Flow Cytometry Coupled with Resuscitation Assays As a High-Resolution Tool to Inform Environmental Management and Disinfection of Settings Affected by Tuberculous Mycobacteria.

Environmental decontamination and water disinfection practices are hallmarks of disease prevention and control in agricultural and public health settings. Informed fit-to-purpose biocontainment is thus dependent on methodologies accurately assessing microbial burden and viability. Also, rigorous evaluation of the efficacy of biocontrol measures implies monitoring microbial inactivation after decontamination/disinfection procedures. In this study, we used flow cytometry coupled with a resuscitation protocol to monitor the metabolic inactivation of bacteria capable of entering non-cultivable states, after the application of a chlorine-based water disinfectant. For this purpose, we used Mycobacterium bovis BCG as a model of slow-growing bacteria able to enter dormancy and representing a multi-host pathogen in a zoonotic disease system-animal tuberculosis-thriving both across temperate and semi-arid regions and involving environmental contamination. The biocide activity of a commercial sodium dichloroisocyanurate (NaDCC) disinfectant against M. bovis BCG was evaluated through mock environmental matrix tests. Using the manufacturer-recommended dosage of NaDCC, BCG cells were apparently inactivated after 24 h upon exposure. However, we show via flow cytometry that, upon exposure to optimal growth conditions, mycobacterial cells were able to regain metabolic activity shortly after, highlighting a sublethal effect of NaDCC at the recommended commercial dosage due to reversible BCG cell damage. In contrast, increasing twice the disinfectant dosage completely inactivated BCG cells after 24 h of exposure, with full irreversible loss of metabolic activity. Methodological workflows based on conventional culture or PCR would have missed the detection of these dormant subpopulations that were in fact able to resume growth when following the recommendations of a commercial disinfectant. This study highlights the superior, high-resolution value of single-cell approaches, such as flow cytometry, to accurately assess the activity of biocides against metabolically heterogeneous and dormant pathogenic bacteria with environmental cycles, supporting data-driven prioritization of environmental management and disinfection options in contaminated vulnerable settings.

Soil salinity regulates spatial-temporal heterogeneity of seed germination and seedbank persistence of an annual diaspore-trimorphic halophyte in northern China.

BACKGROUND AND AIMS: Seed heteromorphism is a plant strategy that an individual plant produces two or more distinct types of diaspores, which have diverse morphology, dispersal ability, ecological functions and different effects on plant life history traits. The aim of this study was to test the effects of seasonal soil salinity and burial depth on the dynamics of dormancy/germination and persistence/depletion of buried trimorphic diaspores of a desert annual halophyte Atriplex centralasiatica. METHODS: We investigated the effects of salinity and seasonal fluctuations of temperature on germination, recovery of germination and mortality of types A, B, C diaspores of A. centralasiatica in the laboratory and buried diaspores in situ at four soil salinities and three depths. Diaspores were collected monthly from the seedbank from December 2016 to November 2018, and the number of viable diaspores remaining (not depleted) and their germinability were determined. RESULTS: Non-dormant type A diaspores were depleted in the low salinity "window" in the first year. Dormant diaspore types B and C germinated to high percentages at 0.3 and 0.1 mol L-1 soil salinity, respectively. High salinity and shallow burial delayed depletion of diaspore types B and C. High salinity delayed depletion time of the three diaspore types and delayed dormancy release of types B and C diaspores from autumn to spring. Soil salinity modified the response of diaspores in the seedbank by delaying seed dormancy release in autum and winter and by providing a low-salt concentration window for germination of non-dormant diaspores in spring and early summer. CONCLUSIONS: Buried trimorphic diaspores of annual desert halophyte A. centralasiatica exhibited diverse dormancy/germination behavior in respond to seasonal soil salinity fluctuation. Prolonging persistence of the seedbank and delaying depletion of diaspores under salt stress in situ primarily is due to inhibition of dormancy-break. The differences in dormancy/germination and seed persistence in the soil seedbank may be a bet-hadging strategy adapted to stressful temporal and spatial heterogeneity, and allows A. centralasiatica to persist in the unpredictable cold desert enevironment.

