Background Insulin signaling is a conserved regulator of growth, metabolism, and lifespan across metazoans. While its systemic roles are well established, the mechanisms by which insulin coordinates tissue-specific transcriptional programs that underlie distinct functional demands remain incompletely understood. In particular, the differential impact of reduced insulin signaling on different tissues has not been systematically explored. Results We performed a comparative transcriptomic analysis of Drosophila melanogaster olfactory sensory neurons (OSNs) and fat body (Fb) to investigate how reduced insulin signaling remodels gene expression in neural and metabolic tissues. Across both tissue types, insulin reduction suppressed key pathways involved in protein synthesis and mRNA surveillance, indicating shared regulatory responses. However, distinct tissue-specific transcriptional adaptations were also observed. In OSNs, insulin reduction led to the upregulation of synaptic and signaling genes, alongside the downregulation of proteostasis-related factors, suggesting enhanced neural plasticity that may come at the cost of long-term neuronal maintenance. In contrast, the Fb exhibited widespread metabolic suppression accompanied by feedback activation of stress-responsive insulin-like peptide genes, consistent with a shift toward hypometabolic adaptation. Network and pathway analyses revealed that these tissue-specific responses involved distinct regulatory architectures affecting core insulin pathway components and gene families. Conclusions Our findings demonstrate that reduced insulin signaling elicits both shared and divergent transcriptional programs in neural and metabolic tissues of Drosophila melanogaster. These findings reveal how insulin signaling orchestrates tissue-specific transcriptional landscapes that may underlie differential resilience or vulnerability to cognitive and metabolic decline.

ABSTRACT Critical periods of development are time points that are especially sensitive to disruptions. Critical periods are important for microbiome assembly and the development of an effective immune system and, therefore, can have large and lasting impacts on host health, even through later life stages. Here, we investigated how a disruption to the microbiome of amphibians (treatment with a cocktail of six antibiotics and one antifungal compound) during early life and subsequent introduction to microbes at different developmental stages influences microbiome assembly and the development of the immune system (lymphoid tissues thymus and spleen). We found that antimicrobial treatments and introduction to microbes altered microbiome assembly (total microbial richness, antifungal microbial richness, composition, and relative abundances) and these changes were dependent on the timing of microbial introduction. Tadpoles treated with antimicrobials and then introduced to microbes at different developmental stages also had higher scaled abundances of bacteria in the phylum Actinobacteriota. However, after 7.5 weeks of tadpole development, we found no effects of treatment on lymphoid organ (thymus and spleen) size or on lymphoid cell counts. Overall, these results suggest that a disruption to the microbiome during early development, and more specifically, the length of the disruption and timing of reintroduction to microbes, can have significant impacts on microbiome assembly, potentially leading to long term impacts on host health.

Vitamin A is an essential micronutrient that supports vision, immunity, and development, yet excess vitamin A can be toxic. Most vertebrates maintain tightly regulated vitamin A levels by cleaving dietary carotenoids into retinoids via specialized enzymes, including the carotenoid oxygenase Bco2. To what extent genetic changes in carotenoid-metabolism enzymes such as Bco2 drive natural variation in vitamin A homeostasis remains unclear. Here, we show that some cave-adapted populations of the Mexican tetra (Astyanax mexicanus) have evolved loss-of-function mutations in bco2a. The mutations yield enzymatically inactive Bco2a proteins and are associated with dramatic carotenoid and vitamin A accumulation. The bco2a locus shows signatures of selection in these cavefish populations, suggesting that loss of Bco2a function could be advantageous under certain cave conditions. Contrary to expectations from mammalian models in which Bco2 loss induces oxidative damage, cavefish appear to tolerate carotenoid accumulation and may benefit from elevated carotenoid stores in nutrient-variable caves. Our findings reveal that the vitamin A regulatory system is evolutionarily flexible and provide a framework for understanding how animals balance essential nutrient thresholds in extreme environments. VIDEO ABSTRACT.

