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ArXiv Oct 2023Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level...
Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology in order to lend a new perspective on the evolved designs of cells' underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and behavioral patterns describe reaction network function. Applying this pattern language to the E. coli central metabolic reaction network, the yeast pheromone response signaling network, and other examples lends new insights into these systems.
PubMed: 37873010
DOI: No ID Found -
International Journal of Molecular... Apr 2024The Japanese pine sawyer serves as the primary vector for pine wilt disease, a devastating pine disease that poses a significant threat to the sustainable development...
The Japanese pine sawyer serves as the primary vector for pine wilt disease, a devastating pine disease that poses a significant threat to the sustainable development of forestry in the Eurasian region. Currently, trap devices based on informational compounds have played a crucial role in monitoring and controlling the population. However, the specific proteins within involved in recognizing the aforementioned informational compounds remain largely unclear. To elucidate the spatiotemporal distribution of chemosensory-related genes, this study conducted neural transcriptome analyses to investigate gene expression patterns in different body parts during the feeding and mating stages of both male and female beetles. The results revealed that 15 genes in the gustatory receptor (GR) gene family exhibited high expression in the mouthparts, most genes in the odorant binding protein (OBP) gene family exhibited high expression across all body parts, 22 genes in the odorant receptor (OR) gene family exhibited high expression in the antennae, a significant number of genes in the chemosensory protein (CSP) and sensory neuron membrane protein (SNMP) gene families exhibited high expression in both the mouthparts and antennae, and 30 genes in the ionotropic receptors (IR) gene family were expressed in the antennae. Through co-expression analyses, it was observed that 34 genes in the IR gene family were co-expressed across the four developmental stages. The Antenna IR subfamily and IR8a/Ir25a subfamily exhibited relatively high expression levels in the antennae, while the Kainate subfamily, NMDA subfamily, and Divergent subfamily exhibited predominantly high expression in the facial region. is expressed only during the feeding stage of , the gene exhibits specific expression in male beetles, the gene exhibits specific expression during the feeding stage in male beetles, the and genes exhibit specific expression during the feeding stage in female beetles, and is expressed only during two developmental stages in male beetles and during the mating stage in female beetles. The IR gene family exhibits gene-specific expression in different spatiotemporal contexts, laying the foundation for the subsequent selection of functional genes and facilitating the full utilization of host plant volatiles and insect sex pheromones, thereby enabling the development of more efficient attractants.
Topics: Animals; Coleoptera; Male; Transcriptome; Female; Receptors, Odorant; Insect Proteins; Gene Expression Profiling; Arthropod Antennae; Receptors, Ionotropic Glutamate
PubMed: 38674138
DOI: 10.3390/ijms25084553 -
Pathogens (Basel, Switzerland) Nov 2023Pathogens can influence the physiology and behavior of both animal and plant hosts in a manner that promotes their own transmission and dispersal. Recent research... (Review)
Review
Pathogens can influence the physiology and behavior of both animal and plant hosts in a manner that promotes their own transmission and dispersal. Recent research focusing on insects has revealed that these manipulations can extend to the production of pheromones, which are pivotal in chemical communication. This review provides an overview of the current state of research and available data concerning the impacts of bacterial, viral, fungal, and eukaryotic pathogens on chemical communication across different insect orders. While our understanding of the influence of pathogenic bacteria on host chemical profiles is still limited, viral infections have been shown to induce behavioral changes in the host, such as altered pheromone production, olfaction, and locomotion. Entomopathogenic fungi affect host chemical communication by manipulating cuticular hydrocarbons and pheromone production, while various eukaryotic parasites have been observed to influence insect behavior by affecting the production of pheromones and other chemical cues. The effects induced by these infections are explored in the context of the evolutionary advantages they confer to the pathogen. The molecular mechanisms governing the observed pathogen-mediated behavioral changes, as well as the dynamic and mutually influential relationships between the pathogen and its host, are still poorly understood. A deeper comprehension of these mechanisms will prove invaluable in identifying novel targets in the perspective of practical applications aimed at controlling detrimental insect species.
PubMed: 38003813
DOI: 10.3390/pathogens12111350 -
Data in Brief Aug 2023Like many other organisms, ciliates communicate and interact socially via diffusible chemical signals, named pheromones, that are functionally associated with a genetic...
