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Perera, R.

Publications and source records attributed to Perera, R..

At least 19 recordsLinked to original sources

Pathogenesis and host response to a novel Tacaribe virus isolate in experimentally-infected Jamaican fruit bats

Tacaribe virus (TCRV) was the first arenavirus discovered in the New World and was isolated from Artibeus bats in Trinidad and Tobago in the 1950s. One isolate, TRVL-11573, remains but it was passaged by intracranial inoculation of newborn mice 22 times that likely changed its biology. This isolate has been extensively used for arenavirus research, including our previous work that showed it can cause fatal neurological disease in Jamaican fruit bats (Artibeus jamaicensis). Another divergent TCRV, DOM2014, was recently identified in transcriptome data from a Jamaican fruit bat captured in the Dominican Republic that contained TCRV genome. A kidney fragment homogenate from this bat was inoculated into Jamaican fruit bats and all became infected with signs of mild liver disease. Experimental challenge of Jamaican fruit bats with DOM2014 led to nonfatal infection that persisted through the end of the study on day 21 and with contact transmission to naive bats. Histopathology, immunohistochemistry and serum chemistry confirmed infection and mild liver disease, but none of the bats produced neutralizing antibodies. B cell receptor transcripts suggested limited somatic hypermutation that could explain the lack of detectable neutralizing antibodies. Transcriptome profiling of livers and spleens showed signatures of a typical innate antiviral response; however, evidence of adaptive immune suppression was also present. Similarly, liver transcriptome analysis showed signatures of an expected innate antiviral response and metabolic dysfunction. The isolation of TCRV DOM2014 provides a relevant model for the study of a bat reservoir host, and which may challenge the extensive work previously conducted with TRVL-11573. IMPORTANCESeveral New World arenaviruses cause disease in humans and many are BSL-4 agents. TCRV strain TRVL-11573 has been used since the 1950s to study arenavirus biology; however, because it was intracranially passaged in newborn mice and Vero cells, it likely accumulated mutations that changed its biology. This assertion has been reinforced in recent years with discovery of divergent TCRV sequences in wild Artibeus bats that are substantially different than TRVL-11573, thus the prototype strain is unlikely to represent wildtype TCRV. The isolation of a new TCRV strain that has retained its genome fidelity allows a better understanding of TCRVs biology and pathogenic potential. The availability of pathogen-free Jamaican fruit bats and cell lines that are permissive for TCRV DOM2014 will also help retain the biological features of the virus. Collectively, this is among the most tractable bat reservoir host models developed and provides a system for dissection of how bats host viruses. Moreover, it may be a suitable model for the study of therapeutics and vaccines for New World arenaviruses.

microbiology↗

Ultrasound Activated Nanobubbles Induce Durable Systemic Antitumor Immunity

Clinical outcomes in aggressive breast cancer vary widely, in part because the tumor microenvironment is structured to exclude immune infiltration. Low antigen load, dysfunctional antigen-presenting cells, T cell exclusion and exhaustion, and a stiff extracellular matrix that physically restricts immune cell trafficking work together to form a suppressive barrier that current immunotherapies struggle to overcome. We addressed this barrier using ultrasound (US)-activated nanobubbles (NBs), a drug-free intervention based on perfluoropropane-filled nanoparticles. The size and deformable phospholipid shell enable NBs to achieve deep tumor penetration and a uniform distribution throughout the entire tumor. Upon ultrasound activation, NBs generate localized mechanical forces that restore extracellular matrix elasticity, disrupt tumor transport barriers, and drive HMGB1 release, re-engaging endogenous antitumor immunity without pharmacological agents. In a syngeneic triple-negative breast cancer model, US-NB treatment depleted immunosuppressive myeloid cells 3-fold within 3 hours, followed by a greater than 5-fold increase in the ratio of antigen-experienced to suppressive T cells at 48 hours. US-NB drives rapid infiltration of CD4+ and CD8+ T cells within 48 hours. US-NB treatment achieved an 85% cure rate in the D2A1 model; cured animals maintained durable systemic immune memory, rejecting both local and systemic tumor rechallenge. Consistent therapeutic benefit was observed in a luminal B-like mammary tumor model (E0771), supporting activity across breast cancer subtypes. These results establish US-NB mechanical immunomodulation as a drug-free therapeutic strategy capable of generating robust and durable antitumor immunity, acting through biophysical tissue properties rather than tumor-specific molecular targets. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/714247v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@8f274eorg.highwire.dtl.DTLVardef@5da575org.highwire.dtl.DTLVardef@19defborg.highwire.dtl.DTLVardef@7e630e_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

