Biology subjects

Adel, A.

Publications and source records attributed to Adel, A..

8 recordsLinked to original sources

bioRxiv2026

First detection of High pathogenicity Avian Influenza A(H5N1) Clade 2.3.4.4b Genotype EA-2024-DI.2.1 in Egypt associated with migratory wild birds

High pathogenicity avian influenza (HPAI) H5 clade 2.3.4.4b is the main driver of the ongoing unprecedented global panzootic. The recently emerged HPAI H5N1 clade 2.3.4.4b genotype EA-2024-DI.2.1 has become predominant in Europe, with migratory wild birds, particularly waterfowl, playing a major role in its dissemination. Egypt lies along major Afro-Eurasian migratory flyways, which have historically played an important role in the introduction of emerging H5Nx viruses into the country. In this study, targeted surveillance was conducted on 416 wild birds offered for sale in in live bird markets (LBMs) and roadside trading points in northern Egypt, mainly in Damietta and Port Said. Of these, 118 birds showing mild clinical signs were examined post-mortem and lung and tracheal tissues were collected, while oropharyngeal and cloacal swabs were collected from apparently healthy birds. Avian influenza virus was detected by RT-qPCR in 22 wild birds, all from tissue samples, whereas all swabs from apparently healthy birds were negative. Waterfowl accounted for 16 of the 22 positive birds (72.7%), with Eurasian teal showing the lowest Ct values (21-25). Phylogenetic and whole-genome analyses showed that the sequenced wild-bird viruses clustered within the recently emerged EA-2024-DI.2.1 sub-lineage and were closely related to contemporary European viruses. Compared with the EA-2021-AB genotype currently circulating in Egyptian poultry, the EA-2024-DI.2.1 viruses showed several HA amino acid differences, including A83D, L104M and T195A. These findings provide evidence for the introduction of EA-2024-DI.2.1 into Egypt through migratory wild birds and highlight the importance of continued genomic surveillance at the wild bird domestic poultry interface and antigenic evaluation against vaccines currently used in Egypt.

molecular biology↗

bioRxiv2026

A cuffed CRISPR guide RNA for microRNA activity-dependent genome editing

Cells in multicellular eukaryotic systems are diverse biological units, with characteristics and functions determined by their molecular profiles. CRISPR-Cas9 genome editing has been widely used across biology to modulate gene expression and study gene function. However, there is currently no versatile and scalable method for editing a cells genome in response to endogenous cellular signals. Here, we report the engineering of a CRISPR guide RNA that efficiently confers genome editing in response to the catalytic activity of a target microRNA (miRNA) within a cell. miRNAs are short non-coding RNAs that are widely conserved across eukaryotes and can cleave their target RNA through almost perfect base pairing. In mammals, miRNAs are largely involved in development and homeostasis as well as disease progression and developmental disorders. To leverage these properties for genome editing, we developed a cuffed guide RNA (cgRNA) which is composed of a permutated order of sequence domains from the commonly used single guide RNA (sgRNA). These permutated domains were then concatenated with a miRNA target sequence, yielding a warped guide RNA that is inactive until cleaved by a complementary miRNA. We demonstrated that cgRNA enabled efficient miRNA activity-dependent genome editing in human and mouse cell lines. Biochemical and structural analyses revealed three stages of inhibition of the CRISPR genome-editing pathway for unprocessed cgRNA. Utilizing a lentiviral library of cgRNAs containing miRNA targets covering mouse genome-wide miRNAs, we identified miRNA cleavage activities and their sequence specificities in mouse embryonic stem cells and during smooth muscle cell differentiation. Furthermore, we showed that endogenous mRNA expression could be irreversibly recorded into a DNA sequence using a cgRNA targeted by a synthetic miRNA repeat. cgRNA is a simple, robust, miRNA activity-gated genome editing system that could facilitate the development of cell state-specific genome editing, the mapping of miRNA activity and gene expression landscapes, and the recording of molecularly determined cell states during the long-term progression of multicellular systems.

