Bacterial leaf spot and bacterial leaf blight are global threats to the cultivation of cruciferous vegetables, and it is necessary to develop methods to easily detect, identify, and distinguish the ...causative pathogens
Pseudomonas syringae
pv.
maculicola
(
Psm
) and
P
.
cannabina
pv.
alisalensis
(
Pca
). Here, we used the sequence specificity of the exchangeable effector loci flanking the
hrp
gene cluster to design primers that can help detect and discriminate between
Psm
and
Pca
. Primers common to both bacteria (hrpK_fw1 and hrpK_fw2) were designed within
hrpK
at the end of the
hrp
gene cluster.
Psm
-specific primers (MAC_rv1 and MAC_rv2) were designed in
hopPtoB1
and
Pca
-specific primers (ALS_rv1 and ALS_rv2) were designed in
hopX1
adjacent to
hrpK
. PCR using hrpK_fw1 and MAC_rv1 or hrpK_fw2 and MAC_rv2 amplified DNA fragments of only
Psm
,
P
.
syringae
pv.
tomato
(causal agent of tomato bacterial speck), and
P
.
syringae
pv.
spinaciae
(causal agent of spinach bacterial leaf spot), among 76 strains of phytopathogenic bacteria. PCR using hrpK_fw1 and ALS_rv1 or hrpK_2 and ALS_rv2 amplified DNA fragments of only
Pca
. Multiplex PCR with these primers could easily distinguish
Psm
and
Pca
from bacterial colonies isolated on growth media and detect the pathogen in symptomatic leaves. Multiplex nested PCR with the primers detected contamination in one
Psm-
and/or one
Pca-
infected seeds in 1000 seeds. These results suggest that these PCR primers could help detect and discriminate
Psm
and
Pca
.
Key points
•
We investigated Pseudomonas syringae pv. maculicola and P. cannabina pv. alisalensis.
•
Novel primers common to both bacteria were designed following genome comparison.
•
Multiplex PCR with new primers could discriminate Psm and Pca.
The oncogenic microRNAs (miRNAs) miR-21 and miR-31 negatively regulate tumor-suppressor genes. Their potential as serum biomarkers has not been determined in human colorectal cancer (CRC).
To ...determine whether miR-21 and miR-31 are secretory miRNAs, we screened expression in medium from 2 CRC cell lines, which was followed by serum analysis from 12 CRC patients and 12 control subjects. We validated expression of candidate miRNAs in serum samples from an independent cohort of 186 CRC patients, 60 postoperative patients, 43 advanced adenoma patients, and 53 control subjects. We analyzed miR-21 expression in 166 matched primary CRC tissues to determine whether serum miRNAs reflect expression in CRC. Patient survival analyses were performed by Kaplan-Meier analyses and Cox regression models. All statistical tests were two-sided.
Although miR-21 was secreted from CRC cell lines and upregulated in serum of CRC patients, no statistically significant differences were observed in serum miR-31 expression between CRC patients and control subjects. In the validation cohort, miR-21 levels were statistically significantly elevated in preoperative serum from patients with adenomas (P < .001) and CRCs (P < .001). Importantly, miR-21 expression dropped in postoperative serum from patients who underwent curative surgery (P < .001). Serum miR-21 levels robustly distinguished adenoma (area under the curve AUC = 0.813; 95% confidence interval CI = 0.691 to 0.910) and CRC (AUC = 0.919; 95% CI = 0.867 to 0.958) patients from control subjects. High miR-21 expression in serum and tissue was statistically significantly associated with tumor size, distant metastasis, and poor survival. Moreover, serum miR-21 was an independent prognostic marker for CRC (hazard ratio = 4.12; 95% CI = 1.10 to 15.4; P = .03).
Serum miR-21 is a promising biomarker for the early detection and prognosis of CRC.
Background
The prognostic nutritional index (PNI), which is calculated based on the serum albumin concentration and peripheral blood lymphocyte count, is a useful tool for predicting short-term and ...long-term postoperative outcome in patients undergoing cancer surgery. However, few studies have investigated PNI in colorectal cancer surgery. We examined the ability of PNI to predict short- and long-term outcomes in patients with colorectal cancer.
Methods
This retrospective study included 365 patients who underwent resection for colorectal cancer. The prognostic nutritional status was calculated on the basis of admission data as follows: 10 × serum albumin (g/dl) + 0.005 × total lymphocyte count (per mm
3
). The primary outcomes measured were the impact of PNI on overall survival and postoperative complications.
