title: Modeling traumatic brain injury combined with hemorrhagic shock in rats: Neurological assessment and PET imaging with 18F-fluorodeoxyglucaric acid

abstract: Traumatic brain injury (TBI) is a major cause of death and disability worldwide. Hemorrhagic shock (HS) aggravates tissue injury and complicates TBI recovery. We studied the combined insult of mild TBI and HS and investigated the impact of varying loss of blood volume on neurologic deficit and brain lesion volume. A novel positron emission tomography (PET) technique was employed to monitor tissue injury. Male Sprague Dawley rats received mTBI by controlled cortical impact (CCI) followed by withdrawal of 0%, 30-40%, 45%, or 50% of blood (mTBI, mTBI+HS[≤]40%, mTBI+HS45%, and mTBI+HS50%, respectively). Neurological deficit (mNSS= 5.6, 7.6, and 12.3) and mortality (2/12, 2/6, and 7/12) were worse in mTBI+HS[≤]40%, mTBI+HS45%, and mTBI+HS50%, respectively than in mTBI alone rats (no death; mNSS=3.3). Histologic lesion size increased 3.5-fold in mTBI+HS50% compared to mTBI alone and the infarct-avid PET agent 18F-fluorodeoxyglucaric acid (FGA) proportionately detected tissue necrosis in mTBI+HS50% rats. Based on these results, we conclude that HS aggravates mTBI-induced neurological deficits, tissue injury and mortality. PET/18F-FGA as an imaging marker can detect the extent of injury in a non-invasive manner.


title: Simulating brain signals with predefined mutual correlations

abstract: This technical note describes a simple linear algorithm which allows generating arbitrary number of signal time courses whose mutual correlations are defined by a given mathematically consistent correlation matrix. This is achieved by mixing some seed set of waveforms typically reflecting desired specific features of the target brain signals. If needed the resulting signals can be properly tapered to be neurophysiologically plausible. For multi-epoch designs the generated waveforms may also include a "phase-locked" component which does not vary between the epochs.

category: neuroscience


title: A benchmark study of simulation methods for single-cell RNA sequencing data

abstract: Single-cell RNA-seq (scRNA-seq) data simulation is critical for evaluating computational methods for analysing scRNA-seq data especially when ground truth is experimentally unattainable. The reliability of evaluation depends on the ability of simulation methods to capture properties of experimental data. However, while many scRNA-seq data simulation methods have been proposed, a systematic evaluation of these methods is lacking. We developed a comprehensive evaluation framework, SimBench, including a novel kernel density estimation measure to benchmark 12 simulation methods through 35 scRNA-seq experimental datasets. We evaluated the simulation methods on a panel of data properties, ability to maintain biological signals, scalability and applicability. Our benchmark uncovered performance differences among the methods and highlighted the varying difficulties in simulating data characteristics. Furthermore, we identified several limitations including maintaining heterogeneity of distribution. These results, together with the framework and datasets made publicly available as R packages, will guide simulation methods selection and their future development.

category: bioinformatics


title: Identifying strengths and weaknesses of methods for computational network inference from single cell RNA-seq data

abstract: Single-cell RNA-sequencing (scRNA-seq) offers unparalleled insight into the transcriptional programs of different cellular states by measuring the transcriptome of thousands individual cells. An emerging problem in the analysis of scRNA-seq is the inference of transcriptional gene regulatory networks and a number of methods with different learning frameworks have been developed. Here we present an expanded benchmarking study of eleven recent network inference methods on six published single-cell RNA-sequencing datasets in human, mouse, and yeast considering different types of gold standard networks and evaluation metrics. We evaluate methods based on their computing requirements as well as on their ability to recover the network structure. We find that while most methods have a modest recovery of experimentally derived interactions based on global metrics such as AUPR, methods are able to capture targets of regulators that are relevant to the system under study. Based on overall performance we grouped the methods into three main categories and found a combination of information-theoretic and regression-based methods to have a generally high performance. We also evaluate the utility of imputation for gene regulatory network inference and find that a small number of methods benefit from imputation, which further depends upon the dataset. Finally, comparisons to inferred networks for comparable bulk conditions showed that networks inferred from scRNA-seq datasets are often better or at par to those from bulk suggesting that scRNA-seq datasets can be a cost-effective way for gene regulatory network inference. Our analysis should be beneficial in selecting algorithms for performing network inference but also argues for improved methods and better gold standards for accurate assessment of regulatory network inference methods for mammalian systems.


title: Formin's nucleation activity influences actin filament length

abstract: Formins stimulate actin polymerization by promoting both filament nucleation and elongation. Because nucleation and elongation draw upon a common pool of actin monomers, the rate at which each reaction proceeds influences the other. This interdependent mechanism determines the number of filaments assembled over the course of a polymerization reaction, as well as their equilibrium lengths. In this study, we used kinetic modeling and in vitro polymerization reactions to dissect the contributions of filament nucleation and elongation to the process of formin-mediated actin assembly. We found that the rates of nucleation and elongation evolve over the course of a polymerization reaction. The period over which each process occurs is a key determinant of the total number of filaments that are assembled, as well as their average lengths at equilibrium. Inclusion of formin in polymerization reactions speeds filament nucleation, thus increasing the number and shortening the lengths of filaments that are assembled over the course of the reaction. Although variations in elongation rates produce modest changes in the equilibrium lengths of formin-bound filaments, nucleation constitutes the primary mode of monomer consumption over the course of assembly. Sustained elongation of small numbers of formin-bound filaments therefore requires inhibition of nucleation via monomer sequestration and a low concentration of activated formin. Our results underscore the mechanistic advantage for keeping formins nucleation efficiency relatively low in cells, where unregulated actin assembly would produce deleterious effects on cytoskeletal dynamics. Under these conditions, differences in the elongation rates mediated by formin isoforms are most likely to impact the kinetics of actin assembly.

category: biophysics


title: Identification of DIR1-dependant cellular responses required for guard cell systemic acquired resistance

abstract:
After localized invasion by bacterial pathogens, systemic acquired resistance (SAR) is induced in uninfected plant tissues, resulting in enhanced defense against a broad range of pathogens. Although SAR requires mobilization of signaling molecules via the plant vasculature, the specific molecular mechanisms remain elusive. The lipid transfer protein-defective in induced resistance 1-1 (DIR1-1) was identified in Arabidopsis thaliana by screening for mutants that were defective in SAR. Here we demonstrate that stomatal response to pathogens is altered in systemic leaves by SAR, and this guard cell SAR defense requires DIR1. Using a multi-omics approach, we have determined potential SAR signaling mechanisms specific for guard cells in systemic leaves by profiling metabolite, lipid, and protein differences between guard cells in wild type and dir1-1 mutant during SAR. We identified two 18C fatty acids and two 16C wax esters as putative SAR-related molecules dependent on DIR1. Proteins and metabolites related to amino acid biosynthesis and response to stimulus were also changed in guard cells of dir1-1 compared to wild type. Identification of guard cell-specific SAR-related molecules may lead to new avenues of genetic modification/molecular breeding for disease resistant plants.

One-sentence summaryDIR1 affects many biological processes in stomatal guard cells during systemic acquired resistance (SAR), as revealed by multi-omics, and it may function through transporting two 18C fatty acids during SAR.

category: plant biology


title: Hippocampal disinhibition reduces contextual and elemental fear conditioning while sparing the acquisition of latent inhibition

abstract:
Hippocampal neural disinhibition, i.e. reduced GABAergic inhibition, is a key feature of schizophrenia pathophysiology. The hippocampus is an important part of the neural circuitry that controls fear conditioning and can also modulate prefrontal and striatal mechanisms, including dopamine signalling, which play a role in salience modulation. Therefore, hippocampal neural disinhibition may contribute to impairments in fear conditioning and salience modulation reported in schizophrenia. To test this hypothesis, we examined the effect of ventral hippocampus (VH) disinhibition in male rats on fear conditioning and salience modulation, as reflected by latent inhibition (LI), in a conditioned emotional response procedure (CER). A flashing light was used as the conditioned stimulus (CS) and conditioned suppression was used to index conditioned fear. In Experiment 1, VH disinhibition via infusion of the GABA-A receptor antagonist picrotoxin prior to CS pre-exposure and conditioning markedly reduced fear conditioning to both the CS and context; LI was evident in saline-infused controls, but could not be detected in picrotoxin-infused rats due to the low level of fear conditioning to the CS. In Experiment 2, VH picrotoxin infusions prior to CS pre-exposure only did not affect the acquisition of fear conditioning or LI. Together, these findings indicate that VH neural disinhibition disrupts contextual and elemental fear conditioning, without affecting the acquisition of LI. The disruption of fear conditioning resembles aversive conditioning deficits reported in schizophrenia and may reflect disruption of neural processing within the hippocampus and its projection sites.

