title: Abnormal Differentiation and Proliferation of Coronary Arterial Endothelium in Hypoplastic Left Heart Syndrome

abstract:
Hypoplastic left heart syndrome (HLHS) is a severe form of single ventricle congenital heart disease characterized by an underdevelopment of the left ventricle. Early serial postmortem examinations revealed high rate of coronary artery abnormalities in HLHS fetal hearts, which may impact ventricular development and intra-cardiac hemodynamics, leading to a poor prognosis after surgical palliations. Previous study reported that endothelial cells (ECs) lining the coronary vessels showed DNA damage in the left ventricle of human fetal heart with HLHS, indicating that EC dysfunction may contribute to the coronary abnormalities in HLHS.

To investigate the underlying mechanism of HLHS coronary artery abnormalities, we profiled both human fetal heart with an underdeveloped left ventricle (ULV) and ECs differentiated from induced pluripotent stem cells (iPSCs) derived from HLHS patients at single cell resolution. CD144+/NPR3- vascular ECs were selected and further classified as venous EC (NR2F2high), arterial EC (EFNB2high) and late arterial EC (GJA5high) subclusters based on previously reported marker genes. To study the arterial phenotype, we specifically generated iPSC-arterial ECs (AECs, CD34+CDH5+CXCR4+NT5E-/low) derived from three HLHS patients and three age-matched healthy controls to further dissect the phenotype of HLHS-AECs.

As compared to normal human heart and control iPSC-ECs respectively, ULV late arterial EC subcluster and HLHS iPSC-EC arterial clusters showed significantly reduced expression of arterial genes GJA5, DLL4, and HEY1. Pathway enrichment analysis based on differentially expressed genes revealed several defects in late AEC cluster from ULV compared to normal human heart, such as impaired endothelial proliferation, development and Notch signaling. HLHS iPSCs exhibited impaired AEC differentiation as evidenced by the significantly reduced CXCR4+NT5E-/low AEC progenitor population. Consistent with human heart transcriptomic data, matured HLHS iPSC-AECs also showed a lower expression of the arterial genes such as GJA5, DLL4, HEY1 which are also downstream of NOTCH signaling. Additionally, matured HLHS iPSC-AECs showed significantly decreased expression of cell proliferation marker Ki67 and G1/S transition genes (CCND1, CCND2) compared with controls. Interestingly, NOTCH ligand Jag1 treatment significantly rescued this cell proliferation defect in HLHS AECs, accompanied by upregulation of various G1/S transition genes.

In summary, we found that coronary AECs from HLHS showed impaired arterial development and proliferation downstream of NOTCH signaling. These functional defects in HLHS coronary AECs could contribute to the vascular structure malformation and impaired ventricular development.


title: Exploring the kinetic selectivity of drugs targeting the β1-adrenoceptor

abstract:
In this study, we report the {beta}1-adrenoceptor binding kinetics of several clinically relevant {beta}1/2-adrenoceptor ({beta}1/2AR) agonists and antagonists. We demonstrate that the physicochemical properties of a molecule directly affect its kinetic association rate (kon) and affinity for the target. In contrast to our findings at the {beta}2-adrenoceptor, a drugs immobilized artificial membrane partition coefficient (KIAM), reflecting both hydrophobic and electrostatic interactions of the drug with the charged surface of biological membranes, was no better predictor than simple hydrophobicity measurements such as log P or logD7.4, characterized by a distribution between water and a non-aqueous organic phase (e.g. n-octanol) at predicting association rate. Overall, this suggests that hydrophobic interactions rather than a combination of polar and hydrophobic interactions play a more prominent role in dictating the binding of these ligands to the {beta}1-adrenoceptor.

Using a combination of kinetic data, detailed structural and physicochemical information we rationalize the above findings and speculate that the association of positively charged ligands at the {beta}1AR is curtailed somewhat by its predominantly neutral/positive charged extracellular surface. Consequently, hydrophobic interactions in the ligand binding pocket dominate the kinetics of ligand binding. In comparison at the {beta}2AR, a combination of hydrophobicity and negative charge attracts basic, positively charged ligands to the receptors surface promoting the kinetics of ligand binding. Additionally, we reveal the potential role kinetics plays in the on-target and off-target pharmacology of clinically used {beta}-blockers.

category: pharmacology and toxicology


title: Robust designation of meiotic crossover sites by CDK-2 through phosphorylation of the MutSγ complex

abstract: Crossover formation is essential for proper segregation of homologous chromosomes during meiosis. Here we show that C. elegans Cyclin-dependent kinase 2 (CDK-2) forms a complex with cyclin-like protein COSA-1 and supports crossover formation by promoting conversion of meiotic double-strand breaks (DSBs) into crossover-specific recombination intermediates. Further, we identify MutS{gamma} component MSH-5 as a CDK-2 phosphorylation target. MSH-5 has a disordered C-terminal tail that contains 13 potential CDK phosphosites and is required to concentrate crossover-promoting proteins at recombination sites. Phosphorylation of the MSH-5 tail appears dispensable in a wild- type background, but when MutS{gamma} activity is partially compromised, crossover formation and retention of CDK-2/COSA-1 at recombination sites are exquisitely sensitive to phosphosite loss. Our data support a model in which robustness of crossover designation reflects a positive feedback mechanism involving CDK-2-mediated phosphorylation and scaffold-like properties of the MSH-5 C-terminal tail, features that combine to promote full recruitment and activity of crossover-promoting complexes.

category: cell biology


title: A Cytosolic Reductase Pathway is Required for Complete N-Glycosylation of an STT3B-Dependent Acceptor Site.

abstract: N-linked glycosylation of proteins entering the secretory pathway is an essential post-translational modification required for protein stability and function. Previously, it has been shown that there is a temporal relationship between protein folding and glycosylation, which influences the occupancy of specific glycosylation sites. Here we use an in vitro translation system that reproduces the initial stages of secretory protein translocation, folding and glycosylation under defined redox conditions. We found that the efficiency of glycosylation of hemopexin was dependent upon a robust NADPH-dependent cytosolic reductive pathway, which could also be mimicked by the addition of a membrane impermeable reducing agent. The identified hypoglycosylated acceptor site is adjacent to a cysteine involved in a short range disulfide bond, which has been shown to be dependent on the STT3B-containing oligosaccharyl transferase. We also show that efficient glycosylation at this site is dependent on the STT3A-containing oligosaccharide transferase. Our results provide further insight into the important role of the ER redox conditions in glycosylation site occupancy and demonstrate a link between redox conditions in the cytosol and glycosylation efficiency.


title: miR-573 rescues endothelial dysfunction during dengue infection under PPARγ regulation.

abstract: Early prognosis of abnormal vasculopathy is essential for effective clinical management of severe dengue patients. An exaggerated interferon (IFN) response and release of vasoactive factors from endothelial cells cause vasculopathy. This study shows that dengue 2 (DENV2) infection of human umbilical vein endothelial cells (HUVEC) results in differentially regulated miRNAs important for endothelial function. miR-573 was significantly down-regulated in DENV2-infected HUVEC due to decreased Peroxisome Proliferator Activator Receptor Gamma (PPAR{gamma}) activity. Restoring miR-573 expression decreased endothelial permeability by suppressing the expression of vasoactive angiopoietin 2 (ANGPT2). We also found that miR-573 suppressed the proinflammatory IFN response through direct downregulation of toll like receptor 2 (TLR2) expression. Our study provides a novel insight into miR-573 mediated regulation of endothelial function during DENV2 infection which can be further translated into a potential therapeutic and prognostic agent for severe dengue patients.

category: microbiology


title: Microstructured hydrogels to guide self-assembly and function of lung alveolospheres

abstract: Epithelial cell organoids have increased opportunities to probe questions on tissue development and disease in vitro and for therapeutic cell transplantation. Despite their potential, current protocols to grow these organoids almost exclusively depend on culture within three-dimensional (3D) Matrigel, which limits defined culture conditions, introduces animal components, and results in heterogenous organoids (i.e., shape, size, composition). Here, we describe a method that relies on polymeric hydrogel substrates for the generation and expansion of lung alveolar organoids (alveolospheres). Using synthetic hydrogels with defined chemical and physical properties, human induced pluripotent stem cell (iPSC)-derived alveolar type 2 cells (iAT2s) self-assemble into alveolospheres and propagate in Matrigel-free conditions. By engineering pre-defined microcavities within these hydrogels, the heterogeneity of alveolosphere size and structure was reduced when compared to 3D culture while maintaining alveolar type 2 cell fate of human iAT2 and primary mouse tissue-derived progenitor cells. This hydrogel system is a facile and accessible culture system for the culture of primary and iPSC-derived lung progenitors and the method could be expanded to the culture of other epithelial progenitor and stem cell aggregates.

category: bioengineering


title: Bone-Specific Enhancement of Antibody Therapy for Breast Cancer Metastasis to Bone

abstract: Therapeutic antibodies have gone a long way toward realizing their clinical potential and have become very useful for treating a variety of pathologies. Despite the rapid evolution of therapeutic antibodies, their clinical efficacy in treatment of bone tumors has been hampered by the inadequate pharmacokinetics and poor bone tissue accessibility of these large macromolecules. Here, we show that engineering therapeutic antibodies to include bone-homing peptide sequences dramatically enhances their concentration in the bone metastatic niche, resulting in significantly reduced survival and progression of breast cancer bone metastases. To enhance the bone tumor-targeting ability of engineered antibodies, we introduced varying numbers of a bone-homing peptide into permissive internal sites of the anti-HER2 antibody trastuzumab. Compared to the unmodified antibody, the engineered bone-targeting antibodies have similar pharmacokinetics and in vitro cytotoxic activity against HER2-positive cancer cells, but exhibit improved bone tumor distribution in vivo. Accordingly, in xenograft models of breast cancer metastasis to bone sites, engineered antibodies with enhanced bone specificity exhibit increased inhibition of both initial bone metastases and secondary multi-organ metastases from bone lesions. Furthermore, this engineering strategy is also applied to prepare bone-targeting antibody-drug conjugates with enhanced therapeutic efficacy. These results demonstrate that adding bone-specific targeting to antibody therapy results in robust delivery of therapeutic antibodies to the bone tumor niche. This provides a powerful strategy for overcoming inadequate treatment of bone cancer and the development of potentially acquired resistance to therapy.


title: In Silico analysis of PE_PGRS20 (Rv1068c) protein in Mycobacterium tuberculosis H37Rv

abstract:
The genetic makeup of Mycobacterium tuberculosis reveals the presence of an unknown repeat sequence of PE_PGRS family proteins that are responsible for antigenic variations and many unknown functions that includes necrosis of macrophage and apoptosis. The structure and function of these glycine-rich proteins can be predictable by homology modeling, the Ab-initio method, or by using different tools of bioinformatics. In this study, we selected, PE_PGRS20 (Rv1068c) an unknown PE_PGRS protein. We suggest that the PE_PGRS20 gene is linked with the others genes of the espACD operon which are the virulence factors in the M. tuberculosis H37Rv strain. The genes associated with this protein secretion system can perform the synthesis of a special type of fatty acid known as phthioceroldimycocerates (PDIM).

