Latitude or altitude as the future refugium? A case for the future of forests in Asia Minor and its surroundings

At the current juncture with climate change, centennial projections of species distributions in biodiversity hotspots, using dynamic vegetation models may provide vital insight into conservation efforts. This study aims to answer: (1) if climate change progresses under a business-as-usual scenario of anthropogenic emissions for this century, how may the forest ranges be affected? (2) will there be potential regional extinctions of the taxa simulated? (3) may any site emerge as a potential refugium?

STUDY AREA

Anatolian Peninsula and its surroundings, longitudes 24-50° E, latitudes 33-46° N. Time Period: 1961-2100. Major Taxa Studied: 25 woody species and a C3 grass-type.

METHOD

Keeping a spatial window large enough to track potential changes in the vegetation range and composition especially in the mountain ranges within the study area, we parameterized a process-based regional-to-global dynamic vegetation model (LPJ-GUESS v 4.1), forced it with ERA5-Land reanalysis for the historical period, and five different bias-corrected centennial global circulation model (GCM) datasets under SSP5-8.5, and simulated the dynamic responses of key forest species. Bivariate spatio-temporal maps from the simulation results were constructed for final analysis.

RESULTS

A significant increase in woody taxa biomass for the majority of our study area, towards the end of the century was simulated, where temperate taxa with high tolerance for drought and a wider range of temperatures took dominance. The mountain ranges in our study area stood out as critical potential refugia for cold favoring species. There were no regional extinctions of taxa, however, important changes in areal dominance and potential future forest composition were simulated.

MAIN CONCLUSIONS

Our simulation results suggest a high potential for future forest cover in our study region by the end of the century under a high emissions scenario, sans human presence, with important changes in vegetation composition, including encroachment of grasslands ecosystems by woody taxa.

Depolymerization of actin filaments by Cucurbitacin I through binding G-actin

Cucurbitacins have high economic value as they are a major source of food and have pharmacological properties. Cucurbitacin I (CuI) is a plant-derived natural tetracyclic triterpenoid compound that shows an anticancer effect via inhibiting the JAK2-STAT3 signaling pathway. The actin cytoskeleton is the most abundant protein in cells and regulates critical events through reorganization in cells. In this study, it is aimed at determining the direct effect of CuI on actin dynamics. The fluorescence profile of G-actin in the presence of CuI (1-200 nM) shifted to a higher temperature, suggesting that G-actin binds CuI and that G-actin-CuI is more thermally stable than the ligand-free form. CuI dose-dependently inhibited the polymerization of F-actin in vitro and disrupted actin filaments in endothelial cells. Docking and MD simulations suggested that CuI binds to the binding site formed by residues I136, I175, D154, and A138 that are at the interface of monomers in F-actin. The migration ability of cells treated with CuI for 24 h was significantly lower than the control group (p < .001). This study reveals the molecular mechanisms of CuI in the regulation of actin dynamics by binding G-actin. More importantly, this study indicates a novel role of CuI as an actin-targeting drug by binding directly to G-actin and may contribute to the mode of action of CuI on anticancer activities.

Drying of Tarhana dough by Refractance Window™ technology under vacuum/atmospheric conditions: Characterization of physical and quality parameters

This study aimed to produce dried tarhana using a refractance window drying (RWD) system. The drying process was also carried out under vacuum; the current study is the first in the literature. Using different heating mediums, the maximum temperature can be adjusted to a level above that used in RWD studies. Considering results, process time savings in RWD were over 85% and 75% compared to control groups (oven and hot air dryer), respectively. Tarhana samples dried in RWD were also faster (50%) under vacuum conditions than atmospheric ones. The highest preservation of total phenolic content (TPC) and total antioxidant activity (TAA) was for samples dried by RWD at 110°C under atmospheric conditions. Techno-physical properties were better than the control group. The rheological behavior of tarhana soups was similar to pseudoplastic flow behavior and well defined by the Power law and Herschel-Bulkey models. In conclusion, RWD can be a promising technique for tarhana production.