Significance StatementHippocampal disinhibition, reduced GABAergic inhibition, is a feature of schizophrenia, but how this contributes to psychological deficits remains to be clarified. Here, we focused on impairments patients show on classical-conditioning assays: aberrant salience allocation to stimuli that healthy participants have learnt to ignore and reduced fear conditioning, which have been linked to psychosis and negative symptoms, respectively. These impairments may be related to hippocampal disinhibition because the hippocampus modulates neural substrates of salience allocation and is part of the fear-conditioning neural circuit. Combining selective pharmacological manipulation of the hippocampus with a conditioning assay in rats, we found hippocampal disinhibition disrupted fear conditioning, without evidence for aberrant salience allocation. This suggests hippocampal disinhibition contributes to fear conditioning deficits in schizophrenia.


title: Costs dictate strategic investment in dominance interactions

abstract: Dominance is important for access to resources. As dominance interactions are costly, individuals should be strategic in who they interact with. One hypothesis is that individuals should direct costly interactions towards those closest in rank, as they have most to gain--in terms of attaining or maintaining dominance--from winning such interactions. Here, we show that male vulturine guineafowl (Acryllium vulturinum), a gregarious species with steep dominance hierarchies, strategically express higher-cost aggressive interactions towards males occupying ranks immediately below themselves in their groups hierarchy. In contrast, lower-cost aggressive interactions are expressed towards group members further down the hierarchy. By directly evaluating differences in the strategic use of higher- and lower-cost aggressive interactions towards competitors, we show that individuals disproportionately use highest-cost interactions--such as chases--towards males found one to three ranks below themselves. Our results support the hypothesis that the costs associated with different interaction types can determine their expression in social groups with steep dominance hierarchies.

category: animal behavior and cognition


title: PLK1 inhibition selectively kills ARID1A deficient cells through uncoupling of oxygen consumption from ATP production

abstract:
Inhibitors of the mitotic kinase PLK1 yield objective responses in a subset of refractory cancers. However, PLK1 overexpression in cancer does not correlate with drug sensitivity, and the clinical development of PLK1 inhibitors has been hampered by the lack of patient selection marker. Using a high-throughput chemical screen, we discovered that cells deficient for the tumor suppressor ARID1A are highly sensitive to PLK1 inhibition. Interestingly this sensitivity was unrelated to canonical functions of PLK1 in mediating G2-M cell cycle transition. Instead, a whole-genome CRISPR screen revealed PLK1 inhibitor sensitivity in ARID1A deficient cells to be dependent on the mitochondrial translation machinery. We find that ARID1A knocked-out (KO) cells have an unusual mitochondrial phenotype with aberrant biogenesis, increased oxygen consumption/ expression of oxidative phosphorylation genes, but without increased ATP production. Using expansion microscopy and biochemical fractionation, we see that a subset of PLK1 localizes to the mitochondria in interphase cells. Inhibition of PLK1 in ARID1A KO cells further uncouples oxygen consumption from ATP production, with subsequent membrane depolarization and apoptosis. Knockdown of a key subunit of the mitochondrial ribosome reverses PLK1-inhibitor induced apoptosis in ARID1A deficient cells, confirming specificity of the phenotype. Together, these findings highlight a novel interphase role for PLK1 in maintaining mitochondrial fitness under metabolic stress, and a strategy for therapeutic use of PLK1 inhibitors. To translate these findings, we describe a quantitative microscopy assay for assessment of ARID1A protein loss, which could offer a novel patient selection strategy for the clinical development of PLK1 inhibitors in cancer.

Statement of significanceCurrently, no predictive biomarkers have been identified for PLK1 inhibitors in cancer treatment. We show that ARID1A loss sensitizes cells to PLK1 inhibitors through a previously unrecognized vulnerability in mitochondrial oxygen metabolism.

category: cancer biology


title: Co-infection of a novel Chlamydia-like organism and Henneguya sp. (Myxosporea, Myxobolidae) in snakeskin gourami Trichopodus pectoralis (Regan 1910), in Thailand

abstract: The present study describes a simultaneous infection of a novel Chlamydia-like organism (CLO) with a Myxozoa parasite, Henneguya sp. in snakeskin gourami Trichopodus pectoralis in Thailand. A new CLO is proposed "Candidatus Piscichlamydia trichopodus" (CPT) based on 16S rRNA phylogenetic analysis. Systemic intracellular CPT infection was confirmed by histological examination, in situ hybridization, PCR assay, and sequencing of 16S rRNA. This novel pathogen belongs to the order Chlamydiales but differs in certain aspects from other species. The histopathological changes associated with CPT infection were different from the typical pathological lesions of epitheliocystis caused by previously known CLO. Unlike other CLO, CPT localized in the connective tissue rather than in the epithelial cells and formed smaller clumps of intracellular bacteria that stained dark blue with hematoxylin. On the other hand, typical myxospores of the genus Henneguya with tails were observed in the gill sections. Infection with Henneguya sp. resulted in extensive destruction of the gill filaments, most likely leading to respiratory distress. Due to the frequency of co-infections and the unavailability of culture methods for CLO and Henneguya sp, it was difficult to determine which pathogens were directly responsible for the associated mortality. However, co-infections may increase the negative impact on the host and the severity of the disease. Given the commercial importance of the snakeskin gourami and its significant aquaculture potential, the findings of this study are important for further studies on disease prevention.

category: pathology


title: Co-infection of Candidatus Piscichlamydia trichopodus (order Chlamydiales) and Henneguya sp (Myxosporea, Myxobolidae) in snakeskin gourami Trichopodus pectoralis (Regan 1910)


title: Assessing the sensitivity of EEG-based frequency-tagging as a metric for statistical learning

abstract: AO_SCPLOWBSTRACTC_SCPLOWStatistical Learning (SL) is hypothesized to play an important role in language development. However, the behavioral measures typically used to assess SL, particularly at the level of individual participants, are largely indirect and often have low sensitivity. Recently, a neural metric based on frequency-tagging has been proposed as an alternative and more direct measure for studying SL. Here we tested the sensitivity of frequency-tagging measures for studying SL in individual participants in an artificial language paradigm, using non-invasive EEG recordings of neural activity in humans. Importantly, we use carefully constructed controls, in order to address potential acoustic confounds of the frequency-tagging approach. We compared the sensitivity of EEG-based metrics to both explicit and implicit behavioral tests of SL, and the correspondence between these presumed converging operations. Group-level results confirm that frequency-tagging can provide a robust indication of SL for an artificial language, above and beyond potential acoustic confounds. However, this metric had very low sensitivity at the level of individual participants, with significant effects found only in 30% of participants. Conversely, the implicit behavior measures indicated that SL has occurred in 70% of participants, which is more consistent with the proposed ubiquitous nature of SL. Moreover, there was low correspondence between the different measures used to assess SL. Taken together, while some researchers may find the frequency-tagging approach suitable for their needs, our results highlight the methodological challenges of assessing SL at the individual level, and the potential confounds that should be taken into account when interpreting frequency-tagged EEG data.


title: Immune dynamics in a time of covid

abstract: Motivated by curiosities of disease progression seen in the coronavirus pandemic, we analyze a minimalist predator-prey model for the immune system (predator) competing against a pathogen (prey). We find that the mathematical model alone accounts for numerous paradoxical behaviors observed in this and other infections. These include why an exponentially growing pathogen requires an exposure threshold to take hold, how chronic and recurrent infections can arise, and what can allow very sick patients to recover, while healthier patients succumb. We also examine the distinct dynamical roles that specific, "innate," and nonspecific, "adaptive," immunity play, and we describe mathematical effects of infection history on prognosis. Finally, we briefly discuss predictions for some of the effects of timing and strengths of antibiotics or immunomodulatory agents.

category: immunology


title: pUL21 regulation of pUs3 Kinase Activity Influences the Nature of Nuclear Envelope Deformation by the HSV-2 Nuclear Egress Complex

abstract:
It is well established that the herpesvirus nuclear egress complex (NEC) has an intrinsic ability to deform membranes. During viral infection, the membrane-deformation activity of the NEC must be precisely regulated to ensure efficient nuclear egress of capsids. One viral protein known to regulate herpes simplex virus type 2 (HSV-2) NEC activity is the tegument protein pUL21. Cells infected with an HSV-2 mutant lacking pUL21 ({Delta}UL21) produced a slower migrating species of the viral serine/threonine kinase pUs3 that was shown to be a hyperphosphorylated form of the enzyme. Investigation of the pUs3 substrate profile in {Delta}UL21-infected cells revealed a prominent band with a molecular weight consistent with that of the NEC components pUL31 and pUL34. Phosphatase sensitivity and retarded mobility in phos-tag SDS-PAGE confirmed that both pUL31 and pUL34 were hyperphosphorylated by pUs3 in the absence of pUL21. To gain insight into the consequences of increased phosphorylation of NEC components, the architecture of the nuclear envelope in cells producing the HSV-2 NEC in the presence or absence of pUs3 was examined. In cells with robust NEC production, invaginations of the inner nuclear membrane were observed that contained budded vesicles of uniform size. By contrast, nuclear envelope deformations protruding outwards from the nucleus, were observed when pUs3 was included in transfections with the HSV-2 NEC. Finally, when pUL21 was included in transfections with the HSV-2 NEC and pUs3, decreased phosphorylation of NEC components was observed in comparison to transfections lacking pUL21. These results demonstrate that pUL21 influences the phosphorylation status of pUs3 and the HSV-2 NEC and that this has consequences for the architecture of the nuclear envelope.

Author SummaryDuring all herpesvirus infections, the nuclear envelope undergoes deformation in order to enable viral capsids assembled within the nucleus of the infected cell to gain access to the cytoplasm for further maturation and spread to neighbouring cells. These nuclear envelope deformations are orchestrated by the viral nuclear egress complex (NEC), which, in HSV, is composed of two viral proteins, pUL31 and pUL34. How the membrane-deformation activity of the NEC is controlled during infection is incompletely understood. The studies in this communication reveal that the phosphorylation status of pUL31 and pUL34 can determine the nature of nuclear envelope deformations and that the viral protein pUL21 can modulate the phosphorylation status of both NEC components. These findings provide an explanation for why HSV-2 strains lacking pUL21 are defective in nuclear egress. A thorough understanding of how NEC activity is controlled during infection may yield strategies to disrupt this fundamental step in the herpesvirus lifecycle, providing the basis for novel antiviral strategies.

category: microbiology


title: A Functional Menadione Biosynthesis Pathway is Required for Capsule Production by Staphylococcus aureus.

abstract: Staphylococcus aureus is a major human pathogen that utilises a wide array of pathogenic and immune evasion strategies to cause disease. One immune evasion strategy, common to many bacterial pathogens, is the ability of S. aureus to produce a capsule that protects the bacteria from several aspects of the human immune system. To identify novel regulators of capsule production by S. aureus we applied a genome wide association study (GWAS) to a collection of 300 bacteraemia isolates that represent the two major MRSA clones in UK and Irish hospitals: CC22 and CC30. One of the loci associated with capsule production, the menD gene, encodes an enzyme critical to the biosynthesis of menadione. Mutations in this gene that result in menadione auxotrophy induce the slow growing small-colony variant (SCV) form of S. aureus often associated with chronic infections due to their increased resistance to antibiotics and ability to survive inside phagocytes. Utilising such an SCV we functionally verified this association between menD and capsule production. Although the clinical isolates with polymorphisms in the menD gene in our collections had no apparent growth defects, they were more resistant to gentamicin when compared to those with the wild-type menD gene. Our work suggests that menadione plays a critical role in the production of the S. aureus capsule, and that amongst clinical isolates polymorphisms exist in the menD gene that confer the characteristic increased gentamicin resistance, but not the major growth defect associated with SCV phenotype.


