Journal of Biosciences最新文献

Polymerization of branched actin networks by the ARP2/3 complex plays a critical role in diverse cellular processes. ARP2/3 activity is tightly controlled by the upstream CDC-42 GTPase and effectors such as the Wiscott-Aldrich syndrome protein (N-WASP/Wiscott-Aldrich Syndrome Protein (WSP-1)) and members of the F-BAR containing transducer of CDC-42-dependent actin assembly (TOCA) protein family. While the mechanisms governing WASP/N-WASP (neural-WASP) functioning are well understood, the regulatory dynamics of TOCA proteins at the cell cortex remain poorly characterized. Here, using the Caenorhabditis elegans zygote as a model system, we investigated the role of cortical F-actin structures - both branched and linear - in modulating surface dynamics of CeTOCA-1, the nematode ortholog of mammalian TOCA-1. In our in silico analysis, iPTM values associated with the interaction between different domains of CeTOCA-1 and CDC-42 suggested that while the HR-1 domain is essential for this interaction, the SH3 domain is dispensable for complex formation between the two proteins. Further, we experimentally disrupted ARP2/3 and CYK-1/ formin-polymerized F-actin structures in C. elegans zygotes to examine the role of cortical F-actin on CeTOCA-1 assembly dynamics and biophysical properties. Co-localization studies revealed a preferential association between CeTOCA-1 and the pool of F-actin structures polymerized by ARP2/3. Disruption of ARP2/3 led to the formation of larger CeTOCA-1 clusters, prolonged cluster lifetime on the cell surface, and reduced cluster mobility. These findings suggest that distinct F-actin structures play specialized roles in mediating plasma membrane interactions and regulating surface dynamics of CeTOCA-1 clusters.

YAP and TAZ are downstream effectors of the Hippo signaling pathway, known to shuttle between the cytoplasm and nucleus, where they primarily function as transcriptional coactivators. Although their nuclear role has been well characterized, the non-transcriptional functions of YAP/TAZ remain poorly understood. In this study, we report that YAP/TAZ localize to the metaphase spindle in a microtubule-dependent manner. Specifically, we demonstrate that YAP interacts with α-tubulin via its WW domain. Notably, while the spindle localization of YAP/TAZ does not affect the mechanics of mitotic cell division, it does influence the distribution of YAP/TAZ protein levels between the resulting daughter cells. These findings reveal a novel, nontranscriptional role for YAP/TAZ during mitosis.

Psoriasis (PS) is one of the comorbidities of type 2 diabetes mellitus (T2DM). The molecular processes leading to the T2DM-PS comorbidity are not fully understood. Recently, six genes (IL23R, IL12B, IL23A, GSK3B, PTPN1, and STX4) were identified as associated with the T2DM-PS comorbidity. Both diseases are multi-genic disorders with the involvement of thousands of genes. We used an integrative approach by sourcing the genes associated with T2DM and PS from the DISGENET database, the genes associated with the T2DM-PS comorbidity from the literature, the differentially expressed genes in a PS blood sample dataset (GSE55201), and the differentially expressed genes in each of three T2DM gene expression datasets of blood samples (GSE69528, GSE15932, and GSE21321). We constructed pathway networks by importing the enriched pathways of these genes into a biological network simulator software. Simulations of these pathway networks were carried out using the average expression values of cases and controls separately in each T2DM dataset until a steady state was reached. Finally, pathway enrichment analysis of the perturbed genes revealed the perturbed pathways in the T2DM condition in the three datasets of T2DM patients. Five perturbed pathways were common among the three T2DM datasets: the NF-κB signaling pathway, necroptosis pathway, NOD-like receptor signaling pathway, TNF signaling pathway, and Toll-like receptor signaling pathway. The involvement of these pathways in PS is reported in the literature, thereby suggesting potential susceptibility to PS arising in the T2DM condition. This approach offers a holistic view of T2DM conditions and the pathways reported in individual studies with potential susceptibility to PS.

Animals exhibit behavioural responses to environmental stimuli. To date, various experimental assays have been conducted to investigate the molecular and neural mechanisms underlying behavioural responses in Caenorhabditis elegans. However, behavioural outcomes can vary even under the same stimulus due to factors such as past experience, individual circumstances, and modifications in behavioural assay procedures, which complicate the interpretation of results. In this study, we focussed on the composition of the behavioural assay media and compared the behaviours of C. elegans in response to temperature and odour stimuli using three commonly used media: nematode growth medium (NGM), thermotaxis (TTX), and chemotaxis (Chemo) assay media. Our results demonstrated that in thermotaxis, C. elegans exhibited stable behavioural decisions across all examined media. However, the population of worms reaching the preferable areas was smaller in Chemo and TTX media compared with NGM due to prolonged exploration period and reduced migration speed. By contrast, in chemotaxis, we did not observe significant differences across the tested media. This study provides insights into the significant effects on C. elegans behaviour caused by the modifications of the behavioural assay media and emphasises the importance of further studies to explore the detailed neural mechanisms that regulate animal behaviour under diverse environmental factors.

In an earlier editorial (Borges 2022), I had talked about the keystone concept formulated by Robert Paine. This important concept (Paine 1966) emphasised the idea that biodiversity is maintained by a top-down process in which the removal of a keystone predator would allow the unchecked proliferation of herbivores; during this process a dominant herbivore might outcompete another herbivore species, resulting in the removal of the lesser competitor from the community and a reduction in overall species richness (i.e., the number of species present). The keystone predator concept is well-established in community ecology. Are there keystone molecules whose presence can influence the diversity of communities? At an extreme, of course, one may say that oxygen is a most important molecule whose presence has fuelled the diversification of autotrophs such as diatoms and plants, and hence the flowering of life. A key feature of Paine's keystone concept is that the species must exert an impact that is disproportionate to its abundance (Power et al. 1996). By this definition, oxygen, although vital to all life, would fail to be recognised as a keystone chemical or molecule in species communities. Are there chemical compounds that can govern species diversity within trophic levels of an ecological community, as defined by Paine's keystone concept?

