title: Strain and crack propagation of HIV-1 capsids during uncoating

abstract:
Viral replication in HIV-1 relies on a fullerene-shaped capsid to transport genetic material deep into the nucleus of an infected cell. Capsid stability is linked to the presence of cofactors, including inositol hexakisphosphate (IP6) that bind to pores found in the capsid. Using extensive all-atom molecular dynamics simulations of HIV-1 cores imaged from cryo-electron tomography (cryo-ET) in intact virions, which contain IP6 and a ribonucleoprotein complex, we find markedly striated patterns of strain on capsid lattices. The presence of these cofactors also increases rigidity of the capsid. Conformational analysis of capsid (CA) proteins show CA accommodates strain by locally flexing away from structures resolved using x-ray crystallography and cryo-electron microscopy. Then, cryo-ET of HIV-1 cores undergoing endogenous reverse transcription demonstrate that lattice strain increases in the capsid prior to mechanical failure and that the capsid ruptures by crack propagation along regions of high strain. These results uncover HIV-1 capsid properties involved in their critical disassembly process.

Significance statementThe mature capsids of HIV-1 are transiently stable complexes that self-assemble around the viral genome during maturation, and uncoat to release preintegration complexes that archive a double-stranded DNA copy of the virus in the host cell genome. However, a detailed view of how HIV cores rupture remains lacking. Here, we elucidate the physical properties involved in capsid rupture using a combination of large-scale all-atom molecular dynamics simulations and cryo-electron tomography. We find that intrinsic strain on the capsid forms highly correlated patterns along the capsid surface, along which cracks propagate. Capsid rigidity also increases with high strain. Our findings provide fundamental insight into viral capsid uncoating.


title: Strain and rupture of HIV-1 capsids during uncoating

category: biophysics


title: TRICLOSAN IS A KCNQ3 POTASSIUM CHANNEL ACTIVATOR

abstract: KCNQ channels participate in the physiology of several cell types. In neurons of the central nervous system, the primary subunits are KCNQ2, 3 and 5. Activation of these channels silence the neurons, limiting action potential duration and preventing high-frequency action potential burst. Mutation of the KCNQ genes are associated with a wide spectrum of phenotypes characterized by hyperexcitability. Activation of KCNQ channels is an attractive strategy to treat epilepsy and other hyperexcitability conditions as are the evolution of stroke and traumatic brain injury. In this work we show that triclosan, a bactericide widely used in personal care products, activates the KCNQ3 channels but not the KCNQ2. Triclosan induces a voltage shift in the activation, increases the conductance and slows the closing of the channel. The effect is independent of PIP2. The putative binding site is located in the pore region but is distinct from the binding site for retigabine. Our results indicate that triclosan is a new activator for KCNQ channels.


title: The inflammatory accumulation of lipids and ROS in human Nrf1α-deficient hepatoma cells is ameliorated by 2-bromopalmitate

abstract: Since Nrf1 and Nrf2 are essential for regulating the lipid metabolism pathways, their dysregulation was also shown to be critically involved in the non-controllable inflammatory pathology into cancer development. However, it is unknown that the interaction between Nrf1 and Nrf2 in the regulation of lipid metabolism, especially in hepatoma cells. Here, we have further explored the molecular mechanisms underlying their distinct regulation of lipid metabolism, by comparative analysis of changes in those lipid metabolism-related genes in Nrf1-/- and/or Nrf2-/- cell lines relative to wild-type controls. The results revealed that loss of Nrf1 leads to disordered lipid metabolism; its lipid synthesis pathway was up-regulated by JNK-Nrf2-AP1 signaling, while its lipid decomposition pathway was down-regulated by the nuclear receptor PPAR-PGC1 signaling, resulting in severe accumulation of lipids as deposited in lipid droplets. By contrast, knockout of Nrf2 gave rise to decreases in lipid synthesis and uptake capacity. These demonstrate that Nrf1 and Nrf2 contribute to significant differences in the cellular lipid metabolism regulatory profiles and relevant pathological responses. Further experiments unraveled that lipid deposition in Nrf1-/- cells was resulted from CD36 upregulation by activating the PI3K-AKT-mTOR pathway, leading to induction of the inflammatory response. Following treatment of Nrf1-/- cells with 2-bromopaImitate (2BP), it enabled the yield of lipid droplets to be strikingly alleviated, as companied by substantial abolishment of CD36 and critical inflammatory cytokines. Such Nrf1-/--led inflammatory accumulation of lipids and ROS was significantly ameliorated by 2BP. Overall, this study provides a potential strategy for cancer prevention and treatment by precision targeting of Nrf1, Nrf2, or both.

category: cancer biology


title: A phylogenetic and transcriptomic study of the β-1,3-glucanase family in tomato identifies candidate targets for fruit improvement

abstract: Tomato, Solanum lycopersicum, is one of the most cultivated fruits. However, between one-quarter and half of their production is lost during transport and storage. Modifications in cell walls, and specifically pectin composition, delay fruit softening but, so far, the impact of callose metabolism in this process has not been investigated. Callose accumulates in cell walls around plasmodesmata to modify symplasmic transport. It also plays a role in reinforcing cell walls in response to bruising or pathogen invasion. The aim of this work is to identify cell wall {beta}-1,3-glucanases expressed in tomato fruit that can be used as targets to modify callose accumulation during ripening. A phylogenetic analysis identified fifty candidate {beta} -1,3-glucanases in tomato distributed in three clusters (, {beta} and {gamma}) with evolutionary relations previously characterised in the model Arabidopsis thaliana. Analysis of tomato microarray data indicates different regulatory patterns: the expression of a subset of enzymes in cluster  decreased during ripening, while enzymes in cluster {beta} and {gamma} displayed higher expression in white-red stages. qRT-PCR experiments confirm the differential regulation of enzymes in different clusters suggesting evolutionary divergences that correlate with differences in their predicted localization and function. The potential to exploit this information in the selection of targets to modify cell walls and fruit development is discussed.

category: plant biology


title: In vivo production of pederin by labrenzin pathway expansion

abstract: Pederin is a potent polyketide toxin that causes severe skin lesions in humans after contact with insects of genus Paederus. Due to its potent anticancer activities, pederin family compounds have raised the interest of pharmaceutical industry. Despite extensive studies on the cluster of biosynthetic genes responsible for the production of pederin, it has not yet been possible to isolate and cultivate its bacterial endosymbiont producer. However, the marine bacterium Labrenzia sp. PHM005 was recently reported to produce labrenzin, the closest pederin analog. By cloning a synthetic pedO gene encoding one of the three O-methyltraferase of the pederin cluster into Labrenzia sp. PHM005 we have been able to produce pederin for the first time by fermentation in the new recombinant strain.

category: molecular biology


title: Single-cell RNA-seq analysis reveals aberrant CSF1 expression in disease-causing synovial fibroblasts of pigmented villonodular synovitis

abstract:
ObjectivesAlthough the role of the CSF1/CSF1R axis in pigmented villonodular synovitis (PVNS) has been confirmed, the cells that express CSF1 and CSF1R and the underlying mechanism remain unclear. Single-cell RNA sequencing (scRNA-seq) of PVNS obtained through biopsies depicted the cellular diversity of PVNS, revealed specific CSF1/CSF1R-expressing cells and further identified novel gene expression that is associated with the development of PVNS.

MethodsscRNA-seq was performed on tissues obtained from the 6 biopsies of 3 patients with PVNS. Flow cytometry, immunofluorescence and western blot validated the transcriptional results, while co-culture systems revealed the cross talk between fibroblasts and macrophages.

Results8 subsets of fibroblasts and 5 subsets of macrophages were identified from the synovium of patients with PVNS and were found to be related to distinct signaling pathways. The cellular components of localized and diffuse PVNS are overall similar. Moreover, the synovium and nodule of PVNS share similar composition. The specific cells expressing CSF1/CSF1R were also identified. Other than that, unique CXCL12+CSF1+ fibroblasts were revealed to attract macrophages as disease-causing synovial fibroblasts, leading to the formation of masses in PVNS.

ConclusionsPVNS consists of macrophages, fibroblasts, T cells, endothelial cells and mast cells. Among them, the CSF1-expressing fibroblasts appeared to be tumor-like cells that attract macrophages, subsequently forming tumor-like mass in PVNS. This paves the path for novel treatments of PVNS by targeting CXCL12+CSF1+ fibroblasts and the CXCL12-CXCR4 axis.


title: Fast enzymatic HCO3- dehydration supports photosynthetic water oxidation in Photosystem II from pea

abstract: Carbonic anhydrase (CA) activity, associated with Photosystem II (PSII) from Pisum sativum, has been shown to enhance water oxidation. But, the nature of the CA activity, its origin and role in photochemistry has been under debate, since the rates of CA reactions, measured earlier, were less than the rates of photochemical reactions. Here, we demonstrate high CA activity in PSII from Pisum sativum, measured by HCO3- dehydration at pH 6.5 (i.e. under optimal condition for PSII photochemistry), with kinetic parameters Km of 2.7 mM; Vmax of 2.74{middle dot}10-2 mM{middle dot}sec-1; kcat of 1.16{middle dot}103 sec-1 and kcat/Km of 4.1{middle dot}105 M-1 sec-1, showing the enzymatic nature of this activity, which kcat exceeds by [~]13 times the rate of PSII, as measured by O2 evolution. The similar dependence of HCO3- dehydration, of the maximal quantum yield of photochemical reactions and of O2 evolution on the ratio of chlorophyll/photochemical reaction center II demonstrate the interconnection of these processes on the electron donor side of PSII. Since the removal of protons is critical for fast water oxidation, and since HCO3- dehydration consumes a proton, we suggest that CA activity, catalyzing very fast removal of protons, supports efficient water oxidation in PSII and, thus, photosynthesis in general.