title: In Situ Visualization of the pKM101-Encoded Type IV Secretion System Reveals a Highly Symmetric ATPase Energy Center at the Channel Entrance

abstract:
Bacterial conjugation systems are members of the type IV secretion system (T4SS) superfamily. T4SSs can be classified as  minimized or  expanded based on whether assembly requires only a core set of signature subunits or additional system-specific components. The prototypical  minimized systems mediating Agrobacterium tumefaciens T-DNA transfer and conjugative transfer of plasmids pKM101 and R388 are built from 12 subunits generically named VirB1-VirB11 and VirD4. In this study, we visualized the pKM101-encoded T4SS in the native context of the bacterial cell envelope by in situ cryoelectron tomography (CryoET). The T4SSpKM101 is composed of an outer membrane core complex (OMCC) connected by a thin stalk to an inner membrane complex (IMC). The OMCC exhibits 14-fold symmetry and resembles that of the T4SSR388, a large substructure of which was previously purified and analyzed by negative-stain electron microscopy (nsEM). The IMC of the in situ T4SSpKM101 machine is highly symmetrical and exhibits 6-fold symmetry, dominated by a hexameric collar in the periplasm and a cytoplasmic complex composed of a hexamer of dimers of the VirB4-like TraB ATPase. The IMC closely resembles equivalent regions of three  expanded T4SSs previously visualized by in situ CryoET, but strikingly differs from the IMC of the purified T4SSR388 whose cytoplasmic complex instead presents as two side-by-side VirB4 hexamers. Together, our findings support a unified architectural model for all T4SSs assembled in vivo regardless of their classification as  minimized or  expanded: the signature VirB4-like ATPases invariably are arranged as central hexamers of dimers at the entrances to the T4SS channels.

SignificanceBacterial type IV secretion systems (T4SSs) play central roles in antibiotic resistance spread and virulence. By cryoelectron tomography (CryoET), we solved the structure of the plasmid pKM101-encoded T4SS in the native context of the bacterial cell envelope. The inner membrane complex (IMC) of the in situ T4SS differs remarkably from that of a closely-related T4SS analyzed in vitro by single particle electron microscopy. Our findings underscore the importance of comparative in vitro and in vivo analyses of the T4SS nanomachines, and firmly support a unified model in which the signature VirB4 ATPases of the T4SS superfamily function as a central hexamer of dimers to regulate substrate entry into and passage through T4SS channels.


title: Amino acid-derived quorum sensing molecule alanine on the GIT tolerance of the lactobacillus strains in the co-cultured fermentation model

abstract:
As the importance of gut microbiota in health is increasingly recognized, the interest in interventions that can modulate the microbiota and its interactions with its host has soared. The survival status of the probiotics in the gastrointestinal environment and the microbial interactions between the LAB have also received considerable attention. In the present research, the gastrointestinal environment tolerance, adhesion ability, and biofilm formation of the lactobacillus strains in the co-culture system were explored, through the real-time fluorescence-based quantitative PCR, UPLC-MS/MS metabolic profiling analysis and Live/Dead(R) BacLight cell staining methods. The results show that the co-culture system can promote the release of signal molecules and can effectively protect the liability of the Lactobacillus acidophilus in the gastrointestinal environment. Meanwhile, amino acid-derived quorum sensing molecule L-alanine (1 %) can effectively enhance the communication of the cells in the complex fermentation model, which leads to the increase of the liability of the L. acidophilus in the gastrointestinal environment.

ImportanceThe findings of this study provide a clue to the amino acid-derived metabolites in the communication among cells in the GIT environment, which can enhance the communication of the lactobacillus strains in the complex fermentation model. Meanwhile, the liability of Lactobacillus acidophilus could be enhanced in the co-culture system during the gastrointestinal environment stress with the amino acid-derived quorum sensing (QS) components, and it will shed some light to the application of the amino acid-derived QS molecules in the fermentation stater industry.


title: Persistent DNA damage promotes microglial dysfunction in Ataxia-telangiectasia

abstract: The autosomal recessive genome instability disorder Ataxia-telangiectasia, caused by mutations in ATM kinase, is characterised by the progressive loss of cerebellar neurons. We find that DNA damage associated with ATM loss results in dysfunctional behaviour of human microglia, immune cells of the central nervous system. Microglial dysfunction is mediated by the pro-inflammatory RELB/p52 non-canonical NF-{kappa}B transcriptional pathway and leads to excessive phagocytic clearance of neurites. Pathological phagocytosis of neuronal processes by microglia has also been observed in multiple sclerosis, Alzheimers and progranulin deficiency, suggesting a common mechanism that promotes neuronal damage. Activation of the RELB/p52 pathway in ATM-deficient microglia is driven by persistent DNA damage and is dependent on the NIK kinase. These results provide insights into the underlying mechanisms of aberrant microglial behaviour in Ataxia-telangiectasia, potentially contributing to neurodegeneration.

category: cell biology


title: Proteome and functional decline as platelets age in the circulation

abstract: Anucleate platelets circulate in the blood of healthy individuals for approximately 7-10 days during which time their protein composition may change. We hypothesized such changes would be linked to altered structure and function. Here, we separated platelets of different ages based on mRNA content and characterised them using proteomics, immunofluorescence and functional assays. Total protein content was 45{+/-}5% (n=4) lower in old platelets compared to young platelets. Predictive proteomic pathway analysis identified associations with 28 biological processes, notably increased haemostasis in young platelets and apoptosis in old platelets. Further studies confirmed platelet ageing was linked to a reduction decrease in cytoskeletal proteins, a reduction in mitochondria number, and lower calcium dynamics and granule secretion. This work delineates physical and functional changes in platelets as they age and serves as a base to examine differences associated with altered mean age of platelet populations in conditions such as immune thrombocytopenia and diabetes.


title: Extremely bright, near-IR emitting spontaneously blinking fluorophores enable ratiometric multicolor nanoscopy in live cells

abstract: New bright, photostable, emission-orthogonal fluorophores that blink without toxic additives are needed to enable multi-color, live-cell, single-molecule localization microscopy (SMLM), especially for experiments that demand ultra-high-resolution live imaging. Here we report the design, synthesis, and biological evaluation of Yale676sb, a photostable, near-IR emitting fluorophore that achieves these goals in the context of an exceptional quantum yield (0.59). When used alongside HMSiR, Yale676sb enables simultaneous, live-cell, two-color SMLM of two intracellular organelles (ER + mitochondria) with only a single laser and no chemical additives.


title: Blinking fluorescent probes for tubulin nanoscopy in living and fixed cells

abstract: Here we report a small molecule probe for single molecule localisation microscopy (SMLM) of tubulin in living and fixed cells. We explored a series of constructs composed of taxanes and spontaneously blinking far-red dye hydroxymethyl silicon-rhodamine (HMSiR). We found that the linker length profoundly affects the probe permeability and off-targeting. The best performing probe, HMSiR-tubulin, is composed of cabazitaxel and 6-regioisomer of HMSiR bridged by a C6 linker. Microtubule diameters of [≤]50 nm can be routinely measured in SMLM experiments on living and fixed cells. HMSiR-tubulin also performs well in 3D stimulated emission depletion (STED) microscopy, allowing a complementary use of both nanoscopy methods for investigating microtubule functions in living cells.


title: Symbiosis increases population size and buffers environmental fluctuations in a physiologically-structured model parameterized for thyasirid bivalves

abstract: Symbioses whereby one partner provisions a nutritional resource to the other may alter energy allocation towards reproduction and survival in the recipient partner, potentially impacting population dynamics. Asymbiotic thyasirid bivalves feed predominantly on free-living bacteria, which fluctuate in abundance due to seasonality-driven temperature variations. Symbiotic thyasirids are mixotrophs, gaining nutrients from free-living bacteria and symbiotic bacteria that they host on their enlarged gills. Symbiotic bacteria may function as an additional energy reserve for thyasirids, allowing the hosts to allocate more energy to reproduction. We hypothesize that, for symbiotic thyasirids, the symbionts are a nutritional source that mitigates resource limitation. Using Dynamic Energy Budget theory, we built a physiologically-structured population model assuming equal mortality rates in both species. We find that without seasonal fluctuations, symbiotic thyasirids have higher abundances than asymbiotic thyasirids since the symbionts increase reproduction. Both species have similar population sizes in fluctuating environments, suggesting different adaptations to seasonality: asymbiotic thyasirids have adapted their physiology, while symbiotic thyasirids have adapted through mixotrophy. Our results highlight the significance of linking individual energetics and life-history traits to population dynamics and are the first step to-wards understanding the role of symbioses in population and community dynamics.

category: ecology


title: Quantitative proteomic and metabolomic profiling reveals altered mitochondrial metabolism and folate biosynthesis pathways in the aging Drosophila eye

abstract: Aging is associated with increased risk of ocular disease, suggesting that age-associated molecular changes in the eye increase its vulnerability to damage. Although there are common pathways involved in aging at an organismal level, different tissues and cell types exhibit specific changes in gene expression with advanced age. Drosophila melanogaster is an established model system for studying aging and neurodegenerative disease, that also provides a valuable model for studying age-associated ocular disease. Flies, like humans, exhibit decreased visual function and increased risk of retinal degeneration with age. Here, we profiled the aging proteome and metabolome of the Drosophila eye, and compared these data with age-associated transcriptomic changes from both eyes and photoreceptors to identify alterations in pathways that could lead to age-related phenotypes in the eye. Notably, the proteomic and metabolomic changes observed in the aging eye are distinct from those observed in the head or whole fly, suggesting that tissue-specific changes in protein abundance and metabolism occur in the aging fly. Our integration of the proteomic, metabolomic and transcriptomic data reveals that changes in metabolism, potentially due to decreases in availability of B vitamins, together with chronic activation of the immune response, may underpin many of the events observed in the aging Drosophila eye. We propose that targeting these pathways in the genetically tractable Drosophila system may help to identify potential neuroprotective approaches for neurodegenerative and age-related ocular diseases.