bioengineering↗

bioRxiv2025

Cognitive ethology of nest building in a shell-dwelling cichlid

Across animal taxa, nest-building behavior is performed using a generalizable and flexible mental representation of an action sequence - a schema. In order to accomplish its goal (a stable nest), the brain appears to compare intermediate steps in the process to stored mental images, or templates. Deviations from these templates drive progress, preferences, and corrections in the execution of this behavior. The stereotypy vs. plasticity of both schema and mental templates have rarely been defined in an experimentally accessible system. Here we investigated nest building by the cichlid Lamprologus ocellatus, a fish species that manipulates abandoned snail shells to build shelters for breeding and protection. We find that nest building is composed of a sequence of behaviors that are tied together by a series of stimulus-response loops, allowing for restarts and shortcuts as the behavioral program unfolds. The attraction to a shell object is innate, as is the final appearance of the nest. The behavior in an inexperienced animal is initially uncoordinated, but is fine-tuned by repeated building opportunities. Shells need to conform to rigid geometric criteria in order to be acceptable as a potential home. Nest building is accompanied by focused neural activity in brain regions homologous to the mammalian hippocampus and neocortex. In conclusion, we have uncovered the constraints and flexibility of cognitive template matching underlying an instinctive, goal-directed behavior.

animal behavior and cognition↗

bioRxiv2023

Brood care in shell-dwelling cichlids is timed by independent maternal and larval clocks

Successful brood care requires a finely tuned interplay between caregiving parent and offspring. Cichlids are a diverse group of teleost fish known for their extensive parental care of altricial young. Female Lamprologus ocellatus lay their eggs in the protective confines of an abandoned snail shell, where they raise them to free-swimming larvae. Here we investigated whether the transition to larval independence is driven by the behavior of the mother, the offspring, or an interaction between the two. Using 3D printed shells with a window, we were able to observe the behavior of both mother and offspring inside the nest using automated object detection and tracking. We found that, once hatched, the larvae remain in the deep chambers of the shell, and at 9 dpf, actively emerge from the shell during the day. An inversion of larval phototactic behavior from dark- to light-seeking leads up to this emergence. Removal of the mother causes premature emergence of the larvae by a few days. The natural schedule (emergence at 9 dpf) is restored if the larvae are supplied with fresh water in the mothers absence. In cross-fostering experiments, we found that swapping out the mothers own clutch for older larvae forces a delay in emergence, as the foster mother prevents the larvae from leaving at 9 dpf. We conclude that larval and maternal behavior are each controlled by independent internal clocks, which, although normally synchronized, can be experimentally manipulated and brought into conflict. This study has thus revealed an innate sequence of behavioral adaptations that orchestrate brood care in shell-dwelling cichlids.

evolutionary biology↗

bioRxiv2023

Emergence of the Novel Infectious bursal disease viruse Variant in Vaccinated Poultry Flocks in Egypt

Infectious bursal disease viruses (IBDVs) have a profound impact on poultry production worldwide, directly causing mortality rates of up to 100%, and indirectly through their immunosuppressive effects. Since the emergence of the antigenically modified very virulent IBDV (vvIBDV) in Egypt in late 1999, the country has experienced recurrent outbreaks with high mortality rates and typical vvIBDV gross lesions. However, a notable shift occurred in 2023, characterized by a substantial increase in reported subclinical IBDV cases exhibiting atrophied bursa and associated immunosuppression. To assess the field situation, we examined samples from 21 farms in 2023 and 18 farms from 2021 and 2022, all of which experienced IBD outbreaks based on clinical diagnosis. These samples were submitted to our laboratory for confirmatory testing and subsequently subjected to VP2-HVR sequencing. Phylogenetic analysis revealed that all samples collected in 2021 and 2022 clustered with classical virulent strains and very virulent IBDV. In 2023, one sample clustered with the Egyptian vvIBDV, while one sample clustered with classic virulent IBDV, and the remaining 2023 samples clustered with the Chinese novel variant IBDV (nVarIBDV). The alignment of deduced amino acid sequences for VP2 revealed that all Egyptian classic virulent strains were similar to the Winterfield or Leukert strains. In contrast, vvIBDV strains exhibited two out of the three typical residues found in Egyptian antigenically atypical vvIBDV, namely Y220F and G254S, but not A321T, and one sample was identical to the European vvIBDV (emerged in 1989). Meanwhile, all variant strains recognized in the present study exhibited typical residues found in variant IBDV, in addition to the three conserved amino acid residues found only in Chinese variant IBDVs. However, all Egyptian variant strains showed a mutation at position 321 (321V), which represents the most exposed part of the capsid and is known to have a massive impact on IBDV antigenicity, with the exception of one sample that had 318G instead. This report highlights the emergence of a new variant IBDV clustered with the Chinese new variant in Egypt, causing bursa atrophy and spreading subclinically in broiler farms over a wide geographic distance, resulting in massive economic losses due to immunosuppression.