Development of a mouse embryonic stem cell model for investigating the functions of the linker histone H1-4

The linker histone H1 C-terminal domain (CTD) plays a pivotal role in chromatin condensation. De novo frameshift mutations within the CTD coding region of H1.4 have recently been reported to be associated with Rahman syndrome, a neurological disease that causes intellectual disability and overgrowth. To investigate the mechanisms and pathogenesis of Rahman syndrome, we developed a cellular model using murine embryonic stem cells (mESCs) and CRISPR/Cas9 genome engineering. Our engineered mES cells facilitate detailed investigations, such as H1-4 dynamics, immunoprecipitation, and nuclear localization; in addition, we tagged the mutant H1-4 with a photoactivatable GFP (PA-GFP) and an HA tag to facilitate pulldown assays. We anticipate that these engineered cells could also be used for the development of a mouse model to study the in vivo role of the H1-4 protein.

Cellular models in autoinflammatory disease research

Systemic autoinflammatory diseases are a heterogeneous group of rare genetic disorders caused by dysregulation of the innate immune system. Understanding the complex mechanisms underlying these conditions is critical for developing effective treatments. Cellular models are essential for identifying new conditions and studying their pathogenesis. Traditionally, these studies have used primary cells and cell lines of disease-relevant cell types, although newer induced pluripotent stem cell (iPSC)-based models might have unique advantages. In this review, we discuss the three cellular models used in autoinflammatory disease research, their strengths and weaknesses, and their applications to inform future research in the field.

Comparative efficacy of different tenderizing agents and time on Physicochemical textural and organoleptic properties of squid (Todarodes pacificus) muscle

This study aimed to investigate the chemical, physical, textural, and sensory properties of the squid (Todarodes pacificus) muscle during different tenderization agents (yeast, milk, and mineral water) and times (3, 6, 12, and 24 h). The results of the analyses showed that different treatments and their durations affected the dry matter, ash, lipid, and crude protein content of the squid. According to sodium dodecyl sulfate-polyacrylamide gel electrophoresis results, it was observed that there was a slight decrease in band intensities based on different treatments and their durations. However, no significant changes were observed in myosin actin and paramyosin bands. It was found that the hardness (359.7 N), cohesiveness (0.63), and gumminess (233.2 N) parameters increased at the 6th hour, decreased at the 12th hour, and increased again at the 24th hour of the treatment. According to the scanning electron microscopy results, the most affected groups by the application and duration were found to be the mineral water group at the 12th and 24th hours, and the milk group at the 24th hour. Fibers in all marinated squid muscles were observed to spring significantly more compared to the positive and negative control groups. The taste score was found to be significantly higher in the group treated with yeast for 3 h and it was evaluated by the panelists as the most delicious squid among all of the groups. As a result of the study, it was determined that the chemical, physical, and sensory properties of squid could be improved by marinating with yeast, milk, and mineral water for different durations.

Prediction of amputation risk of patients with diabetic foot using classification algorithms: A clinical study from a tertiary center

Diabetic foot ulcers can have vital consequences, such as amputation for patients. The primary purpose of this study is to predict the amputation risk of diabetic foot patients using machine-learning classification algorithms. In this research, 407 patients treated with the diagnosis of diabetic foot between January 2009-September 2019 in Istanbul University Faculty of Medicine in the Department of Undersea and Hyperbaric Medicine were retrospectively evaluated. Principal Component Analysis (PCA) was used to identify the key features associated with the amputation risk in diabetic foot patients within the dataset. Thus, various prediction/classification models were created to predict the "overall" risk of diabetic foot patients. Predictive machine-learning models were created using various algorithms. Additionally to optimize the hyperparameters of the Random Forest Algorithm (RF), experimental use of Bayesian Optimization (BO) has been employed. The sub-dimension data set comprising categorical and numerical values was subjected to a feature selection procedure. Among all the algorithms tested under the defined experimental conditions, the BO-optimized "RF" based on the hybrid approach (PCA-RF-BO) and "Logistic Regression" algorithms demonstrated superior performance with 85% and 90% test accuracies, respectively. In conclusion, our findings would serve as an essential benchmark, offering valuable guidance in reducing such hazards.

