bluuebunny/crossref_metadata_2025 huggingface dataset:
The influence of gastronomic identity factors on food tourism development in the Republic of Serbia and Bosnia and Herzegovina
Authors: Kalenjuk Pivarski Bojana , Paunić Maja , Šarenac Nemanja , Šmugović Stefan , Mlinarević Predrag , Ivanović Velibor , Marjanović Jelena , Pavlović Stevan , Tekić Dragana , Ðerčan Bojan , Tešanović Dragan , Gagić Jaraković Snježana
Published: January 2024

Background and aims

The gastronomic identity of an area is the key factor in tourism development, attracting numerous tourists and generating significant income. Numerous economic actors participate in its use and proper placement, and their perception of the gastronomic potential significantly affects its distribution and use in tourism. The main aim of this study is to investigate the factors of gastronomic identity that influence the development of tourism, observed at two tourist destinations in Southeast Europe [the Republic of Serbia (RS) the city of Novi Sad with Fruška Gora Mountain, n = 305 and Bosnia and Herzegovina (BIH) the city of Sarajevo with Jahorina Mountain, n = 301].

Methods

In order to define the factors that are relevant to food tourism development, a custom-made GastroIdentity scale was created. A survey was conducted among employees in the hospitality and tourism industry as well as employees in educational institutions in the field of hospitality and tourism.

Results

The research results show that employees from the RS area acknowledge the importance of organizing gastronomic events where local products are presented and that they understand that dishes and beverages with unique and recognizable tastes can characterize their area. Employees from the BIH area pointed out that the nutritional quality of their local agricultural and gastronomic products represents an advantage when compared to mass-produced ones and that the local gastronomic culture and tradition are authentic representatives of the culture of the region.

Conclusion

The GastroIdentity scale proved to be dependable, highlighting gastronomic culture and tradition as extremely crucial factors in tourism, using the input provided by the employees from the investigated areas. Noteworthy results were also recorded regarding the need for incentives for food tourism development in the investigated regions.
Identification and virtual screening of novel salty peptides from hydrolysate of tilapia by-product by batch molecular docking
Authors: Ren Hongjun , Zhou Jingxuan , Fu Huixian , Feng Qiaohui , Wang Jionghao , Li Chuan , Xia Guanghua , Shang Wenting , He Yanfu
Published: January 2024

Introduction

Tilapia produces a large number of by-products during processing, which contain potentially flavorful peptides.

Methods

The application of PyRx software enabled batch molecular docking andscreening of 16 potential salty peptides from 189 peptides identified in the enzymaticdigestion of tilapia by-products.

Results

According to sensory analysis, all 16 peptides werepredominantly salty with a threshold of 0.256 - 0.379 mmol/L with some sournessand astringency, among which HLDDALR had the highest salty intensity, followedby VIEPLDIGDDKVR, FPGIPDHL, and DFKSPDDPSRH. I addition, moleculardocking results showed these four core peptides with high salt intensity bound to thesalt receptor TRPV1 mainly via van der Waals interactions, hydrogen bonds, andhydrophobic forces; Arg491, Tyr487, VAL441, and Asp708 were the key sites for thebinding of salty peptides to TRPV1. Therefore, the application of batch moleculardocking using PyRx is effective and economical for the virtual screening of saltypeptides.
Association between tamoxifen and incidence of osteoporosis in Korean patients with ductal carcinoma in situ
Authors: Kim Dooreh , Oh Jooyoung , Lee Hye Sun , Jeon Soyoung , Park Woo-Chan , Yoon Chang Ik
Published: January 2024

Introduction

The partial estrogen-agonist action of tamoxifen on bone receptors has beneficial effects on bone mineral density. However, in premenopausal women, the use of tamoxifen causes systemic estrogen depletion, which has detrimental effects on bone health. We aim to investigate the association between tamoxifen and osteoporosis in the real world using data from a longitudinal nationwide cohort of Korean patients.

Methods

Data were collected from the National Health Insurance claims database in South Korea. Osteoporosis was defined by diagnostic codes accompanying prescription data for osteoporosis. The cumulative incidence was analyzed by Kaplan–Meier survival curves and the risk factors were analyzed using a multivariable Cox proportional hazard regression model.

Results

Between 2009 and 2015, of the 4,654 women with ductal carcinoma in situ (DCIS) without prior osteoporosis, 2,970 were prescribed tamoxifen and 1,684 were not. A total of 356 DCIS survivors were later diagnosed with osteoporosis during a median follow-up period of 84 months. In the overall population, tamoxifen was associated with a low risk of osteoporosis, before and after propensity matching adjusted for age, operation type, and comorbidities (before matching, hazard ratio [HR]=0.69, 95% confidence interval [CI]=0.559–0.851, p<0.001; after matching, HR=0.664, 95% CI=0.513–0.858, p=0.002). In the subgroup analysis, findings were consistent in postmenopausal women but were not evident in the younger age group.

Conclusion

In a nationwide cohort study, a low risk of osteoporosis was associated with the use of tamoxifen. The protective effect of tamoxifen was more profound in older women and was not related to the incidence of osteoporosis in younger women.
Axillary management in patients with clinical node-negative early breast cancer and positive sentinel lymph node: a systematic review and meta-analysis
Authors: Li Changzai , Zhang Pan , Lv Jie , Dong Wei , Hu Baoshan , Zhang Jinji , Zhu Hongcheng
Published: January 2024

Background

The omission of axillary lymph node dissection (ALND) or axillary radiation (AxRT) remains controversial in patients with clinical node-negative early breast cancer and a positive sentinel lymph node.