category: biochemistry


title: DnaK response to expression of protein mutants is dependent on translation rate and stability

abstract: Chaperones play a central part in the quality control system in cells by clearing misfolded and aggregated proteins. The chaperone DnaK acts as a sensor for molecular stress by recognising short hydrophobic stretches of misfolded proteins. As the level of unfolded protein is a function of protein stability, we hypothesised that the level of DnaK response upon overexpression of recombinant proteins would be correlated to stability. Using a set of mutants of the{lambda} -repressor with varying thermal stabilities and a fluorescent reporter system, the effect of stability on DnaK response and protein abundance was investigated. Our results demonstrate that the initial DnaK response is largely dependent on protein synthesis rate but as the recombinantly expressed protein accumulates and homeostasis is approached the response correlates strongly with stability. Furthermore, we observe a large degree of cell-cell variation in protein abundance and DnaK response in more stable proteins.


title: SPF: A Spatial and Functional Data Analytic Approach to cell Imaging data

abstract: The tumor microenvironment (TME), which characterizes the tumor and its surroundings, plays a critical role in understanding cancer development and progression. Recent advances in imaging techniques enable researchers to study spatial structure of the TME at a single-cell level. Investigating spatial patterns and interactions of cell subtypes within the TME provides useful insights into how cells with different biological purposes behave, which may consequentially impact a subjects clinical outcomes. We utilize a class of well-known spatial summary statistics, the K-function and its variants, to explore inter-cell dependence as a function of distances between cells. Using techniques from functional data analysis, we introduce an approach to model the association between these summary spatial functions and subject-level outcomes, while controlling for other clinical scalar predictors such as age and disease stage. In particular, we leverage the additive functional Cox regression model (AFCM) to study the nonlinear impact of spatial interaction between tumor and stromal cells on overall survival in patients with non-small cell lung cancer, using multiplex immunohistochemistry (mIHC) data. The applicability of our approach is further validated using a publicly available Multiplexed Ion beam Imaging (MIBI) triple-negative breast cancer dataset.

category: bioinformatics


title: MotifBoost: k-mer based data-efficient immune repertoire classification method

abstract: The repertoire of T cell receptors encodes various types of immunological information. Machine learning is indispensable for decoding such information from repertoire datasets measured by next-generation sequencing. In particular, the classification of repertoires is the most basic task, which is relevant for a variety of scientific and clinical problems. Supported by the recent appearance of large datasets, efficient but data-expensive methods have been proposed. However, it is unclear whether they can work efficiently when the available sample size is severely restricted as in practical situations. In this study, we demonstrate that the their performances are impaired catastrophically below critical sample sizes. To overcome this, we propose MotifBoost, which exploits the information of short motifs of TCRs. MotifBoost can perform the classification as efficiently as a deep learning method on large datasets while providing more stable and reliable results on small datasets. We also clarify that the robustness of MotifBoost can be attributed to the efficiency of motifs as representation features of repertoires. Finally, by comparing predictions of these methods, we show that the whole sequence identity and sequence motifs encode partially different information and that a combination of such complementary information is necessary for further development of repertoire analysis.


title: Comparative Pathogenesis of Different Phylogroup I Bat Lyssaviruses in a Standardized Mouse Model

abstract:
A plethora of bat-associated lyssaviruses potentially capable of causing the fatal disease rabies are known today. Transmitted via infectious saliva, occasionally-reported spillover infections from bats to other mammals demonstrate the permeability of the species-barrier and highlight the zoonotic potential of bat-related lyssaviruses. However, it is still unknown whether and, if so, to what extent, viruses from different lyssavirus species vary in their pathogenic potential. In order to characterize and systematically compare a broader group of lyssavirus isolates for their viral replication kinetics, pathogenicity, and virus release through saliva-associated virus shedding, we used a mouse infection model comprising a low (102 TCID50) and a high (105 TCID50) inoculation dose as well as three different inoculation routes (intramuscular, intranasal, intracranial). Clinical sings, incubation periods, and survival were investigated. Based on the latter two parameters, a novel pathogenicity matrix was introduced to classify lyssavirus isolates. Using a total of 13 isolates from ten different virus species, this pathogenicity index varied within and between virus species. Interestingly, Irkut virus (IRKV) and Bokeloh bat lyssavirus (BBLV) obtained higher pathogenicity scores (1.14 for IRKV and 1.06 for BBLV) compared to Rabies virus (RABV) isolates ranging between 0.19 and 0.85. Also, clinical signs differed significantly between RABV and other bat lyssaviruses. Altogether, our findings suggest a high diversity among lyssavirus isolates concerning survival, incubation period, and clinical signs. Virus shedding significantly differed between RABVs and other lyssaviruses. Our results demonstrated that active shedding of infectious virus was exclusively associated with two RABV isolates only (92 % for RABV-DogA and 67 % for RABV-Insectbat), thus providing a potential explanation as to why sustained spillovers are solely attributed to RABVs. Interestingly, high-resolution imaging of a selected panel of brain samples from bat-associated lyssaviruses demonstrated a significantly increased percentage of infected astrocytes in mice inoculated with IRKV (10.03 %; SD{+/-}7.39) compared to RABV-Vampbat (2.23 %; SD{+/-}2.4), and BBLV (0.78 %; SD{+/-}1.51), while only individual infected cells were identified in mice infected with Duvenhage virus (DUVV). These results corroborate previous studies on RABV that suggest a role of astrocyte infection in the pathogenicity of lyssaviruses.

Author SummaryGlobally, there are at present 17 different officially recognized lyssavirus species posing a potential threat for human and animal health. Bats have been identified as carriers for the vast majority of those zoonotic viruses, which cause the fatal disease rabies and are transmitted through infectious saliva. The occurrence of sporadic spillover events where lyssaviruses are spread from bats to other mammalian species highlights the importance of studying pathogenicity and virus shedding in regard to a potentially sustained onward cross-species transmission. Therefore, as part of this study, we compared 13 different isolates from ten lyssavirus species in a standardized mouse infection model, focusing on clinical signs, incubation periods, and survival. Based on the latter two, a novel pathogenicity index to classify different lyssavirus species was established. This pathogenicity index varied within and between different lyssavirus species and revealed a higher ranking of other bat-related lyssaviruses in comparison to the tested Rabies virus (RABV) isolates. Altogether, our results demonstrate a high diversity among the investigated isolates concerning pathogenicity and clinical picture. Furthermore, we comparatively analyzed virus shedding via saliva and while there was no indication towards a reduced pathogenicity of bat-associated lyssaviruses as opposed to RABV, shedding was increased in RABV isolates. Additionally, we investigated neuronal cell tropism and revealed that bat lyssaviruses are not only capable of infecting neurons but also astrocytes.

category: pathology


title: The kinesin KIF4 mediates HBV/HDV entry through regulation of surface NTCP localization and can be targeted by RXR agonists in vitro.

abstract:
Intracellular transport via microtubule-based dynein and kinesin family motors plays a key role in viral reproduction and transmission. We show here that Kinesin Family Member 4 (KIF4) plays an important role in HBV/HDV infection. We intended to explore host factors impacting the HBV life cycle that can be therapeutically addressed using siRNA library transfection and HBV/NLuc (HBV/NL) reporter virus infection in HepG2-hNTCP C4 cells. KIF4 silencing resulted in a 3-fold reduction in luciferase activity following HBV/NL infection and suppressed both wild-type HBV and HDV infection. Transient KIF4 depletion reduced surface and raised intracellular NTCP (HBV/HDV entry receptor) levels, according to both cellular fractionation and immunofluorescence analysis (IF). Overexpression of wild-type KIF4 but not ATPase-null KIF4 regains the surface localization of NTCP in these cells. Furthermore, immunofluorescence (IF) revealed KIF4 and NTCP colocalization across microtubule filaments, and a co-immunoprecipitation study showed that KIF4 physically binds to NTCP. KIF4 expression is regulated by FOXM1. Interestingly, we discovered that RXR agonists (Bexarotene, and Alitretinoin) down-regulated KIF4 expression via FOXM1-mediated suppression, resulting in a substantial decrease in HBV-Pre-S1 protein attachment to HepG2-hNTCP cell surface and subsequent suppression of HBV infection in HepG2-hNTCP and primary human hepatocytes (PXB) (Bexarotene, IC50 1.89 {+/-} 0.98 M). Overall, our findings show that human KIF4 is a critical regulator of NTCP surface transport and localization, which is required for NTCP to function as a receptor for HBV/HDV entry. Furthermore, small molecules that suppress or alleviate KIF4 expression would be potential antiviral candidates that target HBV and HDV entry phases.

Author SummaryUnderstanding HBV/HDV entry machinery and the mechanism by which NTCP (HBV/HDV entry receptor) surface expression is regulated is crucial to develop antiviral entry inhibitors. We found that NTCP surface transport is mainly controlled by the motor kinesin KIF4. Surprisingly, KIF4 was negatively regulated by RXR receptors through FOXM1-mediated suppression

This study not only mechanistically correlated the role of RXR receptors in regulating HBV/HDV entry but also suggested a novel approach to develop therapeutic rexinoids for preventing HBV and/or HDV infections in important clinical situations, such as in patients undergoing liver transplantation or those who are at a high risk of HBV infection and unresponsive to HBV vaccination.

category: microbiology


title: Identification of fetal liver stromal subsets in spectral cytometry using the parameter autofluorescence

abstract:
The fetal liver is the main hematopoietic organ during embryonic development. The fetal liver is also the unique anatomical site where hematopoietic stem cells expand before colonizing the bone marrow, where they ensure life-long blood cell production and become mostly resting. The identification of the different cell types that comprise the hematopoietic stroma in the fetal liver is essential to understand the signals required for the expansion and differentiation of the hematopoietic stem cells. We used a panel of monoclonal antibodies to identify fetal liver stromal cells in a 5-laser equipped spectral flow cytometry analyzer. The "Autofluorescence Finder" of SONY ID7000 software identified two distinct autofluorescence emission spectra. Using autofluorescence as a fluorescence parameter we could assign the two autofluorescent signals to three distinct cell types and identified surface markers that characterize these populations. We found that one autofluorescent population corresponds to hepatoblasts and cholangiocytes whereas the other expresses mesenchymal transcripts and was identified as stellate cells. Importantly, after birth, autofluorescence becomes the unique identifying property of hepatoblasts because mature cholangiocytes are no longer autofluorescent.

