Comparative Functional Analysis Research Articles

High-resolution chromosome-level genome of Scylla paramamosain provides molecular insights into adaptive evolution in crabs

BackgroundEvolutionary adaptation drives organismal adjustments to environmental pressures, exemplified in the diverse morphological and ecological adaptations seen in Decapoda crustaceans, particularly brachyuran crabs. Crabs thrive in diverse ecosystems, from coral reefs to hydrothermal vents and terrestrial habitats. Despite their ecological importance, the genetic mechanisms underpinning their developmental processes, reproductive strategies, and nutrient acquisition remain poorly understood.ResultsHere, we report a comprehensive genomic analysis of the green mud crab Scylla paramamosain using ultralong sequencing technologies, achieving a high-quality chromosome-level assembly. The refined 1.21 Gb genome, with an impressive contig N50 of 11.45 Mb, offers a valuable genomic resource. The genome exhibits 33,662 protein-coding genes, enriched in various pathways related to development and environmental adaptation. Gene family analysis shows expansion in development-related pathways and contraction in metabolic pathways, indicating niche adaptations. Notably, investigation into Hox gene regulation sheds light on their role in pleopod development, with the Abd-A gene identified as a linchpin. Post-transcriptional regulation involving novel-miR1317 negatively regulates Abd-A levels. Furthermore, the potential role of fru gene in ovarian development and the identification of novel-miR35 as a regulator of Spfru2 add complexity to gene regulatory networks. Comparative functional analysis across Decapoda species reveals neo-functionalization of the elovl6 gene in the synthesis of long-chain polyunsaturated fatty acids (LC-PUFA), suggesting its importance in environmental adaptation.ConclusionsOur findings shed light on various aspects of crab biology, including genome sequencing, assembly, and annotation, as well as gene family expansion, contraction, and regulatory mechanisms governing crucial developmental processes such as metamorphosis, reproductive strategies, and fatty acid metabolism.

Changes of immune function mediated by Gasdermin-E in the immune microenvironment of primary oral squamous cell carcinoma

In primary oral squamous cell carcinoma (OSCC), the tumor microenvironment (TME) constitutes a highly intricate ecosystem comprised of cellular and acellular elements. The tumor immune microenvironment (TIME) is characterized by the presence of a broad of immune cells, while there is a scarcity of cytotoxic lymphocytes (CTLs) intratumorally. Consequently, the recruitment of a larger cohort of CTLs to infiltrate the tumor core has emerged as a pressing scientific challenge. Gasdermin E (GSDME), as a pivotal effector protein in pyroptosis, plays a significant role in anti-tumor therapy. Here, primary OSCC was induced by Gsdme knockout (KO) mice and wild type (WT) mice of the same strain respectively, using the chemical mutagen 4-Nitroquinoline N-oxide (4-NQO). Through comparative analysis of immune function between the two kinds of mice, intriguing observations have been elucidated, the presence of GSDME was instrumental in augmenting the infiltration of lymphocytes towards the neoplastic site, effectively ameliorating the TIME. Our findings elucidated that the absence of GSDME promotes the development of primary OSCC, accompanied by a notable increase in malignancy. Furthermore, our data delineated a positive inter-relationship between the presence of GSDME and the host organism’s immunological reactivity, which enhances the TIME in primary OSCC.

The HST Large Programme on ω Centauri

We present a study of the white dwarf (WD) cooling sequence (CS) in the globular cluster (GC) Omega Centauri (or NGC 5139; hereafter, ω Cen), the primary goal of a dedicated Hubble Space Telescope (HST) programme. We find that the peak at the termination of the WD CS is located at mF606W = 30.1 ± 0.2 (equivalent to V ∼ 31). The brighter part of ω Cen’s WD CS is consistent with the presence of massive He-core WDs, in agreement with previous HST analyses with ultraviolet and blue filters. Comparative analyses of the WD luminosity function (LF) and theoretical counterparts show that a single-age population for the cluster is compatible with the data. However, an analysis of only the WD LF cannot entirely exclude the possibility of an age range, due to uncertainties in the present-day WD mass function, with a star formation history potentially spanning up to 5 billion years, predominantly comprising stars about 13 Gyr old, with a minority potentially as young as 8 Gyr. This underscores the need for global spectroscopic and photometric investigations that simultaneously include both the WD populations and the previous evolutionary phases, in order to fully understand the cluster’s diverse chemical compositions and ages.