category: biochemistry


title: Efficient Hit-to-Lead Searching of Kinase Inhibitor Chemical Space via Computational Fragment Merging

abstract:
In early stage drug discovery, the hit-to-lead optimization (or "hit expansion") stage entails starting from a newly-identified active compound, and improving its potency or other properties. Traditionally this process relies on synthesizing and evaluating a series of analogs to build up structure-activity relationships. Here, we describe a computational strategy focused on kinase inhibitors, intended to expedite the process of identifying analogs with improved potency. Our protocol begins from an inhibitor of the target kinase, and generalizes the synthetic route used to access it. By searching for commercially-available replacements for the individual building blocks used to make the parent inhibitor, we compile an enumerated library of compounds that can be accessed using the same chemical transformations; these huge libraries can exceed many millions - or billions - of compounds. Because the resulting libraries are much too large for explicit virtual screening, we instead consider alternate approaches to identify the top-scoring compounds. We find that contributions from individual substituents are well-described by a pairwise additivity approximation, provided that the corresponding fragments position their shared core in precisely the same way relative to the binding site. This key insight allows us to determine which fragments are suitable for merging into a single new compounds, and which are not. Further, the use of the pairwise approximation allows interaction energies to be assigned to each compound in the library, without the need for any further structure-based modeling: interaction energies instead can be reliably estimated from the energies of the component fragments, and the reduced computational requirements allow for flexible energy minimizations that allow the kinase to respond to each substitution. We demonstrate this protocol using libraries built from six representative kinase inhibitors drawn from the literature, which target five different kinases: CDK9, CHK1, CDK2, EGFRT790M, and ACK1. In each example, the enumerated library includes additional analogs reported by the original study to have activity, and these analogs are successfully prioritized within the library. We envision that the insights from this work can facilitate the rapid assembly and screening of increasingly large libraries for focused hit-to-lead optimization. To enable adoption of these methods and to encourage further analyses, we disseminate the computational tools needed to deploy this protocol.

Graphical Abstract

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/446684v2_ufig1.gif" ALT="Figure 1">
View larger version (15K):
org.highwire.dtl.DTLVardef@1ccdd9aorg.highwire.dtl.DTLVardef@e8b7b8org.highwire.dtl.DTLVardef@75a4fcorg.highwire.dtl.DTLVardef@1a2da2c_HPS_FORMAT_FIGEXP  M_FIG C_FIG


title: Evaluating sources of technical variability in the mechano-node-pore sensing pipeline and their effect on the reproducibility of single-cell mechanical phenotyping

abstract: Cellular mechanical properties can reveal physiologically relevant characteristics in many cell types, and several groups have developed microfluidics-based platforms to perform single-cell mechanical testing with high throughput. However, prior work has performed only limited characterization of these platforms technical variability and reproducibility. Here, we evaluate the repeatability performance of mechano-node-pore sensing, which is a single-cell mechanical phenotyping platform developed by our research group. We measured the degree to which device-to-device variability and semi-manual data processing affected this platforms measurements of single-cell mechanical properties, and we demonstrated high repeatability across the entire technology pipeline even for novice users. We then compared results from identical mechano-node-pore sensing experiments performed by researchers in two different labs with different analytical instruments, demonstrating that the mechanical testing results from these two locations are in agreement. Our findings quantify the expectation of technical variability in mechano-node-pore sensing even in minimally experienced hands. Most importantly, we find that the repeatability performance we measured is fully sufficient for interpreting biologically relevant single-cell mechanical measurements with high confidence.

category: bioengineering


title: vcf2gwas - Python API for comprehensive GWAS analysis using GEMMA

abstract:
We present a new software package vcf2gwas to perform reproducible genome-wide association studies (GWAS). vcf2gwas is a Python API for bcftools, PLINK and GEMMA. Before running the analysis a traditional GWAS workflow requires the user to edit and format the genotype information from commonly used Variant Call Format (VCF) file and phenotype information. Post-processing steps involve summarizing and visualizing the analysis results. This workflow requires a user to utilize the command-line, manual text-editing and knowledge of one or more programming/scripting languages which can be time-consuming especially when analyzing multiple phenotypes. Our package provides a convenient pipeline performing all of these steps, reducing the GWAS workflow to a single command-line input without the need to edit or format the VCF file beforehand or to install any additional software. In addition, features like reducing the dimensionality of the phenotypic space and performing analyses on the reduced dimensions or comparing the significant variants from the results to specific genes/regions of interest are implemented. By integrating different tools to perform GWAS under one workflow, the package ensures reproducible GWAS while reducing the user efforts significantly.

Availability and implementationThe source code of vcf2gwas is available under the GNU General Public License. The package can be easily installed using conda. Installation instructions and a manual including tutorials can be accessed on the package website at https://github.com/frankvogt/vcf2gwas


title: A subset of CB002 xanthine analogues bypass p53-signaling to restore a p53 transcriptome and target an S-phase cell cycle checkpoint in tumors with mutated-p53

abstract: Mutations in TP53 occur commonly in the majority of human tumors and confer aggressive tumor phenotypes including metastasis and therapy resistance. CB002 and structural-analogues restore p53 signaling in tumors with mutant-p53 but we find that unlike other xanthines such as caffeine, pentoxifylline, and theophylline, they do not deregulate the G2-checkpoint. Novel CB002-analogues induce pro-apoptotic Noxa protein in an ATF3/4-dependent manner, whereas caffeine, pentoxifylline, and theophylline do not. By contrast to caffeine, CB002-analogues target an S-phase checkpoint associated with increased p-RPA/RPA2, p-ATR, decreased Cyclin A, p-histone H3 expression and downregulation of essential proteins in DNA-synthesis and -repair. CB002-analogue #4 enhances cell death, and decreases Ki-67 in patient-derived tumor-organoids without toxicity to normal human cells. Preliminary in vivo studies demonstrate anti-tumor efficacy in mice. Thus, a novel class of anti-cancer drugs show activation of p53 pathway signaling in tumors with mutated p53, and target an S-phase checkpoint.


title: Differential oxidative and pro-apoptotic response of cancer and normal cells to an anti-inflammatory agent CLEFMA

abstract: Selective killing of cancer cells by chemotherapy has been an age old challenge, but certain unique features of cancer cells allow discriminatory response between cancer and normal cells. The objectives of this study was to investigate pro-oxidant and apoptotic effects of CLEFMA, an anti-inflammatory compound with anticancer activity, in lung cancer cells versus normal lung fibroblasts and to establish its maximum tolerated dose (MTD) in mice. We found that CLEFMA preferentially induced reactive oxygen species (ROS)-mediated apoptosis in H441, H1650 and H226 cancer cells, but spared normal CCL151 and MRC9 fibroblasts. Immunoblotting studies revealed that CLEFMA-induced apoptosis is associated with p53 phosphorylation in cancer cells which was not observed in CLEFMA treated normal fibroblasts. CLEFMA showed no effect on NF-{kappa}B p-65 expression in the normal lung fibroblasts, whereas its translocation to nucleus was inhibited in cancer cells. Furthermore, CLEFMA treatment also inhibited the DNA-binding activity of NF-{kappa}B p65 in H441cancer cells, but not in normal CCL151 cells. Preclinical toxicology studies in CD31 mice showed that CLEFMA was not toxic when injected daily for 7 days or injected weekly for 4 weeks. Based on survival data, MTD of CLEFMA was estimated as 30 mg/kg bodyweight. We conclude that CLEFMA exploits the biochemical differences in cancer and normal cells and selectively induces ROS in cancer cells. Secondly, CLEFMA can be safely administered in vivo because its known dose necessary for in vivo efficacy as anti-inflammatory and anti-tumor agent (0.4 mg/kg) is 75 times lower than its MTD.


title: Species-specific effects of cation channel TRPM4 small-molecule inhibitors

abstract:
BackgroundThe Transient Receptor Potential Melastatin member 4 (TRPM4) gene encodes a calcium-activated non-selective cation channel expressed in several tissues. Mutations in TRPM4 have been reported in patients with different types of cardiac conduction defects. It is also linked to immune response and cancers, but the associated molecular mechanisms are still unclear. Thus far, 9-phenanthrol is the most common pharmacological compound used to investigate TRPM4 function. We recently identified two promising aryloxyacyl-anthranilic acid compounds (abbreviated CBA and NBA) inhibiting TRPM4. However, all afore-mentioned compounds were screened using assays expressing human TRPM4, whereas the efficacy on mouse TRPM4 has not been assessed. Mouse models are essential to investigate ion channel physiology and chemical compound efficacy.

AimIn this study, we performed comparative electro-physiology experiments to assess the effect of these TRPM4 inhibitors on human and mouse TRPM4 channels heterologously expressed in TsA-201 cells.

Methods and ResultsWe identified striking species-dependent differences in TRPM4 responses. NBA inhibited both human and mouse TRPM4 currents when applied intracellularly and extracellularly using excised membrane patches. CBA inhibited human TRPM4, both intracellularly and extracellularly. Unexpectedly, the application of CBA had no inhibiting effect on mouse TRPM4 current when perfused on the extracellular side. Instead, it increased mouse TRPM4 current at negative holding potentials. In addition, CBA on the intracellular side altered the outward rectification component of the mouse TRPM4 current. Application of 9-phenanthrol, both intracellularly and extracellularly, inhibited human TRPM4. For mouse TRPM4, 9-phenanthrol perfusion led to opposite effects depending on the site of application. With intracellular 9-phenanthrol, we observed a tendency towards potentiation of mouse TRPM4 outward current at positive holding potentials.