Microwave-assisted extraction optimization of sesquiterpene lactones from Inula helenium roots: A sustainable approach to reduce energy consumption and carbon footprint

Inula helenium roots are consumed as natural flavor components and raw or cooked as food, and their extracts are rich in sesquiterpene lactones such as alantolactone (AL) and isoalantolactone (IAL), which have recently attracted great attention due to their pharmacological properties. The industrial utilization of these compounds requires the development of green, efficient, cost-effective, and sustainable extraction protocols. Therefore, this study focused on the optimization of microwave-assisted extraction (MAE) process variables using Face-Centered Central Composite Design (FC-CCD). Then, maceration was applied as a conventional technique, and these techniques were compared in terms of extraction efficiency, morphological changes, antimicrobial activities, carbon emissions, and energy consumption. As a result, optimal MAE conditions, i.e., EtOH: water ratio (X 1) = 100:0, liquid/sample ratio (X 2) = 30:1 mL/g, microwave power (X 3) = 300 W, and irradiation time (X 4) = 5 min, were obtained with AL and IAL yields of 54.99 ± 0.11 (mg/g) and 48.40 ± 0.19 (mg/g), respectively. The extract obtained by MAE had similar or better activity than positive controls in most cases and formed the largest inhibition zones against E. coli (29.5 ± 0.71 mm) and A. niger (34.75 ± 1.06 mm). Morphological changes of I. helenium roots after extraction were observed by scanning electron microscopy. Additionally, MAE was 43.4 times faster than maceration, resulting in 228.6 times less energy consumption and carbon emissions. Based on these findings, it is recommended to use MAE as an industrial green technique for the extraction of sesquiterpene lactones with potential applications in nutraceuticals and food products in terms of sustainable economy and environmental protection.

Synergistic coupling between 3D bioprinting and vascularization strategies

Three-dimensional (3D) bioprinting offers promising solutions to the complex challenge of vascularization in biofabrication, thereby enhancing the prospects for clinical translation of engineered tissues and organs. While existing reviews have touched upon 3D bioprinting in vascularized tissue contexts, the current review offers a more holistic perspective, encompassing recent technical advancements and spanning the entire multistage bioprinting process, with a particular emphasis on vascularization. The synergy between 3D bioprinting and vascularization strategies is crucial, as 3D bioprinting can enable the creation of personalized, tissue-specific vascular network while the vascularization enhances tissue viability and function. The review starts by providing a comprehensive overview of the entire bioprinting process, spanning from pre-bioprinting stages to post-printing processing, including perfusion and maturation. Next, recent advancements in vascularization strategies that can be seamlessly integrated with bioprinting are discussed. Further, tissue-specific examples illustrating how these vascularization approaches are customized for diverse anatomical tissues towards enhancing clinical relevance are discussed. Finally, the underexplored intraoperative bioprinting (IOB) was highlighted, which enables the direct reconstruction of tissues within defect sites, stressing on the possible synergy shaped by combining IOB with vascularization strategies for improved regeneration.

A zebrafish model for studying the mechanisms of newborn hyperbilirubinemia and bilirubin-induced neurological damage

Unresolved neonatal hyperbilirubinemia may lead to the accumulation of excess bilirubin in the body, and bilirubin in neural tissues may induce toxicity. Bilirubin-induced neurological damage (BIND) can result in acute or chronic bilirubin encephalopathy, causing temporary or lasting neurological dysfunction or severe damage resulting in infant death. Although serum bilirubin levels are used as an indication of severity, known and unknown individual differences affect the severity of the symptoms. The mechanisms of BIND are not yet fully understood. Here, a zebrafish newborn hyperbilirubinemia model is developed and characterized. Direct exposure to excess bilirubin induced dose- and time-dependent toxicity linked to the accumulation of bilirubin in the body and brain. Introduced bilirubin was processed by the liver, which increased the tolerance of larvae. BIND in larvae was demonstrated by morphometric measurements, histopathological analyses and functional tests. The larvae that survived hyperbilirubinemia displayed mild or severe morphologies associated with defects in eye movements, body posture and swimming problems. Interestingly, a plethora of mild to severe clinical symptoms were reproduced in the zebrafish model.

