title: Isolation of the Buchnera aphidicola flagellum basal body from the Buchnera membrane

abstract: Buchnera aphidicola is an intracellular bacterial symbiont of aphids and maintains a small genome of only 600 kbps. Buchnera is thought to maintain only genes relevant to the symbiosis with its aphid host. Curiously, the Buchnera genome contains gene clusters coding for flagellum basal body structural proteins and for flagellum type III export machinery. These structures have been shown to be highly expressed and present in large numbers on Buchnera cells. No recognizable pathogenicity factors or secreted proteins have been identified in the Buchnera genome, and the relevance of this protein complex to the symbiosis is unknown. Here, we show isolation of Buchnera flagella from the cellular membrane of Buchnera, confirming the enrichment of flagellum proteins relative to other proteins in the Buchnera proteome. This will facilitate studies of the structure and function of the Buchnera flagellum structure, and its role in this model symbiosis.


title: Engineering the thermotolerant industrial yeast Kluyveromyces marxianus for anaerobic growth

abstract: Current large-scale, anaerobic industrial processes for ethanol production from renewable carbohydrates predominantly rely on the mesophilic yeast Saccharomyces cerevisiae. Use of thermotolerant, facultatively fermentative yeasts such as Kluyveromyces marxianus could confer significant economic benefits. However, in contrast to S. cerevisiae, these yeasts cannot grow in the absence of oxygen. Response of K. marxianus and S. cerevisiae to different oxygen-limitation regimes were analyzed in chemostats. Genome and transcriptome analysis, physiological responses to sterol supplementation and sterol-uptake measurements identified absence of a functional sterol-uptake mechanism as a key factor underlying the oxygen requirement of K. marxianus. Heterologous expression of a squalene-tetrahymanol cyclase enabled oxygen-independent synthesis of the sterol surrogate tetrahymanol in K. marxianus. After a brief adaptation under oxygen-limited conditions, tetrahymanol-expressing K. marxianus strains grew anaerobically on glucose at temperatures of up to 45 {degrees}C. These results open up new directions in the development of thermotolerant yeast strains for anaerobic industrial applications.

category: biochemistry


title: Frog nest foam as a drug delivery system

abstract: Foams have frequently been used as systems for the delivery of cosmetic and therapeutic molecules; however, there is high variability in the foamability and long-term stability of synthetic foams. The development of pharmaceutical foams that exhibit desirable foaming properties, delivering appropriate amounts of the active pharmaceutical ingredient (API) and that have excellent biocompatibility is of great interest. The production of stable foams is rare in the natural world; however, certain species of frogs have adopted foam production as a means of providing a protective environment for their eggs and larvae from a predators and parasites, to prevent desiccation, to control gaseous exchange, temperature extremes, and to reduce UV damage. These foams show great stability (up to 10 days in tropical environments) and are highly biocompatible due to the sensitive nature of amphibian skin. This work demonstrates for the first time, that nests of the Tungara frog (Engystomops pustulosus) is stable ex situ with useful physiochemical and biocompatible properties and is capable of encapsulating a range of compounds, including antibiotics. These protein foam mixtures share some properties with pharmaceutical foams and may find utility in a range of pharmaceutical applications such as a topical drug delivery systems (DDS).

category: bioengineering


title: Frog nest foams exhibit pharmaceutical foam-like properties


title: Brain connectivity at rest predicts individual differences in normative activity during movie watching

abstract: When multiple individuals are exposed to the same sensory event, some are bound to have less typical experiences than others. These atypical experiences are underpinned by atypical stimulus-evoked brain activity, the extent of which is often indexed by intersubject correlation (ISC). Previous research has attributed individual differences in ISC to variation in trait-like behavioral phenotypes. Here, we extend this line of work by showing that an individuals degree and spatial distribution of ISC are closely related to their brains intrinsic functional architecture. Using resting state and movie watching fMRI data from 176 Human Connectome Project participants, we reveal that resting state functional connectivity (RSFC) profiles can be used to predict cortex-wide ISC with considerable accuracy. Similar region-level analyses demonstrate that the amount of ISC a brain region exhibits during movie watching is associated with its connectivity to others at rest, and that the nature of these connectivity-activity relationships varies as a function of the regions role in sensory information processing. Finally, we show that an individuals unique spatial distribution of ISC, independent of its magnitude, is also related to their RSFC profile. These findings suggest that the brains ability to process complex sensory information is tightly linked to its baseline functional organization and motivate a more comprehensive understanding of individual responses to naturalistic stimuli.

category: neuroscience


title: Onset of sexual maturity of sexually propagated and wild Favites abdita colonies in northwestern Philippines

abstract: Scleractinian corals are modular colonial organisms and are the main framework builders of coral reefs. Most corals reproduce by broadcast spawning with external fertilization and these processes are essential to replenish reef coral populations. Despite decades of research, many aspects of coral reproductive biology remain poorly studied. For example, two important reproductive life history traits, colony size and age at the onset of sexual maturity, are mostly unknown for many reef-building corals. In this study, wild colonies of different size classes and colonies of a known age (i.e. colonies sexually cultured and reared from larvae to adults) of the massive scleractinian Favites abdita were examined for the presence or absence of mature oocytes to determine size and age at the onset of sexual reproduction. Fecundity at the onset of reproductive maturity across size classes of wild colonies was also determined. Surveyed and sampled colonies were grouped into three size classes based on maximum colony diameter (A = 0.1-4.0 cm, B = 4.1-8.0 cm, and C = >8.1 cm). For both wild and sexually propagated colonies, the smallest colonies containing gametes were 1.8 cm in diameter, suggesting that this is the minimum colony size at onset of sexual maturity. Colonies of size class A had lower mean oocyte counts per polyp (44 {+/-} 6.08; mean {+/-} SE) compared to colonies of classes B and C (469 {+/-} 62.41, 278 {+/-} 57.15, respectively). However, mean oocyte geometric mean diameter of size class A colonies was greater (340.38 {+/-} 7.68 m) than classes B and C (283.96 {+/-} 6.94 m, 317.57 {+/-} 9.18 m, respectively). Results of this study bring in to question the widely applied operational definition of coral juveniles being colonies [≤]4.0 cm diameter and suggest that even quite small colonies may play a role in contributing to the natural larval pool on reefs than previously thought.

category: ecology


title: A Multi-dimensional Integrative Scoring Framework for Predicting Functional Regions in the Human Genome

abstract: Attempts to identify and prioritize functional DNA elements in coding and noncoding regions, particularly through use of in silico functional annotation data,continue to increase in popularity. However, specific functional roles may vary widely from one variant to another, making it challenging to summarize different aspects of variant function. Here we propose Multi-dimensional Annotation Class Integrative Estimation (MACIE), an unsupervised multivariate mixed model framework capable of integrating annotations of diverse origin to assess multi-dimensional functional roles for both coding and noncoding variants. Unlike existing one-dimensional scoring methods, MACIE views variant functionality as a composite attribute encompassing multiple characteristics, and estimates the joint posterior functional probability vector of each genomic position, a quantity that offers richer and more interpretable information in the presence of multiple aspects of functionality. Applied to a variety of independent coding and non-coding datasets, MACIE demonstrates powerful and robust performance in discriminating between functional and non-functional variants. We also show an application of MACIE to fine-mapping using lipids GWAS summary statistics data from the European Network for Genetic and Genomic Epidemiology Consortium.

category: genetics


title: A multi-dimensional integrative scoring framework for predicting functional variants in the human genome


title: Review and performance evaluation of trait-based between-community dissimilarity measures

abstract:
O_LIIn the recent years a variety of indices have been proposed with the aim of quantifying functional dissimilarity between communities. These indices follow different approaches to account for between-species similarities in the calculation of community dissimilarity, yet they all have been proposed as straightforward tools.
C_LIO_LIIn this paper we reviewed the trait-based dissimilarity indices available in the literature, contrasted the approaches they follow, and evaluated their performance in terms of correlation with an underlying environmental gradient using individual-based community simulations with different gradient lengths. We tested how strongly dissimilarities calculated by different indices correlate with environmental distances. Using random forest models we tested the importance of gradient length, the choice of data type (abundance vs. presence/absence), the transformation of between-species similarities (linear vs. exponential), and the dissimilarity index in the predicting correlation value.
C_LIO_LIWe found that many indices behave very similarly and reach high correlation with environmental distances. There were only a few indices (e.g. Raos DQ, and representatives of the nearest neighbour approach) which performed regularly poorer than the others. By far the strongest determinant of correlation with environmental distance was the gradient length, followed by the data type. The dissimilarity index and the transformation method seemed not crucial decisions when correlation with an underlying gradient is to be maximized.
C_LIO_LISynthesis: We provide a framework of functional dissimilarity indices and discuss the approaches they follow. Although, these indices are formulated in different ways and follow different approaches, most of them perform similarly well. At the same time, sample properties (e.g. gradient length) determine the correlation between trait-based dissimilarity and environmental distance more fundamentally.
C_LI

category: bioinformatics


title: Immature olfactory sensory neurons provide behaviorally useful sensory input to the olfactory bulb

abstract: Postnatal neurogenesis provides an opportunity to understand how newborn neurons functionally integrate into circuits to restore lost function. Newborn olfactory sensory neurons (OSNs) wire into highly organized olfactory bulb (OB) circuits throughout life, enabling lifelong plasticity and regeneration. Immature OSNs can form functional synapses capable of evoking firing in OB projection neurons. However, what contribution, if any, immature OSNs make to odor processing is unknown. Indeed, because immature OSNs can express multiple odorant receptors, any input that they do provide could degrade the odorant selectivity of input to OB glomeruli. Here, we used a combination of in vivo 2-photon calcium imaging, optogenetics, electrophysiology and behavioral assays to show that immature OSNs provide odor input to the OB, where they form monosynaptic connections with excitatory neurons. Importantly, immature OSNs responded as selectively to odorants as mature OSNs. Furthermore, mice successfully performed odor detection tasks using sensory input from immature OSNs alone. Immature OSNs responded more strongly to low odorant concentrations but their responses were less concentration dependent than those of mature OSNs, suggesting that immature and mature OSNs provide distinct odor input streams to each glomerulus. Together, our findings suggest that sensory input mediated by immature OSNs plays a previously unappreciated role in olfactory-guided behavior.