A Comparative Analysis of Neurocognitive Function in Community- and Hospital-Based Patients With Schizophrenia.

The study compared differences in various neurocognitive characteristics across treatment modalities among schizophrenia patients recruited in one city between July 2020 and June 2023 who were on regular medication. Of the 151 participants, 113 were included in the analysis. Participants were divided into community-based and hospital-based groups, and their demographics and clinical characteristics, including insight, quality of life, positive and negative symptoms, and personal and social functioning, were examined. In addition, several aspects of cognition were assessed using neurocognitive assessments such as the Trail Making Test (TMT), Stroop test, and Wisconsin Card Sorting Test (WCST). After adjusting for age differences between groups, the final analysis included data from 42 participants in the community-based group and 33 participants in the hospital-based group. Hospital-based group participants completed Stroop-W more rapidly, excelled in Rey-Osterrieth Complex Figure Test recall and recognition, and incurred fewer TMT Part B (TMT-B) and Stroop-C errors. Additionally, they outperformed in WCST total, non-persistent errors, and categories completed. Contrastingly, community-based group participants showed superior outcomes in WCST persistent responses and errors, suggesting specific neurocognitive strengths. We found differences in neurocognitive characteristics between the two groups. These differences were consistent across a range of cognitive domains, including attention, visual discrimination, memory, and executive functioning. Further large-scale study is needed to generalize cognitive characteristics across treatment modalities.

Comparing the ecological consequences of globally invasive fishes versus their F1 hybrids in recreational fisheries

Recreational angling is a major introduction pathway for non-native fish into freshwaters, where multiple non-native fishes are often released into waterbodies to diversify the angling opportunities. When these non-native fishes are taxonomically similar, then there is concern that their hybridisation will result in F1 generations comprising of novel phenotypes that outperform their parental species, resulting in the impacts of these ecological engineering species being accelerated. Across two water temperatures (18 °C, 26 °C), comparative functional response analyses (CFR) quantified the consumption patterns of the globally invasive freshwater fish common carp Cyprinus carpio and goldfish Carassius auratus, plus their F1 hybrids, before testing differences in their specific growth rates (SGRs). In CFRs, carp consumed significantly more prey at 18 °C than the other fishes, and with no differences between any of the fishes at 26 °C. SGRs also did not differ substantially between the fishes at either temperature. These results suggest that hybridisation between the high impacting parental species did not produce novel phenotypes of high ecological performance that could accelerate their ecological impacts in invaded ecosystems. Accordingly, the ecological risks of their use in recreational angling remain an issue that is primarily associated with the parent populations, and this can be reflected in their invasion management.

Comparative Analysis and Optimal Selection of Calibration Functions in Pure Rotational Raman Lidar Technique

The pure rotational Raman (PRR) lidar technique relies on calibration functions (CFs) to extract temperature information from raw detection data. The choice of CF significantly impacts the accuracy of the retrieved temperature. In this study, we propose a method that combines multiple Monte Carlo simulation experiments with a statistical analysis, and we first conduct simulated comparisons of the calibration effects of different CFs while considering the impact of noise. We categorized ten common CFs into four groups based on their functional form and the number of calibration coefficients. Based on functional form, specifically, we defined 1/T = f(lnQ) as a forward calibration function (FCF) and lnQ = g(1/T) as a backward calibration function (BCF). Here, T denotes temperature, and Q denotes the signal intensity ratio. Their performance within and outside the calibration interval is compared across different integration times, smoothing methods, and reference temperature ranges. The results indicate that CFs of the same category exhibit similar calibration effects, while those of different categories exhibit notable differences. Within the calibration interval, the FCF performs better, especially with more coefficients. However, outside the calibration interval, the linear calibration function (which can be considered a two-coefficient FCF) has an obvious advantage. Conclusions based on the simulation results are validated with actual data, and the factors influencing calibration errors are discussed. Utilizing these findings to guide CF selection can enhance the accuracy and stability of PRR lidar detection.