These results show that autofluorescence used as a parameter in spectral flow cytometry is a useful tool to identify new cell subsets that are difficult to analyze in conventional flow cytometry.

category: developmental biology


title: Coral assemblages at higher latitudes favour short-term potential over long-term performance

abstract: The current exposure of species assemblages to high environmental variability may grant them resilience to future increases in climatic variability. In globally threatened coral reef ecosystems, management seeks to protect resilient reefs within variable environments. Yet, our lack of understanding for the determinants of coral population performance within variable environments hinders forecasting the future reassembly of coral communities. Here, using Integral Projection Models, we compare the short- (i.e., transient) and long-term (i.e., asymptotic) demographic characteristics of tropical and subtropical coral assemblages to evaluate how thermal variability influences the structural composition of coral communities over time. Exploring spatial variation across the dynamics of functionally different competitive, stress-tolerant, and weedy coral assemblages in Australia and Japan, we show that coral assemblages trade-off long-term performance for transient potential in response to thermal variability. We illustrate how coral assemblages can reduce their susceptibility towards environmental variation by exploiting volatile short-term demographic strategies, thus enhancing their persistence within variable environments. However, we also reveal considerable variation across the vulnerability of competitive, stress-tolerant, and weedy coral assemblages towards future increases in thermal variability. In particular, stress-tolerant and weedy corals possess an enhanced capacity for elevating their transient potential in response to environmental variability. Accordingly, despite their current exposure to high thermal variability, future climatic shifts threaten the structural complexity of coral assemblages, derived mostly from competitive coral taxa within highly variable subtropical environments, emulating the degradation expected across global coral communities.

category: ecology


title: Understanding the relationship between dispersal and range size

abstract: Understanding what drives the vast variability in species range size is still an outstanding question. Among the several processes potentially affecting species ranges, dispersal is one of the most prominent hypothesized predictors. However, the theoretical expectation of a positive dispersal-range size relationship has received mixed empirical support. Here, we synthesized results from 84 studies to investigate in which context dispersal is most important in driving species range size. We found that dispersal traits - proxies for dispersal ability - explain range sizes more often in temperate and subtropical regions than in tropical regions, when considering multiple components of dispersal, and when investigating a large number of species to capture dispersal and range size variation. In plants, positive effects of dispersal on range size were less often detected when examining broad taxonomic levels. In animals, dispersal is more important for range size increase in ectotherms than in endotherms. Our synthesis emphasizes the importance of considering different aspects of the dispersal process -departure, transfer, settlement-, niche aspects and evolutionary components, like time for range expansion and past geological-environmental dynamics. We therefore call for a more integrative view of the dispersal process and its causal relationship with range size.


title: Emerging mosquito resistance to piperonyl butoxide-synergized pyrethroid insecticide and its mechanism

abstract:
Piperonyl butoxide (PBO)-synergized pyrethroid products are widely available for the control of pyrethroid-resistant mosquitoes. To date, no study has formally examined mosquito resistance to PBO-synergized insecticides. We used Culex quinquefasciatus as a model mosquito examined the insecticide resistance mechanisms of mosquitoes to PBO-synergized pyrethroid using modified World Health Organization tube bioassays and biochemical analysis of metabolic enzyme expressions prior- and post-PBO exposure. We measured mosquito mortalities and metabolic enzyme expressions in mosquitoes with/without pre-exposure to different PBO concentrations and exposure durations. We found that field Culex quinquefasciatus mosquitoes were resistant to all insecticides tested, including PBO-synergized pyrethroids (mortality ranged from 3.7{+/-}4.7% to 66.7{+/-}7.7%), except malathion. Field mosquitoes had elevated levels of carboxylesterase (COE, 3.8-fold) and monooxygenase (P450, 2.1-fold) but not glutathione S-transferase (GST) compared to susceptible mosquitoes. When the field mosquitoes were pre-exposed to 4% PBO, the 50% lethal concentration of deltamethrin was reduced from 0.22% to 0.10%, compare to 0.02% for susceptible mosquitoes. Knockdown resistance gene mutation (L1014F) rate was 62% in field mosquitoes. PBO pre-exposure suppressed P450 enzyme expression levels by 25[~]34%, GST by 11%, and had no impact on COE enzyme expression. Even with the optimal PBO concentration and exposure duration, field mosquitoes had significantly higher P450 enzyme expression levels after PBO exposure compared to laboratory controls. These results demonstrate that PBO alone may not be enough to control highly pyrethroid resistant mosquitoes due to the multiple resistance mechanisms. Mosquito resistance to PBO-synergized insecticide should be closely monitored.

Authors SummaryMosquitoes are vectors of many major infectious diseases globally. Insecticides and related products are widely used for mosquito controls and disease preventions. Over time and following repeated use, mosquitoes (including Aedes, Anopheles and Culex) have developed very high resistance to multiple insecticides all over the world. Target site insensitivity due to mutations in the voltage-gated sodium channel gene and overproduction of metabolic detoxification enzymes such as cytochrome P450 (CYP) monooxygenases play critical role in insecticide resistance in mosquitoes. To enhance the killing power of insecticides, synergized insecticides were developed by mixing insecticide synergists with pyrethroids. Discovered in the 1940s, piperonyl butoxide (PBO) is one of the earliest and most commonly used insecticide synergists. Field application of PBO-synergized insecticides performed far better than mono-pyrethroids. PBO-treated long-lasting insecticidal nets (PBO-LLINs), which also use pyrethroids, outperformed regular LLIN for malaria control in many African countries. PBO-LLIN is soon to be rolled out on a large scale for malaria control in Africa. One important question regarding the use of synergized insecticides is whether they will select for vector population resistance to synergized insecticide products, in other words, are PBO-synergized pyrethroids effective against highly insecticide-resistant mosquitoes? To date, no study has formally examined mosquito resistance to PBO-synergized insecticides. Here, we used Culex quinquefasciatus as a model mosquito, we examined its resistance status to different insecticides including PBO-synergized pyrethrins and tested how PBO exposure affect mosquito mortality and the expressions of metabolic enzymes. We found that field Culex quinquefasciatus mosquitoes were resistant to multiple insecticides tested, including PBO-synergized pyrethroids. Field mosquitoes had elevated levels of carboxylesterase (COE) and monooxygenase (P450) but not glutathione S-transferase (GST) enzyme expressions compared to susceptible mosquitoes. Even with optimal PBO concentration and exposure duration, field mosquitoes had significantly higher P450 enzyme expression levels after PBO exposure compared to laboratory controls, and PBO exposure had no impact on COE enzyme expressions. The phenomena of the insecticide-resistant mosquitoes insensitivity to PBO exposure or PBO-synergized insecticides and multiple-resistance mechanisms have also been reported from Aedes and Anopheles mosquitoes in different countries. These results demonstrate that PBO alone is not enough to control highly pyrethroid resistant mosquitoes due to multiple resistance mechanisms. Mosquito resistance to PBO-synergized insecticide should be closely monitored


title: SHAPR - An AI approach to predict 3D cell shapes from 2D microscopic images

abstract: Reconstruction of shapes, forms, and sizes of three-dimensional (3D) objects from two-dimensional (2D) information is one of the most complex functions of the human brain. It also poses an algorithmic challenge and at present is a widely studied subject in computer vision. We here focus on the single cell level and present a neural network-based SHApe PRediction autoencoder SHAPR that accurately reconstructs 3D cellular and nuclear shapes from 2D microscopic images and may have great potential for application in the biomedical sciences.


title: Ex Vivo and In Vivo CD46 Receptor Utilization by Species D Human Adenovirus Serotype 26 (HAdV26)

abstract:
Human adenovirus serotype 26 (Ad26) is used as a gene-based vaccine against SARS-CoV-2 and HIV-1. Yet, its primary receptor portfolio remains controversial, potentially including sialic acid, CAR, integrins, and CD46. We and others have shown that Ad26 can use CD46, but these observations were questioned by the inability to co-crystallize Ad26 fiber with CD46. Recent work demonstrated that Ad26 binds CD46 with its hexon protein rather than its fiber. We examined the functional consequences of Ad26 for infection in vitro and in vivo. Ectopic expression of human CD46 on Chinese hamster ovary cells increased Ad26 infection significantly. Deletion of the complement control protein domains CCP1 or CCP2 or the serine-threonine-proline (STP) region of CD46 reduced infection. Comparing wild type and sialic acid-deficient CHO cells, we show that the usage of CD46 is independent of its sialylation status. Ad26 transduction was increased in CD46 transgenic mice after intramuscular (IM) injection, but not after intranasal (IN) administration. Ad26 transduction was 10-fold lower than Ad5 after intratumoral (IT) injection of CD46-expressing tumors. Ad26 transduction of liver was 1000-fold lower than Ad5 after intravenous (IV) injection. These data demonstrate the use of CD46 by Ad26 under certain situations, but also show that the receptor has little consequence by other routes of administration. Finally, IV injection of high doses of Ad26 into CD46 mice induced release of liver enzymes in the bloodstream and reduced white blood cell counts, but did not induce thrombocytopenia. This suggests that Ad26 virions do not induce direct clotting side effects seen during COVID-19 vaccination with this serotype of adenovirus.

