Deepti Negi, Penelope M. Tsimbouri, Matthew J. Dalby
et al.
Bone is a dynamic tissue with ecological and evolutionary importance, as it can grow and remodel itself in response to mechanical stimuli. In mammals, osteocytes are widely recognised as the central regulators of bone formation and mechanotransduction. However, many advanced teleosts lack these cells yet still exhibit evidence of bone formation and remodelling. This challenges the prevailing view that osteocytes are indispensable for these processes. Notably, these anosteocytic teleosts exhibit clear responses to mechanical loading, suggesting alternative mechanisms at play. African cichlids, known for their remarkable ecological diversification, which occurs in craniofacial bone morphology. However, these differences are based on very few genetic changes, while including interspecific variation in bone remodeling capacities. Thus, cichlid, being anosteocytic, and variable in remodeling abilities based on very few genetic changes, represents an ideal model system for understanding the mechanisms underlying remodeling. This protocol outlines the development of primary cell cultures from cichlid jaw bones that can be applied across species, establishing a foundation for future research aimed at elucidating the cellular and molecular mechanisms underlying bone formation and remodelling in anosteocytic systems.
Abstract Background E2F/DP is a transcription factor family essential for regulating the cell cycle during plant growth, development, and stress response. However, its role in cotton, a crop of significant economic importance, particularly concerning salt tolerance, remains unexplored. Results We systematically identified 70 E2F/DP genes across four cotton species, including the allopolyploids Gossypium hirsutum and G. barbadense, as well as the parental diploids A-genome G. arboreum and D-genome G. raimondii. Phylogenetic analysis classified these genes into three subfamilies (E2F, DP, and DEL), with notable expansion of the E2F subfamily in tetraploid cotton through local duplication events rather than tandem duplication. Promoter analysis revealed enrichment of stress- and hormone-responsive cis-elements, suggesting functional roles in environmental adaptation. Tissue-specific and salt stress expression profiling highlighted GhDEL1_D08 as a key candidate, exhibiting rapid induction under salt stress. Functional validation using virus- induced gene silencing in cotton and overexpression in Arabidopsis thaliana demonstrated that GhDEL1_D08 negatively regulates salt tolerance by modulating antioxidant enzyme activities and membrane lipid peroxidation. Conclusions These findings provide a comprehensive view of the E2F/DP gene family in cotton and identify GhDEL1_D08 as a critical regulator of salt stress response, offering potential targets for breeding stress-resilient cotton varieties.
Lactylation, a recently identified epigenetic modification derived from lactate metabolism, has emerged as a key regulator linking cellular metabolic states to chromatin remodeling and gene transcription. Acting through histone and non-histone protein lactylation (for example, Histone H3 Lysine 9 Lactylation [H3K9la], Histone H3 Lysine 18 Lactylation [H3K18la]), this modification reshapes chromatin accessibility and activates transcriptional programs, thereby driving tumor progression, metabolic reprogramming, immune evasion, and chemoresistance in digestive system malignancies. This review comprehensively summarizes the latest advances in lactylation across esophageal cancer (EC), gastric cancer (GC), colorectal cancer (CRC), hepatocellular carcinoma (HCC), pancreatic cancer (PC), and gallbladder cancer (GBC), emphasizing its role in epigenetic regulation of oncogenic signaling and metabolic–epigenetic crosstalk. Moreover, we discuss potential biomarkers, therapeutic targets, and pharmacologic strategies aimed at modulating lactylation. Despite promising translational potential, key challenges remain in standardizing detection methods and validating clinical efficacy. The intricate mechanisms of lactylation not only deepen our understanding of digestive tumor biology but also unveil a rich landscape of novel therapeutic targets. Future investigations should focus on deciphering lactylation-mediated epigenetic mechanisms in tumor immunotherapy and precision medicine, providing new directions for research and clinical insights for the early diagnosis and tailored treatment of digestive system tumors.
