Abstract Maize (Zea mays L.) kernel mutants are valuable tools for investigating kernel development. In this study, we employed ethyl methanesulfonate (EMS) mutagenesis of pollen on five inbred lines, which displayed varying performance after treatment. Over 400 independent kernel mutants were generated, showing a wide range of defects in both type and severity. Bulked segregant analysis (BSA) combined with whole‐genome sequencing was employed to map two representative mutants. For a shrunken kernel mutant, a missense mutation (P155L) was identified in the classical ZmBT1 gene, which encodes an ADP‐glucose transporter. For a small kernel mutant, a start‐lost mutation (M1?) was discovered in the ZmTOP6A gene, which encodes the DNA topoisomerase VI subunit A. Allelic verification of ZmBT1 and ZmTOP6A confirmed their association with the mutant phenotypes. Furthermore, we analyzed the protein conservation, expression patterns, and subcellular localization of both genes. Our study highlights the effectiveness of combining EMS mutagenesis with BSA for mining maize kernel genes. The mutants and the identified genes will advance our understanding of maize kernel development.
Background: Angiogenesis is a key mechanism in metastatic colorectal cancer (mCRC). Novel agents targeting this pathway, like cabozantinib, are of great therapeutic need. Patients and methods: We conducted an open-label, single-arm phase II trial to assess the antitumor activity of cabozantinib in patients with pretreated mCRC who had progressed following at least two prior lines of therapy. The primary endpoint was the progression-free survival (PFS) rate at 16 weeks, whereas secondary endpoints included median PFS, overall survival (OS), response rate, disease control rate, and safety. DNA- and RNA-based translational analyses were carried out on biological samples. Results: From October 2019 to January 2023, 33 patients were treated with oral cabozantinib, 60 mg daily. The primary endpoint was met: 11/33 assessable patients (33%) were progression-free at 16 weeks. Median PFS was 2.27 months [95% confidence interval (CI) 1.71-3.65 months], median OS was 6.25 months (95% CI 3.81-10.26 months). Disease control rate was 45.5%. Cabozantinib was generally fairly tolerated. Exploratory analyses investigating the effect of clinical disease features on PFS showed no significant correlation. Comprehensive genomic profiling on 30 patients (tissues and plasma) suggested that absence of TP53 mutations and tumor mutational burden (TMB) ≥4 mutations/Mb positively correlated with response (PFS >16 weeks). Additionally, for a subset of 18 (54.5%) patients, RNA sequencing from archival formalin-fixed paraffin-embedded samples was carried out. Molecular subtypes 4 (CMS4) was the most represented transcriptional subtype (10/18 cases). To verify if other transcriptional features were associated with treatment benefit, for each sample we computed gene set variation analysis. For epithelial-mesenchymal transition (EMT) and angiogenesis gene sets, we identified a trend toward higher scores in tumors from patients with longer PFS. Conclusion: Within the limitations of a single-arm phase II trial, cabozantinib demonstrates both safety and antitumor activity in mCRC. The observed correlation between specific molecular features, such as EMT activation and angiogenesis, and cabozantinib activity is hypothesis-generating and warrants further investigation.