title: An awareness-dependent saliency map in the human visual system

abstract: The bottom-up contribution to the allocation of exogenous attention is a saliency map. However, how the saliency map is distributed when multiple salient stimuli are presented simultaneously and how this distribution interacts with awareness remain unclear. These questions were addressed here using visible and invisible stimuli that consisting of two salient foregrounds: the high one served as the target and the low one served as the distractor, which did or did not interfere the target saliency, indicating a gradient or winner-take-all manner, respectively. By combining psychophysics, fMRI, and effective connectivity analysis, we found that the saliency map was distributed as a gradient or winner-take-all manner with and without awareness, respectively. Crucially, we further revealed that the gradient manner was derived by feedback from pIPS, whereas the winner-take-all manner was constructed in V1. Together, our findings indicate an awareness-dependent saliency map and reconcile previous, seemingly contradictory findings on the saliency map.


title: Wide distribution of alternatively coded Lak megaphages in animal microbiomes

abstract: Lak phages with alternatively coded ~540 kbp genomes were recently reported to replicate in Prevotella in the gut microbiomes of humans that consume a non-western diet, baboons and some pigs. Here, we investigate the diversity and broader distribution of Lak phages in human and animal microbiomes using diagnostic PCR and genome-resolved metagenomics. Lak phages were detected in 13 different animal types and are particularly prevalent in pigs, with significant enrichment in the hindgut compared to foregut. We reconstructed 34 new Lak genomes, including six curated complete genomes, all of which are alternatively coded. The most deeply branched Lak is from a horse faecal sample and is the largest phage genome from an animal microbiome (~660 kbp). From the Lak genomes, we identified families of hypothetical proteins associated with specific animal types. Overall, we substantially expanded Lak phage diversity and demonstrate their occurrence in a variety of human and animal microbiomes.

category: microbiology


title: Concentration-dependent duality of bFGF in regulation of barrier properties of human brain endothelial cells

abstract: Multiple paracrine factors regulate barrier properties of human brain capillary endothelial cells (BCECs). Understanding precise mode of action of these factors remains a challenging task because of the limited availability of functionally competent BCECs and use of serum-containing medium. In the present study we employed defined protocol for producing BCECs from human inducible pluripotent stem cells. We found that autocrine secretion of basic fibroblast growth factor (bFGF) is necessary for the establishment a tight BCECs barrier, as revealed by measurements of trans-endothelial electric resistance (TEER). In contrast, exogenous bFGF in concentrations exceeding 4 ng/ml inhibited TEER and proliferation of BCECs in a concentration-dependent manner. Exogenous bFGF did not significantly affect expression and distribution of tight junction proteins claudin-5, occludin and ZO-1. Treatment with FGF receptor blocker PD173074 (15 M) suppressed inhibitory effects of bFGF and induced nuclear translocation of protein ZO-1. Inhibition of phosphoinositide 3-Kinase (PI-3K) with LY294002 (25 M) significantly potentiated inhibitory effect of bFGF on TEER indicating that PI-3K signalling pathway partially suppress inhibitory effects of bFGF on TEER. In conclusion we show that autocrine bFGF secretion is necessary for the proper barrier function of BCECs, whereas exogenous bFGF suppresses barrier resistance in a concentration-dependent manner. Our findings demonstrate a dual role for bFGF in the regulation of BCEC barrier function.

category: molecular biology


title: Occupancy-collection models: Towards bias-corrected modeling of species' distributions using unstructured occurrence data from museums and herbaria

abstract: The digitization of museum collections as well as an explosion in citizen science initiatives has resulted in a wealth of data that can be useful for understanding the global distribution of biodiversity, provided that the well-documented biases inherent in unstructured opportunistic data are accounted for. While traditionally used to model imperfect detection using structured data from systematic surveys of wildlife, occupancy-detection models provide a framework for modelling the imperfect collection process that results in digital specimen data. In this study, we explore methods for adapting occupancy-detection models for use with biased opportunistic occurrence data from museum specimens and citizen science platforms using 7 species of Anacardiaceae in Florida as a case study. We explored two methods of incorporating information about collection effort to inform our uncertainty around species presence: (1) filtering the data to exclude collectors unlikely to collect the focal species and (2) incorporating collection covariates (collection type and history of previous detections) into a model of collection probability. We found that the best models incorporated both the background data filtration step as well as the incorporation of collector covariates associated with the probability of collection. We found that month, method of collection and whether a collector had previously collected the focal species were important predictors of collection probability. Efforts to standardize meta-data associated with data collection will improve efforts for modeling the spatial distribution of a variety of species.


title: From lethal to beneficial - contrasting dietary effects of freshwater mixotrophs on zooplankton

abstract:
O_LIThe importance of mixotrophic algae as key bacterivores in microbial food webs is increasingly acknowledged, but their effects on the next trophic level remain poorly understood. Their high stoichiometric food quality is contrasted by anti-grazing strategies.
C_LIO_LIWe tested the quality of freshwater mixotrophs as prey for zooplankton, using four non-colonial chrysophyte species and a cryptophyte as a high quality reference food. We (1) analyzed the stoichiometric and biochemical (fatty acid) composition of the mixotrophs, and (2) quantified their dietary effects on Daphnia longispina survival.
C_LIO_LISurvival of D. longispina significantly depended on the identity of species provided as food, ranging from higher to lower as compared to starvation. This was not reflected in differences in cellular stoichiometry or fatty acid profiles of the mixotrophs. We suggest that toxicity may be the driver for the observed differences.
C_LIO_LIGeneralization of the dietary effects of mixotrophic chrysophytes does not appear straightforward. Besides fundamental species-specific differences, potential toxic effects may vary depending on environmental cues or physiological strategies. Notably in our study, Ochromonas tuberculata, a species previously reported to be deleterious turned out to be a beneficial food source, in terms of enabling high survival of D. longispina.
C_LIO_LIWe challenge the generality of the assumption that chrysophytes are of low value as food for zooplankton. We recommend that future studies test how environmental conditions and physiological strategies shape the quality of mixotrophs as food for consumers at higher trophic levels, specifically focusing on effects of dietary toxicity.
C_LI


title: From adverse to beneficial - contrasting dietary effects of freshwater mixotrophs on zooplankton


title: Antibiotic treatment increases yellowness of carotenoid feather coloration in greenfinches (Chloris chloris)

abstract: Carotenoid plumage coloration is an important signal of quality, and plays an important role in mate choice in many bird species. However, it remains unclear what mechanism makes carotenoids an honest signal. Here, we test the hypothesis that carotenoid plumage coloration might indicate gut health. Parasitic and microbial infections can affect nutrient absorption due to decreased gut surface or by altered gut microbiome. We took an advantage of a naturally occurring coinfection of parasites inhabiting the upper and lower portions of the digestive track to distinguish between the direct and indirect effects of parasites on carotenoid acquisition. Protozoan coccidian intestinal parasites are widespread in greenfinches (Chloris chloris) and the majority of greenfinches are infected in nature. Trichomonosis is an emerging disease of the upper digestive track that causes high mortality among greenfinches. We captured wild greenfinches (N=71) and administered anticoccidial medication toltrazuril (TOLTRA) to one group, antibiotic metronidazole (METRO) that is also effective for treating Trichomonas gallinea, to the second group, and third group received no medication. In the METRO group, feathers grown during the experiment had significantly higher chroma of yellow parts, but there was no effect of TOLTRA on feather chroma. These results suggest that METRO increased the efficiency of carotenoid modification or deposition to the feathers rather than nutrient acquisition, and/or freed energy resources that could be invested in coloration. Alternatively, in accordance with shared pathway hypothesis, increase in efficiency of vital cellular processes might have occurred, as many microbial metabolites can modulate mitochondrial and immune function.


title: Using genomic prediction to detect microevolutionary change of a quantitative trait

abstract: Detecting microevolutionary responses to natural selection by observing temporal changes in individual breeding values is challenging. The collection of suitable datasets can take many years and disentangling the contributions of the environment and genetics to phenotypic change is not trivial. Furthermore, pedigree-based methods of obtaining individual breeding values have known biases. Here, we apply a genomic prediction approach to estimate breeding values of adult weight in a 35-year dataset of Soay sheep (Ovis aries). During the study period adult body weight decreased, but the underlying genetic component of body weight increased, at a rate that is unlikely to be attributable to genetic drift. Thus cryptic microevolution of greater adult body weight has probably occurred. Using genomic prediction to study microevolution in wild populations can remove the requirement for pedigree data, potentially opening up new study systems for similar research.

category: evolutionary biology


title: In vivo deciduous dental eruption in LuiKotale bonobos and Gombe chimpanzees

abstract: Existing data on bonobo and chimpanzee dental eruption timing are derived predominantly from captive individuals or deceased wild individuals. However, recent advances in noninvasive photographic monitoring of living, wild apes have greatly expanded our knowledge of chimpanzee dental eruption in relatively healthy individuals under naturalistic conditions. We employ similar methods to expand on this knowledge by reporting deciduous dental eruption ages in living, wild bonobos and chimpanzees from LuiKotale, Democratic Republic of the Congo and Gombe National Park, Tanzania, respectively. Deciduous dental eruption ages in our sample generally fall within the range of variation previously documented for captive chimpanzees. We also found substantial variation in deciduous canine eruption timing, particularly among bonobos. One bonobo had a deciduous canine present by 227 days old while another did not have a deciduous canine present at 477 days old. As more data accumulate from these populations, future studies should consider sources of variation in deciduous canine eruption timing and relationships with other aspects of life history.


title: Contraction-expansion dynamics of reef species in response to sea-level changes

abstract: The contraction-expansion model (CEM) describes the dynamics of species that survived in refugia during the last glacial maximum (LGM) and expanded their range when environmental conditions slowly improved from the Late Glacial through to the Holocene. The CEM has been proposed to describe the dynamics of reef species in response to sea-level fluctuations from a range of disciplines, but genetic inferences rather suggest stable population sizes since the last glacial period. Here, we address this paradox by providing a new model of modern reef development, by assessing the effect of LGM bottlenecks using genetic simulations, and by using a survey of the literature on reef species to compile both estimates of times to expansion and applied rates of molecular evolution. Using previously published radiocarbon dates of core data, we propose a synthetic model for the dynamics of modern coral reefs in the Indo-Pacific region. This model describes both an initiation at 9.9 ka and subsequent development that confirms a strong influence of sea-level fluctuations on reef dynamics. Simulations based on mtDNA datasets showed that pre-LGM genetic signatures of expansion are lost. Recent literature shows that, although genetic expansions of tropical marine species are frequent (>95%), the onset of these expansions is old (median ~110 ka), which indicates that most populations have remained stable since before the LGM. These pre-LGM expansions are explained by the low mutation rates (1.66% changes/site/Myr) known to be inadequate to calibrate time at population level. Specific calibrations should help solve the paradox and generalise the CEM for reef species.