Methods

We conducted a comprehensive review by searching PubMed, Embase, Web of Science, and Cochrane databases (up to November 2023). Our primary outcomes were overall survival (OS), disease-free survival (DFS), locoregional recurrence (LRR), and axillary recurrence (AR).

Results

We included 26 studies encompassing 145,548 women with clinical node-negative early breast cancer and positive sentinel lymph node. Pooled data revealed no significant differences between ALND and sentinel lymph node biopsy (SLNB) alone in terms of OS (hazard ratio [HR]0.99, 95% confidence interval [CI] 0.91-1.08, p=0.84), DFS (HR 1.04, 95% CI 0.90-1.19, p=0.61), LRR (HR 0.76, 95% CI 0.45-1.20, p=0.31), and AR (HR 1.01, 95% CI 0.99-1.03, p=0.35). Similarly, no significant differences were observed between AxRT and SLNB alone for OS (HR 0.57, 95% CI 0.32-1.02, p=0.06) and DFS (HR 0.52, 95% CI 0.26-1.05, p=0.07). When comparing AxRT and ALND, a trend towards higher OS was observed the AxRT group (HR 0.08, 95% CI 0.67-1.15), but the difference did not reach statistical significance (p=0.35, I2 = 0%). Additionally, no significant differences significance observed for DFS or AR (p=0.13 and p=0.73, respectively) between the AxRT and ALND groups.

Conclusion

Our findings suggest that survival and recurrence rates are not inferior in patients with clinical node-negative early breast cancer and a positive sentinel lymph node who receive SLNB alone compared to those undergoing ALND or AxRT.
Management and outcomes of brain metastases from pancreatic adenocarcinoma: a pooled analysis and literature review
Authors: Gouton Etienne , Gilabert Marine , Launay Simon , Loir Elika , Tyran Marguerite , Rochigneux Philippe , Turrini Olivier , Garnier Jonathan , Mitry Emmanuel , Chanez Brice
Published: January 2024

Background

Brain metastases (BM) are rare in pancreatic ductal adenocarcinoma (PDAC) and little data exists concerning these patients and their outcomes.

Aim

We aimed to analyze the management, practices, and outcomes of patients presenting BM from PDAC both in our institution and in all cases reported in the literature.

Methods

We conducted a retrospective, monocentric analysis using a data mining tool (ConSoRe) to identify all patients diagnosed with PDAC and BM in our comprehensive cancer center (Paoli-Calmettes Institute), from July 1997 to June 2022 (cohort 1). Simultaneously, we reviewed and pooled the case reports and case series of patients with PDAC and BM in the literature (cohort 2). The clinical characteristics of patients in each cohort were described and survival analyses were performed using the Kaplan-Meier method.

Results

In cohort 1, 19 patients (0.3%) with PDAC and BM were identified with a median age of 69 years (range: 39-81). Most patients had metastatic disease (74%), including 21% with BM, at diagnosis. Lung metastases were present in 58% of patients. 68% of patients had neurological symptoms and 68% were treated by focal treatment (surgery: 21%, radiotherapy: 42%, Gamma Knife radiosurgery: 5%). In cohort 2, among the 61 PDAC patients with BM described in the literature, 59% had metastatic disease, including 13% with BM at diagnosis. Lung metastases were present in 36% of patient and BM treatments included: surgery (36%), radiotherapy (36%), radiosurgery (3%), or no local treatment (25%). After the pancreatic cancer diagnosis, the median time to develop BM was 7.8 months (range: 0.0-73.9) in cohort 1 and 17.0 months (range: 0.0-64.0) in cohort 2. Median overall survival (OS) in patients of cohort 1 and cohort 2 was 2.9 months (95% CI [1.7,4.0]) and 12.5 months (95% CI [7.5,17.5]), respectively.

Conclusion

BM are very uncommon in PDAC and seem to occur more often in younger patients with lung metastases and more indolent disease. BM are associated with poor prognosis and neurosurgery offers the best outcomes and should be considered when feasible.
Acupuncture in musculoskeletal pain: analysis of changes in pain perception using the NRS (Numeric Rating Scale)
Authors: Fracchia Lorenzo , Olivero Alda Maria , Rustichelli Riccardo , Pedrali Tiziana
Published: January 2024

Objectives

This study is based on data collected at the Acupuncture clinic of the Local Health Authority (ASL) in Turin from 2008 to 2022 and aims at evaluating the effectiveness of acupuncture in the treatment of musculoskeletal pain using the Numeric Rating Scale (NRS) which analyzes changes in pain perceived by patients in different body regions.

Methods

The database consists of data provided by patients during the initial visit and the last session. Only patients who provided data at the beginning and end of treatment were included. The data were processed using JASP 0.17.2.1 software. The sample consisted of 932 patients with musculoskeletal conditions, excluding 254 subjects with internal medical conditions, who were treated during the same period. The selected population includes individuals aged 23–94, comprising 242 men and 690 women. Patients followed a therapeutic protocol based on the initial diagnosis and underwent an initial cycle of six weekly sessions, with the possibility of four additional sessions if needed. Acupuncture was performed by experienced medical personnel following Traditional Chinese Medicine guideline.