Comparative analysis of modulation transfer function in various intraocular lenses under normal, decentration, and tilt conditions

PurposeThis study aims to compare the modulation transfer function (MTF) of different intraocular lenses (IOLs) under normal, decentration, and tilt conditions to evaluate their optical performance. DesignExperimental setting. MethodsA total of 12 IOL models (+20 D diopter, n = 3 each) were measured for MTF using the OptiSpheric IOL system with a 3 mm aperture diameter at a water temperature of 35 °C. Measurements were made with a spatial frequency of 0 - 200 lp/mm at the normal, decentration of 0.5 mm, and tilt of 5° positions. ResultsThe MTF values were significantly different between normal and decentration conditions for XY1A (monofocal, toric) (P = 0.03), Tecnis ZCB00V (P = 0.0009), and NS-60YG (P = 0.004). Differences were significant between normal and tilt conditions for MP70 (P = 0.009), XY1 (P = 0.0005), and Clareon (P = 0.049), and were significant between decentration and tilt conditions only for LentisComfort (bifocal) (P = 0.01). With normal condition, MTF of Eyhance DIB00V (extended depth of focus) showed significant differences with 11 other IOLs (P < 0.0001), while LentisComfort exhibited differences with 10 other IOLs (P < 0.0001) except for XY1A (P = 0.0002). Similarly, with decentration condition, Eyhance DIB00V differed significantly from 11 other IOLs (P < 0.0001). With tilt condition, Eyhance DIB00V showed significant differences with 10 other IOLs (P < 0.0001) except for LentisComfort, which itself differed significantly from 10 other IOLs (P < 0.0001). ConclusionsIn the experimental settings, while specialized IOLs can address specific visual issues, monofocal IOLs remain superior in terms of overall contrast transfer quality and resolution even in the implanted IOL position is not ideal. These results provide a basis for recommending the use of monofocal IOLs in cases where the anterior chamber depth and lens position are prone to instability, such as in eyes with weakened zonules or following glaucoma filtering surgery.

Comparative Analysis of Circular RNAs Expression and Function between Aortic and Intracranial Aneurysms.

An aneurysm is an abnormal enlargement or bulging of the wall of a blood vessel. Most often, aneurysms occur in large blood vessels - the aorta (Thoracic Aortic Aneurysm (TAA) and Abdominal Aortic Aneurysm (AAA)) and brain vessels (Intracranial Aneurysm (IA)). Despite the presence of significant differences in the pathogenesis of the development and progression of IA and TAA/AAA, there are also similarities. For instance, both have been shown to be strongly influenced by shear stress, inflammatory processes, and enzymatic destruction of the elastic lamellae and extracellular matrix (ECM) proteins of the vascular wall. Moreover, although IA and TAA are predominantly considered arteriopathies with different pathological mechanisms, they share risk factors with AAA, such as hypertension and smoking. However, there is a need for a more in- -depth study of the key elements that may influence the formation and progression of a particular aneurysm to find ways of therapeutic intervention or search for a diagnostic tool. Today, it is known that the disruption of gene expression is one of the main mechanisms that contribute to the development of aneurysms. At the same time, growing evidence suggests that aberrant epigenetic regulation of gene function is strongly related to the genesis of aneurysms. Although much has been studied of the known protein-coding genes, circular RNAs (circRNAs), a relatively new and rapidly evolving large family of transcripts, have recently received much scientific attention. CircRNAs regulate gene expression through the sponging of microRNAs (miRNAs) and can also be used as therapeutic targets and biomarkers. Increasing evidence has implicated circRNAs in the pathogenesis of multiple cardiovascular diseases, including the development of aneurysms. However, the mechanism of dysregulation of certain circRNAs in a particular aneurysm remains to be studied. The discovery of circRNAs has recently advanced our understanding of the latest mode of miRNAs/target genes regulation in the development and progression of IA and TAA/AAA. The aim of this study is to compare the expression profiles of circRNAs to search for similar or different effects of certain circRNAs on the formation and progression of IA and TAA/AAA.

