title: The emergence of a collective sensory response threshold in ant colonies

abstract: The sensory response threshold is a fundamental biophysical property of biological systems that underlies many physiological and computational functions, and its systematic study has played a pivotal role in uncovering the principles of neural computation. Here, we show that ant colonies, which perform computational tasks at the group level, have emergent collective sensory response thresholds. Colonies respond collectively to step changes in temperature and evacuate the nest during severe perturbations. This response is characterized by a group-size dependent threshold, and the underlying dynamics are dominated by social feedback between the ants. Using a binary network model, we demonstrate that a balance between short-range excitatory and long-range inhibitory interactions can explain the emergence of the collective response threshold and its size dependency. Our findings illustrate how simple social dynamics allow insect colonies to integrate information about the external environment and their internal state to produce adaptive collective responses.

category: animal behavior and cognition


title: Accessible, Open-source Hardware and Process Designs for 3D Bioprinting and Culturing Channels Lined with iPSC-derived Vascular Endothelial Cells

abstract: Indirect bioprinting for cell culture requires the use of several technologies and techniques which currently prevent many researchers not specialized in electrical engineering or materials science from accessing these new tools. In this paper, a printer and all necessary associated hardware was developed and tested for the purpose of seeding human induced Pluripotent Stem Cell (iPSC)-derived endothelial cells (iECs) onto all surfaces of a fibringelatin channel. Immature iECs were seeded onto all channel surfaces and completed differentiation along channel walls. All required tools and methods, including engineering drawing, printable files, code, and hand-tool templates, have been provided with sufficient clarity to enable full, open-source replication of all technique employed.

category: bioengineering


title: Quantitative model suggests both intrinsic and contextual features contribute to the transcript coding ability determination in cells

abstract: Gene transcription and protein translation are two key steps of the "central dogma". It is still a major challenge to quantitatively deconvolute factors contributing to the coding ability of transcripts in mammals. Here, we propose Ribosome Calculator (RiboCalc) for quantitatively modeling the coding ability of RNAs in human genome. In addition to effectively predicting the experimentally confirmed coding abundance via sequence and transcription features with high accuracy, RiboCalc provides interpretable parameters with biological information. Large-scale analysis further revealed a number of transcripts with a variety of coding ability for distinct types of cells (i.e., context-dependent coding transcripts, CDCTs), suggesting that, contrary to conventional wisdom, a transcripts coding ability should be modeled as a continuous spectrum with a context-dependent nature.

category: bioinformatics


title: Emergence of an adaptive epigenetic cell state in human bladder urothelial carcinoma evolution

abstract: Intratumor heterogeneity (ITH) of bladder cancer (BLCA) facilitates therapy resistance and immune evasion to affect clinical prognosis directly. However, the molecular and cellular mechanism generating ITH in BLCA remains elusive. Here we show that a TM4SF1-positive cancer subpopulation (TPCS) drives ITH diversification in BLCA. By extensive profiling of the epigenome and transcriptome of BLCA from 79 donors across all stages, we elucidated the evolution trajectories of luminal and basal BLCA. TPCS emerges from the basal trajectory and shows extensive transcriptional plasticity with a distinct epigenomic landscape. Clinically, TPCS were enriched in advanced stage patients and associated with poor prognosis. Our results showed how cancer adapts to its environment by adopting a stem cell-like epigenomic landscape.

category: cancer biology


title: A novel mechanism of Euonymine inhibits in-stent restenosis through enhancing contractile phenotype of VSMCs by targeting AKT1 and p38MAPK

abstract:
This study aimed to examine the inhibitory effects of Euonymine on in-stent restenosis (ISR) after percutaneous coronary intervention (PCI) and oxidized low-density lipoprotein (ox-LDL)-induced proliferation, migration, and pro-apoptotic of vascular smooth muscle cells (VSMCs) in vitro, and its potential mechanisms. Euonymine is a monomer component extracted from Tripterygium hypoglaucum (Levl) Hutch. Using in vitro models of rabbit carotid balloon injury and porcine atherosclerotic coronary implantation, we confirmed that Euonymine inhibited ISR after PCI. Furthermore, Euonymine inhibited VSMC phenotypic transformation by targeting AKT1 to regulate the PTEN/AKT1/m TOR signaling pathway, with exertion of anti-proliferative, anti-migratory, and pro-apoptotic effects on ox-LDL-induced cell injury model. Additionally, the study demonstrated that Euonymine induced apoptosis of VSMCs via the p38MAPK-related mitochondria-dependent apoptotic pathway. Collectively, these findings indicated that Euonymine drug-eluting stents inhibited ISR after PCI by targeting AKT1 and p38MAPK to enhance the contractile phenotype of VSMCs to prevent intimal hyperplasia development. This provides insights into a potential therapeutic strategy involving the beneficial effect of Euonymine drug-eluting stent on ISR.

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category: pharmacology and toxicology


title: Combination of successor representation-based appetitive learning and individual representation-based aversive learning is a good strategy and can be implemented in the cortico-basal ganglia circuits

abstract: The direct and indirect pathways of the basal ganglia (BG) have been suggested to learn mainly from positive and negative feedbacks, respectively. Since these pathways unevenly receive inputs from different cortical neuron types and/or regions, they may preferentially use different state/action representations. We explored whether such combined use of different representations coupled with appetitive or aversive learning has computational benefits. We simulated reward learning tasks in dynamic environments, and examined the performance of animal modeled as an agent equipped with two learning systems, each of which used individual representation (IR) or successor representation (SR) of states. With varying the combination of IR or SR and also the learning rates from positive and negative reward prediction errors (RPEs) in each system, we found that combination of an SR-based system learning mainly from positive RPEs and an IR-based system learning mainly from negative RPEs could achieve good performance, as compared to other combinations, in many situations. The architecture of such a combination provides a novel coherent explanation for the functional significance and underlying mechanism of diverse findings about the cortico-BG circuits. These results suggest that combining different representations with appetitive and aversive learning is an effective learning strategy adopted by the brain.

category: neuroscience


title: Opponent learning with different representations in the cortico-basal ganglia circuits


title: WY14643 Increases Herpesvirus Replication Independent of PPARα Expression and Inhibits IFNβ Production

abstract:
Peroxisome proliferator activated receptor (PPAR) agonists are commonly used to treat metabolic disorders in humans because they regulate fatty acid oxidation and cholesterol metabolism. In addition to their roles in controlling metabolism, PPAR agonists also regulate inflammation and are immunosuppressive in models of autoimmunity. We aimed to test whether activation of PPAR with clinically relevant ligands could impact herpesvirus infection using the model strain murine gammaherpesvirus-68. We found that PPAR agonists WY14643 and fenofibrate increased herpesvirus replication in vitro. In vivo, WY14643 increased viral replication and caused lethality in mice. Unexpectedly, these effects proved independent of PPAR. Investigating the mechanism of action for WY14643, we found that it suppresses production of type I interferon by inhibiting stimulator of interferon (STING), which lies downstream of the cytoplasmic DNA sensor cGAS. Thus, WY14643 regulates interferon downstream of cytoplasmic DNA recognition and increases herpesvirus replication in a PPAR-independent manner. Taken together, our data indicate that caution should be employed when using PPAR agonists in immuno-metabolic studies, as they can have off-target effects on viral replication.

ImportancePPAR agonists are used clinically to treat both metabolic and inflammatory disorders. Because viruses are known to rewire host metabolism to their own benefit, the intersection of immunity, metabolism, and virology is an important research area. Our article is an important contribution to this field because for two reasons. First, it shows a role for PPAR agonists in altering virus detection by cells. Second, it shows that PPAR agonists can affect virus replication in a manner unrelated to their expected genetic function. This knowledge is valuable for anyone seeking to use PPAR agonists as a research tool.

category: immunology


title: Transcriptional burst kinetics are linked to short term transcriptional memory

abstract: Transcriptional bursting is thought to be a stochastic process that allows the dynamic regulation of most genes. The random telegraph model assumes the existence of two states, ON and OFF. However recent studies indicate the presence of additional ON states, suggesting that bursting kinetics and their regulation can be quite complex. We have developed a system to study transcriptional bursting in the context of p53 biology using the endogenous p21 gene tagged with MS2 in human cells. Remarkably, we find that transcriptional bursts from the p21 gene contain multiple ON and OFF states that can be regulated by elevation of p53 levels. Distinct ON states are characterized by differences in burst duration, classified as Short and Long, with long bursts associated with higher Pol II initiation rates. Importantly, the different ON states display memory effects that allow us to predict the likelihood of properties of future bursting events. Long bursting events result in faster re-activation, longer subsequent bursts and higher transcriptional output in the future compared to short bursts. Bursting memory persists up to 2 hours suggesting a stable inheritable promoter architecture. Bursting memory at the p21 gene is the strongest under basal conditions and is suppressed by UV and inhibition of H3K9me1/2, which also increase transcriptional noise. Stabilization of p53 by Nutlin-3a partially reverses suppression of bursting memory suggesting that higher p53 levels may be a key in enforcing memory under conditions of cellular stress. Overall our data uncover a new found bursting property termed Short-Term Transcriptional Memory (STTM) that has the potential to fine-tune transcriptional output at the p21 gene.

category: cell biology


title: High-Speed Imaging Reveals the Bimodal Nature of Dense Core Vesicle Exocytosis and Jet Flow through the Fusion Pore

abstract: During exocytosis, the fusion of secretory vesicle with plasma membrane forms a pore that regulates release of neurotransmitter and peptide. Osmotic forces contribute to exocytosis but release through the pore is thought to occur by diffusion. Heterogeneity of fusion pore behavior has also suggested stochastic variation in a common exocytic mechanism, implying a lack of biological control. Imaging at millisecond resolution to observe the first events in exocytosis, we find that fusion pore duration is bimodal rather than stochastic. Loss of calcium sensor synaptotagmin 7 increases the proportion of slow events without changing the intrinsic properties of either class, indicating the potential for independent regulation. In addition, dual imaging shows a delay in the entry of external dye relative to release that indicates discharge at high velocity rather than strictly by diffusion.


title: Transcriptional evaluation of the ductus arteriosus at the single-cell level uncovers a requirement for vimentin for complete closure

abstract:
OBJECTIVEFailure to close the ductus arteriosus immediately post-birth, patent ductus arteriosus (PDA), accounts for up to 10% of all congenital heart defects. Despite significant advances in PDA management options, including pharmacological treatment targeting the prostaglandin pathway, a proportion of patients fail to respond and must undergo surgical intervention. Thus, further refinement of the cellular and molecular mechanisms that govern vascular remodeling of this vessel is required.