Results

The average NRS values were 7.49 at the beginning and 4.27 at the end, with a 43% reduction in pain. The data were analyzed using the Wilcoxon test, confirming statistical significance (p < 0.001). They were then divided by body region, showing a reduction in pain ranging from 40% to 55%. Statistical analysis among different conditions was performed using the Kruskal–Wallis test, with further comparisons using the Dunn test.

Discussion

The study demonstrates that acupuncture is effective in reducing musculoskeletal suffering, with a significant decrease in pain perceived by patients. The results suggest that acupuncture can be a valid treatment for a wide range of conditions, with pain reduction ranging from 40% to 55% and greater effectiveness for elbow-related conditions. However, it is important to note that sample size may influence the results, and further research is needed to confirm and expand these findings, especially for less-represented conditions by the sample.
An analysis of Pompe newborn screening data: a new prevalence at birth, insight and discussion
Authors: Colburn Ryan , Lapidus David
Published: January 2024

This study includes over 11.6M newborns screened (NBS) for Pompe Disease (PD) from 29 distinct universal screening programs across 8 countries and 4 continents. The birth prevalence of PD is 1:18,711, with no evidence of difference across populations of European, Latin American, or Asian ancestry, though differences may exist for PD subtypes. This study also compares these results, based on direct detection of disease and analyzed using a binomial method along with power analysis, with other methods for estimating the ‘frequency’ of rare genetic diseases (such as utilizing Hardy-Weinberg equilibrium on allele frequency and confidence interval analysis). This comparison demonstrates the implications of sample size and frames a discussion on its influence on the reliability of results when extrapolating to a population beyond the study dataset.

Objectives

Primary: Establish a new figure for prevalence at birth for Pompe disease by collecting and analyzing the largest relevant dataset to date and using that result to project population prevalence at birth in a novel way. Secondary: Compare these results to previous analyses to offer a framework for evaluating ‘frequency’ data that can be applied to other rare, genetic diseases, along with methods to assess quality of estimates.
End-of-life decision-making in the neonatal intensive care unit
Authors: Morillo Palomo Ana , Esquerda Aresté Montse , Riverola de Veciana Ana , Cambra Lasaosa Francisco José
Published: January 2024

Most paediatric deaths occur in the neonatal period, many of them in neonatal intensive care units after withdrawal of life support or the decision not to initiate new treatments. In these circumstances, discussions with families and decision-making are fundamental elements of the care and attention given to newborn babies. In this context, bioethical deliberation can help us to identify the values at stake, the different courses of action to be taken, and the means to ensure that family-shared decision-making is appropriate to the patient's situation and in accordance with the family's values.
Neuroprotective effects and possible mechanisms of berberine in animal models of Alzheimer’s disease: a systematic review and meta-analysis
Authors: Dan Lijuan , Hao Yanwei , Li Jiaxin , Wang Tianyuan , Zhao Weiwei , Wang Hui , Qiao Liyan , Xie Peijun
Published: January 2024

Background: Recently, multiple preclinical studies have reported the beneficial effect of berberine in the treatment of Alzheimer’s disease (AD). Nevertheless, the neuroprotective effects and possible mechanisms of berberine against AD are not universally recognized. This study aimed to conduct a systematic review and meta-analysis by integrating relevant animal studies to assess the neuroprotective effects and potential mechanisms of berberine on AD.

Methods: We systematically searched PubMed, Embase, Scopus and Web of Science databases that reported the effects of berberine on AD models up to 1 February 2023. The escape latency, times of crossing platform, time spent in the target quadrant and pro-oligomerized amyloid beta 42 (Aβ1-42) were included as primary outcomes. The secondary outcomes were the Tau-ps 204, Tau-ps 404, β-site of APP cleaving enzyme (BACE1), amyloid precursor protein (APP), acetylcholine esterase (AChE), tumor necrosis factor ⍺ (TNF-α), interleukin 1β (IL-1β), IL-6, nitric oxide (NO), glial fibrillary acidic protein (GFAP), malonaldehyde (MDA), glutathione S-transferase (GST), glutathione (GSH), glutathione peroxidase (GPx), Beclin-1 and neuronal apoptosis cells. This meta-analysis was conducted using RevMan 5.4 and STATA 15.1. The SYRCLE’s risk of bias tool was used to assess the methodological quality.

Results: Twenty-two studies and 453 animals were included in the analysis. The overall results showed that berberine significantly shortened the escape latency (p < 0.00001), increased times of crossing platform (p < 0.00001) and time spent in the target quadrant (p < 0.00001), decreased Aβ1-42 deposition (p < 0.00001), Tau-ps 202 (p < 0.00001) and Tau-ps 404 (p = 0.002), and improved BACE1, APP, AChE, Beclin-1, neuronal apoptosis cells, oxidative stress and inflammation levels.