In vivo tracking of CAR-T cells in tumors via nanobubble-based contrastenhanced ultrasound

CAR-T cell therapy has led to remarkable advances in the outcomes of patients with acute lymphoblastic leukemia (ALL), B cell lymphomas, and multiple myeloma. Given these successes in hematologic malignancies, extensive efforts are now focused on developing CAR-T cell therapies for the treatment of solid tumors. The treatment of solid tumors poses significant hurdles with cell trafficking that is necessary to achieve efficacy and minimize off-tumor side effects. The development of simple, safe and inexpensive modalities to track CAR-T cell distribution in humans could provide critical insights to facilitate the development of improved CAR-T products for solid tumors. Here we demonstrate a strategy to monitor CAR-T cells in vivo using ultrasound imaging and nanobubble (NB) labeled cells. NBs are ultrasound contrast agents composed of a lipid shell and a C4F10 gas core that can be efficiently internalized into cells. This approach enables us to image the CAR-T cells using nonlinear contrast-enhanced ultrasound (CEUS). Utilizing this method, we found that CAR-T cells can be visualized after injection into both tumor bearing and non-tumor bearing mice. In summary, our ultrasound-based tracking approach can effectively monitor the trafficking of CAR-T cells in vivo, offering a valuable new strategy that can further enable the development of new CAR-T products and strategies to modulate cell trafficking.

bioengineering↗

BRCA2 C-terminal clamp restructures RAD51 dimers to bind B-DNA for replication fork stability

Tumor suppressor protein BRCA2 acts with RAD51 in replication-fork protection (FP) and homology-directed DNA break repair (HDR). Critical for cancer etiology and therapy resistance, BRCA2 C-terminus was thought to stabilize RAD51-filaments after they assemble on single-stranded (ss)DNA. Here we determined the detailed crystal structure for BRCA2 C-terminal interaction-domain (TR2i) with ATP-bound RAD51 prior to DNA binding. In contrast to recombinogenic RAD51-filaments comprising extended ATP-bound RAD51 dimers, TR2i unexpectedly reshapes ATP-RAD51 into a unique dimer conformation accommodating double-stranded B-DNA binding unsuited for HDR initiation. Structural, biochemical, and molecular results with interface-guided mutations uncover TR2is FP mechanism. Proline-driven secondary-structure stabilizes residue triads and spans the RAD51 dimer engaging pivotal interactions of RAD51 M210 and BRCA2 S3291/P3292, the cyclin-dependent kinase (CDK) phosphorylation site that toggles between FP during S-phase and HDR in G2. TR2i evidently acts as an allosteric clamp switching RAD51 from ssDNA to double-stranded and B-DNA binding enforcing FP over HDR.

