bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring the acute cardiovascular effects of Floatation-REST
Authors: Flux M. C. , Fine Thomas H. , Poplin Tate , Al Zoubi Obada , Schoenhals William A. , Schettler Jesse , Refai Hazem H. , Naegele Jessyca , Wohlrab Colleen , Yeh Hung-Wen , Lowry Christopher A. , Levine Jason C. , Smith Ryan , Khalsa Sahib S. , Feinstein Justin S.
Published: December 2022

The central nervous system (CNS) exerts a strong regulatory influence over the cardiovascular system in response to environmental demands. Floatation-REST (Reduced Environmental Stimulation Therapy) is an intervention that minimizes stimulation from the environment, yet little is known about the autonomic consequences of reducing external sensory input to the CNS. We recently found that Floatation-REST induces a strong anxiolytic effect in anxious patients while paradoxically enhancing their interoceptive awareness for cardiorespiratory sensations. To further investigate the physiologic nature of this anxiolytic effect, the present study measured acute cardiovascular changes during Floatation-REST using wireless and waterproof equipment that allowed for concurrent measurement of heart rate, heart rate variability (HRV), breathing rate, and blood pressure. Using a within-subjects crossover design, 37 clinically anxious participants with high levels of anxiety sensitivity and 20 non-anxious comparison participants were randomly assigned to undergo a 90-min session of either Floatation-REST or an exteroceptive comparison condition that entailed watching a relaxing nature film. Measures of state anxiety and serenity were collected before and after each session, while indices of autonomic activity were measured throughout each session. HRV was calculated using both time-series and frequency domain analyses. Linear mixed-effects modeling revealed a significant main effect of condition such that relative to the film condition, Floatation-REST elicited significant decreases (p< 0.001) in diastolic blood pressure, systolic blood pressure, breathing rate, and certain metrics of HRV including the standard deviation of the interbeat interval (SDNN), low-frequency HRV, and very low-frequency HRV. Heart rate showed a non-significant trend (p= 0.073) toward being lower in the float condition, especially toward the beginning of the session. The only metric that showed a significant increase during Floatation-REST was normalized high-frequency HRV (p< 0.001). The observed physiological changes were consistent across both anxious and non-anxious participants, and there were no significant group by condition interactions. Blood pressure was the only cardiac metric significantly associated with float-related reductions in state anxiety and increases in serenity. These findings suggest that Floatation-REST lowers sympathetic arousal and alters the balance of the autonomic nervous system toward a more parasympathetic state.

Clinical trial registration

[https://clinicaltrials.gov/show/NCT03051074], identifier [NCT03051074].
A novel BCL11A polymorphism influences gene expression, therapeutic response and epilepsy risk: A multicenter study
Authors: Wang Shitao , Cai Xuemei , Liu Shiyong , Zhou Qixin , Wang Ting , Du Sunbing , Wang Dan , Yang Fei , Wu Qian , Han Yanbing
Published: December 2022

Background

Genetic factors have been found to be associated with the efficacy and adverse reactions of antiseizure medications. BCL11A is an important regulator of the development of neuronal networks. However, the role of BCL11A in epilepsy remains unclear. This study aimed to evaluate the genetic association of BCL11A with the susceptibility to develop epileptic seizures and therapeutic response of patients with epilepsy in Han Chinese.

Methods

We matched 450 epilepsy cases with 550 healthy controls and 131 drug-resistant epilepsy patients with 319 drug-responsive epilepsy patients from two different centers. Genetic association analysis, genetic interaction analysis, expression quantitative trait loci analysis and protein–protein interaction analysis were conducted.

Results

Our results showed that rs2556375 not only increases susceptibility to develop epileptic seizures (OR = 2.700, 95% = 1.366–5.338, p = 0.004 and OR = 2.984, 95% = 1.401–6.356, p = 0.005, respectively), but also increases the risk of drug resistance(OR = 21.336, 95%CI =2.489–183.402, p = 0.005). The interaction between rs2556375 and rs12477097 results in increased risk for pharma coresistant. In addition, rs2556375 regulated BCL11A expression in human brain tissues (p = 0.0096 and p = 0.033, respectively). Furthermore, the protein encoded by BCL11A interacted with targets of approved antiepileptic drugs.

Conclusion

BCL11A may be a potential therapeutic target for epilepsy. Rs2556375 may increase the risks of epilepsy and drug resistance by regulating BCL11A expression in human brain tissues. Moreover, the interaction between rs2556375 and rs12477097 results in increased risk for drug resistance.
Improving nutrition through biofortification–A systematic review
Authors: Ofori Kelvin F. , Antoniello Sophia , English Marcia M. , Aryee Alberta N. A.
Published: December 2022