ConclusionAltogether, these results suggest that pharmacological compounds screened using "humanised assays" should be extensively characterised before application in in vivo mouse models.

category: pharmacology and toxicology


title: In-phase and in-antiphase connectivity in EEG

abstract: Zero-lag synchrony is generally discarded from functional connectivity studies to eliminate the confounding effect of volume conduction. Demonstrating genuine and significant unlagged synchronization between distant brain regions would indicate that most electroencephalography (EEG) connectivity studies neglect an important mechanism for neuronal communication. We previously demonstrated that local field potentials recorded intracranially tend to synchronize with no lag between homotopic brain regions. This synchrony occurs most frequently in antiphase, potentially supporting corpus callosal inhibition and interhemispheric rivalry. We are now extending our investigation to EEG. By comparing the coherency in a recorded and a surrogate dataset, we confirm the presence of a significant proportion of genuine zero-lag synchrony unlikely to be due to volume conduction or to recording reference artifacts. These results stress the necessity for integrating zero-lag synchrony in our understanding of neural communication and for disentangling volume conduction and zero-lag synchrony when estimating EEG sources and their functional connectivity.


title: Live whole-eye, ex vivo imaging and laser-induced micro injury of the corneal basal epithelium and visualization of resident macrophage responses

abstract:
PurposeIn this paper, we describe a novel live-imaging approach to visualize the short-term response of the mouse cornea to basal epithelial cell damage. Laser scanning confocal microscopy was used to induce precisely-defined, localized corneal basal epithelial cell damage and the live macrophage response to this damage was visualized and analyzed.

MethodsLipophilic fluorescent dyes, SGC5 or FM 4-64, were injected into the anterior chamber of enucleated eyes and imaged live in whole-mount using confocal laser scanning microscopy. Laser-induced damage was performed by focusing onto a defined region of the corneal basal epithelium for a brief period using a high laser power setting and then returning to low laser power for imaging. Eyes from CX3CR1+/GFP mice were used to observe macrophage responses to laser damage in real-time.

ResultsSGC5 or FM 4-64 dyes injected into the anterior chamber readily enter the cornea and are taken up by the stromal layer and labeled the outer membranes of corneal epithelial cells and remained stable when visualized using low laser power. Subjecting a defined region of the basal epithelium to high laser power for 1 minute or longer led to a rapid internalization of dye in the exposed basal epithelium cells and overall increase in cellular fluorescence. This change in fluorescence was also accompanied by cell swelling and contraction. Cellular internalization of the non-lipophilic, dye Alexa 647 hydrazide, indicated that membranes were compromised indicating that exposure to high power laser stimulation causes cellular damage to the basal epithelium. Visualization of corneal resident macrophages close to the site of laser-induced damage showed that within minutes, projecting macrophage filopodia extended towards the damaged region at a rate of 0.75{micro}m/min for roughly 40 minutes.

ConclusionWe have developed a novel approach to image the live cornea and its response to damage. Laser-scanning confocal microscopy can be utilized to induce localized damage to mouse corneal basal epithelium and elicit a macrophage morphological response. This approach represents a useful tool for studying corneal wound healing and cellular responses to damage using live whole-mount imaging.


title: Genomic evidence that blind cavefishes are not wrecks of ancient life

abstract: Cavefishes often have modified eyes, from small but otherwise functional, to highly degenerate structures embedded in a connective tissue and covered by skin. Darwin assumed that these animals are  wrecks of ancient life, but several genomic studies suggests they are not  ancient. The most radical dating shift is for populations of a Mexican cavefish, Astyanax mexicanus, that have been recently estimated to be at the most a few tens of thousands years old. Despite having highly degenerate eyes, the eye-specific genes of A. mexicanus have low levels of decay. Other blind cavefishes we have examined so far are even older, but also can be dated to the Pleistocene. Here, we estimated the age of blindness of two additional fish species by the level of decay of eye-specific genes. Many pseudogenes were identified in the amblyopsid Typhlichthys subterraneus, suggesting that blindness evolved a few million years ago. In contrast, the blind cichlid Lamprologus lethops appears to be a new case of very recent and rapid eye regression, which occurred in deep river water, an environment similar to caves. Genome-wide analyses support the hypothesis that blindness in cavefishes is never very ancient, and ranges from the Early Pliocene to Late Pleistocene. Together with the description of hundreds of cavefish species, our results suggest that surface fishes were able to recurrently and rapidly adapt to caves and similar small dark ecosystems but the resulting highly specialized blind species with a limited distribution may be evolutionary dead-ends in a relatively short time.

category: evolutionary biology


title: Genome-wide association mapping of transcriptome variation in Mimulus guttatus indicates differing patterns of selection on cis- versus trans-acting mutations

abstract: We measured the floral bud transcriptome of 151 fully sequenced lines of Mimulus guttatus from one natural population. Thousands of single nucleotide polymorphisms (SNPs) are implicated as transcription regulators, but there is a striking difference in the Allele Frequency Spectrum (AFS) of cis-acting and trans-acting mutations. Cis-SNPs have intermediate frequencies (consistent with balancing selection) while trans-SNPs exhibit a rare-alleles model (consistent with purifying selection). This pattern only becomes clear when transcript variation is normalized on a gene-to-gene basis. If a global normalization is applied, as is typically in RNAseq experiments, asymmetric transcript distributions combined with "rarity disequilibrium" produce a super-abundance of false positives for trans-acting SNPs. To explore the cause of purifying selection on trans-acting mutations, we identified gene expression modules as sets of co-expressed genes. The extent to which trans-acting mutations influence modules is a strong predictor of allele frequency. Mutations altering expression of genes with high "connectedness" (those that are highly predictive of the representative module expression value) have the lowest allele frequency. The expression modules can also predict whole-plant traits such as flower size. We find that a substantial portion of the genetic (co)variance among traits can be described as an emergent property of genetic effects on expression modules.

category: genetics


title: Birth Order Differences in Education Are Environmental in Origin

abstract: Siblings share many environments and much of their genetics. Yet, siblings turn out different. Intelligence and education are influenced by birth order, with earlier-born siblings outperforming later-borns. We investigate whether birth order differences in education are caused by biological differences present at birth, that is, genetic differences or in-utero differences. Using family data that spans two generations, combining registry, survey, and genotype information, this study is based on the Norwegian Mother, Father and Child Cohort Study (MoBa). We show that there are no genetic differences by birth order as captured by polygenic scores (PGSs) for educational attainment. Furthermore, we show that earlier-born have lower birth weight than later-born, indicating worse uterine environments. Educational outcomes are still higher for earlier-born children when we adjust for PGSs and in utero variables, indicating that birth order differences arise post-natally. Finally, we consider potential environmental influences, such as differences according to maternal age, parental educational attainment, and sibling genetic nurture. We show that birth order differences are not biological in origin, but pinning down their specific causes remains elusive.


title: Birth Order Differences in Education Originate in Post-Natal Environments


title: Significant (Z|-4|) admixture signal with a source from ancient Wusun observed in contemporary Bulgarians.

abstract:
We report the presence of significant Central Asian ancestry in both contemporary Bulgarians and in early medieval population from SMC (Saltovo Mayaky Culture).

The existence of Chalcolithic-Iran (Hajj-Fruz) and Wusun related ancestral component in contemporary Bulgarians comes as a surprise and sheds light on both migration route and ethnic origins of Proto-Bulgarians. We interpret these results as an evidence for a Central -Asian connection for the tribes, constituting the population of SMC and Kubrats Old Great Bulgaria in Pontic steppe from 6th-7th century AD.

We identify Central Asian Wusun tribes as carriers of this component on the base from the results from f3 and f4 statistics. We suggest that Wusun-related tribes must have played role (or might have even been the backbone) in what became known as the Hunnic migration to Europe during 3rd-5th century AD. Same population must have taken part in the formation of the SMC (Saltovo-Mayaki Culture) and Great Old Bulgarian during 6th-9th century AD in Pontic - Caspian steppe.

We also explore the genomic origins of Thracians and their relations to contemporary Europeans. We conclude that contemporary Bulgarians do not harbor Thracian-specific ancestry, since ancient Thracian samples share more SNPs with contemporary Greeks and even contemporary Icelanders than with contemporary Bulgarians.

category: genomics


title: Acetylated Chromatin Domains Link Chromosomal Organization to Cell- and Circuit-level Dysfunction in Schizophrenia and Bipolar Disorder

abstract: To explore modular organization of chromosomes in schizophrenia (SCZ) and bipolar disorder (BD), we applied  population-scale correlational structuring of 739 histone H3-lysine 27 acetylation and H3-lysine 4 trimethylation profiles, generated from the prefrontal cortex (PFC) of 568 cases and controls. Neuronal histone acetylomes and methylomes assembled as thousands of cis-regulatory domains (CRDs), revealing fine-grained, kilo-to megabase scale chromatin organization at higher resolution but firmly integrated into Hi-C chromosomal conformations. Large clusters of domains that were hyperacetylated in disease shared spatial positioning within the nucleus, predominantly regulating PFC projection neuron function and excitatory neurotransmission. Hypoacetylated domains were linked to inhibitory interneuron- and myelination-relevant genes. Chromosomal modular architecture is affected in SCZ and BD, with hyperacetylated domains showing unexpectedly strong convergences defined by cell type, nuclear topography, genetic risk, and active chromatin state across a wide developmental window.


title: Colocalized, Bidirectional Optogenetic Modulations in Freely Behaving Animals with a Wireless Dual-Color Optoelectronic Probe

abstract: The precise control of neural activities at both cellular and circuit levels reveals significant impacts on the fundamental neuroscience explorations and medical applications. Optogenetic methods provide efficient cell-specific modulations, and the ability of simultaneous neural activation and inhibition in the same brain region of freely moving animals is highly desirable and being actively researched. Here we report bidirectional neuronal activity manipulation accomplished by a wireless, dual-color optogenetic probe in synergy with the co-expression of two spectrally distinct opsins (ChrimsonR and stGtACR2) in a rodent model. Based on vertically assembled, thin-film microscale light-emitting diodes (micro-LEDs) with a lateral dimension of 125 x 180 {micro}m2 on flexible substrates, the dual-color probe shows colocalized red and blue emissions and allows chronic in vivo operations with desirable biocompatibilities. In addition, we discover that neurons co-expressing the two opsins can be deterministically evoked or silenced under red or blue irradiations. Implanted in behaving mice, the wirelessly controlled dual-color probe interferes with dopaminergic neurons in the ventral tegmental area (VTA), increasing or decreasing dopamine levels with colocalized red and blue stimulations. Such bidirectional regulations further generate rewarding and aversive behaviors of freely moving mice in a place preference test and interrogate social interactions among multiple mice. The technologies established here will create numerous opportunities and profound implications for brain research.