Neoplasms. Tumors. Oncology. Including cancer and carcinogens
Carolina Dos Santos Passos, Robert Cohen, Tingting Yao
Double-strand breaks (DSBs) are lesions in DNA that, if not properly repaired, can cause genomic instability, oncogenesis, and cell death. Multiple chromatin posttranslational modifications (PTMs) play a role in the DNA damage response to DSBs. Among these, RNF168-mediated ubiquitination of lysines 13 or 15 at the N-terminal tail of histone H2A (H2AK13/15Ub) is essential for the recruitment of effectors of both the non-homologous end joining (NHEJ) and the homologous recombination (HR) repair pathways. Thus, tools and techniques to track the spatiotemporal dynamics of H2AK13/15 ubiquitination at DNA DSBs are important to facilitate studies of DNA repair. Previous work from other groups used the minimal focus-forming region (FFR) of the NHEJ effector 53BP1 to detect H2AK15Ub generated upon damage induced by gamma or laser irradiation in live cells. However, 53BP1-FFR only binds nucleosomes modified with both H2AK15Ub and dimethylation of lysine 20 on histone H4 (H4K20me2); thus, 53BP1-FFR does not recognize H2AK13Ub–nucleosomes or nucleosomes that contain H2AK15Ub but lack methylation of H4K20 (H4K20me0). To overcome this limitation, we developed an avidity-based sensor that binds H2AK13/15Ub without dependence on the methylation status of histone H4K20. This sensor, called Reader1.0, detects DNA damage-associated H2AK13/15Ub in live cells with high sensitivity and selectivity. Here, we present a protocol to detect the formation of H2AK13/15Ub at laser-induced DSBs using Reader1.0 as a live-cell reporter for this histone PTM.Graphic abstract:
The development of methods increasing plant water use efficiency (WUE) would enhance the ability to grow wild aromatic and medicinally important species. The aim of this research was to determine the effect of plant growth regulators (PGRs) applied by spraying on stress resistance and WUE of fennel subjected to water stress. Plants in the generative stage were more drought tolerant than those in the vegetative stage. Water stress at vegetative stage decreased plant biomass and grain yield by 60% and 61%, respectively. Severe water stress in vegetative stage reduced grain production by 56%, and grains had 43% lower mass than those from non-stressed plants. Application of PGRs at both stages of growth increased grain yield and biomass, but the magnitude of increase depended on the type and application time of PGRs. Plants grown in well-watered conditions and sprayed with methyl jasmonate during the vegetative stage had the highest grain production (2.7 g plant<sup>−1</sup>), whereas under moderate water stress, plants yielded the best (2.1 g plant<sup>−1</sup>) when sprayed with epibrassinolide. The maximum WUE for grain (0.91 g L<sup>−1</sup>) and essential oil production (20 mg L<sup>−1</sup>) was noted in plants exposed to moderate stress and treated with methyl jasmonate during the vegetative stage.
Yashar Bashirzadeh, Hossein Moghimianavval, Allen P. Liu
Summary: Cell shape changes from locomotion to cytokinesis are, to a large extent, driven by myosin-driven remodeling of cortical actin patterns. Passive crosslinkers such as α-actinin and fascin as well as actin nucleator Arp2/3 complex largely determine actin network architecture and, consequently, membrane shape changes. Here we reconstitute actomyosin networks inside cell-sized lipid bilayer vesicles and show that depending on vesicle size and concentrations of α-actinin and fascin actomyosin networks assemble into ring and aster-like patterns. Anchoring actin to the membrane does not change actin network architecture yet exerts forces and deforms the membrane when assembled in the form of a contractile ring. In the presence of α-actinin and fascin, an Arp2/3 complex-mediated actomyosin cortex is shown to assemble a ring-like pattern at the equatorial cortex followed by myosin-driven clustering and consequently blebbing. An active gel theory unifies a model for the observed membrane shape changes induced by the contractile cortex.