APPROACH AND RESULTSAs anticipated, single-cell RNA sequencing on the ductus arteriosus in mouse embryos at E18.5, P0.5, and P5, revealed broad transcriptional alterations in the endothelial, smooth muscle, and fibroblast cell compartments. Making use of these data sets, vimentin emerged as an interesting candidate for further investigation. Subsequent studies demonstrated that, in fact, mice with genetic deletion of vimentin fail to complete vascular remodeling of the ductus arteriosus, as per presence of a functional lumen.

CONCLUSIONSThrough single-cell RNA-sequencing and by tracking closure of the ductus arteriosus postnatally in mice, we uncovered the unexpected contribution of vimentin in driving complete closure of the ductus arteriosus potentially through regulation of the Notch signaling pathway.

HIGHLIGHTSO_LISingle-cell RNA-sequencing on the ductus arteriosus at E18.5, P0.5, and P5 reveals how the ductus arteriosus undergoes drastic transcriptional changes at the single-cell level.
C_LIO_LIEndothelial cells increase levels of Vimentin, Notch1 and Jag1 transcripts soon after birth (P0.5), concurrent with ductus arteriosus closure.
C_LIO_LILoss of vimentin, the major intermediate filament protein of endothelial cells, prevents proper permanent closure of the ductus arteriosus.
C_LI

category: developmental biology


title: An arachnid's guide to be an ant: morphological and behavioural mimicry in ant-mimicking spiders

abstract: Batesian mimicry imposes several challenges to mimics and evokes adaptations in multiple sensory modalities. Myrmecomorphy, morphological and behavioral resemblance to ants, is seen in over 2000 arthropod species. Ant-like resemblance is observed in at least 13 spider families despite spiders having a distinct body plan compared to ants. Quantifying the extent to which spiders shape, size, and behavior resemble model ants will allow us to comprehend the evolutionary pressures that have facilitated myrmecomorphy. Myrmaplata plataleoides are  accurate mimics of the weaver ants, Oecophylla smaragdina. In this study, we quantify the speed of movement of model, mimic, and non-mimetic jumping spiders. We use traditional and geometric morphometrics to quantify traits such as foreleg and hindleg size, body shape between the model ant, mimic, and non-mimics. Our results suggest that while the mimics closely resemble the model ants in speed of movement, they occupy an intermediate morphological space compared to the model ants and non-mimics. We suggest that ant-mimicking spiders are better at mimicking ants locomotory movement than morphology and overall body shape. Our study provides a framework to understand the multimodal nature of mimicry and helps discern the relative contributions of such traits that drive mimetic accuracy in ant-mimicking spiders.


title: Development of a novel bioluminescent activity assay for peptide ligases

abstract: In recent years, some peptide ligases have been identified, such as bacterial sortases and certain plant asparaginyl or prolyl endopeptidases. Peptide ligases have wide applications in protein labeling and cyclic peptide synthesis. To characterize known peptide ligases or identify new ones, we propose a novel bioluminescent activity assay via the genetic fusion of a recognition motif of a peptide ligase to the C-terminus of an inactive large NanoLuc fragment (LgBiT) and the chemical introduction of a nucleophilic motif preferred by the peptide ligase to the N-terminus of the low-affinity SmBiT complementation tag. When the inactive ligation version LgBiT protein was ligated with the low-affinity ligation version SmBiT tag by the expected peptide ligase, its luciferase activity would be restored and could be quantified sensitively according to the measured bioluminescence. In the present study, we first validated the novel bioluminescent activity assay using bacterial sortase A and plant butelase-1. Subsequently, we screened novel peptide ligases from crude extracts of selected plants using two LgBiT-SmBiT ligation pairs. Among 80 common higher plants, we identified that five of them likely express asparaginyl endopeptidase-type peptide ligase and four of them likely express prolyl endopeptidase-type peptide ligase, suggesting that peptide ligases are not so rare in higher plants and more of them await discovery. The novel bioluminescent activity assay is ultrasensitive, convenient for use, and resistant to protease interference, and thus would have wide applications for characterizing known peptide ligases or screening new ones from various sources in future studies.

category: biochemistry


title: Ratiometric 4Pi single molecule localization with optimal resolution and color assignment

abstract: 4Pi single molecule localization microscopy (4Pi-SMLM) with two opposing objectives achieves sub-10 nm isotropic 3D resolution with as few as 250 photons collected by each objective. Here, we developed a new ratiometric multi-color imaging strategy for 4Pi-SMLM which employed the intrinsic multi-phase interference intensity without increasing the complexity of the system and achieved both optimal 3D resolution and color separation. By partially linking the photon parameters between channels with interference difference of {pi} during global fitting of the multi-channel 4Pi single molecule data, we showed on simulated data that the loss of the localization precision is minimal compared with the theoretical minimum uncertainty, the Cramer-Rao lower bound (CRLB).

category: biophysics


title: Oligomerization state of the functional bacterial twin arginine translocation (Tat) receptor complex

abstract: The twin-arginine translocation (Tat) system transports folded proteins across bacterial and plastid energy transducing membranes. Ion leaks are generally considered to be mitigated by the creation and destruction of the translocation conduit in a cargodependent manner, a mechanism that enables tight sealing around a wide range of cargo shapes and sizes. In contrast to the variable stoichiometry of the active translocon, the oligomerization state of the receptor complex is considered more consistently stable, but has proved stubbornly difficult to establish. Here, using a single molecule photobleaching analysis of individual inverted membrane vesicles, we demonstrate that Tat receptor complexes are tetrameric in native membranes with respect to both TatB and TatC. This establishes a maximal diameter for a resting state closed pore. A large percentage of Tat-deficient vesicles explains the typical low transport efficiencies observed. This individual reaction chamber approach will facilitate examination of the effects of stochastically distributed molecules.


title: Calcium fluctuations drive morphological patterning at the onset of Hydra morphogenesis

abstract: Morphogenesis in animal development involves significant morphological transitions leading to the emerging body plan of a mature animal. Understanding how the collective physical processes drive robust morphological patterning requires a coarse-grained description of the dynamics and the characterization of the underlying fields. Here I show that calcium spatial fluctuations serve as an integrator field of the electrical-mechanical processes of morphogenesis in whole-body Hydra regeneration and drive the morphological dynamics. We utilize external electric fields to control the developmental process and study a critical transition in morphogenesis, from the initial spheroidal shape of the tissue to an elongated cylindrical shape defining the body plan of a mature animal. Morphogenesis paused under external voltage is associated with a significant increase of the calcium activity compared with the activity supporting normal development. The enhanced calcium activity is characterized by intensified spatial fluctuations, extended spatial correlations across the tissue and faster temporal fluctuations. In contrast, the normal morphogenesis process is characterized by relatively moderate calcium fluctuation activity and restrained spatial correlations. Long-range communication however, is essential for development. Blocking gap-junctions halts morphogenesis by suppressing the long-range electrical communication, severely reducing the overall calcium activity and enhancing its localization in the tissue. Normal calcium activity is resumed following the wash of the blocker drug, leading to a morphological transition characterizing a normal regeneration process and the emergence of a mature animal. Our methodology of controlling morphogenesis by a physical electric field allows us to gain a global statistical view of the dynamics. It shows that the normalized calcium spatial fluctuations exhibit a universal shape distribution, across tissue samples and conditions, suggesting the existence of a global constrain over these fluctuations. Studying the correlations in space and time of the calcium fluctuation field at the onset of morphogenesis opens a new vista on this process and paints a picture of development analogous to a dynamical phase transition.


title: Vitamin A and vitamin E metabolites comodulate amyloid-β aggregation

abstract: Alzheimers disease is characterized by the presence in the brain of amyloid plaques formed by the aberrant deposition of the amyloid-{beta} peptide (A{beta}). Since many vitamins are dysregulated in this disease, we explored whether these molecules participate in protein homeostasis by modulating A{beta} aggregation. By screening 18 fat-soluble and water-soluble vitamins, we found that retinoic acid and -tocopherol, two metabolites of vitamin A and vitamin E, respectively, affect A{beta} aggregation both in vitro and in a C. elegans model of Alzheimers disease. We also show that effects of these two vitamin metabolites in combination can cancel each other out, suggesting that the complex composition of the cellular environment could have a protective role against protein aggregation through the simultaneous presence of aggregation promoters and inhibitors. Taken together, these results indicate that vitamins and their metabolites may be added to the list of components of the quality control system that regulate protein aggregation.


title: Silencing neuronal activity is required for developmental circuit remodeling

abstract:
Postnatal refinement of neuronal connectivity shapes the mature nervous system. Pruning of exuberant connections involves both cell autonomous and non-cell autonomous mechanisms, such as neuronal activity. While the role of neuronal activity in the plasticity of excitatory synapses has been extensively studied, the involvement of inhibition is less clear. Furthermore, the role of activity during stereotypic developmental remodeling, where competition is not as apparent, is not well understood.