Assessing Falling Number Stability Increases the Genomic Prediction Ability of Pre-Harvest Sprouting Resistance in Common Winter Wheat.

Pre-harvest sprouting (PHS) resistance is a complex trait, and many genes influencing the germination process of winter wheat have already been described. In the light of interannual climate variation, breeding for PHS resistance will remain mandatory for wheat breeders. Several tests and traits are used to assess PHS resistance, i.e., sprouting scores, germination index, and falling number (FN), but the variation of these traits is highly dependent on the weather conditions during field trials. Here, we present a method to assess falling number stability (FNS) employing an after-ripening period and the wetting of the kernels to improve trait variation and thus trait heritability. Different genome-based prediction scenarios within and across two subsequent seasons based on overall 400 breeding lines were applied to assess the predictive abilities of the different traits. Based on FNS, the genome-based prediction of the breeding values of wheat breeding material showed higher correlations across seasons (r=0.505-0.548) compared to those obtained for other traits for PHS assessment (r=0.216-0.501). By weighting PHS-associated quantitative trait loci (QTL) in the prediction model, the average predictive abilities for FNS increased from 0.585 to 0.648 within the season 2014/2015 and from 0.649 to 0.714 within the season 2015/2016. We found that markers in the Phs-A1 region on chromosome 4A had the highest effect on the predictive abilities for FNS, confirming the influence of this QTL in wheat breeding material, whereas the dwarfing genes Rht-B1 and Rht-D1 and the wheat-rye translocated chromosome T1RS.1BL exhibited effects, which are well-known, on FN per se exclusively.

Dormancy of a specialist herbivore, Anthonomus rufipennis (Coleoptera: Curculionidae), in a dry tropical forest.

The life history aspects of dormancy of the weevil Anthonomus rufipennis LeConte (Coleoptera: Curculionidae) were studied a 57-month period in a seasonally dry tropical forest of central Mexico. Weevil populations and their physiological status were monitored on both the reproductive host tree, Senna polyantha (Collad.) H.S: Irwin & Barneby (Fabales: Fabaceae) and the highly favored refuge host, Tillandsia recurvata L. (Poales: Bromeliaceae) or "ball moss." During the dry season, weevils were only found on the refuge host with a mean total density of 1.014 ± 2.532 individuals/ball moss (N = 1,681). Weevil densities on T. recurvata between early and late dry seasons were not significantly different, suggesting that dry season survival was relatively high. Weevils collected during these seasons revealed little reproductive development and relatively high-fat accumulation in both sexes. During 5 of 6 yr, densities of the weevils in T. recurvata dropped significantly during the early rainy seasons, when the reproductive host trees leafed out and began producing oviposition sites (flower buds). At this time, more males than females initially moved to vegetative trees and showed significant signs of reproductive development. Recolonization of ball moss by weevils began during the late rainy season when oviposition sites (flower buds) were still available. A proportion of the weevils remained on the reproductive host, suggesting that A. rufipennis is facultatively multivoltine. The methodologies and results of the study can serve as a model system for future studies of the dormancy of other insects in dry tropical forests and provide insight into the dormancy of other anthonomine weevils of economic importance.

Regulation of seed germination: ROS, epigenetic, and hormonal aspects.

