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Simple Summary: Technological advancements and growing interest in farm animal health have led to the development of various biometric devices. Among these, bolus-type biosensors have been extensively used to monitor adult cattle, but their application in calves remains limited. In this study, we evaluated a newly developed miniature bolus biosensor, equipped with a triaxial accelerometer and temperature sensor, to monitor physiological changes in beef and dairy calves. The biosensor was orally administered shortly after birth and monitored for retention and data accuracy. Our findings showed that most calves have successfully retained the biosensor, which provided valuable data on calf activity, body temperature, and responses to the stressful weaning period. Significant changes in these parameters indicate the possibility of using such biosensors for early health monitoring. While occasional regurgitation of the device was noted, this study highlights the potential of these biosensors for improving calf health management, though further validation is needed. In this study, a newly developed small wireless bolus biosensor, equipped with a triaxial accelerometer and temperature sensors, was applied to assess physiological changes in calves. The biosensor was orally implanted in calves, and its retention rate and location in the forestomach were examined. Data transmitted at 10 min intervals were analyzed to determine the characteristics of the calves at 10 and 100 days of age. Additionally, the daily averages of the vector magnitude (DV), changes in V over time (DV1), and reticular temperature (DRT) were analyzed during the experimental period. The biosensor was orally administered to twelve calves (six beef and six dairy) within 22 days of birth. Except for two regurgitated devices, the sensors transmitted data normally in a wireless manner for 15 weeks, recording physiological changes in the calves. The location of the biosensors was confirmed to be the reticulum. The analysis revealed that the V and V1 values were influenced by the physical characteristics of the biosensor's location. During weaning, DV and DV1 values first increased and then decreased compared to pre-weaning, while the DRT increased post-weaning and remained elevated. These findings suggest that these types of biosensors can be used for monitoring calf health; however, further research is needed to determine their ability to detect pathological states. [ABSTRACT FROM AUTHOR]

An often-overlooked aspect of biology is formed by the outliers of the protein length distribution, specifically those proteins with more than 5000 amino acids, which we refer to as huge proteins (HPs). By examining UniprotKB, we discovered more than 41 000 HPs throughout the tree of life, with the majority found in eukaryotes. Notably, the phyla with the highest propensity for huge proteins are Apicomplexa and Fornicata. Moreover, we observed that certain bacteria, such as Elusomicrobia or Planctomycetota, have a higher tendency for encoding huge proteins, even more than the average eukaryote. To investigate if these macro-polypeptides represent "real" proteins, we explored several indirect metrics. Additionally, orthology analyses reveals thousands of clusters of homologous sequences of HPs, revealing functional groups related to key cellular processes such as cytoskeleton organization and functioning as chaperones or as E3-ubiquitin ligases in eukaryotes. In the case of bacteria, the major clusters have functions related to Non-Ribosomomal peptide synthesis/Polyketide synthesis, followed by pathogen-host attachment or recognition surface proteins. Further exploration of the annotations for each HPs supported the previously identified functional groups. These findings underscore the need for further investigation of the cellular and ecological roles of these HPs and their potential impact on biology and biotechnology. Author summary: In our study we focused on a fascinating and often overlooked aspect of biology: proteins that stand out due to their extraordinary length, with more than 5000 amino acids in size. These exceptional proteins, aptly named "huge proteins", have been found in surprising abundance across various life forms, with over 41 000 identified. Astonishingly, most of these HPs belong to eukaryotes. Within this group, specific branches like Apicomplexa and Fornicata exhibit a remarkable tendency to encode for these HPs. Besides, certain types of bacteria, like Elusomicrobia and Planctomycetota, encode these HPs even more than the average eukaryote. To confirm the significance of these findings, we used various methods and discovered that these mega-molecules are indeed authentic proteins with crucial roles in cellular activities. In eukaryotes, they participate in vital processes such as maintaining the cell's structure and acting as cellular caretakers. For bacteria, these proteins are involved in intricate tasks like producing essential compounds and interacting with host organisms. This study sheds light on these enigmatic biological giants, urging further exploration into their roles, opening new avenues in the realms of biology and biotechnology. [ABSTRACT FROM AUTHOR]