While multi-omics integration is the gold standard for precision oncology, its clinical utility is severely hampered by the incomplete data problem, where cost and technical barriers often leave researchers with only single-omics profiles. Our manuscript introduces CSIE (cancer subtyping via inference and ensemble), a framework that bridges this gap by using a novel transformer-based inference module which incorporates systems-level knowledge to accurately infer missing omics layers from gene expression data. Furthermore, CSIE employs an ensemble clustering module that simultaneously integrates multi-omics data via different similarity metrics and clustering algorithms to capture molecular patterns of cancer subtypes. The robustness of CSIE is validated through extensive benchmarking against 12 state-of-the-art methods across 66 cancer datasets with over 15 000 patients and 22 diverse data modalities/platforms. Our results demonstrate that CSIE significantly outperforms existing tools, particularly in scenarios with incomplete data. This work shifts the paradigm from requiring exhaustive data collection to leveraging biological intelligence for data completion, offering a scalable solution for high-resolution cancer subtyping in real-world clinical settings. All source code of CSIE and scripts for regenerating results reported in this article are available at https://github.com/tinnlab/CSIE.

IntroductionWild trait introgression is a valuable breeding tool for increasing tomato salinity tolerance. However, this process often results in deleterious linkage drag. Understanding the physiological and molecular mechanisms underlying salinity response can aid in developing salt-tolerant cultivars while minimizing undesirable traits. This study investigates the salinity response of the tomato cultivar OH8245, Solanum galapagense accession LA1141, and two derived introgression lines (ILs SG18_197 and SG18_247) that were previously screened for salt tolerance traits.MethodsThe physiological and molecular responses of OH8245, LA1141, and the two ILs were analyzed under salinity stress. Key salinity tolerance traits were evaluated, including root characteristics, water status, ion homeostasis, stomatal density, photosynthetic rate, and relative growth rate. Differential gene expression analysis was conducted to identify genes associated with salinity tolerance, comparing the number and uniqueness of differentially expressed genes (DEGs) across genotypes.ResultsS. galapagense LA1141 exhibited multiple salinity tolerance traits, such as higher specific root length, increased root hydraulic conductivity, and improved plant water status. It also maintained better ion homeostasis and had lower stomatal density compared to OH8245. In contrast, OH8245 demonstrated traits supporting greater biomass accumulation, including a higher photosynthetic rate and relative growth rate. Differential gene expression analysis revealed that LA1141 had the fewest DEGs (706), whereas OH8245 had one of the highest (2524), suggesting a constitutive set of genes contributing to salinity or abiotic stress tolerance. Additionally, 40 DEGs were uniquely found in LA1141 under salinity, with nine and 16 of these transferred to ILs SG18_197 and SG18_247, respectively.DiscussionSalinity tolerance is a complex trait that imposes an energy cost on the plant. However, key beneficial traits, including improved plant water potential, higher photosynthetic rate, and a lower sodium/potassium ratio, were successfully transferred from LA1141 to at least one of the ILs. These findings provide valuable insights for tomato breeding programs aimed at enhancing salinity tolerance while balancing growth and stress resistance traits.

The cytochrome P450 enzymes of the CYP4G subfamily are some of the most enigmatic insect P450s. The dipterans with sequenced genomes have two CYP4G paralogs. In Drosophila melanogaster , CYP4G1 is highly expressed in the oenocytes and catalyzes the last enzymatic step in the biosynthesis of cuticular hydrocarbons. In contrast, CYP4G15 is expressed in the brain glial cells, but its function is unknown. The Aedes aegypti genome encodes two CYP4Gs: CYP4G36 (ortholog of DmCYP4G1) and CYP4G35 (ortholog of DmCYP4G15). Here, we show that CYP4G35 is highly expressed in mosquito antennae, and the RNAi knockdown of CYP4G35 results in delayed host-seeking. Ae. aegypti CYP4G knockout lines confirmed delayed host-seeking behavior in CYP4G35 knockout females. Proteomics analysis of CYP4G35 KO females also corroborates the physiological findings and shows upregulation of proteins related to olfaction and other CYP4Gs to compensate for the lack of CYP4G35. Immunohistochemistry and in situ hybridization were used to localize CYP4G35 and demonstrated its expression in the sensilla lymph of the antennae and the tip of the proboscis. CYP4G35 and CYP4G36 fusion proteins with cytochrome P450 reductase demonstrated that, unlike CYP4G36, CYP4G35 lacks an oxidative decarbonylase function. Together, our data support a novel function of CYP4G35 in modulating olfactory response.