BACKGROUND: The whole life of a plant is regulated by complex environmental or hormonal signaling networks that control genomic stability, environmental signal transduction, and gene expression affecting plant development and viability. Seed germination, responsible for the transformation from seed to seedling, is a key initiation step in plant growth and is controlled by unique physiological and biochemical processes. It is continuously modulated by various factors including epigenetic modifications, hormone transport, ROS signaling, and interaction among them. ROS showed versatile crucial functions in seed germination including various physiological oxidations to nucleic acid, protein, lipid, or chromatin in the cytoplasm, cell wall, and nucleus. AIM: of review: This review intends to provide novel insights into underlying mechanisms of seed germination especially associated with the ROS, and considers how these versatile regulatory mechanisms can be developed as useful tools for crop improvement. KEY SCIENTIFIC CONCEPTS OF REVIEW: We have summarized the generation and elimination of ROS during seed germination, with a specific focus on uncovering and understanding the mechanisms of seed germination at the level of phytohormones, ROS, and epigenetic switches, as well as the close connections between them. The findings exhibit that ROS plays multiple roles in regulating the ethylene, ABA, and GA homeostasis as well as the Ca2+ signaling, NO signaling, and MAPK cascade in seed germination via either the signal trigger or the oxidative modifier agent. Further, ROS shows the potential in the nuclear genome remodeling and some epigenetic modifiers function, although the detailed mechanisms are unclear in seed germination. We propose that ROS functions as a hub in the complex network regulating seed germination.

Exploring the potential of Paris polyphylla var. yunnanensis pollen manipulation in modifying seed dormancy.

Paris polyphylla var. yunnanensis, a well-known Chinese medicinal herb, shows a unique physiological trait characterized by the cyclic opening and closing of its anthers after pollen maturation. The aim of this study was to explore the implications of this phenomenon on breeding. RNA sequencing coupled with methylation sequencing was used to scrutinize and compare gene expression profiles and methylation alterations in pollen and seeds during anther opening and closing, along with cold exposure. Genes enriched within Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were examined to identify gene clusters susceptible to temperature-related methylation changes in both pollen and seeds. Four pollen treatment models, namely, normal control, "pollen protected from low temperatures," "pollen from just-opened anther," and "pollen from close-blocked anther," were used to produce corresponding seeds via artificial pollination. Subsequently, qRT-PCR was used to validate modifications in the expression patterns of marker genes in pollinated seeds under diverse treatment scenarios. Genes exhibiting significant differences in expression between anthers and normal tissues, along with gene regions linked to methylation variations attributed to low-temperature-treated pollen and seeds, were identified through transcriptomic analysis. Convergence was observed in three signaling pathways: oxidative phosphorylation (ko00190), plant hormone signal transduction (Ko04075), and zeatin biosynthesis (ko00908). Notably, gene clusters prone to temperature-induced methylation changes, such as NADH-ubiquinone oxidoreductase chain 5, plasma membrane ATPase 4, cytochrome c oxidase subunit 2, cis-zeatin O-glucosyltransferase, ABSCISIC ACID-INSENSITIVE 5-like protein 4, and indole-3-acetic acid-amido synthetase (IAAS), were identified. Evaluation using various pollen pollination models revealed altered expression patterns of five dormancy-regulating marker genes: IAAS, sucrose synthase (SUS), gibberellin 2-oxidase (GA2ox), ABA INSENSITIVE 2 (ABI2), and auxin-repressed protein (ARP), in seeds pollinated with pollen from close-blocked anthers, cold-protected pollen, and pollen from freshly opened anthers. The close-blocked anther treatment led to significantly upregulated expression of IAAS, SUS, GA2ox, and ABI2, whereas ARP expression decreased markedly, indicating a propensity toward prolonged seed dormancy. Conversely, in the low-temperature-protected anther model, SUS, ARP, GA2ox, and IAAS exhibited reduced expression levels, whereas the expression of ABI2 was upregulated, overall facilitating seed germination.

Evolutionary reversal of physical dormancy to nondormancy: evidence from comparative seed morphoanatomy of Argyreia species (Convolvulaceae).

