, soil physicochemical properties and extracellular enzyme activities, while the second investigated the response of the root-associated fungal community. Both biochars stimulated five extracellular enzyme activities, with increases of between 67% and 446%. Structural equation modelling identified increases to dissolved organic carbon and soil moisture as potential mechanisms of biochars effects on enzyme activities. Tree growth and survival were negatively affected by biochar application, depending on the tree species and biochar applied, which may have been due to induced nitrogen limitation. High-throughput sequencing showed that biochar decreased the diversity of root-associated fungal communities, with the ectomycorrhizal species Wilcoxina mikolae reaching levels of hyper-dominance on balsam fir in response to one of the biochars. Further studies should investigate how biochar can be harnessed to remediate specific soil quality issues or restructure soil ecosystems in ways that improve crop performance.