IMPORTANCEHuman species D Ad26 is being pursued as a low seroprevalence vector for oncolytic virotherapy and gene-based vaccination against HIV-1 and SARS-CoV-2. However, there is debate in the literature about its tropism and receptor utilization, which directly influence its efficiency for certain applications. This work was aimed at determining which receptor(s) this virus uses for infection, and its role in virus biology, vaccine efficacy, and importantly, in vaccine safety.

category: pharmacology and toxicology


title: Towards integration of time-resolved confocal microscopy of a 3D in vitro microfluidic platform with a hybrid multiscale model of tumor angiogenesis

abstract: The goal of this study is to calibrate a multiscale model of tumor angiogenesis with time-resolved data to allow for systematic testing of mathematical predictions of vascular sprouting. The multi-scale model consists of an agent-based description of tumor and endothelial cell dynamics coupled to a continuum model of vascular endothelial growth factor concentration. First, we calibrate ordinary differential equation models to time-resolved protein expression data to estimate the rates of secretion and consumption of vascular endothelial growth factor by endothelial and tumor cells, respectively. These parameters are then input into the multiscale tumor angiogenesis model, and the remaining model parameters are then calibrated to time resolved confocal microscopy images obtained within a 3D vascularized microfluidic platform. The microfluidic platform mimics a functional blood vessel with a surrounding collagen matrix seeded with inflammatory breast cancer cells, which induce tumor angiogenesis. Once the multi-scale model is fully parameterized, we forecast the spatiotemporal distribution of vascular sprouts at future time points and directly compare the predictions to experimentally measured data. We assess the ability of our model to globally recapitulate angiogenic vasculature density, resulting in an average relative calibration error of 17.7% {+/-} 6.3% and an average prediction error of 20.2% {+/-} 4% and 21.7% {+/-} 3.6% using one and four calibrated parameters, respectively. We then assess the models ability to predict local vessel morphology (individualized vessel structure as opposed to global vascular density), initialized with the first time point and calibrated with two intermediate time points. To the best of our knowledge, this represents the first study to integrate well-controlled, experimental data into a mechanism-based, multiscale, mathematical model of angiogenic sprouting to make specific, testable predictions.

category: systems biology


title: A preclinical randomized multicenter trial of anti-IL-17A treatment for acute ischemic stroke

abstract: Multiple consensus statements have called for preclinical randomized controlled trials (pRCT) to improve translation in stroke research. Here, we investigated the efficacy of IL-17A neutralizing antibodies in a multicentric pRCT using a murine stroke model. C57/Bl.6 mice were subjected to transient middle cerebral artery occlusion (tMCAO). Mice were randomly allocated (1:1). Either anti-IL-17A (500 {micro}g) or isotype antibody (500 {micro}g) were administered 1 h after tMCAO. Primary analysis of infarct volumes was done by MRI after three days. Secondary analysis included mortality, neurological score, neutrophil infiltration and the impact of the gut microbiome on treatment effects. Out of 136 mice, 109 mice were included in the analysis. Mixed model analysis revealed that the IL-17A neutralization significantly reduced infarct sizes (anti IL-17A: 61.77 {+/-} 31.04 mm3; IgG control: 75.66 {+/-} 34.79 mm3; p=0.01). Secondary outcome measures showed a decrease in mortality (Hazard Ratio=3.43, 95% CI = 1.157 - 10.18; p=0.04) and neutrophil invasion into ischemic cortices. There was no difference in the neurological score. The analysis of the gut microbiome showed significant differences between centers. Taken together, this is the first positive pRCT in an ischemia reperfusion model. It suggests IL-17A neutralization as a potential target in stroke.

category: neuroscience


title: Non-parametric Functional Muscle Network as a Robust Biomarker of Fatigue

abstract: The possibility of muscle fatigue detection using surface electromyography has been explored and multiple biomarkers, such as median frequency, have been suggested. However, there are contradictory reports in the literature which results in an inconsistent understanding of the biomarkers of fatigue. Thus, there is an unmet need for a statistically robust sEMG-based biomarker for fatigue detection. This paper, for the first time, demonstrates the superior capability of a non-parametric muscle network to reliably detect fatigue-related changes. Seven healthy volunteers completed a lower limb exercise protocol, which consisted of 30s of a sit-to-stand exercise before and after the completion of fatiguing leg press sets. A non-parametric muscle network was constructed, using Spearmans power correlation and showed a very reliable decrease in network metrics associated with fatigue (degree, weighted clustering coefficient (WCC)). The network metrics displayed a significant decrease at the group level (degree, WCC: p < 0.001), individual subject level (degree: p < 0.035 WCC: p < 0.004) and particular muscle level (degree: p < 0.017). Regarding the decrease in mean degree connectivity at particular muscles, all seven subjects followed the group trend. In contrast to the robust results achieved by the proposed non-parametric muscle network, classical spectrotemporal measurements showed heterogeneous trends at the particular muscle and individual subject levels. Thus, this paper for the first time shows that non-parametric muscle network is a reliable biomarker of fatigue and could be used in a broad range of applications.


title: Modeling spatial, developmental, physiological, and topological constraints on human brain connectivity

abstract: The complex connectivity of nervous systems is thought to have been shaped by competitive selection pressures to minimize wiring costs and support adaptive function. Accordingly, recent modeling work indicates that stochastic processes, shaped by putative trade-offs between the cost and value of each connection, can successfully reproduce many topological properties of macroscale human connectomes measured with diffusion magnetic resonance imaging. Here, we derive a new formalism with the aim to more accurately capture the competing pressures of wiring cost minimization and topological complexity. We further show that model performance can be improved by accounting for developmental changes in brain geometry and associated wiring costs, and by using inter-regional transcriptional or microstructural similarity rather than topological wiring-rules. However, all models struggled to capture topologies spatial embedding. Our findings highlight an important role for genetics in shaping macroscale brain connectivity and indicate that stochastic models offer an incomplete account of connectome organization.


title: Disrupted dynamic network reconfiguration of the executive and reward networks in internet gaming disorder: Why IGD subjects cannot control their gaming cravings

abstract:
BackgroundStudies have shown that people with internet gaming disorder (IGD) show impaired executive control over their gaming cravings; however, the neural mechanisms underlying this process remain unknown. In addition, these conclusions were based on the hypothesis that brain networks were temporally stationary and neglected changes in cognitive processes.

MethodsResting-state fMRI data were collected from 402 subjects (162 subjects with IGD and 240 recreational game users (RGUs)). The community structure (recruitment and integration) of the executive control network and the basal ganglia network (BGN, representing the reward network) of patients with IGD and healthy controls were analyzed and compared. Mediation effects were analyzed among the different networks.

ResultsWhen compared to RGUs, subjects with IGD had a lower recruitment coefficient within the right executive control network (ECN). Further analysis showed that only male subjects had a lower recruitment coefficient. Mediation analysis showed that the integration coefficient of the right ECN mediated the relationship between the recruitment coefficients of both the right ECN and the BGN in RGUs.

ConclusionsSubjects with IGD had a lower recruitment coefficient than RGUs, and this feature was only observed in male subjects, making them less efficient at impulse control. The meditation results suggest a top-down control mechanism of the ECN is missing in subjects with IGD. All of these findings could explain why subjects with IGD have impaired executive control over their gaming cravings.


title: Differential effects of intra-modal and cross-modal reward value on visual perception: ERP evidence

abstract: Stimuli associated with high reward modulate perception and such value-driven effects have been shown to originate from the modulation of the earliest stages of sensory processing in the brain. In natural environments objects comprise multiple features (imagine a rolling soccer ball, with its black and white patches and the swishing sound made during its motion), where each feature may signal different associations with previously encountered rewards. How perception of such an object is affected by the value associations of its constituent parts is unknown. The present study compares intra- and cross-modal value-driven effects on behavioral and electrophysiological correlates of visual perception. Human participants first learned the reward associations of visual and auditory cues. Subsequently, they performed a visual orientation discrimination task in the presence of previously rewarded visual or auditory cues (intra- and cross-modal cues, respectively) that were concurrently presented with the target stimulus. During the conditioning phase, when reward associations were learned and reward cues were the target of the task, reward value of both modalities enhanced the electrophysiological correlates of sensory processing in visual cortex. During the post-conditioning phase, when reward delivery was halted and previously rewarded stimuli were task-irrelevant, cross-modal value-enhanced behavioral measures of visual sensitivity whereas intra-modal value led to a trend for suppression. A similar pattern of modulations was found in the simultaneously recorded event-related potentials (ERPs) of posterior electrodes. We found an early (90-120 ms) suppression of ERPs evoked by high-value, intra-modal stimuli. Cross-modal cues led to a later value-driven modulation, with an enhancement of response positivity for high-compared to low-value stimuli starting at the N1 window (180-250 ms) and extending to the P3 (300-600 ms) responses of the posterior electrodes. These results indicate that visual cortex is modulated by the reward value of visual as well as auditory cues. Previously rewarded, task-irrelevant cues from the same or different sensory modality have a different effect on visual perception, as intra-modal high-value cues may interfere with the target processing, whereas cross-modal high-value cues boost the perception of the target.


title: Higher-order olfactory neurons in the lateral horn supports odor valence and odor identity coding in Drosophila

abstract: Understanding neuronal representations of odor-evoked activities and their progressive transformation from the sensory level to higher brain centers features one of the major aims in olfactory neuroscience. Here, we investigated how odor information is transformed and represented in higher-order neurons of the lateral horn, one of the higher olfactory centers implicated in determining innate behavior, using Drosophila melanogaster. We focused on a subset of third-order glutamatergic lateral horn neurons (LHNs) and characterized their odor coding properties in relation to their presynaptic partner neurons, the projection neurons (PNs) by two-photon functional imaging. We found that odors evoke reproducible, stereotypic and odor-specific response patterns in LHNs. Notably, odor-evoked responses in these neurons are valence-specific in a way that their response amplitude is positively correlated with innate odor preferences. We postulate that this valence-specific activity is the result of integrating inputs from multiple olfactory channels through second-order neurons. GRASP and micro-lesioning experiments provide evidence that glutamatergic LHNs obtain their major excitatory input from uniglomerular PNs, while they receive an odor-specific inhibition through inhibitory multiglomerular PNs. In summary, our study indicates that odor representations in glutamatergic LHNs encode hedonic valence and odor identity and primarily retain the odor coding properties of second-order neurons.


title: The European Prevention of Alzheimer's Dementia (EPAD) MRI Dataset and Processing Workflow

abstract:
The European Prevention of Alzheimer Dementia (EPAD) is a multi-center study that aims to characterize the preclinical and prodromal stages of Alzheimers Disease. The EPAD imaging dataset includes core (3D T1w, 3D FLAIR) and advanced (ASL, diffusion MRI, and resting-state fMRI) MRI sequences.

Here, we give an overview of the semi-automatic multimodal and multisite pipeline that we developed to curate, preprocess, quality control (QC), and compute image-derived phenotypes (IDPs) from the EPAD MRI dataset. This pipeline harmonizes DICOM data structure across sites and performs standardized MRI preprocessing steps. A semi-automated MRI QC procedure was implemented to visualize and flag MRI images next to site-specific distributions of QC features -- i.e. metrics that represent image quality. The value of each of these QC features was evaluated through comparison with visual assessment and step-wise parameter selection based on logistic regression. IDPs were computed from 5 different MRI modalities and their sanity and potential clinical relevance were ascertained by assessing their relationship with biological markers of aging and dementia.