Like many other organisms, ciliates communicate and interact socially via diffusible chemical signals, named pheromones, that are functionally associated with a genetic mating-type mechanism of cell self/not-self recognition. In species, pheromones form species-specific families of small, globular, and disulfide-rich proteins folding into exclusively helical secondary structures. Each is specified by one of a series of high-multiple alleles that are inherited in Mendelian fashion with relationships of co-dominance at the so-called genetic locus of the cell transcriptionally inert micronuclear genome, and expressed in the transcriptionally active macronuclear genome as individual DNA molecules in which the central coding region is flanked by 5'-leader and 3'-trailer noncoding regions ending with CA/TG telomeric repeats. In , a cosmopolitan marine species with a long tradition in the study of ciliate mating systems and breeding patterns, oligonucleotides specific to amino acid sequences of pheromones E-1 and E-α were previously used to clone and sequence a first set of four structurally distinct macronuclear () pheromone coding genes, and , from two interbreeding strains, L-2D and POR-73. The use of these oligonucleotides in PCR amplifications of macronuclear DNA preparations from three other interbreeding strains, ES10, Fava4 and MN4, has now resulted in the characterization of a second set of eight new pheromone coding genes, ec- and . Multiple alignment between previously and newly determined pheromone-gene sequences reinforces the concept that the pheromone-gene family includes two sub-families, which likely reflect a duplication of the micronuclear gene locus and represent an apomorphic trait of the clade. Members of one sub-family (each identified with a Greek letter) show a 500-bp 5'-leader noncoding region rich in AGGA/AGGGA repetitions, and encode 56-amino acid pheromones with eight conserved Cys residues. Members of the other sub-family (each identified with an Arabic numeral) show an 800-bp 5'-leader noncoding region without AGGA/AGGGA repetitions, and encode 45-amino acid pheromones with ten conserved Cys residues.
PubMed: 37538957
DOI: 10.1016/j.dib.2023.109430 -
International Journal of Molecular... Jul 2023species are known for their ability to form biofilms, which contributes to their survival in extreme environments and involvement in persistent bacterial infections,... (Review)
Review
species are known for their ability to form biofilms, which contributes to their survival in extreme environments and involvement in persistent bacterial infections, especially in the case of multi-drug-resistant strains. This review aims to provide a comprehensive understanding of the mechanisms underlying biofilm formation in clinically important species such as and the less studied but increasingly multi-drug-resistant , and explores potential strategies for their eradication. Biofilm formation in involves a complex interplay of genes and virulence factors, including gelatinase, cytolysin, Secreted antigen A, pili, microbial surface components that recognize adhesive matrix molecules (MSCRAMMs), and DNA release. Quorum sensing, a process of intercellular communication, mediated by peptide pheromones such as Cob, Ccf, and Cpd, plays a crucial role in coordinating biofilm development by targeting gene expression and regulation. Additionally, the regulation of extracellular DNA (eDNA) release has emerged as a fundamental component in biofilm formation. In , the autolysin N-acetylglucosaminidase and proteases such as gelatinase and serin protease are key players in this process, influencing biofilm development and virulence. Targeting eDNA may offer a promising avenue for intervention in biofilm-producing infections. Overall, gaining insights into the intricate mechanisms of biofilm formation in may provide directions for anti-biofilm therapeutic research, with the purpose of reducing the burden of -associated infections.
Topics: Enterococcus; Biofilms; Enterococcus faecalis; Quorum Sensing; Gelatinases; Bacterial Proteins
PubMed: 37511337
DOI: 10.3390/ijms241411577 -
Annual Review of Entomology Jan 2024Dengue, caused by the dengue virus, is the most widespread arboviral infectious disease of public health significance globally. This review explores the communicative... (Review)
Review
Dengue, caused by the dengue virus, is the most widespread arboviral infectious disease of public health significance globally. This review explores the communicative function of olfactory cues that mediate host-seeking, egg-laying, plant-feeding, and mating behaviors in and , two mosquito vectors that drive dengue virus transmission. has adapted to live in close association with humans, preferentially feeding on them and laying eggs in human-fabricated water containers and natural habitats. In contrast, is considered opportunistic in its feeding habits and tends to inhabit more vegetative areas. Additionally, the ability of both mosquito species to locate suitable host plants for sugars and find mates for reproduction contributes to their survival. Advances in chemical ecology, functional genomics, and behavioral analyses have improved our understanding of the underlying neural mechanisms and reveal novel and specific olfactory semiochemicals that these species use to locate and discriminate among resources in their environment. Physiological status; learning; and host- and habitat-associated factors, including microbial infection and abundance, shape olfactory responses of these vectors. Some of these semiochemicals can be integrated into the toolbox for dengue surveillance and control.
Topics: Humans; Animals; Dengue; Aedes; Ecology; Pheromones
PubMed: 37625116
DOI: 10.1146/annurev-ento-020123-015755 -
Neuroscience and Biobehavioral Reviews Jan 2024Animals respond to changes in the environment which affect their internal state by adapting their behaviors. Social isolation is a form of passive environmental stressor... (Review)
Review
Animals respond to changes in the environment which affect their internal state by adapting their behaviors. Social isolation is a form of passive environmental stressor that alters behaviors across animal kingdom, including humans, rodents, and fruit flies. Social isolation is known to increase violence, disrupt sleep and increase depression leading to poor mental and physical health. Recent evidences from several model organisms suggest that social isolation leads to remodeling of the transcriptional and epigenetic landscape which alters behavioral outcomes. In this review, we explore how manipulating social experience of fruit fly Drosophila melanogaster can shed light on molecular and neuronal mechanisms underlying isolation driven behaviors. We discuss the recent advances made using the powerful genetic toolkit and behavioral assays in Drosophila to uncover role of neuromodulators, sensory modalities, pheromones, neuronal circuits and molecular mechanisms in mediating social isolation. The insights gained from these studies could be crucial for developing effective therapeutic interventions in future.