Neoplasms. Tumors. Oncology. Including cancer and carcinogens
Abstract Background Leaf morphology traits determine photosynthetic efficiency, high-density planting tolerance, and grain yield in maize (Zea mays L.). Understanding the genetic basis of these traits is of great practical significance for optimizing plant architecture and enhancing photosynthetic capacity to improve grain yield. Results In this study, six maternal and paternal testcrossing (TC/M and TC/P) populations were developed from recombinant inbred line (RIL) populations using three inbred lines—Y46 (tropical), Ye107 (temperate), and MON2 (subtropical)—in pairwise crosses. The inbreds represented the most representative lines from the three major heterotic groups: Suwan, Reid, and Non-Reid. Each RIL population was backcrossed to maternal and paternal parents, to generate TC/M and TC/P populations, respectively. All individuals from these testcross populations (TCM/Ps) were genotyped using genotyping-by-sequencing technology. Phenotyping for mid-parent heterosis of leaf morphology traits—leaf length (LL), leaf width (LW), and leaf angle (LA)—in these populations were evaluated over two years and across two field locations in China. The inclusive composite interval mapping (ICIM) approach was used to identify quantitative trait loci (QTLs) and candidate genes associated with heterosis for leaf morphological traits. The results showed that more QTLs for LL were identified in the Suwan × Non-Reid and Reid × Non-Reid heterotic groups than in Suwan × Reid heterotic groups. However, the largest QTL effects—with a phenotypic variance explained (PVE) of 23.31% for LL—were observed in the Reid × Non-Reid heterotic group. For LW and LA, more QTLs were detected in the Reid × Non-Reid and Suwan × Reid heterotic groups than in the Suwan x Non-Reid heterotic groups. The largest QTL effects were observed in the Reid × Non-Reid heterotic group, with a PVE of 32.32% for LW and 23.13% for LA. In total, seven stable QTLs and 14 candidate genes were identified. Through gene expression analysis, six candidate pleiotropic genes—the ones expressed in maize leaves—were identified, among which Zm00001d022618 and Zm00001d008625 play crucial roles in regulating heterosis formation of leaf morphological traits. Conclusion These findings provide insights into the complexity of heterosis determination in leaf morphological traits and may support precision breeding to optimize plant architecture and harness heterosis in maize.
Abstract Background Oocyte maturation is a critical process responsible for supporting preimplantation embryo development and full development to term. Understanding oocyte gene expression is relevant given the unique molecular mechanism present in this gamete. Comparative transcriptome analysis across species offers a powerful approach to uncover conserved and species-specific genes involved in the molecular regulation of oocyte maturation throughout evolution. Results Transcriptome analysis identified 4,625, 3,824, 4,972 differentially expressed genes (DEGs) between the germinal vesicle (GV) and metaphase II (MII) stage in human, porcine and mouse oocytes respectively. These DEGs showed dynamic changes associated with oocyte maturation. Functional enrichment analysis revealed that the DEGs in all three species were mainly involved in DNA replication, cell cycle and redox regulation. Comparative transcriptome analysis identified 551 conserved DEGs in the three species with significant enrichment in mitochondria and mitochondrial intima. Conclusions This study provides a systematic comparative analysis of oocyte meiotic maturation in humans, pigs and mice identifying both conserved and species-specific patterns during oocyte meiosis. Our findings also implied that the selection of oocyte expressed genes among these three species could form a basis for further exploring their functional roles in human oocyte maturation.
LI Ke, OUYANG Runkun, SU Yun, HOU Aixiang, LI Jie, LI Zongjun
As the key to microbial fermentation, fermented grains have a decisive influence on the quality and flavor of Baijiu. In recent years, the research on fermented grains has received extensive attention from the academic community, especially in terms of the influence of microbial populations and their metabolic activities on the quality of Baijiu. Based on the bibliometric method, from multiple dimensions such as the number of published articles, journal distribution, author and institutional cooperation network, keywords co-occurrence and cluster analysis, the 1 373 related literatures published on China National Knowledge Infrastructure (CNKI) from 2014 to 2023 were systematically sorted out and visualized using CiteSpace V6.3.R1 software. The aim was to reveal the current hotspots and development trends of fermented grains research. The results showed that the main topics of fermented grains research focus on flavor substances, microorganisms and their fermentation processes, and microorganisms and flavor substances were the hot spots in the field of fermented grains. The study provided important references and guidance for researchers in the field of fermented grains, promoted further exploration and innovation in the field, and advanced the sustainable development of China's fermented grains industry.
Oran Wasserman, Mallory R. Wootton, Spencer Fairbanks
et al.
Summary: Solitary bee cocoons serve as protective barriers against parasitoids, yet their puncture resistance properties remain understudied. Here, we present a protocol for measuring puncture resistance in Osmia lignaria cocoons using custom 3D-printed fixtures. We describe steps for determining bee sex, preparing cocoon segments, measuring segment thickness, testing puncture resistance using 27.5-gauge sharp needles on an MTS Synergie 100 mechanical testing instrument, and analyzing the data. The protocol generates quantitative data on puncture resistance properties and thickness measurements for comparative studies. : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.
