Biology Open最新文献

Regulation of gene expression is critical for fate commitment of stem and progenitor cells during tissue formation. In the context of mammalian brain development, a plethora of studies have described how changes in the expression of individual genes characterize cell types across ontogeny and phylogeny. However, little attention has been paid to the fact that different transcripts can arise from any given gene through alternative splicing (AS). Considered a key mechanism expanding transcriptome diversity during evolution, assessing the full potential of AS on isoform diversity and protein function has been notoriously difficult. Here, we capitalize on the use of a validated reporter mouse line to isolate neural stem cells, neurogenic progenitors and neurons during corticogenesis and combine the use of short- and long-read sequencing to reconstruct the full transcriptome diversity characterizing neurogenic commitment. Extending available transcriptional profiles of the mammalian brain by nearly 50,000 new isoforms, we found that neurogenic commitment is characterized by a progressive increase in exon inclusion resulting in the profound remodeling of the transcriptional profile of specific cortical cell types. Most importantly, we computationally infer the biological significance of AS on protein structure by using AlphaFold2, revealing how radical protein conformational changes can arise from subtle changes in isoforms sequence. Together, our study reveals that AS has a greater potential to impact protein diversity and function than previously thought, independently from changes in gene expression.

Although some budding yeasts have proved tractable and intensely studied models, others are more recalcitrant. Debaryomyces hansenii, an important yeast species in food and biotechnological industries with curious physiological characteristics, has proved difficult to manipulate genetically and remains poorly defined. To remedy this, we have combined live cell fluorescent dyes with high-resolution imaging techniques to define the sub-cellular features of D. hansenii, such as the mitochondria, nuclei, vacuoles and the cell wall. Using these tools, we define biological processes like the cell cycle, organelle inheritance and various membrane trafficking pathways of D. hansenii for the first time. Beyond this, reagents designed to study Saccharomyces cerevisiae proteins were used to access proteomic information about D. hansenii. Finally, we optimised the use of label-free holotomography to image yeast, defining the physical parameters and visualising sub-cellular features like membranes and vacuoles. Not only does this work shed light on D. hansenii but this combinatorial approach serves as a template for how other cell biological systems, which are not amenable to standard genetic procedures, can be studied.

Complex behavioral sequences such as courtship displays are often multimodal, and coordination between modalities is critically important. In learned and variable behavioural sequences such as songs, individual variability may also extend to multimodal coordination and the associations between modalities. However, individual variability in complex multimodal sequences and in coordination between distinct behaviours remains underexplored. Here, we report that budgerigars, which continuously learn and modify their complex warble songs, exhibit associations between body movements and song notes during courtship. Some associations are unique to individuals, and others are universal across individuals. Additionally, some individuals exhibit more unique associations than others. We also find that birds warbling in the absence of body movements emit all notes with broadly similar odds ratios. Our data suggest a hierarchy of associations, some individual-specific and others common to all individuals, between body movements and songs. We propose that these associations may be learnt and modified through social interactions, resulting in individual variability.

Stress during laboratory experiments can affect the outcomes of ecophysiological studies. The serum corticosterone concentration (CORT), the leukocyte profile, heterophil/lymphocyte ratio (H/L), and the presence of blood endoparasites were analyzed as a proxy of stress and immunological state in adult males of the lizard Liolaemus attenboroughi, endemic to Patagonia, Argentina. The results of the ecophysiological variables (preferred temperature, running speed, locomotor endurance, and body condition index, BCI) were analyzed in relation to stress indicators obtained from blood samples taken at three different times: at capture, and on the third and seventh days in the laboratory. Males at capture showed a high percentage of lymphocytes and heterophils and a low of basophils, monocytes, and eosinophils. Haemogregorina-type endoparasites have been recorded in the genus Liolaemus for the first time. The proportion of infected males remained stable during captivity; however, these males showed higher CORT levels, increased percentages of basophils, and decreased percentages of lymphocytes. There was a significant increment in CORT and H/L, and a decrease in BCI during laboratory experiments, compared with baseline values at capture. The performance was not related to the CORT or the repeated blood sampling. The BCI decreased, possibly due to energy reserve mobilization caused by acute stress. This study shows that blood extraction and ecophysiological experiments over 7 days have a minor effect on the stress indicators used.

Maternal inheritance of mitochondrial DNA (mtDNA) is a widespread phenomenon in eukaryotes. Our earlier research indicated that sperm mtDNA is removed prior to fertilization in mice, and Endonuclease G (ENDOG) orchestrates the degradation of sperm mitochondria in Caenorhabditis elegans. However, the mechanisms underlying sperm mtDNA disposal in mammals remain poorly understood. To investigate the potential role of ENDOG in sperm mtDNA elimination, we created Endog knockout (Endog-/-) mice. Our findings revealed that Endog-/- mice maintained normal spermatogenesis and fertility. Most strikingly, we detected no substantial discrepancy in sperm mtDNA copy number between Endog-/- and control mice. Furthermore, we noted that sperm mtDNA copy numbers were unchanged in both less motile and motile sperm isolated by Percoll gradient centrifugation from Endog-/- and control mice. Taken together, our results indicate that ENDOG is not essential for spermatogenesis or the elimination of sperm mtDNA in mice.