Topics: Animals; Humans; Drosophila melanogaster; Drosophila; Social Isolation; Loneliness; Sleep
PubMed: 38061597
DOI: 10.1016/j.neubiorev.2023.105504 -
Cellular and Molecular Life Sciences :... Jul 2023Male moths utilize their pheromone communication systems to distinguish potential mates from other sympatric species, which contributes to maintaining reproductive...
Male moths utilize their pheromone communication systems to distinguish potential mates from other sympatric species, which contributes to maintaining reproductive isolation and even drives speciation. The molecular mechanisms underlying the evolution of pheromone communication systems are usually studied between closely-related moth species for their similar but divergent traits associated with pheromone production, detection, and/or processing. In this study, we first identified the functional differentiation in two orthologous pheromone receptors, OR14b, and OR16, in four Helicoverpa species, Helicoverpa armigera, H. assulta, H. zea, and H. gelotopoeon. To understand the substrate response specificity of these two PRs, we performed all-atom molecular dynamics simulations of OR14b and OR16 based on AlphaFold2 structural prediction, and molecular docking, allowing us to predict a few key amino acids involved in substrate binding. These candidate residues were further tested and validated by site-directed mutagenesis and functional analysis. These results together identified two hydrophobic amino acids at positions 164 and 232 are the determinants of the response specificity of HarmOR14b and HzeaOR14b to Z9-14:Ald and Z9-16:Ald by directly interacting with the substrates. Interestingly, in OR16 orthologs, we found that position 66 alone determines the specific binding of Z11-16:OH, likely via allosteric interactions. Overall, we have developed an effective integrated method to identify the critical residues for substrate selectivity of ORs and elucidated the molecular mechanism of the diversification of pheromone recognition systems.
Topics: Animals; Male; Receptors, Pheromone; Molecular Docking Simulation; Pheromones; Moths
PubMed: 37421463
DOI: 10.1007/s00018-023-04837-1 -
Frontiers in Endocrinology 2023Neuropeptides are involved in almost all physiological activities of insects. Their classification is based on physiological function and the primary amino acid... (Review)
Review
Neuropeptides are involved in almost all physiological activities of insects. Their classification is based on physiological function and the primary amino acid sequence. The pyrokinin (PK)/pheromone biosynthesis activating neuropeptides (PBAN) are one of the largest neuropeptide families in insects, with a conserved C-terminal domain of FXPRLamide. The peptide family is divided into two groups, PK1/diapause hormone (DH) with a WFGPRLa C-terminal ending and PK2/PBAN with FXPRLamide C-terminal ending. Since the development of cutting-edge technology, an increasing number of peptides have been sequenced primarily through genomic, transcriptomics, and proteomics, and their functions discovered using gene editing tools. In this review, we discussed newly discovered functions, and analyzed the distribution of genes encoding these peptides throughout different insect orders. In addition, the location of the peptides that were confirmed by PCR or immunocytochemistry is also described. A phylogenetic tree was constructed according to the sequences of the receptors of most insect orders. This review offers an understanding of the significance of this conserved peptide family in insects.
Topics: Humans; Animals; Phylogeny; Amino Acid Sequence; Insecta; Neuropeptides; Pheromones
PubMed: 38161974
DOI: 10.3389/fendo.2023.1274750 -
Nature Communications May 2024Currently, there is no pesticide available for the selective control of the pine processionary moth (Thaumetopoea pityocampa-specific), and conventional methods...
Currently, there is no pesticide available for the selective control of the pine processionary moth (Thaumetopoea pityocampa-specific), and conventional methods typically rely on mechanical techniques such as pheromone traps or broad-spectrum larvicidal chemicals. As climate change increases the range and dispersion capacity of crop and forest pests, outbreaks of the pine processionary occur with greater frequency and significantly impact forestry and public health. Our study is carried out to provide a T. pityocampa-specific pesticide targeting the Allatostatin Type-C Receptor (AlstR-C). We use a combination of computational biology methods, a cell-based screening assay, and in vivo toxicity and side effect assays to identify, for the first time, a series of AlstR-C ligands suitable for use as T. pityocampa-specific insecticides. We further demonstrate that the novel AlstR-C targeted agonists are specific to lepidopteran larvae, with no harmful effects on coleopteran larvae or adults. Overall, our study represents an important initial advance toward an insect GPCR-targeted next-generation pesticide design. Our approach may apply to other invertebrate GPCRs involved in vital metabolic pathways.
Topics: Animals; Moths; Insecticides; Larva; Insect Proteins; Receptors, G-Protein-Coupled; Humans; Ligands; Neuropeptides
PubMed: 38730017
DOI: 10.1038/s41467-024-48156-w