Here we use the Drosophila mushroom body as a model to show that regulated silencing of neuronal activity is required for developmental axon pruning of the {gamma}-Kenyon cells. We demonstrate that silencing neuronal activity is mechanistically achieved by cell autonomous expression of the inward rectifying potassium channel (irk1) combined with inhibition by the GABAergic APL neuron. These results support the Hebbian-like rule  use it or lose it, where inhibition can destabilize connectivity and promote pruning while excitability stabilizes existing connections.


title: A versatile mitochondria isolation- and analysis-pipeline generates 3D nano-topographies and mechano-physical surface maps of single organelles

abstract: Living eukaryotic cells typically contain large quantities of highly dynamic mitochondria, which sustain the cells energy and redox homeostasis. Growing evidence suggests that mitochondria can functionally differ among but also within cells. The extent and biological significance of mitochondrial diversity is still largely unexplored, due to technical limitations that hamper profiling of individual organelles. Previous measurements of the cells interior have shown that membrane-bound compartments respond to metabolic manipulation by changes in their surface stiffness, suggesting that mechano-physical properties are a valuable readout of mitochondrial function. We here present the establishment of a robust multi-step analysis pipeline that allows one to profile mechano-physical properties of single mitochondria at the nanoscale using Atomic Force Microscopy (AFM). Firstly, we developed a rapid cell-type specific isolation protocol (mRACE), which selectively functionalizes mitochondria with biotin, facilitating isolation by streptavidin decorated microbeads. We established the technique for human and rat cell cultures, the invertebrate Caenorhabditis elegans, and the model plant Arabidopsis thaliana. Based on this versatile tool, we detected diversity of mitochondrially associated proteins among different tissues, reflecting the trophic condition of the source material. Secondly, a rapid filtration-based mitochondria isolation protocol was established, which was combined with mRACE. Lastly, we established an AFM analysis platform, which generates 3D maps of the nano-topography and mechano-physical properties of individual mitochondria. The comparison of mitochondria with each other revealed an unprecedented diversity in their mechano-physical properties and suggests that shape is not the sole determining parameter for outer membrane stiffness. We expect our results to not only introduce a new dimension for basic mitochondrial research, but in addition to open the door for the exploitation of individual mitochondria for diagnostic characterization.

category: plant biology


title: Directional selection at gene expression level contributes to the speciation of Asian rice cultivars

abstract: Differences in expression levels play important roles in phenotypic variation across species, especially those closely related species with limited genomic differences. Therefore, studying gene evolution at expression level is important for illustrating phenotypic differentiation between species, such as the two Asian rice cultivars, Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica. In this study, we evaluated the gene expression variation at inter-subspecies and intra-subspecies level using transcriptome data from seedlings of three indica and japonica rice and defined four groups of genes under different natural selections. We found a substantial of genes (about 79%) that are under stabilizing selection at the expression level in both subspecies, while about 16% of genes are under directional selection. Genes under directional selection have higher expression level and lower expression variation than those under stabilizing selection, which suggest a potential explanation to subspecies adaptation to different environments and interspecific phenotypic differences. Subsequent functional enrichment analysis of genes under directional selection shows that indica rice have experienced the adaptation to environmental stresses, and also show differences in biosynthesis and metabolism pathways. Our study provide an avenue of investigating indica-japonica differentiation through gene expression variation, which may guide to rice breeding and yield improvement.


title: Plasmotype condition nuclear pleiotropic effects on clock and fitness in barley

abstract: In plants, the role of chloroplasts and mitochondria (plasmotype) in controlling circadian clock plasticity and overall plant robustness has not been elucidated. In this study, we investigated the rhythmicity of chlorophyll fluorescence (Chl F) clock output, and fitness in the field at optimal and elevated temperatures, in three different barley populations. First, we examined a reciprocal DH population between two wild barley (Hordeum vulgare ssp. spontaneum), in which we identified two pleiotropic QTLs (frp2.1 and amp7.1) that modulate clock and fitness including conditioning of these effects by plasmotype diversity. In the second population, a complete diallel consisting of 11 genotypes (reciprocal hybrids differing in plasmotype), we observed a gradual reduction in plasmotype, ranging from 26% and 15% for Chl F and clock measurements to 5.3% and 3.7% for growth and reproductive traits, respectively. The third population studied was a collection of cytolines in which nine different wild plasmotypes replaced the cultivated Noga (H. vulgare) plasmotype. Here, the order and magnitude of the effects of the plasmotypes differed from what we observed in the diallel population, with the greatest effect of plasmotype diversity observed for clock period and amplitude. Comparison of the chloroplast sequences suggests several candidate genes in the plastid-encoded RNA polymerase (PEP) complex that may be responsible for the observed plasmotype effects. Overall, our results unravel previously unknown cytonuclear epistatic interactions that controls clock performance while also having pleiotropic effects on a plant field characteristics.


title: Genetic control of rhizosheath formation in pearl millet

abstract:
The rhizosheath, the layer of soil that adheres strongly to roots, influences water and nutrients acquisition. Pearl millet is a cereal crop that plays a major role for food security in arid regions of sub Saharan Africa and India. We previously showed that root-adhering soil mass is a heritable trait in pearl millet and that it correlates with changes in rhizosphere microbiota structure and functions. Here, we studied the correlation between root-adhering soil mass and root hair development, root architecture, and symbiosis with arbuscular mycorrhizal fungi and we analysed the genetic control of this trait using genome wide association (GWAS) combined with bulk segregant analysis and gene expression studies. Root-adhering soil mass was weakly correlated only to root hairs traits in pearl millet. Twelve QTLs for rhizosheath formation were identified by GWAS. Bulk segregant analysis on a biparental population validated five of these QTLs. Combining genetics with a comparison of global gene expression in the root tip of contrasted inbred lines revealed candidate genes that might control rhizosheath formation in pearl millet. Our study indicates that rhizosheath formation is under complex genetic control in pearl millet and suggests that it is mainly regulated by root exudation.

HighlightFormation of the rhizosheath, a layer of soil adhering to the root, is under complex genetic control in pearl millet and is mainly regulated by root exudation.


title: Conservation and divergence in cortical cellular organization between human and mouse revealed by single-cell transcriptome imaging

abstract: The human cerebral cortex has tremendous cellular diversity and complex cellular organization that are essential for brain function. How different types of cells are organized and interact with each other in the human cortex, and how cellular organizations and interaction patterns vary across species are, however, unclear. Here, we performed spatially resolved single-cell expression profiling of 4,000 genes in human middle and superior temporal gyrus using multiplexed error-robust fluorescence in situ hybridization (MERFISH). We identified >100 neuronal and non-neuronal cell populations with distinct transcriptional signatures, generated a molecularly defined and spatially resolved cell atlas of these brain regions, and analyzed cell-cell interactions in a cell-type-specific manner. Comparison with the mouse cortex showed conservation in the laminar organization of cells and substantial divergence in cell-cell interactions between human and mouse. Notably, our data revealed a drastic increase in interactions between neurons and non-neuronal cells in the human cortex, uncovered human-specific cell-cell interaction patterns, and identified potential ligand-receptor basis of microglia-neuron interactions.


title: Plasmids as donors of Insertion Sequence elements mediating colistin resistance in Klebsiella pneumoniae

abstract:
Colistin is a last resort antibiotic for the treatment of carbapenemase producing Klebsiella pneumoniae (CRKP). In line with rising colistin use worldwide, colistin resistant Klebsiella pneumoniae (K. pneumoniae) isolates have emerged. The disruption of mgrB by insertion sequences (ISs) has been widely reported worldwide representing a mechanism mediating colistin resistance. Evidence suggests plasmids encode mobilizable IS elements which preferentially integrate into the mgrB gene in K. pneumoniae causing gene inactivation and colistin resistance.

Recognised IS elements targeting mgrB include ISL3 (ISKpn25), IS5 (ISKpn26), ISKpn14 and IS903B-like elements. K. pneumoniae represents the single largest species carrying plasmids encoding these IS elements. For IS presence among species, 1000 BLASTn hits were downloaded and filtered for plasmids. Additionally, the top 120 BLASTn non-duplicate circularised plasmid contig hits for each IS element were typed for incompatibility (Inc) group and carbapenemase gene presence.

IS903B was found in 28 unique Inc groups, while ISKpn25 was largely carried by IncFIB(pQil) plasmids. ISKpn26 and ISKpn14 were most often found associated with IncFII(pHN7A8) plasmids. Of the 34 unique countries which contained any of the IS elements, ISKpn25 was identified from 26. ISKpn26, ISKpn14, and IS903B insertion sequences were identified from 89.3%, 44.9% and 23.9% plasmid samples from China.

Plasmids carrying ISKpn25, ISKpn14, and ISKpn26 IS elements are 12.18, 27.0, and 44.43 times more likely to carry carbapenemase genes relative to plasmids carrying the IS element IS903B. Moreover, plasmids carrying ISKpn26, ISKpn25, and ISKpn14 were 6.10, 28.82, and 31.47 times more likely to be sourced from a clinical environmental setting than the environment relative to IS903B IS harboring plasmid.

ISKpn25 present on IncFIB(pQil) sourced from clinical settings is established across multiple countries, while ISKpn26, ISKpn14, and IS903B appear most often in China. High carbapenemase presence in tandem with IS elements may help promote an extensively drug resistant profile in K. pneumoniae limiting already narrow therapeutic treatment options.

category: microbiology


title: Quorum sensing signal autoinducer-2 inhibits sporulation of Bacillus by interacting with RapC and functions across species

abstract:
Collective behavior of bacteria is regulated by quorum sensing (QS). Bacterial cells sense the density of the population and induce corresponding traits and developmental processes. Autoinducer-2 (AI-2) is a common QS signal that regulates behavior of both Gram-positive and Gram-negative bacteria. In spite of the plethora of processes described to be influenced by AI-2 in diverse Gram-negative bacteria, the AI-2-regulated processes in Bacilli are relatively unexplored. Previously, we demonstrated that AI-2 regulates root colonization of Bacillus velezensis SQR9, a well-studied plant beneficial rhizobacterium. Here, we describe a novel function for AI-2 in B. velezensis SQR9 related to development of dormant spores. AI-2 inhibited the initiation of spore development throught the phosphatase RapC and the DNA binding regulator ComA. Using mutant strains and protein-protein interaction studies, we demonstrate that AI-2 interacts with RapC to stimulate its binding to ComA and therefore inactive ComA. We further demonstrate that ComA is essential for Spo0A-regulated sporulation in B. velezensis SQR9. Finally, the AI-2 molecule could be shared cross species for inhibiting Bacillus sporulation. Our study revealed a novel function and regulation mechanism of AI-2 in sporulation inhibition of Bacilli that overall suggests sporulation to be a population-level decision process in Bacilli rather than just a individual cell behavior.