Canonical Wnt and TGF-β/BMP signaling enhance melanocyte regeneration but suppress invasiveness, migration, and proliferation of melanoma cells

Melanoma is the deadliest form of skin cancer and develops from the melanocytes that are responsible for the pigmentation of the skin. The skin is also a highly regenerative organ, harboring a pool of undifferentiated melanocyte stem cells that proliferate and differentiate into mature melanocytes during regenerative processes in the adult. Melanoma and melanocyte regeneration share remarkable cellular features, including activation of cell proliferation and migration. Yet, melanoma considerably differs from the regenerating melanocytes with respect to abnormal proliferation, invasive growth, and metastasis. Thus, it is likely that at the cellular level, melanoma resembles early stages of melanocyte regeneration with increased proliferation but separates from the later melanocyte regeneration stages due to reduced proliferation and enhanced differentiation. Here, by exploiting the zebrafish melanocytes that can efficiently regenerate and be induced to undergo malignant melanoma, we unravel the transcriptome profiles of the regenerating melanocytes during early and late regeneration and the melanocytic nevi and malignant melanoma. Our global comparison of the gene expression profiles of melanocyte regeneration and nevi/melanoma uncovers the opposite regulation of a substantial number of genes related to Wnt signaling and transforming growth factor beta (TGF-β)/(bone morphogenetic protein) BMP signaling pathways between regeneration and cancer. Functional activation of canonical Wnt or TGF-β/BMP pathways during melanocyte regeneration promoted melanocyte regeneration but potently suppressed the invasiveness, migration, and proliferation of human melanoma cells in vitro and in vivo. Therefore, the opposite regulation of signaling mechanisms between melanocyte regeneration and melanoma can be exploited to stop tumor growth and develop new anti-cancer therapies.

Mapping of the gene in tomato conferring resistance to root-knot nematodes at high soil temperature

Root-knot nematodes (RKNs, Meloidogyne spp.) can cause severe yield losses in tomatoes. The Mi-1.2 gene in tomato confers resistance to the Meloidogyne species M. incognita, M. arenaria and M. javanica, which are prevalent in tomato growing areas. However, this resistance breaks down at high soil temperatures (>28°C). Therefore, it is imperative that new resistance sources are identified and incorporated into commercial breeding programmes. We identified a tomato line, MT12, that does not have Mi-1.2 but provides resistance to M. incognita at 32°C soil temperature. An F2 mapping population was generated by crossing the resistant line with a susceptible line, MT17; the segregation ratio showed that the resistance is conferred by a single dominant gene, designated RRKN1 (Resistance to Root-Knot Nematode 1). The RRKN1 gene was mapped using 111 Kompetitive Allele Specific PCR (KASP) markers and characterized. Linkage analysis showed that RRKN1 is located on chromosome 6 and flanking markers placed the locus within a 270 kb interval. These newly developed markers can help pyramiding R-genes and generating new tomato varieties resistant to RKNs at high soil temperatures.

TRAIL promotes the polarization of human macrophages toward a proinflammatory M1 phenotype and is associated with increased survival in cancer patients with high tumor macrophage content

Background

TNF-related apoptosis-inducing ligand (TRAIL) is a member of the TNF superfamily that can either induce cell death or activate survival pathways after binding to death receptors (DRs) DR4 or DR5. TRAIL is investigated as a therapeutic agent in clinical trials due to its selective toxicity to transformed cells. Macrophages can be polarized into pro-inflammatory/tumor-fighting M1 macrophages or anti-inflammatory/tumor-supportive M2 macrophages and an imbalance between M1 and M2 macrophages can promote diseases. Therefore, identifying modulators that regulate macrophage polarization is important to design effective macrophage-targeted immunotherapies. The impact of TRAIL on macrophage polarization is not known.

Methods

Primary human monocyte-derived macrophages were pre-treated with either TRAIL or with DR4 or DR5-specific ligands and then polarized into M1, M2a, or M2c phenotypes in vitro. The expression of M1 and M2 markers in macrophage subtypes was analyzed by RNA sequencing, qPCR, ELISA, and flow cytometry. Furthermore, the cytotoxicity of the macrophages against U937 AML tumor targets was assessed by flow cytometry. TCGA datasets were also analyzed to correlate TRAIL with M1/M2 markers, and the overall survival of cancer patients.