molecular biology↗

Perturbed pediatric serum metabolome in mild and severe dengue disease

Dengue viruses (DENVs) are the most prevalent arboviruses affecting humans. Four billion people are at risk of infection and this burden is rapidly increasing due to geographic expansion of the mosquito vector. Infection with any of the four serotypes of DENV can result in a self-limiting disease but debilitating febrile illness (DF), and some infections progress to severe disease with manifestations such as hemorrhage and shock. DENV infection drives the metabolic state of host cells for viral benefit and induces a host-immune response that has metabolic implications that link to disease. In this study, a dynamic metabolic response to DENV infection and disease was measured in 535 pediatric patient sera using liquid chromatography-mass spectrometry. The metabolome was interrogated to discover biochemical pathways and identify key metabolites perturbed in severe dengue disease. A biomarker panel of thirty-two perturbed metabolites was utilized to classify DF, and severe dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS) with high sensitivity and specificity equating to a balanced accuracy of 96.9%. Some metabolites that were structurally confirmed here belong to important biochemical pathways of omega-3 and omega-6 fatty acids, sphingolipids, purines, and tryptophan metabolism. A previously reported trend between serotonin and platelets in DHF patients has been expanded upon here to reveal a major depletion of serotonin, but not platelets, in DSS patients. This study differentiated and classified DF and DHF/DSS using a serum metabolic biomarker panel based on perturbed biochemical pathways that have potential implications for severe dengue disease. One sentence summary: Metabolic biomarkers distinguish dengue hemorrhagic fever and dengue shock syndrome from dengue fever and lend insight to severe disease pathology

systems biology↗

Assessing Tumor Microenvironment Characteristics and Stratifying EPR with a Nanobubble Companion Nanoparticle via Contrast-Enhanced Ultrasound Imaging

The tumor microenvironment is characterized by dysfunctional endothelial cells, resulting in heightened vascular permeability. Many nanoparticle-based drug delivery systems attempt to use this enhanced permeability combined with impaired lymphatic drainage (a concept known as the enhanced permeability and retention effect or EPR effect) as the primary strategy for drug delivery, but this has not proven to be as clinically effective as anticipated. The specific mechanisms behind the inconsistent clinical outcomes of nanotherapeutics have not been clearly articulated, and the field has been hampered by a lack of accessible tools to study EPR-associated phenomena in clinically relevant scenarios. While medical imaging has tremendous potential to contribute to this area, it has not been broadly explored. This work examines, for the first time, the use of multiparametric dynamic contrast-enhanced ultrasound (CEUS) with a novel nanoscale contrast agent to examine tumor microenvironment characteristics noninvasively and in real-time. We demonstrate that CEUS imaging can: (1) evaluate tumor microenvironment features and (2) be used to help predict the distribution of doxorubicin-loaded liposomes in the tumor parenchyma. CEUS using nanobubbles (NBs) was carried out in two tumor types of high (LS174T) and low (U87) vascular permeability, and time-intensity curve (TIC) parameters were evaluated in both models prior to injection of doxorubicin liposomes. Consistently, LS174T tumors showed significantly different TIC parameters, including area under the rising curve (2.7x), time to peak intensity (1.9x) and decorrelation time (DT, 1.9x) compared to U87 tumors. Importantly, the DT parameter successfully predicted tumoral nanoparticle distribution (r = 0.86 {+/-} 0.13). Ultimately, substantial differences in NB-CEUS generated parameters between LS174T and U87 tumors suggest that this method may be useful in determining tumor vascular permeability and could be used as a biomarker for identifying tumor characteristics and predicting sensitivity to nanoparticle-based therapies. These findings could ultimately be applied to predicting treatment efficacy and to evaluating EPR in other diseases with pathologically permeable vasculature.

bioengineering↗

Pyrethroid susceptibility reversal in Aedes aegypti: a longitudinal study in Tapachula, Mexico