Author summaryQuorum sensing (QS) regulates many bacterial social behavior. Bacteria cells could moniter and respond cell density by sensing the self produced QS signals. While most QS signals are unique for either Gram-positive or Gram-negative bacteria, autoinducer-2 (AI-2) is a QS signal that could produced by both bacteria groups. However, knowledge of the mechanism of AI-2 affecting bacterial behavior is poorly understood. Here, we found AI-2 inhibite Bacillus velezensis SQR9 sporulation, a generally known bacterial individual behavior. We further revealed the mechanism of AI-2 influencing sporulation of B. velezensis SQR9 was dependent on RapC and ComA. AI-2 interacts with RapC to stimulate its binding to ComA and therefore inactive ComA, and then inhibited the Spo0A-regulated sporulation. Interestingly, we show B. velezensis SQR9 could also sense the AI-2 produced by other bacteria and reduce their own sporulation. Taken together we discovered the novel function of AI-2 in sporulation, which will expand the significance of QS signal that they regulate not only social behavior but also individual behavior of bacteria.


title: E-cigarette aerosol exacerbates cardiovascular oxidative stress in mice with an inactive aldehyde dehydrogenase 2 enzyme

abstract:
AimsE-cigarette aerosol containing aldehydes, including acetaldehyde, are metabolized by the enzyme aldehyde dehydrogenase 2 (ALDH2). However, little is known how aldehyde exposure from e-cigarettes, when coupled with an inactivating ALDH2 genetic variant, ALDH2*2 (present in 8% of the world population), affects cardiovascular oxidative stress. The aim of this study was to determine how e-cigarette aerosol exposure, when coupled with genetics, impacts cardiovascular oxidative stress in wild type ALDH2 and ALDH2*2 knock-in mice.

Methods and ResultsUsing selective ion flow mass spectrometry, we determined that e-cigarette aerosol contains acetaldehyde that are 10-fold higher than formaldehyde or acrolein. Next, using wild type ALDH2 and ALDH2*2 knock-in rodents, we identified organ-specific differences in ALDH2 with the heart having ~1.5-fold less ALDH2 enzyme activity relative to the liver and lung. In isolated cardiac myocytes, acetaldehyde exposure (30 seconds, 0.1-1 M) caused a 4-fold greater peak in calcium levels for ALDH2*2 relative to ALDH2 cardiomyocytes. ALDH2*2 cardiomyocytes exposed to acetaldehyde also demonstrated a 2-fold increase in ROS production and 2.5-fold increase in 4HNE protein adducts relative to ALDH2 cardiomyocytes. For intact rodents, ALDH2*2 knock-in mice exposed to e-cigarette aerosol had an increased heart rate beginning 5 days after exposure compared to wild type ALDH2 mice (775{+/-}30 bpm versus 679{+/-}33 bpm, respectively, *p<0.01, n=7-8/group). E-cigarette aerosol exposure also exacerbated oxidative stress in ALDH2*2 heart homogenates, including a 1.3-fold higher protein carbonyl level, a 1.7-fold higher lipid peroxide level and 1.5-fold greater phosphorylation of NF-{kappa}B relative to wild type ALDH2 homogenates.

ConclusionsThe increased oxidative stress from e-cigarette aerosol aldehydes triggers the proinflammatory NF-{kappa}B pathway. As ALDH2 expression and activity is lower in the heart relative to the lung, the heart could be more susceptible to increases in cardiovascular oxidative stress from e-cigarette aerosol; particularly for those carrying an ALDH2*2 genetic variant which limits acetaldehyde metabolism.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/466292v1_ufig1.gif" ALT="Figure 1">
View larger version (50K):
org.highwire.dtl.DTLVardef@cbba2borg.highwire.dtl.DTLVardef@12b8470org.highwire.dtl.DTLVardef@3ffb8org.highwire.dtl.DTLVardef@89b10b_HPS_FORMAT_FIGEXP  M_FIG C_FIG E-cigarette aerosol exposure triggers increases in ROS that lead to increased protein carbonylation, MDA production, and elevates phosphorylated NF-kB. This exposure to e-cigarette aerosol leads to increases in cardiovascular oxidative stress. For the ALDH2*2 variant, there is limited ability to metabolize the reactive aldehydes from e-cigarette aerosol and with increased levels of oxidative stress at baseline relative to wild type ALDH2, e-cigarette aerosol increased oxidative stress, protein carbonylation, and phosphorylation of NF-kB relative to wild type ALDH2 rodents.


title: When Yeast Cells Change their Mind: Cell Cycle 'Start' is Reversible under Starvation

abstract:
Eukaryotic cells decide in late G1 whether to commit to another round of genome duplication and division. This point of irreversible cell cycle commitment is a molecular switch termed "Restriction Point" in mammals and "Start" in budding yeast. At Start, yeast cells integrate multiple signals such as pheromones, osmolarity, and nutrients. If sufficient nutrients are lacking, cells will not pass Start. However, how the cells respond to nutrient depletion after they have made the Start decision, remains poorly understood.

Here, we analyze by live cell imaging how post-Start yeast cells respond to nutrient depletion. We monitor fluorescently labelled Whi5, the cell cycle inhibitor whose export from the nucleus determines Start. Surprisingly, we find that cells that have passed Start can re-import Whi5 back into the nucleus. This occurs when cells are faced with starvation up to 20 minutes after Start. In these cells, the positive feedback loop is interrupted, Whi5 re-binds DNA, and CDK activation occurs a second time once nutrients are replenished. Cells which re-import Whi5 also become sensitive to mating pheromone again, and thus behave like pre-Start cells. In summary, we show that upon starvation the commitment decision at Start can be reversed. We therefore propose that in yeast, as has been suggested for mammalian cells, cell cycle commitment is a multi-step process, where irreversibility in face of nutrient signaling is only reached approximately 20 minutes after CDK activation at Start.


title: Haspin participates in Aurora phosphorylation at centromeres and contributes to chromosome congression in male mouse meiosis

abstract: Chromosome segregation requires that centromeres properly attach to spindle microtubules. This is an essential step towards the accuracy of cell division and therefore must be precisely regulated in both mitosis and meiosis. One of the main centromeric regulatory signaling pathways is the Haspin-H3T3ph-chromosomal passenger complex (CPC) cascade, which is responsible for the recruitment of the CPC to the centromeres. In mitosis, Haspin kinase phosphorylates H3 at threonine 3 (H3T3ph), the essential histone mark that recruits the CPC whose catalytic component is Aurora B kinase. To date, no data has yet been presented about the action of the centromeric Haspin-H3T3ph-CPC pathway in mammalian male meiosis. We have analyzed the consequences of Haspin chemical inhibition in cultured spermatocytes using LDN-192960. Our in vitro studies suggest that Haspin kinase activity is required for proper chromosome congression during both meiotic divisions and for the recruitment of phosphorylated Aurora B at meiotic centromeres. These results have been confirmed by the characterization of the meiotic phenotype of the genetic mouse model Haspin-/-, which displays similar defects. In addition, our work demonstrates that the absence of H3T3ph histone mark does not alter SGO2 localization to meiotic centromeres. These results add new and relevant information regarding the regulation of centromere function during meiosis.


title: Immunoglobulin-producing AT2-like cells secrete IgA into the extracellular matrix in pulmonary fibrosis

abstract: Pulmonary fibrosis is an interstitial lung disease that can be caused by various factors. Here, we first observed extensive IgA deposition in the extracellular matrix (ECM) of the lungs of mice with pulmonary fibrosis induced by silica inhalation. Consistent with this phenomenon, spatial transcriptomic sequencing of fresh mouse lung tissues from control mice and model mice showed that Igha transcripts were highly expressed in the lesion area. Single-cell RNA sequencing (scRNA-seq) and reconstruction of B cell receptor (BCR) sequences revealed a new cluster of cells with a shared BCR and high expression of genes related to immunoglobulin IgA production. Surprisingly, these clonal cells had more characteristics of AT2 (alveolar epithelial cell type 2) cells than B cells; thus, these cells were named AT2-like cells. Therefore, we propose that secretion of IgA into the ECM by AT2-like cells is an important process that occurs during lung fibrosis.


title: The expression of essential selenoproteins during zebrafish development requires SECIS binding protein 2-like

abstract: The dietary requirement for selenium is based on its incorporation into selenoproteins, which contain the amino acid selenocysteine (Sec). The Sec insertion sequence (SECIS) is an RNA structure found in the 3 UTR of all selenoprotein mRNAs, and it is required to convert in-frame UGA codons from termination to Sec-incorporating codons. There are two proteins that bind to SECIS elements, but only one, SECIS binding protein 2 (Sbp2), has been shown to be required for Sec incorporation. The Sbp2 paralogue, SECIS binding protein 2-like (Secisbp2l) is conserved in all vertebrates and shares many features with Sbp2, but its function is unknown. Here we set out to determine the relative roles of Sbp2 and Secisbp2l by introducing CRISPR mutations in both genes in zebrafish. By monitoring selenoprotein synthesis with 75Se labeling during embryogenesis, we found that sbp2-/- embryos still make a select subset of selenoproteins but secisbp2l-/- embryos retain the full complement. Abrogation of both genes completely prevents selenoprotein synthesis and juveniles die at 14 days post fertilization. Embryos lacking Sbp2 are sensitive to oxidative stress and express the stress marker vtg1. We propose a model where Secisbp2l is required to promote essential selenoprotein synthesis during stress.


title: Soil microbes mediate the effects of environmental variability on plant invasion

abstract: Many studies indicate that increases in resource variability promote plant invasion. However, it remains unknown to what extent these effects might indirectly be mediated by other organisms. To test this, we grew eight alien species in pot-mesocosms with five different native communities under eight combinations of two nutrient-availability, two nutrient-fluctuation and two soil-microbe treatments. We found that when plants grew in sterilized soil, nutrient fluctuation promoted the dominance of alien plants under low nutrient availability, whereas its effect was minimal under high nutrient availability. However, the opposite pattern was found when plants grew in living soil. Analysis of the soil microbial community suggests that this might reflect that nutrient fluctuation strongly increased the soil fungal pathogen diversity under high nutrient availability, but slightly decreased it under low nutrient availability. Our findings indicate that besides its direct influence, environmental variability could also indirectly affect plant invasion via changes in soil-microbial communities.