Conclusion: Berberine may be a promising drug for the treatment of AD based on preclinical evidence (especially when the dose was 5–260 mg/kg). The potential mechanisms for these protective effects may be closely related to anti-neuroinflammation, anti-oxidative stress, modulation of autophagy, inhibition of neuronal apoptosis and protection of cholinergic system. However, these results may be limited by the quality of existing research. Larger and methodologically more rigorous preclinical research are needed to provide more convincing evidence.
Efficacies and ADME properties of redox active methylene blue and phenoxazine analogues for use in new antimalarial triple drug combinations with amino-artemisinins
Authors: Watson Daniel J. , Laing Lizahn , Petzer Jacobus P. , Wong Ho Ning , Parkinson Christopher J. , Wiesner Lubbe , Haynes Richard K.
Published: January 2024

Efforts to develop new artemisinin triple combination therapies effective against artemisinin-tolerant strains of Plasmodium falciparum based on rational combinations comprising artemisone or other amino-artemisinins, a redox active drug and a third drug with a different mode of action have now been extended to evaluation of three potential redox partners. These are the diethyl analogue AD01 of methylene blue (MB), the benzo [α]phenoxazine PhX6, and the thiosemicarbazone DpNEt. IC50 values in vitro against CQ-sensitive and resistant P. falciparum strains ranged from 11.9 nM for AD01–41.8 nM for PhX6. PhX6 possessed the most favourable pharmacokinetic (PK) profile: intrinsic clearance rate CLint was 21.47 ± 1.76 mL/min/kg, bioavailability was 60% and half-life was 7.96 h. AD01 presented weaker, but manageable pharmacokinetic properties with a rapid CLint of 74.41 ± 6.68 mL/min/kg leading to a half-life of 2.51 ± 0.07 h and bioavailability of 15%. DpNEt exhibited a half-life of 1.12 h and bioavailability of 8%, data which discourage its further examination, despite a low CLint of 10.20 mL/min/kg and a high Cmax of 6.32 µM. Efficacies of AD01 and PhX6 were enhanced synergistically when each was paired with artemisone against asexual blood stages of P. falciparum NF54 in vitro. The favourable pharmacokinetics of PhX6 indicate this is the best partner among the compounds examined thus far for artemisone. Future work will focus on extending the drug combination studies to artemiside in vitro, and conducting efficacy studies in vivo for artemisone with each of PhX6 and the related benzo[α]phenoxazine SSJ-183.
Mechanism of Wuzhuyu decoction on alcohol-induced gastric ulcers using integrated network analysis and metabolomics
Authors: Wang Xin , Chen Lisheng , Chang Lei , He Yong , He Tingting , Wang Ruilin , Wei Shizhang , Jing Manyi , Zhou Xuelin , Li Haotian , Zhao Yanling
Published: January 2024

Background: Gastric ulcers (GUs) are prevalent digestive disorders worldwide. Wuzhuyu Decoction (WZYT) is a traditional Chinese medicine that has been employed for centuries to alleviate digestive ailments like indigestion and vomiting. This study aims to explore the potential effects and underlying mechanisms of WZYT on alcohol induced gastric ulcer treatment.

Methods: We employed macroscopic assessment to evaluate the gastric ulcer index (UI), while the enzyme-linked immunosorbent assay (ELISA) was utilized for detecting biochemical indicators. Pathological tissue analysis involved hematoxylin-eosin (H&E) staining and Periodic Acid-Schiff (PAS) staining to assess gastric tissue damage. Additionally, the integration of network analysis and metabolomics facilitated the prediction of potential targets. Validation was conducted using Western blotting.

Results: The research revealed that WZYT treatment significantly reduced the gastric ulcer index (UI) and regulation of alcohol-induced biochemical indicators levels. Additionally, improvements were observed in pathological tissue. Network analysis results indicated that 62 compounds contained in WZYT modulate alcohol-induced gastric ulcers by regulating 183 genes. The serum metabolomics indicated significant changes in the content of 19 metabolites after WZYT treatment. Two pivotal targets, heme oxygenase 1 (HMOX1) and albumin (ALB), are believed to assume a significant role in the treatment of gastric ulcers by the construction of “compounds-target-metabolite” networks. Western blot analysis confirmed that WZYT has the capacity to elevate the expression of HMOX1 and ALB targets.

Conclusion: The integration of network analysis and metabolomics provides a scientific basis to propel the clinical use of WZYT for GUs. Our study provides a theoretical basis for the use of Wuzhuyu decoction in the treatment of gastric ulcers.
Effects of biological therapies on patients with Type-2 high asthma and comorbid obesity
Authors: Garg Diya , Que Loretta G. , Ingram Jennifer L.
Published: January 2024

Over 20 million adults and 6 million children in the United States (US) have asthma, a chronic respiratory disease characterized by airway inflammation, bronchoconstriction, and mucus hypersecretion. Obesity, another highly prevalent disease in the US, is a major risk factor for asthma and a significant cause of diminished asthma control, increased submucosal eosinophilia, and reduced quality of life. A large subgroup of these patients experiences severe symptoms and recurrent exacerbations despite maximal dosage of standard asthma therapies. In the past two decades, the development of biological therapies has revolutionized the field and advanced our understanding of type 2 inflammatory biomarkers. However, patients with obesity and comorbid asthma are not principally considered in clinical trials of biologics. Large landmark cluster analyses of patients with asthma have consistently identified specific asthma phenotypes that associate with obesity but may be differentiated by age of asthma onset and inflammatory cell profiles in sputum. These patterns suggest that biologic processes driving asthma pathology are heterogenous among patients with obesity. The biological mechanisms driving pathology in patients with asthma and comorbid obesity are not well understood and likely multifactorial. Future research needs to be done to elicit the cellular and metabolic functions in the relationship of obesity and asthma to yield the best treatment options for this multiplex condition. In this review, we explore the key features of type 2 inflammation in asthma and discuss the effectiveness, safety profile, and research gaps regarding the currently approved biological therapies in asthma patients with obesity.
Vitamin D3 promotes gastric cancer cell autophagy by mediating p53/AMPK/mTOR signaling
Authors: Wang Yanan , He Qingmin , Rong Kang , Zhu Mingyang , Zhao Xiaoxiao , Zheng Pengyuan , Mi Yang
Published: January 2024

Objective: Vitamin D3 has the general properties of a lipid-soluble vitamin, but is also an active steroid hormone that can regulate the proliferation, apoptosis and differentiation of many tumor cells, and exerts anticancer activity against numerous malignancies. However, the mechanism underlying the effects of vitamin D3 on tumors is not fully understood. Here, we used network pharmacology and in vitro experimental approaches to explore the mechanism of vitamin D3 activity in the context of gastric cancer.

