Biology subjects

Haddad, A.

Publications and source records attributed to Haddad, A..

5 recordsLinked to original sources

bioRxiv2026

Continuous thermal sensitivity of gene expression following acclimation in Drosophila subobscura

The physiology of ectotherms can change substantially during acclimation to changing environmental temperature. The role of transcription in acclimation responses has been well-established, but it remains unclear whether transcriptional regulation generally reflects abrupt changes after surpassing temperature thresholds, or whether transcript abundance is a relatively monotonic, continuous function of acclimation temperature. In this study we exposed adult male Drosophila subobscura flies to four different 96-hour acclimation treatments at temperatures that were not acutely stressful but ranged from relatively cold (10{degrees}C) to relatively warm (27{degrees}C) with respect to standard rearing conditions. Transcriptome sequencing of whole-body homogenates (mRNAseq) revealed a massive, transcriptome-wide response across acclimation temperatures, with a marked overrepresentation of genes that were continuously and monotonically up- and down-regulated in response to increasing acclimation temperature. Though some genes showed more complex relationships consistent with putative threshold responses, a high percentage of the differentially expressed transcriptome (42%) showed continuous and strictly monotonic relationships. Functional enrichment suggested continuous up-regulation of spermatogenesis-related transcripts with increasing temperature and continuous up-regulation of oxidative phosphorylation-related transcripts with decreasing temperature, illustrating contrasting patterns consistent with previous studies of thermal sensitivity of male reproduction and metabolic compensation in the cold. Thus, continuous thermal sensitivity of transcription is a hallmark of acclimation in D. subobscura that likely underlies the continuous thermal sensitivity of downstream physiological processes. We also provide evidence for shared transcriptomic responses across short-term acclimation (this study) vs. published results for long-term, developmental acclimation.

evolutionary biology↗

bioRxiv2026

Emergence of a novel hypervirulent extensively drug-resistant ST383 Klebsiella pneumoniae lineage carrying ICEKp5 in Lebanon

Klebsiella pneumoniae ST383 has emerged as a high-risk clone, characterized by carbapenem resistance and increasing detection of hypervirulence determinants. We describe a novel ST383 lineage in Lebanon, defined by the acquisition of ICEKp5, which carries the yersiniabactin locus. Three ST383 K. pneumoniae clinical isolates (LBN_CAKp91, LBN_CTKp3, LBN_CTKp11) recovered from a Lebanese medical center were subjected to whole-genome sequencing. Comparative genomic analysis included regional ST383 strains and previously characterized Lebanese isolates. The study isolates formed a tight, monophyletic cluster (3-9 SNPs) that is phylogenetically distinct from the previously reported Lebanese ST383 clone (>164 SNPs) and grouped most closely to an Egyptian ST383 strain (59-65 SNPs). All three isolates carried ICEKp5 with yersiniabactin lineage ybt14, a feature absent in the earlier Lebanese ST383 clone. The isolates were the only ST383 strains to harbor the full spectrum of hypervirulence determinants to date, including capsule regulators (rmpA, rmpA2), aerobactin (iucABCD, iutA), yersiniabactin, and the hypervirulence biomarker peg-344. All isolates carried dual carbapenemases (blaOXA-48 and blaNDM-5) in addition to blaCTX-M-15 and blaCTX-M-14b. The genetic environments of blaOXA-48 and blaNDM-5 were highly conserved across geographically diverse ST383 isolates, indicating common plasmid origins. This study documents the emergence of a novel hypervirulent extensively drug-resistant (XDR) ST383 K. pneumoniae lineage in Lebanon. The acquisition of ICEKp5, combined with plasmid-borne hypervirulence and resistance determinants, reveals the concerning convergence of hypervirulence and XDR. Enhanced surveillance and infection control measures are urgently needed to monitor this emerging high-risk clone.

genomics↗

bioRxiv2021

Identification of Cancer-Associated Fibroblasts in Glioblastoma and Defining Their Pro-tumoral Effects

Despite their identification in some cancers, pro-tumoral cancer-associated fibroblasts (CAFs) were presumed absent in glioblastoma given the lack of brain fibroblasts. Serial trypsinization of primary glioblastoma cultures yielded cells with CAF morphology, CAF transcriptomic profile, and mesenchymal lineage in single-cell RNA-seq. Glioblastoma CAFs were attracted to glioblastoma stem cells (GSCs) and CAFs enriched GSCs. We created a resource of inferred crosstalk by mapping expression of receptors to their cognate ligands, identifying PDGF-{beta} and TGF-{beta} as mediators of GSC effects on CAFs, and osteopontin and hepatocyte growth factor as mediators of CAF-induced GSC enrichment. Glioblastoma CAFs also induced M2 macrophage polarization by producing the EDA fibronectin variant. Glioblastoma CAFs were enriched in the subventricular zone which houses neural stem cells that produce GSCs. Including CAFs in GSC-derived xenografts induced in vivo growth. These findings are among the first to identify glioblastoma CAFs and their GSC interactions, making them an intriguing target.

