Developmental Stage Affects Nutrient Uptake by Four Snapdragon Cultivars

Nutrient uptake by `Apache', `Jersey City', `Peoria', and `Philadelphia' snapdragons (Antirrhinum majus L.) was compared at three developmental stages: Stage I, vegetative to bud initiation; Stage II, bud initiation to visible bud; and Stage III, visible bud to anthesis. Significant differences in uptake occurred between one or more developmental stages for all nutrients tested: \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{NO}_{3}^{-}\mathrm{-}\mathrm{N},\mathrm{NH}_{4}^{+}\mathrm{-}\mathrm{NB}\) \end{document}, B, Ca, Cu, Fe, K, Mg, Mn, Mo, P, and Zn. Uptake of most of the nutrients increased or remained high during Stage III. These results indicate that the current cultural practice of stopping fertilization at bud elongation should be reexamined. Differences in uptake between cultivars were found only for \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{NO}_{3}^{-}\mathrm{-}\mathrm{N}\) \end{document}, as uptake by `Apache' was significantly higher than uptake by `Philadelphia'.

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Identification of biomarkers and functional modules from genomic data in stage-wise breast cancer

Current Bioinformatics ◽

10.2174/1574893615999200922123104 ◽

2020 ◽

Vol 15 ◽

Author(s):

Athira K ◽

Vrinda C ◽

Sunil Kumar P V ◽

Gopakumar G

Keyword(s):

Breast Cancer ◽

Expression Patterns ◽

Differential Expression Analysis ◽

Predictive Biomarkers ◽

Stage I ◽

Stage Ii ◽

Stage Iii ◽

Functional Modules ◽

Incidence And Mortality ◽

Multiple Stages

Background: Breast cancer is the most common cancer in women across the world, with high incidence and mortality rates. Being a heterogeneous disease, gene expression profiling based analysis plays a significant role in understanding breast cancer. Since expression patterns of patients belonging to the same stage of breast cancer vary considerably, an integrated stage-wise analysis involving multiple samples is expected to give more comprehensive results and understanding of breast cancer. Objective: The objective of this study is to detect functionally significant modules from gene co-expression network of cancerous tissues and to extract prognostic genes related to multiple stages of breast cancer. Methods: To achieve this, a multiplex framework is modelled to map the multiple stages of breast cancer, which is followed by a modularity optimization method to identify functional modules from it. These functional modules are found to enrich many Gene Ontology terms significantly that are associated with cancer. Result and Discussion: predictive biomarkers are identified based on differential expression analysis of multiple stages of breast cancer. Conclusion: Our analysis identified 13 stage-I specific genes, 12 stage-II specific genes, and 42 stage-III specific genes that are significantly regulated and could be promising targets of breast cancer therapy. That apart, we could identify 29, 18 and 26 lncRNAs specific to stage I, stage II and stage III respectively.

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Cardiac transthyretin wild-type amyloidosis (ATTRwt): a prospective study of 400 patients followed at the Italian referral center

European Heart Journal ◽

10.1093/ehjci/ehaa946.2144 ◽

2020 ◽

Vol 41 (Supplement_2) ◽

Author(s):

P Milani ◽

L Obici ◽

R Mussinelli ◽

M Basset ◽

G Manfrinato ◽

...

Keyword(s):