category: ecology


title: The influence of unmeasured confounding on the MR Steiger approach

abstract: The Mendelian Randomization (MR) Steiger approach is used to determine the direction of a possible causal effect between two phenotypes [1]. For two phenotypes, denoted phenotype 1 and 2, the MR Steiger approach is composed of two parts: (1) MR is performed for a set of single nucleotide polymorphisms (SNPs) that serve as instrumental variables for phenotype 1 and (2) the difference of two correlations, the correlation between the SNPs and phenotype 1 and the correlation between the SNPs and phenotype 2, is calculated. These two parts are then used to determine the direction of a possible causal effect between the two phenotypes. The original MR Steiger paper [1] shows that unmeasured confounding of the two phenotypes affects the validity of the MR Steiger approach, but does not elucidate as to how this occurs. In particular, it was argued that if the magnitude of the observational variance explained between the two phenotypes is above 0.2, the MR Steiger method may return the incorrect causal direction due to unmeasured confounding. This may initially seem surprising since unmeasured confounding does not induce spurious associations between the SNP and phenotype 2, as we demonstrate using directed acyclic graphs. In this note, we show that this is because unmeasured confounding may rescale the magnitude of a non-zero association, and thereby distort the comparison of the correlation between the SNP and phenotype 2 and the correlation between the SNP and phenotype 1. We will end with a number of cautionary remarks on the MR Steiger method, which are partly motivated by this and mentioned in the original MR Steiger paper [1].

category: genetics


title: Maize root-associated microbes likely under adaptive selection by the host to enhance phenotypic performance

abstract: The root-associated microbiome (rhizobiome) plays a non-negligible role in determining plant health, stress tolerance, and nutrient use efficiency. However, it remains unclear to what extent the composition of the rhizobiome is governed by intraspecific variation in host plant genetics in the field and the degree to which host plant selection can reshape the composition of the rhizobiome. Here we quantify the rhizosphere microbial communities associated with a replicated diversity panel of 230 maize (Zea mays L.) genotypes grown in agronomically relevant conditions under high N (+N) and low N (-N) treatments. We show that the abundance of many root-associated microbes within a functional core microbial community of 150 abundant and consistently reproducible microbial groups is explainable by natural genetic variation in the host plant, with a greater proportion of microbial variance attributable to plant genetic variation in low N conditions. Population genetic approaches identify signatures of purifying selection in the maize genome associated with the abundance of several groups of microbes in the maize rhizobiome. Genome-wide association studies conducted using rhizobiome phenotypes identified n = 467 microbe-associated plant loci (MAPLs) in the maize genome linked to variation in the abundance of n = 115 microbial groups in the maize rhizosphere. In 62/115 cases, which is more than expected by chance, the abundance of these same microbial groups was correlated with variation in plant vigor indicators derived from high throughput phenotyping of the same field experiment. This study provides insights into harnessing the full potential of root-associated microbial symbionts in maize production.


title: DNA-free CRISPR-Cas9 gene editing of tetraploid tomatoes using protoplast regeneration

abstract:
Wild tomatoes are important genomic resources for tomato research and breeding. Development of a foreign DNA-free CRISPR-Cas delivery system has potential to mitigate public concern about genetically modified organisms. Here, we established a DNA-free protoplast regeneration and CRISPR-Cas9 genome editing system for Solanum peruvianum, an important resource for tomato introgression breeding. We generated mutants for genes involved in small interfering RNAs (siRNA) biogenesis, RNA-DEPENDENT RNA POLYMERASE 6 (SpRDR6) and SUPPRESSOR OF GENE SILENCING 3 (SpSGS3); pathogen-related peptide precursors, PATHOGENESIS-RELATED PROTEIN-1 (SpPR-1) and PROSYSTEMIN (SpProsys); and fungal resistance (MILDEW RESISTANT LOCUS O, SpMlo1) using diploid or tetraploid protoplasts derived from in vitro-grown shoots. The ploidy level of these regenerants was not affected by PEG-calcium-mediated transfection, CRISPR reagents, or the target genes. By karyotyping and whole genome sequencing analysis, we confirmed that CRISPR-Cas9 editing did not introduce chromosomal changes or unintended genome editing sites. All mutated genes in both diploid and tetraploid regenerants were heritable in the next generation. spsgs3 null T0 regenerants and sprdr6 null T1 progeny had wiry, sterile phenotypes in both diploid and tetraploid lines. The sterility of the spsgs3 null mutant was partially rescued, and fruits were obtained by grafting to wild-type stock and pollination with wild-type pollen. The resulting seeds contained the mutated alleles. Tomato yellow leaf curl virus proliferated at higher levels in spsgs3 and sprdr6 mutants than in the wild type. Therefore, this protoplast regeneration technique should greatly facilitate tomato polyploidization and enable the use of CRISPR-Cas for S. peruvianum domestication and tomato breeding.

One-sentence summaryDNA-free CRISPR-Cas9 genome editing in wild tomatoes creates stable and inheritable diploid and tetraploid regenerants.


title: Pseudomonas syringae  pv. tomato DC3000 Effector HopG1 is a multi-faceted protein that Triggers Necrotic Cell Death that is attenuated by the Nonhost Resistance 2B (AtNHR2B) Protein

abstract: The plant pathogenic bacterium Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) has become a paradigm in plant-bacteria interactions due to its ability to cause disease in the model plant Arabidopsis thaliana. Pst DC3000 uses the type III secretion system to deliver type III secreted effectors (T3SEs) directly into the plant cytoplasm. Pst DC3000 T3SEs contribute to pathogenicity by suppressing plant defense responses and targeting plants physiological processes. Although the complete repertoire of effectors encoded in the Pst DC3000 genome have been identified, the specific function for most of them remains to be elucidated. The mitochondrial-localized T3E HopG1, suppresses plant defense responses and promotes the development of disease symptoms. Here, we show that HopG1 triggers necrotic cell death that enables the growth of non-adapted pathogens. We further showed that HopG1 interacts with the plant immunity-related protein AtNHR2B and that AtNHR2B attenuates HopG1-virulence functions.


title: Multi-area recordings and optogenetics in the awake, behaving marmoset

abstract: The common marmoset has emerged as a key primate model in neuroscience. Marmosets are small in size, show great potential as transgenic models and exhibit complex behaviors. These advantages place the marmoset model in the critical gap between rodents and larger primates. Thus, it is necessary to develop technology that enables monitoring and manipulation of the neural circuits underlying the behavior of the marmoset. Here, we present a novel approach to record and optogenetically manipulate neural activity in the awake, behaving marmoset. Our design utilizes a light-weight, 3D printed titanium chamber that can house several high-density silicon probes for semi-chronic recordings, while enabling simultaneous optogenetic stimulation. Surgical procedures are streamlined via custom 3D printed guides and implantation holders. We demonstrate the application of our method by recording multi- and single-unit data from areas V1 and V6 with 192 channels simultaneously, and show for the first time that optogenetic activation of excitatory neurons in area V6 can influence behavior in a detection task. Together, the work presented here will support future studies investigating the neural basis of perception and behavior in the marmoset.


title: Distinct representation of cue-outcome association by D1 and D2 neurons in the olfactory striatum

abstract: Positive and negative associations acquired through olfactory experience are thought to be especially strong and long-lasting. The conserved direct olfactory sensory input to the ventral striatal olfactory tubercle (OT) and its convergence with dense dopaminergic input to the OT could underlie this privileged form of associative memory, but how this process occurs is not well understood. We imaged the activity of the two canonical types of striatal neurons, expressing D1 or D2 type dopamine receptors, in the OT at cellular resolution while mice learned odor-outcome associations ranging from aversive to rewarding. D1 and D2 neurons both responded to rewarding and aversive odors. D1 neurons in the OT robustly and bidirectionally represented odor valence, responding similarly to odors predicting similar outcomes regardless of odor identity. This valence representation persisted even in the absence of a licking response to the odors and in the absence of the outcomes, indicating a true transformation of odor sensory information by D1 OT neurons. In contrast, D2 neuronal representation of the odor-outcome associations was weaker, contingent on a licking response by the mouse, and D2 neurons were more selective for odor identity than valence. Stimulus valence coding in the OT was modality-sensitive, with separate sets of D1 neurons responding to odors and sounds predicting the same outcomes, suggesting that integration of multimodal valence information happens downstream of the OT. Our results point to distinct representation of identity and valence of odor stimuli by D1 and D2 neurons in the OT.


title: Distinct representation of cue-outcome association by D1 and D2 neurons in the ventral striatum's olfactory tubercle


title: Consequences of endogenous and virally-induced hyperphosphorylated tau on behavior and cognition in a rat model of Alzheimer's disease

abstract:
BackgroundThe locus coeruleus (LC) is one of the earliest brain regions to accumulate hyperphosphorylated tau, but a lack of animal models that recapitulate this pathology has hampered our ability to understand its contributions to the pathophysiology of Alzheimers disease (AD).

ObjectiveWe previously reported that TgF344-AD rats, which overexpress mutant human amyloid precursor protein and presenilin-1, accumulate early endogenous hyperphosphorylated tau in the LC. Here, we used TgF344-AD rats and a wild-type (WT) human tau virus to interrogate the effects of endogenous hyperphosphorylated rat tau and human tau in the LC on AD-related neuropathology and behavior.

MethodsTwo-month old TgF344-AD and WT rats received bilateral LC infusions of WT human tau or mCherry control virus driven by the noradrenergic-specific PRSx8 promoter. Rats were subsequently assessed at 6 and 12 months for arousal (sleep latency), anxiety-like behavior (open field, elevated plus maze, novelty-suppressed feeding), passive coping (forced swim task), and learning and memory (Morris water maze and fear conditioning). Hippocampal microglia, astrocyte, and AD pathology were evaluated using immunohistochemistry.

ResultsIn general, the effects of age were more pronounced than genotype or treatment; older rats displayed greater hippocampal pathology, took longer to fall asleep, had reduced locomotor activity, floated more, and had impaired cognition compared to younger animals. TgF344-AD rats showed increased anxiety-like behavior and impaired learning and memory. The tau virus had negligible influence on most measures.

