Biology subjects

Salem, M.

Publications and source records attributed to Salem, M..

10 recordsLinked to original sources

bioRxiv2026

QTL spanning the TGF-β2 locus is associated with muscle fiber hypertrophy in rainbow trout

BackgroundSkeletal muscle growth is a key determinant of body size and market value in salmonid aquaculture, yet the mechanisms linking genomic variation to muscle fiber hypertrophy remain poorly resolved. Myofiber cross-sectional area (CSA) provides a quantitative cellular proxy for fiber size and a direct link to macroscopic growth traits. MethodsWe performed histological phenotyping of white skeletal muscle from rainbow trout (Oncorhynchus mykiss) representing divergent fillet-yield selection lines (ARS-FY-H and ARS-FY-L), quantifying mean myofiber CSA and fiber number using high-throughput image analysis. Genome-wide association analysis (GWAS) was conducted using low-pass whole-genome sequencing ([~]1x) with genotype imputation and functional variant annotation. RNA sequencing was performed on fish representing high and low CSA extremes to identify differentially expressed genes and enriched biological pathways. ResultsMean myofiber CSA was significantly associated with body weight, muscle weight, visceral weight, and body length (p < 0.05), while fiber count showed no significant association with most growth traits, implicating hypertrophy as the primary driver of muscle mass variation. GWAS identified a significant QTL spanning [~]4.76 Mb on chromosome 2 (117 significant SNPs; Bonferroni-adjusted P [≤] 0.05; {lambda} = 1.02). Associated variants were predominantly noncoding, enriched in intronic, intergenic, and enhancer-annotated regions. A high density of SNPs colocalized with the TGF-{beta}2 locus, overlapping strong and genic enhancer elements in white muscle. Transcriptomic comparisons revealed that high-CSA muscle showed elevated expression of genes related to contractile function, cytoskeletal organization, and translation, while low-CSA muscle exhibited upregulation of extracellular matrix and immune-related genes consistent with a tissue remodeling state. ConclusionsNoncoding regulatory variation within a significant QTL spanning the TGF-{beta}2 locus is associated with distinct transcriptional programs linked to muscle fiber hypertrophy in rainbow trout. By integrating genetic variation, chromatin-state annotation, and transcriptomic profiling, this study identifies candidate regulatory loci associated with variation in muscle cellularity and growth-related phenotypes in rainbow trout.

genomics↗

bioRxiv2026

Homologous ABA-independent kinase tracks coalesced into osmotic stress circuits during plant terrestrialization

Land plants possess a unique system for responding to environmental stressors. How this system evolved during plant terrestrialization remains one of the major questions in plant evolutionary biology. To retrace this process, it is essential to study both land plants and their closest algal relatives, the zygnematophytes. Using the single-celled zygnematophyte Mesotaenium, we integrated physiological stress experiments with phosphoproteomics, genome-wide transcription factor binding analyses, and protein-protein interaction studies to investigate the architecture of a key stress response pathway: the signaling cascade homologous to the plant abscisic acid (ABA)-mediated pathway. Our results highlight the roles of histidine kinases (HKs) and calcium-dependent protein kinases (CDPKs) in osmotic stress signaling. Focusing on SnRK2 and ABF, key components at the downstream end of the canonical ABA signaling pathway, we provide evidence that ABF plays a central role in osmotic stress responses even in the absence of ABA. Together, our data reveal the coordinated action of parallel functional modules that were likely integrated into the ABA response cascade during plant terrestrialization.

evolutionary biology↗

bioRxiv2026

Age Dependent Immunopathology Drives Pneumonia-Associated Cardiac Dysfunction During Streptococcus pneumoniae Infection