Argyreia is the most recently evolved genus in the Convolvulaceae, and available information suggests that most species in this family produce seeds with physical dormancy (PY). Our aim was to understand the evolution of seed dormancy in this family via an investigation of dormancy, storage behaviour, morphology and anatomy of seeds of five Argyreia species from Sri Lanka. Imbibition, germination and dye tracking of fresh intact and manually scarified seeds were studied. Scanning electron micrographs and hand sections of the hilar area and the seed coat away from the hilar area were compared. Scarified and intact seeds of A. kleiniana, A. hirsuta and A. zeylanica imbibed water and germinated to a high percentage, but only scarified seeds of A. nervosa and A. osyrensis did so. Thus, seeds of the three former species are non-dormant (ND), while those of the latter two have physical dormancy (PY); this result was confirmed by dye-tracking experiments. Since >90% of A. kleiniana, A. hirsuta and A. zeylanica seeds survived desiccation to 10% moisture content (MC) and >90% of A. nervosa and A. osyrensis seeds with a dispersal MC of ~12% were viable, seeds of the five species were desiccation-tolerant. A. nervosa and A. osyrensis have a wide geographical distribution and PY, while A. kleiniana, A. hirsuta and A. zeylanica have a restricted distribution and ND. Although seeds of A. kleiniana are ND, their seed coat anatomy is similar to that of A. osyrensis with PY. These observations suggest that the ND of A. kleiniana, A. hirsuta and A. zeylanica seeds is the result of an evolutionary reversal from PY and that ND may be an adaptation of these species to the environmental conditions of their wet aseasonal habitats.

Long days induce adaptive secondary dormancy in the seeds of the Mediterranean plant Aethionema arabicum.

Secondary dormancy is an adaptive trait that increases reproductive success by aligning seed germination with permissive conditions for seedling establishment. Aethionema arabicum is an annual plant and member of the Brassicaceae that grows in environments characterized by hot and dry summers. Aethionema arabicum seeds may germinate in early spring when seedling establishment is permissible. We demonstrate that long-day light regimes induce secondary dormancy in the seeds of Aethionema arabicum (CYP accession), repressing germination in summer when seedling establishment is riskier. Characterization of mutants screened for defective secondary dormancy demonstrated that RGL2 mediates repression of genes involved in gibberellin (GA) signaling. Exposure to high temperature alleviates secondary dormancy, restoring germination potential. These data are consistent with the hypothesis that long-day-induced secondary dormancy and its alleviation by high temperatures may be part of an adaptive response limiting germination to conditions permissive for seedling establishment in spring and autumn.

Therapy-induced senescence is finally escapable, what is next?

Several breakthrough articles have recently confirmed the ability of tumor cells to escape the stable cell cycle arrest imposed by Therapy-Induced Senescence (TIS). Subsequently, accepting the hypothesis that TIS is escapable should encourage serious reassessments of the fundamental roles of senescence in cancer treatment. The potential for escape from TIS undermines the well-established tumor suppressor function of senescence, proposes it as a mechanism of tumor dormancy leading to disease recurrence and invites for further investigation of its unfavorable contribution to cancer therapy outcomes. Moreover, escaping TIS strongly indicates that the elimination of senescent tumor cells, primarily through pharmacological means, is a suitable approach for increasing the efficacy of cancer treatment, one that still requires further exploration. This commentary provides an overview of the recent evidence that unequivocally demonstrated the ability of therapy-induced senescent tumor cells in overcoming the terminal growth arrest fate and provides future perspectives on the roles of TIS in tumor biology.

Developing a dormancy-associated ECM signature in TNBC that is linked to immunosuppressive tumor microenvironment and selective sensitivity to MAPK inhibitors.

