title: A B cell actomyosin arc network couples integrin co-stimulation to mechanical force-dependent immune synapse formation

abstract: B-cell activation and immune synapse (IS) formation with membrane-bound antigens are actin-dependent processes that scale positively with the strength of antigen-induced signals. Importantly, ligating the B-cell integrin, LFA-1, with ICAM-1 promotes IS formation when antigen is limiting. Whether the actin cytoskeleton plays a specific role in integrin-dependent IS formation is unknown. Here we show using super-resolution imaging of mouse primary B cells that LFA-1: ICAM-1 interactions promote the formation of an actomyosin network that dominates the B-cell IS. This network is created by the formin mDia1, organized into concentric, contractile arcs by myosin 2A, and flows inward at the same rate as B-cell receptor (BCR): antigen clusters. Consistently, individual BCR microclusters are swept inward by individual actomyosin arcs. Under conditions where integrin is required for synapse formation, inhibiting myosin impairs synapse formation, as evidenced by reduced antigen centralization, diminished BCR signaling, and defective signaling protein distribution at the synapse. Together, these results argue that a contractile actomyosin arc network plays a key role in the mechanism by which LFA-1 co-stimulation promotes B-cell activation and IS formation.

category: immunology


title: Tissue-wide metabolomics reveals wide impact of gut microbiota on mice metabolite composition

abstract: The essential role of gut microbiota in health and disease is well-recognized, but the biochemical details underling beneficial impact remain largely undefined. Dysbiosis of gut bacteria results in the alteration of certain microbial and host metabolites, and identifying these markers could enhance the early detection of certain diseases. We report LC-MS based non-targeted metabolic profiling to demonstrate a large effect of gut microbiota on mammalian tissue metabolites. It was hypothesized that gut microbiota influences the overall biochemistry of the host metabolome and this effect is tissue-specific. Thirteen different tissues from germ-free and conventional mice were selected and their metabolic differences were analyzed. Our study demonstrated a large effect of the microbiome on mammalian biochemistry at different tissue levels and resulted in significant modulation of metabolites from multiple metabolic pathway (p [≤] 0.05). A vast metabolic response of host to metabolites generated by the microbiota was observed, Hundreds of molecular features were detected exclusively in one mouse group, with the majority of these being unique to specific tissue, suggesting direct impact gut microbiota on host metabolism.

category: microbiology


title: Diversification by CofC and control by CofD govern biosynthesis and evolution of coenzyme F420 and its derivative 3PG-F420

abstract:
Coenzyme F420 is a microbial redox cofactor that is increasingly used for biocatalytic applications. Recently, diversified biosynthetic routes to F420 and the discovery of a derivative, 3PG-F420, were reported. 3PG-F420 is formed via activation of 3-phospho-D-glycerate (3-PG) by CofC, but the structural basis of substrate binding, its evolution, as well as the role of CofD in substrate selection remained elusive.

Here, we present a crystal structure of the 3-PG-activating CofC from Mycetohabitans sp. B3 and define amino acids governing substrate specificity. Site-directed mutagenesis enabled bidirectional switching of specificity and thereby revealed the short evolutionary trajectory to 3PG-F420 formation. Furthermore, CofC stabilized its product, thus confirming the structure of the unstable molecule, revealing its binding mode and suggesting a substrate channeling mechanism to CofD. The latter enzyme was shown to significantly contribute to the selection of related intermediates to control the specificity of the combined biosynthetic CofC/D step. Taken together, this work closes important knowledge gaps and opens up perspectives for the discovery, enhanced biotechnological production, and engineering of coenzyme F420 derivatives in the future.

ImportanceThe microbial cofactor F420 is crucial for processes like methanogenesis, antibiotics biosynthesis, drug resistance, and biocatalysis. Recently, a novel derivative of F420 (3PG-F420) was discovered, enabling the production and use of F420 in heterologous hosts.

By analyzing the crystal structure of a CofC homolog whose substrate choice leads to formation of 3PG-F420, we defined amino acid residues governing the special substrate selectivity. A diagnostic residue enabled reprogramming of the substrate specificity, thus mimicking the evolution of the novel cofactor derivative and successfully guiding the identification of further 3-PG-activating enzymes.

Furthermore, a labile reaction product of CofC was revealed that has not been directly detected so far and CofD was shown to provide as another layer of specificity of the combined CofC/D reaction, thus controlling the initial substrate choice of CofC. The latter finding resolves a current debate in the literature about the starting point of F420 biosynthesis in various organisms.


title: Escaping from multiple visual threats: Modulation of escape responses in Pacific staghorn sculpin (Leptocottus armatus).

abstract:
Fish perform rapid escape responses to avoid sudden predatory attacks. During escape responses, fish bend their bodies into a C-shape and quickly turn away from the predator and accelerate. The escape trajectory is determined by the initial turn (Stage 1) and a contralateral bend (Stage 2). Previous studies have used a single threat or model predator as a stimulus. In nature, however, multiple predators may attack from different directions simultaneously or in close succession. It is unknown whether fish are able to change the course of their escape response when startled by multiple stimuli at various time intervals. Pacific staghorn sculpin (Leptocottus armatus) were startled with a left and right visual stimulus in close succession. By varying the timing of the second stimulus, we were able to determine when and how a second stimulus could affect the escape response direction. Four treatments were used: a single visual stimulus (control); or two stimuli coming from opposite sides separated by a 0 ms (simultaneous treatment); a 33 ms; or a 83 ms time interval. The 33 ms and 83 ms time intervals were chosen to occur shortly before and after a predicted 60 ms visual escape latency (i.e. during Stage 1). The 0 ms and 33 ms treatments influenced both the escape trajectory and the Stage 1 turning angle, compared to a single stimulation, whereas the 83 ms treatment had no effect on the escape response. We conclude that Pacific staghorn sculpin can modulate their escape response only between stimulation and the onset of the response, but that escape responses are ballistic after the body motion has started.

SUMMARY STATEMENTUsing double stimulation from opposite sides at different time intervals to simulate coordinated predatory attacks, Pacific staghorn sculpin escape away from the first stimulus, but were unable to turn away from the second stimulus while the escape response was in progress.

category: animal behavior and cognition


title: MetaLogo: a generator and aligner for multiple sequence logos

abstract: Sequence logos are used to visually display conservations and variations in short sequences. They can indicate the fixed patterns or conserved motifs in a batch of DNA or protein sequences. However, most of the popular sequence logo generators are based on the assumption that all the input sequences are from the same homologous group, which will lead to an overlook of the heterogeneity among the sequences during the sequence logo making process. Heterogeneous groups of sequences may represent clades of different evolutionary origins, or genes families with different functions. Therefore, it is essential to divide the sequences into different phylogenetic or functional groups to reveal their specific sequence motifs and conservation patterns. To solve these problems, we developed MetaLogo, which can automatically cluster the input sequences after multiple sequence alignment and phylogenetic tree construction, and then output sequence logos for multiple groups and aligned them in one figure. User-defined grouping is also supported by MetaLogo to allow users to investigate functional motifs in a more delicate and dynamic perspective. MetaLogo can highlight both the homologous and nonhomologous sites among sequences. MetaLogo can also be used to annotate the evolutionary positions and gene functions of unknown sequences, together with their local sequence characteristics. We provide users a public MetaLogo web server (http://metalogo.omicsnet.org), a standalone Python package (https://github.com/labomics/MetaLogo), and also a built-in web server available for local deployment. Using MetaLogo, users can draw informative, customized and publishable sequence logos without any programming experience to present and investigate new knowledge on specific sequence sets.

category: bioinformatics


title: MetaLogo: a heterogeneity-aware sequence logo generator and aligner


title: MetaProFi: A protein-based Bloom filter for storing and querying sequence data for accurate identification of functionally relevant genetic variants

abstract: Technological advances of next-generation sequencing present new computational challenges to develop methods to store and query these data in time- and memory-efficient ways. We present MetaProFi (https://github.com/kalininalab/metaprofi), a Bloom filter-based tool that, in addition to supporting nucleotide sequences, can for the first time directly store and query amino acid sequences and translated nucleotide sequences, thus bringing sequence comparison to a more biologically relevant protein level. Owing to the properties of Bloom filters, it has a zero false-negative rate, allows for exact and inexact searches, and leverages disk storage and Zstandard compression to achieve high time and space efficiency. We demonstrate the utility of MetaProFi by indexing UniProtKB datasets at organism- and at sequence-level in addition to the indexing of Tara Oceans dataset and the 2585 human RNA-seq experiments, showing that MetaProFi consumes far less disk space than state-of-the-art-tools while also improving performance.


title: Cancer cell hyper-proliferation disrupts the topological invariance of epithelial monolayers

abstract: Although the polygonal shape of epithelial cells has drawn the attention of scientists for several centuries, only recently, it has been demonstrated that distributions of polygon types (DOPTs) are similar in proliferative epithelia of many different plant and animal species. In this study we show that hyper-proliferation of cancer cells disrupts this universality paradigm and results in random epithelial structures. Examining non-synchronized and synchronized HeLa cervix cells, we suppose that the cell size spread is the single parameter controlling the DOPT in these monolayers. We test this hypothesis by considering morphologically similar random polygonal packings. By analyzing the differences between tumoral and non-tumoral epithelial monolayers, we uncover that the latter have more ordered structures and argue that the relaxation of mechanical stresses associated with cell division induces more effective ordering in the epithelia with lower proliferation rates. The proposed theory also explains the specific highly ordered structures of some post-mitotic unconventional epithelia.