Natural History ◽

Median Survival ◽

Troponin I ◽

Stage I ◽

Stage Ii ◽

Stage Iii ◽

Wild Type ◽

Staging Systems ◽

Significant Difference ◽

History Of

Abstract Background Cardiac wild type transthyretin (ATTRwt) amyloidosis, formerly known as senile systemic amyloidosis, is an increasingly recognized, progressive, and fatal cardiomyopathy. Two biomarkers staging systems were proposed based on NT-proBNP (in both cases) and troponin or estimated glomerular filtration rate, that are able to predict survival in this population. The availability of novel effective treatments requires large studies to describe the natural history of the disease in different populations. Objective To describe the natural history of the disease in a large, prospective, national series. Methods Starting in 2007, we protocolized data collection in all the patients diagnosed at our center (n=400 up to 7/2019). Results The referrals to our center increased over time: 5 cases (1%) between 2007–2009, 33 (9%) in 2010–2012, 90 (22%) in 2013–2015 and 272 (68%) in 2016–2019. Median age was 76 years [interquartile range (IQR): 71–80 years] and 372 patients (93%) were males. One hundred and seventy-three (43%) had atrial fibrillation, 63 (15%) had a history of ischemic cardiomyopathy and 64 (15%) underwent pacemaker or ICD implantation. NYHA class was I in 58 subjects (16%), II in 225 (63%) and III in 74 (21%). Median NT-proBNP was 3064 ng/L (IQR: 1817–5579 ng/L), troponin I 0.096 ng/mL (IQR: 0.063–0.158 ng/mL), eGFR 62 mL/min (IQR: 50–78 mL/min). Median IVS was 17 mm (IQR: 15–19 mm), PW 16 mm (IQR: 14–18 mm) and EF 53% (IQR: 45–57%). One-hundred and forty-eight subjects (37%) had a concomitant monoclonal component in serum and/or urine and/or an abnormal free light chain ratio. In these patients, the diagnosis was confirmed by immunoelectron microscopy or mass spectrometry. In 252 (63%) the diagnosis was based on bone scintigraphy. DNA analysis for amyloidogenic mutations in transthyretin and apolipoprotein A-I genes was negative in all subjects. The median survival of the whole cohort was 59 months. The Mayo Clinic staging based on NT-proBNP (cutoff: 3000 ng/L) and troponin I (cutoff: 0.1 ng/mL) discriminated 3 different groups [stage I: 131 (35%), stage II: 123 (32%) and stage III: 127 (33%)] with different survival between stage I and II (median 86 vs. 81 months, P=0.04) and between stage II and III (median 81 vs. 62 months, P<0.001). The UK staging system (NT-proBNP 3000 ng/L and eGFR 45 mL/min), discriminated three groups [stage I: 170 (45%), stage II: 165 (43%) and stage III: 45 (12%)] with a significant difference in survival: between stage I and stage II (86 vs. 52 months, P<0.001) and between stage II and stage III (median survival 52 vs. 33 months, P=0.045). Conclusions This is one of the largest series of patients with cardiac ATTRwt reported so far. Referrals and diagnoses increased exponentially in recent years, One-third of patients has a concomitant monoclonal gammopathy and needed tissue typing. Both the current staging systems offered good discrimination of staging and were validated in our independent cohort. Funding Acknowledgement Type of funding source: None

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Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza

Scientific Reports ◽

10.1038/s41598-020-79298-8 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yuping Li ◽

Xiaoju Liang ◽

Xuguo Zhou ◽

Yu An ◽

Ming Li ◽

...

Keyword(s):

Gene Expression ◽

Developmental Stage ◽

Reference Genes ◽

Developmental Stages ◽

Individual Factors ◽

Congeneric Species ◽

Spatio Temporal ◽

The Stability ◽

Different Tissues ◽

Selection Of

AbstractGlycyrrhiza, a genus of perennial medicinal herbs, has been traditionally used to treat human diseases, including respiratory disorders. Functional analysis of genes involved in the synthesis, accumulation, and degradation of bioactive compounds in these medicinal plants requires accurate measurement of their expression profiles. Reverse transcription quantitative real-time PCR (RT-qPCR) is a primary tool, which requires stably expressed reference genes to serve as the internal references to normalize the target gene expression. In this study, the stability of 14 candidate reference genes from the two congeneric species G. uralensis and G. inflata, including ACT, CAC, CYP, DNAJ, DREB, EF1, RAN, TIF1, TUB, UBC2, ABCC2, COPS3, CS, R3HDM2, were evaluated across different tissues and throughout various developmental stages. More importantly, we investigated the impact of interactions between tissue and developmental stage on the performance of candidate reference genes. Four algorithms, including geNorm, NormFinder, BestKeeper, and Delta Ct, were used to analyze the expression stability and RefFinder, a comprehensive software, provided the final recommendation. Based on previous research and our preliminary data, we hypothesized that internal references for spatio-temporal gene expression are different from the reference genes suited for individual factors. In G. uralensis, the top three most stable reference genes across different tissues were R3HDM2, CAC and TUB, while CAC, CYP and ABCC2 were most suited for different developmental stages. CAC is the only candidate recommended for both biotic factors, which is reflected in the stability ranking for the spatio (tissue)-temporal (developmental stage) interactions (CAC, R3HDM2 and DNAJ). Similarly, in G. inflata, COPS3, R3HDM2 and DREB were selected for tissues, while RAN, COPS3 and CS were recommended for developmental stages. For the tissue-developmental stage interactions, COPS3, DREB and ABCC2 were the most suited reference genes. In both species, only one of the top three candidates was shared between the individual factors and their interactions, specifically, CAC in G. uralensis and COPS3 in G. inflata, which supports our overarching hypothesis. In summary, spatio-temporal selection of reference genes not only lays the foundation for functional genomics research in Glycyrrhiza, but also facilitates these traditional medicinal herbs to reach/maximize their pharmaceutical potential.