title: Plasma-derived cell-free DNA methylomes might not enable detection and discrimination of intracranial tumors

abstract: Intracranial tumors are both hard to detect and diagnose, resulting in poor patient outcomes. For that reason, non-invasive methods enabling detection and discrimination of intracranial tumors have significant clinical potential. Recently Nassiri et al.1 propose plasma-derived cell-free DNA methylomes as such a method. Here I show that the results have been misinterpreted, and for many comparisons, no evidence supporting the conclusions are actually presented. While my analysis highlights the potential of plasma-derived cell-free DNA methylomes, the evidence provided by Nassiri et al.1 is simply currently insufficient.


title: Defining the activation profile and fate trajectory of adult Scleraxis-lineage cells during tendon healing by combining lineage tracing and spatial transcriptomics

abstract: The tendon healing process is regulated by the coordinated interaction of multiple cell types and molecular processes. However, these processes are not well-defined leading to a paucity of therapeutic approaches to enhance tendon healing. Scleraxis-lineage (ScxLin) cells are the major cellular component of adult tendon and make time-dependent contributions to the healing process. Prior work from our lab and others suggests heterogeneity within the broader ScxLin population over the course of tendon healing; therefore delineating the temporal and spatial contributions of these cells is critical to understanding and improving the healing process. In the present study we utilize lineage tracing of the adult aScxLin population to determine whether these cells undergo cellular activation and subsequent myofibroblast differentiation, which is associated with both proper healing and fibrotic progression in many tissues. We show that adult aScxLin cells undergo transient activation in the organized cellular bridge at the tendon repair site, contribute to the formation of an organized neotendon, and contribute to a persistent myofibroblast population in the native tendon stubs. The mechanisms dictating this highly specialized spatial response are unknown. We therefore utilized spatial transcriptomics to better define the spatio-molecular program of tendon healing. Integrated transcriptomic analyses across the healing time-course identifies five distinct molecular regions, including key interactions between the inflammatory bridging tissue and highly reactive tendon tissue at the repair site, with adult ScxLin cells being a central player in the transition from native tendon to reactive, remodeling tendon. Collectively, these data provide important insights into both the role of adult ScxLin cells during healing as well as the molecular mechanisms that underpin and coordinate the temporal and spatial healing phenotype, which can be leveraged to enhance the healing process.


title: FLAME: a web tool for functional and literature enrichment analysis of multiple gene lists

abstract:
Functional enrichment is a widely used method for interpreting experimental results by identifying classes of proteins/genes associated with certain biological functions, pathways, diseases or phenotypes. Despite the variety of existing tools, most of them can process a single list per time, thus making a more combinatorial analysis more complicated and prone to errors. In this article, we present FLAME, a web tool for combining multiple lists prior to enrichment analysis. Users can upload several lists of preference and use interactive UpSet plots, as an alternative to Venn diagrams, to handle unions or intersections among the given input files. Functional and literature enrichment along with gene conversions are offered by g:Profiler and aGOtool applications for 197 organisms. In its current version, FLAME can analyze genes/proteins for related articles, Gene Ontologies, pathways, annotations, regulatory motifs, domains, diseases, phenotypes while it can also generate protein-protein interactions derived from STRING. We have herein validated FLAME by interrogating gene expression data associated with the sensitivity of the distal part of the large intestine to experimental colitis-propelled colon cancer. The FLAME application comes with an interactive user-friendly interface which allows easy list manipulation and exploration, while results can be visualized as interactive and parameterizable heatmaps, barcharts, Manhattan plots, networks and tables.

AvailabilityFLAME application: http://flame.pavlopouloslab.info

Codehttps://github.com/PavlopoulosLab/FLAME


title: Relative Affinities of Protein-Cholesterol Interactions from Equilibrium Molecular Dynamics Simulations

abstract: Specific interactions of lipids with membrane proteins contribute to protein stability and function. Multiple lipid interactions surrounding a membrane protein are often identified in molecular dynamics (MD) simulations and are, increasingly, resolved in cryo-EM densities. Determining the relative importance of specific interaction sites is aided by determination of lipid binding affinities by experimental or simulation methods. Here, we develop a method for determining protein-lipid binding affinities from equilibrium coarse-grained MD simulations using binding saturation curves, designed to mimic experimental protocols. We apply this method to directly obtain affinities for cholesterol binding to multiple sites on a range of membrane proteins and compare our results with free energies obtained from density-based equilibrium methods and with potential of mean force calculations, getting good agreement with respect to the ranking of affinities for different sites. Thus, our binding saturation method provides a robust, high-throughput alternative for determining the relative consequence of individual sites seen in e.g. cryo-EM derived membrane protein structures surrounded by a plethora of ancillary lipid densities.


title: Characterizing Hydrogen Bonds in Intact RNA from MS2 Bacteriophage Using Solid State Magic Angle Spinning NMR

abstract: Ribonucleic acid (RNA) is a polymer with pivotal functions in many biological processes. RNA structure determination is thus a vital step towards understanding its function. The secondary structure of RNA is stabilized by hydrogen bonds formed between nucleotide base pairs and it defines the positions and shapes of functional stem-loops, internal loops, bulges, and other functional and structural elements. In this work we present a methodology for studying large intact RNA biomolecules using homonuclear 15N solid state nuclear magnetic resonance (NMR) spectroscopy. We show that Proton Driven Spin Diffusion (PDSD) experiments with long mixing times, up to 16s, improved by the incorporation of multiple rotor-synchronous 1H inversion pulses (termed Radiofrequency Dipolar Recoupling, RFDR, pulses), reveal key hydrogen-bond contacts. In the full-length RNA isolated from MS2 phage, we observed strong and dominant contributions of G-C Watson-Crick base pairs, and beyond these common interactions, we observe a significant contribution of the G-U wobble base pairs. Moreover, we can differentiate base-paired and non-base-paired nitrogen atoms. Using the improved technique facilitates characterization of hydrogen-bond types in intact large-scale RNA using solid-state NMR. It can be highly useful to guide secondary structure prediction techniques, and possibly structure determination methods.


title: Free energies of stalk formation in the lipidomics era

abstract: Many biological membranes are asymmetric and exhibit complex lipid composition, comprising hundreds of distinct chemical species. Identifying the biological function and advantage of this complexity is a central goal of membrane biology. Here, we study how membrane complexity controls the energetics of the first steps of membrane fusions, that is, the formation of a stalk. We first present a computationally efficient method for simulating thermodynamically reversible pathways of stalk formation at near-atomic resolution. The new method reveals that the inner leaflet of a typical plasma membrane is far more fusogenic than the outer leaflet, which is likely an adaptation to evolutionary pressure. To rationalize these findings by the distinct lipid compositions, we computed ~200 free energies of stalk formation in membranes with different lipid head groups, tail lengths, tail unsaturations, and sterol content. In summary, the simulations reveal a drastic influence of the lipid composition on stalk formation and a comprehensive fusogenicity map of many biologically relevant lipid classes.


title: Staring at the naked Goddess. Unraveling structure and reactivity of Artemis endonuclease interacting with a DNA double strand.

abstract: Artemis is an endonuclease responsible for breaking hairpin DNA strand during immune system adaptation and maturation as well as the processing of potentially toxic DNA lesions. Thus, Artemis may be an important target in the development of anticancer therapy, both for the sensitization of radiotherapy and for immunotherapy. Despite its importance its structure has been resolved only recently, and important questions concerning the arrangement of its active center, the interaction with the DNA substrate, or the catalytic mechanism remain unanswered. In this contribution, by performing extensive molecular dynamic simulation, both classically and at hybrid quantum mechanics/ molecular mechanics level, we evidence the stable interaction modes of Artemis with a model DNA strand. We also analyze the catalytic cycle providing the free energy profile and key transition states for the DNA cleavage reaction.


title: Hitting more birds with one stone: CD70 as an actionable immunotherapeutic target in recurrent glioblastoma

abstract:
PurposeGlioblastoma (GBM) patients suffer from a dismal prognosis, with standard of care therapy inevitably leading to therapy-resistant recurrent tumors. The presence of brain tumor initiating cells (BTICs) drives the extensive heterogeneity seen in GBM, prompting the need for novel therapies specifically targeting this subset of tumor-driving cells. Here we identify CD70 as a potential therapeutic target for recurrent GBM BTICs.

Experimental DesignIn the current study, we identified the relevance and functional influence of CD70 on primary and recurrent GBM cells, and further define its function using established stem cell assays. We utilize CD70 knockdown studies, subsequent RNAseq pathway analysis, and in vivo xenotransplantation to validate CD70s role in GBM. Next, we developed and tested an anti-CD70 CAR-T therapy, which we validated in vitro and in vivo using our established preclinical model of human GBM. Lastly, we explored the importance of CD70 in the tumor immune microenvironment (TIME) by assessing the presence of its receptor, CD27, in immune infiltrates derived from freshly resected GBM tumor samples.

ResultsCD70 expression is elevated in recurrent GBM and CD70 knockdown reduces tumorigenicity in vitro and in vivo. CD70 CAR-T therapy significantly improves prognosis in vivo. We also found CD27 to be present on the cell surface of multiple relevant GBM TIME cell populations.

ConclusionCD70 plays a key role in recurrent GBM cell aggressiveness and maintenance. Immunotherapeutic targeting of CD70 significantly improves survival in animal models and the CD70/CD27 axis may be a viable poly-therapeutic avenue to co-target both GBM and its TIME.


title: Cardiac and respiratory muscle responses to dietary N-acetylcysteine in rats consuming a high-saturated fat, high-sucrose diet

abstract:
BACKGROUNDExertional dyspnea is a significant clinical concern in individuals with overweight or obesity. The pathophysiology of dyspnea is multifactorial and complex. Previous data suggest that diaphragm and cardiac abnormalities should be considered as likely contributors to obesity-related exertional dyspnea. Additionally, oxidative stress is a causative factor in the general etiology of obesity as well as skeletal and cardiac muscle pathology. Thus, this preclinical study aimed to define diaphragm and cardiac morphological and functional alterations following an obesogenic diet in rats and the therapeutic potential of an antioxidant supplement, N-acetylcysteine (NAC).