Nutritious foods are essential for human health and development. However, malnutrition and hidden hunger continue to be a challenge globally. In most developing countries, access to adequate and nutritious food continues to be a challenge. Although hidden hunger is less prevalent in developed countries compared to developing countries where iron (Fe) and zinc (Zn) deficiencies are common. The United Nations (UN) 2nd Sustainable Development Goal was set to eradicate malnutrition and hidden hunger. Hidden hunger has led to numerous cases of infant and maternal mortalities, and has greatly impacted growth, development, cognitive ability, and physical working capacity. This has influenced several countries to develop interventions that could help combat malnutrition and hidden hunger. Interventions such as dietary diversification and food supplementation are being adopted. However, fortification but mainly biofortification has been projected to be the most sustainable solution to malnutrition and hidden hunger. Plant-based foods (PBFs) form a greater proportion of diets in certain populations; hence, fortification of PBFs is relevant in combating malnutrition and hidden hunger. Agronomic biofortification, plant breeding, and transgenic approaches are some currently used strategies in food crops. Crops such as cereals, legumes, oilseeds, vegetables, and fruits have been biofortified through all these three strategies. The transgenic approach is sustainable, efficient, and rapid, making it suitable for biofortification programs. Omics technology has also been introduced to improve the efficiency of the transgenic approach.
Communication about early palliative care: A qualitative study of oncology providers’ perspectives of navigating the artful introduction to the palliative care team
Authors: Collins Anna , Gurren Lorna , McLachlan Sue-Anne , Wawryk Olivia , Philip Jennifer
Published: December 2022

Background

Despite robust evidence for the integration of early palliative care for patients with advanced cancer, many patients still access this approach to care late. Communication about the introduction of Early Palliative Care is an important skill of healthcare providers working in this setting. In the context of limited community understanding about palliative care, patients and their families may express fear or negative reactions to its early introduction. Health professionals may lack the confidence or skill to describe the role and benefits of early palliative care.

Aim

This study sought to explore clinicians’ perspectives on communication about referral to early palliative care, specifically identifying facilitators in undertaking this communication task.

Methods

An exploratory qualitative study set within a tertiary oncology service in Victoria, Australia. Semi-structured interviews were conducted with purposively sampled oncology clinicians exploring their perspectives on communication about referral to early palliative care. A reflexive thematic analysis was undertaken by two researchers, including both latent and semantic coding relevant to the research question. Reporting of the research was guided by the Consolidated Criteria for Reporting Qualitative Research (COREQ) checklist.

Results

Twelve oncology clinicians (58% female, with 67% > 15 years clinical experience) from medical oncology, surgical oncology, and haematology participated. The artful navigation of communication about early palliative care was characterised by the need for a ‘spiel’ involving the adoption of a series of strategies or ‘tactics’ when introducing this service. These themes included: 1) Using carefully selected and rehearsed language; 2) Framing in terms of symptom control; 3) Framing as additive to patient care; 4) Selling the service benefits of early palliative care; 5) Framing acceptance of referral as an altruistic act; and 6) Adopting a phased approach to delivering information about palliative care.

Implications

This study highlights the wide ranging and innovative communication strategies and skills required by health professionals to facilitate referral to early palliative care for cancer patients and their families. Future focus on upskilling clinicians around communication of this topic will be important to ensure successful implementation of models of early palliative care in routine cancer care.
Case report: Olaparib as an experimental therapy in a BRCA2-mutated patient with metastatic ovarian adenocarcinoma that originated from liver cancer
Authors: Li Caixia , Ye Wenlei , Zhou Wenni , Ye Zhikang , Yang Weihong , Cheng Zhongping
Published: December 2022

Secondary ovarian tumor [secondary tumor of the ovary (STO)] is not a frequent disease. To date, there is still a lack of standard treatment for STO due to the relative heterogeneity. Liver cancer metastasis to the ovary is extremely rare, with only 17 living cases having been reported so far, making it impossible to launch large-scale prospective studies and formulate the standard intervention for patients. We herein report a rare case of STO with liver primary cancer metastasis to the ovary and omentum in a 66-year-old woman. The patient underwent debulking surgery with the removal of the uterus, bilateral fallopian tubes, bilateral ovaries, appendix, and a large part of the omentum majus. Next-generation sequencing was conducted after the operation, identifying BRCA2 mutation. Because strongly refusing chemotherapy, she received olaparib as an experimental therapy. After the administration of surgery and olaparib, the serum value of cancer antigen 125 (CA125) and alpha fetoprotein (AFP) decreased dramatically and basically remained within the normal range. So far, she has achieved nearly 2-year survival and lives a relatively normal life with good quality.
Ferroptosis and triple-negative breast cancer: Potential therapeutic targets
Authors: Xu Na , Li Baohong , Liu Yong , Yang Cui , Tang Siqi , Cho William C. , Huang Zunnan
Published: December 2022

Purpose

Triple-negative breast cancer (TNBC) is an aggressive tumor with poor prognosis, it has higher recurrence and metastatic rates than other breast cancer subtypes. This study aims to investigate biomarkers and potential targets for TNBC related to ferroptosis through data mining and bioinformatics analysis. The findings may provide new insights for treating TNBC.

Methods

The TNBC patients’ data from the Cancer Genome Atlas (TCGA) database were extracted for differential expression and prognosis analysis. Consensus genes obtained by intersecting differential expressed and ferroptosis-related genes was used to establish the prognostic model by the univariate and multivariate Cox analyses. Besides, TNBC data from the Gene Expression Omnibus (GEO) database was used to confirm the reliability of the prognosis model. Moreover, clinical information was analyzed by multifactorial independent analysis to identify independent prognostic factors. The expression of genes constituting the prognostic model was further validated using the Human Protein Atlas (HPA) database. Finally, the Comparative Toxicogenomic Data (CTD) database was used to explore possible treatment drugs for TNBC.