Metabolic syndrome has become a global epidemic, affecting all developed countries and communities with growing economies. Worldwide, increasing efforts have been directed at curbing this growing problem. Mice deleted of the gene encoding Type 1 Transient Receptor Potential Canonical Channel (Trpc1) were found to weigh heavier than controls. They had fasting hyperglycemia and impaired glucose tolerance compared with wild-type controls. Beyond 1 year of age, plasma triglyceride level in Trpc1-/- mice was elevated. Plasma cholesterol levels tended to be higher than in controls. The livers of Trpc1-/- mice were heavier, richer in triglyceride, and more echogenic than those of controls on ultrasound evaluation. Hematocrit was lower in Trpc1-/- mice of both genders beginning at the second to third months of age in the absence of bleeding or hemolysis. Measured by the indirect tail-cuff method or by the direct arterial cannulation, blood pressures in null mice were lower than controls. We conclude that TRPC1 gene regulates body metabolism and that except for hypertension, phenotypes of mice after deletion of the Trpc1 gene resemble mice with metabolic syndrome, suggesting that this could be a good experimental model for future investigation of the pathogenesis and management of this disorder.

The African spiny mouse (Acomys cahirinus) is a unique mammalian model of tissue regeneration, regenerating 4 mm ear-hole punches with cartilage, adipocytes, hair follicles, and muscle. However, the time to regenerate ear tissue varies from 20 to 90 days and muscle regeneration is inconsistent. Some report that older spiny mice have delayed regeneration without investigation on the regenerative capacity of muscle. We thought that delayed regeneration and inconsistent muscle regeneration could be linked via age-related nerve degeneration. While the current study found that spiny mice aged 6-9 months had delayed regeneration compared to 3-4 month-old spiny mice, the capacity of muscle regeneration was unrelated to age, and there was little evidence for age-related nerve degeneration. Instead, the regeneration of muscle, cartilage and adipocytes was spatially heterogeneous, declining in amount from the proximal to distal region of the regenerated tissue. Also, cartilage regeneration in the distal region was decreased in ≥22-month-old Acomys and adipocyte regeneration was decreased in those older than 6 months, compared to 3-4 month olds. While the underlying mechanisms for delayed and spatially heterogenous regeneration remain unclear, age and the spatial region of the regenerated tissue should be considered in experimental designs with spiny mice.

The multiprotein complexes known as the complex of proteins associated with Set1 (COMPASS) play a crucial role in the methylation of histone 3 lysine 4 (H3K4). In Drosophila, the COMPASS series complexes comprise core subunits Set1, Trx, and Trr, which share several common subunits such as ash2, Dpy30-L1, Rbbp5, and wds, alongside their unique subunits: Wdr82 for Set1/COMPASS, Mnn1 for Trx/COMPASS-like, and Ptip for Trr/COMPASS-like. Our research has shown that flies deficient in any of these common or unique subunits exhibited high lethality at eclosion (the emergence of adult flies from their pupal cases) and significantly shortened lifespans of the few adults that do emerge. Silencing these common or unique subunits led to severe heart morphological and functional defects. Moreover, specifically silencing the unique subunits of the COMPASS series complexes, Wdr82, Mnn1, and Ptip, in the heart results in decreased levels of H3K4 monomethylation and dimethylation, consistent with effects observed from silencing the core subunits Set1, Trx, and Trr. These findings underscore the critical roles of each subunit of the COMPASS series complexes in regulating histone methylation during heart development and provide valuable insights into their potential involvement in congenital heart diseases, thereby informing ongoing research in heart disease.

Bazooka/Par-3 (Baz) is an evolutionarily conserved scaffold protein that functions as a master regulator for the establishment and maintenance of cell polarity in many different cell types. In the vast majority of published research papers Baz has been reported to localize at the cell cortex and at intercellular junctions. However, there have also been several reports showing localization and function of Baz at additional subcellular sites, in particular the nuclear envelope and the neuromuscular junction. In this study we have re-assessed the localization of Baz to these subcellular sites in a systematic manner. We used antibodies raised in different host animals against different epitopes of Baz for confocal imaging of Drosophila tissues. We tested the specificity of these antisera by mosaic analysis with null mutant baz alleles and tissue-specific RNAi against baz. In addition, we used a GFP-tagged gene trap line for Baz and a bacterial artificial chromosome (BAC) expressing GFP-tagged Baz under control of its endogenous promoter in a baz mutant background to compare the subcellular localization of the GFP-Baz fusion proteins to the staining with anti-Baz antisera. Together, these experiments did not provide evidence for specific localization of Baz to the nucleus or the neuromuscular junction.

Viral infectivity depends on multiple factors. Recent studies showed that the interaction between viral RNAs and endogenous microRNAs (miRNAs) regulates viral infectivity; viral RNAs function as a sponge of endogenous miRNAs and result in upregulation of its original target genes, while endogenous miRNAs target viral RNAs directly and result in repression of viral gene expression. In this study, we analyzed the possible interaction between parainfluenza virus RNA and endogenous miRNAs in human and mouse lungs. We showed that the parainfluenza virus can form base pairs with human miRNAs abundantly than mouse miRNAs. Furthermore, we analyzed that the sponge effect of endogenous miRNAs on viral RNAs may induce the upregulation of transcription regulatory factors. Then, we performed RNA-sequence analysis and observed the upregulation of transcription regulatory factors in the early stages of parainfluenza virus infection. Our studies showed how the differential expression of endogenous miRNAs in lungs could contribute to respiratory virus infection and species- or tissue-specific mechanisms and common mechanisms could be conserved in humans and mice and regulated by miRNAs during viral infection.