Advances in food production systems and customer acceptance have led to the commercial launch of dietary proteins produced via modern biotechnological approaches as alternatives to traditional agricultural sources. At the same time, a deeper understanding of how dietary components interact with the gut microbiome has highlighted the importance of understanding the nuances underpinning diet-microbiome interactions. Novel food proteins with distinct post-translational modifications resulting from their respective production systems have not been characterized, nor how they may differ from their traditionally produced counterparts. Here, we have characterized the protein composition and N-glycome of a yeast-synthesized and commercially available whey protein ingredient and compared this novel ingredient to whey protein isolate powder derived from bovine milk. Despite strong similarities in protein composition, we found that the N-glycome significantly differs between the two protein sources, reflecting the biosynthetic machinery of the production systems. Furthermore, the diversity of proteins found in yeast-synthesized whey protein were lower relative to bovine whey protein, despite both being predominantly β-lactoglobulin. Finally, to understand whether these differences in N-glycome profiles may affect the human gut microbiome, we compared these proteins in an in vitro fecal fermentation model. The two whey protein sources generated significant differences among three representative gut microbiomes in vitro, most likely due to differences in N-glycan composition and degradation by these representative microbial communities. This work highlights the need to understand how differences in novel biotechnological systems affect the bioactivity of synthesized proteins and how these differences impact the human gut microbiome. IMPORTANCE:Recent advances in food technology have led to the production of animal-free products from yeast that are traditionally derived from animals, such as milk proteins. These new processes raise important questions about the use of synthetic proteins as a replacement for traditionally sourced protein, especially in the context of the gut microbiome. Importantly, yeast produce N-glycans comprised primarily of mannose, while animals synthesize structurally and compositionally complex N-glycan structures. Given these differences, we characterized a new, yeast-derived whey protein ingredient and compared it to bovine whey protein. We found that yeast-derived whey protein differs in its impact on human gut microbiomes because of differences in N-glycan structures, despite similarity in protein composition. These findings raise important questions as to whether these differences in synthetic proteins lead to significant changes to the gut microbiome in vivo, and whether this may impact the utility of these novel ingredients.

Neurons are almost exclusively cultured in media containing glucose at much higher concentrations than found in the brain. To test whether these "standard" hyperglycemic culture conditions affect neuronal respiration relative to near-euglycemic conditions, we compared neuronal cultures grown with minimal glial contamination from the hippocampus and cortex of neonatal C57BL/6NCrl mice in standard commercially available media (25 mM Glucose) and in identical media with 5 mM glucose. Neuronal growth in both glucose concentrations proceeded until at least 14 days in vitro, with similar morphology and synaptogenesis. Neurons grown in high glucose were highly dependent on glycolysis as their primary source of ATP, measured using ATP luminescence and cellular respirometry assays. In contrast, neurons grown in 5 mM glucose showed a more balanced dependence on glycolysis and mitochondrial oxidative phosphorylation (OXPHOS), greater reserve mitochondrial respiration capacity, and increased mitochondrial population relative to standard media. Our results show that neurons cultured in artificially high glucose-containing media preferentially use glycolysis, opposite to what is known for neurons in vivo as the primary pathway for ATP maintenance. Changes in gene and protein expression levels corroborate these changes in function and additionally suggest that high glucose culture media increases neuronal inflammation. We suggest using neuronal culture systems in 5 mM glucose to better represent physiologically relevant neuronal respiration.