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Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants

Scientific Reports ◽

10.1038/s41598-021-88055-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hangxia Jin ◽

Xiaomin Yu ◽

Qinghua Yang ◽

Xujun Fu ◽

Fengjie Yuan

Keyword(s):

Developmental Stage ◽

Phytic Acid ◽

Differentially Expressed Genes ◽

Transcriptome Analysis ◽

Defense Mechanisms ◽

Developmental Stages ◽

Sucrose Metabolism ◽

Differentially Expressed ◽

Sequencing Analysis ◽

Seed Developmental Stage

AbstractPhytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than one mutated gene (lpa) have lower PA contents than mutants with a single lpa mutant gene. However, little is known about the link between PA pathway intermediates and downstream regulatory activities following the mutation of these genes in soybean. Consequently, we performed a comparative transcriptome analysis using an advanced generation recombinant inbred line with low PA levels [2mlpa (mips1/ipk1)] and a sibling line with homozygous non-mutant alleles and normal PA contents [2MWT (MIPS1/IPK1)]. An RNA sequencing analysis of five seed developmental stages revealed 7945 differentially expressed genes (DEGs) between the 2mlpa and 2MWT seeds. Moreover, 3316 DEGs were associated with 128 metabolic and signal transduction pathways and 4980 DEGs were annotated with 345 Gene Ontology terms related to biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were among the DEGs in 2mlpa. Of these genes, 36 contributed to PA metabolism, including 22 genes possibly mediating the low-PA phenotype of 2mlpa. The expression of most of the genes associated with photosynthesis (81 of 117) was down-regulated in 2mlpa at the late seed developmental stage. In contrast, the expression of three genes involved in sucrose metabolism was up-regulated at the late seed developmental stage, which might explain the high sucrose content of 2mlpa soybeans. Furthermore, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this study, we detected a low PA content as well as changes to multiple metabolites in the 2mlpa mutant. These results may help elucidate the regulation of metabolic events in 2mlpa. Many genes involved in PA metabolism may contribute to the substantial decrease in the PA content and the moderate accumulation of InsP3–InsP5 in the 2mlpa mutant. The other regulated genes related to photosynthesis, starch and sucrose metabolism, and defense mechanisms may provide additional insights into the nutritional and agronomic performance of 2mlpa seeds.

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Actual survival after resection of primary colorectal cancer: results from a prospective multicenter study

World Journal of Surgical Oncology ◽

10.1186/s12957-021-02207-4 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Inge van den Berg ◽

Robert R. J. Coebergh van den Braak ◽

Jeroen L. A. van Vugt ◽

Jan N. M. Ijzermans ◽

Stefan Buettner

Keyword(s):