The EPAD v1500.0 data release encompassed core structural scans from 1356 participants 842 fMRI, 831 dMRI, and 858 ASL scans. From 1356 3D T1w images, we identified 17 images with poor quality and 61 with moderate quality. Five QC features -- Signal to Noise Ratio (SNR), Contrast to Noise Ratio (CNR), Coefficient of Joint Variation (CJV), Foreground-Background energy Ratio (FBER), and Image Quality Rate (IQR) -- were selected as the most informative on image quality by comparison with visual assessment. The multimodal IDPs showed greater impairment in associations with age and dementia biomarkers, demonstrating the potential of the dataset for future clinical analyses.


title: Nanoparticle Shape Governs Immunomodulation of MUC1 Antigen to Develop Anti-cancer Vaccine

abstract: T-cell-dependent immunomodulation of carbohydrate antigens under benign conditions is the most promising approach for carbohydrate-based vaccine development. However, to achieve such adaptive immune responses, well-defined multifunctional nanocarriers loaded with immunogenic materials must be explored. Current efforts to use gold nanoparticles (AuNPs) as antigen carriers in vaccine development have conveniently introduced considerable diversity. Here, we show that the shape of AuNPs markedly influences carbohydrate-based antigen processing in murine dendritic cells (mDCs) and subsequent T-cell activation. In the study, CpG-adjuvant coated sphere-, rod-, and star-shaped AuNPs were conjugated to the tripodal Tn-glycopeptide antigen to study their DC uptake and the activation of T-cells in the DCs/T-cell co-culture assay. Our results showed that sphere- and star-shaped AuNPs displayed relatively weak receptor-mediated uptake but induced a high level of T helper-1 (Th1) biasing immune responses compared with rod-shaped AuNPs, showing that receptor-mediated uptake and cytokine secretion of nanostructures are two independent mechanisms. Significantly, the shapes of AuNPs and antigen/adjuvant conjugation synergistically work together to modulate the effective anti-Tn-glycopeptide immunoglobulin (IgG) antibody response after in vivo administration of the AuNPs. These results show that by varying the shape parameter, one can alter the immunomodulation, leading to the development of carbohydrate vaccines.

category: immunology


title: Human pressures filter out the less resilient demographic strategies in natural populations of plants and animals worldwide

abstract: The exponential growth that has characterised human societies since the industrial revolution has fundamentally modified our surroundings. Examples include rapid increases in agricultural fields, now accounting for 37% of the land surface, as well as increases in urban areas, projected to triple worldwide by 2030. As such, understanding how species have adapted to and will respond to increasing human pressures is of key importance. Resilience, the ability of an ecological system to resist, recover, and even benefit from disturbances, is a key concept in this regard. Here, using a recently develop comparative demographic framework, we examine how the inherent ability of 921 natural populations of 279 plants and 45 animal species worldwide to respond to disturbances correlates with human settlement size and human activities. We develop a spatially and phylogenetically explicit model parameterised with life history traits and metrics of demographic resilience using the open-access COMPADRE and COMADRE databases, coupled with high-resolution human impact information via the Human Footprint database. We expected: (H1) species populations located nearer urban areas to have a greater ability to resist, recover, or benefit from human-related disturbances compared to pristine habitats; (H2) human effects on the responses of animal populations to disturbances to depend on the species ability for long-distance mobility; and (H3): human pressures to constrain the repertoire of life history strategies of animal and plant species via their effects on underlying vital rates and life history traits. We find that: (1) urban areas host a limited diversity of strategies that achieve demographic resilience with, on average, more resistant and faster-recovery populations located near human activities than in pristine habitats; (2) species with limited mobility tend to be more strongly affected by human activities than those with long-distance mobility; and (3) human pressures correlate with a limited set of vital rates and life history traits, including the ability to shrink, and reproduce earlier. Our results provide a tangible picture of how, having drastically transformed terrestrial landscapes, humans have shaped the ways animals and plants respond to disturbances.


title: LOTVS: a global collection of permanent vegetation plots

abstract: Analysing temporal patterns in plant communities is extremely important to quantify the extent and the consequences of ecological changes, especially considering the current biodiversity crisis. Long-term data collected through the regular sampling of permanent plots represent the most accurate resource to study ecological succession, analyse the stability of a community over time and understand the mechanisms driving vegetation change. We hereby present the LOng-Term Vegetation Sampling (LOTVS) initiative, a global collection of vegetation time-series derived from the regular monitoring of vascular plants in permanent plots. With 79 datasets from five continents and 7789 vegetation time-series monitored for at least six years and mostly on an annual basis, LOTVS possibly represents the largest collection of temporally fine-grained vegetation time-series derived from permanent plots and made accessible to the research community. As such, it has an outstanding potential to support innovative research in the fields of vegetation science, plant ecology and temporal ecology.


title: Characterization of morpho-functional traits in mesophotic corals reveals optimized light capture and photosynthesis

abstract: The morphology and skeleton architecture of photosynthetic corals modulates the light capture and functioning of the coral-algal symbiosis on shallow-water corals. Since corals can thrive on mesophotic reefs under extreme light-limited conditions, we hypothesized that microskeletal coral features optimize light capture under low-light environments. Using micro-computed tomography scanning, we conducted a comprehensive three-dimensional (3D) assessment of small-scale skeleton morphology of the depth-generalist coral Stylophora pistillata collected from shallow (5 m) and mesophotic (45 m) depths. We detected a high phenotypic diversity between depths, resulting in two distinct morphotypes, with calyx diameter, theca height, and corallite marginal spacing contributing to most of the variation between depths. To determine whether such depth-specific morphotypes affect coral light capture and photosynthesis on the corallite-scale, we developed 3D simulations of light propagation based on photosynthesis-irradiance parameters. We found that corals associated with shallow morphotypes dissipated excess light through self-shading microskeletal features; while mesophotic morphotypes facilitated enhanced light absorption and photosynthesis under low-light conditions. We conclude that the mesophotic coral architecture provides a greater ability to trap solar energy and efficiently exploit the limited light conditions, and suggest that morphological modifications play a key role in the photoadaptation response to low-light.


title: Supergene formation is associated with a major shift in genome-wide patterns of diversity in a butterfly

abstract: Selection shapes genetic diversity around target mutations, yet little is known about how selection on specific loci affects the genetic trajectories of populations, including their genome-wide patterns of diversity and demographic responses. Adaptive introgression provides a way to assess how adaptive evolution at one locus impacts whole-genome biology. Here we study the patterns of genetic variation and geographic structure in a neotropical butterfly, Heliconius numata, and its closely related allies in the so-called melpomene-silvaniform subclade. H. numata is known to have evolved a supergene via the introgression of an adaptive inversion about 2.2 million years ago, triggering a polymorphism maintained by balancing selection. This locus controls variation in wing patterns involved in mimicry associations with distinct groups of co-mimics, and butterflies show disassortative mate preferences and heterozygote advantage at this locus. We contrasted patterns of genetic diversity and structure 1) among extant polymorphic and monomorphic populations of H. numata, 2) between H. numata and its close relatives, and 3) between ancestral lineages in a phylogenetic framework. We show that H. numata populations which carry the introgressed inversions in a balanced polymorphism show markedly distinct patterns of diversity compared to all other taxa. They show the highest diversity and demographic estimates in the entire clade, as well as a remarkably low level of geographic structure and isolation by distance across the entire Amazon basin. By contrast, monomorphic populations of H. numata as well as its sister species and their ancestral lineages all show the lowest effective population sizes and genetic diversity in the clade, and higher levels of geographical structure across the continent. This suggests that the large effective population size of polymorphic populations could be a property associated with harbouring the supergene. Our results are consistent with the hypothesis that the adaptive introgression of the inversion triggered a shift from directional to balancing selection and a change in gene flow due to disassortative mating, causing a general increase in genetic diversity and the homogenisation of genomes at the continental scale.

category: evolutionary biology


title: Phenotypic plasticity, life cycles and the evolutionary transition to multicellularity

abstract: Understanding the evolutionary transition to multicellularity is a key problem in evolutionary biology (1,2). While around 25 independent instances of the evolution of multicellular existence are known across the tree of life (3), the ecological conditions that drive such transformations are not well understood. The first known transition to multicellularity occurred approximately 2.5 billion years ago in cyanobacteria (4-6), and todays cyanobacteria are characterized by an enormous morphological diversity, ranging from single-celled species over simple filamentous to highly differentiated filamentous ones (7,8). While the cyanobacterium Cyanothece sp. ATCC 51142 was isolated from the intertidal zone of the U.S. Gulf Coast as a unicellular species (9), we are first to additionally report a phenotypically mixed strategy where multicellular filaments and unicellular stages alternate. We experimentally demonstrate that the facultative multicellular life cycle depends on environmental conditions, such as salinity and population density, and use a theoretical model to explore the process of filament dissolution. While results predict that the observed response can be caused by an excreted compound in the medium, we cannot fully exclude changes in nutrient availability (as in (10,11)). The best fit modeling results demonstrate a nonlinear effect of the compound, which is characteristic for density-dependent sensing systems (12,13). Further, filament fragmentation is predicted to occur by means of connection cleavage rather than by cell death of every alternate cell. The phenotypic switch between the single-celled and multicellular morphology constitutes an environmentally dependent life cycle, which likely represents an important step en route to permanent multicellularity.


title: Tools for Drawing Informative Idiograms

abstract: Each species has a typical karyotype, which represents the phenotypic appearance of the somatic chromosomes including number, size, and morphology. Idiogram is a diagrammatic representation of the chromosomes showing their relative size, homologous groups and different cytogenetic landmarks. Chromosomal analysis of cytological preparations is an essential component of many investigations which involves the calculation of karyotypic parameters and generation of idiogram. Although various tools are available for karyotype analysis, here we demonstrate karyotype analysis using our recently developed tool named KaryoMeasure. KaryoMeasure is a semi-automated free and user-friendly karyotype analysis software that facilitates data collection from different digital images of the metaphase chromosome spreads and calculates a wide variety of chromosomal and karyotypic parameters along with the related standard errors. KaryoMeasure draws idiograms of both diploid and allopolyploid species into a vector-based SVG or PDF image file.

category: genetics


title: Quantifying mediation between omics layers and complex traits

abstract:
BackgroundHigh-dimensional omics datasets provide valuable resources to determine the causal role of molecular traits in mediating the path from genotype to phenotype. Making use of quantitative trait loci (QTL) and genome-wide association studies (GWASs) summary statistics, we developed a multivariable Mendelian randomization (MVMR) framework to quantify the connectivity between three omics layers (DNA methylome (DNAm), transcriptome and proteome) and their cascading causal impact on complex traits and diseases.