Mapping World: A Comparative Analysis of Functionality and Usability between QGIS and ArcGIS

The current review conducts a comprehensive comparison of Quantum GIS (QGIS) and ArcGIS in the context of healthcare applications, aiming to assist users in selecting the most appropriate GIS platform for their specific needs. Geographic Information Systems (GIS) are essential tools in healthcare, providing capabilities for spatial analysis, disease mapping, and resource allocation. Driven by the need to improve healthcare delivery and public health strategies, this study compares the functionalities, costs, and support systems of QGIS and ArcGIS. The major objective is to determine which GIS platform offers the best balance of cost-efficiency and performance across various healthcare scenarios. The methodology encompasses a detailed comparative analysis, incorporating quantitative data from user satisfaction surveys, performance evaluations, and real-world case studies. Findings reveal that QGIS, as an open-source GIS software, is highly cost-effective and customizable, making it particularly advantageous for budget-limited projects and smaller organizations requiring flexibility. Its extensibility via plugins and robust user community fosters continuous innovation and improvement. QGIS proves exceptionally effective in healthcare applications such as disease mapping and accessibility analysis, where customization and cost-efficiency are critical. Conversely, ArcGIS is distinguished by its advanced analytical capabilities and strong performance in handling complex, large-scale studies. Its sophisticated tools and comprehensive spatial analysis functionalities are essential for thorough healthcare research and planning. Although ArcGIS incurs higher costs, its extensive feature set, professional support, and exhaustive documentation justify the investment for large organizations and research institutions engaged in detailed GIS projects. In conclusion, both QGIS and ArcGIS exhibit significant strengths in key healthcare applications. QGIS excels in affordability and flexibility, while ArcGIS provides superior analytical power and support for extensive projects. Future research should focus on integrating real-time data and enhancing user experience to further optimize GIS applications in healthcare.

Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations.

The ability to generate multiple RNA transcript isoforms from the same gene is a general phenomenon in eukaryotes. However, the complexity and diversity of alternative isoforms in natural populations remain largely unexplored. Using a newly developed full-length transcript enrichment protocol with 5' CAP selection, we sequenced full-length RNA transcripts of 48 individuals from outbred populations and subspecies of Mus musculus, and from the closely related sister species Mus spretus and Mus spicilegus as outgroups. The data set represents the most extensive full-length high-quality isoform catalog at the population level to date. In total, we reliably identify 117,728 distinct isoforms, of which only 51% were previously annotated. We show that the population-specific distribution pattern of isoforms is phylogenetically informative and reflects the segregating single nucleotide polymorphism (SNP) diversity between the populations. We find that ancient housekeeping genes are a major source of the overall isoform diversity, and that the generation of alternative first exons plays a major role in generating new isoforms. Given that our data allow us to distinguish between population-specific isoforms and isoforms that are conserved across multiple populations, it is possible to refine the annotation of the reference mouse genome to a set of about 40,000 isoforms that should be most relevant for comparative functional analysis across species.