category: biophysics


title: Sleep spindles, ripples, and interictal epileptiform discharges in the human anterior and mediodorsal thalamus

abstract: Sleep spindles are major oscillatory components of Non-Rapid Eye Movement (NREM) sleep, reflecting hyperpolarization-rebound sequences of thalamocortical neurons, the inhibition of which is caused by the NREM-dependent activation of GABAergic neurons in the reticular thalamic nucleus. Reports suggest a link between sleep spindles and several forms of interictal epileptic discharges (IEDs) which are considered as expressions of pathological off-line neural plasticity in the central nervous system. Here we investigated the relationship between thalamic sleep spindles, IEDs and ripples in the anterior and mediodorsal nuclei (ANT and MD) of epilepsy patients. Whole-night LFP from the ANT and MD were co-registered with scalp EEG/polysomnography by using externalized leads in 15 epilepsy patients undergoing Deep Brain Stimulation protocol. Slow ([~]12 Hz) and fast ([~]14 Hz) sleep spindles were present in the human ANT and MD. Roughly, one third of thalamic sleep spindles were associated with IEDs or ripples. Both IED- and ripple-associated spindles were longer than pure spindles. IED-associated thalamic sleep spindles were characterized by broadband increase in thalamic and cortical activity, both below and above the spindle frequency range, whereas ripple-associated thalamic spindles exceeded pure spindles in terms of 80-200 Hz thalamic, but not cortical activity as indicated by time-frequency analysis. These result show that thalamic spindles coupled with IEDs are reflected at the scalp slow and beta-gamma oscillation as well. IED density during sleep spindles in the MD, but not in the ANT was identified as correlates of years spent with epilepsy, whereas no signs of pathological processes were correlated with measures of ripple and spindle association. Furthermore, the density of ripple-associated sleep spindles in the ANT showed a positive correlation with general intelligence. Our findings indicate the complex and multifaceted role of the human thalamus in sleep spindle-related physiological and pathological neural plasticity.

category: neuroscience


title: Aged mouse ovarian immune milieu shows a shift towards adaptive immunity and attenuated cell function

abstract: The immune system plays a major role in maintaining many physiological processes in the reproductive system. However, a complete characterization of the immune milieu in the ovary, and particularly how it is affected by maternal aging, is still lacking. In this work, we utilize single-cell RNA sequencing and flow cytometry to construct a complete description of the murine ovarian immune system and its changes along with pre-estropause aging. We show that the ovarian immune cells composition undergoes an extensive shift with age towards adaptive immunity. We analyze the effect of aging on gene expression and chemokine and cytokine networks and show an overall decreased expression of inflammatory mediators together with an increased senescent cells recognition. Our results reveal the changes in the aging ovarian immune system of the fertile female as it copes with the inflammatory stimulations during repeated cycles and the increasing need for clearance of accumulating atretic follicles.


title: Phase transition specified by a binary code patterns the vertebrate eye cup

abstract: The developing vertebrate eye cup is partitioned into the neural retina (NR), the retinal pigmented epithelium (RPE) and the ciliary margin (CM). By single cell analysis, we showed that a gradient of FGF signaling regulates demarcation and subdivision of the CM and controls its stem cell-like property of self-renewal, differentiation and survival. This regulation by FGF is balanced by an evolutionarily conserved Wnt signaling gradient induced by the lens ectoderm and the periocular mesenchyme, which specifies the CM and the distal RPE. These two morphogen gradients converge in the CM where FGF signaling promotes Wnt signaling by stabilizing {beta}-catenin in a GSK3{beta}-independent manner. We further showed that activation of Wnt signaling converts the NR to either the CM or the RPE depending on the level of FGF signaling. Conversely, activation of FGF transforms the RPE to the NR or CM dependent on Wnt activity. We demonstrated that the default fate of the eye cup is the NR, but synergistic FGF and Wnt signaling promotes CM formation both in vivo and in retinal organoid culture of human iPS cells. Our study reveals that the vertebrate eye develops through phase transition determined by a combinatorial code of FGF and Wnt signaling.

category: developmental biology


title: Temperature and nutrients drive complex eco-phenotypic dynamics in a microbial food web

abstract: Anthropogenic increases in temperature and nutrient loads will likely impact food web structure and stability. Though their independent effects have been well studied, their joint effects-- particularly on coupled ecological and phenotypic dynamics--remain poorly understood. Here we experimentally manipulated temperature and nutrient levels in microbial food webs and used time-series analysis to quantify the strength and causality of reciprocal effects between ecological and phenotypic dynamics across species. We found that i) temperature and nutrients have more complex effects on ecological dynamics at higher trophic levels, ii) temperature and nutrients interact antagonistically to shift the relative strength of top-down vs. bottom-up control, iii) phenotypic dynamics have stronger impacts on ecological dynamics than vice versa (especially at higher temperature), and iv) rapid phenotypic change mediates observed ecological responses to changes in temperature and nutrients. Our results expose how feedbacks between ecological and phenotypic dynamics mediate food web responses to environmental change.

category: ecology


title: Increases in multiple resources promote plant invasion

abstract: Invasion by alien plants is frequently attributed to increased resource availabilities. Still, our understanding is mainly based on effects of single resources despite the fact that plants rely on multiple resources. How multiple resources affect success of alien plants remains largely unexplored. Here, with two common garden experiments, one in China and one in Germany, we tested whether nutrient and light availabilities affected the competitive outcomes between alien and native plants. We found that under low resource availabilities or with addition of only one type of resource aliens were not more competitive than natives. However, with a joint increase of nutrients and light intensity, aliens outcompeted natives. Our finding indicates that addition of multiple resources could greatly reduce the number of limiting factors (i.e. niche dimensionality), and that this favors the dominance of alien species. It also indicates that habitats experiencing multiple global changes might be more vulnerable to plant invasion.


title: Next generation restoration metrics: Using soil eDNA bacterial community data to measure trajectories towards rehabilitation targets

abstract: In post-mining rehabilitation, successful mine closure planning requires specific, measurable, achievable, relevant and time-bound (SMART) completion criteria, such as returning ecological communities to match a target level of similarity to reference sites. Soil microbiota are fundamentally linked to the restoration of degraded ecosystems, helping to underpin ecological functions and plant communities. High-throughput sequencing of soil eDNA to characterise these communities offers promise to help monitor and predict ecological progress towards reference states. Here we demonstrate a novel methodology for monitoring and evaluating ecological restoration using three long-term (> 25 year) case study post-mining rehabilitation soil eDNA-based bacterial community datasets. Specifically, we developed rehabilitation trajectory assessments based on similarity to reference data from restoration chronosequence datasets. Recognising that many alternative options for microbiota data processing have potential to influence these assessments, we comprehensively examined the influence of standard versus compositional data analyses, different ecological distance measures, sequence grouping approaches, eliminating rare taxa, and the potential for excessive spatial autocorrelation to impact on results. Our approach reduces the complexity of information that often overwhelms ecologically-relevant patterns in microbiota studies, and enables prediction of recovery time, with explicit inclusion of uncertainty in assessments. We offer a step change in the development of quantitative microbiota-based SMART metrics for measuring rehabilitation success. Our approach may also have wider applications where restorative processes facilitate the shift of microbiota towards reference states.


title: Deep Learning Classification of Lake Zooplankton

abstract: Plankton are effective indicators of environmental change and ecosystem health in freshwater habitats, but collection of plankton data using manual microscopic methods is extremely labor-intensive and expensive. Automated plankton imaging offers a promising way forward to monitor plankton communities with high frequency and accuracy in real-time. Yet, manual annotation of millions of images proposes a serious challenge to taxonomists. Deep learning classifiers have been successfully applied in various fields and provided encouraging results when used to categorize marine plankton images. Here, we present a set of deep learning models developed for the identification of lake plankton, and study several strategies to obtain optimal performances, which lead to operational prescriptions for users. To this aim, we annotated into 35 classes over 17900 images of zooplankton and large phytoplankton colonies, detected in Lake Greifensee (Switzerland) with the Dual Scripps Plankton Camera. Our best models were based on transfer learning and ensembling, which classified plankton images with 98% accuracy and 93% F1 score. When tested on freely available plankton datasets produced by other automated imaging tools (ZooScan, FlowCytobot and ISIIS), our models performed better than previously used models. Our annotated data, code and classification models are freely available online.


title: Analysis of wild plant pathogen populations reveals a signal of adaptation in genes evolving for survival in agriculture in the beet rust pathogen (Uromyces beticola)

abstract:
Improvements in crop resistance to pathogens can reduce yield losses and address global malnourishment today. Gene-for-gene -type interactions can identify new sources of resistance but genetic resistance is often short lived. Ultimately an understanding of how pathogens rapidly adapt will allow us to both increase resistance gene durability and more effectively target chemical treatments. Until recently all agricultural pathogens were living on wild hosts. To understand crop pathogen evolution, we compared genetic diversity in agricultural and wild populations. Wild reservoirs may be the source of emergent pathogen lineages, but here we outline a strategy for comparison of wild and agricultural pathogen populations to highlight genes adapting to agriculture. To address this, we have selected and developed the beet rust system (Beta vulgaris, Uromyces beticola, respectively) as our wild-agricultural model. Our hypothesis is that pathogen adaptation to agricultural crops will be evident as divergence in comparisons of wild and agricultural plant pathogen populations. We sampled isolates in both the wild and agriculture, sequenced and assembled and annotated a large fungal genome and analysed genetic diversity in 42 re-sequenced rust isolates. We found population differentiation between isolates in the wild compared to a predominantly agricultural group. Fungal effector genes are co-evolving with host resistance and are important for successful colonisation. We predicted (and found) that these exhibit a greater signal of diversification and adaptation and more importantly displayed increased wild agricultural divergence. Finding a signal of adaptation in these genes highlights this as an important strategy to identify genes which are key to pathogen success, that analysis of agricultural isolates alone cannot.