Abstract Background A balanced and optimized amount of nutrients in bread, which is the main food in many countries, is necessary to maintain human health. Considering the importance of nutritional values of bread in the food basket of Iranian households, the purpose of this study was to determine the nutrients and their concentrations in breads consumed in Iran. Methods This systematic review study was performed to determine the types of nutrients in breads consumed in Iran by searching reputable international databases including Scopus and Google scholar, PubMed, Science direct, ISI (Web of Science). Data were collected according to inclusion and exclusion criteria and by searching for relevant keywords, emphasizing the types of nutrients in breads consumed in Iran. Qualitative data were collected using the standard PRISMA checklist (preferential reporting items for systematic reviews and meta-analysis). After verifying the quality of the articles, the information was entered into a checklist such as the name of the first author and year of publication of the research, type of study, number of samples, type of nutrition, type of bread and amount of nutrition measured. Results After reviewing the information and quality of articles, 10 articles were qualified for systematic review. The review of the articles showed that different breads were experimented, including: Sangak, Barbari, Taftoon, Lavash, French and local bread. The highest number of experimented bread samples was Sangak. Examination of the articles showed that 6 nutrients were experimented in different breads such as Fe, K, Mg, Ca, Cu and Zn. The highest number of experimented in breads was related to the amount of Zn (13 times) and Cu (10 times), respectively. The results of quality assessment of articles showed that most of the studies were of good quality. The results of articles on the amount of nutrients measured in different breads showed that only in two articles the amount of nutrients was reported to be desirable. In most articles, the amount of nutrients in breads was reported to be lower or higher than standard. Conclusion The results of this study showed that the concentration of nutrients in most articles was undesirable. It is suggested that optimal methods of enrichment of breads and flours be done with interdisciplinary cooperation between food hygiene, environmental health, nutrition, farmers and bakers. It is recommended that food hygiene and environmental health researchers investigate other nutrients (including phosphorus, selenium, manganese, boron and molybdenum) in breads and other staple foods used by people to constructive and practical measures to increase public health.
Nutritional diseases. Deficiency diseases, Public aspects of medicine
To understand the biological complexity of life, one needs to investigate how biomolecules behave and interact with each other at a molecular level [...]
Maximilian Schweinsberg, Fabian Gösser, Ralph Tollrian
Abstract Corals have evolved a variety of stress responses to changing conditions, many of which have been the subject of scientific research. However, polyp bailout has not received widespread scientific attention, despite being described more than 80 years ago. Polyp bailout is a drastic response to acute stress in which coral colonies break down, with individual and patches of polyps detaching from the colony and the calcareous skeleton Polyps retain their symbiotic partners, have dispersal ability, and may undergo secondary settlement and calcification. Polyp bailout has been described worldwide in a variety of anthozoan species, especially in Scleractinia. It can be induced by multiple natural stressors, but also artificially. Little is known about the evolutionary and ecological potential and consequences of breaking down modularity, the dispersal ability, and reattachment of polyps resulting from polyp bailout. It has been shown that polyp bailout can be used as a model system, with promise for implementation in various research topics. To date, there has been no compilation of knowledge on polyp bailout, which prompted us to review this interesting stress response and provide a basis to discuss research topics and priorities for the future.
Mauro Falconieri, Serena Gagliardi, Flaminia Rondino
et al.
Impulsive stimulated Raman scattering (ISRS) is a nonlinear pump–probe spectroscopy technique particularly suitable to study vibrational intermolecular and intramolecular modes in complex systems. For the latter, recent studies of ISRS microscopy with low-energy laser sources have attracted attention for investigation of photosensitive or biological samples. Following this stream of interest, in this paper, we report an investigation on the relationship between femtosecond ISRS data and pump–probe Z-scan measurements, showing that the latter technique is capable of capturing the Kerr nonlinearities induced by the molecular vibrational modes. To this aim, firstly, spectrally filtered and Raman-induced Kerr ISRS signals were simultaneously acquired to determine the sample nonlinear response and to establish the reference data for the Z-scan analysis. Then, by adopting a suitable experimental arrangement to avoid thermo-optical effects, we were able to unambiguously observe the Raman-induced effects in Z-scan measurements, thus obtaining a consistent picture between ISRS and Z-scan for the first time, to the best of our knowledge. Practical applications of the proposed method include calibrated measurements of the contribution of the internal (Raman) and external molecular modes to the nonlinear refractive index.