GEPAF: A non-monotonic generalized activation function in neural network for improving prediction with diverse data distributions characteristics

The world today has made prescriptive analytics that uses data-driven insights to guide future actions. The distribution of data, however, differs depending on the scenario, making it difficult to interpret and comprehend the data efficiently. Different neural network models are used to solve this, taking inspiration from the complex network architecture in the human brain. The activation function is crucial in introducing non-linearity to process data gradients effectively. Although popular activation functions such as ReLU, Sigmoid, Swish, and Tanh have advantages and disadvantages, they may struggle to adapt to diverse data characteristics. A generalized activation function named the Generalized Exponential Parametric Activation Function (GEPAF) is proposed to address this issue. This function consists of three parameters expressed: α, which stands for a differencing factor similar to the mean; σ, which stands for a variance to control distribution spread; and p, which is a power factor that improves flexibility; all these parameters are present in the exponent. When p=2, the activation function resembles a Gaussian function. Initially, this paper describes the mathematical derivation and validation of the properties of this function mathematically and graphically. After this, the GEPAF function is practically implemented in real-world supply chain datasets. One dataset features a small sample size but exhibits high variance, while the other shows significant variance with a moderate amount of data. An LSTM network processes the dataset for sales and profit prediction. The suggested function performs better than popular activation functions when a comparative analysis of the activation function is performed, showing at least 30% improvement in regression evaluation metrics and better loss decay characteristics.

Abstract B084: Comparative functional analysis of TP53 alleles in pancreatic ductal adenocarcinoma in vivo

Abstract TP53 is the second most mutated gene in pancreatic ductal adenocarcinoma (PDAC), bearing both truncal loss-of-function and missense point mutations. TP53 encodes a stress-induced transcription factor (p53) capable of activating tumor suppressive pathways mediating cell cycle arrest, apoptosis, senescence, and metabolic reprogramming. Despite high mutational frequency, how TP53 mutants function to suppress pancreatic tumorigenesis in vivo remains unclear. Previous studies indicate that the most frequent point mutations observed in human PDAC (TP53 R175H and R273H; mouse homologues Trp53 R172H and R270H) exhibit both dominant-negative (e.g., response to radiation in leukemia cells) and gain-of-function (e.g., increased liver metastasis in advanced PDAC models) roles compared to p53 null cells in various contexts. To rigorously explore the differential functions of p53 point and deletion mutants in PDAC progression, we performed an isogenic comparative analysis of Trp53 alleles in vivo using Mosaic Analysis with Double Markers (MADM) in mice. MADM uses stochastic mitotic recombination to induce two genotypically distinct daughter cells – created at 1-to-1 ratios – expressing different Trp53 variants dependent on the genotype of the mouse (+/+ vs. -/-, R172H/R172H vs. +/+, R172H/R172H vs. -/-, R270H/R270H vs. +/+, R270H/R270H vs. -/-) and simultaneously label them with unique genetically encoded fluorescent markers (TdTomato vs. GFP). We integrated MADM into a faithful Kras-driven model of pancreatic tumorigenesis (KC: Kras LSL-G12D/+ ; Pdx1-Cre) and used fluorescence microscopy to trace subclonal populations with various Trp53 alleles within the same mouse. By analyzing the ratio of TdTomato+ to GFP+ cells, we studied the functional differences between alleles in driving tumor initiation and expansion at various stages of progression. Strikingly, we found that Trp53 -/- cells exhibited greater expansion in preinvasive pancreatic intraepithelial neoplasias (PanINs) compared to not only Trp53 +/+ cells but also cells harboring either point mutation (Trp53 R172H/R172H or Trp53 R270H/R270H ). While Trp53 R270H/R270H cells predominated over Trp53 +/+ in PanINs, Trp53 R172H/R172H cells were surprisingly indistinguishable from Trp53 +/+ cells, suggesting that p53R172H retains tumor suppressive properties in early PDAC progression. Conversely, both Trp53 R172H/R172H and Trp53 R270H/R270H cells progressed to advanced PDAC with comparable PDAC incidence and survival as Trp53 -/- , arguing that Trp53 R172H is a separation-of-function mutant concordant with a distinct transcriptional profile relative to Trp53 -/- tumor cells. Together, these studies offer the strongest evidence to date for stage-specific functional differences between TP53 mutant variants in cancer progression in vivo and provide a faithful MADM-based PDAC model to define molecular mechanisms (through ongoing transcriptomic, epigenomic, and metabolomic studies) that govern functional differences amongst these diverse alleles. Citation Format: Sherry S. Agabiti, Andy Tang, Timothy Nottoli, Mandar D. Muzumdar. Comparative functional analysis of TP53 alleles in pancreatic ductal adenocarcinoma in vivo [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr B084.