Results

We obtained 13,245 differential expressed genes, and 177 consensus genes. 98 genes with prognostic implication were obtained by univariable Cox. Then, a prognostic model including 12 ferroptosis-related genes was constructed by multivariable Cox. The area under curve (AUC) value of the prognostic model for TNBC was 0.82. The GEO database validated that the model (AUC = 0.77) could predict the patient outcomes. The staining results of 10 out of 12 prognostic model genes in HPA database showed that their expression was consistent with our predictions. Clinical risk analysis indicated that risk score of patients could act as an independent prognostic factor. Finally, six drugs that may have interaction with 12 ferroptosis-related genes were obtained using the CTD database.

Conclusion

The prognostic model composed of 12 ferroptosis-related genes could predict the prognosis of TNBC patients, and seven genes (ASNS, LAMP2, CAV1, DPP4, HELLS, TF, ZFP69B) could be potential new therapeutic targets for TNBC, and two drugs (1-methyl-3-isobutylxanthine, rosiglitazone) could act as potential therapeutic drugs for the treatment of TNBC.
Cancer informatics analysis indicates high CHAC2 associated with unfavorable prognosis in breast cancer
Authors: Chand Subhash , Mehta Vikrant , Sharma Ratnesh K. , Anvikar Anupkumar R. , Chander Harish
Published: December 2022

Breast cancer remains the most commonly diagnosed cancer worldwide and exhibits a poor prognosis. The induction of genetic changes deregulates several genes that increase the disposal towards this life-threatening disease. CHAC2, a member of the glutathione degrading enzyme family has been shown to suppress gastric and colorectal cancer progression, however, the expression of CHAC2 in breast cancer has not been reported. We did an analysis of CHAC2 expression in breast cancer patients from various online tools like UALCAN, GEPIA2, GENT2, TIMER2, and bcGenExminer v4.8. Further, we used the Kaplan-Meier plotter to establish the significance of CHAC2 in BC patient survival and prognosis while TISIDB and TIMER databases were used to investigate the filtration of immune cells. The results showed that CHAC2 levels were high in breast cancer patients and elevated CHAC2 was associated with low overall survival. Taken together, the results of the present study show that like its paralog CHAC1, CHAC2 may also be an important biomarker and could have a potential therapeutic implication in breast cancer.
Construction and validation of a novel web-based nomogram for patients with lung cancer with bone metastasis: A real-world analysis based on the SEER database
Authors: Yin Mengchen , Guan Sisi , Ding Xing , Zhuang Ruoyu , Sun Zhengwang , Wang Tao , Zheng Jiale , Li Lin , Gao Xin , Wei Haifeng , Ma Junming , Huang Quan , Xiao Jianru , Mo Wen
Published: December 2022

Purpose

Patients with lung cancer with bone metastasis (LCBM) often have a very poor prognosis. The purpose of this study is to characterize the prevalence and associated factors and to develop a prognostic nomogram to predict the overall survival (OS) and cancer-specific survival (CSS) for patients with LCBM using multicenter population-based data.

Methods

Patients with LCBM at the time of diagnosis were identified using the Surveillance, Epidemiology, and End Results (SEER) Program database of the National Cancer Institute (NCI) from 2010 to 2015. Multivariable and univariate logistic regression analyses were performed to identify factors associated with all-cause mortality and lung cancer (LC)–specific mortality. The performance of the nomograms was evaluated with the calibration curves, area under the curve (AUC), and decision curve analysis (DCA). Kaplan–Meier analysis and log-rank tests were used to estimate the survival times of patients with LCBM.

Results

We finally identified 26,367 patients with LCBM who were selected for survival analysis. Multivariate analysis demonstrated age, sex, T stage, N stage, grade, histology, radiation therapy, chemotherapy, primary site, primary surgery, liver metastasis, and brain metastasis as independent predictors for LCBM. The AUC values of the nomogram for the OS prediction were 0.755, 0.746, and 0.775 in the training cohort; 0.757, 0.763, and 0.765 in the internal validation cohort; and 0.769, 0.781, and 0.867 in the external validation cohort. For CSS, the values were 0.753, 0.753, and 0.757 in the training cohort; 0.753, 0.753, and 0.757 in the internal validation cohort; and 0.767, 0.774, and 0.872 in the external validation cohort.

Conclusions

Our study constructs a new prognostic model and clearly presents the clinicopathological features and survival analysis of patients with LCBM. The result indicated that the nomograms had favorable discrimination, good consistency, and clinical benefits in patients. In addition, our constructed nomogram prediction models may assist physicians in evaluating individualized prognosis and deciding on treatment for patients.
Mechanisms of retinal ganglion cell injury following acute increases in intraocular pressure
Authors: Garner Mary Anne , Strickland Ryan G. , Girkin Christopher A. , Gross Alecia K.
Published: December 2022

The maintenance of intraocular pressure (IOP) is critical to preserving the pristine optics required for vision. Disturbances in IOP can directly impact the optic nerve and retina, and inner retinal injury can occur following acute and chronic IOP elevation. There are a variety of animal models that have been developed to study the effects of acute and chronic elevation of IOP on the retina, retinal ganglion cell (RGC) morphology, intracellular signaling, gene expression changes, and survival. Acute IOP models induce injury that allows for the study of RGC response to well characterized injury and potential recovery. This review will focus on the initial impact of acute IOP elevation on RGC injury and recovery as these early responses may be the best targets for potential therapeutic interventions to promote RGC survival in glaucoma.
Effect of postbiotic-toothpaste on salivary levels of IgA in 6- to 12-year-old children: Study protocol for a randomized triple-blind placebo-controlled trial
Authors: Basir Leila , Moghimipour Eskandar , Saadatzadeh Afrooz , Cheraghian Bahman , Khanehmasjedi Samaneh
Published: December 2022

Background

Children in mixed dentition are highly at risk for dental caries, which is a major health issue worldwide. Despite their effect in controlling dental caries, using probiotics can be challenging. Therefore, it has been advised to use their inanimate forms, called postbiotics. We hypothesize that postbiotics can enhance the oral immunity.