Author SummaryAs quickly as we develop new strategies for crop defence, pathogens evolve to circumvent them. Novel crop pathogen strains emerge periodically and sweep through the agricultural system. However, because of the (often) clonal nature of these crop pathogens it is difficult to identify the trait that is key to their success. In other words, if there is a trait that is key for success in agriculture, all agricultural isolates will have it (or die without it). What we need is a case and control system where we identify genes important to pathogen success in agricultural by comparing them to pathogens that live in the wild. Here we exemplify this strategy by focussing on genes already known to specifically adapt for the successful colonisation of the host, the fungal effector genes. We find that these genes appear to be evolving quickly and that they are more different between the wild and agriculture than other non-effector genes. These differences between wild and agricultural pathogens suggest we are observing adaptation to agriculture. We do this work in the sugar beet rust system because of its tractability to sample but this understanding about how to identify genetic variation that is key to pathogen success in agriculture is applicable to crop systems where pathogen reservoirs exist as well as other pathogen reservoir systems (e.g. zoonoses).

category: evolutionary biology


title: Uncertainty avoidance versus conditioned reinforcement: exploring paradoxical choice in rats

abstract: Paying a cost to reduce uncertainty can be adaptive, because better informed decision-makers can align their preferences to opportunities. However, birds and mammals display an appetite for information that they cannot use to functionally alter behaviour or its outcomes. We explore two putative motivational mechanisms for this paradoxical behaviour. The  information hypothesis, proposes that reducing uncertainty is reinforcing per se, consistent with the concept of curiosity: a motivation to know, in the absence of instrumental benefits. In contrast, the  conditioned reinforcement hypothesis sees information-seeking as a consequence of asymmetries in secondarily acquired reinforcement: responding increments caused by post-choice stimuli announcing positive outcomes (S+) exceed decrements caused by stimuli signalling absence of reward (S-). We contrast these hypotheses experimentally. Rats chose between two equally profitable options delivering food probabilistically after a fixed delay. In the informative option (Info), the outcome (food/no food) was signalled immediately after choice, whereas in the non-informative option (NoInfo) outcomes were uncertain until the delay lapsed. Subjects preferred Info when (1) outcomes were signalled by salient auditory cues, (2) only the absence of reward was signalled, and (3) only reward was signalled, though acquisition was slower when rewards were not explicitly signalled. Our results show that a salient good news signal is not required as a conditioned reinforcer to generate paradoxical preferences. Terminal preferences support the information hypothesis but the slower acquisition of Info preference when S+ is not present is consistent with the conditioning account. We conclude that both uncertainty reduction and conditioned reinforcement influence choice.


title: "Devil's stairs", Poisson's Statistics, and Patient Sorting via Variabilities for Oxygenation: All from Arterial Blood Gas Data

abstract: This report deals with arterial oxygen saturation (SaO2) for healthy adults. A comparably small data set (20 persons) holds 3-minute records of SaO2. The sample rate was 200 Hz. The charts have the looks of a "devils stairs." A few (from 1 to 10) detectable oxygenation levels form the stairs treads, more or less long. "The risers" have two types (up and down), and all have virtually the same height, about 1 %. The inter-level shifts ( 0 to 42 switches per record) turned out a rare event at the actual sample rate. The number of switchings meets the Poisson distribution. There were found three visibly varied intensities for the switch-overs within the data set. Histograms also show the co-existing of no fewer than three subsets into the data set. The subsets differ by the intensity of switch-overs, amounts of possible levels, relative frequencies of most probable levels (modes), etcetera. In short, those all are diverse variability quantifiers. The higher variability subset has about 25 %, the lower one - 45%.


title: Structurally distinct polymorphs of Tau aggregates revealed by nanoscale infrared spectroscopy

abstract: Aggregation of the tau protein plays a central role in several neurodegenerative diseases collectively known as tauopathies, including Alzheimers and Parkinsons disease. Tau misfolds into fibrillar beta sheet structures that constitute the paired helical filaments found in Neurofibrillary tangles. It is known that there can be significant structural heterogeneities in tau aggregates associated with different diseases. However, while structures of mature fibrils have been studied, the structural distributions in early stage tau aggregates is not well understood. In the present study, we use AFM-IR to investigate nanoscale spectra of individual tau fibrils at different stages of aggregation and demonstrate the presence of multiple fibrillar polymorphs that exhibit different secondary structures. We further show that mature fibrils contain significant amounts of antiparallel beta sheets. Our results are the very first application of nanoscale infrared spectroscopy to tau aggregates and underscore the promise of spatially resolved infrared spectroscopy for investigating protein aggregation.


title: Safety Assessment of Broadband Laser Exposure in μOCT

abstract: Micro-optical coherence tomography ({micro}OCT) improves the spatial resolution of in vivo OCT imaging by utilizing sophisticated focusing schemes and broadband illumination. This study explores the safety of coronary and trachea tissue exposure to {micro}OCT illumination. (C) 2021 The Authors


title: Bending-torsional elasticity and energetics of the plus-end microtubule tip

abstract: Microtubules (MTs), mesoscopic cellular filaments, grow primarily by the addition of GTP-bound tubulin dimers at their dynamic flaring plus-end tips. They operate as chemomechanical energy transducers with stochastic transitions to an astounding shortening motion upon hydrolyzing GTP to GDP. Time-resolved dynamics of the MT tip - a key determinant of this behavior - as a function of nucleotide state, internal lattice strain, and stabilizing lateral interactions have not been fully understood. Here, we use atomistic simulations to study the spontaneous relaxation of complete GTP-MT and GDP-MT tip models from unfavorable straight to relaxed splayed conformations and to comprehensively characterize the elasticity of MT tips. Our simulations reveal the dominance of viscoelastic dynamics of MT protofilaments during the relaxation process, driven by the stored bending-torsional strain and counterbalanced by the inter-protofilament interactions. We show that the post-hydrolysis MT tip is exposed to higher activation energy barriers for straight lattice formation, which translates into its inability to elongate. Our study provides an  information ratchet mechanism for the elastic energy conversion and release by MT tips and offers new insights into the mechanoenzymatics of MTs.


title: Rumen disappearance of tannins from tropical tannin-rich plants: interplay between degradability, methane production and adherent rumen microbiota

abstract: AO_SCPLOWBSTRACTC_SCPLOWCondensed tannins in plants are found free and attached to protein and fibre but it is not known whether these fractions influence rumen degradation and microbial colonization. This study explored the rumen degradation of tropical tannins-rich plants and the relationship between condensed tannins fractions disappearance and microbial communities colonising plant particles. Leaves from Calliandra calothyrsus, Gliricidia sepium, and Leucaena leucocephala, pods from Acacia nilotica and the leaves of two agricultural by-products: Manihot esculenta and Musa spp. were incubated in situ in the rumen of dairy cows. An in vitro approach was also used to assess the effects of these plants on rumen fermentation parameters. All plants contained more than 100 g/kg of condensed tannins with a large proportion (32 to 61%) bound to proteins. Calliandra calothyrsus had the highest concentration of condensed tannins at 361 g/kg, whereas Acacia nilotica was particularly rich in hydrolysable tannins (350 g/kg). Hydrolysable and free condensed tannins from all plants completely disappeared after 24 h incubation in the rumen. Disappearance of protein-bound condensed tannins was variable with values ranging from 93% for Gliricidia sepium to 21% for Acacia nilotica. In contrast, fibre-bound condensed tannins disappearance averaged ~82% and did not vary between plants. Disappearance of bound fractions of condensed tannins was not associated with degradability of plant fractions. The presence of tannins interfered with the microbial colonisation of plants. Each plant had distinct bacterial and archaeal communities after 3 and 12 h of incubation in the rumen and distinct protozoal communities at 3 h. Adherent communities in tannin-rich plants had a lower relative abundance of fibrolytic microbes, notably Fibrobacter spp. Whereas, archaea diversity was reduced in high tannin-containing Calliandra calothyrsus and Acacia nilotica at 12 h of incubation. Concurrently, in vitro methane production was lower for Calliandra calothyrsus, Acacia nilotica and Leucaena leucocephala although for the latter total volatile fatty acids production was not affected and was similar to control. Here we show that the total amount of hydrolysable and condensed tannins contained in a plant govern the interaction with rumen microbes affecting degradability and fermentation. The effect of protein- and fibre-bound condensed tannins on degradability is less important.

category: zoology


title: Microbial colonization of tannin-rich tropical plants: interplay between degradability, methane production and tannin disappearance in the rumen


title: Carbon Fiber Electrodes for Intracellular Recording and Stimulation

abstract: To understand neural circuit dynamics, it is critical to manipulate and record from many neurons, ideally at the single neuron level. Traditional recording methods, such as glass microelectrodes, can only control a small number of neurons. More recently, devices with high electrode density have been developed, but few of them can be used for intracellular recording or stimulation in intact nervous systems, rather than on neuronal cultures. Carbon fiber electrodes (CFEs) are 8 micron-diameter electrodes that can be organized into arrays with pitches as low as 80 {micro}m. They have been shown to have good signal-to-noise ratios (SNRs) and are capable of stable extracellular recording during both acute and chronic implantation in vivo in neural tissue such as rat motor cortex. Given the small fiber size, it is possible that they could be used in arrays for intracellular stimulation. We tested this using the large identified and electrically compact neurons of the marine mollusk Aplysia californica. The cell bodies of neurons in Aplysia range in size from 30 to over 250 {micro}m. We compared the efficacy of CFEs to glass microelectrodes by impaling the same neurons cell body with both electrodes and connecting them to a DC coupled amplifier. We observed that intracellular waveforms were essentially identical, but the amplitude and SNR in the CFE were lower than in the glass microelectrode. CFE arrays could record from 3 to 8 neurons simultaneously for many hours, and many of these recordings were intracellular as shown by recording from the same neuron using a glass microelectrode. Stimulating through CFEs coated with platinum-iridium had stable impedances over many hours. CFEs not within neurons could record local extracellular activity. Despite the lower SNR, the CFEs could record synaptic potentials. Thus, the stability for multi-channel recording and the ability to stimulate and record intracellularly make CFEs a powerful new technology for studying neural circuit dynamics.