Pyrethroid resistance in Aedes aegypti has become widespread after almost two decades of frequent applications to reduce the transmission of mosquito-borne diseases. Because few insecticide classes are available for public health use, insecticide resistance management (IRM) is proposed as a strategy to retain their use. A key hypothesis of IRM assumes that negative fitness is associated with resistance, and when insecticides are removed from use, susceptibility is restored. In Tapachula, Mexico, pyrethroids (PYRs) were used exclusively by dengue control programs for 15 years, thereby contributing to selection for high PYR resistance in mosquitoes and failure in dengue control. In 2013, PYRs were replaced by organophosphates--insecticides from a class with a different mode of action. To test the hypothesis that PYR resistance is reversed in the absence of PYRs, we monitored Ae. aegyptis PYR resistance from 2016 to 2021 in Tapachula. We observed significant declining rates in the lethal concentration 50 (LC50), for permethrin and deltamethrin. For each month following the discontinuation of PYR use by vector control programs, we observed increases in the odds of mosquitoes dying by 1.5% and 8.4% for permethrin and deltamethrin, respectively. Also, knockdown-resistance mutations (kdr) in the voltage-gated sodium channel explained the variation in the permethrin LC50s, whereas variation in the deltamethrin LC50s was only explained by time. This trend was rapidly offset by application of a mixture of neonicotinoid and PYRs by vector control programs. Our results suggest that IRM strategies can be used to reverse PYR resistance in Ae. aegypti; however, long-term commitment by operational and community programs will be required for success. Author summaryThe mosquito Aedes aegypti is the principal urban vector of the viruses that cause three globally significant diseases: dengue fever, chikungunya, and Zika fever, for which vaccines and effective treatments are currently absent. The only way to control dengue, chikungunya, and Zika fever outbreaks is to diminish vector populations. During epidemics, the most frequent way of targeting adult mosquitoes is outdoor spatial spraying of insecticides. Control of Ae. aegypti is difficult because limited insecticide classes are available for public health, leading to operational practices that overuse single molecules for long periods of time, imposing great selection pressure on mosquito populations for insecticide resistance. Insecticide resistance management (IRM) is proposed as a strategy to prevent resistance and avoid depleting the susceptibility resource in mosquito populations. IRM strategies assume that alternation of insecticides with different toxicological modes of action will prevent the selection of resistance. Unfortunately, very few field evaluations have reported IRM schemes to control Ae. aegypti. In our study, the exclusive use of pyrethroids in vector control programs in Mexico from 1999 to 2013, led in the selection of knockdown resistance (kdr) to pyrethroid insecticides. To address this issue, vector control programs temporarily phased out pyrethroids from 2013 to 2019, substituting them with an insecticide class with a different mode of action: organophosphates (OPs). During six years, we monitored pyrethroid resistance in 24 mosquito populations from Tapachula, Mexico. We show that discontinuing pyrethroids for six years led in pyrethroid resistance reversal in Ae. aegypti in the field. However, high levels of pyrethroid resistance continue to jeopardize operational application, necessitating longer periods of pyrethroid cessation and novel IRM strategies to achieve lower resistance thresholds.

evolutionary biology↗

BRDriver: Breast Cancer Driver Gene Predictor

The breast cancer mortality rate is high in developing countries as the early detection of cancer is deficient in patients. The identification of the genes that drive cancer is one of the major approaches in the early detection of breast cancer. Several computational tools have been developed to predict the cancer driver genes. However, there is no gold-standard method for identifying breast cancer driver genes. Therefore, this study aims to develop a model to predict high-confidence breast cancer diver genes using already-developed computational tools and already-produced breast cancer data. Primary breast cancer data were retrieved from the Cancer Genome Atlas Program (TCGA). Here we use twenty-seven different gene prediction tools that calculate each genes effect and variant in the primary gene dataset. The primary dataset feeds as the input for each tool. The results retrieved from each tool are recorded as the secondary dataset. The latest breast cancer driver gene set was retrieved from DriverDBv3 and included as the target attribute. Training and testing subsets were selected using k-fold cross-validation from the secondary dataset. Attributes from the secondary dataset were ranked according to their correlation with breast cancer driver genes. The ranked data were trained using different supervised machine-learning algorithms. The attributes and the learning algorithm which produced the highest classification accuracy were selected to build the new model, BReast cancer Driver (BRDriver). The new model BRDriver achieved 0.999 area under the curve and 0.999 classification accuracy on breast invasive carcinoma data. TP53 was the most predicted breast cancer drive gene (n=246) predicted by BRDriver. Interestingly, our BRDriver model predicted CDKN2A and NFE2L2 genes as new breast cancer driver genes. Further in vivo and in vitro studies are required to determine whether these genes are indeed cancer-driver genes. Many computational tools developed to identify the cancer driver genes and variants. A few methodologies were developed to combine these tools and increase efficiency for detecting breast cancer driver genes. Our BRDriver overcomes the difficulties and produces high-confidence breast cancer driver genes.