Colorectal Cancer ◽

Postoperative Complications ◽

Multicenter Study ◽

Survival Data ◽

Standard Therapy ◽

Tumor Grade ◽

National Registry ◽

Stage I ◽

Stage Iii ◽

Curative Intent

Abstract Background Colorectal cancer is the third most common type of cancer in the world. We characterize a cohort of patients who survived up to 5 years without recurrence and identify factors predicting the probability of cure. Methods We analyzed data of patients who underwent curative intent surgery for stage I–III CRC between 2007 and 2012 and who had had been included in a large multicenter study in the Netherlands. Cure was defined as 5-year survival without recurrence. Survival data were retrieved from a national registry. Results Analysis of data of 754 patients revealed a cure rate of 65% (n = 490). Patients with stage I disease and T1- and N0-tumor had the highest probability of cure (94%, 95% and 90%, respectively). Those with a T4-tumor or N2-tumor had the lowest probability of cure (62% and 50%, respectively). A peak in the mortality rate for older patients early in follow-up suggests early excess mortality as an explanation. A similar trend was observed for stage III disease, poor tumor grade, postoperative complications, sarcopenia, and R1 resections. Patients with stage III disease, poor tumor grade, postoperative complications, sarcopenia, and R1 resections show a similar trend for decrease in CSS deaths over time. Conclusion In the studied cohort, the probability of cure for patients with stage I–III CRC ranged from 50 to 95%. Even though most patients will be cured from CRC with standard therapy, standard therapy is insufficient for those with poor prognostic factors, such as high T- and N-stage and poor differentiation grade.

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Single Ventricle Palliation in a Developing Sub-Saharan African Country: What Should be Improved?

World Journal for Pediatric and Congenital Heart Surgery ◽

10.1177/2150135118822671 ◽

2019 ◽

Vol 10 (2) ◽

pp. 164-170 ◽

Cited By ~ 3

Author(s):

Valdano Manuel ◽

Humberto Morais ◽

Aida L. R. Turquetto ◽

Gade Miguel ◽

Leonardo A. Miana ◽

...

Keyword(s):

Confidence Interval ◽

African Country ◽

Single Ventricle ◽

Hazard Ratio ◽

Stage I ◽

Stage Ii ◽

Stage Iii ◽

Lost To Follow Up ◽

Single Ventricle Palliation

Introduction: Single ventricle physiology management is challenging, especially in low-income countries. Objective: To report the palliation outcomes of single ventricle patients in a developing African country. Methods: We retrospectively studied 83 consecutive patients subjected to single ventricle palliation in a single center between March 2011 and December 2017. Preoperative data, surgical factors, postoperative results, and survival outcomes were analyzed. The patients were divided by palliation stage: I (pulmonary artery banding [PAB] or Blalock–Taussig shunt [BTS]), II (Glenn procedure), or III (Fontan procedure). Results: Of the 83 patients who underwent palliation (stages I-III), 38 deaths were observed (31 after stage I, six after stage II, and one after stage III) for an overall mortality of 45.7%. The main causes of operative mortality were multiple organ dysfunction due to sepsis, shunt occlusion, and cardiogenic shock. Twenty-eight survivors were lost to follow-up (22 after stage I, six after stage II). Thirteen stage II survivors are still waiting for stage III. The mean follow-up was 366 ± 369 days. Five-year survival was 28.4 % for PAB and 30.1% for BTS, while that for stage II and III was 49.8% and 57.1%, respectively. Age (hazard ratio, 0.61; 95% confidence interval: 0.47-0.7; P = .000) and weight at surgery (hazard ratio, 0.45; 95% confidence interval: 0.31-0.64; P = .002) impacted survival. Conclusion: A high-mortality rate was observed in this initial experience, mainly in stage I patients. A large number of patients were lost to follow-up. A task force to improve outcomes is urgently required.

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Impact of the Number of Dissected Lymph Nodes on Survival for Gastric Cancer after Distal Subtotal Gastrectomy

Gastroenterology Research and Practice ◽

10.1155/2011/476014 ◽

2011 ◽

Vol 2011 ◽

pp. 1-7 ◽

Cited By ~ 8

Author(s):

Chang-Ming Huang ◽

Jian-Xian Lin ◽

Chao-Hui Zheng ◽

Ping Li ◽

Jian-Wei Xie ◽

...

Keyword(s):

Gastric Cancer ◽

Survival Rate ◽

Lymph Nodes ◽

Distal Gastrectomy ◽

Stage I ◽

Stage Ii ◽

Stage Iii ◽

Prognostic Impact ◽

Term Survival

Objectives. To investigate the prognostic impact of the number of dissected lymph nodes (LNs) in gastric cancer after curative distal gastrectomy.Methods. The survival of 634 patients who underwent curative distal gastrectomy from 1995 to 2004 was retrieved. Long-term surgical outcomes and associations between the number of dissected LNs and the 5-year survival rate were investigated.Results. The number of dissected LNs was one of the most important prognostic indicators. Among patients with comparable T category, the larger the number of dissected LNs was, the better the survival would be (). The linear regression showed that a significant survival improvement based on increasing retrieved LNs for stage II, III and IV (). A cut-point analysis yields the greatest variance of survival rate difference at the levels of 15 LNs (stage I), 25 LNs (stage II) and 30 LNs (stage III).Conclusion. The number of dissected LNs is an independent prognostic factor for gastric cancer. To improve the long-term survival of patients with gastric cancer, removing at least 15 LNs for stage I, 25 LNs for stage II, and 30 LNs for stage III patients during curative distal gastrectomy is recommended.