title: Subtle alterations in neonatal neurodevelopment following early or late exposure to prenatal maternal immune activation

abstract: Prenatal exposure to maternal immune activation (MIA) is a risk factor for a variety of neurodevelopmental and psychiatric disorders. The timing of MIA-exposure has been shown to affect adolescent and adult offspring neurodevelopment, however, less is known about these effects in the neonatal period. To better understand the impact of MIA-exposure on neonatal brain development, we first assess neonate communicative abilities with the ultrasonic vocalization task, followed by high-resolution ex vivo magnetic resonance imaging (MRI) on the neonatal (postnatal day 8) brain. Early exposed offspring displayed decreased communicative ability, while brain anatomy appeared largely unaffected, apart from some subtle alterations. By integrating MRI and behavioural assays to investigate the effects of MIA-expsoure on neonatal neurodevelopment we show that offspring neuroanatomy and behaviour are only subtly affected by both early and late exposure. This suggests that the deficits often observed in later stages of life may be dormant, not yet developed in the neonatal period, or not as easily detectable using a cross-sectional approach.


title: Gut bacteria regulate the pathogenesis of Huntington's disease in Drosophila

abstract: Changes in the composition of gut microbiota are implicated in the pathogenesis of several neurodegenerative disorders. Here, we investigated whether gut bacteria affect the progression of Huntingtons disease (HD) in transgenic Drosophila melanogaster (fruit fly) models expressing human full-length or N-terminal fragments of mutant huntingtin (HTT) protein, here referred to as HD flies. We find that elimination of commensal gut bacteria by antibiotics reduces the aggregation of amyloidogenic N-terminal fragments of HTT and delays the development of motor defects. Conversely, colonization of HD flies with Escherichia coli (E. coli), a known pathobiont of human gut with links to neurodegeneration, accelerates HTT aggregation, aggravates immobility and shortens lifespan. Similar to antibiotics, treatment of HD flies with small compounds such as luteolin, a flavone, or crocin a beta-carotenoid, ameliorates disease phenotypes and promotes survival. Crocin prevents colonization of E. coli in the gut and alters the abundance of commensal bacteria, which may be linked to its protective effects. The opposing effects of E. coli and crocin on HTT aggregation, motor defects and survival in transgenic Drosophila models support the involvement of gut-brain networks in the pathogenesis of HD.


title: Gut bacteria regulate the pathogenesis of Huntington's disease in Drosophila model


title: Stoney vs. Histed: Quantifying the Spatial Effects of Intracortical Microstimulation

abstract:
BackgroundIntracortical microstimulation (ICMS) is used to map neural circuits and restore lost sensory modalities such as vision, hearing, and somatosensation. The spatial effects of ICMS remain controversial: Stoney and colleagues proposed that the volume of somatic activation increased with stimulation intensity, while Histed et al. suggested activation density, but not somatic activation volume, increases with stimulation intensity.

ObjectiveWe used computational modeling to quantify the spatial effects of ICMS intensity and unify the apparently paradoxical findings of Histed and Stoney.

MethodsWe implemented a biophysically-based computational model of a cortical column comprising neurons with realistic morphology and representative synapses. We quantified the spatial effects of single pulse ICMS, including the radial distance to activated neurons and the density of activated neurons as a function of stimulation intensity.

ResultsAt all amplitudes, the dominant mode of somatic activation was by antidromic propagation to the soma following axonal activation, rather than via trans-synaptic activation. There were no occurrences of direct activation of somata or dendrites. The volume over which antidromic action potentials were initiated grew with stimulation amplitude, while the volume of somatic activations did not. However, the density of somatic activation within the activated volume increased with stimulation amplitude.

ConclusionsThe results resolve the apparent paradox between Stoney and Histeds results by demonstrating that the volume over which action potentials are initiated grows with ICMS amplitude, consistent with Stoney. However, the volume occupied by the activated somata remains approximately constant, while the density of activated neurons within that volume increase, consistent with Histed.

HIGHLIGHTSO_LIImplemented a biophysically-based computational model of cortical column comprising cortical neurons with realistic morphology and representative synapses.
C_LIO_LIQuantified the spatial patterns of neural activation by intracortical microstimulation to resolve the paradoxical findings of Stoney et al., 1968 and Histed et al., 2009.
C_LIO_LIThe dominant mode of neural activation near the electrode was direct (i.e., via antidromic propagation from direct activation of the axon) and not trans-synaptic.
C_LIO_LIThe dominant effect of increased ICMS intensity was to increase the density of activated neurons but not the volume of activation.
C_LI


title: RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results

abstract: Despite being one of the most fundamental biological processes, the process of speciation remains poorly understood in many groups of organisms. Mouse lemurs are a species-rich genus of small primates endemic to Madagascar, whose diversity has only recently been uncovered using genetic data and is primarily found among morphologically cryptic, allopatric populations. To assess to what extent described species represent reproductively isolated entities, studies are needed in areas where mouse lemur taxa come into contact. Hybridization has previously been reported in a contact zone between two closely related mouse lemur species (Microcebus murinus and M. griseorufus) based on microsatellite data. Here, we revisit this system using RADseq data for populations in, near, and far from the contact zone, including many of the individuals that had previously been identified as hybrids. Surprisingly, we find no evidence for admixed nuclear ancestry in any of the individuals. Re-analyses of microsatellite data and simulations suggest that previously inferred hybrids were false positives and that the program NewHybrids can be particularly sensitive to erroneously inferring hybrid ancestry. Using coalescent-bases analyses, we also show an overall lack of recent gene flow between the two species, and low levels of ancestral gene flow. Combined with evidence for local syntopic occurrence, these data indicate that M. murinus and M. griseorufus are reproductively isolated. Finally, we estimate that they diverged less than a million years ago, suggesting that completion of speciation is relatively rapid in mouse lemurs. Future work should focus on the underpinnings of reproductive isolation in this cryptic primate radiation, which are mostly unknown. Our study also provides a cautionary tale for the inference of hybridization with microsatellite data.


title: A low-cost greenhouse-based high-throughput phenotyping platform for genetic studies: a case study in maize under inoculation with plant growth-promoting bacteria

abstract:
Greenhouse-based high-throughput phenotyping (HTP) presents a useful approach for studying novel plant growth-promoting bacteria (PGPB). Despite the potential of this approach to leverage genetic variability for breeding new maize cultivars exhibiting highly stable symbiosis with PGPB, greenhouse-based HTP platforms are not yet widely used because they are highly expensive; hence, it is challenging to perform HTP studies under a limited budget. In this study, we built a low-cost greenhouse-based HTP platform to collect growth-related image-derived phenotypes. We assessed 360 inbred maize lines with or without PGPB inoculation under nitrogen-limited conditions. Plant height, canopy coverage, and canopy volume obtained from photogrammetry were evaluated five times during early maize development. A plant biomass index was constructed as a function of plant height and canopy coverage. Inoculation with PGPB promoted plant growth. Phenotypic correlations between the image-derived phenotypes and manual measurements were at least 0.6. The genomic heritability estimates of the image-derived phenotypes ranged from 0.23 to 0.54. Moderate-to-strong genomic correlations between the plant biomass index and shoot dry mass (0.24-0.47) and between HTP-based plant height and manually measured plant height (0.55-0.68) across the developmental stages showed the utility of our HTP platform. Collectively, our results demonstrate the usefulness of the low-cost HTP platform for large-scale genetic and management studies to capture plant growth.

Core ideasO_LIA low-cost greenhouse-based HTP platform was developed.
C_LIO_LIImage-derived phenotypes presented moderate to high genomic heritabilities and correlations.
C_LIO_LIPlant growth-promoting bacteria can improve plant resilience under nitrogen-limited conditions.
C_LI

category: genetics


title: The impact of evolutionary processes in shaping the genetics of complex traits in East Asia and Europe: a specific contribution from Denisovan and Neanderthal introgression

abstract: Evidence of how human evolution shaped the polygenicity of human traits and diseases has been extensively studied in populations of European descent. However, limited information is currently available about its impact on other ancestry groups. Here, we investigated how different evolutionary processes affected the common variant heritability of traits and diseases in East Asians. Leveraging genome-wide association statistics from the Biobank Japan (up to 158,284 participants), we assessed natural selection (negative and positive), archaic introgression from Neanderthal and Denisova, and several genomic functional categories with respect to the heritability of physiological and pathological conditions. Similar to reports in European descent populations, the heritability estimates for East Asian traits were ubiquitously enriched for negative selection annotations (false discovery rate, FDR q<0.05). Enrichment of Denisovan introgression was identified in coronary artery disease (1.69-fold enrichment, p=0.003). We followed up these enrichments by conducting a phenome-wide association study (PheWAS) of Denisovan and Neanderthal alleles in participants of six ancestral backgrounds from the UK Biobank. In East Asians, Denisovan-inherited alleles were associated with 22 phenotypes, including metabolic, immunological, cardiovascular, endocrine, and dermatological traits. The strongest association was observed for the Denisovan-inherited locus rs59185462 with rheumatoid arthritis (beta=0.82, p=1.91x10-105). In summary, our study provides the first evidence regarding the impact of evolutionary processes on the genetics of complex traits in worldwide populations, highlighting the specific contribution of Denisovan introgression in East Asian populations.


title: Applying Machine Learning to Classify the Origins of Gene Duplications

abstract: Nearly all lineages of land plants have experienced at least one whole genome duplication (WGD) in their history. The legacy of these ancient WGDs is still observable in the diploidized genomes of extant plants. Genes originating from WGD--paleologs--can be maintained in diploidized genomes for millions of years. These paleologs have the potential to shape plant evolution through sub- and neofunctionalization, increased genetic diversity, and reciprocal gene loss among lineages. Current methods for classifying paleologs often rely on only a subset of potential genomic features, have varying levels of accuracy, and often require significant data and/or computational time. Here we developed a supervised machine learning approach to classify paleologs from a target WGD in diploidized genomes across a broad range of different duplication histories. We collected empirical data on syntenic block sizes and other genomic features from 27 plant species each with a different history of paleopolyploidy. Features from these genomes were used to develop simulations of syntenic blocks and paleologs to train a gradient boosted decision tree. Using this approach, Frackify (Fractionation Classify), we were able to accurately identify and classify paleologs across a broad range of parameter space, including cases with multiple overlapping WGDs. We then compared Frackify with other paleolog inference approaches in six species with paleotetraploid and paleohexaploid ancestries. Frackify provides a way to combine multiple genomic features to quickly classify paleologs while providing a high degree of consistency with existing approaches.