ResultsEvaluating 50 complex traits, we found that on average 37.8% (95% CI: [36.0%-39.5%]) of DNAm-to-trait effects were mediated through transcripts in the cis-region, while only 15.8% (95% CI: [11.9%-19.6%]) are mediated through proteins in cis. DNAm sites typically regulate multiple transcripts, and while found to predominantly decrease gene expression, this was only the case for 53.4% across {approx} 47,000 significant DNAm-transcript pairs. The average mediation proportion for transcript-to-trait effects through proteins (encoded for by the assessed transcript or located in trans) was estimated to be 5.27% (95%CI: [4.11%-6.43%]). Notable differences in the transcript and protein QTL architectures were detected with only 22% of protein levels being causally driven by their corresponding transcript levels. Several regulatory mechanisms were hypothesized including an example where cg10385390 (chr1:8022505) increases the risk of irritable bowel disease by reducing PARK7 transcript and protein expression.

ConclusionsThe proposed integrative framework identified putative causal chains through omics layers providing a powerful tool to map GWAS signals. Quantification of causal effects between successive layers indicated that molecular mechanisms can be more complex than what the central dogma of biology would suggest.

category: genomics


title: Reduced motivation for social contact in Disrupted-in-schizophrenia transgenic rats

abstract: The Disrupted-in-schizophrenia 1 (DISC1) signaling pathway is considered to play a key role in schizophrenia, depression, autism and other psychiatric disorders. DISC1 is involved in regulating the dopaminergic neurotransmission in, among others, the mesolimbic reward system. A transgenic rat line tgDISC1 has been introduced as a model system to study behavioral phenotypes associated with abnormal DISC1 pathways. Here, we evaluated the impact of impaired DISC1 signaling on social (social interaction) and non-social (sucrose) reward preferences in the tgDISC1 animal model. In a plus-maze setting, rats chose between the opportunity for social interaction with an unfamiliar juvenile conspecific (social reward) or drinking sweet solutions with variable sucrose concentrations (non-social reward). tgDISC1 rats differed from wild-type rats in their social, but not in their non-social reward preferences. Specifically, DISC1 rats showed a lower interest in interaction with the juvenile conspecific, but did not differ from wild-type rats in their preference for higher sucrose concentrations. These results suggest that disruptions of the DISC1 pathway that is associated with altered dopamine transmission in the brain result in selective deficits in social motivation seen in neuropsychiatric illness.

category: animal behavior and cognition


title: Real-time Noise-suppressed Wide-Dynamic-Range Compression in Ultrahigh-Resolution Neuronal Imaging

abstract: With a limited dynamic range of an imaging system, there are always regions with signal intensities comparable to the noise level, if the signal intensity distribution is close to or even wider than the available dynamic range. Optical brain/neuronal imaging is such a case where weak-intensity ultrafine structures, such as, nerve fibers, dendrites and dendritic spines, often coexist with ultrabright structures, such as, somas. A high fluorescence-protein concentration makes the soma order-of-magnitude brighter than the adjacent ultrafine structures resulting in an ultra-wide dynamic range. A straightforward enhancement of the weak-intensity structures often leads to saturation of the brighter ones, and might further result in amplification of high-frequency background noises. An adaptive illumination strategy to real-time-compress the dynamic range demands a dedicated hardware to operate and owing to electronic limitations, might encounter a poor effective bandwidth especially when each digitized pixel is required to be illumination optimized. Furthermore, such a method is often not immune to noise-amplification while locally enhancing a weak-intensity structure. We report a dedicated-hardware-free method for rapid noise-suppressed wide-dynamic-range compression so as to enhance visibility of such weak-intensity structures in terms of both contrast-ratio and signal-to-noise ratio while minimizing saturation of the brightest ones. With large-FOV aliasing-free two-photon fluorescence neuronal imaging, we validate its effectiveness by retrieving weak-intensity ultrafine structures amidst a strong noisy background. With compute-unified-device-architecture (CUDA)-acceleration, a time-complexity of <3 ms for a 1000x1000-sized 16-bit data-set is secured, enabling a real-time applicability of the same.

category: bioengineering


title: Genome graphs detect human polymorphisms in active epigenomic states during influenza infection

abstract: Genetic variants, including mobile element insertions (MEIs), are known to impact the epigenome. We hypothesized that the use of a genome graph, which encapsulates genetic diversity, could reveal missing epigenomic signal. Given the contributions of mobile elements to the evolution of primate innate immunity, we tested this in monocyte-derived macrophages obtained from 35 individuals before and after Influenza virus infection. After characterizing genetic variants in this cohort using linked-reads, including 5140 Alu, 316 L1, 94 SVAs and 48 ERVs, we incorporated them into a genome graph. Mapping epigenetic data to this graph revealed 2.5%, 3.0% and 2.3% novel peaks for H3K4me1 and H3K27ac ChIP-seq and ATAC-seq respectively. Notably, using a genome graph also modified quantitative trait loci estimates and we observed 375 polymorphic MEIs in active epigenomic state. For example, we found an AluYh3 polymorphism whose chromatin state changed after infection and that was associated with the expression of TRIM25, a gene that restricts influenza RNA synthesis. Our results demonstrate that graph genomes can reveal regulatory regions that would have been overlooked by other approaches.


title: Multi-omics and deep learning provide a multifaceted view of cancer

abstract:
Cancer is a complex disease with a large financial and healthcare burden on society. One hallmark of the disease is the uncontrolled growth and proliferation of malignant cells. Unlike Mendelian diseases which may be explained by a few genomic loci, a deeper molecular and mechanistic understanding of the development of cancer is needed. Such an endeavor requires the integration of tens of thousands of molecular features across multiple layers of information encoded in the cells. In practical terms, this implies integration of multi omics information from the genome, transcriptome, epigenome, proteome, metabolome, and even micro-environmental factors such as the microbiome. Finding mechanistic insights and biomarkers in such a high dimensional space is a challenging task. Therefore, efficient machine learning techniques are needed to reduce the dimensionality of the data while simultaneously discovering complex but meaningful biomarkers. These markers then can lead to testable hypotheses in research and clinical applications. In this study, we applied advanced deep learning methods to uncover multi-omic fingerprints that are associated with a wide range of clinical and molecular features of tumor samples. Using these fingerprints, we can accurately classify different cancer types, and their subtypes. Non-linear multi-omic fingerprints can uncover clinical features associated with patient survival and response to treatment, ranging from chemotherapy to immunotherapy. In addition, multi-omic fingerprints may be deconvoluted into a meaningful subset of genes and genomic alterations to support clinically relevant decisions.

Graphical Abstract

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title: Integrative genomics uncover mechanisms of renal medullary carcinoma transformation, microenvironment landscape and therapeutic vulnerabilities.

abstract:
Renal medullary carcinoma (RMC) is an aggressive desmoplastic tumour driven by bi-allelic loss of SMARCB1, however the cell-of-origin, the oncogenic mechanism and the features of its microenvironment remain poorly understood. Using single-cell and multi-region sequencing of human RMC, we defined transformation of thick ascending limb (TAL) cells into at least three RMC cell states along an epithelial-mesenchymal gradient through a transcriptional switch involving loss of renal transcription factor TFCP2L1 and gain of a NFE2L2-associated ferroptosis resistance program. SMARCB1 re-expression in cultured RMC cells reactivates TFCP2L1 that relocates SWI/SNF from the promoters of the MYC-driven oncogenic program to the enhancers of TAL identity genes followed by ferroptotic cell death. We further show that RMC is associated with abundant M2-type macrophages and cancer-associated fibroblasts (CAFs) and we identify key regulatory cross-talks that shape this immunosuppressive microenvironment. Together our data describe the molecular events of RMC transformation and identify novel therapeutically targetable vulnerabilities.

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category: cancer biology


title: Hemodynamic Correlates of Fluctuations in Neuronal Excitability: A Simultaneous Paired Associative Stimulation (PAS) and functional Near Infra-Red Spectroscopy (fNIRS) Study

abstract:
BackgroundThe relationship between task-related hemodynamic activity and brain excitability is poorly understood in humans as it is technically challenging to combine simultaneously non-invasive brain stimulation and neuroimaging modalities. Cortical excitability corresponds to the readiness to become active and as such it may be linked to metabolic demand.

HypothesesCortical excitability and hemodynamic activity are positively linked so that increases in hemodynamic activity correspond to increases in excitability and vice-versa.

MethodsFluctuations of excitability and hemodynamic activity were investigated via simultaneous Transcranial Magnetic Stimulation (TMS) and functional Near Infrared Spectroscopy (fNIRS). Sixteen healthy subjects participated in a sham-controlled, pseudorandomized, counterbalanced study with PAS (PAS10/PAS25/Sham) on the right primary motor cortex (M1). The relationship between M1 excitability (Motor Evoked Potentials, MEP) and hemodynamic responses to finger tapping reconstructed via personalized fNIRS was assessed.

ResultsHemodynamic activity exhibited a significant correlation with cortical excitability: increased HbO and HbR (absolute amplitude) corresponded to increased excitability and vice-versa (r=0.25; p=0.03 and r=0.16; p=0.17, respectively). The effect of PAS on excitability and hemodynamic activity showed a trend of positive correlation: correlation of MEP ratios (post-PAS/pre-PAS) with HbO and HbR ratios (r=0.19, p=0.29; r=0.18, p=0.30, respectively).