ConclusionEffects of hyperphosphorylated tau on AD-like neuropathology and behavioral symptoms were subtle. Further investigation of different forms of tau is warranted.


title: Alpha oscillations are involved in localizing touch on hand-held tools

abstract: The sense of touch is not restricted to the body but can also extend to external objects. When we use a hand-held tool to contact an object, we feel the touch on the tool and not in the hand holding the tool. The ability to perceive touch on a tool actually extends along its entire surface, allowing the user to accurately localize where it is touched similarly as they would on their body. While the neural mechanisms underlying the ability to localize touch on the body have been largely investigated, those allowing to localize touch on a tool are still unknown. We aimed to fill this gap by recording the EEG signal of participants while they localized tactile stimuli on a hand-held rod. We focused on oscillatory activity in the alpha (7-14 Hz) and beta (15-30 Hz) range, as they have been previously linked to distinct spatial codes used to localize touch on the body. Beta activity reflects the mapping of touch in skin-based coordinates, whereas alpha activity reflects the mapping of touch in external space. We found that alpha activity was solely modulated by the location of tactile stimuli applied on a hand-held rod. Source reconstruction suggested that this alpha power modulation was localized in a network of fronto-parietal regions previously implicated in higher-order tactile and spatial processing. These findings are the first to implicate alpha oscillations in tool-extended sensing and suggest an important role for processing touch in external space when localizing touch on a tool.


title: Btbd11 is an inhibitory interneuron specific synaptic scaffolding protein that supports excitatory synapse structure and function

abstract: Synapses in the brain exhibit cell-type-specific differences in basal synaptic transmission and plasticity. Here, we evaluated cell-type-specific differences in the composition of glutamatergic synapses, identifying Btbd11, as an inhibitory interneuron-specific synapse-enriched protein. Btbd11 is highly conserved across species and binds to core postsynaptic proteins including Psd-95. Intriguingly, we show that Btbd11 can undergo liquid-liquid phase separation when expressed with Psd-95, supporting the idea that the glutamatergic post synaptic density in synapses in inhibitory and excitatory neurons exist in a phase separated state. Knockout of Btbd11 from inhibitory interneurons decreased glutamatergic signaling onto parvalbumin-positive interneurons. Further, both in vitro and in vivo, we find that Btbd11 knockout disrupts network activity. At the behavioral level, Btbd11 knockout from interneurons sensitizes mice to pharmacologically induced hyperactivity following NMDA receptor antagonist challenge. Our findings identify a cell-type-specific protein that supports glutamatergic synapse function in inhibitory interneurons--with implication for circuit function and animal behavior.


title: An Immunogold Single Extracellular Vesicular RNA and Protein (AuSERP) Biochip to Predict Responses to Immunotherapy in Non-Small Cell Lung Cancer Patients

abstract: Conventional PD-L1 immunohistochemical tissue biopsies only predict 20~40% of non-small cell lung cancer (NSCLC) patients that will respond positively to anti-PD-1/PD-L1 immunotherapy. Herein, we present an immunogold biochip to quantify single extracellular vesicular RNA and protein (AuSERP) as a non-invasive alternative. With only 3 L of serum, PD-1/PD-L1 proteins on the surface of extracellular vesicles (EVs) and EV PD-1/PD-L1 messenger RNA (mRNA) cargo were detected at a single-vesicle resolution and exceeded the sensitivities of ELISA and qRT-PCR by 1000 times. By testing a cohort of 27 non-responding and 27 responding NSCLC patients, AuSERP indicated that the single-EV mRNA biomarkers surpass the single-EV protein biomarkers at predicting patient responses to immunotherapy. Dual single-EV PD-1/PD-L1 mRNA detection differentiated responders from non-responders with an accuracy of 72.2% and achieved an NSCLC diagnosis accuracy of 93.2%, suggesting the potential for AuSERP to provide enhanced immunotherapy predictions and cancer diagnoses within the clinical setting.


title: Impact of Protein Identity on Tumor-Associated Antigen Uptake into Infiltrating Immune Cells: A Comparison of Different Fluorescent Proteins as Model Antigens

abstract:
Effective immune responses depend on efficient antigen uptake in the periphery, transport of those antigens to, and presentation in draining lymph nodes (LNs). These processes have been studied intensively using stable fluorescent proteins (FPs) as model antigens. To date, ZsGreen is the only FP that can be tracked efficiently towards LNs, hence, it is difficult to compare studies using alternated tracking proteins.

Here, we systematically compared six different FPs. We included ZsGreen, ZsYellow, DsRed, AsRed, mCherry, and mRFP based on sequence homology and/or origin species, and generated FP-expressing tumor cell lines. Stability of fluorescent signal was assessed in vitro over time, across different pH environments, and in vivo through FP antigen uptake and transfer to immune cells isolated from tumors and tumor-draining LNs.

ZsGreen could be detected in high percentages of all analyzed tumor-infiltrating immune cells, with highest amounts in tumor-associated macrophages (TAMs) and type 2 conventional dendritic cells (cDC2s). ZsYellow, AsRed, and DsRed followed a similar pattern, but percentages of FP-containing immune cells in the tumor were lower than for ZsGreen. Strikingly, mRFP and mCherry demonstrated a  non-canonical antigen uptake pattern where percentages of FP-positive tumor-infiltrating immune cells were highest for cDC1s not TAMs and cDC2s despite comparable stabilities and localization of all FPs. Analysis of antigen-containing cells in the LN was hindered by intracellular degradation of FPs. Only ZsGreen could be efficiently tracked to the LN, though some signal was measurable for ZsYellow and DsRed.

In summary, we find that detection of antigen uptake and distribution is subject to variabilities related to fluorophore nature. Future experiments need to consider that these processes might be impacted by protein expression, stability, or other unknown factors. Thus, our data sheds light on potential under-appreciated mechanisms regulating antigen transfer and highlights potential uses and necessary caveats to interpretation based on FP use.


title: The use of disinfectant in barn cleaning alters microbial composition and increases carriage of Campylobacter jejuni in broiler chickens

abstract: To maintain food safety and flock health in broiler chicken production, biosecurity approaches to keep chicken barns free of pathogens are important. Canadian broiler chicken producers must deep clean their barns with chemical disinfectants at least once annually (full disinfection; FD) and may wash with water (water-wash; WW) throughout the year. However, many producers use FD after each flock, assuming a greater efficacy of more stringent cleaning protocols, although little information is known regarding how these two cleaning practices affect pathogen population and gut microbiota. In the current study, a cross-over experiment over four production cycles was conducted in seven commercial chicken barns to compare WW and FD. We evaluated the effects of barn cleaning method on the commercial broiler performance, cecal microbiota composition, pathogen occurrence and abundance, as well as short-chain fatty acid concentrations in the month-old broiler gut. The 30-day body weight and mortality rate were not affected by the barn cleaning methods. The WW resulted in a modest but significant effect on the structure of broiler cecal microbiota (weighted-UniFrac; adonis p = 0.05, and unweighted-UniFrac; adonis p = 0.01), with notable reductions in Campylobacter jejuni occurrence and abundance. In addition, the WW group had increased cecal acetate, butyrate and total short-chain fatty acid concentrations, which were negatively correlated with C. jejuni abundance. Our results support the use of WW over FD to enhance the activity of the gut microbiota and potentially reduce zoonotic transmission of C. jejuni in broiler production without previous disease challenges.


title: Transcriptional regulation of cyclophilin D by BMP/SMAD signaling and its role in osteogenic differentiation

abstract: Cyclophilin D (CypD) promotes opening of the mitochondrial permeability transition pore (MPTP) which plays a key role in both cell physiology and pathology. It is, therefore beneficial for cells to tightly regulate CypD and MPTP but little is known about such regulation. We have reported before that CypD is downregulated and MPTP deactivated during differentiation in various tissues. Herein, we identify BMP/Smad signaling, a major driver of differentiation, as a transcriptional repressor of the CypD gene, Ppif. Using osteogenic induction of mesenchymal lineage cells as a model of BMP/Smad-dependent differentiation, we show that CypD is in fact transcriptionally repressed during this process. The importance of such CypD downregulation is evidenced by the negative effect of CypD  rescue via gain-of-function on osteogenesis both in vitro and in vivo. In sum, we characterized BMP/Smad signaling as a regulator of CypD expression and elucidated the role of CypD downregulation during cell differentiation.


title: Separable mechanisms drive local and global polarity establishment in the C. elegans intestinal epithelium

abstract:
Apico-basolateral polarization is essential for epithelial cells to function as selective barriers and transporters, and to provide mechanical resiliency to organs. Epithelial polarity is established locally, within individual cells to establish distinct apical, junctional, and basolateral domains, and globally, within a tissue where cells coordinately orient their apico-basolateral axes. Using live imaging of endogenously tagged proteins and tissue specific protein depletion in the C. elegans embryonic intestine, we found that local and global polarity establishment are temporally and genetically separable. Local polarity is initiated prior to global polarity and is robust to perturbation. PAR-3 is required for global polarization across the intestine but is not required for local polarity establishment as small groups of cells are able to correctly establish polarized domains in PAR-3 depleted intestines in an HMR-1/E-cadherin dependent manner. Despite belonging to the same apical protein complex, we additionally find that PAR-3 and PKC-3/aPKC have distinct roles in the establishment and maintenance of local and global polarity. Together, our results indicate that different mechanisms are required for local and global polarity establishment in vivo.

SUMMARY STATEMENTLive-imaging and intestine specific protein depletion reveal that apico-basolateral polarity establishment can be temporally and genetically separated at the local level of individual cells and globally, across a tissue.


title: Computational simulations reveal that Abl activity controls cohesiveness of actin networks in growth cones

abstract:
Extensive studies of growing axons have revealed many individual components and protein interactions that guide neuronal morphogenesis. Despite this, however, we lack any clear picture of the emergent mechanism by which this nanometer-scale biochemistry generates the multi-micron scale morphology and cell biology of axon growth and guidance in vivo. To address this, we studied the downstream effects of the Abl signaling pathway using a computer simulation software (MEDYAN) that accounts for mechanochemical dynamics of active polymers. Previous studies implicate two Abl effectors, Arp2/3 and Enabled, in Abl-dependent axon guidance decisions. We now find that Abl alters actin architecture primarily by activating Arp2/3, while Enabled plays a more limited role. Our simulations show that simulations mimicking modest levels of Abl activity bear striking similarity to actin profiles obtained experimentally from live-imaging of actin in wild type axons in vivo. Using a graph-theoretical filament-filament contact analysis, moreover, we find that networks mimicking hyperactivity of Abl (enhanced Arp2/3) are fragmented into smaller domains of actin that interact weakly with each other, consistent with the pattern of actin fragmentation observed upon Abl overexpression in vivo. Two perturbative simulations further confirm that high Arp2/3 actin networks are mechanically disconnected and fail to mount a cohesive response to perturbation. Taken together, these data provide a molecular-level picture of how the large-scale organization of the axonal cytoskeleton arises from the biophysics of actin networks.