Methods

The aim of this triple-blind, randomized, placebo-controlled trial is to investigate the effect of postbiotic-toothpaste (Bifidobacterium animalis subsp. animalis) on salivary levels of Immunoglobulin A (IgA) and pH in children. Using comparing two means formula to calculate the sample size, for this trial 80 healthy 6- to 12-year-old children during mixed dentition with no cavitated dental caries will be selected by convenience sampling method and randomly allocated to two groups, postbiotic-toothpaste or placebo-toothpaste. Saliva samples will be gathered at baseline and four weeks after the intervention. The level of salivary IgA will be determined by ELISA and salivary pH will be measured using a pH meter. Data will be compared within and between groups using independent t-test and paired t-test, in case of normality, with a p < 0.05 as statistically significant.

Discussion

If postbiotics-toothpaste prove to be effective in improving the oral immunity, they can be used to prevent dental caries and other oral diseases. The result of this study can help researchers who are working on the immunomodulatory effects of postbiotics in children.

Trial registration number

Iranian Registry of Clinical Trials (IRCT), IRCT20191016045128N2. Registered on 7 March 2022.
The critical roles and therapeutic implications of tuft cells in cancer
Authors: Li Lin , Ma Mengmeng , Duan Ting , Sui Xinbing
Published: December 2022

Tuft cells are solitary chemosensory epithelial cells with microvilli at the top, which are found in hollow organs such as the gastrointestinal tract, pancreas, and lungs. Recently, an increasing number of studies have revealed the chemotactic abilities and immune function of the tuft cells, and numerous efforts have been devoted to uncovering the role of tuft cells in tumors. Notably, accumulating evidence has shown that the specific genes (POU2F3, DCLK1) expressed in tuft cells are involved in vital processes related with carcinogenesis and cancer development. However, the interaction between the tuft cells and cancer remains to be further elucidated. Here, based on an introduction of biological functions and specific markers of the tuft cells, we have summarized the functional roles and potential therapeutic implications of tuft cells in cancers, including pancreatic cancer, lung cancer, gastric cancer, colon cancer, and liver cancer, which is in the hope of inspiring the future research in validating tuft cells as novel strategies for cancer therapies.
Antisense oligonucleotide is a promising intervention for liver diseases
Authors: Lu Kailing , Fan Qijing , Zou Xiaoju
Published: December 2022

As the body’s critical metabolic organ, the liver plays an essential role in maintaining proper body homeostasis. However, as people’s living standards have improved and the number of unhealthy lifestyles has increased, the liver has become overburdened. These have made liver disease one of the leading causes of death worldwide. Under the influence of adverse factors, liver disease progresses from simple steatosis to hepatitis, to liver fibrosis, and finally to cirrhosis and cancer, followed by increased mortality. Until now, there has been a lack of accepted effective treatments for liver disease. Based on current research, antisense oligonucleotide (ASO), as an alternative intervention for liver diseases, is expected to be an effective treatment due to its high efficiency, low toxicity, low dosage, strong specificity, and additional positive characteristics. In this review, we will first introduce the design, modification, delivery, and the mechanisms of ASO, and then summarize the application of ASO in liver disease treatment, including in non-alcoholic fatty liver disease (NAFLD), hepatitis, liver fibrosis, and liver cancer. Finally, we discuss challenges and perspectives on the transfer of ASO drugs into clinical use. This review provides a current and comprehensive understanding of the integrative and systematic functions of ASO for its use in liver disease.
Hitting time for random walks on the Sierpinski network and the half Sierpinski network
Authors: Sun Yu , Liu Xiaobei , Li Xiaoyan
Published: December 2022

We consider the unbiased random walk on the Sierpinski network (Sn◦N) and the half Sierpinski network (HSn◦N), where n is the generation. Different from the existing works on the Sierpinski gasket, Sn◦N is generated by the nested method and HSn◦N is half of Sn◦N based on the vertical cutting of the symmetry axis. We study the hitting time on Sn◦N and HSn◦N. According to the complete symmetry and structural properties of Sn◦N, we derive the exact expressions of the hitting time on the nth generation of Sn◦N and HSn◦N. The curves of the hitting time for the two networks are almost consistent when n is large enough. The result indicates that the diffusion efficiency of HSn◦N has not changed greatly compared with Sn◦N at a large scale.
Antioxidant processes involving epicatechin decreased symptoms of pine wilt disease
Authors: Zhang Ruizhi , Wang Jianan , Xia Rui , Li Danlei , Wang Feng
Published: December 2022

