Miracle-dz/UniFAR-FTUs huggingface dataset:
CAR/CXCR5-T cell immunotherapy is safe and potentially efficacious in promoting sustained remission of SIV infection

During chronic human immunodeficiency virus (HIV) or simian immunodeficiency virus (SIV) infection prior to AIDS progression, the vast majority of viral replication is concentrated within B cell follicles of secondary lymphoid tissues. We investigated whether infusion of T cells expressing an SIV-specific chimeric antigen receptor (CAR) and the follicular homing receptor, CXCR5, could successfully kill viral-RNA+ cells in targeted lymphoid follicles in SIV-infected rhesus macaques. In this study, CD4 and CD8 T cells from rhesus macaques were genetically modified to express antiviral CAR and CXCR5 moieties (generating CAR/CXCR5-T cells) and autologously infused into a chronically infected animal. At 2 days post-treatment, the CAR/CXCR5-T cells were located primarily in spleen and lymph nodes both inside and outside of lymphoid follicles. Few CAR/CXCR5-T cells were detected in the rectum and lung, and no cells were detected in the bone marrow, liver, brain, or ileum. Within follicles, CAR/CXCR5-T cells were found in direct contact with SIV viral RNA+ cells. We next infused CAR/CXCR5-T cells into ART-suppressed SIV-infected rhesus macaques, in which the animals were released from ART at the time of infusion. These CAR/CXCR5-T cells replicated in vivo within both the extrafollicular and follicular regions of lymph nodes and accumulated within lymphoid follicles. CAR/CXR5-T cell concentrations in follicles peaked during the first week post-infusion but declined to undetectable levels after 2 to 4 weeks. Overall, CAR/CXCR5-T cell-treated animals maintained lower viral loads and follicular viral RNA levels than untreated control animals, and no outstanding adverse reactions were noted. These findings indicate that CAR/CXCR5-T cell treatment is safe and holds promise as a future treatment for the durable remission of HIV. Author summary A person infected with human immunodeficiency virus (HIV) has replicating virus concentrated within the follicles of lymphoid tissues. The cells needed to clear the infection, cytotoxic T lymphocytes, have limited access to follicles and, thus, the cytotoxic T lymphocytes are never completely able to clear all of the HIV from the body. In this study, we have produced immunotherapeutic T cells that home to follicles and clear infected cells. These T cells express a viral targeting chimeric antigen receptor (CAR) and a molecule called CXCR5, which leads to homing of the cells to follicles. Upon administration of these CAR T-cells to virus-infected primates, we found that the cells localized to the follicle, replicated, and directly interacted with infected cells. While the cells were not maintained in the animals for more than 4 weeks, most of the treated animals maintained lower levels of virus in the blood and follicles than untreated control animals. This study shows that this immunotherapy has potential as a treatment leading to long-term remission of HIV without the need for antiretroviral drugs.
A multispecies amplicon sequencing approach for genetic diversity assessments in grassland plant species

Grasslands are widespread and economically relevant ecosystems at the basis of sustainable roughage production. Plant genetic diversity (PGD; i.e., within-species diversity) is related to many beneficial effects to the ecosystem functioning of grasslands. The monitoring of PGD in temperate grasslands is complicated by the multiplicity of species present and by a shortage of methods for large-scale assessment. However, the continuous advancement of high-throughput DNA sequencing approaches have improved the prospects of broad, multispecies PGD monitoring. Among them, amplicon sequencing stands out as a robust and cost-effective method. Here we report a set of twelve multispecies primer pairs that can be used for high-throughput PGD assessment in multiple grassland plant species. The loci targeted by the amplicons were selected and tested in two phases: a “discovery phase” based on a sequence capture assay (611 target nuclear loci assessed in 16 grassland plant species), which resulted in the selection of eleven loci; and a “validation phase”, in which the selected loci were targeted and sequenced using twelve multispecies primers in test populations of Dactylis glomerata L. , Lolium perenne L. , Festuca pratensis Huds. , Trifolium pratense L. and T. repens L. The resulting multispecies amplicons had overall nucleotide diversities per species ranging from 5.19 × 10−3 to 1.29 × 10−2, which is in the range of flowering-related genes but slightly lower than pathogen resistance genes. We conclude that the methodology, the DNA sequence resources, and the amplicon-specific primer pairs reported in this study provide the basis for large-scale, multispecies PGD monitoring in grassland plants.
Differential Interactions Between Human ACE2 and Spike RBD of SARS-CoV-2 Variants of Concern