Methods: The Targetnet, SuperPred, SwissTargetPrediction, and PharmMapper databases were screened for potential drug-related targets, while we used data from the PharmGKB, Drugbank, OMIM, DisGeNET, CTD, and GeneCards databases to identify potential targets associated with gastric cancer. Disease-drug crossover genes were obtained by constructing Venn diagrams. Gene ontology and Kyoto Encyclopedia of Genomes (KEGG) enrichment analyses of crossover genes were conducted and STRING was used to generate protein interaction networks and identify core targets. CCK-8 experiments were performed and apoptosis detected to assess the effect of vitamin D3 on gastric cancer cells. Western blotting was applied to detect p53/AMPK/mTOR signaling, as well as autophagy-, cell cycle-, and apoptosis-related proteins.

Results: A total of 485 targets of vitamin D3 activity were obtained and 1200 gastric cancer disease-related targets discovered. Further, 60 potential targets for vitamin D3 in gastric cancer treatment were identified. KEGG analysis indicated that potential targets were mainly involved in the cell cycle, HIF-1 signaling, and the AMPK pathway, among other pathways. These findings were validated using cellular experiments, which demonstrated that the viability of AGS and SGC-7901 cells was impeded by vitamin D3. Further, vitamin D3 promoted apoptosis and inhibited the cell cycle in those cell lines, as well as activating the p53/AMPK/mTOR pathway, which promotes autophagy and inhibits tumor development.

Conclusion: Our network pharmacological analyses provide preliminarily data supporting a role for vitamin D3 in promoting autophagy and apoptosis in gastric cancer cells, and in activating the p53/AMPK/mTOR pathway, which inhibits gastric cancer cell proliferation. Our findings demonstrate the molecular mechanism underlying the effect of vitamin D3 in cure of gastric cancer.
Turkey hen sperm storage tubule transcriptome response to artificial insemination and the presence of semen
Authors: Brady Kristen , Krasnec Katina , Hanlon Charlene , Long Julie A.
Published: January 2024

Introduction: Sperm storage within the uterovaginal junction (UVJ) of avian species occurs in specialized structures termed sperm storage tubules (SSTs) and allows for prolonged storage of semen, though the molecular mechanisms involved in semen preservation are not well understood. Little work has been done examining how function of the SSTs is impacted by insemination and by semen present in the SSTs.

Methods: Transcriptome analysis was performed on isolated SSTs from turkey hens receiving no insemination (control), sham-insemination, or semen-insemination at three timepoints (D1, D30, and D90 post-insemination). Bioinformatic and functional annotation analyses were performed using CLC Genomics Workbench, Database for Annotation, Visualization, and Integrated Discovery (DAVID), and Ingenuity Pathway Analysis (IPA). Pairwise comparisons and k-medoids cluster analysis were utilized to decipher differential expression profiles in the treatment groups.

Results: The SST transcriptome of the semen inseminated group exhibited the greatest differences within the group, with differences detectable for up to 90 days post insemination, while control and sham-inseminated groups were more similar. In the semen-inseminated samples, upregulation of pathways relating to classical and non-classical reproductive signaling, cytoskeletal remodeling, physiological parameters of the local UVJ environment, and cellular metabolism was observed. In the sham-inseminated samples, upregulation of immune pathways and non-reproductive endocrine hormones was observed.

Discussion: This work provides insights into the molecular level changes of the SST in response to insemination as well as to the presence of semen. Results from this study may have direct implications on fertility rates as well as potential strategies for avian semen cryopreservation protocols.
Development and utility of SSR markers based on Brassica sp. whole-genome in triangle of U
Authors: Sun Nairan , Chen Jisuan , Wang Yuqi , Hussain Iqbal , Lei Na , Ma Xinyan , Li Weiqiang , Liu Kaiwen , Yu Hongrui , Zhao Kun , Zhao Tong , Zhang Yi , Yu Xiaolin
Published: January 2024

Introduction

Simple sequence repeats (SSR), also known as microsatellites, are crucial molecular markers in both animals and plants. Despite extensive previous research on SSRs, the development of microsatellite markers in Brassica crops remains limited and inefficient.

Methods

Krait software was used to identify microsatellites by genome-wide and marker development based on three recently sequenced basic species of Brassica crops in the triangle of U (Brassica rapa, B. nigra and B. oleracea), as well as three allotetraploids (B. juncea, B. napus and B. carinata) using public databases. Subsequently, the primers and the characteristics of microsatellites for most of them were accordingly designed on each chromosome of each of the six Brassica species, and their physical locations were identified,and the cross-transferability of primers have been carried out. In addition, a B-genome specific SSR marker was screened out.