bioinformatics↗

Decorrelation Time Mapping as an Analysis Tool for Nanobubble-Based Contrast Enhanced Ultrasound Imaging

Nanobubbles (NBs) are nanoscale ([~]100-500 nm diameter) ultrasound (US) contrast agents that enable new robust applications of contrast enhanced US and US-mediated therapy. Due to their sub-micron size, high particle density, and highly deformable shell, NBs exhibit unique properties. In pathological states of heightened vascular permeability, such as in tumours, NBs can extravasate, enabling extravascular applications not currently possible with clinically available microbubbles ([~]1000-10,000 nm diameter). This ability can be explored to develop imaging biomarkers to improve tumour detection. There is a need for an imaging method that can rapidly and effectively separate intravascular versus extravascular NB signal when imaged using nonlinear dynamic contrast enhanced US. Herein, we demonstrated the use of decorrelation time (DT) mapping to achieve this goal. Two in vitro models were used to explore the roles of NB velocity and diffusion on DTs. Mice bearing prostate specific membrane antigen (PSMA) expressing flank tumours (n = 7) were injected with bubble agents to evaluate the in vivo potential of this technique. The DT was calculated at each pixel of nonlinear contrast videos to produce DT maps. Across all models, long DT correlated with slowly moving or entrapped NBs while short DT correlated with flowing NBs. DT maps were sensitive to NBs in tumour tissue with high average DT in tumour regions ([~]10 s) compared to surrounding normal tissue ([~]1 s). Molecular NB targeting to PSMA extended DT (17 s) compared to non-targeted NBs (12 s), demonstrating sensitivity to NB adherence dynamics. Overall, DT mapping of in vivo NB dynamics produced detailed information of tumour tissue and showed potential for quantifying extravascular NB kinetics. This new NB-contrast enhanced US-based biomarker can be useful in molecular ultrasound imaging, with improved sensitivity and specificity of target tissue detection and potential for use as a predictor of vascular permeability and the enhanced permeability and retention (EPR) effect in tumours.

bioengineering↗

Human sialidase activity is vital for dengue virus serotype 2 infection

The human sialidase enzymes (or neuraminidases, NEU1-4) are glycoside hydrolases that catalyze the removal of sialic acid residues from glycoconjugates, including many bioactive glycoproteins and glycolipids. Through their physiochemical effect on glycoconjugates, sialic acid residues are thought to play vital roles in the control of cellular signaling. In previous studies, it was demonstrated that NEU1-4 activity was increased in cells infected with dengue virus serotype 2 (DENV2). Additionally, it was demonstrated that the DENV2 NS1 protein was sufficient for inducing increased NEU1-4 activity in both in vivo and in vitro models, and that this increased activity was linked to endothelial hyperpermeability and vascular leakage, a hallmark of severe dengue disease. However, the role of increased NEU1-4 activity in the viral lifecycle was not understood. Here, we used siRNA-mediated loss of function studies to evaluate the effect of inhibition of sialidase activity on the DENV2 lifecycle. Our analyses uncovered that apart from their importance for viral pathogenesis, NEU1-4 activity was vital for DENV2 viral replication and egress. Moreover, we characterized the inter-relationship between NEU 1-4, and determined that there was a transcriptional dependency of NEU1-3 on NEU4.

microbiology↗

Shifting a Cellular Metabolic Landscape Identifies a Refractory Environment for Flavivirus Replication