Aging is a major risk factor for severe Streptococcus pneumoniae (Spn) infection and pneumonia-associated - major adverse cardiac events (PA-MACE), yet underlying mechanisms remain unclear. Using young and aged murine models, we show that aging exacerbates bacterial burden, mortality, and cardiac dysfunction following Spn infection, associated with impaired macrophage bacterial killing. Single-cell RNA sequencing infected hearts revealed extensive age-dependent remodeling across immune and stromal compartments. Aged mice exhibited heightened pro-inflammatory myeloid responses, with increased neutrophil infiltration characterized by elevated S100A8/9 and LCN2 and reduced antimicrobial programs. Macrophages displayed defective efferocytosis, including disruption of the GAS6-AXL axis. Aging also drove expansion of an infection-responsive fibroblast population with inflammatory signatures and reduced extracellular matrix gene expression. These changes were linked to oxidative stress and impaired glucose oxidation. Notably, anti-inflammatory treatment rescued cardiac dysfunction, implicating excessive inflammation as a central driver of PA-MACE. Together, these findings define mechanisms linking aging to pneumococcal cardiac complications and identify potential therapeutic targets.

immunology↗

bioRxiv2025

De novo Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants In Pursuit of a Pangenome Reference

Rainbow trout (Oncorhynchus mykiss) exhibit extensive genomic diversity shaped by domestication, life history, and geographic origin. To advance the development of a comprehensive pangenome reference, we present new de novo genome assemblies of two genetically and ecologically distinct lines: Whale Rock (WR; wild, landlocked, Central California) and Keithley Creek (KC; wild, resident, interior Columbia Basin), along with the previously published assemblies of the Arlee (domesticated, Northern California) and Swanson (semi-domesticated, resident, Alaska) lines. All assemblies provide nearly complete coverage of known genes (BUSCO 95.8-99.7%) and are similar in genome size ([~]2.3 Gb), with scaffold N50 values between 3.4 Mb (KC) and 52.4 Mb (Swanson). Comparative whole-genome alignments revealed high sequence conservation (97-98% identity) among assemblies, but also evidence of extensive structural variation of at least 50 bp in length. Structural variant (SV) profiling identified tens of thousands of deletions, insertions, and complex rearrangements largely in noncoding sequences. In an initial assessment of the utility of having multiple de novo genome assemblies for rainbow trout, we found that two strains (Arlee and Swanson; domesticated) share SVs enriched in genes linked with growth, reproduction, and adaptation to domestication, such as GTP binding and ECM-receptor interaction. In comparison, the other two strains (WR and KC; wild origin) share SVs associated with reproductive timing such as GnRH signaling pathway. Both Arlee and WR also have unique SVs potentially related to their geographic origin and unique life history. Additionally, we identified SVs in key regions, such as a QTL for fillet yield on Omy17 and the maturation-associated SIX6/ER{beta}-GPHB5 locus on Omy25q, suggesting the importance of considering SVs when investigating the genomics of complex traits. Together, these assemblies and comparative analyses establish a foundation for a rainbow trout pangenome reference, illuminating how they can be utilized to reveal the structural genomic basis of domestication, adaptation, and other complex traits in O. mykiss.

genomics↗

bioRxiv2025

Splicing Retention and Enhancer Divergence Govern the Evolutionary Fate of Ohnologues Following Whole-Genome Duplication in Rainbow Trout

Whole-genome duplication (WGD) produces gene duplicates--known as ohnologues--that expand evolutionary potential while posing challenges for regulatory coordination and functional balance. While divergence in gene expression has been widely studied post-WGD, the long-term evolutionary dynamics of alternative splicing (AS) and its regulatory basis remain unresolved. Here, we investigate the evolution of AS in rainbow trout (Oncorhynchus mykiss), a species that underwent a salmonid-specific WGD [~]100 million years ago. Using a high-quality genome assembly, transcriptome data across six tissues, and ChIP-seq profiling of histone modifications, we classify ohnologue pairs based on their expression divergence, splicing complexity, and epigenetic signatures. We find that most ohnologues are retained through conservation, with a gradual reduction in AS diversity over time. Contrary to earlier models, a substantial fraction of ohnologues follows an independent splicing model, maintaining splicing complexity similar to their unduplicated ancestors. Strikingly, we show that enhancer-associated histone marks, particularly H3K27ac, diverge significantly between neofunctionalized and independently splicing gene pairs, implicating enhancer rewiring as a key driver of regulatory and functional divergence. These findings reveal that AS evolution after WGD is shaped by both selective pressures and epigenetic modulation, challenging assumptions of rapid splicing loss and highlighting the independent model as a dominant long-term fate. Our results provide a unified framework for understanding how splicing and regulatory landscapes evolve following genome duplication, with broad implications for vertebrate genome evolution and functional innovation.