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current coronavirus disease 2019 (COVID-19) pandemic. It is known that the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 interacts with the human angiotensin-converting enzyme 2 (ACE2) receptor, initiating the entry of SARS-CoV-2. Since its emergence, a number of SARS-CoV-2 variants have been reported, and the variants that show high infectivity are classified as the variants of concern according to the US CDC. In this study, we performed both all-atom steered molecular dynamics (SMD) simulations and microscale thermophoresis (MST) experiments to characterize the binding interactions between ACE2 and RBD of all current variants of concern (Alpha, Beta, Gamma, and Delta) and two variants of interest (Epsilon and Kappa). We report that the RBD of the Alpha (N501Y) variant requires the highest amount of force initially to be detached from ACE2 due to the N501Y mutation in addition to the role of N90-glycan, followed by Beta/Gamma (K417N/T, E484K, and N501Y) or Delta (L452R and T478K) variant. Among all variants investigated in this work, the RBD of the Epsilon (L452R) variant is relatively easily detached from ACE2. Our results combined SMD simulations and MST experiments indicate what makes each variant more contagious in terms of RBD and ACE2 interactions. This study could help develop new drugs to inhibit SARS-CoV-2 entry effectively. TOC Graphic
Bmmp influences wing shape by regulating anterior-posterior and proximal-distal axis development

Insect wings are subject to strong selective pressure, resulting in the evolution of remarkably diverse wing shapes that largely determine flight capacity. However, the genetic basis and regulatory mechanisms underlying wing shape development are not well understood. The silkworm Bombyx mori micropterous (mp) mutant exhibits shortened wing length and enlarged vein spacings, albeit without changes in total wing area. Thus, the mp mutant comprises a valuable genetic resource for studying wing shape development. In this study, we used molecular mapping to identify the gene responsible for the mp phenotype and designated it Bmmp. Phenotype-causing mutations were identified as indels and single nucleotide polymorphisms in non-coding regions. These mutations resulted in decreased Bmmp mRNA levels and changes in transcript isoform composition. Bmmp null mutants were generated by CRISPR/Cas9 and exhibited significantly smaller wings. By examining the expression of genes critical to wing development in wildtype and Bmmp null mutants, we found that Bmmp exerts its function by coordinately modulating anterior-posterior and proximal-distal axis development. We also studied a Drosophila mp mutant and found that Bmmp is functionally conserved in Drosophila. The Drosophila mp mutant strain exhibits curly wings of reduced size and a complete loss of flight capacity. Our results increase our understanding of the mechanisms underpinning insect wing development and reveal potential targets for pest control.
Effect of stimulation time on the expression of human macrophage polarization markers

Macrophages are highly plastic cells that can polarize into functionally distinct subsets in vivo and in vitro in response to environmental signals. The development of protocols to model macrophage polarization in vitro greatly contributes to our understanding of macrophage biology. Macrophages are divided into two main groups: Pro-inflammatory M1 macrophages (classically activated) and anti-inflammatory M2 macrophages (alternatively activated), based on several key surface markers and the production of inflammatory mediators. However, the expression of these common macrophage polarization markers is greatly affected by the stimulation time used. Unfortunately, there is no consensus yet regarding the optimal stimulation times for particular macrophage polarization markers in in vitro experiments. This situation is problematic, (i) as analysing a particular marker at a suboptimal time point can lead to false-negative results, and (ii) as it clearly impedes the comparison of different studies. Using human monocyte-derived macrophages (MDMs) in vitro, we analysed how the expression of the main polarization markers for M1 (CD64, CD86, CXCL9, CXCL10, HLA-DR, IDO1, IL1β, IL12, TNF), M2a (CD200R, CD206, CCL17, CCL22, IL-10, TGM2), and M2c (CD163, IL-10, TGFβ) macrophages changes over time at mRNA and protein levels. Our data establish the most appropriate stimulation time for the analysis of the expression of human macrophage polarization markers in vitro. Providing such a reference guide will likely facilitate the investigation of macrophage polarization and its reproducibility.
The first crested duck genome reveals clues to genetic compensation and crest cushion formation