Docking with different anti TB drugs shows binding with PE_PGRS20 protein which suggests that the target protein may involve in the drug resistance.

category: bioinformatics


title: Modelling the collective mechanical regulation of the structure and morphology of epithelial cell layers

abstract: The morphology and function of epithelial sheets play an important role in healthy tissue development and cancer progression. The maintenance of structure of closely packed epithelial layers requires the coordination of various mechanical forces within the cells and others resulting from interactions with other cells and other tissues or substrates. However, a general model for the combination of mechanical properties which determine the cell shape and the overall structure of epithelial layers remains elusive. Here, we propose a computational model, based on the Cellular Potts Model, to study the interplay between mechanical properties of cells and dynamical transitions in epithelial structures and cell shapes. We map out phase diagrams as functions of cellular properties and the orientation of cell division. Monolayers of squamous, cuboidal, and columnar cells are found when the axis of cell proliferation is perpendicular to the substrate. Monolayer-to-multilayer transition is promoted via cell extrusion, depending on the mechanical properties of cells and the orientation of cell division. The results and model predictions are discussed in the context of experimental observations.

category: biophysics


title: Patient derived organoids reveal that PI3K/AKT signaling is an escape pathway for radioresistance and a target for therapy in rectal cancer.

abstract: Partial or total resistance to preoperative chemoradiotherapy occurs in more than half of locally advanced rectal cancer patients. Several novel or repurposed drugs have been trialled to improve cancer cell sensitivity to radiotherapy, with limited success. To understand the mechanisms underlying this resistance and target them effectively, we initially compared treatment-naive transcriptomes of radiation-resistant and radiation-sensitive patient-derived organoids (PDO) to identify biological pathways involved in radiation resistance. Pathway analysis revealed that PI3K/AKT/mTOR and epithelial mesenchymal transition pathway genes were upregulated in radioresistant PDOs. Moreover, single-cell sequencing of pre & post-irradiation PDOs showed mTORC1 upregulation, which was confirmed by a genome-wide CRSIPR-Cas9 knockout screen using irradiated colorectal cancer (CRC) cell lines. Based on these findings, we evaluated cancer cell viability in vitro when treated with radiation in combination with dual PI3K/mTOR inhibitors apitolisib or dactolisib. Significant AKT phosphorylation was detected in HCT116 cells two hours post-irradiation (p=0.027). Dual PI3K/mTOR inhibitors radiosensitised HCT116 and radiation-resistant PDO lines. The PI3K/AKT/mTOR pathway upregulation contributes to radioresistance and its pharmacological inhibition leads to significant radiosensitisation in an organoid model of CRC and is a target for clinical trials.

category: cancer biology


title: Correlations between metabolites in the synovial fluid and serum: a mouse injury study

abstract: Osteoarthritis, the most common degenerative joint disease, occurs more frequently in joints that have sustained injury. Currently, osteoarthritis is diagnosed with imaging that finds radiographic changes after the disease has already progressed to multiple tissues. The primary objective of this study was to compare potential metabolomic biomarkers of joint injury between the synovial fluid and serum in a mouse model of post-traumatic osteoarthritis. The secondary objective was to gain insight into the pathophysiology of osteoarthritis by examining metabolomic profiles after joint injury. 12-week-old adult female C57BL/6 mice (n=12) were randomly assigned to control, day 1 post injury, or day 8 post injury groups. Randomly selected stifle (i.e., knee) joints were placed into a non-invasive injury apparatus and subjected to a single dynamic axial compression causing anterior translation of the tibia relative to the femur to tear the anterior cruciate ligament. At days 1 and 8 post injury, serum was extracted then mice were immediately euthanized prior to synovial fluid collection. Metabolites were extracted and analyzed by liquid chromatography coupled to mass spectrometry. We detected ~2500 metabolites across serum and synovial fluid. Of these metabolites 179 were positively correlated and 51 were negatively correlated between synovial fluid and serum, indicating potential for the development of metabolomic biomarkers. Synovial fluid appeared to capture differences in metabolomic profiles between injured mice at both day 1 and 8 after injury whereas serum did not. However, synovial fluid and serum were distinct at both days 1 and 8 after injury. In the synovial fluid, pathways of interest across different time points mapped to amino acid synthesis and degradation, bupropion degradation, and the tRNA charging pathway. In the serum, notable pathways across time points were amino acid synthesis and degradation, the phospholipase pathway, and nicotine degradation. These results provide a rich picture of the injury response at early time points following traumatic joint injury. Furthermore, the correlations between synovial fluid and serum metabolites suggest that there is potential to gain insight into intra-articular pathophysiology through analysis of serum metabolites.

category: pathology


title: Chemotherapy in Cases of Trypanosoma cruzi Reinfection: Assessing for Chagas Disease Endemic Areas

abstract: People living in endemic areas of Chagas disease are submitted to multiple infections during their lives. This is an important factor in the development and morbidity of the disease. In the present investigation, evaluate the treatment outcome of triple infection mice with 21SF clones compared to the parental strain and with clones were investigated. Mice were infected and divided into groups: G1, infected with 21SF strain; G2, infected with 3 cloness 21SF strain; and G3, infected with each clone alone. Subsequently, the groups were subdivided in treated and untreated controls. After the treatment the mice were euthanized. Serological tests and parasitological tests were performed. Sections of the heart and skeletal muscle were collected, fixed and then processed for the histopathological study in sections stained with Hematoxilin end Eosin. Parasitological tests for animals treated have shown positive results that varied from 25 to 66.7% and the serology titers varied from 1:10 a 1:280 in treated mice. Cure rates ranged from 11.1 to 30.8%. Histopathological examination revealed that treated animals presented clear reduction of lesions in myocardium and in skeletal muscle. Animals subjected to multiple infections have low rates of cure and worsening of tissue lesions.


title: Movement is governed by rotational population dynamics in spinal motor networks

abstract: Although the generation of movements is a fundamental function of the nervous system, the underlying neural principles remain unclear. Since flexor- and extensor-muscles alternate during rhythmic movements like walking, it is often assumed that the responsible neural circuitry is similarly displaying alternating activity. Here, we present ensemble-recordings of neurons in the lumbar spinal cord that indicate that, rather than alternating, the population is performing a low-dimensional "rotation" in neural space, in which the neural activity is cycling through all phases continuously during the rhythmic behavior. The radius of rotation correlates with the intended muscle force and a perturbation of the low-dimensional trajectory can modify the motor behavior. Since existing models of spinal motor control offer an inadequate explanation of rotation, we propose a new theory of neural generation of movements from which this and other unresolved issues, such as speed regulation, force control, and multi-functionalism, are readily explained.

category: neuroscience


title: Synergistic Effect of Serotonin 1A and Serotonin 1B/D Receptor Agonists in the Treatment of L-DOPA-Induced Dyskinesia in 6-Hydroxydopamine-Lesioned Rats

abstract:
BackgroundThe gold standard for symptomatic relief of Parkinsons disease is L-DOPA. However, long-term treatment often leads to motor complications such as L-DOPA-induced dyskinesia (LID). While amantadine (Gocovri) is the only approved therapy for dyskinesia in people with Parkinsons disease on the American market, it is associated with neurological side effects and limited efficacy. Thus, there remains a high unmet need for addressing LID in Parkinsons disease patients worldwide.

ObjectiveThe objective of this study was to evaluate the efficacy, safety and performance compared to approved treatments of the serotonin receptor 1A (5-HT1A) and 5-HT1B/D agonists buspirone and zolmitriptan in the 6-hydroxydopamine unilaterally lesioned rat model for Parkinsons disease.

MethodsThe hemi-parkinsonian 6-OHDA lesioned rats underwent chronic treatment with L-DOPA to induce dyskinesia and were subsequently used for efficacy testing of buspirone, zolmitriptan and comparison with amantadine, measured as abnormal involuntary movement (AIM) scores after L-DOPA challenge. Safety testing was performed in model and naive animals using forelimb adjusting, rotarod and open field tests.

Results5-HT1A and 5-HT1B/D agonism effectively reduced AIM scores in a synergistic manner. The drug combination of buspirone and zolmitriptan was safe and did not lead to tolerance development following sub-chronic administration. Head-to-head comparison with amantadine showed superior performance of buspirone and zolmitriptan in the model.