Host-targeted therapeutics to control viral infection are gaining prominence given the vulnerability of viral replication at select host-interaction points and the limited possibility of developing drug resistant mutants. Nevertheless, the chemical and biological impact of many host-targeted therapeutics on both the cell and virus has not been elucidated and remains a key complication. Previously, it has been demonstrated that inhibition of fatty acid metabolism has significant antiviral potential. Here, we use a multidisciplinary approach to demonstrate how inhibition of fatty acid biosynthesis creates a metabolically refractory environment that drives viral dependence on alternate metabolic pathways for survival. By profiling the global metabolic landscape following inhibition of fatty acid biosynthesis, we identified additional biochemical pathways that, when inhibited in combination with fatty acid biosynthesis, displayed increased antiviral potential. Our studies also demonstrated that there was a direct link between changes in cellular chemical composition and the ultrastructural membrane architecture induced by viral gene products. Utilizing inhibitors to change these metabolic environments significantly impacted early viral replication and disrupted the membrane architecture critical for the viral life cycle. Here, we have defined at a molecular level how shifting metabolic landscapes can be exploited to identify combinations of therapeutics that have a greater antiviral effect. Author SummaryDengue viruses are transmitted by Aedes aegypti mosquitoes which are prevalent in the tropical and subtropical regions of the world. These viruses cause over 350 million infections annually. There are no antivirals to combat infection and the only vaccine available is suboptimal. Since these viruses are obligate pathogens, they hijack lipid metabolic pathways in host cells to drive new lipid synthesis critically required for their replication. Mechanisms of how lipid synthesis impacts viral replication is unknown. These viruses also rearrange cellular membranes to form platforms for assembly of viral replication complexes. Here, for the first time, we show that virus-hijacking of de novo fatty acid biosynthesis pathways is required for the formation of membranous replication platforms and if inhibited disrupted synthesis of replicative form viral RNA. Importantly, these inhibitors drastically rearranged the metabolic landscape of the cell resulting in an activation of compensatory nucleotide synthesis pathways that allowed the virus to survive at a low level through the inhibition. However, if both pathways were inhibited in combination, infectious virus release was reduced to below detection limits. The study demonstrates how understanding the metabolic landscape altered by specific inhibitors can lead to the discovery of compensatory metabolic pathways and targets that in combination can enhance intervention efficacy.

microbiology↗

Expression of fatty acid synthase genes and their role in development and arboviral infection of Aedes aegypti

BackgroundFatty acids are the building blocks of complex lipids essential for living organisms. In mosquitoes, fatty acids are involved in cell membrane production, energy conservation and expenditure, innate immunity, development, and reproduction. Fatty acids are synthesized by a multifunctional enzyme complex called fatty acid synthase (FAS). Several paralogues of FAS were found in the Aedes aegypti (Ae. aegypti) mosquito. However, the molecular characteristics and the expression of some of these paralogues have not been investigated. MethodsGenome assemblies of Ae. aegypti were analyzed and orthologues of human FAS were identified. Phylogenetic analysis and in silico molecular characterization were performed to identify the functional domains of the Ae. aegypti FAS (AaFAS). Quantitative analysis and loss-of-function experiments were performed to determine the significance of different AaFAS transcripts in various stages of development, expression following different diets and the impact of AaFAS on dengue virus, serotype 2 (DENV2) infection and transmission. ResultsWe identified seven putative FAS genes in the Ae. aegypti genome assembly, based on nucleotide similarity to the FAS proteins (tBLASTn) of humans, other mosquitoes and invertebrates. Bioinformatics and molecular analyses suggested that only five of the FAS genes produce mRNA and therefore represent complete gene models. Expression levels of AaFAS varied among developmental stages and between male and female Ae. aegypti. Quantitative analyses revealed that expression of AaFAS1, the putative orthologue of the human FAS, was highest in adult females. Transient knockdown (KD) of AaFAS1 did not induce a complete compensation by other AaFAS genes but limited DENV2 infection of Aag2 cells in culture and the midgut of the mosquito. ConclusionAaFAS1 is the predominant AaFAS in the adult mosquitoes. It has the highest amino acid similarity to human FAS and contains all enzymatic domains typical of human FAS. AaFAS1 also facilitated DENV2 replication in both cell culture and in mosquito midguts. Our data suggest that AaFAS1 may play a role in transmission of dengue viruses, and could represent a target for intervention strategies.