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Safe-Site Effects on Rhizosphere Bacterial Communities in a High-Altitude Alpine Environment

BioMed Research International ◽

10.1155/2014/480170 ◽

2014 ◽

Vol 2014 ◽

pp. 1-9 ◽

Cited By ~ 9

Author(s):

Sonia Ciccazzo ◽

Alfonso Esposito ◽

Eleonora Rolli ◽

Stefan Zerbe ◽

Daniele Daffonchio ◽

...

Keyword(s):

High Altitude ◽

Developmental Stage ◽

Bacterial Communities ◽

Developmental Stages ◽

Gene Diversity ◽

Intergenic Spacer ◽

Intermediate Stage ◽

Plant Colonization ◽

Early Developmental Stage ◽

Rrna Gene

The rhizosphere effect on bacterial communities associated with three floristic communities (RW, FI, and M sites) which differed for the developmental stages was studied in a high-altitude alpine ecosystem. RW site was an early developmental stage, FI was an intermediate stage, M was a later more matured stage. The N and C contents in the soils confirmed a different developmental stage with a kind of gradient from the unvegetated bare soil (BS) site through RW, FI up to M site. The floristic communities were composed of 21 pioneer plants belonging to 14 species. Automated ribosomal intergenic spacer analysis showed different bacterial genetic structures per each floristic consortium which differed also from the BS site. When plants of the same species occurred within the same site, almost all their bacterial communities clustered together exhibiting a plant species effect. Unifrac significance value (P<0.05) on 16S rRNA gene diversity revealed significant differences (P<0.05) between BS site and the vegetated sites with a weak similarity to the RW site. The intermediate plant colonization stage FI did not differ significantly from the RW and the M vegetated sites. These results pointed out the effect of different floristic communities rhizospheres on their soil bacterial communities.

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Differentiation of the sexual characters and onset of maturity in the males of the "red claw" crayfish, Cherax quadricarinatus (Von Martens, 1898) (Astacidea, Astacida, Parastacidae)

Animal Biology ◽

10.1163/157075610x491734 ◽

2010 ◽

Vol 60 (2) ◽

pp. 195-208 ◽

Cited By ~ 3

Author(s):

Laura Susana López Greco ◽

Fernanda Jimena Vazquez

Keyword(s):

Sexual Maturity ◽

Vas Deferens ◽

Developmental Stages ◽

Stage I ◽

Early Event ◽

Cherax Quadricarinatus ◽

Secondary Sexual Characters ◽

Single Structure ◽

Red Claw Crayfish ◽

Secondary Sexual

AbstractThe differentiation of the male reproductive system, the copulatory structures, "red patch" and onset of sexual maturity were studied in Cherax quadricarinatus. For this characterization 353 males were observed, dissected and processed for histological analysis. Three developmental stages were identified. At stage I the testes are two parallel cords with a few lobes or acinii, connected medially by a short thin bridge (X-shape) and the vasa deferentia are straight transparent cords. In the second stage, more lobulated testes present an H-shape and the vas deferens begins to differentiate into three distinct regions: proximal, medial and distal. In the last stage testes are two parallel cords tending to fuse along their entire length and become a single structure. From this stage, the development of the "red patch" occurs and spermatophore formation is observed in the vas deferens giving it white colour. These primary and secondary sexual characters could indicate the onset of sexual maturity. The morphology of the copulatory structure is lobular at stage I and it differentiates into an elongated structure during stage II. This study shows that in C. quadricarinatus the differentiation of primary and secondary sexual characters of males starts simultaneously and very early in development (0.09-0.10g achieved nearly 1 month old) and that acquisition of sexual maturity is also an early event (6g achieved nearly 3 month old). The compared features within Astacidea and Decapoda and the possible applications in the analysis of phylogenetic relationships between different taxa are discussed.

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