Oxidative stress-mediated retinal pigment epithelium (RPE) degeneration plays a vital role in retinal degeneration with irreversible visual impairment, most notably in age-related macular degeneration (AMD), but a key pathogenic factor and the targeted medical control remain controversial and unclear. In this work, by sophisticated high-throughput sequencing and biochemistry investigations, the major pathologic processes during RPE degeneration in the sodium iodate-induced oxidative stress model has been identified to be heme oxygenase-1 (HO-1)-regulated ferroptosis, which is controlled by the Nrf2–SLC7A11–HO-1 hierarchy, through which ferrous ion accumulation and lethal oxidative stress cause RPE death and subsequently photoreceptor degeneration. By direct knockdown of HO-1 or using HO-1 inhibitor ZnPP, the specific inhibition of HO-1 overexpression has been determined to significantly block RPE ferroptosis. In mice, treatment with ZnPP effectively rescued RPE degeneration and achieved superior therapeutic effects: substantial recovery of the retinal structure and visual function. These findings highlight that targeting HO-1-mediated RPE ferroptosis could serve as an effectively retinal-protective strategy for retinal degenerative diseases prevention, including AMD.
Malwina Mularczyk, Izabela Michalak, Krzysztof Marycz
Bioactive compounds of natural origin are gaining increasing popularity. High biological activity and bioavailability, beneficial effects on health and safety of use are some of their most desirable features. Low production and processing costs render them even more attractive. Microorganisms have been used in the food, medicinal, cosmetic and energy industries for years. Among them, microalgae have proved to be an invaluable source of beneficial compounds. <i>Haematococcus pluvialis</i> is known as the richest source of natural carotenoid called astaxanthin. In this paper, we focus on the cultivation methods of this green microalga, its chemical composition, extraction of astaxanthin and analysis of its antioxidant, anti-inflammatory, anti–diabetic and anticancer activities. <i>H. pluvialis</i>, as well as astaxanthin can be used not only for the treatment of human and animal diseases, but also as a valuable component of diet and feed.
Jesús Rodrigo-Comino, Jesús Barrena-González, Manuel Pulido-Fernández
et al.
Monitoring soil erosion processes and measuring soil and water yields allow supplying key information to achieve land degradation neutrality challenges. Vineyards are one of the most affected agricultural territories by soil erosion due to human and natural factors. However, the spatial variability of soil erosion, the number of sampling points, and plot size necessary to estimate accurate soil erosion rates remains unclear. In this research, we determine how many inter-rows should be surveyed to estimate the soil mobilization rates in the viticulture area of Tierra de Barros (Extremadura, SW Spain) using the Improved Stock Unearthing Method (ISUM). This method uses the graft union of the vines as a passive biomarker of the soil surface level changes since the time of plantation and inter-row measures. ISUM was applied to three inter-row and four rows of vines (5904 sampling points) in order to determine how many surfaces and transects must be surveyed as all the previous surveys were done with only one inter-row. The results showed average values of soil depletion reaching −11.4, −11.8, and −11.5 cm for the inter-rows 1, 2, and 3, respectively. The current soil surface level descended 11.6 cm in 20 years. The inter-rows 1, 2, and 3 with a total area of 302.4 m<sup>2</sup> each one (2016 points) recorded 71.4, 70.8, and 74.0 Mg ha<sup>−1</sup> yr<sup>−1</sup>, respectively. With the maximum number of sampling points (5904), 71.2 Mg ha<sup>−1</sup> yr<sup>−1</sup> were obtained. The spatial variability of the soil erosion was shown to be very small, with no statistically significant differences among inter-rows. This could be due to the effect of the soil profile homogenization as a consequence of the intense tillage. This research shows the potential predictability of ISUM in order to give an overall overview of the soil erosion process for vineyards that follow the same soil management system. We conclude that measuring one inter-row is enough to get an overview of soil erosion processes in vineyards when the vines are under the same intense tillage management and topographical conditions. Moreover, we demonstrated the high erosion rates in a vineyard within the viticultural region of the Tierra de Barros, which could be representative for similar vineyards with similar topographical conditions, soil properties, and a possible non-sustainable soil management system.