genomics↗

bioRxiv2024

On the same side: The immune regulatory protein Vista and its ligands interact in cis

VISTA, an essential immune checkpoint regulatory protein, regulates peripheral T-cell quiescence and tolerance. Despite its potential as a target for anti-tumor and autoimmune disease therapies, uncertainty regarding VISTAs binding mode and membrane orientation has hindered these developments. Contrary to the prevailing paradigm, we found using cell aggregation assays that VISTA cannot interact with its ligands in trans (between cells). Using MST and flow cytometry, we showed that soluble VISTA binds to its ligands, suggesting that VISTAs membrane orientation restricts trans interactions. In contrast, split luciferase complementation assays showed that VISTA interacts with its ligands in cis. We propose that a disulfide bond bends VISTAs Ig domain towards the membrane in an orientation that prevents trans while enabling cis interactions. Co-expression data analysis from the cancer genome atlas showed a strong correlation between VISTA and its ligand, PSGL-1, consistent with our in-vitro cis interaction data. Our findings reveal VISTAs binding mechanism and suggest an intrinsic inhibition signaling pathway independent of additional cells. Importantly, our experimental framework provides a platform for identifying novel VISTA-targeted therapeutics.

immunology↗

bioRxiv2023

Functional microRNA-Targeting Drug Discovery by Graph-Based Deep Learning

MicroRNAs are recognized as key drivers in many cancers, but targeting them with small molecules remains a challenge. We present RiboStrike, a deep learning framework that identifies small molecules against specific microRNAs. To demonstrate its capabilities, we applied it to microRNA-21 (miR-21), a known driver of breast cancer. To ensure the selected molecules only targeted miR-21 and not other microRNAs, we also performed a counter-screen against DICER, an enzyme involved in microRNA biogenesis. Additionally, we used auxiliary models to evaluate toxicity and select the best candidates. Using datasets from various sources, we screened a pool of nine million molecules and identified eight, three of which showed anti-miR-21 activity in both reporter assays and RNA sequencing experiments. One of these was also tested in mouse models of breast cancer, resulting in a significant reduction of lung metastases. These results demonstrate RiboStrikes ability to effectively screen for microRNA-targeting compounds in cancer.

cancer biology↗

bioRxiv2021

sRNAs enriched in outer membrane vesicles of pathogenic Flavobacterium psychrophilum interact with immune genes of rainbow trout

Outer membrane vesicles (OMVs) released by gram-negative bacteria during host-pathogen interactions harbor cargos, such as DNA, RNA, toxins, and virulence factors. We hypothesized that sRNAs carried within OMVs of Flavobacterium psychrophilum interact with host immune genes and affect their expression. OMVs were isolated from F. psychrophilum and visualized using transmission electron microscopy (TEM). RNA-Seq datasets generated from whole-cell F. psychrophilum and their OMVs indicated enrichment of specific sRNAs in the OMVs compared to the parent cell. Fluorescent in situ hybridization (FISH) and confocal microscopy confirmed the expression of a randomly chosen sRNA. Integrated RNA-Seq analyses of host transcriptome and bacterial sRNAs on day 5 post-infection of F. psychrophilum-resistant and -susceptible rainbow trout genetic lines revealed 516 protein-coding, 595 lncRNA, and 116 bacterial sRNA differentially expressed (DE) transcripts. Integrated and network analyses of these DE transcripts revealed immune genes targeted by bacterial sRNAs. On the top of these genes, an isoform encoding anaphase-promoting complex subunit 13 (ANAPC13_1) was highly upregulated and exhibited interaction and reciprocal expression with 21 DE sRNAs enriched in OMVs and/or located in pathogenicity islands (PAIs). In vitro treatment of the rainbow trout epithelial cell line RTgill-W1 with OMVs showed signs of cell autolysis accompanied by dynamic changes in expression of host genes when profiled 24h following treatment. The OMV-enriched sRNAs, soFE013584 and soFE002123, showed high interactions with the protection of telomeres 1 gene (POT1); essential for chromosome stability and cellular viability. Modulation of the host gene expression following OMV-treatment, which favors elements from the phagocytic, endocytic, and antigen presentation pathways in addition to HSP70, HSP90, and cochaperone proteins, provided evidence for a potential role of OMVs in boosting the host immune response. In conclusion, our work identified novel microbial targets and inherent characteristics of OMVs that could open up new avenues of treatment and prevention of fish infections.