Applications for plastic polymers can be found all around the world, often discarded without any prior care, exacerbating the environmental issue. When large waste materials are released into the environment, they undergo physical, biological, and photo-degradation processes that break them down into smaller polymer fragments known as microplastics (MPs). The time it takes for residual plastic to degrade depends on the type of polymer and environmental factors, with some taking as long as 600 years or more. Due to their small size, microplastics can contaminate food and enter the human body through food chains and webs, causing gastrointestinal (GI) tract pain that can range from local to systemic. Microplastics can also acquire hydrophobic organic pollutants and heavy metals on their surface, due to their large surface area and surface hydrophobicity. The levels of contamination on the microplastic surface are significantly higher than in the natural environment. The gut-brain axis (GB axis), through which organisms interact with their environment, regulate nutritional digestion and absorption, intestinal motility and secretion, complex polysaccharide breakdown, and maintain intestinal integrity, can be altered by microplastics acting alone or in combination with pollutants. Probiotics have shown significant therapeutic potential in managing various illnesses mediated by the gut-brain axis. They connect hormonal and biochemical pathways to promote gut and brain health, making them a promising therapy option for a variety of GB axis-mediated illnesses. Additionally, taking probiotics with or without food can reduce the production of pro-inflammatory cytokines, reactive oxygen species (ROS), neuro-inflammation, neurodegeneration, protein folding, and both motor and non-motor symptoms in individuals with Parkinson's disease. This study provides new insight into microplastic-induced gut dysbiosis, its associated health risks, and the benefits of using both traditional and next-generation probiotics to maintain gut homeostasis
Although tissue engineering offered new approaches to repair bone defects, it remains a great challenge to create a bone-friendly microenvironment and rebuild bone tissue rapidly by a scaffold with a bionic structure. In this study, a multifunctional structurally optimized hydrogel scaffold was designed by integrating polyvinyl alcohol (PVA), gelatin (Gel), and sodium alginate (SA) with aspirin (ASA) and nano-hydroxyapatite (nHAP). The fabrication procedure is through a dual-crosslinking process. The chemical constitution, crystal structure, microstructure, porosity, mechanical strength, swelling and degradation property, and drug-release behavior of the hydrogel scaffold were analyzed. Multi-hydrogen bonds, electrostatic interactions, and strong “egg-shell” structure contributed to the multi-network microstructure, bone tissue-matched properties, and desirable drug-release function of the hydrogel scaffold. The excellent performance in improving cell viability, promoting cell osteogenic differentiation, and regulating the inflammatory microenvironment of the prepared hydrogel scaffold was verified using mouse pre-osteoblasts (MC3T3-E1) cells. And the synergistic osteogenic and anti-inflammatory functions of aspirin and nano-hydroxyapatite were also verified. This study provided valuable insights into the design, fabrication, and biological potential of multifunctional bone tissue engineering materials with the premise of constructing a bone-friendly microenvironment.
Tooba Mahboob, Polrat Wilairatana, Mohammed Rahmatullah
et al.
Background: Propolis is a natural resinous mixture produced by bees. It provides beneficial effects on human health in the treatment/management of many diseases. The present study was performed to demonstrate the anti-Acanthamoeba activity of ethanolic extracts of Propolis samples from Iran. The interactions of the compounds and essential proteins of Acanthamoeba were also visualized through docking simulation. Methods: The minimal inhibitory concentrations (MICs) of Propolis extract against Acanthamoeba trophozoites and cysts was determined in vitro. In addition, two-fold dilutions of each of agents were tested for encystment, excystment and adhesion inhibitions. Three major compounds of Propolis extract such as chrysin, tectochrysin and pinocembrin have been selected in molecular docking approach to predict the compounds that might be responsible for encystment, excystment and adhesion inhibitions of A. castellanii. Furthermore, to confirm the docking results, molecular dynamics (MD) simulations were also carried out for the most promising two ligand-pocket complexes from docking studies. Results: The minimal inhibitory concentrations (MICs) 62.5 and 125 µg/mL of the most active Propolis extract were assessed in trophozoites stage of Acanthamoeba castellanii ATCC30010 and ATCC50739, respectively. At concentrations lower than their MICs values (1/16 MIC), Propolis extract revealed inhibition of encystation. However, at 1/2 MIC, it showed a potential inhibition of excystation and anti-adhesion. The molecular docking and dynamic simulation revealed the potential capability of Pinocembrin to form hydrogen bonds with A. castellanii Sir2 family protein (AcSir2), an encystation protein of high relevance for this process in Acanthamoeba. Conclusions: The results provided a candidate for the development of therapeutic drugs against Acanthamoeba infection. In vivo experiments and clinical trials are necessary to support this claim.