Since the pine wood nematode (PWN, Bursaphelenchus xylophilus) invasion of Northeast China, both symptomatic and asymptomatic PWN carriers have been found. Asymptomatic PWN carriers, which are more dangerous than symptomatic carriers, constitute a source of infection in the following spring. The simultaneous presence of symptomatic and asymptomatic PWN carriers indicates that Pinus koraiensis has different tolerance levels to PWN. In this study, validity of susceptibility testing discovered differential types of P. koraiensis including Latent Reservoirs, Low Susceptibles, High Susceptibles and Bell Ringers. Among those types, the Low Susceptibles and Latent Reservoirs were asymptomatic PWN carriers, and Latent Reservoirs were the most dangerous. Transcriptome and metabolomic data showed that 5 genes (3 ans and 2 anr gene) involved in the epicatechin (EC) synthesis pathway were significantly upregulated, which increased the content of EC antioxidants in Latent Reservoirs. Hydrogen peroxide (H2O2) staining and content determination showed that the hypersensitive response (HR) and H2O2, which functions as a signaling molecule in systemic acquired resistance, decreased in Latent Reservoirs. However, low contents of EC and high contents of H2O2 were found in the High Susceptibles of P. koraiensis. RT-PCR results showed that the expression of ans and anr was upregulated together only in Latent Reservoirs. These results show that the susceptibility of P. koraiensis to PWN differed among different individuals, although no resistant individuals were found. Latent Reservoirs, in which more PWNs resided without visible symptoms via prolonged incubation period, inhibited the symptoms caused by H2O2 because of increased contents of the EC antioxidants.
Revealing the transfer pathways of cyanobacterial-fixed N into the boreal forest through the feather-moss microbiome
Authors: Arróniz-Crespo María , Bougoure Jeremy , Murphy Daniel V. , Cutler Nick A. , Souza-Egipsy Virginia , Chaput Dominique L. , Jones Davey L. , Ostle Nicholas , Wade Stephen C. , Clode Peta L. , DeLuca Thomas H.
Published: December 2022

Introduction

Biological N2 fixation in feather-mosses is one of the largest inputs of new nitrogen (N) to boreal forest ecosystems; however, revealing the fate of newly fixed N within the bryosphere (i.e. bryophytes and their associated organisms) remains uncertain.

Methods

Herein, we combined 15N tracers, high resolution secondary ion mass-spectrometry (NanoSIMS) and a molecular survey of bacterial, fungal and diazotrophic communities, to determine the origin and transfer pathways of newly fixed N2 within feather-moss (Pleurozium schreberi) and its associated microbiome.

Results

NanoSIMS images reveal that newly fixed N2, derived from cyanobacteria, is incorporated into moss tissues and associated bacteria, fungi and micro-algae.

Discussion

These images demonstrate that previous assumptions that newly fixed N2 is sequestered into moss tissue and only released by decomposition are not correct. We provide the first empirical evidence of new pathways for N2 fixed in feather-mosses to enter the boreal forest ecosystem (i.e. through its microbiome) and discuss the implications for wider ecosystem function.
Extensive reorganization of the chloroplast genome of Corydalis platycarpa: A comparative analysis of their organization and evolution with other Corydalis plastomes
Authors: Raman Gurusamy , Nam Gi-Heum , Park SeonJoo
Published: December 2022

Introduction

The chloroplast (cp) is an autonomous plant organelle with an individual genome that encodes essential cellular functions. The genome architecture and gene content of the cp is highly conserved in angiosperms. The plastome of Corydalis belongs to the Papaveraceae family, and the genome is comprised of unusual rearrangements and gene content. Thus far, no extensive comparative studies have been carried out to understand the evolution of Corydalis chloroplast genomes.

Methods

Therefore, the Corydalis platycarpa cp genome was sequenced, and wide-scale comparative studies were conducted using publicly available twenty Corydalis plastomes.

Results

Comparative analyses showed that an extensive genome rearrangement and IR expansion occurred, and these events evolved independently in the Corydalis species. By contrast, the plastomes of its closely related subfamily Papaveroideae and other Ranunculales taxa are highly conserved. On the other hand, the synapomorphy characteristics of both accD and the ndh gene loss events happened in the common ancestor of the Corydalis and sub-clade of the Corydalis lineage, respectively. The Corydalis-sub clade species (ndh lost) are distributed predominantly in the Qinghai-Tibetan plateau (QTP) region. The phylogenetic analysis and divergence time estimation were also employed for the Corydalis species.

Discussion

The divergence time of the ndh gene in the Corydalis sub-clade species (44.31 – 15.71 mya) coincides very well with the uplift of the Qinghai-Tibet Plateau in Oligocene and Miocene periods, and maybe during this period, it has probably triggered the radiation of the Corydalis species.

Conclusion

To the best of the authors’ knowledge, this is the first large-scale comparative study of Corydalis plastomes and their evolution. The present study may provide insights into the plastome architecture and the molecular evolution of Corydalis species.
Changing winter climate and snow conditions induce various transcriptional stress responses in Scots pine seedlings
Authors: Vuosku Jaana , Martz Françoise , Hallikainen Ville , Rautio Pasi
Published: December 2022