title: Sciviewer enables interactive visual interrogation of single-cell RNA-Seq data from the Python programming environment

abstract:
SummaryVisualizing two-dimensional (2D) embeddings (e.g. UMAP or tSNE) is a key step in interrogating single-cell RNA sequencing (scRNA-Seq) data. Subsequently, users typically iterate between programmatic analyses (e.g. clustering and differential expression) and visual exploration (e.g. coloring cells by interesting features) to uncover biological signals in the data. Interactive tools exist to facilitate visual exploration of embeddings such as performing differential expression on user-selected cells. However, the practical utility of these tools is limited because they dont support rapid movement of data and results to and from the programming environments where the bulk of data analysis takes place, interrupting the iterative process. Here, we present the Single-cell Interactive Viewer (Sciviewer), a tool that overcomes this limitation by allowing interactive visual interrogation of embeddings from within Python. Beyond differential expression analysis of user-selected cells, Sciviewer implements a novel method to identify genes varying locally along any user-specified direction on the embedding. Sciviewer enables rapid and flexible iteration between interactive and programmatic modes of scRNA-Seq exploration, illustrating a useful approach for analyzing high-dimensional data.

Availability and implementationCode and examples are provided at https://github.com/colabobio/sciviewer


title: Structure of benzothiadiazine at zwitterionic phospholipid cell membranes

abstract: The use of drugs derived from benzothiadiazine, which is a bicyclic heterocyclic benzene derivative, has become a widespread treatment for diseases such as hypertension (treated with diuretics such as bendroflumethiazide or chlorothiazide), low blood sugar (treated with non-diuretic diazoxide) or the human immunodeficiency virus, among others. In this work we have investigated the interactions of benzothiadiazine with the basic components of cell membranes and solvents such as phospholipids, cholesterol, ions and water. The analysis of the mutual microscopic interactions is of central importance to elucidate the local structure of benzothiadiazine as well as the mechanisms responsible for the access of benzothiadiazine to the interior of the cell. We have performed molecular dynamics simulations of benzothiadiazine embedded in three different model zwitterionic bilayer membranes made by dimyristoilphosphatidylcholine, dioleoylphosphatidylcholine, 1,2-dioleoyl-sn-glycero-3-phosphoserine and cholesterol inside aqueous sodium-chloride solution in order to systematically examine microscopic interactions of benzothiadiazine with the cell membrane at liquid-crystalline phase conditions. From data obtained through radial distribution functions, hydrogen-bonding lengths and potentials of mean force based on reversible work calculations, we have observed that benzothiadiazine has a strong affinity to stay at the cell membrane interface although it can be fully solvated by water in short periods of time. Furthermore, benzothiadiazine is able to bind lipids and cholesterol chains by means of single and double hydrogen-bonds of different characteristic lengths.


title: Mapping the peptide binding groove of MHC class I

abstract: An essential element of adaptive immunity is the selective binding of peptide antigens by major histocompatibility complex (MHC) class I proteins and their presentation to cytotoxic T lymphocytes on the cell surface. Using native mass spectrometry, we here analyze the binding of peptides to an empty disulfide-stabilized HLA-A*02:01 molecule. This novel approach allows us to examine the binding properties of diverse peptides. The unique stability of our MHC class I even enables us to determine the binding affinity of complexes, which are suboptimally loaded with truncated or charge-reduced peptides. Notably, a unique erucamide adduct decouples affinity analysis from peptide identity alleviating issues usually attributed to clustering during electrospray ionization. We discovered that two anchor positions at the binding surface between MHC and peptide can be stabilized independently and further identify the contribution of other peptidic amino acids on the binding. We propose this as an alternative, likely universally applicable method to artificial prediction tools to estimate the binding strength of peptides to MHC class I complexes quickly and efficiently. This newly described MHC class I-peptide binding affinity quantitation represents a much needed orthogonal, independent approach to existing computational affinity predictions and has the potential to eliminate binding affinity biases and thus accelerate drug discovery in infectious diseases, autoimmunity, vaccine design, and cancer immunotherapy.


title: Lipid Tails Modulate Antimicrobial Peptide Membrane Incorporation and Activity

abstract:
Antimicrobial peptides (AMPs) are cationic, amphipathic peptides that interact directly with lipid bilayers. AMPs generally interact with anionic lipid head groups, but it is less clear how the lipid tail length and saturation modulates interactions with membranes. Here we used native mass spectrometry to measure the stoichiometry of three different AMPs--LL-37, indolicidin, and magainin-2--in lipid nanodiscs. We also measured the activity of these AMPs in large unilamellar vesicle leakage assays. We found that LL-37 formed specific hexamer complexes but with different assembly pathways and affinities that depended on the bilayer thickness. LL-37 was also most active in lipid bilayers containing longer, unsaturated lipids. In contrast, indolicidin incorporated to a higher degree into more fluid lipid bilayers but was more active with thinner, less fluid bilayers. Finally, magainin-2 incorporated to a higher degree into longer, unsaturated bilayers and showed more activity in these same conditions. Together, these data show that higher amounts of peptide incorporation generally led to higher activity and that AMPs tend to incorporate more into longer unsaturated lipid bilayers. However, the activity of AMPs was not always directly related to amount of peptide incorporated.

Graphical Abstract

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title: Transcriptomic and functional analysis of Aβ1-42 oligomer-stimulated human monocyte-derived microglia-like cells

abstract: Dysregulation of microglial function contributes to Alzheimers disease (AD) pathogenesis. Several genetic and transcriptome studies have revealed microglia specific genetic risk factors, and changes in microglia expression profiles in AD pathogenesis, viz. the human-Alzheimers microglia/myeloid (HAM) profile in AD patients and the disease-associated microglia profile (DAM) in AD mouse models. The transcriptional changes involve genes in immune and inflammatory pathways, and in pathways associated with A{beta} clearance. A{beta} oligomers have been suggested to be the initial trigger of microglia activation in AD. To study the direct response to A{beta} oligomers exposure, we assessed changes in gene expression in an in vitro model for microglia, the human monocyte-derived microglial-like (MDMi) cells. We confirmed the initiation of an inflammatory profile following LPS stimulation, based on increased expression of IL1B, IL6, and TNF. In contrast, the A{beta}1-42 oligomers did not induce an inflammatory profile or a classical HAM or DAM profile. Interestingly, we observed a specific increase in the expression of metallothioneins in the A{beta}1-42 oligomer treated MDMi cells. Metallothioneins are involved in metal ion regulation, protection against reactive oxygen species, and have anti-inflammatory properties. In conclusion, our data suggests that A{beta}1-42 oligomers may trigger a protective response both in vitro and in vivo.


title: Ecdysone exerts biphasic control of regenerative signaling, coordinating the completion of regeneration with developmental progression

abstract:
In Drosophila melanogaster, loss of regenerative capacity in wing imaginal discs coincides with an increase in systemic levels of the steroid hormone ecdysone, a key coordinator of their developmental progression. Regenerating discs release the relaxin hormone Dilp8, which limits ecdysone synthesis and extends the regenerative period. Here, we describe how regenerating tissues produce a biphasic response to ecdysone levels: lower concentrations of ecdysone promote local and systemic regenerative signaling, whereas higher concentrations suppress regeneration through the expression of broad splice isoforms. Ecdysone also promotes the expression of wingless during both regeneration and normal development through a distinct regulatory pathway. This dual role for ecdysone explains how regeneration can still be completed successfully in dilp8- mutant larvae: higher ecdysone levels increase the regenerative activity of tissues, allowing regeneration to reach completion in a shorter time. From these observations, we propose that ecdysone hormone signaling functions to coordinate regeneration with developmental progression.

Summary StatementEcdysone coordinates regenerative activity with developmental progression through the biphasic, concentration-dependent activation, and suppression of regenerative signaling.


title: Quantifying microbial associations of dissolved organic matter under global change

abstract: Microbes play a critical role in regulating the size, composition, and turnover of dissolved organic matter (DOM), which is one of the largest pools of carbon in aquatic ecosystems. Global change may alter DOM-microbe associations with implications for biogeochemical cycles, although disentangling these complex interactions remains a major challenge. Here we develop a framework called Energy-Diversity-Trait integrative Analysis (EDTiA) to examine the associations between DOM and bacteria along temperature and nutrient gradients in a manipulative field experiment on mountainsides in contrasting subarctic and subtropical climates. In both study regions, the chemical composition of DOM correlated with bacterial communities, and was primarily controlled by nutrients and to a lesser degree by temperature. At a molecular-level, DOM-bacteria associations depended strongly on the molecular traits of DOM, with negative associations indicative of decomposition as molecules are more biolabile. Using bipartite networks, we further demonstrated that negative associations were more specialized than positive associations indicative of DOM production. Nutrient enrichment promoted specialization of positive associations, but decreased specialization of negative associations particularly at warmer temperatures in subtropical climate. These global change drivers influenced specialization of negative associations most strongly via molecular traits, while both molecular traits and bacterial diversity similarly affected positive associations. Together, our framework provides a quantitative approach to understand DOM-microbe associations and wider carbon cycling across scales under global change.