BackgroundAstyanax mexicanus is a single species of fish that consists of river-dwelling (surface) and cave-dwelling morphotypes. Little is known about how sexual determination, differentiation or reproduction have evolved in the surface morphs or cavefish, though divergence in reproductive strategy is expected as the latter have adapted to the novel cave environment. Evolution of the gonad transcriptome may underlie the differences in gamete morphology, fertility, and fecundity previously reported between morphotypes.ResultsWe compared the ovary and testis transcriptome of surface fish and cavefish at juvenile and adult stages. We found that samples clustered by developmental stage, sex, and morphotype identity. Several key genes that are typically associated with the female gonad in other vertebrates showed a reversal in sexual dimorphism or were not differentially expressed between sexes in A. mexicanus. In contrast, gene expression typically associated with male gonads was largely conserved and consistent with vertebrate testicular expression profiles. Transcriptional and physiological differences between surface fish and cavefish morphotypes were observed in gonads from both sexes. Cavefish ovaries exhibited unique upregulation of neuron development and differentiation genes, and extensive innervation of the ovarian epithelium, while cavefish testes showed increased expression of angiogenesis regulating genes, and greater vasculature density compared to surface fish testes.ConclusionsThese results reveal significant gene expression differences between A. mexicanus surface fish and cavefish morphotypes that may have functional consequences in gonad morphogenesis and fertility. Our findings provide a foundation for investigating the evolution of sex regulatory pathways and reproductive strategies in animals adapting to new and challenging environments in which nutrient availability, temperature, and mate selection are suboptimal.

Starvation is a complex physiological state that induces changes in protein expression to ensure survival. The insect midgut is sensitive to changes in dietary content as it is at the forefront of communicating information about incoming nutrients to the body via hormones. Therefore, a DIA proteomics approach was used to examine starvation physiology and, specifically, the role of midgut neuropeptide hormones in a representative lepidopteran, Manduca sexta. Proteomes were generated from midguts of M. sexta fourth-instar caterpillars, starved for 24 h and 48 h, and compared to fed controls. A total of 3047 proteins were identified, and 854 of these were significantly different in abundance. KEGG analysis revealed that metabolism pathways were less abundant in starved caterpillars, but oxidative phosphorylation proteins were more abundant. In addition, six neuropeptides or related signaling cascade proteins were detected. Particularly, neuropeptide F1 (NPF1) was significantly higher in abundance in starved larvae. A change in juvenile hormone-degrading enzymes was also detected during starvation. Overall, our results provide an exploration of the midgut response to starvation in M. sexta and validate DIA proteomics as a useful tool for quantifying insect midgut neuropeptide hormones.

Retinal progenitor cells (RPCs) are a multipotent and highly proliferative population that give rise to all retinal cell types during organogenesis. Defining their molecular signature is a key step towards identifying suitable approaches to treat visual impairments. Here, we performed RNA sequencing of whole eyes from Xenopus at three embryonic stages and used differential expression analysis to define the transcriptomic profiles of optic tissues containing proliferating and differentiating RPCs during retinogenesis. Gene Ontology and KEGG pathway analyses showed that genes associated with developmental pathways (including Wnt and Hedgehog signaling) were upregulated during the period of active RPC proliferation in early retinal development (Nieuwkoop Faber st. 24 and 27). Developing eyes had dynamic expression profiles and shifted to enrichment for metabolic processes and phototransduction during RPC progeny specification and differentiation (st. 35). Furthermore, conserved adult eye regeneration genes were also expressed during early retinal development, including sox2, pax6, nrl, and Notch signaling components. The eye transcriptomic profiles presented here span RPC proliferation to retinogenesis and include regrowth-competent stages. Thus, our dataset provides a rich resource to uncover molecular regulators of RPC activity and will allow future studies to address regulators of RPC proliferation during eye repair and regrowth.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of coronavirus disease 2019 (COVID-19), has posed significant challenges to global health. While much attention has been directed towards understanding the primary mechanisms of SARS-CoV-2 infection, emerging evidence suggests co-infections or superinfections with other viruses may contribute to increased morbidity and mortality, particularly in severe cases of COVID-19. Among viruses that have been reported in patients with SARS-CoV-2, seropositivity for Human cytomegalovirus (HCMV) is associated with increased COVID-19 risk and hospitalization. HCMV is a ubiquitous beta-herpesvirus with a seroprevalence of 60-90 % worldwide and one of the leading causes of mortality in immunocompromised individuals. The primary sites of latency for HCMV include CD14+ monocytes and CD34+ hematopoietic cells. In this study, we sought to investigate SARS-CoV-2 infection of CD14+ monocytes latently infected with HCMV. We demonstrate that CD14+ cells are susceptible and permissive to SARSCoV-2 infection and detect subgenomic transcripts indicative of replication. To further investigate the molecular changes triggered by SARS-CoV-2 infection in HCMV-latent CD14+ monocytes, we conducted RNA sequencing coupled with bioinformatic differential gene analysis. The results revealed significant differences in cytokine-cytokine receptor interactions and inflammatory pathways in cells superinfected with replicationcompetent SARS-CoV-2 compared to the heat-inactivated and mock controls. Notably, there was a significant upregulation in transcripts associated with pro-inflammatory response factors and a decrease in antiinflammatory factors. Taken together, these findings provide a basis for the heightened inflammatory response, offering potential avenues for targeted therapeutic interventions among HCMV-infected severe cases of COVID-19. Summary: COVID-19 patients infected with secondary viruses have been associated with a higher prevalence of severe symptoms. Individuals seropositive for human cytomegalovirus (HCMV) infection are at an increased risk for severe COVID-19 disease and hospitalization. HCMV reactivation has been reported in severe COVID-19 cases with respiratory failure and could be the result of co-infection with SARS-CoV-2 and HCMV. In a cell culture model of superinfection, HCMV has previously been shown to increase infection of SARS-CoV-2 of epithelial cells by upregulating the human angiotensin-converting enzyme-2 (ACE2) receptor. In this study, we utilize CD14+ monocytes, a major cell type that harbors latent HCMV, to investigate co-infection of SARS-CoV-2 and HCMV. This study is a first step toward understanding the mechanism that may facilitate increased COVID-19 disease severity in patients infected with SARS-CoV-2 and HCMV.