The Chinese crested (CC) duck is a unique indigenous waterfowl breed with a phenotypic crest trait that affects its high survival rate. Therefore, the CC duck is an ideal model to investigate the genetic compensation response to maintain genetic stability. In the present study, we first generated a chromosome-level genome of CC ducks. Comparative genomics revealed genes related to tissue repair, immune function, and tumors were under strong positive selection, which suggested that these adaptive changes might enhance cancer resistance and immune response to maintain the genetic stability of CC ducks. We sub-assembled a Chinese spot-billed duck genome and detected genome-assembled structure variants among three ducks. Functional analysis revealed that a large number of structural variants were related to the immune system, which strongly suggests the occurrence of genetic compensation in the anti-tumor and immune systems to further support the survival of CC ducks. Moreover, we confirmed that the CC duck originated from the mallard ducks. Finally, we revealed the physiological and genetic basis of crest traits and identified a causative mutation in TAS2R40 that leads to crest formation. Overall, the findings of this study provide new insights into the role of genetic compensation in adaptive evolution.
N-VEGF, a proteolytic product of the long isoform of VEGF-A, L-VEGF, shuttles to the nucleus to activate cellular stress survival circuits

Vascular Endothelial Growth Factor A (VEGF-A) is a major angiogenesis stimulator in response to hypoxia. Its first exon possesses an elongated 5’ Untranslated Region (5’UTR) and two Internal Ribosome Entry Sites (IRESs), enabling translation under hypoxia. It also encodes a 180 aa peptide that is in-frame with the classic coding region of VEGF-A. Upon hypoxia, Long VEGF-A (L-VEGF) is translated from this reading-frame concomitant with canonical VEGF-A isoforms. L-VEGF is proteolytically cleaved upstream to the VEGF-A translation initiation site to generate N-VEGF, which under hypoxia shuttles to cells nuclei. Here we show that hypoxia-independent nuclear mobilization of N-VEGF into NIH3T3 cells nuclei followed by RNA-seq leads to the identification of induced key genes associated with angiogenesis, cellular maintenance, and survival. Conversely, CRISPR-Cas9 mediated deletion of N-VEGF followed by RNA-Seq analysis underlined cells fragility under hypoxia supported by experimentations. This novel data highlights the role of this non-canonical VEGF-A isoform in potentiating the initial steps of angiogenesis along with cell survival circuits.
AlphaPept, a modern and open framework for MS-based proteomics

In common with other omics technologies, mass spectrometry (MS)-based proteomics produces ever-increasing amounts of raw data, making their efficient analysis a principal challenge. There is a plethora of different computational tools that process the raw MS data and derive peptide and protein identification and quantification. During the last decade, there has been dramatic progress in computer science and software engineering, including collaboration tools that have transformed research and industry. To leverage these advances, we developed AlphaPept, a Python-based open-source framework for efficient processing of large high-resolution MS data sets. Using Numba for just-in-time machine code compilation on CPU and GPU, we achieve hundred-fold speed improvements while maintaining clear syntax and rapid development speed. AlphaPept uses the Python scientific stack of highly optimized packages, reducing the code base to domain-specific tasks while providing access to the latest advances in machine learning. We provide an easy on-ramp for community validation and contributions through the concept of literate programming, implemented in Jupyter Notebooks of the different modules. A framework for continuous integration, testing, and benchmarking enforces solid software engineering principles. Large datasets can rapidly be processed as shown by the analysis of hundreds of cellular proteomes in minutes per file, many-fold faster than the data acquisiton. The AlphaPept framework can be used to build automated processing pipelines using efficient HDF5 based file formats, web-serving functionality and compatibility with downstream analysis tools. Easy access for end-users is provided by one-click installation of the graphical user interface, for advanced users via a modular Python library, and for developers via a fully open GitHub repository.
Trehalose induces tomato defenses and increases drought tolerance and bacterial wilt disease resistance