ConclusionsThe strong anti-dyskinetic effect found with combined 5-HT1A and 5-HT1B/D agonism renders buspirone and zolmitriptan a potential clinical candidate for LID in Parkinsons disease.


title: NEURON-SPECIFIC CHROMOSOMAL MEGADOMAIN ORGANIZATION IS ADAPTIVE TO RECENT RETROTRANSPOSON EXPANSIONS

abstract: Here, we mapped cell-type specific chromatin domain organization in adult mouse cerebral cortex and report strong enrichment of Endogenous Retrovirus 2 (ERV2) repeat sequences in the neuron-specific heterochromatic  B2NeuN+ megabase-scaling subcompartment. Comparative chromosomal conformation mapping in Mus spretus and Mus musculus revealed neuron-specific reconfigurations tracking recent ERV2 retrotransposon expansions in the murine germline, with significantly higher B2 megadomain contact frequencies at sites with ongoing ERV2 insertions in Mus musculus. Ablation of the retrotransposon silencer Kmt1e/Setdb1 triggered B2 megadomain disintegration and rewiring with open chromatin domains enriched for cellular stress response genes, along with severe neuroinflammation and proviral assembly of ERV2/Intracisternal-A-Particles (IAPs) infiltrating dendrites and spines. We conclude that neuronal megadomain architectures include evolutionarily adaptive heterochromatic organization which, upon perturbation, unleashes ERV proviruses with strong tropism within mature neurons.


title: Population dynamics of the thalamic head direction system during drift and reorientation

abstract: The head direction (HD) system is classically modeled as a ring attractor network1,2 which ensures a stable representation of the animals head direction. This unidimensional description popularized the view of the HD system as the brains internal compass3,4. However, unlike a globally consistent magnetic compass, the orientation of the HD system is dynamic, depends on local cues and exhibits remapping across familiar environments5. Such a system requires mechanisms to remember and align to familiar landmarks, which may not be well described within the classic 1-dimensional framework. To search for these mechanisms, we performed large population recordings of mouse thalamic HD cells using calcium imaging, during controlled manipulations of a visual landmark in a familiar environment. First, we find that realignment of the system was associated with a continuous rotation of the HD network representation. The speed and angular distance of this rotation was predicted by a 2nd dimension to the ring attractor which we refer to as network gain, i.e. the instantaneous population firing rate. Moreover, the 360-degree azimuthal profile of network gain, during darkness, maintained a  memory trace of a previously displayed visual landmark. In a 2nd experiment, brief presentations of a rotated landmark revealed an attraction of the network back to its initial orientation, suggesting a time-dependent mechanism underlying the formation of these network gain memory traces. Finally, in a 3rd experiment, continuous rotation of a visual landmark induced a similar rotation of the HD representation which persisted following removal of the landmark, demonstrating that HD network orientation is subject to experience-dependent recalibration. Together, these results provide new mechanistic insights into how the neural compass flexibly adapts to environmental cues to maintain a reliable representation of the head direction.


title: Axonal length determines distinct homeostatic phenotypes in human iPSC derived motor neurons on a bioengineered platform

abstract: Stem cell-based experimental platforms for neuroscience can effectively model key mechanistic aspects of human development and disease. However, conventional culture systems often overlook the engineering constraints that cells face in vivo. This is particularly relevant for neurons covering long range connections such as spinal motor neurons (MNs). The axons of these neurons extend up to 1m in length and require a complex interplay of mechanisms to maintain cellular homeostasis. It follows that shorter axons in conventional cultures may not faithfully capture important aspects of their longer counterparts. Here we directly address this issue by establishing a bioengineered platform to assemble arrays of human axons ranging from micrometers to centimeters, permitting systematic investigation of the effects of length on human axonal biology for the first time. With this approach, we reveal a link between length and metabolism in human MNs in vitro, where axons above a "threshold" size induce specific molecular adaptations in cytoskeleton composition, functional properties, local translation and mitochondrial homeostasis. Our findings specifically demonstrate the existence of a length-dependent mechanism that switches homeostatic processes within human MNs in order to sustain long axons. Our findings have critical implications for in vitro modelling of several neurodegenerative disorders and reinforce the importance of modelling cell shape and biophysical constraints with fidelity and precision in vitro.


title: Laser Capture Microdissection optimization for high-quality RNA in mouse brain tissue

abstract: Laser Capture Microdissection (LCM) is a method that allows to select and dissecting specific structures, cell populations, or even single cells from different types of tissue to extract DNA, RNA, or proteins. It is easy to perform and precise, avoiding unwanted signals from irrelevant cells, because gene expression may be affected by a bulk of heterogeneous material in a sample. However, despite its efficiency, several steps can affect the sample RNA integrity. In comparison to DNA, RNA is a much more unstable molecule and represents a challenge in the LCM method. Here we describe an optimized protocol to provide good concentration and high-quality RNA in specific structures, such as Dentate Gyrus and CA1 in the hippocampus, basolateral amygdala and anterior cingulate cortex of mouse brain tissue.


title: HCN1 channels mediate mu opioid receptor long-term depression at insular cortex inputs to the dorsal striatum

abstract: Mu opioid receptors (MORs) are expressed in the dorsal striatum, a brain region that mediates goal-directed (via the dorsomedial striatum), and habitual (via the dorsolateral striatum, DLS) behaviors. Our previous work indicates that glutamate transmission is depressed when MORs are activated in the dorsal striatum, inducing MOR-mediated long-term synaptic depression (MOR-LTD) or short-term depression (MOR-STD), depending on the input. In the DLS, MOR-LTD is produced by MORs on anterior insular cortex (AIC) inputs and MOR-STD occurs at thalamic inputs, suggesting input-specific MOR plasticity mechanisms. Here, we evaluated the mechanisms of induction of MOR-LTD and MOR-STD in the DLS using pharmacology and optogenetics combined with patch clamp electrophysiology. We found that cAMP/PKA signaling and protein synthesis are necessary for MOR-LTD expression, similar to previous studies of endocannabinoid-mediated LTD (eCB-LTD) in DLS. However, MOR-LTD does not require mTOR signaling as eCB-LTD does. MOR-STD does not utilize these same mechanisms. We characterized the role of presynaptic HCN1 channels in MOR-LTD induction as HCN1 channels expressed in AIC are necessary for MOR-LTD expression in the DLS. These results suggest a mechanism in which MOR activation needs HCN1 to induce MOR-LTD, suggesting a new target for pharmacological modulation of synaptic plasticity, providing new opportunities to develop novel drugs to treat alcohol and opioid use disorders.


title: Adaptive cognitive maps for curved surfaces in the 3D world

abstract: Terrains in a 3D world can be undulating. Yet, most prior research has exclusively investigated spatial representations on a flat surface, leaving a 2D cognitive map as the dominant model in the field. Here, we investigated whether humans represent a curved surface by building a dimension-reduced flattened 2D map or a full 3D map. Participants learned the location of objects positioned on a flat and curved surface in a virtual environment by driving on the concave side of the surface (Experiment 1), driving and looking vertically (Experiment 2), or flying (Experiment 3). Subsequently, they were asked to retrieve either the path distance or the 3D Euclidean distance between the objects. Path distance estimation was good overall, but we found a significant underestimation bias for the path distance on the curve, suggesting an influence of potential 3D shortcuts, even though participants were only driving on the surface. Euclidean distance estimation was better when participants were exposed more to the global 3D structure of the environment by looking and flying. These results suggest that the representation of the 2D manifold, embedded in a 3D world, is neither purely 2D nor 3D. Rather, it is flexible and dependent on the behavioral experience and demand.


title: β-glucan-induced innate immune memory distinctively affects macrophage activation in response to differential environmental cues

abstract: In vitro, exposure of human primary monocytes to the fungal {beta}-glucan enhances their pro-inflammatory responsiveness towards several pathogens. Yet, the role of environmental condition of this process remains unclear. Here we found that {beta}-glucan-induced innate immune memory counteract the anti-inflammatory status of the macrophages. In response to {beta}-glucan imprinting, M-CSF-(M2-like-) macrophages increase their pro-inflammatory responsiveness to secondary stimuli associated with decrease of the M-CSF differentiation hallmarks. In contrast, in GM-CSF-(M1-like-) environment, {beta}-glucan imprinting reduced the pro-inflammatory canonical feature of the macrophages, together with their terminal differentiation marks. Comparing M-CSF and GM-CSF environment, we observed that {beta}-glucan-imprinted macrophages present comparable functions in terms of cytokine responses, phagocytosis, oxidative burst, and angiogenesis. This effect is mediated through Dectin-1 and associated with altered expression of the master regulators of macrophage terminal differentiation, IRF5 and IRF3. {beta}-glucan-induced innate immune memory skews the commitment of the macrophages in complex environment towards similar and less terminally differentiated cells. Together, these observations suggest a potential therapeutic role for {beta}-glucan-induced modulation of innate memory in different pathological contexts.

category: immunology


title: β-glucan imprinting remodels macrophage function in response to environmental cues


title: HIV-1 Induction of Tolerogenic DCs is Mediated by Cellular Interaction with Suppressive T Cells

abstract:
HIV-1 infection gives rise to a multilayered immune impairment in most infected individuals. The crosstalk between Dendritic cells and T cells plays an important part in the induction of immune responses. The chronic presence of human immunodeficiency virus (HIV)-1 during the dendritic cells (DCs) priming and activation of T cells promotes the expansion of suppressor cells in a contact dependent manner. The mechanism behind the T cell side of this HIV induced impairment is well studied, whereas little is known about the reverse effects exerted on the DCs in this setting.

Here we assessed the phenotype and transcriptome profile of mature DCs that have been in contact with suppressive T cells. The DCs in the HIV exposed DC-T cell coculture obtained a more tolerogenic/suppressive phenotype with increased expression of e.g., PDL1, Gal-9, HVEM, and B7H3, mediated by their cellular interaction with T cells. The transcriptomic analysis showed a clear type I IFN response profile as well as an activation of pathways involved in T cell exhaustion.