Results

A total of 79341, 92089, 125443, 173964, 173604, and 222160 SSR loci have been identified from the whole genome sequences of Brassica crops within the triangle of U crops, B. rapa (AA), B. nigra (BB), B. oleracea (CC), B. napus (AACC), B. juncea (AABB) and B. carinata (BBCC), respectively. Comparing the number distribution of the three allotetraploid SSR loci in the three subgenomes AA, BB and CC, results indicate that the allotetraploid species have significant reduction in the number of SSR loci in the genome compared with their basic diploid counterparts. Moreover, we compared the basic species with their corresponding varieties, and found that the microsatellite characters between the allotetraploids and their corresponding basic species were very similar or almost identical. Subsequently, each of the 40 SSR primers was employed to investigate the polymorphism potential of B. rapa (85.27%), B. nigra (81.33%) and B. oleracea (73.45%), and B. rapa was found to have a higher cross-transfer rate among the basic species in the triangle of U. Meanwhile, a B-genome specific SSR marker, BniSSR23228 possessing the (AAGGA)3 sequence characteristics was obtained, and it located in chromosome B3 with a total length of 97 bp.

Discussion

In this study, results suggest that the pattern of distribution may be highly conserved during the differentiation of basic Brassica species and their allotetraploid counterparts. Our data indicated that the allotetraploidization process resulted in a significant reduction in SSR loci in the three subgenomes AA, BB and CC. The reasons may be partial gene dominated chromosomal homologous recombination and rearrangement during the evolution of basic diploid species into allotetraploids. This study provides a basis for future genomics and genetic research on the relatedness of Brassica species.
A biostimulant prepared from red seaweed Kappaphycus alvarezii induces flowering and improves the growth of Pisum sativum grown under optimum and nitrogen-limited conditions
Authors: Shukla Pushp Sheel , Nivetha Nagarajan , Nori Sri Sailaja , Kumar Sawan , Critchley Alan T. , Suryanarayan Shrikumar
Published: January 2024

Nitrogen (N) is one of the critical elements required by plants and is therefore one of the important limiting factors for growth and yield. To increase agricultural productivity, farmers are using excessive N fertilizers to the soil, which poses a threat to the ecosystem, as most of the applied nitrogen fertilizer is not taken up by crops, and runoff to aquatic bodies and the environment causes eutrophication, pollution, and greenhouse gas emissions. In this study, we used LBS6, a Kappaphycus alvarezii-based biostimulant as a sustainable alternative to improve the growth of plants under different NO3- fertigation. A root drench treatment of 1 ml/L LBS6 significantly improved the growth of Pisum sativum plants grown under optimum and deficient N conditions. No significant difference was observed in the growth of LBS6-treated plants grown with excessive N. The application of LBS6 induced flowering under optimum and deficient N conditions. The total nitrogen, nitrate and ammonia contents of tissues were found to be higher in treated plants grown under N deficient conditions. The LBS6 treatments had significantly higher chlorophyll content in those plants grown under N-deficient conditions. The root drench application of LBS6 also regulated photosynthetic efficiency by modulating electron and proton transport-related processes of leaves in the light-adapted state. The rate of linear electron flux, proton conductivity and steady-state proton flux across the thylakoid membrane were found to be higher in LBS6-treated plants. Additionally, LBS6 also reduced nitrogen starvation-induced, reactive oxygen species accumulation by reduction in lipid peroxidation in treated plants. Gene expression analysis showed differential regulation of expression of those genes involved in N uptake, transport, assimilation, and remobilization in LBS6-treated plants. Taken together, LBS6 improved growth of those treated plants under optimum and nitrogen-limited condition by positively modulating their biochemical, molecular, and physiological processes.
Enhancing estimation of cover crop biomass using field-based high-throughput phenotyping and machine learning models
Authors: Bai Geng , Koehler-Cole Katja , Scoby David , Thapa Vesh R. , Basche Andrea , Ge Yufeng
Published: January 2024

Incorporating cover crops into cropping systems offers numerous potential benefits, including the reduction of soil erosion, suppression of weeds, decreased nitrogen requirements for subsequent crops, and increased carbon sequestration. The aboveground biomass (AGB) of cover crops strongly influences their performance in delivering these benefits. Despite the significance of AGB, a comprehensive field-based high-throughput phenotyping study to quantify AGB of multiple cover crops in the U.S. Midwest has not been found. This study presents a two-year field experiment carried out in Eastern Nebraska, USA, to estimate AGB of five different cover crop species [canola (Brassica napus L.), rye (Secale cereale L.), triticale (Triticale × Triticosecale L.), vetch (Vicia sativa L.), and wheat (Triticum aestivum L.)] using high-throughput phenotyping and Machine Learning (ML) models. Destructive AGB sampling was performed three times during each spring season in 2022 and 2023. An array of morphological, spectral, thermal, and environmental features from the sensors were utilized as feature inputs of ML models. Moderately strong linear correlations between AGB and the selected features were observed. Four ML models, namely Random Forests Regression (RFR), Support Vector Regression (SVR), Partial Least Squares Regression (PLSR), and Artificial Neural Network (ANN), were investigated. Among the four models, PLSR achieved the highest Coefficient of Determination (R2) of 0.84 and the lowest Root Mean Squared Error (RMSE) of 892 kg/ha (Normalized RMSE (NRMSE) = 8.87%), indicating that PLSR could be the most appropriate method for estimating AGB of multiple cover crop species. Feature importance analysis ranked spectral features like Normalized Difference Red Edge (NDRE), Solar-induced Fluorescence (SIF), Spectral Reflectance at 485 nm (R485), and Normalized Difference Vegetation Index (NDVI) as top model features using PLSR. When utilizing fewer feature inputs, ANN exhibited better prediction performance compared to other models. Using morphological and spectral parameters as input features alone led to a R2 of 0.80 and 0.77 for AGB prediction using ANN, respectively. This study demonstrated the feasibility of high-throughput phenotyping and ML techniques for accurately estimating AGB of multiple cover crop species. Further enhancement of model performance could be achieved through additional destructive sampling conducted across multiple locations and years.
Compressed variance component mixed model reveals epistasis associated with flowering in Arabidopsis
Authors: Han Le , Shen Bolin , Wu Xinyi , Zhang Jin , Wen Yang-Jun
Published: January 2024