title: The effect of weak clonal interference on average fitness trajectories in the presence of macroscopic epistasis

abstract: Adaptation dynamics on fitness landscapes is often studied theoretically in the strong-selection, weak-mutation (SSWM) regime. However, in a large population, multiple beneficial mutants can emerge before any of them fixes in the population. Competition between mutants is known as clonal interference, and how it affects the form of long-term fitness trajectories in the presence of epistasis is an open question. Here, by considering how changes in fixation probabilities arising from weak clonal interference affect the dynamics of adaptation on fitness-parameterized landscapes, we find that the change in the form of fitness trajectory arises only through changes in the supply of beneficial mutations (or equivalently, the beneficial mutation rate). Furthermore, a depletion of beneficial mutations as a population climbs up the fitness landscape can speed up the functional form of the fitness trajectory, while an enhancement of the beneficial mutation rate does the opposite of slowing down the form of the dynamics. Our findings suggest that by carrying out evolution experiments in both regimes (with and without clonal interference), one could potentially distinguish the different sources of macroscopic epistasis (fitness effect of mutations vs. change in fraction of beneficial mutations).


title: Single Tube qPCR detection and quantitation of hotspot mutations down to 0.01% VAF

abstract: Clinically and biologically, rare DNA sequence variants are significant and informative. However, existing detection technologies are either complex in workflow, or restricted in the limit of detection (LoD), or do not allow for multiplexing. Blocker displacement amplification (BDA) method can stably and effectively detect and enrich multiple rare variants with LoD around 0.1% variant allele fraction (VAF). Nonetheless, the detailed mutation information has to be identified by additional sequencing technologies. Here, we present allele-specific BDA (As-BDA), a method combining BDA with allele-specific TaqMan (As-TaqMan) probes for effective variant enrichment and simultaneous SNV profiling. We demonstrated that As-BDA could detect mutations down to 0.01% VAF. Further, As-BDA could detect up to four mutations with low to 0.1% VAF per reaction using only 15 ng DNA input. The median error of As-BDA in VAF determination is approximately 9.1%. Comparison experiments using As-BDA and droplet digital PCR (ddPCR) on peripheral blood mononuclear cell (PBMC) clinical samples showed 100% concordance for samples with mutations at [≥] 0.1% VAF. Hence, we have shown that As-BDA can achieve simultaneous enrichment and identification of multiple targeted mutations within the same reaction with high clinical sensitivity and specificity, thus helpful for clinical diagnosis.

category: bioengineering


title: mebipred: identifying metal-binding potential in protein sequences.

abstract:
Metal-binding proteins have a central role in maintaining life processes. Nearly one-third of known protein structures contain metal ions that are used for a variety of needs, such as catalysis, DNA/RNA binding, protein structure stability, etc. Identifying metal-binding proteins is thus crucial for understanding the mechanisms of cellular activity. However, experimental annotation of protein metal-binding potential is severely lacking, while computational techniques are often imprecise and of limited applicability.

We developed a novel machine learning-based method, mebipred, for identifying metal-binding proteins from sequence-derived features. This method is nearly 90% accurate in recognizing proteins that bind metal ions and ion containing ligands. Moreover, the identity of ten ubiquitously present metal ions and ion-containing ligands can be annotated. mebipred is reference-free, i.e. no sequence alignments are involved, and outperforms other prediction methods, both in speed and accuracy. mebipred can also identify protein metal-binding capabilities from short sequence stretches and, thus, may be useful for the annotation of metagenomic samples metal requirements inferred from translated sequencing reads. We performed an analysis of microbiome data and found that ocean, hot spring sediments and soil microbiomes use a more diverse set of metals than human host-related ones. For human-hosted microbiomes, physiological conditions explain the observed metal preferences. Similarly, subtle changes in ocean sample ion concentration affect the abundance of relevant metal-binding proteins. These results are highlight mebipreds utility in analyzing microbiome metal requirements.

mebipred is available as a web server at services.bromberglab.org/mebipred and as a standalone package at https://pypi.org/project/mymetal/


title: Optimizing Polymerase Chain Reaction (PCR) using Machine Learning

abstract: Despite substantial standardization, polymerase chain reaction (PCR) experiments frequently fail. Troubleshooting failed PCRs can be costly in both time and money. Using a crowdsourced data set spanning 290 real PCRs from six active research laboratories, we investigate the degree to which PCR success rates can be improved by machine learning. While human designed PCRs succeed at a rate of 55-63%, we find that a machine learning model can accurately predict reaction outcome 81% of the time. We validate this level of improvement by then using the model to guide the design and predict the outcome of 39 new PCR experiments. In addition to improving outcomes, the model identifies 15 features of PCRs that researchers did not optimize well compared to the learned model. These results suggest that PCR success rates can easily be improved by 17-26%, potentially saving millions of dollars and thousands of hours of researcher time each year across the scientific community. Other common laboratory methods may benefit from similar data-driven optimization effort.


title: A practical framework RNMF for the potential mechanism of cancer progression with the analysis of genes cumulative contribution abundance

abstract: Mutational signatures can reveal the mechanism of tumorigenesis. We developed the RNMF software for mutational signatures analysis, including a key model of cumulative contribution abundance (CCA) which was designed to highlight the association between genes and mutational signatures. Applied it to 1073 esophageal squamous cell carcinoma (ESCC) and found that APOBEC signatures (SBS2* and SBS13*) mediated the occurrence of PIK3CA E545k mutation. Furthermore, we found that age signature is strongly linked to the TP53 R342* mutation. In addition, the CCA matrix image data of genes in the signatures New, SBS3* and SBS17b* were helpful for the preliminary evaluation of shortened survival outcome. In a word, RNMF can successfully achieve the correlation analysis of genes and mutational signatures, proving a strong theoretical basis for the study of tumor occurrence and development mechanism and clinical adjuvant medicine.


title: Temporal properties of painful contrast enhancement using repetitive stimulation

abstract:
Offset analgesia is characterized by a disproportionately large reduction in pain following a small decrease in a heat stimulus and is based on the phenomenon of temporal pain contrast enhancement (TPCE). The aim of this study is to investigate whether this phenomenon can also be induced by repetitive stimulation, i.e., by stimuli that are clearly separated in time. With this aim, the repetitive TPCE paradigm was induced in healthy, pain-free subjects (n=33) at the volar non-dominant forearm using heat stimuli. This paradigm was performed applying three different interstimulus intervals (ISIs): 5, 15, and 25 seconds. All paradigms were contrasted with a control paradigm without temperature change. Participants continuously rated the perceived pain intensity. In addition, electrodermal activity was recorded as a surrogate measure of autonomic arousal. Temporal pain contrast enhancement was confirmed for both ISI 5 seconds (p < 0.001) and ISI 15 seconds (p = 0.005), but not for ISI 25 seconds (p = 0.07), however the magnitude of TPCE did not differ between ISIs (p = 0.11). Electrodermal activity was consistent previous pain ratings, but showing significantly higher autonomic activity being measured. Thus, the phenomenon of temporal contrast enhancement of pain can also be induced by repetitive stimulation. Both the involvement of the autonomic nervous system and the involvement of habituation processes are conceivable, which consequently points to both central and peripheral mechanisms of TPCE.

SummaryThe temporal contrast enhancement of pain and electrodermal activity can be provoked by stimuli that are clearly separated in time.


title: Humanoid robots are perceived as an evolutionary threat

abstract: In the grand challenges of successful social encounters with socially sophisticated robots and shaping the future development of robots in socially acceptable ways, we need to quantify people perception to the robots. The critical assumption at the perception to humanoid robots, namely that people perceive humanoid robots as an evolutionary threat, has not been directly confirmed. We assume the existence of behavioral and neural automaticity for humanoid robots that were previously only evident for evolutionary threats. Here, we observed a monocular advantage for the perception of humanoid robots the same as an evolutionary threat (i.e., snakes). Our neuroimaging analysis indicated that unconscious presentation of humanoid robot vs. human images led to significant left amygdala activation that was associated with negative implicit attitude to humanoid robots. After successfully weakening negative attitude, the left amygdala response to unconscious presentation of humanoid robot images decreased, and the decrease of left amygdala response was positively associated with the decrease of negative attitude. Our results reveal that processing of information about humanoid robots displays automaticity with regard to recruitment of visual pathway and amygdala activation. Our findings that humans may perceive humanoid robots as an evolutionary threat will guide the future direction of robots development and bring us closer to interacting with socially sophisticated robots.


title: A-GHN: Attention-based Fusion of Multiple GraphHeat Networks for Structural to Functional Brain Mapping

abstract: Over the last decade, there has been growing interest in learning the mapping from structural connectivity (SC) to functional connectivity (FC) of the brain. The spontaneous fluctuations of the brain activity during the restingstate as captured by functional MRI (rsfMRI) contain rich non-stationary dynamics over a relatively fixed structural connectome. Among the modeling approaches, graph diffusion-based methods with single and multiple diffusion kernels approximating static or dynamic functional connectivity have shown promise in predicting the FC given the SC. However, these methods are computationally expensive, not scalable, and fail to capture the complex dynamics underlying the whole process. Recently, deep learning methods such as GraphHeat networks along with graph diffusion have been shown to handle complex relational structures while preserving global information. In this paper, we propose a novel attention-based fusion of multiple GraphHeat networks (A-GHN) for mapping SC-FC. A-GHN enables us to model multiple heat kernel diffusion over the brain graph for approximating the complex Reaction Diffusion phenomenon. We argue that the proposed deep learning method overcomes the scalability and computational inefficiency issues but can still learn the SC-FC mapping successfully. Training and testing were done using the rsfMRI data of 100 participants from the human connectome project (HCP), and the results establish the viability of the proposed model. Furthermore, experiments demonstrate that A-GHN outperforms the existing methods in learning the complex nature of human brain function.


title: Enhanced negative response to stress following morphine administration increases wanting of social reward

abstract:
Animal research suggests a central role of the -opioid receptor (MOR) system in regulating affiliative behaviors and in mediating the stress-buffering function of social contact. However, the neurochemistry of stress-related social contact seeking in humans is still poorly understood. In a randomized, double-blind, between-subject design, healthy female volunteers (N = 80) received either 10 mg of the -opioid agonist morphine sulfate, or a placebo. Following a standardized psychosocial stress induction, participants engaged in a social reward task, in which the motivation to obtain skin-to-skin social touch and the hedonic reactions elicited by such touch were assessed.