cancer biology↗

bioRxiv2020

Early Classification of Motor Tasks Using Dynamic Functional Connectivity Graphs from EEG

ObjectiveClassification of electroencephalography (EEG) signals with high accuracy using short recording intervals has been a challenging problem in developing brain computer interfaces (BCIs). This paper presents a novel feature extraction method for EEG recordings to tackle this problem. ApproachThe proposed approach is based on the concept that the brain functions in a dynamic manner, and utilizes dynamic functional connectivity graphs. The EEG data is first segmented into intervals during which functional networks sustain their connectivity. Functional connectivity networks for each identified segment are then localized, and graphs are constructed, which will be used as features. To take advantage of the dynamic nature of the generated graphs, a Long Short Term Memory (LSTM) classifier is employed for classification. Main resultsFeatures extracted from various durations of post-stimulus EEG data associated with motor execution and imagery tasks are used to test the performance of the classifier. Results show an average accuracy of 85.32% about only 500 ms after stimulus presentation. SignificanceOur results demonstrate, for the first time, that using the proposed feature extraction method, it is possible to classify motor tasks from EEG recordings using a short interval of the data in the order of hundreds of milliseconds (e.g. 500 ms).This duration is considerably shorter than what has been reported before. These results will have significant implications for improving the effectiveness and the speed of BCIs, particularly for those used in assistive technologies.

neuroscience↗

bioRxiv2019

Targeting of mitochondrial and cytosolic substrates of tRNA isopentenyltransferases: selection of differential tRNA-i6A37 identity subsets

tRNA isopentenyltransferases (IPTases), which add an isopentenyl group to N6 of adenosine-37 (i6A37) of certain tRNAs, are among a minority of modification enzymes that act on both cytosolic and mitochondrial substrates. The Caenorhabditis elegans mitochondrial IPTase impacts life expectancy, and pathogenic mutations to human IPTase (TRIT1) that decrease i6A37 levels cause mitochondrial insufficiency and neurodevelopmental disease. Understanding of IPTase broad function should consider the differential identities of the tRNAs selected for i6A37 formation and their cognate codons, which vary among species in both their nuclear- and mitochondria-encoded tRNAs. Substrate selection is principally by recognition of the A36-A37-A38 sequence but can be negatively impacted by certain anticodons, and by ill-defined properties of the IPTase. Thus, tRNAs-i6A37 comprise a modification code system whose principles are incompletely understood. While Saccharomyces cerevisiae uses alternative translation initiation to target IPTase to mitochondria, our analyses indicate that TRIT1 uses a single initiation site to produce a mitochondrial targeting sequence (MTS) that we demonstrate by point mutagenesis using GFP imaging in human cells. We also examined cytosolic and mitochondrial tRNA modification by TRIT1 in Schizosaccharomyces pombe using tRNA-mediated suppression and i6A37-sensitive northern blotting. The TRIT1 MTS mutations indeed decrease mitochondrial-tRNA modification in S. pombe. We also show TRIT1 modification deficiency specific for tRNATrpCCA despite A36-A37-A38, consistent with the negative effect of the CCA anticodon as was described for Mod5 IPTase. This TRIT1 deficiency can be countered by over-expression. We propose a model of tRNA-i6A37 identity selection in eukaryotes that includes sensitivity to substrates with YYA anticodons.\n\nAUTHOR SUMMARYtRNA isopentenyltransferases (IPTases) are tRNA modification enzymes that are conserved in bacteria and eukaryotes. They add an isopentenyl group to the Adenosine base at position 37, adjacent to the anticodon of specific subsets of tRNAs that decode codons that begin with Uridine. This modification stabilizes the otherwise weak adjacent codon-anticodon basepair and increases the efficiency of decoding of the corresponding codons of the genetic code. IPTases belong to a group of enzymes that modify both cytoplasmic and mitochondrial tRNAs of eukaryotic cells. Interestingly, during evolution there were changes in the way that IPTases are targeted to mitochondria as well as changes in the relative numbers and identities of IPTase tRNA substrates in the cytoplasm vs. mitochondria, the latter consistent with phenotypic consequences of IPTase deficiencies in fission and budding yeasts, and mammals. Pathogenic mutations to human IPTase (TRIT1) cause mitochondrial insufficiency and neurodevelopmental disease, principally due to decreased modification of the mt-tRNA substrates. In this study, we identify the way human TRIT1 is targeted to mitochondria. We also show that TRIT1 exhibits a tRNA anticodon identity-specific substrate sensitivity. The work leads to new understanding of the IPTases and the variable codon identities of their tRNA substrates found throughout nature.

genetics↗