Results

TRAIL increased the expression of M1 markers at both mRNA and protein levels while decreasing the expression of M2 markers at the mRNA level in human macrophages. TRAIL also shifted M2 macrophages towards an M1 phenotype. Our data showed that both DR4 and DR5 death receptors play a role in macrophage polarization. Furthermore, TRAIL enhanced the cytotoxicity of macrophages against the AML cancer cells in vitro. Finally, TRAIL expression was positively correlated with increased expression of M1 markers in the tumors from ovarian and sarcoma cancer patients and longer overall survival in cases with high, but not low, tumor macrophage content.

Conclusions

TRAIL promotes the polarization of human macrophages toward a proinflammatory M1 phenotype via both DR4 and DR5. Our study defines TRAIL as a new regulator of macrophage polarization and suggests that targeting DRs can enhance the anti-tumorigenic response of macrophages in the tumor microenvironment by increasing M1 polarization.

Dynamic changes occur in the cell wall composition and related enzyme activities during flower development in Rosa damascena

The flowering period of oil-bearing rose is short and many physiological processes occur during flower development. Changes in the cell wall composition and associated enzyme activities are important as they allow cells to divide, differentiate and grow. In the present study, changes in seven cell wall components and six cell wall-related enzyme activities at five flower development stages were investigated and the relationships between these parameters and flowering were examined. Ash content did not change between stages I to II but decreased at later stages. Neutral detergent fiber (NDF), acid detergent fiber (ADF) and hemicellulose contents increased after stage I but did not change significantly at the other developmental periods. Total pectin content increased throughout flower development. An "increase-decrease" trend was observed in total cellulose content and a "decrease-increase" pattern in uronic acid content. The activities of both glycosidases (β-galactosidase, β-glucosidase and endoglucanase) and pectinases (pectin lyase, pectin methyl esterase and polygalacturonase) increased until stage IV and decreased significantly at stage V of flower development. Correlation analysis revealed 14 positive and one negative correlation with the studied parameters. Cell wall enzymes showed positive correlations with each other. Principal component analysis (PCA) showed that ADF, NDF and cellulose content were significantly altered at stage II of flower development, and significant changes occurred in all cell wall enzyme activities between stages III and V. Overall, blooming is correlated closely with increased pectin and decreased cellulose contents, and changes in cell wall glucosidase and pectin hydrolysis enzyme activities. These results show that cell wall modifying enzymes are part of the flower development process in oil-bearing rose. Therefore, remodeling of cell wall components in petals is a process of flower development.

Identification of collateral sensitivity and evolutionary landscape of chemotherapy-induced drug resistance using cellular barcoding technology

Background: One of the most significant challenges impeding cancer treatment effectiveness is drug resistance. Combining evolutionary understanding with drug resistance can pave the way for the identification of second-line drug options that can overcome drug resistance. Although capecitabine and irinotecan are commonly used therapeutic agents in the treatment of CRC patients, resistance to these agents is common. The underlying clonal dynamics of resistance to these agents using high-resolution barcode technology and identification of effective second-line drugs in this context remain unclear. Methods and materials: Caco-2 and HT-29 cell lines were barcoded, and then capecitabine and irinotecan resistant derivatives of these cell lines were established. The frequencies of barcodes from resistant cell lines and harvested medium, longitudinally, were determined. Collateral drug sensitivity testing was carried out on resistant Caco-2 and HT-29 cell lines using single agents or drug combinations. The SyngeryFinder tool was used to analyse drug combination testing. Results: In Caco-2 and HT-29 cell lines, barcode frequency measurements revealed clonal dynamics of capecitabine and irinotecan formed by both pre-existing and de novo barcodes, indicating the presence of polyclonal drug resistance. The temporal dynamics of clonal evolution in Caco-2 and HT-29 cell lines were demonstrated by longitudinal analysis of pre-existing and de novo barcodes from harvested medium. In Caco-2 and HT-29 cell lines, collateral drug sensitivity revealed a number of drugs that were effective alone and in combination. Conclusion: The use of barcoding technology reveals the clonal dynamics of chemotherapy-induced drug resistance not only from harvested cell populations, but also from longitudinal sampling throughout the course of clonal evolution. Second-line drugs that sensitize drug-resistant CRC cell lines are identified through collateral drug testing.