In northern boreal forests the warming winter climate leads to more frequent snowmelt, rain-on-snow events and freeze-thaw cycles. This may be harmful or even lethal for tree seedlings that spend even a half of the year under snow. We conducted a snow cover manipulation experiment in a natural forest to find out how changing snow conditions affect young Scots pine (Pinus sylvestris L.) seedlings. The ice encasement (IE), absence of snow (NoSNOW) and snow compaction (COMP) treatments affected ground level temperature, ground frost and subnivean gas concentrations compared to the ambient snow cover (AMB) and led to the increased physical damage and mortality of seedlings. The expression responses of 28 genes related to circadian clock, aerobic and anaerobic energy metabolism, carbohydrate metabolism and stress protection revealed that seedlings were exposed to different stresses in a complex way depending on the thickness and quality of the snow cover. The IE treatment caused hypoxic stress and probably affected roots which resulted in reduced water uptake in the beginning of the growing season. Without protective snowpack in NoSNOW seedlings suffered from cold and drought stresses. The combination of hypoxic and cold stresses in COMP evoked unique transcriptional responses including oxidative stress. Snow cover manipulation induced changes in the expression of several circadian clock related genes suggested that photoreceptors and the circadian clock system play an essential role in the adaptation of Scots pine seedlings to stresses under different snow conditions. Our findings show that warming winter climate alters snow conditions and consequently causes Scots pine seedlings various abiotic stresses, whose effects extend from overwintering to the following growing season.
Transcriptional regulation of the raffinose family oligosaccharides pathway in Sorghum bicolor reveals potential roles in leaf sucrose transport and stem sucrose accumulation
Authors: McKinley Brian A. , Thakran Manish , Zemelis-Durfee Starla , Huang Xinyi , Brandizzi Federica , Rooney William L. , Mansfield Shawn D. , Mullet John E.
Published: December 2022

Bioenergy sorghum hybrids are being developed with enhanced drought tolerance and high levels of stem sugars. Raffinose family oligosaccharides (RFOs) contribute to plant environmental stress tolerance, sugar storage, transport, and signaling. To better understand the role of RFOs in sorghum, genes involved in myo-inositol and RFO metabolism were identified and relative transcript abundance analyzed during development. Genes involved in RFO biosynthesis (SbMIPS1, SbInsPase, SbGolS1, SbRS) were more highly expressed in leaves compared to stems and roots, with peak expression early in the morning in leaves. SbGolS, SbRS, SbAGA1 and SbAGA2 were also expressed at high levels in the leaf collar and leaf sheath. In leaf blades, genes involved in myo-inositol biosynthesis (SbMIPS1, SbInsPase) were expressed in bundle sheath cells, whereas genes involved in galactinol and raffinose synthesis (SbGolS1, SbRS) were expressed in mesophyll cells. Furthermore, SbAGA1 and SbAGA2, genes that encode neutral-alkaline alpha-galactosidases that hydrolyze raffinose, were differentially expressed in minor vein bundle sheath cells and major vein and mid-rib vascular and xylem parenchyma. This suggests that raffinose synthesized from sucrose and galactinol in mesophyll cells diffuses into vascular bundles where hydrolysis releases sucrose for long distance phloem transport. Increased expression (>20-fold) of SbAGA1 and SbAGA2 in stem storage pith parenchyma of sweet sorghum between floral initiation and grain maturity, and higher expression in sweet sorghum compared to grain sorghum, indicates these genes may play a key role in non-structural carbohydrate accumulation in stems.
Retrotransposons: How the continuous evolutionary front shapes plant genomes for response to heat stress
Authors: Papolu Pradeep K. , Ramakrishnan Muthusamy , Mullasseri Sileesh , Kalendar Ruslan , Wei Qiang , Zou Long−Hai , Ahmad Zishan , Vinod Kunnummal Kurungara , Yang Ping , Zhou Mingbing
Published: December 2022

Long terminal repeat retrotransposons (LTR retrotransposons) are the most abundant group of mobile genetic elements in eukaryotic genomes and are essential in organizing genomic architecture and phenotypic variations. The diverse families of retrotransposons are related to retroviruses. As retrotransposable elements are dispersed and ubiquitous, their “copy-out and paste-in” life cycle of replicative transposition leads to new genome insertions without the excision of the original element. The overall structure of retrotransposons and the domains responsible for the various phases of their replication is highly conserved in all eukaryotes. The two major superfamilies of LTR retrotransposons, Ty1/Copiaand Ty3/Gypsy, are distinguished and dispersed across the chromosomes of higher plants. Members of these superfamilies can increase in copy number and are often activated by various biotic and abiotic stresses due to retrotransposition bursts. LTR retrotransposons are important drivers of species diversity and exhibit great variety in structure, size, and mechanisms of transposition, making them important putative actors in genome evolution. Additionally, LTR retrotransposons influence the gene expression patterns of adjacent genes by modulating potential small interfering RNA (siRNA) and RNA-directed DNA methylation (RdDM) pathways. Furthermore, comparative and evolutionary analysis of the most important crop genome sequences and advanced technologies have elucidated the epigenetics and structural and functional modifications driven by LTR retrotransposon during speciation. However, mechanistic insights into LTR retrotransposons remain obscure in plant development due to a lack of advancement in high throughput technologies. In this review, we focus on the key role of LTR retrotransposons response in plants during heat stress, the role of centromeric LTR retrotransposons, and the role of LTR retrotransposon markers in genome expression and evolution.
Mixed-litter effects of fresh leaf semi-decomposed litter and fine root on soil enzyme activity and microbial community in an evergreen broadleaf karst forest in southwest China
Authors: Mao Bing , Cui Tingting , Su Tongqing , Xu Qiangsheng , Lu Feng , Su Hongxin , Zhang Jianbing , Xiao Shuangshuang
Published: December 2022