title: Increasing calling accuracy, coverage, and read depth in sequence data by the use of haplotype blocks

abstract:
High-throughput genotyping of large numbers of lines remains a key challenge in plant genetics, requiring geneticists and breeders to find a balance between data quality and the number of genotyped lines under a variety of different existing technologies when resources are limited. In this work, we are proposing a new imputation pipeline ("HBimpute") that can be used to generate high-quality genomic data from low read-depth whole-genome-sequence data. The key idea of the pipeline is the use of haplotype blocks from the software HaploBlocker to identify locally similar lines and merge their reads locally. The effectiveness of the pipeline is showcased on a dataset of 321 doubled haploid lines of a European maize landrace, which were sequenced with 0.5X read-depth. Overall imputing error rates are cut in half compared to the state-of-the-art software BEAGLE, while the average read-depth is increased to 83X, thus enabling the calling of structural variation. The usefulness of the obtained imputed data panel is further evaluated by comparing the performance in common breeding applications to that of genomic data from a 600k array. In particular for genome-wide association studies, the sequence data is shown to be performing slightly better. Furthermore, genomic prediction based on the overlapping markers from the array and sequence is leading to a slightly higher predictive ability for the imputed sequence data, thereby indicating that the data quality obtained from low read-depth sequencing is on par or even slightly higher than high-density array data. When including all markers for the sequence data, the predictive ability is slightly reduced indicating overall lower data quality in non-array markers.

Author summaryHigh-throughput genotyping of large numbers of lines remains a key challenge in plant genetics and breeding. Cost, precision, and throughput must be balanced to achieve optimal efficiencies given available technologies and finite resources. Although genotyping arrays are still considered the gold standard in high-throughput quantitative genetics, recent advances in sequencing provide new opportunities for this. Both the quality and cost of genomic data generated based on sequencing are highly dependent on the used read depth. In this work, we are proposing a new imputation pipeline ("HBimpute") that uses haplotype blocks to detect individuals of the same genetic origin and subsequently uses all reads of those individuals in the variant calling. Thus, the obtained virtual read depth is artificially increased, leading to higher calling accuracy, coverage, and the ability to all copy number variation based on relatively cheap low-read depth sequencing data. Thus, our approach makes sequencing a cost-competitive alternative to genotyping arrays with the additional benefit of the potential use of structural variation.


title: ConVarT: a search tool for orthologous variants: A method and server for functional inference of human genetic variants

abstract: The availability of genetic variants, together with phenotypic annotations from model organisms, facilitates comparing these variants with equivalent variants in humans. However, existing databases and search tools do not make it easy to scan for equivalent variants, namely "matching variants" (MatchVars) between humans and other organisms. Therefore, we developed an integrated search engine called ConVarT (http://www.convart.org/) for matching variants between humans, mice, and C. elegans. ConVarT incorporates annotations (including phenotypic and pathogenic) into variants, and these previously unexploited phenotypic MatchVars from mice and C. elegans can give clues about the functional consequence of human genetic variants. Our analysis shows that many phenotypic variants in different genes from mice and C. elegans, so far, have no counterparts in humans, and thus, can be useful resources when evaluating a relationship between a new human mutation and a disease.


title: ConVarT: a search engine for orthologous variants and functional inference of human genetic variants


title: ConVarT: a search engine for matching human genetic variants with variants from non-human species


title: Structural and mechanistic insights into the Artemis endonuclease and strategies for its inhibition

abstract: Artemis (DCLRE1C) is an endonuclease that plays a key role in development of B- and T-lymphocytes and in DNA double-strand break repair by non-homologous end-joining (NHEJ). Artemis is phosphorylated by DNA-PKcs and acts to open DNA hairpin intermediates generated during V(D)J and class-switch recombination. Consistently, Artemis deficiency leads to radiosensitive congenital severe immune deficiency (RS-SCID). Artemis belongs to a structural superfamily of nucleases that contain conserved metallo-{beta}-lactamase (MBL) and {beta}-CASP (CPSF-Artemis-SNM1-Pso2) domains. Here, we present crystal structures of the catalytic domain of wild type and variant forms of Artemis that cause RS-SCID Omenn syndrome. The truncated catalytic domain of the Artemis is a constitutively active enzyme that with similar activity to a phosphorylated full-length protein. Our structures help explain the basis of the predominantly endonucleolytic activity of Artemis, which contrast with the predominantly exonuclease activity of the closely related SNM1A and SNM1B nucleases. The structures also reveal a second metal binding site in its {beta}-CASP domain that is unique to Artemis. By combining our structural data that from a recently reported structure we were able model the interaction of Artemis with DNA substrates. Moreover, co-crystal structures with inhibitors indicate the potential for structure-guided development of inhibitors.


title: The topological free energy of proteins

abstract: Protein folding, the process by which proteins attain a 3-dimensional conformation necessary for their function, remains an important unsolved problem in biology. A major gap in our understanding is how local properties of proteins relate to their global properties. In this manuscript, we use the Writhe and Torsion to introduce a new local topological/geometrical free energy that can be associated to 4 consecutive residues along protein backbone. By analyzing a culled protein dataset from the PDB, our results show that high local topological free energy conformations are independent of sequence and may be involved in the rate limiting step in protein folding. By analyzing a set of 2-state single domain proteins, we find that the total local topological free energy of these proteins correlates with the experimentally observed folding rates reported in [29].


title: Free Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitor Using Metadynamics

abstract: Aromatic side-chains (phenylalanine and tyrosine) of a protein flip by 180{degrees} around the C{beta} - C{gamma} axis ({chi}2 dihedral of side-chain) producing two symmetry-equivalent states. The ring-flip dynamics act as an NMR probe to understand local conformational fluctuations. Ring-flips are categorized as slow (ms onwards) or fast (ns to near ms) based on timescales accessible to NMR experiments. In this study, we investigated the ability of the infrequent metadynamics approach to discriminate between slow and fast ring-flips for eight individual aromatic side-chains (F4, Y10, Y21, F22, Y23, F33, Y35, F45) of basic pancreatic trypsin inhibitor (BPTI). Well-tempered metadynamics simulations were performed to observe ring-flipping free energy surfaces for all eight aromatic residues. The results indicate that{chi} 2 as a standalone collective variable (CV) is not sufficient to classify fast and slow ring-flips. Most of the residues needed{chi} 1 (N - C) as a complementary CV, indicating the importance of librational motions in ring-flips. Multiple pathways and mechanisms were observed for residues F4, Y10, and F22. Recrossing events are observed for residues F22 and F33, indicating a possible role of friction effects in the ring-flipping. The results demonstrate the successful application of the metadynamics based approach to estimate ring-flip rates of aromatic residues in BPTI and identify certain limitations of the approach.

category: biophysics


title: Myeloperoxidase-induced fibrinogen unfolding and clotting

abstract:
Fibrinogen is a major protein of blood coagulation system and is a promising component of biomaterials and protein matrixes. Conformational changes of fibrinogen underlie the important mechanism of thrombin mediated fibrinogen clotting but also may induce the loss of its biological activity and (amyloid) aggregation. Understanding and controlling of fibrinogen unfolding is important for the development of fibrinogen based materials with tunable properties. We have discovered that myeloperoxidase induces denaturation of fibrinogen molecules followed by fibrinogen clotting, which is not thrombin-dependent. This is the first example of ATP-independent, non-targeted protein-induced protein denaturation. The morphological structure of unfolded fibrinogen molecules and "non-conventional" fibrinogen clots has been characterized using high-resolution atomic force microscopy and scanning electron microscopy techniques. Circular dichroism (CD) spectroscopy has shown no significant changes of the secondary structure of the fibrinogen clots. The absorbance spectrophotometry has demonstrated that the kinetics of myeloperoxidase induced fibrinogen clotting strongly decays with growth of ionic strength indicating a major role of the Debye screening effect in regulating of this process. The obtained results provide with the novel concepts of protein unfolding and open new insights into fibrinogen clotting. Moreover, they give new possibilities in biotechnological and biomedical applications, e.g., for regulation of fibrinogen clotting and platelet adhesion and for the development of fibrinogen-based matrices.

The organization of a protein molecule is characterized by different hierarchical levels such as primary, secondary, tertiary and quaternary structure. Protein unfolding or denaturation, i.e. its transformation to a lower order structure (and loss of a higher order structure), is a biologically and biotechnologically relevant process. Protein unfolding is a prerequisite for an alternative folding pathway including amyloid aggregation 1,2. Unfolded proteins may be used in development of protein films and coatings with special properties such as enhanced mechanical stability 3-5, resistance to protein adsorption or platelet adhesion 6,7 and other advantages 8. Unfolding of a protein molecule may lead to the loss of its biological function 9 that has important consequences in biosensor 10,11 and pharmaceutical applications 12.


title: T cell stiffness is enhanced upon formation of immunological synapse

abstract: T cells are activated by cognate target cells via an intimate contact, termed immunological synapse (IS). Cellular mechanical properties, especially stiffness, are essential to regulate cell functions, T cell stiffness at a subcellular level at the IS still remains largely elusive. In this work, we established an atomic force microscopy (AFM)-based elasticity mapping method on whole T cells to obtain an overview of the stiffness with a resolution of ~ 60 nm. Using Jurkat T-cells and primary human CD4+ T cells, we show that in the T cells in contact with functionalized surfaces, the lamellipodia are stiffer than the cell body. Upon IS formation, T cell stiffness is substantially enhanced both at the lamellipodia and in cell body. Chelation of intracellular Ca2+ abolishes IS-induced stiffening at the lamellipodia but has no influence on cell body-stiffening, suggesting different regulatory mechanism of IS-induced stiffening between the lamellipodia and the cell body.