Age-related transversal changes in craniofacial sutures of the anterior viscerocranium in growing rats

Objective: To evaluate the dimensional changes that occur in the internasal and nasopremaxillary sutures, and related transverse craniofacial dimensions, of rats from 4 to 38-weeks of age. Methods: Four groups of twelve male Wistar rats were sacrificed at different ages [4-weeks (immature), 16-weeks (adolescent), 26-weeks (young adult), 38-weeks (adult)]. The rats were scanned with a high-resolution micro-computed tomography imaging device with 90 µm voxel size and 45 mm × 45 mm field of view (FOV) to obtain images of the viscreocranium, and with 10 µm voxel size and 5 mm × 5 mm FOV to obtain images of the internasal and left nasopremaxillary sutures. The nasal bone width, transverse width between the nasopremaxillary sutures and interzygomatic width were measured as craniofacial measurements. The endocranial, ectocranial and mean suture widths (cross-sectional area between endocranial and ectocranial borders/suture height), and suture height were measured at 5 frontal planes with 1.2 mm intervals. Outcomes were compared at different ages, and correlation coefficients were used to assess the relationship between craniofacial and suture changes. Results: All transverse craniofacial dimensions increased significantly from 4-16 weeks of age (p < 0.001). After 16-weeks of age, the only significant increase was observed in interzygomatic width (p = 0.02), between 26 and 38 weeks. In both the internasal and nasopremaxillary sutures, the endocranial suture mean widths decreased from 4-16 weeks (p < 0.001 and p = 0.002, respectively), but did not show any significant change after 16-weeks of age. The ectocranial internasal suture width decreased from 4-16 weeks (p < 0.001), increased until 26-weeks (p = 0.035), and subsequently decreased (p < 0.001). The nasopremaxillary suture widths decreased from 4-38 weeks to varying degrees in different frontal planes. Except for the internasal ectocranial suture width, all suture measurements were found highly and negatively correlated with the transverse craniofacial dimensions. The height of the sutures increased with time, with the most significant changes occurring between 4 and 16 weeks of age (p < 0.001). Conclusion: Although the internasal and nasopremaxillary endocranial suture widths nearly reach their final widths during adolescence, the changes in the ectocranial and mean suture widths continue into early adulthood. These results may serve as a reference for future studies aiming to evaluate the effects of functional demands on suture development and dimensional changes of the viscerocranium.

Construction of a high-density genetic linkage map and QTL mapping for bioenergy-related traits in sweet sorghum [Sorghum bicolor (L.) Moench]

Sorghum is an important but arguably undervalued cereal crop, grown in large areas in Asia and Africa due to its natural resilience to drought and heat. There is growing demand for sweet sorghum as a source of bioethanol as well as food and feed. The improvement of bioenergy-related traits directly affects bioethanol production from sweet sorghum; therefore, understanding the genetic basis of these traits would enable new cultivars to be developed for bioenergy production. In order to reveal the genetic architecture behind bioenergy-related traits, we generated an F₂ population from a cross between sweet sorghum cv. 'Erdurmus' and grain sorghum cv. 'Ogretmenoglu'. This was used to construct a genetic map from SNPs discovered by double-digest restriction-site associated DNA sequencing (ddRAD-seq). F₃ lines derived from each F₂ individual were phenotyped for bioenergy-related traits in two different locations and their genotypes were analyzed with the SNPs to identify QTL regions. On chromosomes 1, 7, and 9, three major plant height (PH) QTLs (qPH1.1, qPH7.1, and qPH9.1) were identified, with phenotypic variation explained (PVE) ranging from 10.8 to 34.8%. One major QTL (qPJ6.1) on chromosome 6 was associated with the plant juice trait (PJ) and explained 35.2% of its phenotypic variation. For fresh biomass weight (FBW), four major QTLs (qFBW1.1, qFBW6.1, qFBW7.1, and qFBW9.1) were determined on chromosomes 1, 6, 7, and 9, which explained 12.3, 14.5, 10.6, and 11.9% of the phenotypic variation, respectively. Moreover, two minor QTLs (qBX3.1 and qBX7.1) of Brix (BX) were mapped on chromosomes 3 and 7, explaining 8.6 and 9.7% of the phenotypic variation, respectively. The QTLs in two clusters (qPH7.1/qBX7.1 and qPH7.1/qFBW7.1) overlapped for PH, FBW and BX. The QTL, qFBW6.1, has not been previously reported. In addition, eight SNPs were converted into cleaved amplified polymorphic sequences (CAPS) markers, which can be easily detected by agarose gel electrophoresis. These QTLs and molecular markers can be used for pyramiding and marker-assisted selection studies in sorghum, to develop advanced lines that include desirable bioenergy-related traits.