Johanna von Seth, Tom van der Valk, Edana Lord
et al.
Abstract Background Understanding the micro-evolutionary response of populations to demographic declines is a major goal in evolutionary and conservation biology. In small populations, genetic drift can lead to an accumulation of deleterious mutations, which will increase the risk of extinction. However, demographic recovery can still occur after extreme declines, suggesting that natural selection may purge deleterious mutations, even in extremely small populations. The Chatham Island black robin (Petroica traversi) is arguably the most inbred bird species in the world. It avoided imminent extinction in the early 1980s and after a remarkable recovery from a single pair, a second population was established and the two extant populations have evolved in complete isolation since then. Here, we analysed 52 modern and historical genomes to examine the genomic consequences of this extreme bottleneck and the subsequent translocation. Results We found evidence for two-fold decline in heterozygosity and three- to four-fold increase in inbreeding in modern genomes. Moreover, there was partial support for temporal reduction in total load for detrimental variation. In contrast, compared to historical genomes, modern genomes showed a significantly higher realised load, reflecting the temporal increase in inbreeding. Furthermore, the translocation induced only small changes in the frequency of deleterious alleles, with the majority of detrimental variation being shared between the two populations. Conclusion Our results highlight the dynamics of mutational load in a species that recovered from the brink of extinction, and show rather limited temporal changes in mutational load. We hypothesise that ancestral purging may have been facilitated by population fragmentation and isolation on several islands for thousands of generations and may have already reduced much of the highly deleterious load well before human arrival and introduction of pests to the archipelago. The majority of fixed deleterious variation was shared between the modern populations, but translocation of individuals with low mutational load could possibly mitigate further fixation of high-frequency deleterious variation.
Apert syndrome (AS) is characterized by synostosis of coronal sutures, midfacial hypoplasia,abnormity of brain, syndactyly of hands and feet. Majority of AS is caused by gain-of-function mutation of fibro‐blast growth factor receptor 2 (FGFR2). To date, the treatment of AS is surgical correction for the deformed skull.The reconstruction of sutures is often executed several times, because of constant premature of sutures. Some dis‐eased tissues, such as brain, are difficult to treat with surgery. CRISPR/Cas9 gene editing technology exhibits pow‐erful prospect in the treatment of human genetic diseases. In this study, small guiding RNA (gRNA) specificallytargeting the Fgfr2 gene was screened and lentivirus mediated Cas9/gRNA was employed to treat mice (Fg‐fr2+/P253R) that mimicking human Apert syndrome in primary calvarial cells, calvarial explants or calvarial bone. Incultured primary calvarial cells, Cas9/gRNA reduced the phosphorylation of ERK1/2 and P38, and resultantly inhibited osteoblastic differentiation and matrix mineralization. Besides, Cas9/gRNA attenuated the premature closure ofcoronal suture and the decreased calvarial bone volume calvarial explants and AS mice. This study provides exper‐imental basis of gene therapy for Apert syndrome, and is prospective to provide new strategies for the treatment ofskeletal genetic diseases.
Chenyin Feng, Christopher L. Frewin, Md Rubayat-E Tanjil
et al.