Litter decomposition is the main process that affects nutrient cycling and carbon budgets in mixed forests. However, knowledge of the response of the soil microbial processes to the mixed-litter decomposition of fresh leaf, semi-decomposed leaf and fine root is limited. Thus, a laboratory microcosm experiment was performed to explore the mixed-litter effects of fresh leaf, semi-decomposed leaf and fine root on the soil enzyme activity and microbial community in an evergreen broadleaf karst forest in Southwest China. Fresh leaf litter, semi-decomposed litter and fine root in theParakmeria nitidaandDayaoshania cotinifoliaforests, which are unique protective species and dominant species in the evergreen broadleaf forest, were decomposed alone and in all possible combinations, respectively. Our results showed that the mass loss of fresh leaf litter in three mixed-litter treatment was significantly higher than that in two mixed-litter treatment in theP. nitidaandD. cotinifoliaforests. Mass loss of fine root in the single litter treatment was significantly lower in theP. nitidaforest and higher in theD. cotinifoliaforest compared to that in the other litter treatments. There were insignificant differences in the activities of β-glucosidase (BG) and leucine aminopeptidase (LAP) between control and mixed-litter treatment in theP. nitidaforest and between control and single litter treatment in theD. cotinifoliaforest. The N-acetyl-β-D-glucosaminidase (NAG) activity was significantly increased by the single litter decomposition of fresh leaf and fine root and three mixed-litter decomposition in theP. nitidaandD. cotinifoliaforests. The activity of acid phospomonoesterase (AP) in the decomposition of fresh leaf litter was lower in theP. nitidaforest and higher in theD. cotinifoliaforest compared to that in control. The most dominant soil bacteria wereProteobacteriain theP. nitidaforest and wereActinobacteriaandProteobacteriain theD. cotinifoliaforest. Shannon, Chao1, ACE and PD indexes in the mixed-litter decomposition of fresh leaf and semi-decomposition litter were higher than that in control inP. nitidaforest. There were insignificant differences in observed species and indexes of Chao1, ACE and PD between litter treatments in theD. cotinifoliaforest. Richness of mixed-litter significantly affected mass loss, soil enzyme activity and microbial diversity in theP. nitidaforest. Litter N concentration and the presence of fresh leaf litter were significantly correlated with the mass loss and soil enzyme activity in theP. nitidaandD. cotinifoliaforests. These results indicated that the presence of fresh leaf litter showed a non-negligible influence on mixed-litter decomposition and soil enzyme activity, which might be partly explained by litter initial quality in theP. nitidaandD. cotinifoliaforests.
Elevated CO2 concentration induces changes in plant growth, transcriptome, and antioxidant activity in fennel (Foeniculum vulgare Mill.)
Authors: Jo Na-Yeon , Lee Junkyung , Byeon Ji-Eun , Park Hong-Jin , Ryoo Jong-Won , Hwang Sun-Goo
Published: December 2022

Introduction

Fennel (Foeniculum vulgare Mill.) is widely used to produce natural bio-materials. Elevated CO2(eCO2) concentrations in the atmosphere improve the net photosynthesis of plants.

Methods

The aim of the present study was to investigate distinct changes in fennel growth characteristics and phytonutrient contents under different CO2concentrations. The effects of 400 and 800 ppm concentrations on plant growth and antioxidant activity were observed under hydroponics.

Results and Discussion

Plant growth was improved by eCO2concentrations. We also observed diverse changes in nutrient solution (pH, electrical conductivity, and dissolved oxygen) and environmental factors (temperature and humidity) in greenhouse under light or dark conditions. Electrical conductivity increased under dark and eCO2conditions, whereas the pH decreased. Additionally, we performed transcriptome analysis and identified CO2-responsive differentially expressed genes. In the 800 ppm group, genes involved in photosynthesis and Karrikin response were upregulated whereas those involved in syncytium formation were downregulated. Four upregulated differentially expressed genes involved in flavonoid biosynthesis and total flavonoid content were relatively increased under the 800 ppm CO2condition. In contrast, antioxidant activity, including total phenolic content, scavenging activity, ferric ion reducing antioxidant power, and reducing power were decreased in fennel under relatively high eCO2concentrations. Moreover, different light intensities of 12 or 24 lx did not affect the growth and antioxidant activity of fennel, suggesting eCO2has a stronger effect on plant improvement than light intensity. The results of the present study enhance our understanding of the positive effects of CO2on the growth and antioxidant activity of fennel.
Comprehensive resistance evaluation of 15 blueberry cultivars under high soil pH stress based on growth phenotype and physiological traits
Authors: Yang Hao , Wu Yaqiong , Zhang Chunhong , Wu Wenlong , Lyu Lianfei , Li Weilin
Published: December 2022