title: Comparison between slow, anisotropic LE4PD fluctuations and thePrincipal Component Analysis modes of Ubiquitin

abstract: Proteins biological function and folding mechanisms are often guided by large-scale, slow motions, which involve crossing high energy barriers. In a simulation trajectory, these slow fluctuations are commonly identified using a principal component analysis (PCA). Despite the popularity of this method, a complete analysis of its predictions based on the physics of protein motion has been so far limited. This study formally connects the PCA to a Langevin model of protein dynamics and analyzes the contributions of energy barriers and hydrodynamic interactions to the slow PCA modes of motion. To do so, we introduce an anisotropic extension of the Langevin Equation for Protein Dynamics, called the LE4PD-XYZ, which formally connects to the PCA  essential dynamics. The LE4PD-XYZ is an accurate coarse-grained diffusive method to model protein motion, which describes anisotropic fluctuations in the proteins alpha-carbons. The LE4PD accounts for hydrodynamic effects and mode-dependent free-energy barriers. This study compares large-scale anisotropic fluctuations identified by the LE4PD-XYZ to the mode-dependent PCAs predictions, starting from a microsecond-long alpha-carbon molecular dynamics atomistic trajectory of the protein ubiquitin. We observe that the inclusion of free-energy barriers and hydrodynamic interactions has important effects on the identification and timescales of ubiquitins slow modes.


title: Single cell proteomics of tumor compartments identifies differential kinase activities defining sensitivity to mTOR-PI3-kinase inhibition

abstract: Cancer therapy often results in heterogeneous responses in different metastatic lesions in the same patient. Inter- and intra-tumor heterogeneity in proteomic signaling within the various tumor compartments and its impact on therapy are not well characterized due to the limited sensitivity of single cell proteomic approaches. To overcome this barrier, we applied single cell mass cytometry with a customized 29-antibody panel [against cell states, receptor tyrosine kinases (RTK) and phosphoinositide 3-kinase/mammalian target of rapamycin (PI3K/mTOR)-, mitogen-activated protein kinase (MAPK)-, and cytokine-signaling] to PTEN-deleted orthotopic prostate cancer xenograft models to measure the evolution of kinase activities in different tumor compartments during metastasis and upon drug treatment. Compared with primary tumors and circulating tumor cells (CTCs), bone metastases but not lung and liver metastases exhibited elevated PI3K/mTOR signaling and RTKs including c-Met protein, which, when suppressed, impaired tumor growth in the bone. Intra-tumoral heterogeneity within tumor compartments also arises from highly proliferative EpCAMhigh epithelial cells with increased PI3K and mTOR kinase activities co-existing with poorly proliferating EpCAMlow mesenchymal populations with reduced kinase activities, findings recapitulated in epithelial and mesenchymal CTC populations in metastatic prostate and breast cancer patients. Increased kinase activity in EpCAMhigh cells rendered them more sensitive to PI3K/mTOR inhibition and drug resistant EpCAMlow populations with reduced kinase activity emerged over time. Taken together, single cell proteomics identified microenvironment- and cell state-dependent activation of kinase networks creating heterogeneity and differential drug sensitivity among and within tumor populations across different sites, defining a new paradigm of drug responses to kinase inhibitors.

category: cancer biology


title: Network Analysis Reveals Synergistic Genetic Dependencies for Rational Combination Therapy in Philadelphia Chromosome-like Acute Lymphoblastic Leukemia

abstract: Systems biology approaches can identify critical targets in complex cancer signaling networks to inform therapy combinations and overcome conventional treatment resistance. Herein, we developed a data-driven, network controllability-based approach to identify synergistic key regulator targets in Philadelphia chromosome-like B-acute lymphoblastic leukemia (Ph-like B-ALL), a high-risk leukemia subtype associated with hyperactive signal transduction and chemoresistance. Integrated analysis of 1,046 childhood B-ALL cases identified 14 dysregulated network nodes in Ph-like ALL involved in aberrant JAK/STAT, Ras/MAPK, and apoptosis pathways and other critical processes. Consistent with network controllability theory, combination small molecule inhibitor therapy targeting a pair of key nodes shifted the transcriptomic state of Ph-like ALL cells to become less like kinase-activated BCR-ABL1-rearranged (Ph+) B-ALL and more similar to prognostically-favorable childhood B-ALL subtypes. Functional validation experiments further demonstrated enhanced anti-leukemia efficacy of combining the BCL-2 inhibitor venetoclax with tyrosine kinase inhibitors ruxolitinib or dasatinib in vitro in human Ph-like ALL cell lines and in vivo in multiple patient-derived xenograft models. Our study represents a broadly-applicable conceptual framework for combinatorial drug discovery, based on systematic interrogation of synergistic vulnerability pathways with pharmacologic targeted validation in sophisticated preclinical human leukemia models.


title: Multiomics Integration Elucidates Metabolic Modulators of Drug Resistance in Lymphoma

abstract:
BackgroundDiffuse large B-cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma (NHL). B-cell NHLs rely on Brutons tyrosine kinase (BTK) mediated B-cell receptor signaling for survival and disease progression. However, they are often resistant to BTK inhibitors or soon acquire resistance after drug exposure resulting in the drug tolerant form. The drug tolerant clones proliferate faster, have increased metabolic activity, and shift to oxidative phosphorylation; however, how this metabolic programming occurs in the drug resistant tumor is poorly understood.

MethodsIn this study, we explored for the first time the metabolic regulators of ibrutinib-resistant activated B-cell (ABC) DLBCL using a  multi-omics analysis that integrated metabolomics (using high-resolution mass spectrometry) and transcriptomic (gene expression analysis). Overlay of the unbiased statistical analyses, genetic perturbation and pharmaceutical inhibition, were further used to identify the key players that contribute to the metabolic reprograming of the drug resistant clone.

ResultsGene-metabolite integration revealed interleukin 4 induced 1 (IL4I1) at the crosstalk of two significantly altered metabolic pathways involved in the production of various amino acids. We showed for the first time that drug resistant clones undergo metabolic reprogramming from glycolysis towards oxidative phosphorylation & is activated via the BTK-PI3K-AKT-IL4I1 axis and can be targeted therapeutically.

ConclusionsOur report shows how these cells become dependent on PI3K/AKT signaling for survival after acquiring ibrutinib resistance and shift to sustained Oxidative phosphorylation, additionally we outline the compensatory, pathway that regulates this metabolic reprogramming in the drug resistant cells. These findings from our unbiased analyses highlight the role of metabolic reprogramming during drug resistance development. Furthermore, our work demonstrates that a multi-omics approach can be a powerful and unbiased strategy to uncover genes and pathways that drive metabolic dysregulation in cancer cells.


title: Fibronectin-mediated inflammatory signaling through integrin α5 in vascular remodeling

abstract: Adhesion of vascular endothelial cells (ECs) to the underlying basement membrane potently modulates EC inflammatory activation. The normal basement membrane proteins laminin and collagen IV attenuate inflammatory signaling in part through integrin 2{beta}1. In contrast, fibronectin, the provisional matrix protein found in injured, remodeling or inflamed vessels, sensitizes ECs to inflammatory stimuli through integrins 5{beta}1and and v{beta}3. A chimeric integrin in which the cytoplasmic domain of 5 is replaced with that of 2 pairs with {beta}1 and binds fibronectin but signals like 2{beta}1. Here, we examined mice in which integrin 5 is replaced with the 5/2 chimera, using the transverse aortic constriction (TAC) and partial carotid ligation (PCL) models of vessel remodeling. Following TAC and PCL surgery, WT mice showed increased fibronectin deposition and expression of inflammatory markers, which were strongly attenuated in a5/2 mice. 5/2 mice also showed reduced artery wall hypertrophy in the TAC model and diminished inward remodeling in the PCL model. Acute atherosclerosis after PCL in hyperlipidemic ApoE-/- mice on a high fat diet was dramatically decreased in 5/2 mice. These results underscore the key role for integrin 5 signaling in pathological vascular remodeling and support its potential as a therapeutic target.

category: physiology


title: Coordinated overexpression of OsSUT1, OsSWEET11 and OsSWEET14 in rice impairs carbohydrate metabolism that has implications in plant growth, yield and susceptibility to Xanthomonas oryzae pv oryzae (Xoo)

abstract: Enhancing carbohydrate export to sink tissues is considered as a feasible approach for improving photosynthetic efficiency and crop yield. In Oryza sativa Sucrose Transporter OsSUT1 located in companion cells and Sugars Will Eventually be Exported Transporters (SWEETs); OsSWEET11 and OsSWEET14 present in phloem parenchyma mesophyll cell plasma membranes are involved in long distance sucrose transport. OsSWEET11 and OsSWEET14 also play important role in host-pathogen interaction of rice plants and Xanthomonas oryzae pv oryzae (Xoo) that causes bacterial leaf blight. Three genes, OsSUT1, OsSWEET11, and OsSWEET14 were overexpressed under the control of their native promoters in rice to modulate long distance sugar transport and disease resistance. The transgenics displayed several phenotypic aberrations such as reduced plant height and seed weight due to altered sucrose transport and metabolism. Lower sucrose transport rate in transgenics than the WT resulted in reduced sucrose, fructose and glucose and increased starch accumulation in their leaves at the end of dark period. Transcriptional analysis revealed a reduction in the expression of genes involved in sucrose synthesis pathway in transgenics. Normal growth and development of transgenic seedlings were restored in growth media supplemented with 3% sucrose demonstrating in planta sucrose limitation. Remarkably, transgenic lines had diminished susceptibility to Xoo than the WTs due to low sugar content in the leaves demonstrating that rice plants maintain an optimum level of SWEETs for proper plant growth and development, and upregulation of these SWEETs in rice mimicks Xoo attack impelling plants to reduce sugar content in the apoplasm to inhibit pathogen growth.

category: plant biology


title: Corynebacterium glutamicum regulation beyond transcription: Organizing principles and reconstruction of an extended regulatory network incorporating regulations mediated by small RNA and protein-protein interactions

abstract: Corynebacterium glutamicum is a Gram-positive bacterium found in soil where the condition changes demand plasticity of the regulatory machinery. The study of such machinery at the global scale has been challenged by the lack of data integration. Here, we report three regulatory network models for C. glutamicum: strong (3040 interactions) constructed solely with regulations previously supported by directed experiments; all evidence (4665 interactions) containing the strong network, regulations previously supported by non-directed experiments, and protein-protein interactions with a direct effect on gene transcription; and sRNA (5222 interactions) containing the all evidence network and sRNA-mediated regulations. Compared to the previous version (2018), the strong and all evidence networks increased by 75 and 1225 interactions, respectively. We analyzed the system-level components of the three networks to identify how they differ and compared their structures against those for the networks of more than 40 species. The inclusion of the sRNAs regulations changed the proportions of the system-level components and increased the number of modules but decreased their size. The C. glutamicum regulatory structure contrasted with other bacterial regulatory networks. Finally, we used the strong networks of three model organisms to provide insights and future directions of the C. glutamicum regulatory network characterization.