microbiology↗

RNase L-mediated RNA decay alters 3' end formation and splicing of host mRNAs

The antiviral endoribonuclease, RNase L, is a vital component of the mammalian innate immune response that destroys host and viral RNA to reduce viral gene expression. Herein, we show that a consequence of RNase L-mediated decay of cytoplasmic host RNAs is the widespread re-localization of RNA-binding proteins (RBPs) from the cytoplasm to the nucleus, due to the presence of nuclear RNA. Concurrently, we observe global alterations to host RNA processing in the nucleus, including alterations of splicing and 3 end formation, with the latter leading to downstream of gene (DoG) transcripts. While affecting many host mRNAs, these alterations are pronounced in mRNAs encoding type I and type III interferons and coincide with the retention of their mRNAs in the nucleus. Similar RNA processing defects also occur during infection with either dengue virus or SARS-CoV-2 when RNase L is activated. These findings reveal that the distribution of RBPs between the nucleus and cytosol is fundamentally dictated by the availability of RNA in each compartment and thus viral infections that trigger cytoplasmic RNA degradation alter RNA processing due to the nuclear influx of RNA binding proteins.

immunology↗

Acyl-CoA Thioesterases; a rheostat that controls activated fatty acids modulates dengue virus serotype 2 replication

During infection with dengue viruses (DENVs), the lipid landscape within host cells is significantly altered to assemble membrane platforms that support viral replication and particle assembly. Fatty acyl-CoAs are key intermediates in the biosynthesis of complex lipids that form these membranes. They also function as key signaling lipids in the cell. Here, we carried out loss of function studies on acyl-CoA thioesterases (ACOTs), a family of enzymes that hydrolyze fatty acyl-CoAs to free fatty acids and coenzyme A, to understand their influence on the lifecycle of DENVs. Loss of function of the type I ACOTs 1 (cytoplasmic) and 2 (mitochondrial) together significantly increased DENV serotype 2 (DENV2) viral replication and infectious particle release. However, isolated knockdown of mitochondrial ACOT2 significantly decreased DENV2 protein translation, genome replication, and infectious virus release. Furthermore, loss of ACOT7 function, a mitochondrial type II ACOT, similarly suppressed DENV2. As ACOT1 and ACOT2 are splice variants, these data suggest that location (cytosol and mitochondria, respectively) rather than function of these proteins may account for the differences in DENV2 infection phenotype. Additionally, loss of mitochondrial ACOT2 and ACOT7 expression also altered the expression of several ACOTs located in multiple organelle compartments within the cell highlighting a complex relationship between ACOTs in the DENV2 virus lifecycle.

microbiology↗

Expectations boost the reconstruction of auditory features from electrophysiological responses to noisy speech

Online speech processing imposes significant computational demands on the listening brain, the underlying mechanisms of which remain poorly understood. Here, we exploit the perceptual pop-out phenomenon (i.e. the dramatic improvement of speech intelligibility after receiving information about speech content) to investigate the neurophysiological effects of prior expectations on degraded speech comprehension. We recorded electroencephalography and pupillometry from 21 adults while they rated the clarity of noise-vocoded and sine-wave synthesised sentences. Pop-out was reliably elicited following visual presentation of the corresponding written sentence, but not following incongruent or neutral text. Pop-out was associated with improved reconstruction of the acoustic stimulus envelope from low-frequency EEG activity, implying that improvements in perceptual clarity were mediated via top-down signals that enhance the quality of cortical speech representations. Spectral analysis further revealed that pop-out was accompanied by a reduction in theta-band power, consistent with predictive coding accounts of acoustic filling-in and incremental sentence processing. Moreover, delta-band power, alpha-band power, and pupil diameter were all increased following the provision of any written sentence information, irrespective of content. Together, these findings reveal distinctive profiles of neurophysiological activity that differentiate the content-specific processes associated with degraded speech comprehension from the context-specific processes invoked under adverse listening conditions.

neuroscience↗

Coupled small molecules target RNA interference and JAK/STAT signaling to reduce Zika virus infection in Aedes aegypti