Beyond complete remission: A comparative analysis of long-term laryngeal function in patients with hypopharyngeal and laryngeal cancer following radiotherapy and concurrent chemoradiation.

This study evaluates functional larynx preservation in patients with hypopharyngeal cancer (HPC) and laryngeal cancer (LC) who achieved complete remission following radiotherapy (RT) or concurrent chemoradiation (CCRT). HPC and LC patients treated with RT/CCRT from 1999 to 2017 were retrospectively analyzed. Severe late dysphagia and tracheostomy cases were assessed to determine laryngeal function. Long-term preservation rate of functional larynx and associated factors were evaluated. Of 152 patients (55 HPC, 97 LC), nine developed severe dysphagia, occurring on average 58.2 months post-treatment. HPC and cervical node metastasis significantly increased the risk of laryngeal function impairment (p < 0.001 and p = 0.014, respectively), presenting a continued decline in functional larynx preservation rate beyond 10 years. Patients with HPC and cervical node metastasis demonstrate an increased risk for long-term laryngeal function impairment despite successful oncologic outcomes. This risk extends beyond 10 years, underscoring the need for prolonged monitoring and comprehensive support.

Comparative chemical profiling and functional analysis of Scutellaria baicalensis: Precision-boiled powder vs. traditional decoction pieces using UHPLC-q-orbitrap MS/MS

This study aimed to investigate the potential benefits of using precise boiling techniques on the solubility of two forms of Scutellaria baicalensis (S. baicalensis) powder, Scutellaria precision-boiled powder (SPBP) and Scutellaria traditional decoction pieces (STDP), using UHPLC-Q-Orbitrap MS/MS technology. The UHPLC-Q-Orbitrap MS/MS technique, along with data-analysis methodologies, were employed to compare the active components between SPBP and STDP. A total of ninety-three chemical components were detected in S. baicalensis. By comparing the weights of extracts, conducting a weighted analysis, and using network pharmacology, SPBP demonstrated a higher concentration of active components and improved beneficial benefits compared to STDP. The quality and potential effectiveness of SPBP were evaluated by comparing its chemical components with those of STDP. These findings lay a foundational framework for in-depth exploration of the mechanisms underlying the decoction of S. baicalensis powder, offering significant potential for future research in functional foods and nutraceuticals.

Enhancing solar energy conversion efficiency: Thermophysical property predicting of MXene/Graphene hybrid nanofluids via bayesian-optimized artificial neural networks

Accurately predicting thermo-physical properties (TPPs) of MXene/graphene-based nanofluids is crucial for photovoltaic/thermal solar systems, driving focused research on developing precise TPP predictive models. This study presents optimized multi-layer perceptron neural network (MLPNN) models, leveraging Bayesian optimization to refine architectural and training hyperparameters, including hidden layers, neurons, activation functions, standardization, and regularization terms. A comparative analysis of Bayesian acquisition functions—the probability of improvement (POI), lower confidence bound (LCB), expected improvement (EI), expected improvement plus (EIP), expected improvement per second plus (EIPSP), and expected improvement per second (EIPS)—demonstrated that the POI-MLPNN achieves the most accurate results, as evidenced by the lowest MAPE of 1.0923 % and exceptional consistency with an R-value of 0.99811. The EI-MLPNN and EIP-MLPNN models recorded the same outputs. The EI/EIP-MLPNN (R = 0.99668) model excels in consistency over LCB-MLPNN (R = 0.99529) and EIPSP-MLPNN (R = 0.99667). The optimized models offer a reliable, cost-efficient alternate for experimental and computational TPP analyses. Leveraging insights from these models enables better control over nanofluid TPPs in solar systems, enhancing energy conversion efficiency.