Ralstonia solanacearum causes plant bacterial wilt disease, leading to severe crop losses. Xylem sap from R. solanacearum-infected tomato is enriched in host produced trehalose. Water stressed plants accumulate the disaccharide trehalose, which increases drought tolerance via abscisic acid (ABA) signaling networks. Because infected plants have reduced water flow, we hypothesized that bacterial wilt physiologically mimics drought stress, which trehalose could mitigate. Transcriptomic responses of susceptible vs. resistant tomato plants to R. solanacearum infection revealed differential expression of drought-associated genes, including those involved in ABA and trehalose metabolism. ABA was enriched in xylem sap from R. solanacearum-infected plants. Treating roots with ABA lowered stomatal conductance and reduced R. solanacearum stem colonization. Treating roots with trehalose increased ABA in xylem sap and reduced plant water use by reducing stomatal conductance and temporarily improving water use efficiency. Further, trehalose-treated plants were more resistant to bacterial wilt disease. Trehalose treatment also upregulated expression of salicylic acid (SA)-dependent defense genes, increased xylem sap levels of SA and other antimicrobial compounds, and increased wilt resistance of SA-insensitive NahG tomato plants. Additionally, trehalose treatment increased xylem concentrations of jasmonic acid and related oxylipins. Together, these data show that exogenous trehalose reduced both water stress and bacterial wilt disease and triggered systemic resistance. This suite of responses revealed unexpected linkages between plant responses to biotic and abiotic stress and suggests that that R. solanacearum-infected tomato plants produce more trehalose to improve water use efficiency and increase wilt disease resistance. In turn, R. solanacearum degrades trehalose as a counter-defense.
Evaluating the Feasibility and Efficacy of a Dual-Modality Nanoparticle Contrast Agent (Nanotrast-CF800) for Image-Guided Sentinel Lymph Node Mapping in the Oral Cavity of Healthy Dogs

A combination of pre- and intraoperative sentinel lymph node (SLN) mapping techniques has been suggested to optimize SLN detection. A novel liposomal nanoparticle, Nanotrast-CF800 (CF800), utilizes computed tomography lymphography (CTL) and near infrared fluorescence imaging (NIRF) for image-guided surgery and SLN mapping. This novel tracer agent has not been evaluated in companion animals. The objective of this study was to evaluate the feasibility and efficacy of CF800 for SLN mapping in the oral cavity of healthy dogs and to report any local adverse effects. Six healthy adult purpose-bred research dogs randomly received either 1 mL (group 1) or 2 mL (group 2) of CF800 injected into the submucosa at the level of the right canine maxillary tooth. CTL and percutaneous NIRF were performed at 1, 3, and 10 minutes, then 1, 2, 4, 7, and 10 days post-injection (p.i). Overall, both CTL and NIRF identified SLNs in all dogs. The overall peak mean contrast enhancement of the SLNs was 73.98 HU (range 63.45-86.27 HU) at 2 days p.i. Peak fluorescence of the SLN occurred at 1 day p.i. The agent was retained within the SLN for at least 7 days for CTL and 4 days for NIRF. No adverse effects were observed. Local administration of CF800 was simple and feasible for the detection of SLNs using CTL+NIRF in the head and neck of healthy dogs and was not associated with significant local adverse events.
Disentangling key species interactions in diverse and heterogeneous communities: A Bayesian sparse modelling approach

Modeling species interactions in diverse communities traditionally requires a prohibitively large number of species-interaction coefficients, especially when considering environmental dependence of parameters. We implemented Bayesian variable selection via sparsity-inducing priors on non-linear species abundance models to determine which species-interactions should be retained and which can be represented as an average heterospecific interaction term, reducing the number of model parameters. We evaluated model performance using simulated communities, computing out-of-sample predictive accuracy and parameter recovery across different input sample sizes. We applied our method to a diverse empirical community, allowing us to disentangle the direct role of environmental gradients on species’ intrinsic growth rates from indirect effects via competitive interactions. We also identified a few neighboring species from the diverse community that had non-generic interactions with our focal species. This sparse modeling approach facilitates exploration of species-interactions in diverse communities while maintaining a manageable number of parameters.
Reward-Dependent Selection of Feedback Gains Impacts Rapid Motor Decisions