Sainfoin (Onobrychis spp.) crop ontology: supporting germplasm characterization and international research collaborations

Sainfoin (Onobrychis spp.) is a perennial forage legume that is also attracting attention as a perennial pulse with potential for human consumption. The dual use of sainfoin underpins diverse research and breeding programs focused on improving sainfoin lines for forage and pulses, which is driving the generation of complex datasets describing high dimensional phenotypes in the post-omics era. To ensure that multiple user groups, for example, breeders selecting for forage and those selecting for edible seed, can utilize these rich datasets, it is necessary to develop common ontologies and accessible ontology platforms. One such platform, Crop Ontology, was created in 2008 by the Consortium of International Agricultural Research Centers (CGIAR) to host crop-specific trait ontologies that support standardized plant breeding databases. In the present study, we describe the sainfoin crop ontology (CO). An in-depth literature review was performed to develop a comprehensive list of traits measured and reported in sainfoin. Because the same traits can be measured in different ways, ultimately, a set of 98 variables (variable = plant trait + method of measurement + scale of measurement) used to describe variation in sainfoin were identified. Variables were formatted and standardized based on guidelines provided here for inclusion in the sainfoin CO. The 98 variables contained a total of 82 traits from four trait classes of which 24 were agronomic, 31 were morphological, 19 were seed and forage quality related, and 8 were phenological. In addition to the developed variables, we have provided a roadmap for developing and submission of new traits to the sainfoin CO.

A comparison of urinary bladder weight in male and female mice across five models of diabetes and obesity

Introduction: Diabetes often leads to lower urinary tract dysfunction. The most frequently assessed parameter of urinary bladder dysfunction in animal models of diabetes is an enlargement of the bladder, which is consistently observed in type 1 and less consistently in type 2 diabetes. The vast majority of studies on bladder weight in animal models of diabetes and obesity has been performed in males, and no studies have directly compared this outcome parameter between sexes. Methods: Therefore, we have compared bladder weight and bladder/body weight ratio in five mouse models of obesity and diabetes (RIP-LCMV, db/db, ob/ob (two studies), insulin receptor substrate 2 (IRS2) knock-out mice and mice on a high-fat diet; pre-specified secondary analysis of a previously reported study). Results: In a pooled analysis of the control groups of all studies, females exhibited slightly lower glucose levels, lower body weight, and lower bladder weight, but bladder/body weight ratio was similar in both sexes (0.957 vs. 0.986 mg/g, mean difference 0.029 [-0.06; 0.118]). Among the six diabetic/obese groups, bladder/body weight ratio was similar in both sexes in three but smaller in female mice in three other groups. The mRNA expression of a panel of genes implied in the pathophysiology of bladder enlargement and/or fibrosis and inflammation did not differ systematically between sexes. Conclusions: We conclude that sex differences in diabetes/obesity-associated bladder enlargement may be model dependent.