Highlight summaryHow do single-molecule dynamics produce multi-micron scale changes in actin organization in an extending axon? Comparison of computational simulations to in vivo data suggests that Abl kinase and Arp2/3 expand actomyosin networks by fragmenting into multiple domains, thus toggling the axon between states of local vs global internal connectivity.


title: Evolution of reduced mate-harming tendency of males in Drosophila melanogaster populations selected for faster life history

abstract:
Detrimental effect of males on female, often termed mate harm, is a hallmark of sexual conflict. Allowed to evolve unchecked, mate harming traits are predicted to bring down average fitness of a population, unless mitigated by the evolution of resistance in females. In addition, life history may also modulate sexual conflict, but the mechanism is not clearly understood. Here we investigated the evolution of mate harm in a set of experimentally evolved laboratory populations of Drosophila melanogaster wherein a faster aging has evolved in response to >1000 generations of selection for faster development and early reproduction. We quantified mortality and fecundity of Oregon R females held with evolved (ACO) and ancestral males (CO) to show that the evolved males are significantly less detrimental to their mates. We compared our results from the ACO males with that from a phenocopied version of the ancestral regime (CCO) to show that only part of the observed difference in mate harm can be attributed to the evolved difference in body size. We further show that the reduction in mate harming ability evolved despite an increase in courtship activity, especially early in life. We discuss the causative role of an evolved reproductive schedule and altered breeding ecology.

Significance statementSexually antagonistic male effects can significantly bring down female fitness. Along with female counter evolution of resistance traits, life history has been conjectured to impose constrains on the evolution of such harming ability in males. Here, we report the evolution of mate harming ability in males of a set of five replicate Drosophila melanogaster populations that evolved smaller size and faster aging as a result of >1000 generations of experimental evolution for faster development and early reproduction. We show that in spite of ample scope of sexual selection, the faster aging males have evolved reduced mate harming ability despite being more active in courting their mates. To the best of our knowledge, this is one of the first clear evidences demonstrating the causal relationship between evolution of life history and reduction in sexual antagonism in a population.

category: evolutionary biology


title: orthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

abstract: Molecular evolution studies, such as phylogenomic studies and genome-wide surveys of positive selection, often rely on gene families of single-copy orthologs (SC-OGs). In contrast, large gene families with multiple homologs in one or more species--a phenomenon observed among several important families of genes such as transporters and transcription factors--are often ignored because identifying and retrieving SC-OGs nested within them is challenging. To address this issue and increase the number of markers used in molecular evolution studies, we developed orthoSNAP, a software that uses a phylogenetic framework to simultaneously split gene families into SC-OGs and prune species-specific inparalogs. We term SC-OGs identified by orthoSNAP as SNAP-OGs because they are identified using a splitting and pruning procedure. From 46,645 orthologous groups of genes inferred using graph-based clustering of sequence similarity scores across four separate eukaryotic datasets, we identified 6,634 SC-OGs; using orthoSNAP on the remaining 40,011 orthologous groups of genes, we identified an additional 6,630 SNAP-OGs. Comparison of SNAP-OGs and SC-OGs revealed that their phylogenetic information content was similar. orthoSNAP is useful for increasing the number of markers used in molecular evolution data matrices, a critical step for robustly inferring and exploring the tree of life.


title: Manual curation and phylogenetic analysis of chitinase family genes in the Asian citrus psyllid, Diaphorina citri

abstract: Chitinases are enzymes that digest the polysaccharide polymer chitin. Chitin is a major component of insect exoskeletons, which must be replaced multiple times during growth and development in a process known as molting. Insect genomes usually have multiple chitinase genes, some of which are required for molting and some whose functions are still unknown. Since knockdown of the chitinases required for molting causes high levels of lethality, chitinase genes have drawn interest as targets for RNAi-based pest control methods. The Asian citrus psyllid, Diaphorina citri, carries the bacterium that causes Huanglongbing, also known as citrus greening disease, which is devastating the citrus industry worldwide. We have identified and annotated 12 chitinase family genes from D. citri as part of a community effort to create high quality gene models to facilitate the design of interdictory molecules for pest control. Using predicted protein domain content and phylogenetic analysis, we categorized the D. citri chitinases according to a previously established classification scheme and re-evaluated the classification of chitinases in other hemipterans. In addition to chitinases belonging to known groups, we identified a novel class of chitinases present in D. citri and several related hemipterans that appears to be the result of horizontal gene transfer.


title: Early-Stage Identification and Avoidance of Antisense Oligonucleotides Causing Species-Specific Inflammatory Responses in Human Volunteers Peripheral Blood Mononuclear Cells

abstract: A human peripheral blood mononuclear cell (PBMC)-based assay was developed to identify antisense oligonucleotide (ASO) with the potential to activate a cellular innate immune response outside of an acceptable level. The development of this assay was initiated when ISIS 353512 targeting the mRNA for human C-reactive protein was tested in a phase I clinical trial in which healthy human volunteers unexpectedly experienced increases in interleukin-6 (IL-6) and C-reactive protein. This level of immune stimulation was not anticipated following rodent and non-human primate safety studies in which no evidence of exaggerated proinflammatory effects were observed. The IL-6 increase induced by ISIS 353512 was caused by activation of B-cells. The IL-6 induction was inhibited by chloroquine pretreatment of the PBMC and the nature of the ASOs suggested that the response is mediated by a toll like receptor, in all likelihood TLR9. While assessing the inter PBMC donor variability, two class of responders to ISIS 353512 were identified (discriminator and non-discriminators). The discriminator source of PBMC was shown to produce low level of IL-6 after 24 hours in culture in absence of ASO treatment. The PBMC assay using discriminator donors was shown to be reproducible allowing to assess reliably the immune potential of ASOs via comparison to known benchmark ASO controls that were previously shown to be either safe or inflammatory in clinical trials.


title: Core circadian clock and light signalling genes brought into genetic linkage across the green lineage

abstract:
The circadian clock ensures that biological processes are phased to the correct time of day. In plants the circadian clock is conserved at both the level of transcriptional networks as well as core genes. In the model plant Arabidopsis thaliana, the core circadian singleMYB (sMYB) genes CCA1 and RVE4 are in genetic linkage with the PSEUDO-RESPONSE REGULATOR (PRR) genes PRR9 and PRR7 respectively. Leveraging chromosome-resolved plant genomes and syntenic ortholog analysis it was possible to trace this genetic linkage back to the basal angiosperm Amborella and identify an additional evolutionarily conserved genetic linkage between PIF3 and PHYA. The LHY/CCA1-PRR5/9, RVE4/8-PRR3/7 and PIF3-PHYA genetic linkages emerged in the bryophyte lineage and progressively moved within several genes of each other across an array of higher plant families representing distinct whole genome duplication and fractionation events. Soybean maintains all but two genetic linkages, and expression analysis revealed the PIF3-PHYA linkage overlapping with the E4 maturity group locus was the only pair to robustly cycle with an evening phase in contrast to the sMYB-PRR morning and midday phase. While most monocots maintain the genetic linkages, they have been lost in the economically important grasses (Poaceae) such as maize where the genes have been fractionated to separate chromosomes and presence/absence variation results in the segregation of PRR7 paralogs across heterotic groups. The evolutionary conservation of the genetic linkage as well as its loss in the grasses provides new insight in the plant circadian clock, which has been a critical target of breeding and domestication.

Summary SentenceThe genetic linkage of the core circadian clock components has evolutionary origins in bryophytes and sheds light on the current functioning and selection on the circadian clock in crops.


title: Type 1 interferon supports B cell responses to polysaccharide antigens but is not required for MPL/TDCM adjuvant effects on innate B cells

abstract:
We previously described monophosphoryl lipid A (MPL) and synthetic cord factor, trehalose-6,6-dicorynomycolate (TDCM) significantly increases antibody (Ab) responses to T cell independent type 2 antigens (TI-2 Ags) in a manner dependent on B cell-intrinsic TLR4 expression as well as MyD88 and TRIF adapter proteins. Given the requirement for TRIF in optimal MPL/TDCM adjuvant effects and the capacity of MPL to drive type I IFN production, we aimed to investigate the extent to which adjuvant effects on TI-2 Ab responses depend on type I IFN receptor (IFNAR) signaling. We found IFNAR-/- mice had impaired early TI-2 Ag-induced B cell activation and expansion and that B cell-intrinsic type I IFN signaling on B cells was essential for normal antibody responses to TI-2 Ags, including haptenated Ficoll and the pneumococcal vaccine, Pneumovax23. However, MPL/TDCM significantly increased TI-2 IgM and IgG responses in IFNAR-/- mice. MPL/TDCM enhanced TI-2 Ab production primarily by activating innate B cells (B-1b and splenic CD23- B cells) as opposed to CD23+ enriched follicular B cells. In summary, our study highlights an important role for type I IFN in supporting early B cell responses to TI-2 Ags through B cell-expressed IFNAR, but nonetheless demonstrates an MPL/TDCM adjuvant significantly increases TI-2 Ab responses independently of type I IFN signaling and does so by predominantly supporting increased polysaccharide-specific Ab production by innate B cell populations.