microbiology↗

bioRxiv2018

Genome-wide association analysis with a 50K transcribed gene SNP-chip identifies QTL affecting muscle yield in rainbow trout

Detection of coding/functional SNPs that change the biological function of a gene may lead to identification of putative causative alleles within QTL regions and discovery of genetic markers with large effects on phenotypes. Two bioinformatics pipelines, GATK and SAMtools, were used to identify ~21K transcribed SNPs with allelic imbalances associated with important aquaculture production traits including body weight, muscle yield, muscle fat content, shear force, and whiteness in addition to resistance/susceptibility to bacterial cold-water disease (BCWD). SNPs were identified from pooled RNA-Seq data collected from ~620 fish, representing 98 families from growth- and 54 families from BCWD-selected lines with divergent phenotypes. In addition, ~29K transcribed SNPs without allelic-imbalances were strategically added to build a 50K Affymetrix SNP-chip. SNPs selected included two SNPs per gene from 14K genes and ~5K non-synonymous SNPs. The SNP-chip was used to genotype 1728 fish. The average SNP calling-rate for samples passing quality control (QC; 1,641 fish) was [≥] 98.5%. Genome-wide association (GWA) study on 878 fish (representing 197 families from 2 consecutive generations) with muscle yield phenotypes and genotyped for 35K polymorphic markers (passing QC) identified several QTL regions explaining together up to 28.40% of the additive genetic variance for muscle yield in this rainbow trout population. The most significant QTLs were on chromosomes 14 and 16 with 12.71% and 10.49% of the genetic variance, respectively. Many of the annotated genes in the QTL regions were previously reported as important regulators of muscle development and cell signaling. No major QTLs were identified in a previous GWA study using a 57K genomic SNP chip on the same fish population. These results indicate improved detection power of the transcribed gene SNP-chip in the target trait and population, allowing identification of large-effect QTLs for important traits in rainbow trout.

genomics↗

bioRxiv2017

Supplement comprising of laccase and citric acid as an alternative for antibiotics - in vitro triggers of melanin production

An indiscriminate use of antibiotics in humans and animals has led to a widespread selection of antibiotic-resistant bacterial strains. A possible solution to counter this problem could be to develop alternatives that may boost the host immunity, thus reducing in the quantity and frequency of antibiotic use. In this work, for the first time, citric acid and laccase were used as extracellular inducers of melanin production in yeast cells and human cell lines. It is proposed that the formulation of laccase and citric acid together could further promote melatonin stimulated melanocyte derived melanin production. Melanization test as a probe of immunity, described in this study, is an easy and a quicker test than the other immunity tests and is statistically significant. The results showed the synergistic effect of citric acid and laccase on melanin production by the yeast cells, with significant statistical differences compared to all other tested conditions (P: 0.0005- 0.005). Laccase and citric acid together boosted melanin production after 8 days of incubation. An increase in melanin production by two colon human cells lines (Cacao-2/15 and HT-29) was observed when both laccase and citric acid were present in cell growth medium. A formulation with citric acid and laccase may prove to be an excellent alternative to reduce the antibiotic load in human and animal subjects.\n\nSummary statementThis study shows, for the first time, that production of melanin in yeast and human intestinal cells is induced by extracellular addition of laccase and citric acid.

immunology↗