Aims: Cellular dormancy is a state of quiescence subpopulation of tumor cells, characterized by low differentiation and lack of mitotic activity. They could evade chemotherapy and targeted therapy, leading to drug resistance and disease recurrence. Recent studies have shown a correlation between dormant cancer cells and unique extracellular matrix (ECM) composition, which is critical in regulating cell behavior. However, their interacting roles in TNBC patients remains to be characterized. Main methods: Dormant cancer cells in MDA-MB-231 cell line with highest PKH26 dye-retaining were FACS-sorted and gene expression was then analyzed. Dormant associated ECM (DA-ECM) signature was characterized by pathway analysis. Unsupervised hierarchical clustering was used to define distinct ECM features for TNBC patients. ECM-specific tumor biology was defined by integration of bulk RNA-seq with single-cell RNA-seq data, analysis of ligand-receptor interactions and enriched biological pathways, and in silico drug screening. We validated the sensitivity of dormant cancer cells to MAPK inhibitors by flow cytometry in vitro. Key findings: We observed that dormant TNBC cells preferentially expressed ∼10 % DA-ECM genes. The DA-ECM High subtype defined by unsupervised hierarchical clustering analysis was associated with immunosuppressive tumor microenvironment. Moreover, ligand-receptor interaction and pathway analysis revealed that the DA-ECM High subtype may likely help maintain tumor cell dormancy through MAPK, Hedgehog and Notch signaling pathways. Finally, in silico drug screening against the DA-ECM signature and in vitro assay showed dormant cancer cells were relatively sensitive to the MAPK pathway inhibitors, which may represent a potential therapeutic strategy for treating TNBC. Significance: Collectively, our research revealed that dormancy-associated ECM characterized tumor cells possess significant ECM remodeling capacity, and treatment strategies towards these cells could improve TNBC patient outcome.

Mycobacterial biofilms: A therapeutic target against bacterial persistence and generation of antibiotic resistance.

Mycobacterium tuberculosis (M. tb) is the causative agent of Tuberculosis, one of the deadliest infectious diseases. According to the WHO Report 2023, in 2022, approximately 10.6 million people got infected with TB, and 1.6 million died. It has multiple antibiotics for treatment, but the major drawback of anti-tuberculosis therapy (ATT) is, its prolonged treatment duration. The major contributors to the lengthy treatment period are mycobacterial persistence and drug tolerance. Persistent M. tb is phenotypically drug tolerant and metabolically slow down which makes it difficult to be eliminated during ATT. These persisting bacteria are a huge reservoir of impending disease, waiting to get reactivated upon the onset of an immune compromising state. Directly Observed Treatment Short-course, although effective against replicating bacteria; fails to eliminate the drug-tolerant persisters making TB still the second-highest killer globally. There are different mechanisms for the development of drug-tolerant mycobacterial populations being investigated. Recently, the role of biofilms in the survival and host-evasion mechanism of persisters has come to light. Therefore, it is crucial to understand the mechanism of adaptation, survival and attainment of drug tolerance by persisting M. tb-populations, in order to design better immune responses and therapeutics for the effective elimination of these bacteria by reducing the duration of treatment and also circumvent the generation of drug-resistance to achieve the goal of global eradication of TB. This review summarizes the drug-tolerance mechanism and biofilms' role in providing a niche to dormant-M.tb. We also discuss methods of targeting biofilms to achieve sterile eradication of the mycobacteria and prevent its reactivation by achieving adequate immune responses.

Voltinism of a solitary bee was influenced by temperature but not provision size.

Changes in the timing and duration of life cycles are distinctive fingerprints of environmental change. Yet, the biotic and abiotic cues underpinning phenology and voltinism, i.e., number of generations per year, are poorly understood. Here, I experimentally test how temperature and provision size influence voltinism and survival to emergence in a solitary bee Colletes validus, and how temperature influences voltinism in the brood parasite Tricrania sanguinipennis. Within the same population, univoltine individuals emerge after 1 year (1-year form), whereas semivoltine individuals enter prolonged dormancy and emerge after 2 years (2-year form). I reared field-collected bees under 2 × 2 factorial experiments with cool (18.5 °C ± 0.5 °C) vs. warm (24 °C ± 0.5 °C) temperature treatments (bees and beetles) and no supplement vs. supplemental food treatments (+ 20% ± 5% pollen provision by mass); beetles were reared under temperature treatments only. Cool temperatures consistently increased the proportion of 2-year bees regardless of provision size, a finding that was consistent with three years of field observations. There was a demographic cost to prolonged dormancy in that both 1- and 2-year bees survived to emergence as adults, but survival of 2-year bees was approximately 50% lower than 1-year bees. Two-year beetles were produced under cooler temperatures, but unlike bees, beetles had nearly perfect survival to emergence in all treatments. This experiment advances our mechanistic understanding of the environmental drivers of voltinism in diverse insect taxa and underscores the importance of considering cryptic life stages when interpreting responses to environmental change.