category: systems biology


title: Optogenetic activation of Gq signaling in astrocytes yields stimulation-specific effects on basal hippocampal synaptic excitation and inhibition

abstract: Astrocytes play active roles at synapses and can monitor, respond, and adapt to local synaptic activity. To investigate this relationship, more tools that can selectively activate native G protein signaling pathways in astrocytes with both spatial and temporal precision are needed. Here, we tested AAV8-GFAP-Opto1AR-eYFP (Opto1AR), a viral vector to enable activation of Gq signaling in astrocytes via light-sensitive 1-adrenergic receptors. To determine if stimulating astrocytic Opto1AR modulates hippocampal synaptic transmission, recordings were made in CA1 pyramidal cells with surrounding astrocytes expressing Opto1AR, channelrhodopsin (ChR2), or GFP. Both high-frequency (20 Hz, 45-ms light pulses, 5 mW, 5 min) and low-frequency (0.5 Hz, 1-s pulses at increasing 1, 5, and 10 mW intensities, 90 s per intensity) blue light stimulation were tested. 20 Hz Opto1AR stimulation increased both inhibitory and excitatory postsynaptic current (IPSC and EPSC) frequency, and the mIPSC effect was largely reversible within 20 min. By contrast, low-frequency stimulation of Opto1AR did not modulate either IPSCs or EPSCs, whereas the same stimulation of astrocytic ChR2 was effective. These data demonstrate that Opto1AR activation in astrocytes changes synaptic excitation and inhibition in a stimulation-sensitive manner, demonstrating the efficacy and utility of GFAP-Opto1AR as a tool in studying astrocyte-neuron interactions.


title: Evaluating the efficacy of Optoα1AR activation in astrocytes in modulating basal hippocampal synaptic excitation and inhibition


title: An edge-centric model for harmonizing multi-relational network datasets

abstract: Functional and structural connections vary across conditions, measurements, and time. However, how to resolve multi-relational measures of connectivity remains an open challenge. Here, we propose an extension of structural covariance and morphometric similarity methods to integrate multiple estimates of connectivity into a single edge-centric network representation. We highlight the utility of this method through two applications: an analysis of multi-task functional connectivity data and multi-measure structural networks. In these analyses, we use data-driven clustering techniques to identify collections of edges that covary across tasks and measures, revealing overlapping mesoscale architecture. We also link these features to node-level properties such as modularity and canonical descriptors of brain systems. We further demonstrate that, in the case of multi-task functional networks, edge-level features are consistent across individuals yet exhibit subject-specificity. We conclude by highlighting other instances where the edge-centric model may be useful.


title: Macrophage depletion impairs neonatal tendon regeneration

abstract: Tendons are dense connective tissues that transmit muscle forces to the skeleton. After adult injury, healing potential is generally poor and dominated by scar formation. Although the immune response is a key feature of healing, the specific immune cells and signals that drive tendon healing have not been fully defined. In particular, the immune regulators underlying tendon regeneration are almost completely undetermined due to a paucity of tendon regeneration models. Using a mouse model of neonatal tendon regeneration, we screened for immune-related markers and identified upregulation of several genes associated with inflammation, macrophage chemotaxis, and TGF{beta} signaling after injury. Depletion of macrophages using AP20187 treatment of MaFIA mice resulted in impaired functional healing, reduced cell proliferation, reduced ScxGFP+ neo-tendon formation, and altered tendon gene expression. Collectively, these results show that inflammation is a key component of neonatal tendon regeneration and demonstrate a requirement for macrophages in effective functional healing.

category: immunology


title: Role of T cells in intrauterine administration of activated peripheral blood mononuclear cells in recurrent implantation failure.

abstract: Over the last few years, intrauterine administration of autologous peripheral blood mononuclear cells (PBMC) has been proposed as new immunotherapy for patients with unexplained recurrent implantation failure (RIF). In these patients, administration of activated PBMC before embryo transfer results in a 2-fold increase in live birth rates(Yang et al., 2020). In this study we evaluated the role of T cells to promotes human endometrial receptivity. On the day of ovulation, PBMC were isolated from and activated with T cells mitogen, the phytohemagglutinin (PHA) and hCG for 48-h in a conditioned culture medium. Distributions of CD4+ T cells were characterized in 157 patients by flow cytometry before and after PHA/hCG activation. Cytokine production was analyzed by cytometric beads array. We observed in RIF patients a significant decrease in Th2 and natural Treg cells before activation with PHA/hCG and an increase of Th17 cells after activation compared to intrauterine sperm insemination (IUI) and in vitro fertilization (IVF) groups. Furthermore, the hCG/PHA treatment increases anti-inflammatory T cells (Th2 and Treg cells) compared to non-treated T cells. Principal component analysis (PCA) performed on CD4 T cell subtypes revealed a different cellular profile in the RIF compared to the IUI and IVF groups. This inflammatory state change could explain how endometrium immunomodulation by hCG-activated PBMC helps patients with unexplained RIF to reach implantation.


title: The molecular principles of Piwi-mediated co-transcriptional silencing through the dimeric SFiNX complex

abstract: Nuclear Argonaute proteins, guided to nascent target RNAs by their bound small RNAs, elicit co-transcriptional silencing through heterochromatin formation at transposon insertions and repetitive genomic loci. The molecular mechanisms involved in this process are incompletely understood. Here, we propose that the SFiNX complex, a silencing mediator downstream of nuclear Piwi-piRNA complexes in Drosophila, enables co-transcriptional silencing via the formation of molecular condensates. Condensate formation is stimulated by nucleic acid binding and requires SFiNX dimerization, mediated by the dynein light chain protein, LC8/Cutup. LC8s function within SFiNX can be bypassed with a heterologous dimerization domain, suggesting that dimerization is a constitutive feature of SFiNX. Mutations preventing LC8-mediated SFiNX dimerization result in loss of condensate formation in vitro and inability of Piwi to initiate heterochromatin formation and silence transposons in vivo. Formation of molecular condensates might be a general mechanism that underlies effective heterochromatin establishment at small RNA target loci in a co-transcriptional manner.


title: The effects of chromosome fusions on genetic diversity and evolutionary turnover of functional loci consistently depends on chromosome size

abstract: Major changes in chromosome number and structure are linked to a series of evolutionary phenomena, including intrinsic barriers to gene flow or suppression of recombination due to chromosomal rearrangements. However, chromosome rearrangements can also affect the fundamental dynamics of molecular evolution within populations by changing relationships between linked loci and altering rates of recombination. Here, we build chromosome-level assembly Eueides isabella and, together with the chromosome-level assembly of Dryas iulia, examine the evolutionary consequences of multiple chromosome fusions in Heliconius butterflies. These assemblies pinpoint fusion points on 10 of the 21 autosomal chromosomes and reveal striking differences in the characteristics of fused and unfused chromosomes. The ten smallest autosomes in D. iulia and E. isabella, which have each fused to a longer chromosome in Heliconius, have higher repeat and GC content, and longer introns than predicted by their chromosome length. Following fusion, these characteristics change to become more in line with chromosome length. The fusions also led to reduced diversity, which likely reflects increased background selection and selection against introgression between diverging populations, following a reduction in per-base recombination rate. We further show that chromosome size and fusion impact turnover rates of functional loci at a macroevolutionary scale. Together these results provide further evidence that chromosome fusion in Heliconius likely had dramatic effects on population level processes shaping rates of neutral and adaptive divergence. These effects may have impacted patterns of diversification in Heliconius, a classic example of an adaptive radiation.


title: Chromosome fusion affects genetic diversity and evolutionary turnover of functional loci, but consistently depends on chromosome size


title: The impact of PNPLA3 and TM6SF2 in cirrhosis related complications

abstract: Patatin-like phospholipase domain-containing 3 (PNPLA3) and transmembrane 6-superfamily member 2 (TM6SF2) polymorphisms have major impact for fibrosis due to steatohepatitis. However, there are scant data about correlations between cirrhosis-related complications and the polymorphisms of these genes. Therefore, we aimed to determine the role of the PNPLA3 and TM6SF2 polymorphisms in fibrosis progression for patients with liver cirrhosis. A multicenter study was performed at six hospitals in Japan enrolling 400 patients with liver cirrhosis caused by virus (n = 157), alcohol (n = 104), nonalcoholic fatty liver disease (NAFLD) (n = 106), or autoimmune disease (n = 33). These cirrhotic patients included those with complications of variceal bleeding, hepatic ascites, and/or hepatic encephalopathy and those without. To assess the role of the PNPLA3 and TM6SF2 polymorphisms in patients with cirrhosis related complications, we calculated the odds ratio and relative risk for the rs738409 and rs58542926 polymorphisms. We also accessed whether or not the interaction between these two polymorphisms contributed to cirrhosis related complications. As a result, the odds ratio for complications in the NAFLD group significantly increased in the presence of the rs738409 GG genotype when the CC genotype was used as the reference. There were no significant risks between complications and the presence of the rs738409 G allele in the virus or alcohol groups. There were no significant risks of complications in the frequency of the rs58542926 T polymorphism regardless of the etiology of liver cirrhosis. The interaction between the rs738409 and rs58542926 polymorphisms had the highest odds ratio of 2.415 for complications in the rs738409 GG + rs58542926 (CT+TT) group when rs738409 (CC+CG) + TM6SF2 CC was used as the reference in the NAFLD group although there was no statistically interaction between these gene polymorphisms (P=0.085).