The Human Accelerated Region HAR202 Controls NPAS3 Expression in the Developing Forebrain Displaying Differential Enhancer Activity Between Modern and Archaic Human Sequences.

It has been proposed that the phenotypic differences in cognitive abilities between humans and our closest living relatives, chimpanzees, are largely due to changes in the regulation of neurodevelopmental genes. We have previously found that the neurodevelopmental transcription factor gene NPAS3 accumulates the largest number of human accelerated regions (HARs), suggesting it may play some role in the phenotypic evolution of the human nervous system. In this work, we performed a comparative functional analysis of NPAS3-HAR202 using enhancer reporter assays in transgenic zebrafish and mice. We found that the Homo sapiens HAR202 ortholog failed to drive reporter expression to the zebrafish nervous system, in high contrast to the strong expression displayed by the rest of the vertebrate ortholog sequences tested. Remarkably, the HAR202 ortholog from archaic humans (Neanderthals/Denisovans) also displayed a pan-vertebrate expression pattern, despite the fact that archaic and modern humans have only one nucleotide substitution. Moreover, similar results were found when comparing enhancer activity in transgenic mice, where we observed a loss of activity of the modern human version in the mouse developing brain. To investigate the functional importance of HAR202, we generated mice lacking HAR202 and found a remarkable decrease of Npas3 expression in the forebrain during development. Our results place HAR202 as one of the very few examples of a neurodevelopmental transcriptional enhancer displaying functional evolution in the brain as a result of a fast molecular evolutionary process that specifically occurred in the human lineage.

Genomic Sequencing and Functional Analysis of the Ex-Type Strain of Malbranchea zuffiana.

Malbranchea is a genus within the order Onygenales (phylum Ascomycota) that includes predominantly saprobic cosmopolitan species. Despite its ability to produce diverse secondary metabolites, no genomic data for Malbranchea spp. are currently available in databases. Therefore, in this study, we obtained, assembled, and annotated the genomic sequence of the ex-type strain of Malbranchea zuffiana (CBS 219.58). For the genomic sequencing, we employed both the Illumina and PacBio platforms, followed by hybrid assembly using MaSuRCA. Quality assessment of the assembly was performed using QUAST and BUSCO tools. Annotation was conducted using BRAKER2, and functional annotation was completed with InterProScan. The resulting genome was of high quality, with a size of 26.46 Mbp distributed across 38 contigs and a BUSCO completion rate of 95.7%, indicating excellent contiguity and assembly completeness. A total of 8248 protein-encoding genes were predicted, with functional annotations assigned to 73.9% of them. Moreover, 82 genes displayed homology with entries in the Pathogen Host Interactions (PHI) database, while 494 genes exhibited similarity to entries in the Carbohydrate-Active Enzymes (CAZymes) database. Furthermore, 30 biosynthetic gene clusters (BGCs) were identified, suggesting significant potential for the biosynthesis of diverse secondary metabolites. Comparative functional analysis with closely related species unveiled a considerable abundance of domains linked to enzymes involved in keratin degradation, alongside a restricted number of domains associated with enzymes engaged in plant cell wall degradation in all studied species of the Onygenales. This genome-based elucidation not only enhances our comprehension of the biological characteristics of M. zuffiana but also furnishes valuable insights for subsequent investigations concerning Malbranchea species and the order Onygenales.

Comparative Genomic and Functional Analysis of c-di-GMP Metabolism and Regulatory Proteins in Bacillus velezensis LQ-3.