Introduction

Epistasis is currently a topic of great interest in molecular and quantitative genetics. Arabidopsis thaliana, as a model organism, plays a crucial role in studying the fundamental biology of diverse plant species. However, there have been limited reports about identification of epistasis related to flowering in genome-wide association studies (GWAS). Therefore, it is of utmost importance to conduct epistasis in Arabidopsis.

Method

In this study, we employed Levene’s test and compressed variance component mixed model in GWAS to detect quantitative trait nucleotides (QTNs) and QTN-by-QTN interactions (QQIs) for 11 flowering-related traits of 199 Arabidopsis accessions with 216,130 markers.

Results

Our analysis detected 89 QTNs and 130 pairs of QQIs. Around these loci, 34 known genes previously reported in Arabidopsis were confirmed to be associated with flowering-related traits, such as SPA4, which is involved in regulating photoperiodic flowering, and interacts with PAP1 and PAP2, affecting growth of Arabidopsis under light conditions. Then, we observed significant and differential expression of 35 genes in response to variations in temperature, photoperiod, and vernalization treatments out of unreported genes. Functional enrichment analysis revealed that 26 of these genes were associated with various biological processes. Finally, the haplotype and phenotypic difference analysis revealed 20 candidate genes exhibiting significant phenotypic variations across gene haplotypes, of which the candidate genes AT1G12990 and AT1G09950 around QQIs might have interaction effect to flowering time regulation in Arabidopsis.

Discussion

These findings may offer valuable insights for the identification and exploration of genes and gene-by-gene interactions associated with flowering-related traits in Arabidopsis, that may even provide valuable reference and guidance for the research of epistasis in other species.
Deep learning architectures for diagnosing the severity of apple frog-eye leaf spot disease in complex backgrounds
Authors: Liu Bo , Fan Hongyu , Zhang Yuting , Cai Jinjin , Cheng Hong
Published: January 2024

Introduction

In precision agriculture, accurately diagnosing apple frog-eye leaf spot disease is critical for effective disease management. Traditional methods, predominantly relying on labor-intensive and subjective visual evaluations, are often inefficient and unreliable.

Methods

To tackle these challenges in complex orchard environments, we develop a specialized deep learning architecture. This architecture consists of a two-stage multi-network model. The first stage features an enhanced Pyramid Scene Parsing Network (L-DPNet) with deformable convolutions for improved apple leaf segmentation. The second stage utilizes an improved U-Net (D-UNet), optimized with bilinear upsampling and batch normalization, for precise disease spot segmentation.

Results

Our model sets new benchmarks in performance, achieving a mean Intersection over Union (mIoU) of 91.27% for segmentation of both apple leaves and disease spots, and a mean Pixel Accuracy (mPA) of 94.32%. It also excels in classifying disease severity across five levels, achieving an overall precision of 94.81%.

Discussion

This approach represents a significant advancement in automated disease quantification, enhancing disease management in precision agriculture through data-driven decision-making.
Non-coding deep learning models for tomato biotic and abiotic stress classification using microscopic images
Authors: Choudhary Manoj , Sentil Sruthi , Jones Jeffrey B. , Paret Mathews L.
Published: January 2024

Plant disease classification is quite complex and, in most cases, requires trained plant pathologists and sophisticated labs to accurately determine the cause. Our group for the first time used microscopic images (×30) of tomato plant diseases, for which representative plant samples were diagnostically validated to classify disease symptoms using non-coding deep learning platforms (NCDL). The mean F1 scores (SD) of the NCDL platforms were 98.5 (1.6) for Amazon Rekognition Custom Label, 93.9 (2.5) for Clarifai, 91.6 (3.9) for Teachable Machine, 95.0 (1.9) for Google AutoML Vision, and 97.5 (2.7) for Microsoft Azure Custom Vision. The accuracy of the NCDL platform for Amazon Rekognition Custom Label was 99.8% (0.2), for Clarifai 98.7% (0.5), for Teachable Machine 98.3% (0.4), for Google AutoML Vision 98.9% (0.6), and for Apple CreateML 87.3 (4.3). Upon external validation, the model’s accuracy of the tested NCDL platforms dropped no more than 7%. The potential future use for these models includes the development of mobile- and web-based applications for the classification of plant diseases and integration with a disease management advisory system. The NCDL models also have the potential to improve the early triage of symptomatic plant samples into classes that may save time in diagnostic lab sample processing.
The role of symbiotic fungi in the life cycle of Gastrodia elata Blume (Orchidaceae): a comprehensive review
Authors: Liu Jia-Jia , Yang Xiao-Qi , Li Zong-Yang , Miao Jia-Yun , Li Shi-Bo , Zhang Wen-Ping , Lin Yi-Cen , Lin Lian-Bing
Published: January 2024