Key pointsO_LIB cell-intrinsic IFNAR expression promotes TI-2 Ab responses.
C_LIO_LIMPL/TDCM adjuvant effects are independent of type 1 IFN.
C_LIO_LIMPL/TDCM promotes TI-2 Ab responses by innate B cells.
C_LI


title: Prophylactic Treatment of Undernourished Mice with Cotrimoxazole Induces a Different Profile of Dysbiosis with Functional Metabolic Alterations

abstract: 1.Childhood malnutrition affects physiology and development, it increases infection rate which may not present clinical signs in severe cases. To overcome this issue, the World Health Organization recommends prophylactic treatment with Cotrimoxazole (SXT) along with nutritional recovery. This treatment is controversial since evidence of reduction in morbidity and mortality is not a consensus and could induce the development of antibiotic resistant bacteria. Moreover, the impact of the use of this wide-spectrum antibiotic on gut microbiota, in a critical period of development and weakness, is unknown. To understand how SXT prophylaxis could affect gut microbiota in undernutrition, we induced protein-energy undernutrition in weaning C57BL/6 mice for three weeks and treated animals with SXT for two weeks. Using 16S rRNA gene sequencing we compared the taxonomic composition and metabolic pathways of control mice, animals submitted to undernutrition (UND), treated with SXT, or undernourished and SXT treated (UND+SXT). Undernutrition protocol was responsible for increasing Bacteroidetes and decreasing Firmicutes abundance. We identified that UND mice had a significant increase in predicted pathways related to metabolic syndromes later in life. The prophylactic SXT treatment alone resulted in significant loss in community richness and beta diversity. In addition, we identified the reduction of 6 families in SXT treated mice, including the butyrate producers Lachnospiraceae and Ruminococcaceae. The double challenge (UND+SXT) resulted in a reduction in Clostridiaceae family and in the urea cycle pathway, both related to the fermentation of amino acids, the intestinal epithelial permeability, and the healthy gut environment. Our results show that SXT prophylaxis during an undernourishment period in young mice did not re-establish the undernourished microbiota community composition similar to healthy controls, but induces a distinct dysbiotic profile, with functional metabolic consequences.


title: Cholesterol and sphingomyelin are critical for Fcγ receptor-mediated phagocytosis of Cryptococcus neoformans by macrophages

abstract: Cryptococcus neoformans is a fungal pathogen that causes life-threatening meningoencephalitis in lymphopenic patients. Pulmonary macrophages comprise the first line of host defense upon inhalation of fungal spores, whereby macrophages either aid in clearance or serve as a niche for its dissemination. Given that macrophages play a key role in the outcome of a cryptococcal infection, it is crucial to understand factors that mediate phagocytosis of C. neoformans. Since lipid rafts (high order plasma membrane domains enriched in cholesterol and sphingomyelin) have been implicated in facilitating phagocytosis, we evaluated whether these ordered domains govern macrophages ability to phagocytose C. neoformans. We found that cholesterol or sphingomyelin depletion resulted in significantly deficient IgG-mediated phagocytosis of the fungus. Moreover, repletion of macrophage cells with a raft-promoting sterol (7-dehydrocholesterol) rescued this phagocytic deficiency while a raft-inhibiting sterol (coprostanol) significantly decreased IgG-mediated phagocytosis of C. neoformans. Using a photoswitchable sphingomyelin (AzoSM), we observed that the raft-promoting conformation (trans-AzoSM) resulted in efficient phagocytosis whereas raft-inhibiting conformation (cis-AzoSM) significantly blunted phagocytosis in a reversible manner. We observed that the effect on phagocytosis may be mediated by facilitating Fc{gamma} receptor (Fc{gamma}R) function, whereby IgG immune complexes cross-link to Fc{gamma}RIII, resulting in tyrosine phosphorylation of FcR {gamma}-subunit (FcR{gamma}), an important accessory protein in the Fc{gamma}R signaling cascade. Correspondingly, cholesterol or sphingomyelin depletion resulted in decreased FcR{gamma} phosphorylation. Repletion with 7-dehydrocholesterol restored phosphorylation, whereas repletion with coprostanol showed FcR{gamma} phosphorylation comparable to unstimulated cells. Together, these data suggest that lipid rafts are critical for facilitating Fc{gamma}RIII-mediated phagocytosis of C. neoformans.


title: Effect of plant tissues on DNA quantity and quality of barley (Hordeum vulgare) validating through PCR technique

abstract: The use of molecular techniques to deal with plant molecular breeding requires the extraction of genomic DNA in good quantity and quality, which can be influenced by method of extraction and source of DNA (plant species, plant part or tissues). However, this research focuses on plant tissue source and tried to describe the quality and quantity of DNA isolated from different tissues of barley crop. CTAB protocol was used for the isolation of DNA and both the quality and quantity of this DNA was validated through gel electrophoresis, Qubit quantification and PCR amplifications. The result showed that DNA could be successfully extracted from all tissues of plants and the yield of DNA obtained was variable ranging from 179ng l-1 in stem to 750ng l-1 in young leave. Band intensity of genomic and PCR amplified DNA was good for DNA isolated from young and matured leave. Faint band was observed in the PCR amplification for DNA isolated from stem but no to unreliable amplification was obtained for seeds and roots, respectively. Thus, for any molecular technique in barley crop research, the best tissue for DNA isolation using modified CTAB, is young or matured leave and alternatively stem can be used as DNA source.

category: molecular biology


title: Statistical inference in population genomics

abstract: The field of population genomics has grown rapidly in response to the recent advent of affordable, large-scale sequencing technologies. As opposed to the situation during the majority of the 20th century, in which the development of theoretical and statistical population-genetic insights out-paced the generation of data to which they could be applied, genomic data are now being produced at a far greater rate than they can be meaningfully analyzed and interpreted. With this wealth of data has come a tendency to focus on fitting specific (and often rather idiosyncratic) models to data, at the expense of a careful exploration of the range of possible underlying evolutionary processes. For example, the approach of directly investigating models of adaptive evolution in each newly sequenced population or species often neglects the fact that a thorough characterization of ubiquitous non-adaptive processes is a prerequisite for accurate inference. We here describe the perils of these tendencies, present our consensus views on current best practices in population genomic data analysis, and highlight areas of statistical inference and theory that are in need of further attention. Thereby, we argue for the importance of defining a biologically relevant baseline model tuned to the details of each new analysis, of skepticism and scrutiny in interpreting model-fitting results, and of carefully defining addressable hypotheses and underlying uncertainties.


title: Recommendations for improving statistical inference in population genomics


title: Efficacy of longevity interventions in C. elegans is determined by early life activity of RNA splicing factors

abstract:
Geroscience aims to target the aging process to extend healthspan. However, even isogenic individuals show heterogeneity in natural aging rate and responsiveness to pro-longevity interventions, limiting translational potential. Using in vivo mini gene reporters in isogenic C. elegans, we show that alternative splicing of mRNAs related to lipid metabolism in young animals is coupled to subsequent life expectancy. Further, activity of RNA splicing factors REPO-1 and SFA-1 early in life modulates effectiveness of specific longevity interventions via POD-2/ACC1 and regulation of lipid utilization. In addition, early inhibition of REPO-1 renders animals refractory to late onset suppression of the TORC1 pathway. Together these data suggest that activity of RNA splicing factors and the metabolic landscape early in life can modulate responsiveness to longevity interventions and may explain variance in efficacy between individuals.

One Sentence SummaryEfficacy of pro-longevity interventions in C. elegans is determined by the activity of splicing factors and the lipid metabolic landscape early in the life of the individual.


title: CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching

abstract:
Adaptive immune receptor (AIR) repertoires (AIRRs) record past immune encounters with exquisite specificity. Therefore, identifying identical or similar AIR sequences across individuals is a key step in AIRR analysis for revealing convergent immune response patterns that may be exploited for diagnostics and therapy. Existing methods for quantifying AIRR overlap do not scale with increasing dataset numbers and sizes. To address this limitation, we developed CompAIRR, which enables ultra-fast computation of AIRR overlap, based on either exact or approximate sequence matching. CompAIRR improves computational speed 1000-fold relative to the state of the art and uses only one-third of the memory: on the same machine, the exact pairwise AIRR overlap of 104 AIRRs with 105 sequences is found in [~]17 minutes, while the fastest alternative tool requires 10 days. CompAIRR has been integrated with the machine learning ecosystem immuneML to speed up various commonly used AIRR-based machine learning applications.

Availability and implementationCompAIRR code and documentation are available at https://github.com/uio-bmi/compairr. Docker images are available at https://hub.docker.com/r/torognes/compairr. The scripts used for benchmarking and creating figures, and all raw data, may be found at https://github.com/uio-bmi/compairr-benchmarking.


title: Elementary vectors and autocatalytic sets for computational models of cellular growth

abstract:
Traditional (genome-scale) metabolic models of cellular growth involve an approximate biomass "reaction", which specifies biomass composition in terms of precursor metabolites (such as amino acids and nucleotides). On the one hand, biomass composition is often not known exactly and may vary drastically between conditions and strains. On the other hand, the predictions of computational models crucially depend on biomass. Also elementary flux modes (EFMs), which generate the flux cone, depend on the biomass reaction.

To better understand cellular phenotypes across growth conditions, we introduce and analyze new classes of elementary vectors for comprehensive (next-generation) metabolic models, involving explicit synthesis reactions for all macromolecules. Elementary growth modes (EGMs) are given by stoichiometry and generate the growth cone. Unlike EFMs, they are not support-minimal, in general, but cannot be decomposed "without cancellations". In models with additional (capacity) constraints, elementary growth vectors (EGVs) generate a growth polyhedron and depend also on growth rate. However, EGMs/EGVs do not depend on the biomass composition. In fact, they cover all possible biomass compositions and can be seen as unbiased versions of elementary flux modes/vectors (EFMs/EFVs) used in traditional models.

To relate the new concepts to other branches of theory, we consider autocatalytic sets of reactions. Further, we illustrate our results in a small model of a self-fabricating cell, involving glucose and ammonium uptake, amino acid and lipid synthesis, and the expression of all enzymes and the ribosome itself. In particular, we study the variation of biomass composition as a function of growth rate. In agreement with experimental data, low nitrogen uptake correlates with high carbon (lipid) storage.

Author summaryNext-generation, genome-scale metabolic models allow to study the reallocation of cellular resources upon changing environmental conditions, by not only modeling flux distributions, but also expression profiles of the catalyzing proteome. In particular, they do no longer assume a fixed biomass composition. Methods to identify optimal solutions in such comprehensive models exist, however, an unbiased understanding of all feasible allocations is missing so far. Here we develop new concepts, called elementary growth modes and vectors, that provide a generalized definition of minimal pathways, thereby extending classical elementary flux modes (used in traditional models with a fixed biomass composition). The new concepts provide an understanding of all possible flux distributions and of all possible biomass compositions. In other words, elementary growth modes and vectors are the unique functional units in any comprehensive model of cellular growth. As an example, we show that lipid accumulation upon nitrogen starvation is a consequence of resource allocation and does not require active regulation. Our work puts current approaches on a theoretical basis and allows to seamlessly transfer existing workflows (e.g. for the design of cell factories) to next-generation metabolic models.

category: systems biology