title: Barth syndrome cellular models have dysregulated respiratory chain complex I and mitochondrial quality control due to abnormal cardiolipin

abstract: Barth syndrome (BTHS) is an X-linked genetic condition caused by defects in TAZ, which encodes a transacylase involved in the remodeling of the inner mitochondrial membrane phospholipid, cardiolipin (CL). As such, CL has been implicated in numerous mitochondrial functions, and the role of defective CL in the clinical pathology of BTHS is under intense investigation. We used untargeted proteomics, shotgun lipidomics, gene expression analysis, and targeted metabolomics to identify novel areas of mitochondrial dysfunction in a new model of TAZ deficiency in HEK293 cells. Functional annotation analysis of proteomics data revealed abnormal regulation of mitochondrial respiratory chain complex I (CI), driven by the reduced abundance of 6 CI associated proteins in TAZ-deficient HEK293 cells: MT-ND3, NDUFA5, NDUFAB1, NDUFB2, NDUFB4, and NDUFAF1. This resulted in reduced assembly and function of CI in TAZ-deficient HEK293 cells as well as BTHS patient derived lymphoblast cells. We also identified increased abundance of PARL, a rhomboid protein involved in the regulation of mitophagy and apoptosis, and abnormal downstream processing of PGAM5, another mediator of mitochondrial quality control, in TAZ-deficient cells. Lastly, we modulated CL via the phospholipase inhibitor bromoenol lactone and the CL targeted SS-peptide, SS-31, and showed that each is able to remediate abnormalities in CI abundance as well as PGAM5 processing. Thus, mitochondrial respiratory chain CI and PARL/PGAM5 regulated mitochondrial quality control, both of whose functions localize to the inner mitochondrial membrane, are dysregulated due to TAZ deficiency and are partially remediated via modulation of CL.


title: Transcriptomic profiles of Plasmodium falciparum and Plasmodium vivax-infected individuals in Indonesia

abstract: Malaria is one of the leading causes of illness and death globally. The vast majority of transcriptomic studies of the impact of malaria on human hosts have been conducted on populations of African ancestry suffering from Plasmodium falciparum infection, making it unclear whether biological responses observed in these studies can be generalised to other populations. Here, we perform differential expression analysis between healthy controls and malaria-infected patients within Indonesia, a country of over 260 million people which has substantial morbidity due to endemic malaria. We find that in samples infected with P. falciparum and P. vivax, there is an upregulation of genes involved in inflammation, the immediate early immune response, translation, and apoptosis. When comparing these findings to transcriptomic studies conducted in Africa (on P. falciparum) and South America (on P. vivax), we find that many pathways are shared. This is particularly apparent for receptor recognition and inflammation-related genes in P. falciparum and innate immune and chemokine-related genes in P. vivax infection. However, we also find that many genes are unique to the Indonesian population, particularly those involved in RNA processing, splicing, and cell surface receptor genes. This study provides a more comprehensive view of malaria infection outside of Africa and contributes to a better characterisation of malaria pathogenesis within humans across a range of genetic architectures.

category: genomics


title: A co-culture microplate for real-time measurement of microbial interactions

abstract: The dynamic structures of microbial communities emerge from the complex network of interactions between their constituent microbial organisms. Quantitative measurements of these microbial interactions are important for understanding and engineering microbial community structure. Here, we present the development and application of the BioMe plate, a redesigned microplate device in which pairs of wells are separated by porous membranes. BioMe facilitates the measurement of dynamic microbial interactions and integrates easily with standard laboratory equipment. We first applied BioMe to recapitulate recently characterized, natural symbiotic interactions between bacteria isolated from the D. melanogaster gut microbiome. Specifically, the BioMe plate allowed us to observe the benefit provided by two Lactobacilli strains to an Acetobacter strain. We next explored the use of BioMe to gain quantitative insight into the engineered obligate syntrophic interaction between a pair of E. coli amino acid auxotrophs. We integrated experimental observations with a mechanistic computational model to quantify key parameters associated with this syntrophic interaction, including metabolite secretion and diffusion rates. This model also allowed us to explain the slow growth observed for auxotrophs growing in adjacent wells, by demonstrating that under the relevant range of parameters, local exchange between auxotrophs is essential for efficient growth. The BioMe plate provides a scalable and flexible approach for the study of dynamic microbial interactions.


title: Compartmentalized three-dimensional human neuromuscular tissue models fabricated on a well-plate-format microdevice

abstract: Engineered three-dimensional models of neuromuscular tissues are promising for use in mimicking their disorder states in vitro. Although several models have been developed, it is still challenging to mimic the physically separated structures of motor neurons (MNs) and skeletal muscle (SkM) fibers in the motor units in vivo. In this study, we aimed to develop microdevices for precisely compartmentalized coculturing of MNs and engineered SkM tissues. The developed microdevices, which fit a well of 24 well plates, had a chamber for MNs and chamber for SkM tissues. The two chambers were connected by microtunnels for axons, permissive to axons but not to cell bodies. Human iPSC (hiPSC)-derived MN spheroids in one chamber elongated their axons into microtunnels, which reached the tissue-engineered human SkM in the SkM chamber, and formed functional neuromuscular junctions with the muscle fibers. The cocultured SkM tissues with MNs on the device contracted spontaneously in response to spontaneous firing of MNs. The addition of a neurotransmitter, glutamate, into the MN chamber induced contraction of the cocultured SkM tissues. Selective addition of tetrodotoxin or vecuronium bromide into either chamber induced SkM tissue relaxation, which could be explained by the inhibitory mechanisms. We also demonstrated the application of chemical or mechanical stimuli to the middle of the axons of cocultured tissues on the device. Thus, compartmentalized neuromuscular tissue models fabricated on the device could be used for phenotypic screening to evaluate the cellular type specific efficacy of drug candidates and would be a useful tool in fundamental research and drug development for neuromuscular disorders.


title: Periodicity in the embryo: emergence of order in space, diffusion of order in time

abstract: Does embryonic development exhibit characteristic temporal features? This is apparent in evolution, where evolutionary change has been shown to occur in bursts of activity. Using two animal models (Nematode, Caenorhabditis elegans and Zebrafish, Danio rerio) and simulated data, we demonstrate that temporal heterogeneity exists in embryogenesis at the cellular level, and may have functional consequences. Cell proliferation and division from cell tracking data is subject to analysis to characterize specific features in each model species. Simulated data is then used to understand what role this variation might play in producing phenotypic variation in the adult phenotype. This goes beyond a molecular characterization of developmental regulation to provide a quantitative result at the phenotypic scale of complexity.


title: Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface

abstract: The three-dimensional organization of chromatin is expected to play critical roles in regulating genome functions. High-resolution characterization of its structure and dynamics could improve our understanding of gene regulation mechanisms but has remained challenging. Using a near-atomistic model that preserves the chemical specificity of protein-DNA interactions at residue and base-pair resolution, we studied the stability and folding pathways of a tetra-nucleosome. Dynamical simulations performed with an advanced sampling technique uncovered multiple pathways that connect open chromatin configurations with the zigzag crystal structure. Intermediate states along the simulated folding pathways resemble chromatin configurations reported from in situ experiments. We further determined a six-dimensional free energy surface as a function of the inter-nucleosome distances via a deep learning approach. The zigzag structure can indeed be seen as the global minimum of the surface. However, it is not favored by a significant amount relative to the partially unfolded, in situ configurations. Chemical perturbations such as histone H4 tail acetylation and thermal fluctuations can further tilt the energetic balance to stabilize intermediate states. Our study provides insight into the connection between various reported chromatin configurations and has implications on the in situ relevance of the 30nm fiber.


title: Counting individual bacteria during high-throughput growth in microfluidic droplets

abstract: Bacterial growth in microfluidic droplets is relevant in biotechnology, in microbial ecology, and in understanding stochastic population dynamics in small populations. However, it has proved challenging to automate measurement of absolute bacterial numbers within droplets, forcing the use of proxy measures for population size. Here we present a microfluidic device and imaging protocol that allows high-resolution imaging of thousands of droplets, such that individual bacteria stay in the focal plane and can be counted automatically. Using this approach, we track the stochastic growth of hundreds of replicate Escherichia coli populations within droplets. We find that, for early times, the statistics of the growth trajectories obey the predictions of the Bellman-Harris model, in which there is no inheritance of division time. Our approach should allow further testing of models for stochastic growth dynamics, as well as contributing to broader applications of droplet-based bacterial culture.


title: Tracking the stochastic growth of bacterial populations in microfluidic droplets


title: Microwell array-based opto-electrochemical detections revealing co-adaptation of rheological properties and oxygen metabolism in budding yeast

abstract: Microdevices composed of microwell arrays integrating nanoelectrodes (OptoElecWell) were developed to achieve dual high-resolution optical and electrochemical detections on single Saccharomyces cerevisiae budding yeast cells. Each array consists in 1.6 x 105 microwells of 8 {micro}m diameter and 5 {micro}m height, with a platinum nanoring electrode for in-situ electrochemistry, all integrated on a transparent thin wafer for further high-resolution live-cell imaging. After optimizing the filling rate, 32% of cells were effectively trapped within microwells. This allowed to analyse S. cerevisiae metabolisms associated with basal respiration while simultaneously measuring optically other cellular parameters. In this study, we focused on the impact of glucose concentration on respiration and intracellular rheology. We found that while oxygen uptake rate decreased with increasing glucose concentration, diffusion of tracer nanoparticles increased. Our OptoElecWell based respiration methodology provided similar results compared to the commercial gold-standard Seahorse XF analyser, while using 20 times lesser biological samples, paving the way to achieve single cell metabolomics. In addition, it facilitates an optical route to monitor the contents within single cells. The proposed device, in combination with the dual detection analysis, opens up new avenues for measuring cellular metabolism, and relating it to various cellular physiological and rheological indicators at single cell level.


title: The renal inflammatory network of nephronophthisis.

abstract:
STRUCTURED ABSTRACTO_ST_ABSBACKGROUNDC_ST_ABSThe majority of genetic kidney disease leading to kidney failure is caused by mutations in ciliary genes. How cilia malfunction leads to progressive kidney damage is poorly understood, but recent evidence links ciliopathy genes to CCL2 dependent macrophage recruitment in autosomal dominant polycystic kidney disease (ADPKD), the most studied renal ciliopathy. Whether or not renal inflammation is involved in other renal ciliopathies is unclear.

METHODSWe combined mice models with kidney biopsies and renal epithelial cells sampled from human urine to characterize the renal inflammatory network of nephronophthisis (NPH), the most frequent renal ciliopathy in children.