A tree peony RING-H2 finger protein, PsATL33, plays an essential role in cold-induced bud dormancy release by regulating gibberellin content.

Bud dormancy is crucial for woody perennial plants to resist low-temperature stress in winter. However, the molecular regulatory mechanisms underlying bud dormancy release are largely unclear. Here, a tree peony (Paeonia suffruticosa) transcript ARABIDOPSIS TOXICOS EN LEVADURA 33 (PsATL33), encoding a RING-H2 finger protein, was selected from previously generated RNA sequencing data of chilling-treated buds. The objective of this study is to investigate the role of PsATL33 in the regulation of cold-induced bud dormancy release. Subcellular localization assay revealed that PsATL33 was localized to the nucleus and plasma membrane. Reverse transcription-quantitative PCR analysis showed that PsATL33 was dramatically upregulated during cold-triggered bud dormancy release. Exogenous treatments with gibberellin (GA3) increased, but abscisic acid (ABA) inhibited the transcription of PsATL33. Ectopic transformation assay indicated that overexpression of PsATL33 in petunia promoted seed germination, plant growth, and axillary bud break. Silencing of PsATL33 in tree peony through virus-induced gene silencing assay delayed bud dormancy release. tobacco rattle virus (TRV)-PsATL33-infected buds exhibited reduced expression levels of dormancy break-related genes EARLY BUD-BREAK 1 (PsEBB1) and CARBOXYLESTERASE 15 (PsCXE15). Silencing of PsATL33 decreased the accumulation of bioactive GAs, GA1 and GA3, rather than ABA. Transcript levels of several genes involved in GA biosynthesis and signaling, including GA20-OXIDASE 1 (PsGA20ox1), GA3-OXIDASE 1 (PsGA3ox1), PsGA3ox3, GA2-OXIDASE 1 (PsGA2ox1), and GA-INSENSITIVE 1A (PsGAI1A), were changed by PsATL33 silencing. Taken together, our data suggest that PsATL33 functions as a positive regulator of cold-induced bud dormancy release by modulating GA production.

Methodological and Physiological Study during Seed Dormancy Release of Symplocos paniculata.

Symplocos paniculata are reported to exhibit seed dormancy, which impedes its cultivation and widespread adoption. In this study, a comprehensive method was established to overcome seed dormancy by subjecting seeds to scarification in 98% H2SO4 for 10 min, followed by 1000 mg·L-1 GA3 soaking for 48 h and stratification at 4 °C for 100 days. The seed germination percentage has increased significantly, to a peak of 42.67%, though the seeds could not germinate timely by NaOH scarification. Additionally, the dynamic changes of key stored substances (proteins, soluble sugars, starches, and fats), associated enzyme activities (amylases, peroxidase, and catalase), and endogenous hormones (abscisic acid, gibberellic acid, and indole-3-acetic acid) in seeds were investigated. The results demonstrated a continuous degradation of starch and fat in S. paniculata seeds, while the levels of protein and soluble sugar exhibited fluctuations, which probably facilitated seed dormancy breaking through energy supply and transformation. The enzymatic activities underwent rapid changes, accompanied by a gradual decrease in ABA content within the seeds with increasing stratification time. Notably, GA3, GA3/ABA, and (GA3 + IAA)/ABA showed significant increases, indicating their positive regulatory roles in seed germination. This study clarified the dormancy mechanism and established an effective method for the release dormancy of S. paniculata seeds.

Physical Seed Dormancy in Legumes: Molecular Advances and Perspectives.