The recent global Zika epidemics have revealed the significant threat that mosquito-borne viruses pose. There are currently no effective vaccines or prophylactics to prevent Zika virus (ZIKV) infection. Limiting exposure to infected mosquitoes is best way to reduce disease incidence. Recent studies have focused on targeting mosquito reproduction and immune responses to reduce transmission. In particular, previous work evaluated the effect of insulin signaling on antiviral JAK/STAT and RNAi in vector mosquitoes. In this work, we demonstrate that targeting insulin signaling through the repurposing of small molecule drugs results in the activation of both of these antiviral pathways. Activation of this coordinated response additively reduced ZIKV levels in Aedes aegypti mosquitoes. This effect included a quantitatively greater reduction in salivary gland ZIKV levels relative to single pathway activation, indicating the potential for field delivery of these small molecules to substantially reduce virus transmission.

microbiology↗

Intracellular Vesicle Entrapment of Nanobubble Ultrasound Contrast Agents Targeted to PSMA Promotes Prolonged Enhancement and Stability In Vivo and In Vitro

Previous work has shown that active targeting of nanobubble (NB) ultrasound contrast agents to the prostate-specific membrane antigen (PSMA) significantly prolongs ultrasound signal enhancement in PSMA-expressing prostate cancer. However, the specific mechanism behind this effect is not well understood. Furthermore, prior studies were carried out using clinical ultrasound scanners in a single imaging plane. Because tumor heterogeneity can have a drastic effect on bubble kinetics and resulting contrast enhancement, a single region of interest in one imaging plane over time may not fully represent the contrast dynamics of the entire tumor. Accordingly, in the current work, we used high-frequency dynamic parametric contrast-enhanced ultrasound (DCE-US) imaging to gain a detailed understanding of NB kinetics in prostate tumors in mice. Specifically, we examined the differences in enhancement between the tumor periphery and tumor core in the same imaging plane. We also quantified intact nanobubble retention in the entire tumor volume. To better understand the mechanism behind prolonged tumor enhancement, intracellular retention and the acoustic activity of PSMA-NB were evaluated in cell culture. DCE-US US data suggest that both tumor wash-in and retention of PSMA-NB are delayed due to biomarker interaction and binding. The longer retention of PSMA-NB signal in tumor core supported target-driven bubble extravasation. In vitro studies demonstrated a higher level of internalization and prolonged-acoustic activity of internalized PSMA-NB. GC/MS analysis confirmed gas persistence in the cells after PSMA-NB internalization. The active-targeting of NB results in cellular internalization via receptor-mediated endocytosis, and the location with intracellular vesicles (late-stage endosomes/lysosomes) significantly prolongs gas retention within the cells. These features can enable background-free diagnostic imaging of the target cells/tissues, as well as highly focused ultrasound-modulated therapeutic interventions.

cancer biology↗

Rapid decay of host basal mRNAs during SARS-CoV-2 infection perturbs host antiviral mRNA biogenesis and export

A key feature of the mammalian innate immune response to viral infection is the transcriptional induction of interferon (IFN) genes, which encode for secreted proteins that prime the antiviral response and limit viral replication and dissemination. A hallmark of severe COVID-19 disease caused by SARS-CoV-2 is the low presence of IFN proteins in patient serum despite elevated levels of IFN-encoding mRNAs, indicative of post-transcriptional inhibition of IFN protein production. Herein, we show SARS-CoV-2 infection limits type I and type III IFN biogenesis by preventing the release of mRNA from their sites of transcription and/or triggering their nuclear degradation. In addition, SARS-CoV-2 infection inhibits nuclear-cytoplasmic transport of IFN mRNAs as a consequence of widespread cytosolic mRNA degradation mediated by both activation of the host antiviral endoribonuclease, RNase L, and by the SARS-CoV-2 protein, Nsp1. These findings argue that inhibition of host and/or viral Nsp1-mediated mRNA decay, as well as IFN treatments, may reduce viral-associated pathogenesis by promoting the innate immune response.

immunology↗