Taken together, our data indicate that the prolonged and strong IFN type I signaling induced by the presence of HIV during DC-T cell cross talk could play an important role in the induction of the tolerogenic DCs and suppressed immune response.


title: Redox-mediated inactivation of the transcriptional repressor C3600 makes uropathogenic Escherichia coli exquisitely resistant to reactive chlorine species

abstract:
The ability to overcome stressful environments is critical for pathogen survival in the host. One challenge for bacteria is the exposure to reactive chlorine species (RCS), which are generated by innate immune cells as critical part of the oxidative burst. Hypochlorous acid (HOCl) is the most potent antimicrobial RCS and associated with extensive macromolecular damage in the phagocytized pathogen. However, bacteria have evolved defense strategies to alleviate the effects of HOCl-mediated damage. Among these are RCS-sensing transcriptional regulators that control the expression of HOCl-protective genes under non- and HOCl stress. Uropathogenic Escherichia coli (UPEC), the major causative agent of urinary tract infections (UTIs), is particularly exposed to infiltrating neutrophils during pathogenesis, however, their responses to and defenses of HOCl are still completely unexplored. Here, we present evidence that UPEC strains tolerate higher levels of HOCl and are better protected from neutrophil-mediated killing compared to other E. coli. Transcriptomic analysis of HOCl-stressed UPEC revealed the upregulation of an operon consisting of three genes, one of which encodes the transcriptional regulator C3600. We identified C3600 as a HOCl-sensing transcriptional repressor, which, under non-stress conditions, is bound to the operator and represses the expression of its target genes. During HOCl exposure, however, the repressor forms reversible intermolecular disulfide bonds and dissociates from the DNA resulting in the de-repression of the operon. Deletion of one of the target genes renders UPEC significantly more susceptible to HOCl indicating that the HOCl-mediated induction of the regulon plays a major role for UPECs HOCl resistance.

IMPORTANCEHow do pathogens deal with antimicrobial oxidants produced by the innate immune system during infection? Uropathogenic Escherichia coli (UPEC), the most common etiological agent of urinary tract infections (UTIs), is particularly exposed to infiltrating neutrophils and, therefore, must counter elevated levels of the antimicrobial oxidant HOCl to establish infection. Our study provides fundamentally new insights into a defense mechanism that enables UPEC to fend off the toxic effects of HOCl stress. Intriguingly, the defense system is predominantly found in UPEC and absent in non-invasive enteropathogenic E. coli. Our data suggest that expression of the target gene c3601 is exclusively responsible for UPECs increased HOCl tolerance in culture and therefore potentially contributes to UPECs survival during phagocytosis. Thus, this novel HOCl stress defense system could potentially serve as an attractive drug target to increase the bodys own capacity to fight UTIs.


title: Characterization of opposing responses to phenol by Bacillus subtilis chemoreceptors

abstract:
Bacillus subtilis employs ten chemoreceptors to move in response to chemicals in its environment. While the sensing mechanisms have been determined for many attractants, little is known about the sensing mechanisms for repellents. In this work, we investigated phenol chemotaxis in B. subtilis. Phenol is an attractant at low, micromolar concentrations, and a repellent at high, millimolar concentrations. McpA was found to be the principal chemoreceptor governing the repellent response to phenol and other related aromatic compounds. In addition, the chemoreceptors McpC and HemAT were found to the govern the attractant response to phenol and related compounds. Using receptor chimeras, McpA was found to sense phenol using its signaling domain rather than its sensing domain. These observations were substantiated in vitro, where direct binding of phenol to the signaling domain of McpA was observed using saturation-transfer difference nuclear magnetic resonance. These results further advance our understanding of B. subtilis chemotaxis and demonstrate that the signaling domain of B. subtilis chemoreceptors can directly sense chemoeffectors.

IMPORTANCEBacterial chemotaxis is commonly thought to employ a sensing mechanism involving the extracellular sensing domain of chemoreceptors. Some ligands, however, appear to be sensed by the signaling domain. Phenolic compounds, commonly found in soil and root exudates, provide environmental cues for soil microbes like Bacillus subtilis. We show that phenol is sensed both as an attractant and a repellent. While mechanism for sensing phenol as an attractant is still unknown, we found that phenol is sensed as a repellent by the signaling domain of the chemoreceptor McpA. This study furthers our understanding of the unconventional sensing mechanisms employed by the B. subtilis chemotaxis pathway.


title: Towards discrimination of mammary pathogenic Escherichia coli (MPEC) in cattle based on possession of different iron acquisition systems

abstract:
Most efforts to elucidate virulence mechanisms of mammary pathogenic Escherichia coli (MPEC), causative agent of bovine clinical mastitis, have been failed but some recent studies introduced iron acquisition systems as major role players in pathogenicity. Here, we investigated the different iron uptake systems genotypes and assessed how they relate to virulence potential of MPEC. In total, 217 E. coli isolates (MPEC= 157, fecal isolates= 60) were screened for the presence of nine genes related to iron acquisition (iroN, iutA, fecA, fyuA, sitA, irp2, iucD, chuA and tonB) and phylogenetic groups were also determined. Next, bacterial growth potential and survival in raw and UHT milk which are representative for crucial steps in mastitis development were evaluated. In addition, the mineral consumption of E. coli cultured in milk were measured. The results showed that MPEC strains considerably tend to possess fecA (93%, p= 0.000) and belong to phylogenetic group A (42%, p= 0.042). The fecA+ strains from both mastitis and fecal E. coli had a significant (p= 0.000) growth potential in raw and UHT milk. Interestingly, for the first time, it was shown that fecA+ isolates consumed less amounts of iron and other metal ions. Overall, it seems that the uptake systems related to fecA contributes to overcoming harsh conditions of milk and genetic lineages could also affect pathogenicity of MPEC. These findings could lead us to define MPEC with more clarity based on genotypes or growth potential in milk and possibly promote novel solutions to control mastitis more effectively in future.

ImportanceMastitis is one of the most costly concerns in bovine medicine and the main cause of antibiotic use in dairy herds worldwide. As a rule of thumb, it was believed that extraintestinal pathogenic E. coli expands iron acquisition virulence arsenal to enhance pathogenic potential in the environments of the host outside the intestines. The present study indicated that the long believed idea of possession of diverse mineral acquisition systems and siderophores in all ExPEC groups could be a fairy tale. Along with recent studies, the present research showed that the fec operon could be the minimal necessary factor to overcome the harsh conditions of milk with limiting mineral concentrations. Obviously, the fecA+ isolates were fast-growing and consumed less amounts of minerals. It seems that the fec locus and its related metabolic pathways could be the potential targets for diagnostic, preventive, and therapeutic purposes.


title: Systematic shifts in the variation among host individuals must be considered in climate-disease theory

abstract: To make more informed predictions of host-pathogen interactions under climate change, studies have incorporated the thermal performance of host, vector, and pathogen traits into disease models. However, this body of work has ignored the fact that disease spread and long-term patterns of host population dynamics are largely determined by the variation in susceptibility among individuals in the host population. Furthermore, and especially for ectothermic host species, variation in susceptibility is likely to be plastic, influenced by variables such as environmental temperature. Quantifying the relationship between temperature and among-host trait variation will therefore be critical for predicting how climate change and disease will interact to influence host-pathogen population dynamics. Here, we demonstrate how short-term effects of temperature on the variation of host susceptibility drive epidemic characteristics, fluctuations in host population sizes, and probabilities of host extinction. We use this quantitative analysis as a basic framework to suggest that more research is needed in disease ecology to understand the mechanisms that shape trait variation, not just trait averages.

category: ecology


title: The effect of non-linear competitive interactions on quantifying niche and fitness differences

abstract: The niche and fitness differences of modern coexistence theory separate mechanisms into stabilizing and equalizing components. Although this decomposition can help us predict and understand species coexistence, the extent to which mechanistic inference is sensitive to the method used to partition niche and fitness differences remains unclear. We apply two alternative methods to assess niche and fitness differences to four well known community models. We show that because standard methods based on linear approximations do not capture the full community dynamics, they can sometimes lead to incorrect predictions of coexistence and misleading interpretations of stabilizing and equalizing mechanisms. Conversely, a more recently developed method to decompose niche and fitness differences, that accounts for the full nonlinear dynamics of competition, consistently identifies the correct contribution of stabilizing and equalizing components. This approach further reveals that when the true complexity of the system is taken into account, essentially all mechanisms comprise both stabilizing and equalizing components. Amidst growing interest in the role of non-additive and higher-order interactions in regulating species coexistence, we propose that the effective decomposition of niche and fitness differences will become increasingly reliant on methods that account for the inherent non-linearity of community dynamics.


title: Edible fire buffers: mitigation of wildfire with multifunctional landscapes

abstract: Wildfires ravage lands in seasonally-dry regions, imposing high costs on infrastructure maintenance and human habitation at the wildland-urban interface (WUI). Current fire mitigation approaches present upfront costs with uncertain long-term payoffs. Instead, we show that a simple landscape intervention on human-managed wildlands - buffers of a low-flammability crop species such as banana irrigated using recycled water - can mitigate wildfires, produce food profitably, and provide additional ecosystem services. Recreating a recent, major fire in simulation, we find that a medium-sized banana buffer decreases fireline intensity by 96%, similar to prescribed burns and mechanical thinning combined, and delays the fire by 316 minutes, enabling safe and effective firefighting. We find that under climate change, despite worsened fires, banana buffers will still have a protective effect. We also find that banana buffers with average yield could produce a profit of $56k USD/hectare through fruit sales, in addition to fire mitigation and other benefits.


title: Targeting current species ranges and carbon stocks fails to conserve biodiversity in a changing climate: opportunities to support climate adaptation under 30x30

abstract: Protecting areas for climate adaptation will be essential to ensuring greater opportunity for species conservation well into the future. However, many proposals for protected areas expansion focus on our understanding of current spatial patterns, which may be ineffective surrogates for future needs. A science-driven call to address the biodiversity and climate crises by conserving at least 30% of lands and waters by 2030, 30x30, presents new opportunities to inform the siting of new protections globally and in the U.S. Here we identify climate refugia and corridors based on a weighted combination of currently available models; compare them to current biodiversity hotspots and carbon-rich areas to understand how 30x30 protections siting may be biased by data omission; and compare identified refugia and corridors to the Protected Areas Database to assess current levels of protection. Available data indicate that 20.5% and 27.5% of identified climate adaptation areas (refugia and/or corridor) coincides with current imperiled species hotspots and carbon-rich areas, respectively. With only 12.5% of climate refugia and corridors protected, a continued focus on current spatial patterns in species and carbon richness will not inherently conserve places critical for climate adaptation. However, there is ample opportunity for establishing future-minded protections: 52% of the contiguous U.S. falls into the top quartile of values for at least one class of climate refugia. Nearly 27% is already part of the protected areas network but managed for multiple uses that may limit their ability to contribute to the goals of 30x30. Additionally, nearly two-thirds of nationally identified refugia coincide with ecoregion-specific refugia suggesting representation of nearly all ecoregions in national efforts focused on conserving climate refugia. Based on these results, we recommend that land planners and managers make more explicit policy priorities and strategic decisions for future-minded protections and climate adaptation.