AbstractBackgroundAstyanax mexicanusis a single species of fish that consists of river-dwelling (surface) and cave-dwelling morphotypes. Little is known about how sexual determination, differentiation or reproduction have evolved in the surface morphs or cavefish, though divergence in reproductive strategy is expected as the latter have adapted to the novel cave environment. Evolution of the gonad transcriptome may underlie the differences in gamete morphology, fertility, and fecundity previously reported between morphotypes.ResultsWe compared the ovary and testis transcriptome of surface fish and cavefish at juvenile and adult stages. We found that samples clustered by developmental stage, sex, and morphotype identity. Several key genes that are typically associated with the female gonad in other vertebrates showed a reversal in sexual dimorphism or were not differentially expressed between sexes inA. mexicanus. In contrast, while gene expression typically associated with male gonads was largely conserved and consistent with vertebrate testicular expression profiles. Transcriptional and physiological differences between surface fish and cavefish morphotypes were observed in gonads from both sexes. Cavefish ovaries exhibited unique upregulation of neuron development and differentiation genes, and extensive innervation of the ovarian epithelium, while cavefish testes showed increased expression of angiogenesis regulating genes, and greater vasculature density compared to surface fish testes.ConclusionsThese results reveal significant gene expression differences betweenA. mexicanussurface fish and cavefish morphotypes that may have functional consequences in gonad morphogenesis and fertility. Our findings provide a foundation for investigating the evolution of sex regulatory pathways and reproductive strategies in animals adapting to new and challenging environments in which nutrient availability, temperature, and mate selection are suboptimal.

This manuscript describes the development of a resource module that is part of a learning platform named 'NIGMS Sandbox for Cloud-based Learning' (https://github.com/NIGMS/NIGMS-Sandbox). The module delivers learning materials on Cloud-based Consensus Pathway Analysis in an interactive format that uses appropriate cloud resources for data access and analyses. Pathway analysis is important because it allows us to gain insights into biological mechanisms underlying conditions. But the availability of many pathway analysis methods, the requirement of coding skills, and the focus of current tools on only a few species all make it very difficult for biomedical researchers to self-learn and perform pathway analysis efficiently. Furthermore, there is a lack of tools that allow researchers to compare analysis results obtained from different experiments and different analysis methods to find consensus results. To address these challenges, we have designed a cloud-based, self-learning module that provides consensus results among established, state-of-the-art pathway analysis techniques to provide students and researchers with necessary training and example materials. The training module consists of five Jupyter Notebooks that provide complete tutorials for the following tasks: (i) process expression data, (ii) perform differential analysis, visualize and compare the results obtained from four differential analysis methods (limma, t-test, edgeR, DESeq2), (iii) process three pathway databases (GO, KEGG and Reactome), (iv) perform pathway analysis using eight methods (ORA, CAMERA, KS test, Wilcoxon test, FGSEA, GSA, SAFE and PADOG) and (v) combine results of multiple analyses. We also provide examples, source code, explanations and instructional videos for trainees to complete each Jupyter Notebook. The module supports the analysis for many model (e.g. human, mouse, fruit fly, zebra fish) and non-model species. The module is publicly available at https://github.com/NIGMS/Consensus-Pathway-Analysis-in-the-Cloud. This manuscript describes the development of a resource module that is part of a learning platform named ``NIGMS Sandbox for Cloud-based Learning'' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.