Physical dormancy of seeds is a form of dormancy due to the presence of an impermeable seed coat layer, and it represents a feature for plants to adapt to environmental changes over an extended period of phylogenetic evolution. However, in agricultural practice, physical dormancy is problematic. because it prevents timely and uniform seed germination. Therefore, physical dormancy is an important agronomical trait to target in breeding and domestication, especially for many leguminous crops. Compared to the well-characterized physiological dormancy, research progress on physical dormancy at the molecular level has been limited until recent years, due to the lack of suitable research materials. This review focuses on the structure of seed coat, factors affecting physical dormancy, genes controlling physical dormancy, and plants suitable for studying physical dormancy at the molecular level. Our goal is to provide a plethora of information for further molecular research on physical dormancy.

Effective anti-tumor immune response against HCC is orchestrated by immune cell partnership network that functions through hepatic homeostatic pathways, not direct cytotoxicity.

The liver harbors a diverse array of immune cells during both health and disease. The specific roles of these cells in nonalcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC) remain unclear. Using a systems immunology approach, we demonstrate that reciprocal cell-cell communications function through dominant-subdominant pattern of ligand-receptor homeostatic pathways. In the healthy control, hepatocyte-dominated homeostatic pathways induce local immune responses to maintain liver homeostasis. Chronic intake of a Western diet (WD) alters hepatocytes and induces hepatic stellate cell (HSC), cancer cell and NKT cell-dominated interactions during NAFLD. During HCC, monocytes, hepatocytes, and myofibroblasts join the dominant cellular interactions network to restore liver homeostasis. Dietary correction during NAFLD results in nonlinear outcomes with various cellular rearrangements. When cancer cells and stromal cells dominate hepatic interactions network without inducing homeostatic immune responses, HCC progression occurs. Conversely, myofibroblast and fibroblast-dominated network orchestrates monocyte-dominated HCC-preventive immune responses. Tumor immune surveillance by 75% of immune cells successfully promoting liver homeostasis can create a tumor-inhibitory microenvironment, while only 5% of immune cells manifest apoptosis-inducing functions, primarily for facilitating homeostatic liver cell turnover rather than direct tumor killing. These data suggest that an effective immunotherapy should promote liver homeostasis rather than direct tumor killing.

Deep learning with a small dataset predicts chromatin remodelling contribution to winter dormancy of apple axillary buds.

Epigenetic changes serve as a cellular memory for cumulative cold recognition in both herbaceous and tree species, including bud dormancy. However, most studies have discussed predicted chromatin structure with respect to histone marks. In the present study, we investigated the structural dynamics of bona fide chromatin to determine how plants recognise prolonged chilling during the initial stage of bud dormancy. The vegetative axillary buds of the 'Fuji' apple, which shows typical low temperature-dependent, but not photoperiod, dormancy induction, were used for the chromatin structure and transcriptional change analyses. The results were integrated using a deep-learning model and interpreted using statistical models, including Bayesian estimation. Although our model was constructed using a small dataset of two time points, chromatin remodelling due to random changes was excluded. The involvement of most nucleosome structural changes in transcriptional changes and the pivotal contribution of cold-driven circadian rhythm-dependent pathways regulated by the mobility of cis-regulatory elements were predicted. These findings may help to develop potential genetic targets for breeding species with less bud dormancy to overcome the effects of short winters during global warming. Our artificial intelligence concept can improve epigenetic analysis using a small dataset, especially in non-model plants with immature genome databases.

Ectodermal origin and tissue dedifferentiation in the podocyst production by the polyps of the Asian moon jelly (Aurelia coerulea).

The histological origin of podocysts in scyphozoans has long been undetermined, with uncertainty whether they arise from mesenchymal amoebocytes or stalk and pedal disc ectoderm in polyps. Histological investigation on the pedal disc was difficult due to the settlement of polyps on hard substrates. In this study, we investigated the histological characteristics of polyps during podocyst production in Asian moon jelly (Aurelia coerulea) with utilizing those attached on thin polystyrene substrates. Fine histological features of the pedal disc became possible after the substrates were decomposed during histological processing. Our findings unequivocally demonstrate that the cell mass of podocysts originates from the ectoderm of the pedal disc and the stalk without the involvement of amoebocytes in the mesoglea. Preceding the podocyst formation, the pedal disc undergoes enlargement facilitated by the elongated stalk ectodermal cells, which attach to a substrate. Subsequently, the pedal disc ectoderm give rise to the primary podocyst cells with accumulating nutrient granules in the cytoplasm and forming the cyst capsule cooperatively with the invaginated pedal disc ectoderm. Direct transformation from the ectodermal cells to podocyst cells suggests that podocyst formation involves tissue dedifferentiation. Throughout the period of podocyst production, the gastrodermis of polyps is physically separated from the ectoderm by the mesoglea and shows no histological changes, and no amoebocytes appear in the mesoglea. These histological properties are totally different from those in other modes of asexual reproduction, which incorporate the endoderm of polyps, suggesting the developmental and evolutionary differences between these asexual reproductions and podocyst production in Scyphozoa.