Yuichi Shichino, Yoko Otsubo, Yoshitaka Kimori
et al.
Accurate and extensive regulation of meiotic gene expression is crucial to distinguish germ cells from somatic cells. In the fission yeast Schizosaccharomyces pombe, a YTH family RNA-binding protein, Mmi1, directs the nuclear exosome-mediated elimination of meiotic transcripts during vegetative proliferation. Mmi1 also induces the formation of facultative heterochromatin at a subset of its target genes. Here, we show that Mmi1 prevents the mistimed expression of meiotic proteins by tethering their mRNAs to the nuclear foci. Mmi1 interacts with itself with the assistance of a homolog of Enhancer of Rudimentary, Erh1. Mmi1 self-interaction is required for foci formation, target transcript elimination, their nuclear retention, and protein expression inhibition. We propose that nuclear foci formed by Mmi1 are not only the site of RNA degradation, but also of sequestration of meiotic transcripts from the translation machinery.
Jordan Hodgkinson, Leon Grayfer, Miodrag Belosevic
Macrophages are found across all vertebrate species, reside in virtually all animal tissues, and play critical roles in host protection and homeostasis. Various mechanisms determine and regulate the highly plastic functional phenotypes of macrophages, including antimicrobial host defenses (pro-inflammatory, M1-type), and resolution and repair functions (anti-inflammatory/regulatory, M2-type). The study of inflammatory macrophages in immune defense of teleosts has garnered much attention, and antimicrobial mechanisms of these cells have been extensively studied in various fish models. Intriguingly, both similarities and differences have been documented for the regulation of lower vertebrate macrophage antimicrobial defenses, as compared to what has been described in mammals. Advances in our understanding of the teleost macrophage M2 phenotypes likewise suggest functional conservation through similar and distinct regulatory strategies, compared to their mammalian counterparts. In this review, we discuss the current understanding of the molecular mechanisms governing teleost macrophage functional heterogeneity, including monopoetic development, classical macrophage inflammatory and antimicrobial responses as well as alternative macrophage polarization towards tissues repair and resolution of inflammation.
Tri Ratna Saridewi, Setia Hadi, Akhmad Fauzi
et al.
Spatial planning has already been stipulated in Ciliwung Watershed, but its implementation is often not in line with the rapid development activities. To fulfill space demand, agricultural and forest areas are converted into open or built-up areas because the economic appreciation of forest and agricultural land is lower than that of open or built-up areas. Payment for Environmental Services (PES) is a tool designed to overcome environment mismanagement, which is beneficial for the lives of rural communities.  PES should be considered in the formulation of spatial planning. This study was aimed to develop optimum land use pattern in reducing flood in Ciliwung Watershed, using PES approach. This study used a dynamic system approach, consisting of submodels for land use pattern change, runoff, value of farmland, upstream subsidy policy, population dynamics and environmental services. The results showed that the PES policy should be able to maintain the existence of paddy fields and dryland farming areas and to reduce runoff if it is implemented in the form of a guaranteed access to the market, and held in conjunction with efforts to prevent land conversion and to implement reforestation policies. The optimum land use pattern under this condition shall be reached in 2023, which consisted of 0.82% water bodies, 10.74% forest areas, 70.34 % built-up areas, 8.16% dryland farming areas, 4.97% grassland areas, 2.39% paddy fields areas and 2.58% open areas. This land use pattern can reduce runoff in Ciliwung River from 972.04 to 850 cm, and this level is considered to be flood-free. Communities living in the upstream areas are the most effective managers of the watershed.