Morphine prevented the increase of salivary cortisol typically observed following acute stress exposure. Notably, this altered HPA axis responsivity was associated with increased negative affect in response to psychosocial stress, and with enhanced subjective wanting of highly rewarding social contact.

These findings provide novel evidence on the effect of exogenous opioids administration on the reactions to psychosocial stress and point to a state-dependent regulation of social motivation.


title: Opioid-blunted cortisol response to stress is associated to increased negative mood and wanting of social reward


title: Learning from the path not taken: Sensory prediction errors are sufficient for implicit adaptation of withheld movements

abstract: Prediction errors guide many forms of learning, providing teaching signals that help us improve our performance. Implicit motor adaptation, for instance, is driven by sensory prediction errors (SPEs), which occur when the expected and observed consequences of a movement differ. Traditionally, SPE computation is thought to require movement execution. However, recent work suggesting that the brain generates and accounts for sensory predictions based on motor imagery or planning alone calls this assumption into question. Here, by measuring implicit adaptation during a visuomotor task, we tested whether motor planning and well-timed sensory feedback are sufficient for SPE computation. Human participants were cued to reach to a target and were, on a subset of trials, rapidly cued to withhold these movements. Errors displayed both on trials with and without movements induced single-trial implicit learning. Learning following trials without movements persisted even when movement trials had never been paired with errors, and when the direction of movement and sensory feedback trajectories were decoupled. These observations demonstrate that the brain can compute SPEs without generating overt movements, leading to the adaptation of planned movements even when they are not performed.


title: Learning from the path not taken: Sensory prediction error computation and implicit motor adaptation proceed without movement


title: Movement planning and feedback are sufficient for sensory prediction error computation and motor adaptation


title: Identification of a MarR subfamily that regulates arsenic resistance genes

abstract:
Members of the family of Multiple Antibiotic Resistance Regulators (MarR) often regulate genes that encode antibiotic resistance in bacteria. In this study, comprehensive analyses were performed to determine the function of an atypical MarR homolog in Achromobacter sp. As-55. Genomic analyses showed that this marR is located in an arsenic gene island in Achromobacter sp. As-55 adjacent to an arsV gene. ArsV is a flavin-dependent monooxygenase that confers resistance to the antibiotic methylarsenite (MAs(III)), the organoarsenic compound roxarsone(III) (Rox(III)), and the inorganic antimonite (Sb(III)). Similar marR genes are widely distributed in arsenic-resistant bacteria. Phylogenetic analyses showed that these MarRs are found in operons predicted to be involved in resistance to inorganic and organic arsenic species, so the subfamily was named MarRars. MarRars orthologs have three conserved cysteine residues, which are Cys36, Cys37 and Cys157 in Achromobacter sp. As-55, mutation of which compromises the response to MAs(III)/Sb(III). GFP-fluorescent biosensor assays show that AdMarRars (MarR protein of Achromobacter deleyi As-55) responds to trivalent As(III) and Sb(III) but not to pentavalent As(V) or Sb(V). The results of RT-qPCR assays show that arsV is expressed constitutively in a marR deletion mutant, indicating that marR represses transcription of arsV. Moreover, electrophoretic mobility shift assays (EMSA) demonstrate that AdMarRars binds to the promoters of both marR and arsV in the absence of ligands and that DNA binding is relieved upon binding of As(III) and Sb(III). Our results demonstrate that AdMarRars is a novel As(III)/Sb(III)-responsive transcriptional repressor that controls expression of arsV, which confers resistance to MAs(III), Roxarsone(III) and Sb(III). AdMarRars and its orthologs form a subfamily of MarR proteins that regulate genes conferring resistance to arsenic-containing antibiotics.

IMPORTANCEIn this study, a MarR family member, AdMarRars was shown to regulate the arsV gene, which confers resistance to arsenic-containing antibiotics. It is a founding member of a distinct subfamily that we refer to as MarRars, regulating genes conferring resistance to arsenic and antimony antibiotic compounds. AdMarRars was shown to be a repressor containing conserved cysteine residues that are required to bind As(III) and Sb(III), leading to a conformational change and subsequent derepression. Here we show that members of the MarR family are involved in regulating arsenic-containing compounds.


title: Transcriptional profiling of early differentiation of primary human mesenchymal stem cells into chondrocytes

abstract: Articular cartilage has only very limited regenerative capacities in humans. Tissue engineering techniques for cartilage damage repair are limited in the production of hyaline cartilage. Mesenchymal stem/stromal cells (MSCs) are multipotent stem cells and can be differentiated into mature cartilage cells, chondrocytes, which could be used for repairing damaged cartilage. Chondrogenesis is a highly complex, relatively inefficient process lasting over 3 weeks in vitro. In order to better understand chondrogenic differentiation, especially the commitment phase, we have performed transcriptional profiling of MSC differentiation into chondrocytes from early timepoints starting 15 minutes after induction to 16 hours and fully differentiated chondrocytes at 21 days. Transcriptional gene regulatory networks (GRN) were identified using time-course clustering and upstream-regulator predictions which revealed that cells start epigenetic reprogramming as early as 2 hours after induction and commit to differentiation within 4-6 hours. After that they adapt their gene expression to cater for differentiation specific protein production. These results suggest that interventions to improve the frequency and efficiency of differentiation should target early processes.

category: molecular biology


title: O-GlcNAcylation is essential for rapid Pomc expression and cell proliferation in corticotropic tumor cells

abstract:
Pituitary adenomas have a staggering 16.7% lifetime prevalence and can be devastating in many patients due to profound endocrine and neurologic dysfunction. To date, no clear genomic or epigenomic markers correlates with their onset or severity. Herein, we investigate the impact of the O-GlcNAc post-translational modification in their etiology. Found in over 5000 human proteins to date, O-GlcNAcylation dynamically regulates proteins in critical signaling pathways, and its deregulation is involved in cancers progression and endocrine diseases such as diabetes.

In this study, we demonstrate that O-GlcNAcylation enzymes were upregulated, particularly in aggressive ACTH-secreting tumors, suggesting a role for O-GlcNAcylation in pituitary adenoma etiology. In addition to the demonstration that O-GlcNAcylation was essential for their proliferation, we show that the endocrine function of pituitary adenoma is also dependent on O-GlcNAcylation. In corticotropic tumors, hyper-secretion of the proopiomelanocortin (POMC)-derived hormone ACTH leads to Cushings disease, materialized by severe endocrine disruption and increased mortality. We demonstrate that Pomc mRNA is stabilized in an O-GlcNAc-dependent manner in response to corticotropic-stimulating hormone (CRH). By impacting Pomc mRNA splicing and stability, O-GlcNAcylation contributes to this new mechanism of fast hormonal response in corticotropes. Thus, this study stresses the essential role of O-GlcNAcylation in ACTH-secreting adenomas pathophysiology, including cellular proliferation and hypersecretion.

category: cell biology


title: The small and large intestine contain transcriptionally related mesenchymal stromal cell subsets that derive from embryonic Gli1+ mesothelial cells

abstract: Intestinal fibroblasts (FB) play essential roles in intestinal homeostasis. Here we show that the small and large intestinal lamina propria (LP) contain similar FB subsets that locate in specific anatomical niches and express distinct arrays of epithelial support genes. However, there were tissue specific differences in the transcriptional profile of intestinal FB subsets in the two sites. All adult intestinal LP mesenchymal stromal cells (MSC), including FB, smooth muscle cells (SMC) and pericytes derive from Gli1-expressing embryonic precursors which we identify as mesothelial cells. Trajectory analysis suggested that adult SMC and FB derive from distinct embryonic intermediates, and that adult FB subsets develop in a linear trajectory from CD81+ FB. Finally, we show that colonic subepithelial PDGFRhi FB comprise several functionally and anatomically distinct populations that originate from an Fgfr2-expressing FB intermediate. Collectively our results provide novel insights into MSC diversity, location, function and ontogeny, with implications for our understanding of intestinal development, homeostasis and disease.


title: Immunoglobulin heavy constant gamma gene evolution is modulated by both the divergent and birth-and-death evolutionary models

abstract:
Immunoglobulin G (IgG) is one of the five antibody classes produced in mammals as part of the humoral responses. This high-affinity antibody produced late in a primary immune response is responsible for protecting the organisms from infection. This proteins heavy chain constant region is encoded by the Ig gamma gene (Ig{gamma}). In Humans, IgG has evolved into four subclasses with specialized effector functions. However, in Platyrrhini, IgG has been reported to be encoded by a single-copy gene. Here, we analyzed data from 38 primate genome sequences to identify Ig{gamma} genes and describe the evolution of this immunoglobulin in this group. Ig{gamma} belongs to a multigene family that evolves by the birth-death evolutionary model in primates. Whereas Strepsirrhini and Platyrrhini have a single-copy gene, in Catarrhini species it has expanded to having several paralogs in their genomes; some have been deleted or have become pseudogenes. Furthermore, episodic positive selection might promote a specialized species-specific IgG effector function. A hypothesis for the Ig{gamma} evolution has been proposed, suggesting that IgG has evolved to reach an optimal number of copies per genome to adapt their humoral immune responses to different environmental conditions.