Bigger isn't always better: Challenging assumptions about the associations between diapause, body weight, and overwintering survival.

During the winter, animals face limited food availability. Many animals enter dormancy to reduce their winter energy expenditure. Most insects spend the winter in diapause, a state of programmed dormancy. It is often assumed that diapausing insects need nutrient stores to fuel their many months of basal metabolism and must grow heavier than their non-diapause-programmed counterparts. However, the extent to which food limitation affects body weight during overwintering preparation as well as the likelihood and duration of diapause remains unclear. We limited the duration of the feeding period and thus the total quantity of food available to diapause-destined larvae of the pupal-diapausing flesh fly, Sarcophaga crassipalpis, to test how food limitation affects body weight in the context of diapause programming. We also tested the extent to which food deprivation and body weight affect the likelihood and duration of diapause. We hypothesized that diapause-destined larvae grow more quickly and pupariate at a heavier body weight than non-diapause larvae. We also hypothesized that body weight is more dramatically reduced by food limitations when a larva is programmed for diapause. Finally, we hypothesized that larvae with lighter body weight (i.e., food limited) are less likely to enter pupal diapause and also stay in diapause for a shorter duration than heavier, well-fed, individuals. Contrary to our hypotheses that diapausing insects are heavier than their non-diapausing counterparts, we found diapausing pupae weighed less than non-diapausing pupae, especially when larvae received limited food. We found light pupae did not abort their diapause program. In both diapausing and non-diapausing pupae, body weight was positively correlated with simulated winter survival. However, above a weight threshold, body weight no longer affected simulated winter survival in diapausing pupae. Contrary to our predictions and the general consensus in much of the diapause literature, we also found that lighter pupae stayed in diapause longer than heavier pupae. Overall, our results challenge the precept that body weight and diapause are positively associated. The relationship between body weight and diapause is complex and may be affected by the availability of food before and after winter, the availability of high-quality overwintering sites, and the life history of a particular insect.

Identification of ARF Genes and Elucidation of the Regulatory Effects of PsARF16a on the Dormancy of Tree Peony Plantlets.

The low survival rate of transplanted plantlets, which has limited the utility of tissue-culture-based methods for the rapid propagation of tree peonies, is due to plantlet dormancy after rooting. We previously determined that the auxin response factor PsARF may be a key regulator of tree peony dormancy. To clarify the mechanism mediating tree peony plantlet dormancy, PsARF genes were systematically identified and analyzed. Additionally, PsARF16a was transiently expressed in the leaves of tree peony plantlets to examine its regulatory effects on a downstream gene network. Nineteen PsARF genes were identified and divided into four classes. All PsARF genes encoded proteins with conserved B3 and ARF domains. The number of motifs, exons, and introns varied between PsARF genes in different classes. The overexpression of PsARF16a altered the expression of NCED, ZEP, PYL, GA2ox1, GID1, and other key genes in abscisic acid (ABA) and gibberellin (GA) signal transduction pathways, thereby promoting ABA synthesis and decreasing GA synthesis. Significant changes to the expression of some key genes contributing to starch and sugar metabolism (e.g., AMY2A, BAM3, BGLU, STP, and SUS2) may be associated with the gradual conversion of sugar into starch. This study provides important insights into PsARF functions in tree peonies.