microbiology↗

bioRxiv2023

Reinstatement of CDX2 as a differentiation therapy for colorectal cancers

Despite advances in artificial intelligence (AI) within cancer research, its application toward realizing differentiation therapy in solid tumors remains limited. Using colorectal cancer (CRC) as a model, we developed a machine learning (ML) framework, CANDiT (Cancer Associated Nodes for Differentiation Targeting), to selectively induce differentiation and death of cancer stem cells (CSCs)--a key obstacle to durable response. Centering on one node, CDX2, a master differentiation factor lost in high-risk, poorly differentiated CRCs, we built a transcriptomic network to identify therapeutic strategies for CDX2 restoration. Network-based prioritization identified PRKAB1, a stress polarity sensor, as a top target. A clinical-grade PRKAB1 agonist reprogrammed transcriptional networks, induced crypt differentiation, and selectively eliminated CDX2-low CSCs in CRC cell lines, xenografts and patient-derived organoids (PDOs). Multivariate analyses in PDOs revealed a strong therapeutic index, linking efficacy (IC) to the biomarker-defined CDX2-low state. A 50-gene response signature--derived from an integrated analyses of all three models and trained across multiple datasets--revealed that CDX2 restoration therapy may translate into a [~]50% reduction in recurrence and mortality risk. Mechanistically, treatment activated a differentiation-associated stress polarity signaling axis while dismantling Wnt and YAP-driven stemness programs essential to CSC survival. Thus, CANDiT offers a scalable path to CSC-directed therapy in solid tumors by translating transcriptomic vulnerabilities into precision treatments. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=174 SRC="FIGDIR/small/557628v4_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@16eeb1eorg.highwire.dtl.DTLVardef@10e308borg.highwire.dtl.DTLVardef@9512f0org.highwire.dtl.DTLVardef@10e74eb_HPS_FORMAT_FIGEXP M_FIG C_FIG One sentence summaryIn this work, Sinha et al. introduce a machine learning-guided framework to identify and target transcriptomic vulnerabilities in colorectal cancer, demonstrating that differentiation therapy selectively eliminates cancer stem cells and reduces recurrence risk. HighlightsO_LIAn ML framework (CANDiT) identifies target for differentiation therapy for CRCs C_LIO_LITherapy induces crypt differentiation and CSC-specific cytotoxicity C_LIO_LICDX2-low state predicts therapeutic response; restoration improves prognosis C_LIO_LITherapy dismantles stemness via reactivation of stress polarity signaling C_LI

cancer biology↗

bioRxiv2023

A multi-kingdom genetic barcoding system for precise target clone isolation

Clonal heterogeneity underlies diverse biological processes, including cancer progression, cell differentiation, and microbial evolution. Cell tagging strategies with DNA barcodes have recently enabled analysis of clone size dynamics and clone-restricted transcriptomic landscapes of heterogeneous populations. However, isolating a target clone that displays a specific phenotype from a complex population remains challenging. Here, we present a new multi-kingdom genetic barcoding system, CloneSelect, in which a target cell clone can be triggered to express a reporter gene for isolation through barcode-specific CRISPR base editing. In CloneSelect, cells are first barcoded and propagated so their subpopulation can be subjected to a given experiment. A clone that shows a phenotype or genotype of interest at a given time can then be isolated from the initial or subsequent cell pools stored throughout the experimental timecourse. This novel CRISPR-barcode genetics platform provides many new ways of analyzing and manipulating mammalian, yeast, and bacterial systems. TeaserA multi-kingdom CRISPR-activatable barcoding system enables the precise isolation of target barcode-labeled clones from a complex cell population.

synthetic biology↗

bioRxiv2022

License to cut: Smart RNA guides for conditional control of CRISPR-Cas9

The Cas9 enzyme is a programmable endonuclease, whose target sequence is directed by a companion RNA guide. Cas9 and RNA guides have revolutionized biology, enabling facile editing of the genome in almost all organisms. Controlling where and when Cas9 and the guide operate is indispensable for many fields ranging from developmental biology to therapeutics, but it remains a challenge. Most methods focus on controlling Cas9 with physico-chemical means (which lack finesse, precision or multiplexing), or transcriptional tools (which are slow and difficult to design). Rather than directly engineering Cas9, engineering the RNA guide itself has emerged as a more general and potent way to manage the activity of Cas9. Here we report smart RNA guides that are conditionally activated by the presence of a specific RNA opener. Contrary to most previous approaches, the design affords ample freedom as spacer and the opener are independent. We demonstrate this flexibility by operating SmartGuides activated by a panel of miRNA relevant for human health, and by composing SmartGuides in Boolean logic circuits. Lastly, we test the SmartGuides in mammalian cells - validating the basics tenets of the design, but also highlighting the challenges that remain to be lifted for in-vivo operation.

bioengineering↗