In this study, we analyzed the regulatory properties of 26 (twenty-six) genes associated with nonsyndromic male infertility. We applied an in silico analysis in order to determine the number and distribution of promoters and identify relevant promoter consensus sequences and potential transcription factors. Underlining the concept of alternative transcriptional initiation (ATI), we have found that 65.4% of genes associated with nonsyndromic male infertility have 1 (one) to 6 (six) promoters, located in the region 1 kb upstream of the TSS, and 41% of them are located at a position below −500 bp. Although the TATA box consensus sequence TAWAAA, such as W is A or T, appears at a common location in all genes, it is shifted for at least 10 bp in the EFCAB9 gene. The C2H2 zinc finger is found to be the most significant common transcription factor, binding genes' promoters GLIS1, ZSCAN21, GLIS3, GLIS1, ZNF770, ZNF780A, ZNF81, and ZNF264. On the other hand, basic leucine zipper factors (bZIPs) bind the JUNB gene promoter specifically, exhibiting unique regulatory properties of all genes associated with nonsyndromic male infertility. Two genes, NANOS1 and ZMYND15, are expected to be less susceptible to DNA methylation, due to the high density of CpG content found in their promoter regions. [ABSTRACT FROM AUTHOR]

TOR (target of rapamycin), a ubiquitous protein kinase central to cellular homeostasis maintenance, fundamentally regulates ribosome biogenesis in part by its target La-related protein 1 (LARP1). Among other target transcripts, LARP1 specifically binds TOP (terminal oligopyrimidine) mRNAs encoding all 80 ribosomal proteins in a TOR-dependent manner through its C-terminal region containing the DM15 module. Though the functional implications of the LARP1 interaction with target mRNAs is controversial, it is clear that the TOP-LARP1-TOR axis is critical to cellular health in humans. Its existence and role in evolutionarily divergent animals remain less understood. We focused our work on expanding our knowledge of the first arm of the axis: the connection between LARP1-DM15 and the 5' TOP motif. We show that the overall DM15 architecture observed in humans is conserved in fruit fly and zebrafish. Both adopt familiar curved arrangements of HEAT-like repeats that bind 5' TOP mRNAs on the same conserved surface, although molecular dynamics simulations suggest that the N-terminal fold of the fruit fly DM15 is predicted to be unstable and unfold. We demonstrate that each ortholog interacts with TOP sequences with varying affinities. Importantly, we determine that the ability of the DM15 region to bind some TOP sequences but not others might amount to the context of the RNA structure, rather than the ability of the module to recognize some sequences but not others. We propose that TOP mRNAs may retain similar secondary structures to regulate LARP1 DM15 recognition. [ABSTRACT FROM AUTHOR]

Chronic obstructive pulmonary disease (COPD) is commonly caused from smoking cigarettes that induce biological stress responses. Previously we found disorganized endoplasmic reticulum (ER) in fibroblasts from COPD with different responses to chemical stressors compared to healthy subjects. Here, we aimed to investigate differences in stress-related gene expressions within lung cells from COPD and healthy subjects. Bronchoalveolar lavage (BAL) cells were collected from seven COPD and 35 healthy subjects. Lung fibroblasts were derived from 19 COPD and 24 healthy subjects and exposed to cigarette smoke extract (CSE). Gene and protein expression and cell proliferation were investigated. Compared to healthy subjects, we found lower gene expression of CHOP in lung fibroblasts from COPD subjects. Exposure to CSE caused inhibition of lung fibroblast proliferation in both groups, though the changes in ER stress-related gene expressions (ATF6, IRE1, PERK, ATF4, CHOP, BCL2L1) and genes relating to proteasomal subunits mostly occurred in healthy lung fibroblasts. No differences were found in BAL cells. In this study, we have found that lung fibroblasts from COPD subjects have an atypical ER stress gene response to CSE, particularly in genes related to apoptosis. This difference in response to CSE may be a contributing factor to COPD progression. [ABSTRACT FROM AUTHOR]

The development of effective vaccines against SARS-CoV-2 remains a critical challenge amidst the ongoing global pandemic. This study introduces a novel approach to enhancing mRNA vaccine efficacy by leveraging the untranslated region (UTR) of TMSB10, a gene identified for its significant mRNA abundance in antigen-presenting cells. Utilizing the GEO database, we identified TMSB10 among nine genes, with the highest mRNA abundance in dendritic cell subtypes. Subsequent experiments revealed that TMSB10's UTR significantly enhances the expression of a reporter gene in both antigen-presenting and 293T cells, surpassing other candidates and a previously optimized natural UTR. A comparative analysis demonstrated that TMSB10 UTR not only facilitated a higher reporter gene expression in vitro but also showed marked superiority in vivo, leading to enhanced specific humoral and cellular immune responses against the SARS-CoV-2 Delta variant RBD antigen. Specifically, vaccines incorporating TMSB10 UTR induced significantly higher levels of specific IgG antibodies and promoted a robust T-cell immune response, characterized by the increased secretion of IFN-γ and IL-4 and the proliferation of CD4+ and CD8+ T cells. These findings underscore the potential of TMSB10 UTR as a strategic component in mRNA vaccine design, offering a promising avenue to bolster vaccine-induced immunity against SARS-CoV-2 and, potentially, other pathogens. [ABSTRACT FROM AUTHOR]