RESULTSIn human, mutations in cilia genes involved in NPH enhance urine excretion of the chemokine CCL2, causing abnormal macrophage recruitment in kidney tissues from NPH patients. Differing from ADPKD, inactivating Ccl2 specifically in mouse tubular cells does not rescue the NPH phenotype, suggesting that other inflammatory mediators are involved. Using transcriptional data from 2 NPH models, we identify a set of pro-inflammatory cytokines upregulated in this disease, independently of CCL2. The majority of detectable transcripts from this set are specifically upregulated in kidney cells from NPH patients. In line with the function of these cytokines, NPH kidneys show disproportionate neutrophils and T cells infiltrates compared to healthy subject or hypertensive and diabetic chronic kidney disease patients.

CONCLUSIONSThis study reveals that inflammation is a central aspect in human NPH and delineates a specific set of inflammatory mediators that regulates immune cell recruitment in human NPH.

SIGNIFICANCE STATEMENTMutations in genes encoding primary cilia proteins are the leading cause of genetic kidney failure. In autosomal dominant polycystic kidney disease (ADPKD), deregulated cilia signaling leads to kidney infiltration by macrophages through the chemokine CCL2. Little is known about renal inflammation in nephronophthisis (NPH), the most frequent pediatric renal ciliopathy. Using NPH mice models, tissues and cells from NPH patients, we unveil renal inflammation as preeminent feature of NPH. Remarkably, the renal inflammatory evoked by ciliary gene mutations in NPH does not overlap with ADPKD: it is CCL2 independent, involves a prominent recruitment of neutrophils and T cells and a specific cytokine signature. This unforeseen findings strengthen the link between primary cilia and renal inflammation.


title: The renal inflammatory network of nephronophthisis


title: Oncofly: A CURE for Cancer

abstract:
Course-based Undergraduate Research Experiences (CUREs) are emerging as a means to engage large numbers of undergraduate students in meaningful inquiry-based research activities. We describe here a simple laboratory exercise as part of an undergraduate genetics course that illustrates the contributions of oncogenes and tumor suppressors to the formation of neoplasms in an invertebrate model system. In addition, students were challenged to investigate whether flies reared on a diet containing a variety of additives display a higher number of invasive tumors in the larval abdomen.

The goal of the exercise was to (i) familiarize students with the multigenic origin of the cancer phenotype, to (ii) introduce some of the fundamental molecular cancer hallmarks, and to (iii) highlight the significance of invertebrate model systems in biomedical research. Furthermore, (iv) students learn to execute a molecular test for transgenic produce and (v) apply statistical tools to test a simple hypothesis.

We evaluated student learning and changes in opinions and attitudes relating to environmental versus genetic causes of cancer and several common misconceptions using a questionnaire before and after completing the exercise.

Overall, significant improvements in the rate of factually correct responses and reductions in uncertainty were demonstrated. Although resistance to change was apparent in regard to identifying some risk factors, there was clear learning and understanding of the core concepts of carcinogenesis and the utility of basic research with model organisms.

category: scientific communication and education


title: Distinct regulation of dopamine D3 receptor in the basolateral amygdala and dentate gyrus during the reinstatement of cocaine CPP induced by drug priming and social stress

abstract: Relapse in cocaine seeking and intake is one of the main challenges when treating its addiction. Among the triggering factors for recurrence of cocaine use are the re-exposure to the drug and stressful events. Cocaine relapse engages the activity of memory-related nuclei, such as the basolateral amygdala (BLA) and the hippocampal dentate gyrus (DG), which are responsible for emotional and episodic memories. Besides, D3 receptor (D3R) antagonists have recently arisen as a potential treatment for preventing drug relapse. Thus, we have assessed the impact of D3R blockade in the expression of some dopaminergic markers and in the activity of the mTOR pathway, that is modulated by D3R, in the BLA and DG during the reinstatement of cocaine-induced CPP evoked by drug priming and social stress. Reinstatement of cocaine-CPP paralleled with a trend to increase of D3R and dopamine transporter (DAT) levels in the BLA. Social stress-but not drug-induced reactivation of cocaine memories was prevented by systemic administration of SB-277011-A (a selective D3R antagonist), that was able, however, to impede D3R and DAT up-regulation in the BLA during CPP reinstatement evoked by both stress and cocaine. Concomitantly with cocaine-CPP reactivation occurred a diminution of mTOR phosphorylation (activation) in the BLA and DG that was inhibited by D3R blockade in both nuclei before the social stress episode, and only in the BLA when CPP reinstatement was provoked by a cocaine prime. Our data, while support a main role for D3R signalling in the BLA in the reactivation of cocaine memories evoked by social stress, indicates that different neural circuits and signalling mechanisms might mediate in the reinstatement of cocaine-seeking behaviours depending upon the triggering stimuli.


title: Silencing and stimulating the medial amygdala impairs ejaculation but not sexual incentive motivation in male rats

abstract: The medial amygdala (MeA) is a sexually dimorphic brain region that integrates sensory information and hormonal signaling, and is involved in the regulation of social behaviors. Lesion studies have shown a role for the MeA in copulation, most prominently in the promotion of ejaculation. The role of the MeA in sexual motivation, but also in temporal patterning of copulation, has not been extensively studied in rats. Here, we investigated the effect of chemogenetic inhibition and stimulation of the MeA on sexual incentive motivation and copulation in sexually experienced male rats. AAV5-CaMKIIa viral vectors coding for Gi, Gq, or no DREADDs (sham) were bilaterally infused into the MeA. Rats were assessed in the sexual incentive motivation test and copulation test upon systemic CNO or vehicle administration. We report that MeA stimulation and inhibition did not affect sexual incentive motivation. Moreover, both stimulation and inhibition of the MeA decreased the number of ejaculations in a 30 minute copulation test and increased ejaculation latency and the number of mounts and intromissions preceding ejaculation, while leaving the temporal pattern of copulation intact. These results indicate that the MeA may be involved in the processing of sensory feedback required to reach ejaculation threshold. The convergence of the behavioral effects of stimulating as well as inhibiting the MeA may reflect opposing behavioral control of specific neuronal populations within the MeA.


title: Dissociating the effect of reward uncertainty and timing uncertainty on neural indices of reward prediction errors: A reward positivity (RewP) event-related potential (ERP) study

abstract: Accurate reward predictions include forecasting both what a reward will be and when a reward will occur. We tested how variations in the certainty of reward outcome and certainty in timing of feedback presentation modulate neural indices of reward prediction errors using the reward positivity (RewP) component of the scalp-recorded brain event-related potential (ERP). In a within-subjects design, seventy-three healthy individuals completed two versions of a cued doors task; one cued the probability of a reward outcome while the other cued the probability of a delay before feedback. Replicating previous results, RewP amplitude was larger for uncertain feedback compared to certain feedback. Additionally, RewP amplitude was differentially associated with uncertainty of presence/absence of reward, but not uncertainty of feedback timing. Findings suggest a dissociation in that RewP amplitude is modulated by reward prediction certainty but is less affected by certainty surrounding timing of feedback.


title: Disrupted PDZ-domain binding motif of the dopamine transporter uniquely alters nanoscale distribution, dopamine homeostasis and reward motivation

abstract: The dopamine transporter (DAT) is part of a presynaptic multi-protein network involving interactions with scaffold proteins via its C-terminal PDZ-domain binding sequence. In a mouse model expressing DAT with mutated PDZ binding sequence (DAT-AAA), we previously demonstrated the importance of this binding sequence for striatal expression of DAT. Here we show by application of direct Stochastic Reconstruction Microscopy (dSTORM) not only that the striatal level of transporter is reduced in DAT-AAA mice, but also that the nanoscale distribution of the transporter is altered with a higher propensity of DAT-AAA to localize to irregular nanodomains in dopaminergic terminals. In parallel, we observe mesostriatal dopamine (DA) adaptations and changes in DA-related behaviors different from those seen in other genetic DAT mouse models. DA levels in striatum are reduced to [~]45% of wild type (WT), accompanied by elevated DA turnover. Nonetheless, Fast-Scan Cyclic Voltammetry recordings on striatal slices reveal a larger amplitude and prolonged clearance rate of evoked DA release in DAT-AAA mice compared to WT mice. Autoradiography and radioligand binding show reduced DA D2 receptor levels while immunohistochemistry and autoradiography show unchanged DA D1 receptor levels. In behavioral experiments, we observe enhanced self-administration of liquid food under both a fixed-ratio (FR1) and progressive-ratio (PR) schedule of reinforcement, but a reduction compared to WT when using cocaine as reinforcer. Summarized, our data demonstrate how disruption of PDZ-domain interactions causes changes in DAT expression and its nanoscopic distribution that in turn alter DA clearance dynamics.


title: Dysregulation of the basal ganglia indirect pathway prior to cell loss in the Q175 mouse model of Huntington's disease

abstract: The psychomotor symptoms of Huntingtons disease (HD) are linked to degeneration of the basal ganglia indirect pathway. To determine how this pathway is perturbed prior to cell loss, optogenetic- and reporter-guided electrophysiological interrogation approaches were applied to early symptomatic 6-month-old Q175 HD mice. Although cortical activity was unaffected, indirect pathway striatal projection neurons were hypoactive in vivo, consistent with reduced cortical input strength and dendritic excitability. Downstream parvalbumin-expressing prototypic external globus pallidus (GPe) neurons were hyperactive in vivo and exhibited elevated autonomous firing ex vivo. Optogenetic inhibition of prototypic GPe neurons ameliorated the abnormal hypoactivity of postsynaptic subthalamic nucleus (STN) and putative arkypallidal neurons in vivo. In contrast to STN neurons, autonomous arkypallidal activity was unimpaired ex vivo. Together with previous studies, these findings demonstrate that basal ganglia indirect pathway neurons are highly dysregulated in Q175 mice through changes in presynaptic activity and/or intrinsic properties 6-12 months before cell loss.