ConclusionsTMS-fNIRS is a suitable technique for simultaneous investigation of excitability and hemodynamic responses and indicates a relationship between these two cortical properties. PAS effect is not limited to cortical excitability but also impacts hemodynamic processes. These findings have an impact on the application of neuromodulatory interventions in patients with neuropsychiatric disorders.


title: Evaluation of calcium-sensitive adenylyl cyclase AC1 and AC8 mRNA expression in the anterior cingulate cortex of mice with neuropathic pain

abstract: The anterior cingulate cortex (ACC) is a critical region of the brain for the emotional and affective components of pain in rodents and humans. Hyperactivity in this region has been observed in neuropathic pain states in both patients and animal models and ablation of this region from cingulotomy, or inhibition with genetics or pharmacology can diminish pain and anxiety. Two adenylyl cyclases (AC), AC1 and AC8 play an important role in regulating nociception and anxiety-like behaviors through an action in the ACC, as genetic and pharmacological targeting of these enzymes reduces mechanical hypersensitivity and anxietylike behavior, respectively. However, the distribution of these ACs in the ACC has not been studied in the context of neuropathic pain. To address this gap in knowledge, we conducted RNAscope in situ hybridization to assess AC1 and AC8 mRNA distribution in mice with spared nerve injury (SNI). Given the key role of AC1 in nociception in neuropathic, inflammatory and visceral pain animal models, we hypothesized that AC1 would be upregulated in the ACC of mice following nerve injury. This hypothesis was also founded on data showing increased AC1 expression in the ACC of mice with zymosan-induced visceral inflammation. We found that AC1 and AC8 are widely expressed in many regions of the mouse brain including the hippocampus, ACC, medial prefrontal cortex and midbrain regions, but AC1 is more highly expressed. Contrary to our hypothesis, SNI causes an increase in AC8 mRNA expression in NMDAR-2B (Nr2b) positive neurons in the contralateral ACC but does not affect AC1 mRNA expression. Our findings show that changes in Adcy1 mRNA expression in the ACC are insufficient to explain the important role of this AC in mechanical hypersensitivity in mice following nerve injury and suggest a potential unappreciated role of AC8 in regulation of ACC synaptic changes after nerve injury.


title: Subcortical Segmentation of the Fetal Brain in 3D Ultrasound using Deep Learning

abstract: The quantification of subcortical volume development from 3D fetal ultrasound can provide important diagnostic information during pregnancy monitoring. However, manual segmentation of subcortical structures in ultra-sound volumes is time-consuming and challenging due to low soft tissue contrast, speckle and shadowing artifacts. For this reason, we developed a convolutional neural network (CNN) for the automated segmentation of the choroid plexus (CP), lateral posterior ventricle horns (LPVH), cavum septum pellucidum et vergae (CSPV), and cerebellum (CB) from 3D ultrasound. As ground-truth labels are scarce and expensive to obtain, we applied few-shot learning, in which only a small number of manual annotations (n = 9) are used to train a CNN. We compared training a CNN with only a few individually annotated volumes versus many weakly labelled volumes obtained from atlas-based segmentations. This showed that segmentation performance close to intra-observer variability can be obtained with only a handful of manual annotations. Finally, the trained models were applied to a large number (n = 278) of ultrasound image volumes of a diverse, healthy population, obtaining novel US-specific growth curves of the respective structures during the second trimester of gestation.


title: Moderate prenatal alcohol exposure modifies sex-specific CRFR1 activity in the central amygdala and anxiety-like behavior in adolescent offspring.

abstract: Anxiety disorders are highly prevalent among individuals with a history of prenatal alcohol exposure (PAE), and adolescent rodents demonstrate anxiety-like behavior following moderate PAE on Gestational Day (G) 12. A likely systemic target of PAE is the stress peptide corticotrophin-releasing factor (CRF), as activation of CRF receptor 1 (CRFR1) in the medial nucleus of the central amygdala (CeM) is known to increase anxiety-like behavior in adults. To determine if CRF-CRFR1 interactions underly PAE-induced anxiety, functional changes in CRF system activity were investigated in adolescent male and female Sprague Dawley rats following G12 PAE. Compared to air-exposed controls, PAE increased basal spontaneous (s) inhibitory post-synaptic current (IPSC) frequency in the CeM of males, but not females. Furthermore, PAE blunted CRFR1-regulated miniature (m) IPSCs in a sex- and dose-specific manner, and only PAE males demonstrated tonic CRFR1 activity in the CeM. It was further determined that G12 PAE decreased CRFR1 mRNA in the CeM of males while increasing regional expression in females. Finally, infusion of a CRFR1 agonist into the CeM of adolescents produced a blunted expression of CRFR1-induced anxiety-like behavior exclusively in PAE males, mirroring the blunted physiology demonstrated by PAE males. Cumulatively, these data suggest that CRFR1 function within the CeM is age- and sex-specific, and PAE not only increases the expression of anxiety-like behavior, but may reduce the efficacy of treatment for PAE-induced anxiety through CRFR1-associated mechanisms. Therefore, future research will be necessary to develop targeted treatment of anxiety disorders in individuals with a history of PAE.


title: Helminth infection is associated with dampened cytokine responses to viral and bacterial stimulations in Tsimane hunter-horticulturalists.

abstract:
BackgroundSoil-transmitted helminth (STH) infections can catalyze immunological changes that affect the response to subsequent infections, particularly those that elicit strong inflammatory responses. As globalization heightens the risk that remote communities with high STH prevalence will encounter novel pathogens, understanding how STHs shape immune responses to these downstream infections becomes increasingly crucial.

MethodologyWe worked with Tsimane forager-horticulturalists in the Bolivian Amazon, where STHs are prevalent. We tested whether STHs and eosinophil levels--most likely indicative of infection in this population--are associated with dampened immune responses to in vitro stimulation with H1N1 and lipopolysaccharide (LPS) antigens. Whole blood samples (n = 179) were treated with H1N1 vaccine and LPS and assayed for 13 cytokines (interferon gamma [INF-{gamma}], interleukin [IL]-1{beta}, IL-2, IL-4, IL-5, IL-6, IL-7, IL-8, IL-10, IL-12p70, IL-13, Granulocyte-macrophage colony-stimulating factor [GM-CSF], and Tumor necrosis factor-alpha [TNF-]). We evaluated how STHs and eosinophil levels affected cytokine responses and T helper (Th) 1 and Th2-cytokine suite responses to stimulation.

ResultsInfection with Ascaris lumbricoides was significantly (p [≤] 0.05) associated with lower response of some cytokines to H1N1 and LPS in women. Eosinophils were significantly negatively associated with some cytokine responses to H1N1 and LPS, with the strongest effects in women, and associated with a reduced Th1- and Th2-cytokine response to H1N1 and LPS in women and men.

Conclusions and implicationsWe find that STHs were associated with dampened cytokine responses to certain viral and bacterial antigens, and suggest that this mitigation of host-induced damage may reduce the incidence of cytokine storms in populations with high STH prevalence.


title: Analysis of centrosomal area actin reorganization and centrosome polarization upon lymphocyte activation at the immunological synapse

abstract: T cell receptor (TCR) and B cell receptor (BCR) stimulation of T and B lymphocytes, by antigen presented on an antigen-presenting cell (APC) induces the formation of the immunological synapse (IS). IS formation is associated with an initial increase in cortical filamentous actin (F-actin) at the IS, followed by a decrease in F-actin density at the central region of the IS, which contains the secretory domain. This is followed by the convergence of secretion vesicles towards the centrosome, and the polarization of the centrosome to the IS. These reversible, cortical actin cytoskeleton reorganization processes occur during lytic granule secretion in cytotoxic T lymphocytes (CTL) and natural killer (NK) cells, proteolytic granules secretion in B lymphocytes and during cytokine-containing vesicle secretion in T-helper (Th) lymphocytes. In addition, several findings obtained in T and B lymphocytes forming IS show that actin cytoskeleton reorganization also occurs at the centrosomal area. F-actin reduction at the centrosomal area appears to be associated with centrosome polarization. In this chapter we deal with the analysis of centrosomal area F-actin reorganization, as well as the centrosome polarization analysis towards the IS.


title: Assessing the Functionality of RNA Interference (RNAi) in the Phloem-feeding Maize pest Dalbulus maidis

abstract: Dalbulus maidis [(DeLong & Wolcott), corn leafhopper], a phloem-feeding insect, is the most efficient vector of maize stunting pathogens (Spiroplasma kunkelii, Maize bushy stunt phytoplasma, and Maize rayado fino virus) in the Americas. Studies involving gene editing in insects are rapidly providing information that can potentially be used for insect vector and plant disease control. RNA interference (RNAi), a sequence-specific gene silencing method, is one of the most widely used molecular tools in functional genomics studies. RNAi uses exogenous double-stranded RNA (dsRNA) or small interfering RNA (siRNA) to prevent the production of proteins by inhibiting the expression of their corresponding messenger RNA (mRNA). In this study, we measured the efficacy of gene silencing, and its effects on D. maidis mortality as proof of concept that RNAi is a viable tool for use in genetic pest control of phloem-feeding insects. Oral delivery of dsRNA using an artificial diet was used to silence two key insect genes, vacuolar ATP synthase subunit B, and subunit D (V-ATPase B and V-ATPase D). Our results showed reduced gene expression of V-ATPase B and V-ATPase D after ingestion of dsRNA, and significantly higher mortality, and wing deformation, associated with reduced gene expression, compared to control insects that were not orally fed dsRNA. These results reveal RNAi as a viable tool for use in genetic pest control of phloem-feeding insects, and a way for further functional genomic studies, such as identification of potential target genes for either population suppression or population replacement of this vector of maize diseases.