title: The information signature of diverging lineages

abstract: The process of forming new species is the driving force behind the diversity of life on Earth. Yet, we have not answered the basic question: why are species unevenly distributed across taxonomic groups and geographic settings? This is because we lack the means to directly compare aspects of population (lineage) divergence across unrelated species because taxon-specific effects make comparisons difficult or impossible. Here, we present a new solution to this challenge by identifying the information signature of diverging lineages, calculated using partial information decomposition (PID), under different evolutionary scenarios. We show in silico how the informational decomposition of genetic metrics varies over time since divergence. Calculating PID over 97,200 lattices reveals that the decomposed nodes of Tajimas D, {theta}W, and {pi} have strong information signatures, while FST was least useful for discriminating among divergence scenarios. The presence or absence of gene flow during divergence was the most detectable signature; mutation rate and effective population size (Ne) were also detectable whereas differences in recombination rate were not. This work demonstrates that PID can reveal evolutionary patterns that are minimally detectable using the raw metrics themselves; it does so by leveraging the architecture of the genome and the partial redundancy of information contained in genetic metrics. Our results demonstrate for the first time how to directly compare characteristics of diverging populations even among distantly related species, providing a foundational tool for understanding the diversity of life across Earth.

category: evolutionary biology


title: Genome-wide identification of sexual-reproduction genes in fission yeast via transposon-insertion sequencing

abstract: Many genes required for sexual reproduction remain to be identified. Moreover, many of the genes that are known have been characterized in distinct experiments using different conditions, which complicates understanding the relative contributions of genes to sex. To address these challenges, we developed an assay in Schizosaccharomyces pombe that couples transposon mutagenesis with high-throughput sequencing (TN-seq) to quantitatively measure the fitness contribution of nonessential genes across the genome to sexual reproduction. This approach identified 532 genes that contribute to sex, including more than 200 that were not previously annotated to be involved in the process, of which more than 150 have orthologs in vertebrates. Among our verified hits was an uncharacterized gene, ifs1 (important for sex), that is required for spore viability. In two other hits, plb1 and alg9, we observed a novel mutant phenotype of poor spore health wherein viable spores are produced, but the spores exhibit low fitness and are rapidly outcompeted by wildtype. Finally, we fortuitously discovered that a gene previously thought to be essential, sdg1 (social distancing gene), is instead required for growth at low cell densities. Our assay will be valuable in further studies of sexual reproduction in S. pombe and identifies multiple candidate genes that could contribute to sexual reproduction in other eukaryotes, including humans.

category: genetics


title: Information-based summary statistics for spatial genetic structure inference

abstract:
O_LIInference of spatial patterns of genetic structure often relies on parameter estimation and model evaluation using a set of summary statistics (SS) that summarise the information present in the data. An important subset of these SS is best described as diversity indices, which are based on information theory principles that can be classified as belonging to three different  families encompassing a spectrum of information measures, qH. These include the richness family of order q = 0, ArSS; the Shannon family of order q = 1, HSS; and the heterozygosity family of order q = 2, HeSS. Although commonly used by ecologists, the Shannon family has been rather neglected by population geneticists and evolutionary biologists. However, recent population genetic studies have advocated their use, yet the power of these SS for spatial structure discrimination has not been systematically assessed.
C_LIO_LIIn this study, we performed a comprehensive assessment of the three families of SS, as well as a fourth family consisting of SS belonging to the Shannon family but expressed in terms of Hill numbers [Formula], for spatial structure inference using simulated microsatellites data under typical spatial scenarios. To give an unbiased evaluation, we used three machine learning methods, Kernel Local Fisher discriminant analysis (KLFDA), random forest classification (RFC), and deep neural network (DL), to test the performance of different SS to discriminate between spatial scenarios, and then identified the most informative metrics for discriminatory power.
C_LIO_LIResults showed that the SS family of order q = 1 expressed in terms of Hill numbers, [Formula], outperformed the other two families (Ar SS, He SS) as well as the untransformed Shannon entropy (H SS) family. Jaccard dissimilarity (J) and its Mantels r showed the highest discriminatory power to discriminate all spatial scenarios, followed by Shannon differentiation {Delta}D and its Mantels r.
C_LIO_LIInformation-based summary statistics, especially the diversity of order q = 1 and Shannon differentiation measures, can increase the power of spatial structure inference. In addition, different sets of SS provide complementary power for discriminating between spatial scenarios.
C_LI


title: Systematic discovery of gene fusions in pediatric cancer by integrating RNA-seq and WGS

abstract:
BackgroundGene fusions are important cancer drivers in pediatric cancer and their accurate detection is essential for diagnosis and treatment. Clinical decision-making requires high confidence and precision of detection. Recent developments show RNA sequencing (RNA-seq) is promising for genome-wide detection of fusion products, but hindered by many false positives that require extensive manual curation and impede discovery of pathogenic fusions.

ResultsWe developed Fusion-sq to detect tumor-specific gene fusions by integrating and "fusing" evidence from RNA-seq and whole genome sequencing (WGS) using intron-exon gene structure. In a pediatric pan-cancer cohort of 130 patients, we identified 165 high confidence tumor-specific gene fusions and their underlying structural variants (SVs). This includes all clinically relevant fusions known to be present in this cohort (30 patients). Fusion-sq distinguishes healthy-occurring from tumor-specific fusions, and resolves fusions in amplified regions and copy number unstable genomes. A high gene fusion burden is associated with copy number instability. We identified 27 potentially pathogenic fusions involving oncogenes or tumor-suppressor genes characterised by underlying SVs or expression changes indicative of activating or disruptive effects.

ConclusionsOur results indicate how clinically relevant and potentially pathogenic gene fusions can be identified and their functional effects investigated by combining WGS and RNA-seq. Integrating RNA fusion predictions with underlying SVs advances fusion detection beyond extensive manual filtering. Taken together, we developed a method for identifying candidate fusions that is suitable for precision oncology applications. Our method provides multi-omics evidence for assessing the pathogenicity of tumor-specific fusions for future clinical decision making.

category: genomics


title: Finding the right fit: A comprehensive evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data

abstract:
A longstanding challenge in human microbiome research is achieving the taxonomic and functional resolution needed to generate testable hypotheses about the gut microbiomes impact on health and disease. More recently, this challenge has extended to a need for in-depth understanding of the pharmacokinetics and pharmacodynamics of clinical microbiome-based interventions. Whole genome metagenomic sequencing provides high taxonomic resolution and information on metagenome functional capacity, but the required deep sequencing is costly. For this reason, short-read sequencing of the bacterial 16S ribosomal RNA (rRNA) gene is the standard for microbiota profiling, despite its poor taxonomic resolution. The recent falling costs and improved fidelity of long-read sequencing warrant an evaluation of this approach for clinical microbiome analysis. We used samples from participants enrolled in a Phase 1b clinical trial of a novel live biotherapeutic product to perform a comparative analysis of short-read and long-read amplicon and metagenomic sequencing approaches to assess their value for generating informative and actionable clinical microbiome data. Comparison of ubiquitous short-read 16S rRNA amplicon profiling to long-read profiling of the 16S-ITS-23S rRNA amplicon showed that only the latter provided strain-level community resolution and insight into novel taxa. Across all methods, overall community taxonomic profiles were comparable and relationships between samples were conserved, highlighting the accuracy of modern microbiome analysis pipelines. All methods identified an active ingredient strain in treated study participants, though detection confidence was higher for long-read methods. Read coverage from both metagenomic methods provided evidence of active ingredient strain replication in some treated participants. Compared to short-read metagenomics, approximately twice the proportion of long reads were assigned functional annotations (63% vs. 34%). Finally, similar bacterial metagenome-assembled genomes (MAGs) were recovered across short-read and long-read metagenomic methods, although MAGs recovered from long reads were more complete. Overall, despite higher costs, long-read microbiome characterization provides added scientific value for clinical microbiome research in the form of higher taxonomic and functional resolution and improved recovery of microbial genomes compared to traditional short-read methodologies.

Data SummaryAll supporting data, code and protocols have been provided within the article or as supplementary data files. Two supplementary figures and four supplementary tables are available with the online version of this article. Sequencing data are accessible in the National Center for Biotechnology Information (NCBI) database under BioProject accession number PRJNA754443. The R code and additional data files used for analysis and figure generation are accessible in a GitHub repository (https://github.com/jeanette-gehrig/Gehrig_et_al_sequencing_comparison).