Kaposi's sarcoma-associated herpesvirus (KSHV) relies on many cellular proteins to complete replication and generate new virions. Paraspeckle nuclear bodies consisting of core ribonucleoproteins splicing factor proline/glutamine-rich (SFPQ), Non-POU domain-containing octamer-binding protein (NONO), and paraspeckle protein component 1 (PSPC1) along with the long non-coding RNA NEAT1, form a complex that has been speculated to play an important role in viral replication. Paraspeckle bodies are multifunctional and involved in various processes including gene expression, mRNA splicing, and anti-viral defenses. To better understand the role of SFPQ during KSHV replication, we performed SFPQ immunoprecipitation followed by mass spectrometry from KSHV-infected cells. Proteomic analysis showed that during lytic reactivation, SFPQ associates with viral proteins, including ORF10, ORF59, and ORF61. These results are consistent with a previously reported ORF59 proteomics assay identifying SFPQ. To test if the association between ORF59 and SFPQ is important for replication, we first identified the region of ORF59 that associates with SFPQ using a series of 50 amino acid deletion mutants of ORF59 in the KSHV BACmid system. By performing co-immunoprecipitations, we identified the region spanning amino acids 101-150 of ORF59 as the association domain with SFPQ. Using this information, we generated a dominant negative polypeptide of ORF59 encompassing amino acids 101-150, that disrupted the association between SFPQ and full-length ORF59, and decreased virus production. Interestingly, when we tested other human herpesvirus processivity factors (EBV BMRF1, HSV-1 UL42, and HCMV UL44) by transfection of each expression plasmid followed by co-immunoprecipitation, we found a conserved association with SFPQ. These are limited studies that remain to be done in the context of infection but suggest a potential association of SFPQ with processivity factors across multiple herpesviruses.

Charcot-Marie-Tooth disease type 1E (CMT1E) is an inherited autosomal dominant peripheral neuropathy caused by mutations in the peripheral myelin protein 22 (PMP22) gene. The identical leucine-to-proline (L16P) amino acid substitution in PMP22 is carried by the Trembler J (TrJ) mouse and is found in CMT1E patients presenting with early-onset disease. Peripheral nerves of patients diagnosed with CMT1E display a complex and varied histopathology, including Schwann cell hyperproliferation, abnormally thin myelin, axonal degeneration, and subaxonal morphological changes. Here, we have taken an unbiased data-independent analysis (DIA) mass spectrometry (MS) approach to quantify proteins from nerves of 3-week-old, age and genetic strain-matched wild-type (Wt) and heterozygous TrJ mice. Nerve proteins were dissolved in lysis buffer and digested into peptide fragments, and protein groups were quantified by liquid chromatography-mass spectrometry (LC-MS). A linear model determined statistically significant differences between the study groups, and proteins with an adjusted p-value of less than 0.05 were deemed significant. This untargeted proteomics approach identified 3759 quality-controlled protein groups, of which 884 demonstrated differential expression between the two genotypes. Gene ontology (GO) terms related to myelin and myelin maintenance confirm published data while revealing a previously undetected prominent decrease in peripheral myelin protein 2. The dataset corroborates the described pathophysiology of TrJ nerves, including elevated activity in the proteasome-lysosomal pathways, alterations in protein trafficking, and an increase in three macrophage-associated proteins. Previously unrecognized perturbations in RNA processing pathways and GO terms were also discovered. Proteomic abnormalities that overlap with other human neurological disorders besides CMT include Lafora Disease and Amyotrophic Lateral Sclerosis. Overall, this study confirms and extends current knowledge on the cellular pathophysiology in TrJ neuropathic nerves and provides novel insights for future examinations. Recognition of shared pathomechanisms across discrete neurological disorders offers opportunities for innovative disease-modifying therapeutics that could be effective for distinct neuropathies.image This study was designed to obtain comprehensive quantitative proteomic data from the sciatic nerves of Trembler J (TrJ) mice that model Charcot-Marie-Tooth type 1E (CMT1E) hereditary peripheral neuropathy. Samples from three-week old, wild-type (Wt), and neuropathic mice, of mixed sexes, were analyzed. The study identified 884 differentially expressed protein groups between the genotypes. Bioinformatics revealed predicted alterations in protein networks involved in myelination, lysosomal degradative mechanisms, and inflammation. Significantly, detailed pathway analyses uncovered previously unrecognized changes in protein and RNA processing, including shared pathomechanisms across discrete neurological disorders.image