Abstract Target reward influences motor planning strategies through modulation of movement vigor. Considering current theories of sensorimotor control suggesting that movement planning consists in selecting a goal-directed control strategy, we sought to investigate the influence of reward on feedback control. Here, we explored this question in three human reaching experiments. First, we altered the explicit reward associated with the goal target and found an overall increase in feedback gains for higher target rewards, highlighted by larger velocities, feedback responses to external loads, and background muscle activity. Then, we investigated whether the differences in target rewards across multiple goals impacted rapid motor decisions during movement. We observed idiosyncratic switching strategies dependent on both target rewards and, surprisingly, the feedback gains at perturbation onset: the more vigorous movements were less likely to switch to a new goal following perturbations. To gain further insight into a causal influence of the feedback gains on rapid motor decisions, we demonstrated that biasing the baseline activity and reflex gains by means of a background load evoked a larger proportion of target switches in the direction opposite to the background load associated with lower muscle activity. Together, our results demonstrate an impact of target reward on feedback control and highlight the competition between movement vigor and flexibility.
Oncogenic c-Myc induces replication stress by increasing cohesins chromatin occupancy

Oncogene-induced replication stress is a major driver of genomic instability in cancer cells, with a central role in both cancer initiation and progression (1). Despite its critical role in cancer development, the mechanisms that lay at the basis of oncogene-induced replication stress remains poorly understood. Here, we investigate the mechanism of c-Myc-induced replication stress. Our data shows that c-Myc induces replication stress by increasing the amount of cohesins bound to chromatin in the G1 phase of the cell cycle. This is independent of previously suggested mechanisms involving deregulation of replication initiation and transcriptional interference. Restoring the amount of chromatin-bound cohesins to control levels, or preventing the accumulation of cohesins at CTCF sites, in cells experiencing oncogenic c-Myc activity prevents replication stress. Increased cohesins chromatin occupancy correlates with a c-Myc-dependent increase in the levels of the cohesion loader Mau2. Preventing c-Myc-induced increase in Mau2 reduces oncogene-induced replication stress. Together our data support a novel mechanism for oncogene-induced replication stress. Since c-Myc activation is a crucial event in many human cancers (2), identifying the mechanisms through which this oncogene promotes replication stress provides critical insights into cancer biology.
Localized Modification of Water Molecule Transport After Focused Ultrasound-Induced Blood–Brain Barrier Disruption in Rat Brain

Interstitial solutes can be removed by various overlapping clearance systems, including blood–brain barrier (BBB) transport and glymphatic clearance. Recently, focused ultrasound (FUS)-induced BBB disruption (BBBD) has been applied to visualize glymphatic transport. Despite evidence that FUS–BBBD might facilitate glymphatic transport, the nature of fluid movement within the sonication region is yet to be determined. In this study, we sought to determine whether FUS–BBBD may facilitate the local movement of water molecules. Two different FUS conditions (0.60–0.65 MPa and 0.75–0.80 MPa) were used to induce BBBD in the caudate-putamen and thalamus regions of healthy Sprague–Dawley rats. The water diffusion caused by FUS–BBBD was analyzed using the apparent diffusion coefficient (ADC), axial diffusivity, radial diffusivity (RD), and fractional anisotropy, obtained at 5 min, 24 and 48 h, as well as the water channel expression of aquaporin-4 (AQP-4) immunostaining at 48 h after FUS-induced BBBD. In addition, hematoxylin and eosin histopathology and Fluoro-Jade C (FJC) immunostaining were performed to analyze brain damage. The signal changes in ADC and RD in the sonication groups showed significant and transient reduction at 5 min, with subsequent increases at 24 and 48 h after FUS-induced BBBD. When we applied higher sonication conditions, the ADC and RD showed enhancement until 48 h, and became comparable to contralateral values at 72 h. AQP-4 expression was upregulated after FUS-induced BBBD in both sonication conditions at 48 h. The results of this study provide preliminary evidence on how mechanical forces from FUS alter water dynamics through diffusion tensor imaging (DTI) measures and AQP4 expression.