Impact StatementAccurate sequencing and analysis are essential for informative microbiome profiling, which is critical for the development of novel microbiome-targeted therapeutics. Recent improvements in long-read sequencing technology provide a promising, but more costly, alternative to ubiquitous short-read sequencing. To our knowledge, a direct comparison of the informational value of short-read and HiFi long-read sequencing approaches has not been reported for clinical microbiome samples. Using samples from participants in a Phase 1b trial of a live biotherapeutic product, we compare microbiome profiles generated from short-read and long-read sequencing for both amplicon-based 16S ribosomal RNA profiling and metagenomic sequencing. Though overall taxonomic profiles were similar across methods, only long-read amplicon sequencing provided strain-level resolution, and long-read metagenomic sequencing resulted in a significantly greater proportion of functionally annotated genes. Detection of a live biotherapeutic active ingredient strain in treated participants was achieved with all methods, and both metagenomic methods provided evidence of active replication of this strain in some participants. Similar taxonomies were recovered through metagenomic assemblies of short and long reads, although assemblies were more complete with long reads. Overall, we show the utility of long-read microbiome sequencing in direct comparison to commonly used short-read methods for clinically relevant microbiome profiling.


title: Temporal inhibition of chromatin looping and enhancer accessibility during neuronal remodeling

abstract: During development, looping of an enhancer to a promoter is frequently observed in conjunction with temporal and tissue-specific transcriptional activation. The chromatin insulator-associated protein Shep promotes Drosophila post-mitotic neuronal remodeling by repressing transcription of master developmental regulators, such as brain tumor (brat), specifically in maturing neurons. Since insulator proteins can promote looping, we hypothesized that Shep antagonizes brat promoter interaction with an as yet unidentified enhancer. Using chromatin conformation capture and reporter assays, we identified two novel enhancer regions that increase in looping frequency with the brat promoter specifically in pupal brains after Shep depletion. The brat promoters and enhancers function independently of Shep, ruling out direct repression of these elements. Moreover, ATAC-seq in isolated neurons demonstrated that Shep restricts chromatin accessibility of a key brat enhancer as well as other enhancers genome-wide in remodeling pupal but not larval neurons. These enhancers are enriched for chromatin targets of Shep and are located at Shep-inhibited genes, suggesting direct Shep inhibition of enhancer accessibility and gene expression during neuronal remodeling. Our results provide evidence for temporal regulation of chromatin looping and enhancer accessibility during neuronal maturation.


title: A terrain treadmill to study small animal locomotion through large obstacles

abstract:
A major challenge to understanding locomotion in complex 3-D terrain with large obstacles is to create tools for controlled, systematic lab experiments. Existing terrain arenas only allow observations at small spatiotemporal scales ([~]10 body length, [~]10 stride cycles). Here, we create a terrain treadmill to enable high-resolution observations of animal locomotion through large obstacles over large spatiotemporal scales. An animal moves through modular obstacles on an inner sphere, while a rigidly-attached, concentric, transparent outer sphere rotated with the opposite velocity via closed-loop feedback to keep the animal on top. During sustained locomotion, a discoid cockroach moved through pillar obstacles for 25 minutes ({approx} 2500 strides) over 67 m ({approx} 1500 body lengths), and was contained within a radius of 4 cm (0.9 body length) for 83% of the duration, even at speeds of up to 10 body length/s. The treadmill enabled observation of diverse locomotor behaviors and quantification of animal-obstacle interaction.

Summary StatementA device keeps a small animal on top of a sphere while it traverses obstacles, creating a "terrain treadmill" to study locomotion over a long time and distance at high-resolution.

category: animal behavior and cognition


title: A terrain treadmill to study animal locomotion through large obstacles


title: Predictive Simulations of Gait with Exoskeletons that Alter Energetics

abstract: Robotic exoskeletons, designed to augment human locomotion, have the potential to restore function in those with mobility impairments and enhance it in able-bodied individuals. However, optimally controlling these devices, to work in concert with complex and diverse human users, is a challenge. Accurate model simulations of the interaction between exoskeletons and walking humans may expedite the design process and improve control. Here, we use predictive gait simulations to investigate the effect of an exoskeleton that alters the energetic consequences of walking. To validate our approach, we re-created an past experimental paradigm where robotic exoskeletons were used to shift peoples energetically optimal step frequency to frequencies higher and lower than normally preferred. To match the experimental controller, we modelled a knee-worn exoskeleton that applied resistive torques that were either proportional or inversely proportional to step frequency--decreasing or increasing the energy optimal step frequency, respectively. We were able to replicate the experiment, finding higher and lower optimal step frequencies than in natural walking under each respective condition. Our simulated resistive torques and objective landscapes resembled the measured experimental resistive torque and energy landscapes. Individual muscle energetics revealed distinct coordination strategies consistent with each exoskeleton controller condition. Predicted step frequency and energetic outcomes were best achieved by increasing the number of virtual participants (varying whole-body anthropometrics), rather than number of muscle parameter sets (varying muscle anthropometrics). In future, our approach can be used to design controllers in advance of human testing, to help identify reasonable solution spaces or tailor design to individual users.


title: Closed-loop optimization of transcranial magnetic stimulation with electroencephalography feedback

abstract:
BackgroundTranscranial magnetic stimulation (TMS) is widely used in brain research and treatment of various brain dysfunctions. However, the optimal way to target stimulation and administer TMS therapies, for example, where and in which electric field direction the stimuli should be given, is yet to be determined.

ObjectiveTo develop an automated closed-loop system for adjusting TMS parameters (in this work, the stimulus orientation) online based on TMS-evoked brain activity measured with electroencephalography (EEG).

MethodsWe developed an automated closed-loop TMS-EEG set-up. In this set-up, the stimulus parameters are electronically adjusted with multi-locus TMS. As a proof of concept, we developed an algorithm that automatically optimizes the stimulation orientation based on single-trial EEG responses. We applied the algorithm to determine the electric field orientation that maximizes the amplitude of the TMS- EEG responses. The validation of the algorithm was performed with six healthy volunteers, repeating the search twenty times for each subject.

ResultsThe validation demonstrated that the closed-loop control worked as desired despite the large variation in the single-trial EEG responses. We were often able to get close to the orientation that maximizes the EEG amplitude with only a few tens of pulses.

ConclusionOptimizing stimulation with EEG feedback in a closed-loop manner is feasible and enables effective coupling to brain activity.


title: Potential Pharmacodynamic Mechanism of the Main ingredients in Licorice for Chronic Obstructive Pulmonary Disease

abstract:
PurposeThis study aimed to investigate the effect of essential ingredients of licorice on the chronic obstructive pulmonary disease (COPD).

MethodThe ingredients information were obtained from PubChem (https://pubchem.ncbi.nlm.nih.gov/), related genes about COPD was collected from geneCards (http://www.genecards.org/). Network pharmacology was utilized in this study.

ResultThe intersection data set contains 20 molecular targets between COPD and liquorice. Protein-protein interaction network showed that there are a total of 58 nodes and 137 edges involved. The link number of AKT1 in PPI network was 39, which is the highest level of interaction. MAPK1 is an important target of Licorice on COPD.

ConclusionMAPK signaling pathway could be the important key target of main ingredients of licorice on COPD.


title: Accurate, high-coverage assignment of in vivo protein kinases to phosphosites from in vitro phosphoproteomic specificity data

abstract: Phosphoproteomic experiments routinely observe thousands of phosphorylation sites. To understand the intracellular signaling processes that generated this data, one or more causal protein kinases must be assigned to each phosphosite. However, limited knowledge of kinase specificity typically restricts assignments to a small subset of a kinome. Starting from a statistical model of a high-throughput, in vitro kinase-substrate assay, I have developed an approach to high-coverage, multi-label kinase-substrate assignment called IV-KAPhE ("In vivo-Kinase Assignment for Phosphorylation Evidence"). Tested on human data, IV-KAPhE outperforms other methods of similar scope. Such computational methods generally predict a densely connected kinase-substrate network, with most sites targeted by multiple kinases, pointing either to unaccounted-for biochemical constraints or significant cross-talk and signaling redundancy. I show that such predictions can potentially identify biased kinase-site misannotations within families of closely related kinase isoforms and they provide a robust basis for kinase activity analysis.


title: De Novo Prediction of RNA 3D Structures with Deep Learning

abstract: We present a Deep Learning approach to predict 3D folding structures of RNAs from their nucleic acid sequence. Our approach combines an autoregressive Deep Generative Model, Monte Carlo Tree Search, and a Score Model to find and rank the most likely folding structures for a given RNA sequence. We confirm the predictive power of our approach by setting new benchmarks for some longer sequences in a simulated blind test of the RNA Puzzles prediction challenge.


title: Cryo-ET of HIV reveals Env positioning on Gag lattice and structural variation among Env trimers

abstract: HIV-1 Env mediates viral entry into host cells and is the sole target for neutralizing antibodies. However, Env structure and organization in its native virion context has eluded detailed characterization. Here we used cryo-electron tomography to analyze Env in mature and immature HIV-1 particles. Immature particles showed distinct Env positioning relative to the underlying Gag lattice, providing insights into long-standing questions about Env incorporation. A 9.1[A] sub-tomogram averaged reconstruction of virion-bound Env in conjunction with structural mass spectrometry revealed unexpected features, including a variable central core of the gp41 subunit, heterogeneous glycosylation between protomers plus a flexible stalk that allows Env tilting and variable exposure of neutralizing epitopes. Together, our results provide an integrative understanding of HIV assembly and structural variation in Env antigen presentation.


title: Mimicking and mitigating the cutaneous response to transcranial electrical stimulation using interferential and combinatorial techniques

abstract: Transcranial electrical stimulation (tES) is a promising adjunct treatment for neurological impairment and mental health disorders. The modulatory effects of tES are small to moderate, and accrue over days to weeks with repeated administration, but these effects are also inconsistent across individuals, which poses a challenge for its clinical administration. Some of the variability in tES may stem from uncontrolled behavioral factors, and inadequate dosing of current across individuals, so new strategies are needed to address these issues. We evaluated the biophysics of emerging techniques for tES and provided new testable hypotheses for the tolerability of interferentail and combinatorial waveforms. Millisecond pulsatile currents may serve as suitable alternatives to alternating currents in modulating neural spike timing from tES. Pulsatile currents limit spike generation in nerves and may be tolerated above the standard limit of 2 mA when combined with a direct current to block nerve activation. Additionally, we posit that combinations of kilohertz interferential currents can mimic the nerve response of different tES waveforms but with minimal modulation of cortical neurons, providing a new strategy for active placebo stimulation. These results will help guide design of interferential tES strategies for better blinding and provide a testable model for evaluating the tolerability of new combinatorial strategies.


title: Molecular determinants of the modulation of the VSD-PD coupling mechanism of the KV7.1 channel by the KCNE1 ancillary subunits

abstract: The IKS current is diffused through the plasma membranes of cardiomyocytes during the last phase of the cardiac action potential. This repolarization current is conducted by a tetrameric protein complex derived from the co-expression of four voltage-gated potassium channel KV7.1 -subunits and KCNE1 ancillary subunits from KCNQ1 and KCNE1 genes, respectively. We studied here the conformational space of KV7.1 in presence and absence of KCNE1, by building transmembrane models of their known Resting, Intermediate, and Activated states. We conducted Molecular Dynamics simulations of these models in lipid bilayers including the phosphatidyl-inositol-4,5-bisphosphate (PIP2) lipids. The comparative analysis of MD trajectories obtained for the KV7.1 and IKS models reveals how KCNE1 shifts the coupling mechanism between the activation state of the Voltage Sensor Domain of the channel and the conformation (open or closed) of its Pore Domain.