Abiotic stresses such as heat, drought, and salinity significantly impact rice cultivation by affecting its yield and quality. Identifying molecular candidates that confer resistance or tolerance to these stresses is crucial. This study identifies unique and overlapping molecular signatures mediated by coding and non-coding RNAs during heat, drought, and salt stresses in rice. It uses RNA-Seq data from 66 rice samples, including those treated with heat, drought, and salt stresses, to identify both unique and shared differentially expressed mRNAs and long non-coding RNAs (lncRNAs). Analyses reveal key regulatory hubs in transcriptional networks, particularly the ERF, DOF, and MYB family transcription factors, which are central to abiotic stress responses. Stress-specific competing endogenous RNA networks reveal conserved regulatory elements that coordinate these responses. Overlap analysis identifies 637 shared mRNAs and 76 lncRNAs among the three stresses. These findings enhance our understanding of the molecular mechanisms underlying stress resilience in rice and provide a foundation for developing stress-resistant cultivars.

Whole-brain calcium imaging combined with multicolor cell identification is a revolutionary technique for elucidating structure-function relationships in the neural network of the nematode Caenorhabditis elegans. Existing genetically encoded calcium indicator (GCaMP) (for calcium imaging) + neuronal polychromatic atlas of landmarks for whole-brain imaging (NeuroPAL) (for cell identification) strains, however, exhibit suboptimal behavioral and neural responses to external stimuli, at least under certain conditions. To address this, we established a new strain of GCaMP + NeuroPAL, KDK94, and found that this new strain showed improved behavioral and/or neural responses to the repulsive odor 2-nonanone and electric stimuli compared with existing strains. Whole-brain calcium and NeuroPAL imaging using the new strain with several technical improvements revealed that in addition to the previously known amphid sensory neuron (ASH) and amphid wing 'B' cells (AWB) sensory neurons, the AWC^OFF neuron responds to both stepwise increases in the water phase and subtle gradual increases in the air phase of 2-nonanone concentration. The improvement of the whole-brain imaging system with cell identification and the transgenic strain for the system may provide new insights into the neural circuit dynamics underlying the basic brain functions, such as learning, decisionmaking, and emotion, of C. elegans.

Marine fungi are the leading producers of bioactive metabolites with medicinal properties against several diseases. However, since marine species survive in diverse climates, they are usually difficult to culture in laboratory setups, making them challenging to study. This study aimed to optimize culture conditions for marine fungi and evaluate the inhibitory action of the marine extract on primary pro-inflammatory cytokines. Culture conditions for marine fungi were optimized using biomass production, hyphal density, and radial extension, considering temperature and humidity. The study isolated a new Aspergillus fumigatus variant, AFK11 (GenBank accession no. JX022941), showing 96% similarity to reported strains. Ethyl acetate extracts of AFK11 significantly inhibited primary pro-inflammatory cytokines, tumor necrosis factor-α, and interleukin-6, in a dose-dependent manner. This research highlights the successful laboratory culture and anti-inflammatory potential of the new strain of Aspergillus, AFK11, emphasizing the need for further research for its potential in various other diseases such as cancer.

Flying fishes (Exocoetidae) are a highly specialized group of Beloniformes, with 4 subfamilies, 7 genera, and 78 species. However,only a small number of species of flying fishes have the mitochondrial genome described sof ar. Considering the importance of mitogenomes in evolution, in this study we aimed to expand the description of mitochondrial genomes and the phylogenetic relationships of Exocoetidae. We used publicly available DNA-Seq libraries to assemble the mitochondrial genomes of 7 species of flying fishes. The mitochondrial genomes of Exocoetidae showed conserved features among all species. With 22 tRNAs, 2 rRNAs, and 13 protein-coding genes, they share common features among vertebrates.Cheilopogon was reconstructedaspolyphyletic, with four clades, which reinforces previous studies that recovered Cheilopogon as non-monophyletic.Werecoveredallfour subfamilies as monophyletic,with Parexocoetinae as the sister group of all other subfamilies.The genetic distance between Exocoetidae species was two times smaller than the genetic distance among the Hyporhamphus species, indicating a low genetic divergence in the family. Hereby, this study expanded the knowledge of mitochondrial genome features and presented one of the most comprehensive mitochondrial genome datasets used for studying flying fishestodate. This was achievable using publicly available data, reinforcing the importanceof the re-use of such data in the fields of mitogenomics and phylogenetics.

'Tortured phrases' (TPs) are a linguistic misrepresentation of established jargon or technical terms, and can thus be considered to be factual errors. By synonymizing jargon, TPs reduce the clarity of the scientific message. Given their unique nature, a growing literature on TPs is emerging, a summary of which is provided in this article. Supplementing this growing body of evidence, a curiously unique dataset is presented, namely, of 'sodium hypocrite', which is meant to represent sodium hypochlorite. Examples of TPs in the biological sciences are introduced. Papers that contain 'tortured phrases' should ideally be corrected to accurately represent the correct scientific terms they are currently misrepresenting. This responsibility falls on the shoulders of authors, editors and publishers.