METHODSMale Wistar rats ([~]7 weeks old) consumed ad libitum either lean (20% protein, 70% carbohydrate, 10% fat) or high-saturated fat, high-sucrose (HFHS, 20% protein, 35% carbohydrate, 45% fat) diets for [~]22 weeks. Rats receiving HFHS diet were randomized to drink control water or water with NAC (2 mg/ml) for the last eight weeks of the dietary intervention: Lean, HFHS, and HFHS+NAC (n = 8 per group). We evaluated diaphragm bundles (in vitro function and histology) and hearts (weights and echocardiography) for all groups.

RESULTSFinal body weights of HFHS rats, but not HFHS+NAC rats, were significantly higher than Lean controls. Neither HFHS diet nor NAC supplementation affected diaphragm specific force (N/cm2), peak power (W/kg), or morphology. In cardiac muscle, right and left ventricle weights (normalized to tibia length) of HFHS rats were greater than those of Lean controls and HFHS+NAC rats. Cardiac functional abnormalities were also present in HFHS rats, with left ventricular fractional shortening (%) and posterior wall maximal shortening velocity (cm/s) increasing compared to Lean controls, but HFHS+NAC rats did not demonstrate these markers of hypercontractility. HFHS rats showed an elevated deceleration rate of early transmitral diastolic velocity (E/DT) consistent with diastolic dysfunction, but NAC eliminated this effect.

CONCLUSIONOur data suggest that an HFHS diet does not compromise diaphragm muscle morphology or in vitro function, suggesting other possible contributors to breathing abnormalities in obesity (e.g., neuromuscular transmission abnormalities). However, an HFHS diet resulted in cardiac hypertrophy, hypercontractility, and diastolic dysfunction. Supplementation with NAC did not affect diaphragm morphology or function but attenuated cardiac abnormalities in the HFHS diet. Our findings support future studies testing NAC supplementation in clinical trials of humans with obesity.

category: physiology


title: A juvenile climbing exercise establishes a muscle memory boosting the effects of exercise in adult rats

abstract: One of the ideas stemming from the discovery of a cellular memory in muscle cells has been that an early exercise period could induce a long-term muscle memory, boosting the effects of exercise later in life. In general muscles are more plastic in younger animals, so we devised a 5-week climbing exercise scheme with food reward administered to juvenile rats (post-natal week 4-9). The juvenile exercise increased fiber cross-sectional area (fCSA), and boosted nuclear accretion. Subsequently the animals were subjected to 10 weeks of detraining (week 9-19, standard caging). During this period fCSA became similar in the animals that had been climbing compared to Naive controls, but the elevated number of myonuclei induced by the climbing were maintained. When the Naive rats were subjected to two weeks of adult exercise (week 19-21) there was little effect on fCSA, while the previously trained rats displayed an increase of 19%. Similarly, when the rats were subjected to unilateral surgical overload in lieu of the adult climbing exercise, the increase in fCSA was 20% (juvenile climbing group) and 11% (Naive rats) compared to the contralateral leg. This demonstrated that juvenile exercise can establish a muscle memory. The juvenile climbing exercise with food reward led to leaner animals with lower body weight. These differences were to some extent maintained throughout the adult detraining period in spite of all animals being fed ad libitum, indicating a form of body weight memory.


title: Modelling brain representations of abstract concepts

abstract: Abstract conceptual representations are critical for human cognition. Despite their importance, key properties of these representations remain poorly understood. Here, we used computational models of distributional semantics to predict multivariate fMRI activity patterns during the activation and contextualization of abstract concepts. We devised a task in which participants had to embed abstract nouns into a story that they developed around a given background context. We found that representations in inferior parietal cortex were predicted by concept similarities emerging in models of distributional semantics. By constructing different model families, we reveal the models learning trajectories and delineate how abstract and concrete training materials contribute to the formation of brain-like representations. These results inform theories about the format and emergence of abstract conceptual representations in the human brain.

category: neuroscience


title: High activity and high functional connectivity are mutually exclusive in resting state zebrafish and human brains

abstract: Active neurons impact cell types with which they are functionally connected. Both activity and functional connectivity are heterogeneous across the brain, but the nature of their relationship is not known. Here we employ brain-wide calcium imaging at cellular resolution in larval zebrafish to record spontaneous activity of >12,000 neurons in the forebrain. By classifying their activity and functional connectivity into three levels (high, medium, low), we find that highly active neurons have low functional connections and highly connected neurons are of low activity. Intriguingly, deploying the same analytical methods on functional magnetic resonance imaging (fMRI) data from the resting state human brain, we uncover a similar relationship between activity and functional connectivity, that is, regions of high activity are non-overlapping with those of high connectivity. These findings reveal a previously unknown and evolutionarily conserved brain organizational principle that have implications for understanding disease states and designing artificial neuronal networks.


title: Evidence for the null hypothesis in functional magnetic resonance imaging using group-level Bayesian inference

abstract: Classical null hypothesis significance testing is limited to the rejection of the point-null hypothesis; it does not allow the interpretation of non-significant results. Moreover, studies with a sufficiently large sample size will find statistically significant results even when the effect is negligible and may be considered practically equivalent to the  null effect. This leads to a publication bias against the null hypothesis. There are two main approaches to assess  null effects: shifting from the point-null to the interval-null hypothesis and considering the practical significance in the frequentist approach; using the Bayesian parameter inference based on posterior probabilities, or the Bayesian model inference based on Bayes factors. Herein, we discuss these statistical methods with particular focus on the application of the Bayesian parameter inference, as it is conceptually connected to both frequentist and Bayesian model inferences. Although Bayesian methods have been theoretically elaborated and implemented in commonly used neuroimaging software, they are not widely used for  null effect assessment. To demonstrate the advantages of using the Bayesian parameter inference, we compared it with classical null hypothesis significance testing for fMRI data group analysis. We also consider the problem of choosing a threshold for a practically significant effect and discuss possible applications of Bayesian parameter inference in fMRI studies. We argue that Bayesian inference, which directly provides evidence for both the null and alternative hypotheses, may be more intuitive and convenient for practical use than frequentist inference, which only provides evidence against the null hypothesis. Moreover, it may indicate that the obtained data are not sufficient to make a confident inference. Because interim analysis is easy to perform using Bayesian inference, one can evaluate the data as the sample size increases and decide to terminate the experiment if the obtained data are sufficient to make a confident inference. To facilitate the application of the Bayesian parameter inference to  null effect assessment, scripts with a simple GUI were developed.


title: Recruitment of representational components of the semantic system distinguishes successful from unsuccessful access to complex factual knowledge

abstract: Our ability to effectively retrieve complex semantic knowledge meaningfully impacts our daily lives, yet the neural processes that underly successful access and transient failures in access remain only partially understood. In this fMRI study, we contrast activation during successful semantic access, unsuccessful semantic access due to transient access-failures (i.e.,  tip-of-the-tongue,  feeling-of-knowing), and trials where the semantic knowledge was not possessed. Twenty-four human participants (14 female) were presented 240 trivia-based questions relating to person, place, object or scholastic knowledge-domains. Analyses of the recall event indicated a relatively greater role of a dorsomedial section of the prefrontal cortex in unsuccessful semantic access and relatively greater recruitment of the pars orbitalis of the inferior frontal gyrus in successful access. Successful access was also associated with increased activation in knowledge-domain selective areas. Generally, knowledge-domain selective areas showed increased responses for both preferred and non-preferred stimulus classes. The exception was place-selective regions (PPA, TOS and RSC), which were recruited during unsuccessful access attempts for all stimulus domains. Collectively, these results suggest that prefrontal semantic control systems and classical spatial-knowledge selective regions work together to locate relevant information and that access to complex knowledge results in a broad activation of semantic representation extending to regions selective for other knowledge domains.


title: Recruitment of control and representational components of the semantic system during successful and unsuccessful access to complex factual knowledge


title: Tumor necrosis factor-α modulates GABAergic and Dopaminergic neurons in the ventral periaqueductal gray of female mice.

abstract:
Neuroimmune signaling is increasingly identified as a critical component of various illnesses, including chronic pain, substance use disorder, and depression. However, the underlying neural mechanisms remain unclear. Proinflammatory cytokines, such as tumor necrosis factor- (TNF-), may play a key role by modulating synaptic function and long-term plasticity. The midbrain structure periaqueductal gray (PAG) plays a well-established role in pain processing, and while TNF- inhibitors have emerged as a potential therapeutic strategy for pain-related disorders, the impact of TNF- on PAG neuronal activity has not been thoroughly characterized. Recent studies have identified subpopulations of ventral PAG (vPAG) with opposing effects on nociception, with DA neurons driving pain relief in contrast to GABA neurons. Therefore, we used ex vivo slice physiology to examine the effects of TNF- on neuronal activity of both subpopulations. We selectively targeted GABA and dopamine neurons using a vGAT-reporter and a TH-eGFP reporter mouse line, respectively. Following exposure to TNF-, the intrinsic properties of GABA neurons were altered, resulting in increased excitability along with a reduction in glutamatergic synaptic drive. In DA neurons, TNF- exposure resulted in a robust decrease in excitability along with a modest reduction in glutamatergic synaptic transmission. Furthermore, the effect of TNF- was specific to excitatory transmission onto DA neurons as inhibitory transmission was unaltered. Collectively, these data suggest that TNF- differentially affects the basal synaptic properties of GABA and DA neurons and enhances our understanding of how TNF- mediated signaling modulates vPAG function.