title: Imaging erythrocyte sedimentation in whole blood

abstract: The erythrocyte sedimentation rate (ESR) is one of the oldest medical diagnostic tools. However, currently there is some debate on the structure formed by the cells during the sedimentation process. While the conventional view is that erythrocytes sediment as separate aggregates, others have suggested that they form a percolating gel, similar to other colloidal suspensions. A direct probing of the structures formed by erythrocytes in blood at stasis is then required to settle these discrepancies. Here, we report observations performed with three different optical imaging techniques: direct light transmission through thin samples, two-photon microscopy and light-sheet microscopy. All techniques revealed a dynamic structure of a channeling gel but with differences in the resolved details. A quantitative analysis of the erythrocyte related processes and interactions during the sedimentation need a further refinement of the experimental set-ups.


title: RNA secondary structure regulates fragments' adsorption onto flat substrates

abstract: RNA is a functionally rich molecule with multilevel, hierarchical structures whose role in the adsorption to molecular substrates is only beginning to be elucidated. Here, we introduce a multiscale simulation approach that combines a tractable coarse-grained RNA structural model with an interaction potential of a structureless flat adsorbing substrate. Within this approach, we study the specific role of stem-hairpin and multibranch RNA secondary structure motifs on its adsorption phenomenology. Our findings identify a dual regime of adsorption for short RNA fragments with and without secondary structure, and underline the adsorption efficiency in both cases as a function of the surface interaction strength. The observed behavior results from an interplay between the number of contacts formed at the surface and the conformational entropy of the RNA molecule. The adsorption phenomenology of RNA seems to persist also for much longer RNAs as qualitatively observed by comparing the trends of our simulations with a theoretical approach based on an ideal semiflexible polymer chain.


title: Quantifying charge state heterogeneity for proteins with multiple ionizable residues

abstract:
Ionizable residues can release and take up protons and this has an influence on protein structure and function. The extent of protonation is linked to the overall pH of the solution and the local environments of ionizable residues. Binding or unbinding of a single proton generates a distinct charge microstate defined by a specific pattern of charges. Accordingly, the overall partition function is a sum over all charge microstates and Boltzmann weights of all conformations associated with each of the charge microstates. This ensemble-of-ensembles description recast as a q-canonical ensemble allows us to analyze and interpret potentiometric titrations that provide information regarding net charge as a function of pH. In the q-canonical ensemble, charge microstates are grouped into mesostates where each mesostate is a collection of microstates of the same net charge. Here, we show that leveraging the structure of the q-canonical ensemble allows us to decouple contributions of net proton binding and release from proton arrangement and conformational considerations. Through application of the q-canonical formalism to analyze potentiometric measurements of net charge in proteins with repetitive patterns of Lys and Glu residues, we are able to determine the underlying mesostate pKa values and, more importantly, we estimate relative mesostate populations as a function of pH. This is a strength of using the q-canonical approach and cannot be obtained using purely site-specific analyses. Overall, our work shows how measurements of charge equilibria, decoupled from measurements of conformational equilibria, and analyzed using the framework of the q-canonical ensemble, provide protein-specific quantitative descriptions of pH-dependent populations of mesostates. This method is of direct relevance for measuring and understanding how different charge states contribute to conformational, binding, and phase equilibria of proteins.

STATEMENT OF SIGNIFICANCEThe net charge of a protein in solution is governed by the overall pH as well as context and conformational contexts. Measurements of net charge are accessible via techniques such as potentiometry that quantify the buffering capacity of a protein solution. Here, we use the formal structure of the q-canonical ensemble to identify charge states that are compatible with a measured net charge profile as a function of pH. Our approach highlights how measurements of charge, decoupled from measurements of conformation, can be used to identify the ensembles of charge states that contribute to the overall population for given solution conditions. The methods introduced will be useful for measuring charge states and interpreting these measurements in different contexts.


title: Quantifying biochemical reaction rates from static population variability within complex networks

abstract: Quantifying biochemical reaction rates within complex cellular processes remains a key challenge of systems biology even as high-throughput single-cell data have become available to characterize snapshots of population variability. That is because complex systems with stochastic and non-linear interactions are difficult to analyze when not all components can be observed simultaneously and systems cannot be followed over time. Instead of using descriptive statistical models, we show that incompletely specified mechanistic models can be used to translate qualitative knowledge of interactions into reaction rate functions from covariability data between pairs of components. This promises to turn a globally intractable problem into a sequence of solvable inference problems to quantify complex interaction networks from incomplete snapshots of their stochastic fluctuations.


title: The sensitivity of magnetic particle imaging and fluorine-19 magnetic resonance imaging for cell tracking

abstract:
PurposeMagnetic particle imaging (MPI) and fluorine-19 (19F) MRI produce images which allow for quantification of labeled cells. MPI is an emerging instrument for cell tracking, which is expected to have superior sensitivity compared to 19F MRI. Our objective is to assess the cellular sensitivity of MPI and 19F MRI for detection of mesenchymal stem cells (MSC) and breast cancer cells.

MethodsCells were labeled with ferucarbotran or perfluoropolyether, for imaging on a preclinical MPI system or 3 Tesla clinical MRI, respectively. In vivo sensitivity with MPI and 19F MRI was evaluated by imaging MSC that were administered by different routes.

ResultsUsing the same imaging time, as few as 4000 MSC (76 ng iron) and 8000 breast cancer cells (74 ng iron) were reliably detected with MPI, and 256,000 MSC (9.01 x 1016 19F atoms) were detected with 19F MRI, with SNR > 5. In vivo imaging revealed reduced sensitivity compared to ex vivo cell pellets of the same cell number.

ConclusionMPI has the potential to be more sensitive than 19F MRI for cell tracking. We attribute reduced MPI and 19F MRI cell detection in vivo to the effect of cell dispersion among other factors, which are described.


title: Co-aggregation and secondary nucleation in the life cycle of human prolactin/galanin functional amyloids

abstract: Synergistic-aggregation and cross-seeding by two different amyloid proteins/peptides are well evident in various neurological disorders. However, this phenomenon is not well studied in functional amyloid aggregation. Here, we show Prolactin (PRL) is associated with lactation in mammals and neuropeptide galanin (GAL), which are co-stored in the lactotrophs facilitates the synergic aggregation in the absence of secretory granules helper molecules glycosaminoglycans (GAGS). Interestingly, although each partner possesses homotypic seeding ability, a unidirectional cross-seeding of GAL aggregation can be mediated by PRL seeds. The specificity of co-aggregation by PRL and GAL along with unidirectional cross-seeding suggests tight regulation of functional amyloid formation during co-storage of these hormones in secretory granule biogenesis of female rat lactotrophs. Further mixed fibrils release the constituent functional hormone much faster than the corresponding individual amyloid formed in presence of GAGs, suggesting that co-aggregation of functionally distant hormones might have evolved for efficient storage, synergistic and rapid release of both hormones upon stimulation. The co-aggregation and cross seeding by two different hormones of completely different structures and sequences (PRL and GAL) suggest a novel mechanism of heterologous amyloid formation both in disease and functional amyloids.


title: JAMMIT Analysis Defines 2 Semi-Independent Immune Processes Common to 29 Solid Tumors

abstract: Immunophenotype of solid tumors has relevance to cancer immunotherapy, as not all patients respond optimally to treatment utilizing monoclonal antibodies. Bioinformatic studies have failed to clearly identify tumor immunophenotype in a way that encompasses a wide variety of tumor types and highlights fundamental differences among them, complicating prediction of patient clinical response. The novel JAMMIT algorithm was used to analyze mRNA data for 33 cancer types in The Cancer Genome Atlas (TCGA). We found that B cells and T cells constitute the principal source of variation in most patient cohorts, and that virtually all solid malignancies formed three hierarchical clustering patterns with similar molecular features. The second main source of variability in transcriptomic studies we attribute to monocytes. We identified the three tumor types as TC1-mediated, TC17-mediated and non-immunogenic immunophenotypes and used a 3-gene signature to approximate infiltration by agranulocytes. Methods of in silico validation such as pathway analysis, Cibersort and published data from treated cohorts were used to substantiate these findings. Monocytic infiltrate is found to be related to patient survival according to immunophenotype, important differences in some solid tumors are identified and deficiencies of common bioinformatic approaches relevant to diagnosis are detailed by this work.


title: Breast tumor IGF-1R regulates cell adhesion and metastasis: Alignment of mouse single cell and human breast cancer transcriptomics

abstract: The acquisition of a metastatic phenotype is the critical event that determines patient survival from breast cancer. Several receptor tyrosine kinases have functions both in promoting and inhibiting metastasis in breast tumors. Although the insulin-like growth factor 1 receptor (IGF-1R) has been considered a target for inhibition in breast cancer, low levels of IGF-1R expression are associated with worse overall patient survival. To determine how reduced IGF-1R impacts tumor phenotype, we used weighted gene correlation network analysis (WGCNA) of METABRIC patient data and identified gene modules specific to cell cycle, adhesion, and immune cell signaling inversely correlated with IGF-1R expression in human breast cancers. Integration of human patient data with data from mouse tumors revealed similar pathways necessary for promoting metastasis in basal-like tumors with reduced signaling or expression of the IGF-1R. Functional analyses revealed the basis for the enhanced metastatic phenotype including alterations in E- and P-cadherins.


title: Impact of charge patches on tumor disposition and biodistribution of therapeutic antibodies

abstract: This study explores the impact of antibody surface charge on tissue distribution into various tissues including tumor. Tumor-bearing mice were dosed intravenously with a mixture comprising three antibodies engineered to carry negative charge patches, a balanced charge distribution, or positive patches, respectively. Tissue levels were analyzed with a specific LC-MS/MS method. In addition, the antibody mix was administered to non-tumor bearing mice. Muscle and skin interstitial fluid were obtained by centrifugation and analyzed by LC-MS/MS. An in-vitro endothelium model was explored for its feasibility to mimic the observed distribution differences. A balanced charge distribution was optimal in terms of total tumor exposure, while in other tissues negatively charged and balanced charged antibodies gave similar results. In contrast, positive charge patches generally result in increased serum clearance but markedly enhance tumor and organ uptake, leading to higher tissue-to-serum ratios. The uptake and availability in the interstitial space were confirmed by specific assessment of antibody levels in the interstitial fluid of muscle and skin, with similar charge impact as in total tissue. The in vitro model was able to differentiate the transport propensity of this series of antibody variants. In summary, our results show the differential effects of charge patches on an antibody surface on biodistribution and tumor uptake. These insights may help in the design of molecules with biodistribution properties tailored to their purpose and an optimized safety profile.