Graphical abstract

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title: Masculinization of the X-chromosome in aphid soma and gonads

abstract: Males and females share essentially the same genome but differ in their optimal values for many phenotypic traits, which can result in intra-locus conflict between the sexes. Aphids display XX/X0 sex chromosomes and combine unusual X chromosome inheritance with cyclical parthenogenesis. Theoretical and empirical works support the hypothesis that the large excess of male-biased genes observed on the aphid X chromosome compared to autosomes has evolved in response to sexual conflicts, by restricting the product of a sexually antagonistic allele to the sex it benefits. However, whether such masculinization of the X affects all tissues (as expected if it evolved in response to sexual conflicts) or reflects tissue specificities (which would contradict the sexual conflict hypothesis) remains an open question. To address it, we measured gene expression in three different somatic and gonadic tissues of males, sexual females and parthenogenetic females of the pea aphid. We observed a masculinization of the X in each of the studied tissues, with male-biased genes being 2.5 to 3.5 more frequent on the X than expected. We also tested the hypothesis that gene duplication can facilitate the attenuation of conflicts by allowing gene copies to neo-or sub-functionalize and reach sex-specific optima. As predicted, X-linked copies of duplicated genes having their other copies on autosomes were more frequently male-biased (40.5% of the genes) than duplicated autosomal genes (6.6%) or X-linked single-copy genes (32.5%). These results highlight a peculiar pattern of expression of X-linked genes in aphids at the tissue level and provide further support for sex-biased expression as a mechanism to attenuate intra-locus sexual conflicts.


title: Efficient identification of trait-associated loss-of-function variants in the UK Biobank cohort by exome-sequencing based genotype imputation

abstract: The large-scale open access whole-exome sequencing (WES) data of the UK Biobank ~200,000 participants is accelerating a new wave of genetic association studies aiming to identify rare and functional loss-of-function (LoF) variants associated with a broad range of complex traits and diseases, however the community is in short of stringent replication of new associations. In this study, we proposed to merge the WES genotypes and the genome-wide genotyping (GWAS) genotypes of 167,000 UKB Caucasian participants into a combined reference panel, and then to impute 241,911 UKB Caucasian participants who had the GWAS genotypes only. We then proposed to use the imputed data to replicate association identified in the discovery WES sample. Using a leave-100-out imputation strategy in the reference panel, we showed that average imputation accuracy measure r2 is modest to high at LoF variants of all minor allele frequency (MAF) intervals including ultra-rare ones: 0.942 at MAF interval [1%, 50%], 0.807 at [0.1%, 1.0%), 0.805 at [0.01%, 0.1%), 0.664 at [0.001%, 0.01%) and 0.410 at (0, 0.001%). As applications, we studied single variant level and gene level associations of LoF variants with estimated heel BMD (eBMD) and 4 lipid traits: high-density-lipoprotein cholesterol (HDL-C), low-density-lipoprotein cholesterol (LDL-C), triglycerides (TG) and total cholesterol (TC). In addition to replicating dozens of previously reported genes such as MEPE for eBMD and PCSK9 for more than one lipid trait, the results also identified 2 novel gene-level associations: PLIN1 (cumulative MAF=0.10%, discovery BETA=0.38, P=1.20x10-13; replication BETA=0.25, P=1.03x10-6) and ANGPTL3 (cumulative MAF=0.10%, discovery BETA=-0.36, P=4.70x10-11; replication BETA=-0.30, P=6.60x10-11) for HDL-C, as well as one novel single variant level association (11:14843853:C:T, MAF=0.11%, discovery BETA=-0.31, P=2.70x10-9; replication BETA=-0.31, P=8.80x10-14, PDE3B) for TG. Our results highlighted the strength of WES based genotype imputation as well as provided useful imputed data within the UKB cohort.


title: Mistargeting of hydrophobic mitochondrial proteins activates a nucleus-mediated posttranscriptional quality control pathway in trypanosomes

abstract: Mitochondrial protein import in the parasitic protozoan Trypanosoma brucei is mediated by the atypical outer membrane translocase, ATOM. It consists of seven subunits including ATOM69, the import receptor for hydrophobic proteins. Ablation of ATOM69, but not of any other subunit, triggers a unique quality control pathway resulting in the proteasomal degradation of non-imported mitochondrial proteins. The process requires a protein of unknown function, an E3 ubiquitin ligase and the ubiquitin-like protein (TbUbL1), which all are recruited to the mitochondrion upon ATOM69 depletion. TbUbL1 is a nuclear protein, a fraction of which is released to the cytosol upon triggering of the pathway. Nuclear release is essential as cytosolic TbUbL1 can bind mislocalised mitochondrial proteins and likely transfers them to the proteasome. Mitochondrial quality control has previously been studied in yeast and metazoans. Finding such a pathway in the highly diverged trypanosomes suggests such pathways are an obligate feature of all mitochondria.

category: biochemistry


title: Unravelling the binding mode of a methamphetamine aptamer: a spectroscopic and calorimetric investigation

abstract: Nucleic acid aptamers are bio-molecular recognition agents that bind to their targets with high specificity and affinity, and hold promise in a range of biosensor and therapeutic applications. In the case of small molecule targets, their small size and limited number of functional groups constitute challenges for their detection by aptamer-based biosensors because bio-recognition events may both be weak and produce poorly transduced signals. The binding affinity is principally used to characterize aptamer-ligand interactions; however a structural understanding of bio-recognition is arguably more valuable in order to design a strong response in biosensor applications. Using a combination of nuclear magnetic resonance, circular dichroism, and isothermal titration calorimetry, we propose a binding model for a new methamphetamine aptamer and determine the main interactions driving complex formation. These measurements reveal only modest structural changes to the aptamer upon binding and are consistent with a conformational selection binding model. The aptamer-methamphetamine complex formation was observed to be entropically driven, apparently involving hydrophobic and electrostatic interactions. Taken together, our results establish a means of elucidating small molecule-aptamer binding interactions, which may be decisive in the development of aptasensors and therapeutics, and may contribute to a deeper understanding of interactions driving aptamer selection.


title: A mathematical framework for analyzing wild tomato root architecture

abstract: The root architecture of wild tomato, Solanum pimpinellifolium, can be viewed as a network connecting the main root to various lateral roots. Several constraints have been proposed on the structure of such biological networks, including minimizing the total amount of wire necessary for constructing the root architecture (wiring cost), and minimizing the distances (and by extension, resource transport time) between the base of the main root and the lateral roots (conduction delay). For a given set of lateral root tip locations, these two objectives compete with each other -- optimizing one results in poorer performance on the other -- raising the question how well S. pimpinellifolium root architectures balance this network design trade-off in a distributed manner. Here, we describe how well S. pimpinellifolium roots resolve this trade-off using the theory of Pareto optimality. We describe a mathematical model for characterizing the network structure and design trade-offs governing the structure of S. pimpinellifolium root architecture. We demonstrate that S. pimpinellifolium arbors construct architectures that are more optimal than would be expected by chance. Finally, we use this framework to quantify structural differences between arbors grown in the presence of salt stress, classify arbors into four distinct architectural ideotypes, and test for heritability of variation in root architecture structure.

category: plant biology


title: Dynamics and impacts of transposable element proliferation during the Drosophila nasuta species group radiation

abstract: Transposable element (TE) mobilization is a constant threat to genome integrity. Eukaryotic organisms have evolved robust defensive mechanisms to suppress their activity, yet TEs can escape suppression and proliferate, creating strong selective pressure for host defense to adapt. This genomic conflict fuels a never-ending arms race that drives the rapid evolution of TEs and recurrent positive selection of genes involved in host defense; the latter has been shown to contribute to postzygotic hybrid incompatibility. However, how TE proliferation impacts genome and regulatory divergence remains poorly understood. Here, we report the highly complete and contiguous (N50=33.8Mb - 38.0Mb) genome assemblies of seven closely-related Drosophila species that belong to the nasuta species group - a poorly studied group of flies that radiated in the last 2 million years. We constructed a high quality de novo TE library and gathered germline RNA-seq data, which allowed us to comprehensively annotate and compare insertion patterns between the species, and infer the evolutionary forces controlling their spread. We find a strong negative association between TE insertion frequency and expression of genes nearby; this likely reflects survivor-bias from reduced fitness impact of TE inserting near lowly expressed, non-essential genes, with limited TE-induced epigenetic silencing. Phylogenetic analyses of insertions of 147 TE families reveal that 53% of them show recent amplification in at least one species. The most highly amplified TE is an non-autonomous DNA element DINE which has gone through multiple bouts of expansions with thousands of full length copies littered throughout each genome. Across all TEs, we find that TEs expansions are significantly associated with high expression in the expanded species consistent with suppression escape. Altogether, our results shed light on the heterogenous and context-dependent nature in which TEs affect gene regulation and the dynamics of rampant TE proliferation amidst a recently radiated species group.


title: Pressure for rapid and accurate mate recognition promotes avian-perceived plumage sexual dichromatism in true thrushes (genus: Turdus)

abstract: Ecological conditions limiting the time to find a compatible mate or increasing the difficulty in doing so likely promote the evolution of traits used for species and mate recognition. Conspicuous traits that signal an individuals species, sex, and breeding status reduce the challenge of identifying a compatible conspecific mate, and should be more common in migratory rather than sedentary species, species with shorter breeding seasons, and species breeding under high sympatry with many closely-related heterospecifics. Here, we tested this recognition hypothesis for promoting plumage sexual dichromatism in the true thrushes (Turdus spp.), a large and diverse genus of passerine birds. We used receptor-noise limited models of avian vision to quantify avian-perceived chromatic and achromatic visual contrasts between male and female plumage patches and tested the influence of breeding season length, spatial distribution, and sympatry with other Turdus species on plumage dichromatism. As predicted, we found that 1) true thrush species with migratory behaviour have greater plumage sexual dichromatism than non-migratory species, 2) species with longer breeding seasons have less plumage sexual dichromatism, and 3) greater numbers of Turdus thrush species breeding in sympatry is associated with more plumage sexual dichromatism. These results suggest that social recognition systems, including species and mate recognition, play a prominent role in the evolution of plumage sexual dichromatism in true thrushes.