Results
Kaplan–Meier analysis and the log rank test revealed that low PNI was significantly associated with poor survival (
P
< 0.0001). In multivariate analysis for survival, preoperative low PNI was an independent prognostic factor for poor survival: odds ratio: 2.25, 95 % confidence interval 1.42–3.59). Moreover, low PNI significantly correlated with the incidence of postoperative complications, especially serious ones.
Conclusions
Preoperative PNI is a useful predictor of postoperative complications and survival in patients with colorectal cancer.
Epithelial folding is a fundamental process governing the transformation of flat epithelial sheets into intricate three-dimensional structures during morphogenesis. This phenomenon plays a pivotal ...role in the development of various organs across biological systems. Despite its importance, the underlying mechanisms of epithelial folding remain incompletely understood due to its dynamic and complex nature. In recent years, computational simulations have emerged as powerful tools to study epithelial folding, providing a means to test theories, generate predictions, and integrate data from various sources. The basic workflow of simulation-based research involves formulating hypotheses grounded in insights derived from experimental observations, constructing mechanical models based on these hypotheses, conducting simulations, and subsequently comparing simulation results with experimental observations. This review encompasses studies exploring how spatial distributions of contractile cells and temporal histories of growth and contraction contribute to the three-dimensionalization of epithelial sheets by modeling the mechanics of tissue growth and cell contractile forces. Additionally, it addresses the studies examining the impact of asymmetry in physical constraints imposed by the surrounding structures of epithelial sheets and the non-uniformity of growth on the undulation pattern formation of epithelial sheets by modeling the mechanical interaction between the growing tissue and the surrounding structures. Furthermore, a recent advancement proposes a new framework where computations are employed for initial stages of hypothesis formation by inferring the causality. In this context, we also discuss a recent study that quantitatively infers differential growth, causing the morphogenesis, solely from pre- and post-growth shape data. Through this comprehensive review, we demonstrate the utility of simulations in studying epithelial folding, emphasizing their potential for synergistic integration with various perspectives and exploring synergistic opportunities.
Neutrophil extracellular traps (NETs) represent extracellular microbial trapping and killing. Recently, it has been implicated in thrombogenesis, autoimmune disease, and cancer progression. The aim ...of this study was to characterize NETs in various organs of a murine sepsis model in vivo and to investigate their associations with platelets, leukocytes, or vascular endothelium. NETs were classified as two distinct forms; cell-free NETs that were released away from neutrophils and anchored NETs that were anchored to neutrophils. Circulating cell-free NETs were characterized as fragmented or cotton-like structures, while anchored NETs were characterized as linear, reticular, membranous, or spot-like structures. In septic mice, both anchored and cell-free NETs were significantly increased in postcapillary venules of the cecum and hepatic sinusoids with increased leukocyte-endothelial interactions. NETs were also observed in both alveolar space and pulmonary capillaries of the lung. The interactions of NETs with platelet aggregates, leukocyte-platelet aggregates or vascular endothelium of arterioles and venules were observed in the microcirculation of septic mice. Microvessel occlusions which may be caused by platelet aggregates or leukocyte-platelet aggregates and heterogeneously decreased blood flow were also observed in septic mice. NETs appeared to be associated with the formation of platelet aggregates or leukocyte-platelet aggregates. These observational findings may suggest the adverse effect of intravascular NETs on the host during a sepsis.
Black rot and bacterial spots threaten the cultivation of cruciferous vegetables worldwide, and the development of a method that can easily detect, identify, and distinguish their respective ...pathogens
Xanthomonas campestris
pv.
campestris
(
Xcc
) and
X
.
campestris
pv.
raphani
(
Xcr
) is required. Multiple whole-genome sequences of
Xcc
and
Xcr
were aligned to identify specific regions and subsequently design gene markers. A region present in
Xcr
, but absent in
Xcc
, was detected, which was approximately 11.5 kbp in length, sandwiched between the serine protease homolog (
SPH
) and nicotinate phosphoribosyltransferase gene (
pncB
). It contained putative cellulose synthesis-related genes, whereas
Xcc
only had a modified cellulose synthase gene. Designed primers were pncB_fw1 and pncB_fw2 (from the
pncB
gene), Xcc_rv1 and Xcc_rv2 (from the modified cellulose synthesis gene), and Xcr_rv1 and Xcr_rv2 (from the putative first and second open reading frames of the gene cluster). PCR using pncB_fw1 and Xcc_rv1, or pncB_fw2 and Xcc_rv2, amplified DNA fragments only in
Xcc
and
X
.
campestris
pv.
incanae
(
Xci
).