Ixodes scapularis, the black-legged tick, is a major arthropod vector that transmits the causative agents of Lyme disease and several other pathogens of human significance. The tick midgut is the main tissue involved in blood acquisition and digestion and the first organ to have contact with pathogens ingested through the blood meal. Gene expression in the midgut before, during, and after a blood meal may vary in response to the physiological changes due to blood feeding. A systems biology approach based on RNA and protein sequencing was used to gain insight into the changes in tick midgut transcripts and proteins during blood ingestion (unfed and partially fed) and digestion (1-, 2-, 7-, and 14 days post detachment from the host) by the Ixodes scapularis female ticks. A total of 2,726 differentially expressed transcripts, and 449 proteins were identified across the time points. Genes involved in detoxification of xenobiotics, proteases, protease inhibitors, metabolism, and immunity were differentially expressed in response to blood feeding. Similarly, proteins corresponding to the same groups were also differentially expressed. Nine genes from major gene categories were chosen as potential vaccine candidates, and, using RNA interference, the effect of these gene knockdowns on tick biology was investigated. Knockdown of these genes had variable negative impacts on tick physiology, such as the inability to engorge fully and to produce eggs and increased mortality. These and additional gene targets provide opportunities to explore novel tick control strategies.

BackgroundAeromedical evacuation provides critical care during long-distance transport of injured victims between medical facilities. Often, these victims sustain muscle trauma related to mechanical insults, such as crush. Understanding the effects of flight on injured muscle is important because the aircraft cabin represents an external environment with mild hypoxia-the cabin's altitude is 2,438 m instead of sea level. Because mild hypobaric hypoxia can alter gene expression in normal muscle and affect recovery patterns, it is beneficial to examine whether this type of hypoxia may also alter injury-related genes.ObjectiveThe objective of this study was to verify the hypothesis that differential gene expression occurs in response to mild hypobaric hypoxia exposure in crush-injured muscle during two early recovery (preregeneration stage) time points.MethodsTwenty-four female mice were anesthetized, and the right gastrocnemius muscle underwent crush injury. Approximately 24 hours later, mice were exposed to normobaric normoxia or hypobaric hypoxia for 8-9 hours. After 32 or 48 hours of recovery, the mice were euthanized, and the right and left lateral gastrocnemius muscles were collected for microarray and bioinformatics analyses.ResultsThe study hypothesis was verified. There were 353 highly upregulated, differentially expressed genes identified in the injured muscle compared to the uninjured muscle. Mid1 was upregulated in both pressure conditions regardless of injury status. There were 52 and 15 differentially expressed genes at 32 and 48 hours postinjury, respectively, in the hypobaric hypoxia-exposed, injured muscle compared to the normobaric normoxia-exposed, injured muscle. The macrophage gene Cd68 correlated with other leukocyte-related genes.DiscussionThese findings expand our understanding of the genetic changes that occur in muscle in response to a crush injury, including those related to the macrophage protein CD68. Nursing interventions addressing adequate functioning after crush muscle injury may need to consider the effects on Cd68 and its closely related genes. In addition, our results suggest a responsiveness of the gene Mid1 to flight-relevant hypobaric hypoxia. Changes in the expression of Mid1 may be appropriate in assessing the long-term health of flight crew members.