category: molecular biology


title: The Daphnia carapace and the origin of novel structures

abstract: Understanding how novel structures arise is a central question in evolution. Novel structures are often defined as structures that are not derived from (homologous to) any structure in the ancestor1. The carapace of the water flea Daphnia magna is a bivalved "cape" of exoskeleton that has been proposed to be one of many novel arthropod structures that arose through repeated co-option of genes that also pattern insect wings2-4. To determine whether the Daphnia carapace is a novel structure, we compare the expression of pannier, araucan, and vestigial between Daphnia, Parhyale, and Tribolium. Our results suggest that the Daphnia carapace did not arise by co-option, but instead derives from an exite (lateral lobe) that emerges from an ancestral proximal leg segment that was incorporated into the Daphnia body wall. The Daphnia carapace therefore appears to be homologous to the Parhyale tergal plate and the insect wing5. Remarkably, the vestigial-positive region that gives rise to the Daphnia carapace appears to be present in Parhyale6 and Tribolium as a small, inconspicuous protrusion. Similarly, the vestigial-positive regions that form thoracic tergal plates in Parhyale appear to be present in Daphnia, even though Daphnia does not form thoracic tergal plates. Thus, rather than a novel structure resulting from gene co-option, the Daphnia carapace appears to have arisen from a shared, ancestral tissue (morphogenetic field) that persists in a cryptic state in other arthropod lineages. Cryptic persistence of unrecognized serial homologs may thus be a general solution for the origin of novel structures.


title: Experimental evidence for the impact of soil viruses on carbon cycling during surface plant litter decomposition

abstract: To date, the potential impact of viral communities on biogeochemical cycles in soil has largely been inferred from indirect evidence, such as virus-driven changes in microbial abundances, viral auxiliary metabolic genes, and correlations with soil physiochemical properties. To more directly test the impact of soil viruses on carbon cycling during plant litter decomposition, we added concentrated viral community suspensions to complex litter decomposer communities in 40-day microcosm experiments. Microbial communities from two New Mexico alpine soils, Pajarito (PJ) and Santa Fe (SF), were inoculated onto grass litter on sand, and three treatments were applied in triplicate to each set of microcosms: addition of buffer (no added virus), addition of live virus (+virus), or killed virus (+killed-virus) fractions extracted from the same soil. Significant differences in respiration were observed between the +virus and +killed-virus treatments in the PJ, but not the SF microcosms. Bacterial and fungal community composition differed significantly by treatment in both PJ and SF microcosms. Combining data across both soils, viral addition altered links between bacterial and fungal diversity, dissolved organic carbon and total nitrogen. Overall, we demonstrate that increasing viral pressure in complex microbial communities can impact terrestrial biogeochemical cycling but is context-dependent.


title: Strong spatial population structure shapes the temporal coevolutionary dynamics of costly female preference and male display

abstract: Female mating preferences for exaggerated male display traits are commonplace. Yet, comprehensive understanding of the evolution and persistence of costly female preference through indirect (Fisherian) selection in finite populations requires some explanation for the persistence of additive genetic variance (Va) underlying sexual traits, given that directional preference is expected to deplete Va in display and hence halt preference evolution. However, the degree to which Va, and hence preference-display coevolution, may be prolonged by spatially variable sexual selection arising solely from limited gene flow and genetic drift within spatially structured populations has not been examined. Our genetically and spatially explicit model shows that spatial population structure arising in an ecologically homogeneous environment can facilitate evolution and long-term persistence of costly preference given small subpopulations and low dispersal probabilities. Here, genetic drift initially creates spatial variation in female preference, leading to persistence of Va in display through "migration-bias" of genotypes maladapted to emerging local sexual selection, thus fuelling coevolution of costly preference and display. However, costs of sexual selection increased the probability of subpopulation extinction, limiting persistence of high preference-display genotypes. Understanding long-term dynamics of sexual selection systems therefore requires joint consideration of coevolution of sexual traits and metapopulation dynamics.


title: Convergent mosaic brain evolution is associated with the evolution of novel electrosensory systems in teleost fishes.

abstract: Brain region size generally scales allometrically with total brain size, but mosaic shifts in brain region size independent of brain size have been found in several lineages and may be related to the evolution of behavioral novelty. African weakly electric fishes (Mormyroidea) evolved a mosaically enlarged cerebellum and hindbrain, yet the relationship to their behaviorally novel electrosensory system remains unclear. We addressed this by studying South American weakly electric fishes (Gymnotiformes) and weakly electric catfishes (Synodontis spp.), which evolved varying aspects of electrosensory systems, independent of mormyroids. If the mormyroid mosaic increases are related to evolving an electrosensory system, we should find similar mosaic shifts in gymnotiforms and Synodontis. Using micro-computed tomography scans, we quantified brain region scaling for multiple electrogenic, electroreceptive, and non-electrosensing species. We found mosaic increases in cerebellum in all three electrogenic lineages relative to non-electric lineages and mosaic increases in torus semicircularis and hindbrain associated with the evolution of electrogenesis and electroreceptor type. These results show that evolving novel electrosensory systems is repeatedly and independently associated with changes in the sizes of individual brain regions independent of brain size, which suggests that selection can impact structural brain composition to favor specific regions involved in novel behaviors.


title: A novel approach to develop wheat chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in doubled haploid introgression lines

abstract:
Many wild relative species are being used in pre-breeding programmes to increase the genetic diversity of wheat. Genotyping tools such as single nucleotide polymorphism (SNP)-based arrays and molecular markers have been widely used to characterise wheat-wild relative introgression lines. However, due to the polyploid nature of the recipient wheat genome, it is difficult to develop SNP-based KASP markers that are codominant to track the introgressions from the wild species. Previous attempts to develop KASP markers have involved both exome- and PCR-amplicon-based sequencing of the wild species. But chromosome-specific KASPs assays have been hindered by homoeologous SNPs within the wheat genome. This study involved whole genome sequencing of the diploid wheat wild relative Amblyopyrum muticum and development of a SNP discovery pipeline that generated [~]38,000 SNPs in single-copy wheat genome sequences. New assays were designed to increase the density of Am. muticum polymorphic KASP markers. With a goal of one marker per 60 Mbp, 335 new KASP assays were validated as functional. Together with assays validated in previous studies, 498 well distributed chromosome-specific markers were used to recharacterize previously genotyped wheat-Am. muticum doubled haploid (DH) introgression lines. The chromosome specific nature of the KASP markers allowed clarification of which wheat chromosomes were involved with recombination events or substituted with Am. muticum chromosomes and the higher density of markers allowed detection of new small introgressions in these DH lines.

Key MessageA novel methodology to generate chromosome-specific SNPs between wheat and its wild relative Amblyopyrum muticum and their use in the development of KASP markers to genotype wheat-Am. muticum introgression lines.


title: A systematic evaluation of 41 DNA methylation predictors across 101 data preprocessing and normalization strategies highlights considerable variation in algorithm performance

abstract:
BackgroundDNA methylation (DNAm) based predictors hold great promise to serve as clinical tools for health interventions and disease management. While these algorithms often have high prediction accuracy and are associated with many disease-related phenotypes, the reliability of their performance remains to be determined. We therefore conducted a systematic evaluation across 101 different data processing strategies that preprocess and normalize DNAm data and assessed how each analytical strategy affects the reliability and prediction accuracy of 41 DNAm-based predictors.

ResultsOur analyses were conducted in a large EPIC DNAm sample of the Jackson Heart Study (N=2,053) that included 146 pairs of technical replicate samples. By estimating the average absolute agreement between replicate pairs, we show that 32 out of 41 predictors (78%) demonstrate excellent test-retest reliability when appropriate data processing and normalization steps are implemented. Across all pairs of predictors, we find a moderate correlation in performance across analytical strategies (mean rho=0.40, SD=0.27), highlighting significant heterogeneity in performance across algorithms within a choice of an analytical pipeline. (Un)successful removal of technical variation furthermore significantly impacts downstream phenotypic association analysis, such as all-cause mortality risk associations.

ConclusionsWe show that DNAm-based algorithms are sensitive to technical variation. The right choice of data processing and normalization pipeline is important to achieve reproducible estimates and improve prediction accuracy in downstream phenotypic association analyses. For each of the 41 DNAm predictors, we report its test-retest reliability and provide the best performing analytical strategy as a guideline for the research community. As DNAm-based predictors become more and more widely used, both for research purposes as well as for clinic applications, our work helps improve their performance and standardize their implementation.


title: The evolutionary trajectory of drosophilid walking

abstract: Neural circuits must both execute the behavioral repertoire of individuals and account for behavioral variation across species. Understanding how this variation emerges over evolutionary time requires large-scale phylogenetic comparisons of behavioral repertoires. Here, we describe the evolution of walking in fruit flies by capturing high-resolution, unconstrained movement from 13 species and 15 strains of drosophilids. We find that walking can be captured in a universal behavior space, the structure of which is evolutionarily conserved. However, the occurrence of, and transitions between, specific movements have evolved rapidly, resulting in repeated convergent evolution in the temporal structure of locomotion. Moreover, a meta-analysis demonstrates that many behaviors evolve more rapidly than other traits. Thus, the architecture and physiology of locomotor circuits can both execute precise individual movements in one species and simultaneously support rapid evolutionary changes in the temporal ordering of these modular elements across clades.


title: Gaussian Network Model Revisited: Effects of Mutation and Ligand Binding on Protein Behavior

abstract: The coarse-grained Gaussian Network model, GNM, considers only the alpha carbons of the folded protein. Therefore it is not directly applicable to the study of mutation or ligand binding problems where atomic detail is required. This shortcoming is improved by including the local effect of heavy atoms in the neighborhood of each alpha carbon into the Kirchoff Adjacency Matrix. The presence of other atoms in the coordination shell of each alpha carbon diminishes the magnitude of fluctuations of that alpha carbon. But more importantly, it changes the graph-like connectivity structure, i.e., the Kirchoff Adjacency Matrix of the whole system which introduces amino acid specific and position specific information into the classical coarse-grained GNM which was originally modelled in analogy with phantom network theory of rubber elasticity. With this modification, it is now possible to make predictions on the effects of mutation and ligand binding on residue fluctuations and their pair-correlations. We refer to the new model as  all-atom GNM. Using examples from published data we show that the all-atom GNM applied to in silico mutated proteins and to their laboratory mutated structures gives similar results. Thus, loss and gain of correlations, which may be related to loss and gain of function, may be studied by using simple in silico mutations only.