Pancreatic cancer: Emerging field of regulatory B-cell-targeted immunotherapies

Pancreatic ductal adenocarcinoma (PDAC), the most common type of pancreatic cancer, is characterized by a high mortality rate and poor prognosis. Current treatments for PDAC, are ineffective due to a prominent immunosuppressive PDAC tumor microenvironment (TME). Although B lymphocytes are highly infiltrated into PDAC, the importance of B lymphocytes in tumorigenesis is largely neglected. B cells play a dual role in the PDAC tumor microenvironment, acting as either anti-tumorigenic or pro-tumorigenic depending on where they are localized. Tumor-infiltrating B cells, which reside in ectopic lymph nodes, namely tertiary lymphoid structures (TLS), produce anti-tumor antibodies and present tumor antigens to T cells to contribute to cancer immunosurveillance. Alternatively, regulatory B cells (Bregs), dispersed inside the TME, contribute to the dampening of anti-tumor immune responses by secreting anti-inflammatory cytokines (IL-10 and IL-35), which promote tumor growth and metastasis. Determining the role of Bregs in the PDAC microenvironment is thus becoming increasingly attractive for developing novel immunotherapeutic approaches. In this minireview, we shed light on the emerging role of B cells in PDAC development and progression, with an emphasis on regulatory B cells (Bregs). Furthermore, we discussed the potential link of Bregs to immunotherapies in PDAC. These current findings will help us in understanding the full potential of B cells in immunotherapy.

Differential regulation of reactive oxygen species in dimorphic chloroplasts of single cell C4 plant Bienertia sinuspersici during drought and salt stress

Single cell C₄ (SCC₄) plants, discovered around two decades ago, are promising materials for efforts for genetic engineering of C₄ photosynthesis into C₃ crops. Unlike C₄ plants with Kranz anatomy, they exhibit a fully functional C₄ photosynthesis in just a single cell and do not require mesophyll and bundle sheath cell spatial separation. Bienertia sinuspersici is one such SCC₄ plant, with NAD-malic enzyme (NAD-ME) subtype C₄ photosynthesis. Its chlorenchyma cell consist of two compartments, peripheral compartment (PC), analogous to mesophyll cell, and central compartment (CC), analogous to bundle sheath cell. Since oxidative stress creates an important constraint for plants under salinity and drought, we comparatively examined the response of enzymatic antioxidant system, H₂O₂ and TBARS contents, peroxiredoxin Q, NADPH thioredoxin reductase C, and plastid terminal oxidase protein levels of PC chloroplasts (PCC) and CC chloroplasts (CCC). Except for protein levels, these parameters were also examined on the whole leaf level, as well as catalase and NADPH oxidase activities, water status and growth parameters, and levels of C₄ photosynthesis related transcripts. Many C₄ photosynthesis related transcript levels were elevated, especially under drought. Activities of dehydroascorbate reductase and especially peroxidase were elevated under drought in both compartments (CCC and PCC). Even though decreases of antioxidant enzyme activities were more prevalent in PCC, and the examined redox regulating protein levels, especially of peroxiredoxin Q, were elevated in CCC under both stresses, PCC was less damaged by either stress. These suggest PCC is more tolerant and has other means of preventing or alleviating oxidative damage.

Bacillus cereus EC9 protects tomato against Fusarium wilt through JA/ET-activated immunity

The mechanisms of action and the limitations of effectiveness of natural biocontrol agents should be determined in order to convert them into end products that can be used in practice. Rhizosphere Bacillus spp. protect plants from various pathogens by displaying several modes of action. However, the ability of Bacillus spp. to control plant diseases depends on the interaction between the bacteria, host, and pathogen, and the environmental conditions. We found that soil drenching of tomato plants with the non-antifungal Bacillus cereus strain EC9 (EC9) enhances plant defense against Fusarium oxysporum f. sp. lycopersici (Fol). To study the involvement of plant defense-related phytohormones in the regulation of EC9-activated protection against Fol, we conducted plant bioassays in tomato genotypes impaired in salicylic acid (SA) accumulation, jasmonic acid (JA) biosynthesis, and ethylene (ET) production, and analyzed the transcript levels of pathways-related marker genes. Our results indicate that JA/ET-dependent signaling is required for EC9-mediated protection against Fol in tomato. We provide evidence that EC9 primes tomato plants for enhanced expression of proteinase inhibitor I (PI-I) and ethylene receptor4 (ETR4). Moreover, we demonstrated that EC9 induces callose deposition in tomato roots. Understanding the involvement of defense-related phytohormones in EC9-mediated defense against Fusarium wilt has increased our knowledge of interactions between non-antifungal plant defense-inducing rhizobacteria and plants.