Brain-specific angiogenesis inhibitor 1 (BAI1) belongs to the adhesion G-protein-coupled receptors, which exhibit large multi-domain extracellular N termini that mediate cell-cell and cell-matrix interactions. To explore the existence of BAI1 isoforms, we queried genomic datasets for markers of active chromatin and new transcript variants in the ADGRB1 (adhesion G-protein-coupled receptor B1) gene. Two major types of mRNAs were identified in human/mouse brain, those with a start codon in exon 2 encoding a full-length protein of a predicted size of 173.5/173.3 kDa and shorter transcripts starting from alternative exons at the intron 17/exon 18 boundary with new or exon 19 start codons, predicting two shorter isoforms of 76.9/76.4 and 70.8/70.5 kDa, respectively. Immunoblots on wild-type and Adgrb1 exon 2-deleted mice, reverse transcription PCR, and promoter-luciferase reporter assay confirmed that the shorter isoforms originate from an alternative promoter in intron 17. The shorter BAI1 isoforms lack most of the N terminus and are very close in structure to the truncated BAI1 isoform generated through GPS processing from the full-length receptor. The cleaved BAI1 isoform has a 19 amino acid extracellular stalk that may serve as a receptor agonist, while the alternative transcripts generate BAI1 isoforms with extracellular N termini of 5 or 60 amino acids. Further studies are warranted to compare the functions of these isoforms and examine the distinct roles they play in different tissues and cell types., (© 2024. The Author(s).)

A certain proportion of genes are regulated by multiple, distinct promoters, revealing a dynamic landscape of the cancer transcriptome. However, the contribution of alternative promoters (APs) in breast cancer (BRCA) remains largely unexplored. Here, we identified 3654 genes with multiple promoters in BRCA patients, and 53 of them could generate distinct AP transcripts that are dysregulated and prognosis-related in BRCA, namely prognosis-related dysregulated AP (prdeAP) transcripts. Interestingly, when we searched for the genomic signatures of these prdeAP genes, we found that the promoter regions of 92% of the prdeAP genes were enriched with abundant DNA methylation signals. Through further bioinformatic analysis and experimental validation, we showed that AP selections of TANK, UNKL, CCL28, and MAP1LC3A were regulated by DNA methylation upon their corresponding promoter regions. Functionally, by overexpressing AP variants of TANK, we found that TANK|55731 could dramatically suppress MDA-MB-231 cell proliferation and migration. Meanwhile, pan-cancer survival analyses suggested that AP variants of TANK provided more accurate prognostic predictive ability than TANK gene in a variety of tumor types, including BRCA. Together, by uncovering the DNA methylation-regulated AP transcripts with tumor prognostic features, our work revealed a novel layer of regulators in BRCA progression and provided potential targets that served as effective biomarkers for anti-BRCA treatment., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Gestation length (GL) in cattle is associated with neonatal health and the subsequent reproductive performance of dams. We performed a genome-wide association study (GWAS) using 25,144 single nucleotide polymorphisms (SNPs) in 4373 animals to detect genetic variants associated with GL as a fetal trait in Japanese Black cattle in Gifu Prefecture. We identified four significant SNPs on chromosome 21 in moderate linkage disequilibrium (LD). The minor allele of the most significant SNP has the effect on -2.47 days GL with a 0.019 allele frequency. Of the 4373 animals, 140 heterozygotes and one homozygote with the minor allele were traced back to a heterozygous sire. The 7.2 Mb LD region harbors three genes: gamma-aminobutyric acid type A receptor subunit beta3 (GABRB3), arrestin domain containing 4 (ARRDC4), and nuclear receptor subfamily 2 group F member 2 (NR2F2, also known as COUP-TFII). RNA expression analysis and its functions suggest that GABRB3, ARRDC4, and NR2F2 (COUP-TFII) are involved in glucose production via the hypothalamic-pituitary-adrenal axis during the fetal stress response at gestation period termination. These results suggest that an increase in the allele frequency of the associated SNPs has an impact on genetic improvement by shortening the GL in the population., (© 2024 Japanese Society of Animal Science.)