Bacillus velezensis is a promising candidate for biocontrol applications. A common second messenger molecule, bis-(3,5)-cyclic-dimeric-guanosine monophosphate (c-di-GMP), has the ability to regulate a range of physiological functions that impact the effectiveness of biocontrol. However, the status of the c-di-GMP signaling pathway in biocontrol strain LQ-3 remains unknown. Strain LQ-3, which was isolated from wheat rhizosphere soil, has shown effective control of wheat sharp eyespot and has been identified as B. velezensis through whole-genome sequencing analyses. In this study, we investigated the intracellular c-di-GMP signaling pathway of LQ-3 and further performed a comparative genomic analysis of LQ-3 and 29 other B. velezensis strains. The results revealed the presence of four proteins containing the GGDEF domain, which is the conserved domain for c-di-GMP synthesis enzymes. Additionally, two proteins were identified with the EAL domain, which represents the conserved domain for c-di-GMP degradation enzymes. Furthermore, one protein was found to possess a PilZ domain, indicative of the conserved domain for c-di-GMP receptors in LQ-3. These proteins are called DgcK, DgcP, YybT, YdaK, PdeH, YkuI, and DgrA, respectively; they are distributed in a similar manner across the strains and belong to the signal transduction family. We selected five genes from the aforementioned seven genes for further study, excluding YybT and DgrA. They all play a role in regulating the motility, biofilm formation, and colonization of LQ-3. This study reveals the c-di-GMP signaling pathway associated with biocontrol features in B. velezensis LQ-3, providing guidance for the prevention and control of wheat sharp eyespot by LQ-3.

Analysis of the Effector Functions of Vδ2 γδ T Cells and NK Cells against Cholangiocarcinoma Cells.

Cholangiocarcinoma (CCA) is a rare disease characterized by malignant cells derived from the epithelial cells of the biliary duct system. Despite extensive treatments, the prognosis for CCA remains poor, emphasizing the critical need for the development of novel treatments. Considerable attention has been directed towards innate immune effector cells, which can recognize tumor cells independently of the major histocompatibility complex, laying the foundation for the development of off-the-shelf drugs. In this study, we cultured innate immune cells obtained from the peripheral blood of healthy adults and conducted a comparative analysis of the effector functions against CCA cell lines by Vδ2 γδ T cells and NK cells. This analysis was performed using standard short- and long-term cytotoxicity assays, as well as ELISA for IFN-γ. Vδ2 γδ T cells demonstrated cytotoxicity and IFN-γ production in response to CCA cells in a TCR-dependent manner, particularly in the presence of tetrakis-pivaloyloxymethyl 2-(thiazole-2-ylamino)ethylidene-1,1-bisphosphonate, a bisphosphonate prodrug. In contrast, direct killing and antibody-dependent cellular cytotoxicity were relatively slow and weak. Conversely, NK cells displayed potent, direct cytotoxicity against CCA cells. In summary, both Vδ2 γδ T cells and NK cells show promise as innate immune effector cells for adoptive transfer therapy in the context of CCA.

Comparative functional analysis reveals differential nucleotide sensitivity between human and mouse UCP1.

Mitochondrial uncoupling protein 1 (UCP1) is a unique protein of brown adipose tissue. Upon activation by free fatty acids, UCP1 facilitates a thermogenic net proton flux across the mitochondrial inner membrane. Non-complexed purine nucleotides inhibit this fatty acid-induced activity of UCP1. The most available data have been generated from rodent model systems. In light of its role as a putative pharmacological target for treating metabolic disease, in-depth analyses of human UCP1 activity, regulation, and structural features are essential. In the present study, we established a doxycycline-regulated cell model with inducible human or murine UCP1 expression and conducted functional studies using respirometry comparing wild-type and mutant variants of human UCP1. We demonstrate that human and mouse UCP1 exhibit similar specific fatty acid-induced activity but a different inhibitory potential of purine nucleotides. Mutagenesis of non-conserved residues in human UCP1 revealed structural components in α-helix 56 and α-helix 6 crucial for uncoupling function. Comparative studies of human UCP1 with other orthologs can provide new insights into the structure-function relationship for this mitochondrial carrier and will be instrumental in searching for new activators.