High soil pH is one of the main abiotic factors that negatively affects blueberry growth and cultivation. However, no comprehensive evaluation of the high soil pH tolerance of different blueberry cultivars has been conducted. Herein, 16 phenotypic and physiological indices of 15 blueberry cultivars were measured through pot experiments, and the high-pH soil tolerance coefficient (HSTC) was calculated based on these indices to comprehensively evaluate the high-soil-pH tolerance of plants. The results demonstrated that high soil pH stress inhibited blueberry 77.growth, and MDA, soluble sugar (SS), and soluble protein (SP) levels increased in leaves. Moreover, in all cultivars, CAT activity in the antioxidant system was enhanced, whereas SOD activity was reduced, and the relative expression levels of the antioxidant enzyme genes SOD and CAT showed similar changes. In addition, the leaf chlorophyll relative content (SPAD), net photosynthetic rate (Pn), transpiration rate (E), and stomatal conductance (Gs) decreased, while changes in the intercellular CO2 concentration (Ci) were noted in different cultivars. Finally, according to the comprehensive evaluation value D obtained from the combination of principal component analysis (PCA) and membership function (MF), the 15 blueberry cultivars can be divided into 4 categories: high soil pH-tolerant type [‘Briteblue’ (highest D value 0.815)], intermediate tolerance type (‘Zhaixuan 9’, ‘Zhaixuan 7’, ‘Emerald’, ‘Primadonna’, ‘Powderblue’ and ‘Chandler’), low high soil pH-tolerant type (‘Brightwell’, ‘Gardenblue’, ‘Plolific’ and ‘Sharpblue’) and high soil pH-sensitive type [‘Legacy’, ‘Bluegold’, ‘Baldwin’ and ‘Anna’ (lowest D value 0.166)]. Stepwise linear regression analysis revealed that plant height, SS, E, leaf length, Ci, SOD, and SPAD could be used to predict and evaluate the high soil pH tolerance of blueberry cultivars.
Grapevine leaf physiology and morphological characteristics to elevated CO2 in the VineyardFACE (Free air Carbon dioxide Enrichment) experiment
Authors: Wohlfahrt Yvette , Krüger Katja , Papsdorf Daniel , Tittmann Susanne , Stoll Manfred
Published: December 2022

Atmospheric carbon dioxide (CO2) concentration has continuously increased since pre-industrial times and has currently reached an average growth rate of 2.3 ppm per year. For the majority of plant species elevated CO2 (eCO2) improves photosynthesis and thus plant biomass production. To investigate the effects of eCO2 on leaf physiology and morphological leaf characteristics two Vitis vinifera L. cultivars, Riesling and Cabernet Sauvignon, grown in the VineyardFACE (Free Air Carbon dioxide Enrichment) system were used. The VineyardFACE is located at Geisenheim, Rheingau comparing future atmospheric CO2-concentrations (eCO2, predicted for the mid-21st century) with current ambient CO2-conditions (aCO2). Experiments were operated under rain-fed conditions for two consecutive years (2015 and 2016). For both varieties and CO2 treatments, leaf gas exchange measurements were performed as well as measures of epidermal flavonoid (Flav) and leaf chlorophyll (Chl) indices by using a portable leaf clip. Furthermore, leaves were sampled for spectrophotometric analysis of the leaf pigments chlorophyll a (Chl a), chlorophyll b (Chl b) and carotenoid (Car). Additionally, leaf cross-sections were produced as permanent preparations to investigate morphological characteristics of the leaf structure. Both cultivars did not differ in leaf chlorophyll meter readings or leaf pigments between the two CO2 treatments while net assimilation was highly stimulated under elevated CO2 for both seasons. Differences found in leaf cross-sections were detected in palisade parenchyma and epidermal thickness of Cabernet Sauvignon under eCO2, whereas Riesling net assimilation increased by 40% under a 20% CO2 enrichment while remaining unaffected in different leaf layer thickness. The observed results within grapevine leaf tissues provide insights to seasonal adaptation strategies of grapevines under elevated CO2 concentrations predicted in future.
Systematic genome-wide and expression analysis of RNA-directed DNA methylation pathway genes in grapes predicts their involvement in multiple biological processes
Authors: Xiang Rui , Ahmad Bilal , Liang Chen , Shi Xiaoxin , Yang Lili , Du Guoqiang , Wang Li
Published: December 2022

RNA-directed DNA methylation (RdDM) is an important epigenetic pathway in plants and mediates transcriptional silencing by siRNAs. Different gene families have role in the regulation of the RdDM pathway and there is a lack of information about these gene families in the grapes (Vitis vinifera L.). Here, we mentioned the genome-wide identification, bioinformatics analysis, evolutionary history, and expression profiling of VvRdDM pathway genes against various stresses, hormonal treatments as well as in different organs. Sixty VvRdDM genes belonging to fourteen different families were identified. All the genes were unevenly distributed and chromosome 4 contained the highest number of genes (7). Most of the genes showed similar exon-intron and motif distribution patterns within the same subfamilies. Out of 14 families, only members of 4 families underwent duplication events during the evolutionary process and 50% of members of the AGO family are the result of duplication events. Based on Ka/Ks ratio all duplicated gene pairs have a negative mode of selection. VvRdDM pathway genes showed differential spatiotemporal expression patterns against different hormone and stress treatments. Further, with multiple transcriptome analysis, some VvRdDM genes showed a broad spectrum of high expression in different organs at various stages, and VvRdDM genes also displayed different expression in seeded and seedless cultivars during different phases of seed development. This proposed that VvRdDM genes may play multiple roles in grape growth and development, especially in seed development. qRT-PCR analysis of selected genes further verified the critical roles of RdDM genes in multiple biological processes, especially in seed development/ovule abortion i.e., VvIDN2a, VvDRD1a, VvRDR1a, and VvRDR6. Our study provides detailed information about VvRdDM genes in perspective of gene structure and evolution, as well as expression pattern against different stress, hormones and in different plants parts. It provides new candidate gene resources for further functional characterization and molecular breeding of grapes.