Gastrodia elata Blume, a fully mycoheterotrophic perennial plant of the family Orchidaceae, is a traditional Chinese herb with medicinal and edible value. Interestingly, G. elata requires symbiotic relationships with Mycena and Armillaria strains for seed germination and plant growth, respectively. However, there is no comprehensive summary of the symbiotic mechanism between fungi and G. elata. Here, the colonization and digestion of hyphae, the bidirectional exchange of nutrients, the adaptation of fungi and G. elata to symbiosis, and the role of microorganisms and secondary metabolites in the symbiotic relationship between fungi and G. elata are summarized. We comprehensively and deeply analyzed the mechanism of symbiosis between G. elata and fungi from three perspectives: morphology, nutrition, and molecules. The aim of this review was to enrich the understanding of the mutualistic symbiosis mechanisms between plants and fungi and lay a theoretical foundation for the ecological cultivation of G. elata.
Regulatory function of the endogenous hormone in the germination process of quinoa seeds
Authors: Zeng Fang , Zheng Chunmei , Ge Wenxuan , Gao Ya , Pan Xin , Ye Xueling , Wu Xiaoyong , Sun Yanxia
Published: January 2024

The economic and health significance of quinoa is steadily growing on a global scale. Nevertheless, the primary obstacle to achieving high yields in quinoa cultivation is pre-harvest sprouting (PHS), which is intricately linked to seed dormancy. However, there exists a dearth of research concerning the regulatory mechanisms governing PHS. The regulation of seed germination by various plant hormones has been extensively studied. Consequently, understanding the mechanisms underlying the role of endogenous hormones in the germination process of quinoa seeds and developing strategies to mitigate PHS in quinoa cultivation are of significant research importance. This study employed the HPLC-ESI-MS/MS internal standard and ELISA method to quantify 8 endogenous hormones. The investigation of gene expression changes before and after germination was conducted using RNA-seq analysis, leading to the discovery of 280 differentially expressed genes associated with the regulatory pathway of endogenous hormones. Additionally, a correlation analysis of 99 genes with significant differences identified 14 potential genes that may act as crucial “transportation hubs” in hormonal interactions. Through the performance of an analysis on the modifications in hormone composition and the expression of associated regulatory genes, we posit a prediction that implies the presence of a negative feedback regulatory mechanism of endogenous hormones during the germination of quinoa seeds. This mechanism is potentially influenced by the unique structure of quinoa seeds. To shed light on the involvement of endogenous hormones in the process of quinoa seed germination, we have established a regulatory network. This study aims to offer innovative perspectives on the breeding of quinoa varieties that exhibit resistance to PHS, as well as strategies for preventing PHS.
The potential of PGPR and Trichoderma-based bioproducts and resistant cultivars as tools to manage clubroot disease in cruciferous crops
Authors: Moreno-Velandia Carlos Andrés , Garcia-Arias Francy Liliana , Dávila-Mora Lorena , Rodríguez Edwin , Villabona-Gélvez Alejandro , Revelo-Gómez Eliana Gisela , Marcillo-Paguay Carlos Alberto , Riascos-Ortiz Donald Heberth , Zuluaga Andrea Paola
Published: January 2024

The objective of this research was to determine the potential use of eco-friendly technologies to reduce the clubroot disease caused by Plasmodiophora brassicae, the main constraint of cruciferous crops worldwide. Two commercial bioproducts were evaluated in susceptible broccoli, one based on the PGPR consortium (Bacillus amyloliquefaciens, Bacillus pumilus, and Agrobacterium radiobacter K84) and the other one based on Trichoderma koningiopsis Th003 (Tricotec® WG). Additionally, the resistant broccoli cv. Monclano® was tested under two concentrations of resting spores (RS) of P. brassicae, 1 × 103 and 1 × 105 RS g−1 of soil. The first phase of evaluations with broccoli was carried out under a greenhouse, while susceptible broccoli, cauliflower, and red cabbage were included in a subsequent field phase. Tebuconazole + Trifloxystrobin mixture and Fluazinam were included as positive controls. The effectiveness of the bioproducts depended on the nature of the biocontrol agent, the concentration of P. brassicae, and the dose of treatment. Tricotec® showed consistent plant growth promotion but no biocontrol effect against clubroot, and the rhizobacteria-based bioproduct significantly reduced the disease in both greenhouse and field experiments. Higher disease severity was observed with the higher dose of Tricotec®. Under field conditions, the rhizobacteria reduced the incidence progress by 26%, 39%, and 57% under high, medium, and low pressure of the pathogen, respectively. However, no reduction of clubroot severity under high pressure of the pathogen was observed. Complete inhibition of club formation in roots was achieved via the fungicide, but a phytotoxic effect was observed under greenhouse conditions. Fungicides reduced the incidence progress of clubroot, but not the severity under high inoculum pressure in the field. The fungicides, the bacterial treatment, and the combination of bioproducts tended to delay the progress of the disease compared with the negative control and Tricotec alone. The resistant broccoli showed a low level of disease under high concentrations of P. brassicae (less than 10% incidence and up to 2% severity). These results suggested the overall potential of commercial tools based on the PGPR consortium and plant resistance to control P. brassicae. The integration of control measures, the role of Trichoderma spp. in P. brassicae–cruciferous pathosystems, and the need to recover highly infested soils will be discussed.