New & NoteworthyThe present study describes the effects of tumor necrosis factor- (TNF-) on two distinct subpopulations of neurons in the ventral periaqueductal gray (vPAG). We show that TNF- alters both neuronal excitability and glutamatergic synaptic transmission on GABA neurons and dopamine neurons within the vPAG. This provides critical new information on the role of TNF- in the potential modulation of pain since activation of vPAG GABA neurons drives nociception, whereas activation of DA neurons drives analgesia.


title: Using top-down gating to optimally balance shared versus separated task representations

abstract: Human adaptive behavior requires continually learning and performing a wide variety of tasks, often with very little practice. To accomplish this, it is crucial to separate neural representations of different tasks in order to avoid interference. At the same time, sharing neural representations supports generalization and allows faster learning. Therefore, a crucial challenge is to find an optimal balance between shared versus separated representations. Typically, models of human cognition employ top- down modulatory signals to separate task representations, but there exist surprisingly little systematic computational investigations of how such modulation is best implemented. We identify and systematically evaluate two crucial features of modulatory signals. First, top-down input can be processed in an additive or multiplicative manner. Second, the modulatory signals can be adaptive (learned) or non-adaptive (random). We cross these two features, resulting in four modulation networks which are tested on a variety of input datasets and tasks with different degrees of stimulus-action mapping overlap. The multiplicative adaptive modulation network outperforms all other networks in terms of accuracy. Moreover, this network develops hidden units that optimally share representations between tasks. Specifically, different than the binary approach of currently popular latent state models, it exploits partial overlap between tasks.


title: Using top-down modulation to optimally balance shared versus separated task representations


title: An atlas of transcriptionally defined cell populations in the rat ventral tegmental area

abstract: The ventral tegmental area (VTA) is a complex brain region that is essential for reward function but is also implicated in neuropsychiatric diseases including substance abuse. While decades of research on VTA function have focused on the role of dopaminergic neurons, recent evidence has identified critical roles for VTA GABAergic and glutamatergic neurons in reward processes as well. Interestingly, molecular characterization has revealed that subsets of these neurons express genes involved in the transport, synthesis, and vesicular packaging of multiple neurotransmitters, providing evidence for co-release neurons. However, these studies have largely relied on low-throughput methods, and the molecular architecture of the VTA has not been comprehensively examined. Here, we performed single nucleus RNA-sequencing (snRNA-seq) on 21,600 VTA cells from male and female Sprague-Dawley rats to generate a transcriptional atlas of the rat VTA. We identified 16 transcriptionally distinct cell types within the VTA, including 7 neuronal populations. Further subclustering revealed several VTA neuronal populations expressing markers for more than one neurotransmitter system, with one cluster exhibiting high expression levels of genes involved in the synthesis and transport of GABA, glutamate, and dopamine. Finally, snRNA-seq enabled the de novo identification of thousands of marker genes for each transcriptionally distinct population, revealing cluster-specific enrichment of gene sets implicated in neuropsychiatric and neurodevelopmental disorders, as well as specific phenotypes associated with alcohol and tobacco use. Together, these results highlight the heterogeneity of cellular populations in the VTA and identify novel markers and disease-linked genes enriched in distinct neuronal subtypes.


title: Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions

abstract: Trophic interactions play a central role in driving microbial community assembly and function. In gut or soil ecosystems, successful inoculants are always facilitated by efficient colonization, however, the metabolite exchanges between inoculants and resident bacteria are rarely studied, particularly in the rhizosphere. Here, we used bioinformatic, genetic, transcriptomic and metabonomic analyses to uncover syntrophic cooperation between inoculant (Bacillus velezensis SQR9) and plant-beneficial indigenous Pseudomonas stutzeri in the cucumber rhizosphere. We found that the synergistic interaction of these two species is highly environmental dependent, the emergence of syntrophic cooperation was only evident in a static nutrient-rich niche, such as pellicle biofilm in addition to the rhizosphere. Our results identified branched-chain amino acids (BCAAs) biosynthesis pathway involved in syntrophic cooperation when forming coculture biofilms. Assaying the metabolome further demonstrated metabolic facilitation among the bacterial strains. In addition, biofilm matrix components from Bacillus were essential for the interaction. Importantly, the two-species consortium promoted plant growth and helped plants alleviate salt stress. In summary, we propose a mechanism in which synergic interactions between a biocontrol bacterium and a partner species promote plant health.


title: Antibacterial Activity and Acute Toxicity Testing of Biosynthesized Silver Nanoparticles against Methicilin-Resistant Staphylococcus aureus and Pseudomonas aeruginosa

abstract: Antibacterial activity of biosynthesized silver nanoparticles was studied using the macrobroth dilution technique. The silver nanoparticles was significantly active (p > 0.05) against the test organisms at an extract concentration of 75 {micro}g/ml. Concentrations [≤] 50 {micro}g/ml were not as effective as the colony forming units at this concentration, 1.61 x 106 for methicillin-resistant Staphylococcus aureus and concentrations [≤] 25 {micro}g/ml 1.45 x 106 for Pseudomonas aeruginosa respectively, were about the same range as the colony forming units of the controls. The silver nanoparticles inhibited Methicillin-Resistant S. aureus more (MIC of 75 {micro}g/ml and MBC of 100 {micro}g/ml) than they inhibited P. aeruginosa (both MIC and MBC was 100 {micro}g/ml). The LD50 of the synthesized silver nanoparticles after oral administration was seen to be greater than 5000 mg/kg body weight and is therefore thought to be safe. This study supports the use of silver nanoparticles as therapeutic agents.


title: Ex vivo infection of human skin with herpes simplex virus 1 reveals mechanical wounds as insufficient entry portals via the skin surface

abstract: Herpes simplex virus 1 (HSV-1) enters its human host via the skin or mucosa. The open question is how the virus invades this highly protective tissue in vivo to approach its receptors in the epidermis and initiate infection. Here, we performed ex vivo infection studies in human skin to investigate how susceptible the epidermis and dermis are to HSV-1 and whether wounding facilitates viral invasion. Upon ex vivo infection of complete skin, only sample edges demonstrated infected cells. After removal of the dermis, HSV-1 efficiently invaded the basal layer, and from there, gained access to suprabasal layers supporting a high susceptibility of the epidermis. In contrast, only single infected cells were detected in the papillary layer of the separated dermis. Interestingly, after wounding, nearly no infection of the epidermis was observed via the skin surface. However, if the wounding of the skin samples led to breaks through the dermis, HSV-1 infected mainly keratinocytes via the wounded dermis. The application of latex beads revealed only occasional entry via the wounded dermis, however, facilitated penetration via the wounded skin surface. Thus, we suggest that the wounded human skin surface allows particle penetration but still provides barriers that prevent HSV-1 invasion.


title: Deep-rooted plant species recruit distinct bacterial communities in 3 m deep subsoil

abstract: Deep-rooted plants can obtain water and nutrients from the subsurface, making them more resilient to climatic changes such as drought. In addition, the deeper root network also allow the plants to recruit bacteria from a larger reservoir in the soil. These bacteria might contribute to nutrient acquisition and provide other plant beneficial traits to the plant. However, the deep rhizosphere communities compositions and their assembly dynamics are unknown. Here, we show, using three perennial crops, Kernza, lucerne and rosinweed, grown in 4 m RootTowers, that deep rhizosphere bacterial communities are plant specific, but clearly distinct from the shallow communities. We found that the diversity decreased with depth in the rhizosphere, whereas abundance of 16S rRNA gene copies did not change with depth in lucerne and rosinweed. Furthermore, we identified a subgroup (4-8%) of ASVs in the rhizosphere communities that could not be retrieved in the corresponding bulk soil communities. The abundances of genes determined by qPCR involved in N-cycling: amoA, nifH, nirK, nirS and nosZ differed significantly between plant species, suggesting differences in N content in the root exudates of the plant species. Our results suggest that colonization of the rhizosphere by bulk soil bacteria is not limited by carbon supply, but rather by dispersal. Furthermore, the abundance of N cycling genes indicate that deep rhizosphere bacteria have the potential to provide N through nitrogen fixation.


title: A Method for Checking Recombinant Protein Quality to Troubleshoot for Discordant Immunoassays

abstract: Discordant results of recombinant protein-based enzyme-linked immunosorbent assays (ELISA) and other antigen detection tests are a common and vexing problem in scientific research and clinical laboratories. The reproducibility of immunoassays based on antibody specificity can be adversely affected by cryptic changes in the composition of the analyte (e.g., the protein antigen). By use of sodium dodecyl sulfate-polyacrylamide gel electrophoresis and mass spectrometry analyses, we found varying levels of purity and the extent of post-translational modifications (PTMs), particularly of N-linked glycosylation and phosphorylation, among varied lots of recombinant glucose-regulated protein 78 (GRP78) expressed in Escherichia coli. We expect these lotto-lot variabilities of both purity and PTMs led to inconsistent results stemming from ELISA assays that measured GRP78 autoantibody levels in patient plasma specimens. We present these analyses to draw readers attention to a potentially common, yet seldom appreciated problem, in laboratory assays using recombinant proteins as antigens for antibody detection, and propose a workflow to detect and troubleshoot for this typical problem.

category: molecular biology


title: Antiviral Effect of Hyunggaeyungyo-tang on A549 Cells Infected with Human Coronavirus

abstract:
BackgroundHerbal medicine is widely recommended to treat viral infectious diseases. Over 123,000,000 individuals have been infected with the coronavirus since a worldwide pandemic was declared in March 2020. We conducted this research to confirm the potential of herbal medicine as a treatment for coronavirus.

MethodsWe infected the A549 cell line with beta coronavirus OC43 then treated with 100 g/mL Hyunggaeyungyo-tang (HGYGT) or distilled water with a control of HGYGT. We measured the mRNA expression levels of pro-inflammatory cytokines and interferon stimulated genes (ISGs) to confirm the effectiveness of HGYGT upon coronavirus infection.

ResultsWe found the effects of HYGYT decrease the expression level of pPKR, peIF2, IFI6, IFI44, IFI44L, IFI27, IRF7, OASL and ISG15 when administered to cells with coronavirus infection. The expressions of IL-1, TNF-, COX-2, NF-{kappa}B, iNOS and IKK mRNA were also significantly decreased in the HGYGT group than in the control group.

ConclusionThrough the reduction of the amount of coronavirus RNA, our research indicates that HGYGT has antiviral effects. The reduction of IKK and iNOS mRNA levels indicate that HGYGT reduces coronavirus RNA expression and may inhibits the replication of coronavirus by acting on NF-kB/Rel pathways to protect oxidative injury. In addition, decreases in mRNA expression levels of pro-inflammatory cytokines indicate that the HGYGT may relieve the symptoms of coronavirus infections.