title: Priming anodal transcranial direct current stimulation attenuates short interval intracortical inhibition and increases time to task failure of a constant workload cycling exercise

abstract: Transcranial direct current stimulation (tDCS), a non-invasive neuromodulatory technique has been shown to increase the excitability of targeted brain area and influence endurance exercise performance. However, tDCS-mediated interaction between corticospinal excitability, GABAA mediated intracortical inhibition and endurance exercise performance remains understudied. In two separate sessions, twelve subjects performed fatigue cycling exercise (80% peak power output) sustained to task failure in a double-blinded design, following either ten minutes of anodal tDCS (atDCS) or sham. Corticospinal excitability and short interval intracortical inhibition (SICI) were measured at baseline, post neuromodulation and post-exercise using paired-pulse transcranial magnetic stimulation (TMS) in a resting hand muscle. There was a greater a decrease in SICI (P < 0.05) post fatigue cycling with atDCS priming compared to sham. Time to task failure (TTF) was significantly increased following atDCS compared to sham (P < 0.05). These findings suggest that atDCS applied over the motor cortex can augment cycling exercise performance; and this outcome may be mediated via a decrease in the excitability of GABAA inhibitory interneurons.


title: Topological impact of negative links on the stability of resting-state brain network

abstract: Stability is a physical attribute that stands opposite the change. However, it is still unclear how the arrangement of links called topology affects network stability. In this study, we tackled this issue in the resting-state brain network using structural balance. Structural balance theory employs the quality of triadic associations between signed links to determine the network stability. In this study, we showed that negative links of the resting-state network make hubs to reduce balance-energy and push the network into a more stable state compared to null-networks with trivial topologies. In this regard, we created a global measure entitled  tendency to make hub to assess the hubness of the network. Besides, we revealed nodal degrees of negative links have an exponential distribution that confirms the existence of negative hubs. Our findings indicate that the arrangement of negative links plays an important role in the balance (stability) of the resting-state brain network.


title: A single- and paired-pulse TMS-EEG investigation of the N100 and long interval cortical inhibition in autism spectrum disorder

abstract:
BackgroundThere is evidence to suggest a disruption of gamma-aminobutyric acid (GABA) in autism spectrum disorder (ASD), but findings are mixed. Concurrent electroencephalography and transcranial magnetic stimulation (TMS-EEG) provides a novel method by which to probe GABA-mediated cortical inhibition.

MethodsWith a particular focus on GABAB-ergic mechanisms, we investigated the N100 peak of the TMS evoked potential (TEP), as well as long interval cortical inhibition (LICIEEG) in adults with ASD (n = 23; 12 female) without intellectual disability, and a neurotypical comparison group (n =22; 12 female) matched for age, sex, and IQ. Seventy-five single-(spTMS) and 75 paired-(ppTMS; 100 ms inter-stimulus-interval) pulses were applied to the right primary motor cortex (M1), right temporoparietal junction (TPJ), and right dorsolateral prefrontal cortex (DLPFC) while EEG was recorded from 20 scalp electrodes. Additionally, electromyography (EMG) was used to investigate corticospinal inhibition following ppTMS to M1 (LICIEMG).

ResultsThere were no group differences in the N100 amplitude or latency following spTMS. LICI outcomes following ppTMS, as measured by either EEG or EMG, also did not differ between groups. These findings were further supported by Bayesian analyses, which provided weak-moderate support for the null hypothesis.

LimitationsData presented here reflect adults without intellectual disability, and the generalisability of these results is therefore limited.

ConclusionsThe findings of this study argue against GABAB-ergic impairment in adults with ASD without intellectual disability, at least at the cortical regions examined. Further research investigating these mechanisms in ASD at various ages, with varying degrees of symptomatology, and at different brain sites is an important factor in understating the role of GABA in the neuropathophysiology of ASD.


title: High-fidelity fast volumetric brain MRI using a hybrid denoising generative adversarial network (HDnGAN)

abstract:
PurposeReducing scan times is important for wider adoption of high-resolution volumetric MRI in research and clinical practice. Emerging fast imaging and deep learning techniques provide promising strategies to accelerate volumetric MRI without compromising image quality. In this study, we aim to leverage an advanced fast imaging technique, wave-controlled aliasing in parallel imaging (Wave-CAIPI), and a novel denoising generative adversarial network (GAN) to achieve accelerated high-fidelity, high-signal-to-noise-ratio (SNR) volumetric MRI.

Methods3D T2-weighted fluid-attenuated inversion recovery (FLAIR) image data were acquired on 33 multiple sclerosis (MS) patients using a prototype Wave-CAIPI sequence (acceleration factor R=3x2, 2.75 minutes) and a standard T2-SPACE FLAIR sequence (R=2, 7.25 minutes). A hybrid denoising GAN entitled "HDnGAN" composed of a 3D generator (i.e., a modified 3D U-Net entitled MU-Net) and a 2D discriminator was proposed to denoise Wave-CAIPI images with the standard FLAIR images as the target. HDnGAN was trained and validated on data from 25 MS patients by minimizing a combined content loss (i.e., mean squared error (MSE)) and adversarial loss with adjustable weight{lambda} , and evaluated on data from 8 patients unseen during training. The quality of HDnGAN-denoised images was compared to those from other denoising methods including AONLM, BM4D, MU-Net, and 3D GAN in terms of their similarity to standard FLAIR images, quantified using MSE and VGG perceptual loss. The images from different methods were assessed by two neuroradiologists using a five-point score regarding sharpness, SNR, lesion conspicuity, and overall quality. Finally, the performance of these denoising methods was compared at higher noise levels using simulated data with added Rician noise.

ResultsHDnGAN effectively denoised noisy Wave-CAIPI images with sharpness and rich textural details, which could be adjusted by controlling{lambda} . Quantitatively, HDnGAN ({lambda}=10-3) achieved low MSE (7.43 x10-4{+/-}0.94x10-4) and the lowest VGG perceptual loss (1.09x10-2{+/-}0.18x10-2). The reader study showed that HDnGAN ({lambda}=10-3) significantly improved the SNR of Wave-CAIPI images (4.19{+/-}0.39 vs. 2.94{+/-}0.24, P<0.001), outperformed AONLM (4.25{+/-}0.56 vs. 3.75{+/-}0.90, P=0.015), BM4D (3.31{+/-}0.46, P<0.001), MU-Net (3.13{+/-}0.99, P<0.001) and 3D GAN ({lambda}=10-3) (3.31{+/-}0.46, P<0.001) regarding image sharpness, and outperformed MU-Net (4.21{+/-}0.67 vs. 3.29{+/-}1.28, P<0.001) and 3D GAN ({lambda}=10-3) (3.5{+/-}0.82, P=0.001) regarding lesion conspicuity. The overall quality score of HDnGAN ({lambda}=10-3) (4.25{+/-}0.43) was significantly higher than those from Wave-CAIPI (3.69{+/-}0.46, P=0.003), BM4D (3.50{+/-}0.71, P=0.001), MU-Net (3.25{+/-}0.75, P<0.001), and 3D GAN ({lambda}=10-3) (3.50{+/-}0.50, P<0.001), with no significant difference compared to standard FLAIR images (4.38{+/-}0.48, P=0.333). The advantages of HDnGAN over other methods were more obvious at higher noise levels.

ConclusionHDnGAN provides robust and feasible denoising while preserving rich textural detail in empirical volumetric MRI data and is superior on both quantitative and qualitative evaluation compared to the original Wave-CAIPI images and images denoised using standard methods. HDnGAN concurrently benefits from the improved image synthesis performance of the 3D convolution and the increased number of samples for training the 2D discriminator from a limited number of subjects. Our study supports the use of HDnGAN in combination with modern fast imaging techniques such as Wave-CAIPI to achieve high-fidelity fast volumetric MRI.


title: High-fidelity fast volumetric brain MRI using synergistic wave-controlled aliasing in parallel imaging and a hybrid denoising generative adversarial network


title: Elementary Integrate-and-Fire Process Underlies Pulse Amplitudes in Electrodermal Activity

abstract:
Electrodermal activity (EDA) is a direct read-out of sweat-induced changes in the skins electrical conductance. Sympathetically-mediated pulsatile changes in skin sweat measured as EDA resemble an integrate-and-fire process, which yields an inverse Gaussian model as the inter-pulse interval distribution. We have previously showed that the inter-pulse intervals in EDA follow an inverse Gaussian distribution. However, the statistical structure of EDA pulse amplitudes has not yet been characterized based on the physiology. Expanding upon the integrate-and-fire nature of sweat glands, we hypothesized that the amplitude of an EDA pulse is proportional to the excess volume of sweat produced compared to what is required to just reach the surface of the skin. We modeled this as the difference of two inverse Gaussian models for each pulse, one which represents the time required to produce just enough sweat to rise to the surface of the skin and one which represents the time requires to produce the actual volume of sweat. We proposed and tested a series of four simplifications of our hypothesis, ranging from a single difference of inverse Gaussians to a single simple inverse Gaussian. We also tested four additional models for comparison, including the lognormal and gamma distributions. All models were tested on EDA data from two subject cohorts, 11 healthy volunteers during 1 hour of quiet wakefulness and a different set of 11 healthy volunteers during approximately 3 hours of controlled propofol sedation. All four models represent simplifications of our hypothesis outperformed other models across all 22 subjects, as measured by Akaikes Information Criterion (AIC), as well as mean and maximum distance from the diagonal on a quantile-quantile plot. Our broader model set of four simplifications offered a useful framework to enhance further statistical descriptions of EDA pulse amplitudes. Some of the simplifications prioritize fit near the mode of the distribution, while others prioritize fit near the tail. With this new insight, we can summarize the physiologically-relevant amplitude information in EDA with at most four parameters. Our findings establish that physiologically based probability models provide parsimonious and accurate description of temporal and amplitude characteristics in EDA.

AUTHOR SUMMARYElectrodermal activity (EDA) is an indirect read-out of the bodys sympathetic nervous system, or fight-or-flight response, measured as sweat-induced changes in the electrical conductance properties of the skin. Interest is growing in using EDA to track physiological conditions such as stress levels, sleep quality, and emotional states. Our previous worked showed that the times in between EDA pulses obeyed a specific statistical distribution, the inverse Gaussian, that arises from the physiology of EDA production. In this work, we build on that insight to analyze the amplitudes of EDA pulses. In an analysis of EDA data recorded in 11 healthy volunteers during quiet wakefulness and 11 different healthy volunteers during controlled propofol sedation, we establish that the amplitudes of EDA pulses also have specific statistical structure, as the differences of inverse Gaussians, that arises from the physiology of sweat production. We capture that structure using a series of progressively simpler models that each prioritize different parts of the pulse amplitude distribution. Our findings show a physiologically-based statistical model provides a parsimonious and accurate description EDA. This enables increased reliability and robustness in analyzing EDA data collected under any circumstance.