title: The non-steroidal anti-inflammatory drug nimesulide kills Gyps vultures at concentrations found in the muscle of treated cattle.

abstract: Throughout South Asia, cattle are regularly treated with non-steroidal anti-inflammatory drugs (NSAIDs) and their carcasses are left for scavengers to consume. Residues of the NSAID diclofenac in cattle carcasses caused widespread mortality and catastrophic population declines in three species of Gyps vulture during the 1990s and 2000s. Diclofenac is now banned, but other NSAIDs are used in its place. Different lines of evidence, including safety testing in Gyps vultures, have shown that some of these other NSAIDs are toxic, or probably toxic, to vultures. The NSAID nimesulide is widely available and commonly used, and has been found in dead vultures with signs of renal failure (i.e. visceral gout) and without the presence of diclofenac and/or other vulture-toxic NSAIDs. Nimesulide is therefore probably toxic to vultures. Here, we report safety testing of nimesulide in Gyps vultures. In a controlled toxicity experiment, we gave two vultures the maximum likely exposure of nimesulide calculated from initial pharmacokinetic and residue experiments in cattle. Two other control birds were given an oral dose of water. Both vultures dosed with nimesulide died within 30 h, after showing outward signs of toxicity and increases in biochemical indicators of renal failure. Post-mortem examinations found extensive visceral gout in both vultures. Both control vultures survived without biochemical indicators of renal failure. With this evidence, we call for an immediate and comprehensive ban of nimesulide throughout South Asia to ensure the survival of the regions Critically Endangered vultures. More generally, testing the impacts of drugs on non-target species should be the responsibility of the pharmaceutical industry, before their veterinary use is licensed.


title: Biomarkers Of Cardiovascular Toxicity Of Benzene Inhalation In Mice

abstract:
Benzene is a ubiquitous environmental pollutant. Recent population-based studies suggest that benzene exposure is associated with an increased risk for cardiovascular disease. However, it is unclear whether benzene exposure is sufficient to induce cardiovascular toxicity. We examined the effects of benzene inhalation (50 ppm, 6 h/day, 5 days/week, 6 weeks) or HEPA-filtered air exposure on the biomarkers of cardiovascular toxicity in male C57BL/6J mice. Benzene inhalation significantly increased the biomarkers of endothelial activation and injury including endothelial microparticles, activated endothelial microparticles, endothelial progenitor cell microparticles, lung endothelial microparticles, and activated lung and endothelial microparticles while having no effect on circulating levels of endothelial adhesion molecules, endothelial selectins, and biomarkers of angiogenesis. To understand how benzene may induce endothelial injury, we exposed human aortic endothelial cells to benzene metabolites. Of metabolites tested, trans,trans-mucondialdehyde (10 M, 18h) was most toxic. It induced caspases-3, -7 and -9 (intrinsic pathway) activation, and enhanced microparticle formation by 2.4-fold. Levels of plateletleukocyte aggregates, platelet macroparticles, and proportion of CD4+ and CD8+ T-cells were also significantly elevated in the blood of the benzene-exposed mice. We also found that benzene exposure increased the transcription of genes associated with endothelial cell and platelet activation in the liver; and induced inflammatory genes and suppressed cytochrome P450s in the lungs and the liver. Together, these data suggest that benzene exposure induces endothelial injury, enhances platelet activation and inflammatory processes; and circulatory levels of endothelial cell and platelet-derived microparticles and platelet-leukocyte aggregates are excellent biomarkers of cardiovascular toxicity of benzene.

HighlightsO_LIInhaled benzene exposure increases the levels of blood endothelial microparticles.
C_LIO_LIIn vitro, benzene metabolite trans, trans-mucondialdehyde induces endothelial cell apoptosis and microparticles formation.
C_LIO_LIInhaled benzene exposure decreases the levels of hematopoietic progenitor cells in the bone marrow.
C_LIO_LIInhaled benzene exposure augments the circulating levels of platelet-leukocyte adducts.
C_LI


title: Multiple Sclerosis Patients have an Altered Gut Mycobiome and Increased Fungal to Bacterial Richness Running Title: RRMS Patients have Gut Fungal Dysbiosis

abstract:
Trillions of microbes such as bacteria, fungi, and viruses exist in the healthy human gut microbiome. Although gut bacterial dysbiosis has been extensively studied in multiple sclerosis (MS), the significance of the fungal microbiome (mycobiome) is an understudied and neglected part of the intestinal microbiome in MS. The aim of this study was to characterize the gut mycobiome of patients with relapsing-remitting multiple sclerosis (RRMS), compare it to healthy controls, and examine its association with changes in the bacterial microbiome. We characterized and compared the mycobiome of 20 RRMS patients and 33 healthy controls (HC) using Internal Transcribed Spacer 2 (ITS2) and compared mycobiome interactions with the bacterial microbiome using 16S rRNA sequencing. Our results demonstrate an altered mycobiome in RRMS patients compared with HC. RRMS patients showed an increased abundance of Basidiomycota and decreased Ascomycota at the phylum level with an increased abundance of Candida and Epicoccum genera along with a decreased abundance of Saccharomyces compared to HC. We also observed an increased ITS2/16S ratio, altered fungal and bacterial associations, and altered fungal functional profiles in MS patients compared to HC.

This study demonstrates that RRMS patients had a distinct mycobiome with associated changes in the bacterial microbiome compared to HC. There is an increased fungal to bacterial ratio as well as more diverse fungal-bacterial interactions in RRMS patients compared to HC. Our study is the first step towards future studies in delineating the mechanisms through which the fungal microbiome can influence MS disease.


title: Stimulus degradation impairs performance in a rodent continuous performance test

abstract: Sustained attention is a core cognitive domain that is often disrupted in neuropsychiatric disorders. Continuous performance tests (CPTs) are the most common clinical assay of sustained attention. In CPTs, participants produce a behavioral response to target stimuli and refrain from responding to non-target stimuli. Performance in CPTs is measured as the ability to discriminate between targets and non-targets. Rodent versions of CPTs (rCPT) have been developed and validated with both anatomical and pharmacological studies, providing a translational platform for understanding the neurobiology of sustained attention. In human studies, using degraded stimuli (decreased contrast) in CPTs impairs performance and patients with schizophrenia experience a larger decrease in performance compared to healthy controls. In this study, we tested multiple levels of stimulus degradation in a touchscreen version of the CPT in mice. We found that stimulus degradation significantly decreased performance in both males and females. The changes in performance consisted of a decrease in stimulus discrimination, measured as d, and increases in hit reaction time and reaction time variability. These findings are in line with the effects of stimulus degradation in human studies. Overall, female mice demonstrated a more liberal response strategy than males, but response strategy was not affected by stimulus degradation. These data extend the utility of the mouse CPT by demonstrating that stimulus degradation produces equivalent behavioral responses in mice and humans. Therefore, the degraded stimuli rCPT has high translational value as a preclinical assay of sustained attention.


title: Coordinated drift of receptive fields during noisy representation learning

abstract: Long-term memories and learned behavior are conventionally associated with stable neuronal representations. However, recent experiments showed that neural population codes in many brain areas continuously change even when animals have fully learned and stably perform their tasks. This representational "drift" naturally leads to questions about its causes, dynamics, and functions. Here, we explore the hypothesis that neural representations optimize a representational objective with a degenerate solution space, and noisy synaptic updates drive the network to explore this (near-)optimal space causing representational drift. We illustrate this idea in simple, biologically plausible Hebbian/anti-Hebbian network models of representation learning, which optimize similarity matching objectives, and, when neural outputs are constrained to be nonnegative, learn localized receptive fields (RFs) that tile the stimulus manifold. We find that the drifting RFs of individual neurons can be characterized by a coordinated random walk, with the effective diffusion constants depending on various parameters such as learning rate, noise amplitude, and input statistics. Despite such drift, the representational similarity of population codes is stable over time. Our model recapitulates recent experimental observations in hippocampus and posterior parietal cortex, and makes testable predictions that can be probed in future experiments.


title: Compensatory reconfiguration of functional networks between white matter and grey matter in Alzheimer's disease

abstract: The temporal synchronization of BOLD signals within white matter (WM) and between WM and grey matter (GM) exhibited intrinsic architecture and cognitive relevance. However, few studies examined the network property within- and between-tissue in Alzheimers disease (AD). The hub regions with high weighted degree (WD) were prone to the neuropathological damage of AD. To systematically investigate the changes of hubs within- and between-tissue functional networks in AD patients, we used the resting-state fMRI data of 30 AD patients and 37 normal older adults (NC) from the ADNI open database, and obtained four types of voxel-based WD metrics and four types of distant-dependent WD metrics (ddWD) based on a series of Euclidean distance ranges with a 20mm increment. We found that AD patients showed decreased within-tissue ddWD in the thalamic nucleus and increased between-tissue ddWD in the occipito-temporal cortex, posterior thalamic radiation, and sagittal stratum, compared to NC. We also found that AD patients showed the increased between-tissue FCs between the posterior thalamic radiation and occipito-temporal cortex, and between the sagittal stratum and the salience and executive networks. The dichotomy of decreased and increased ddWD metrics and their locations were consistent with previous studies on the neurodegnerative and compensatory mechanisms of AD, indicating that despite the disruptions, the brain still strived to compensate for the neural inefficiency by reorganizing functional circuits. Our findings also suggested the short-to-medium ranged ddWD metrics between WM and GM as useful biomarker to detect the compensatory changes of functional networks in AD.