Carbon containing materials, such as graphene, carbon-nanotubes (CNT), and graphene oxide, have gained prominence as possible electrodes in implantable neural interfaces due to their excellent conductive properties. While carbon is a promising electrochemical interface, many fabrication processes are difficult to perform, leading to issues with large scale device production and overall repeatability. Here we demonstrate that carbon electrodes and traces constructed from pyrolyzed-photoresist-film (PPF) when combined with amorphous silicon carbide (<i>a-</i>SiC) insulation could be fabricated with repeatable processes which use tools easily available in most semiconductor facilities. Directly forming PPF on <i>a</i>-SiC simplified the fabrication process which eliminates noble metal evaporation/sputtering and lift-off processes on small features. PPF electrodes in oxygenated phosphate buffered solution at pH 7.4 demonstrated excellent electrochemical charge storage capacity (CSC) of 14.16 C/cm<sup>2</sup>, an impedance of 24.8 ± 0.4 kΩ, and phase angle of −35.9 ± 0.6° at 1 kHz with a 1.9 kµm<sup>2</sup> recording site area.
Christina J. Castro, Rachel L. Marine, Edward Ramos
et al.
Abstract Background Viruses have high mutation rates and generally exist as a mixture of variants in biological samples. Next-generation sequencing (NGS) approaches have surpassed Sanger for generating long viral sequences, yet how variants affect NGS de novo assembly remains largely unexplored. Results Our results from > 15,000 simulated experiments showed that presence of variants can turn an assembly of one genome into tens to thousands of contigs. This “variant interference” (VI) is highly consistent and reproducible by ten commonly-used de novo assemblers, and occurs over a range of genome length, read length, and GC content. The main driver of VI is pairwise identities between viral variants. These findings were further supported by in silico simulations, where selective removal of minor variant reads from clinical datasets allow the “rescue” of full viral genomes from fragmented contigs. Conclusions These results call for careful interpretation of contigs and contig numbers from de novo assembly in viral deep sequencing.
Raquel Jurado-Escobar, Raquel Jurado-Escobar, Inmaculada Doña
et al.
Nonsteroidal anti-inflammatory drugs (NSAIDs) are among the most highly consumed drugs worldwide and the main triggers of drug hypersensitivity reactions. The most frequent reaction, named cross-reactive NSAID-hypersensitivity, is due to the pharmacological activity of these drugs by blocking the cyclooxygenase-1 enzyme. Such inhibition leads to cysteinyl-leukotriene synthesis, mainly LTE4, which are responsible for the reaction. Although the complete molecular picture of the underlying mechanisms remains elusive, the participation of platelet-adherent leukocytes (CD61+) and integrins have been described for NSAID-exacerbated respiratory disease (NERD). However, there is a lack of information concerning NSAID-induced urticaria/angioedema (NIUA), by far the most frequent clinical phenotype. Here we have evaluated the potential role of CD61+ leukocytes and integrins (CD18, CD11a, CD11b, and CD11c) in patients with NIUA, and included the other two phenotypes with cutaneous involvement, NSAID-exacerbated cutaneous disease (NECD) and blended reactions (simultaneous skin and airways involvement). A group NSAID-tolerant individuals was also included. During the acute phase of the reaction, the three clinical phenotypes showed increased frequencies of CD61+ neutrophils, eosinophils, and monocytes compared to controls, which correlated with urinary LTE4 levels. However, no correlation was found between these variables at basal state. Furthermore, increased expressions of CD18 and CD11a were found in the three CD61+ leukocytes subsets in NIUA, NECD and blended reactions during the acute phase when compared with CD61−leukocyte subpopulations. During the acute phase, CD61+ neutrophils, eosinophils and monocytes showed increased CD18 and CD11a expression when compared with CD61+ leukocytes at basal state. No differences were found when comparing controls and CD61+ leukocytes at basal state. Our results support the participation of platelet-adherent leukocytes and integrins in cutaneous cross-hypersensitivity to NSAIDs and provide a link between these cells and arachidonic acid metabolism. Our findings also suggest that these reactions do not involve a systemic imbalance in the frequency of CD61+ cells/integrin expression or levels of LTE4, which represents a substantial difference to NERD. Although further studies are needed, our results shed light on the molecular basis of cutaneous cross-reactive NSAID-hypersensitivity, providing potential targets for therapy through the inhibition of platelet-leukocyte interactions.