Xci
is the causal agent of black rot of garden stock and closely related to
Xcc
. PCR using pncB_fw1 and Xcr_rv1, or pncB_2 and Xcr_rv2, amplified DNA fragments only in
Xcr
. Multiplex PCR analysis easily distinguished
Xcc
and
Xcr
from bacterial colonies isolated on growth media and detected the pathogen in symptomatic leaves. Multiplex nested PCR detected the contamination of one seed with
Xcc
and/or
Xcr
infection from 1000 seeds. Therefore, the PCR primers designed in this study therefore helped detect and discriminate between
Xcc
and
Xcr
.
Key points
• Xanthomonas campestris
pv.
campestris
(
Xcc
)
and
pv.
raphani
(
Xcr
)
were investigated.
• Novel primers were designed following whole-genome comparison analyses.
• Multiplex PCR with new primers distinguished Xcc and Xcr simultaneously.
Slug and Vimentin genes play a critical role in regulating epithelial-mesenchymal transition (EMT) via downregulation of epithelial markers and upregulation of mesenchymal markers. The present study ...evaluated the clinical significance of Slug and Vimentin expression as potential disease biomarkers in colorectal cancer (CRC). At first, the biological role of Slug in CRC was assessed by RNA interference in CRC cell lines to assess tumor progression, invasion and migration. Next, we analyzed Slug and Vimentin expression in surgical tissue specimens from 181 CRC patients (Cohort 1) by quantitative real-time reverse transcription-PCR and 208 patients (Cohort 2) by immunohistochemistry. Knockdown of Slug using small interfering RNA in CRC cell lines resulted in inhibition of EMT, reduced cell proliferation, invasion and migration in CRC cells. Interestingly, Slug and Vimentin expression in cancer tissues was significantly higher in patients with higher T stage, lymph node involvement, liver metastasis and advanced tumor node metastasis stages. A significant correlation was observed between Slug and Vimentin expression in CRC (messenger RNA: ρ = 0.546, protein: ρ = 0.405), and increased expression of Slug and Vimentin was significantly associated with poor prognosis. Furthermore, increased expression of Slug emerged as an independent prognostic factor and a predictive marker of lymph node metastasis in CRC patients. Our data provide novel evidence for the biological and clinical significance of Slug and Vimentin expression as potential predictive biomarkers for identifying patients with lymph node metastasis or poor prognosis in CRC.
The beetle horn primordium is a complex and compactly folded epithelial sheet located beneath the larval cuticle. Only by unfolding the primordium can the complete 3D shape of the horn appear, ...suggesting that the morphology of beetle horns is encoded in the primordial folding pattern. To decipher the folding pattern, we developed a method to manipulate the primordial local folding on a computer and clarified the contribution of the folding of each primordium region to transformation. We found that the three major morphological changes (branching of distal tips, proximodistal elongation, and angular change) were caused by the folding of different regions, and that the folding mechanism also differs according to the region. The computational methods we used are applicable to the morphological study of other exoskeletal animals.
Despite recent advances in colorectal cancer (CRC) treatment, the prognosis of patients suffering from this malignancy still remains substandard, and metastatic recurrence following curative surgery ...is the leading cause of mortality. Therefore, it is imperative to identify prognostic markers to predict the clinical outcome of CRC patients. Recent evidence revealed the new role of small nucleolar RNAs (snoRNAs) in oncogenesis. Herein, we systematically evaluated dysregulation of snoRNAs in CRC and clarified their biomarker potential and biological significance in CRC.
We analysed expression levels of 4 snoRNAs in 274 colorectal tissues from 3 independent cohorts and 6 colon cancer cell lines. The functional characterisation for the role of SNORA42 in CRC was investigated through a series of in vitro and in vivo experiments.
In the screening phase, expression levels of all four snoRNAs were significantly elevated in CRC tissues than in corresponding normal mucosa. In the clinical validation cohort, increased SNORA42 expression was an independent prognostic factor for overall survival and disease-free survival, and was a risk factor for distant metastasis. SNORA42 expression negatively correlated with overall survival in an additional independent cohort and identified the patients with high risk for recurrence and poor prognosis in stage II CRC. Furthermore, in vitro and in vivo analyses showed that SNORA42 overexpression resulted in enhanced cell proliferation, migration, invasion, anoikis resistance and tumorigenicity.
SNORA42 appears to be a novel oncogene and could serve as a promising predictive biomarker for recurrence and prognosis in patients with CRC.
Background
Metastasis is a major cause of death in patients with gastric cancer (GC). MicroRNAs (miRNAs) relating to the epithelial–mesenchymal transition (EMT) control GC progression and metastasis. ...The aim of this study was to evaluate serum EMT-associated miRNAs for metastatic and prognostic noninvasive biomarkers in GC.
Methods
In the first step of this study (preliminary experiments), we selected candidate miRNAs associated with metastasis by analyzing the expression of the miR-200 family (miR-200a, miR-200b, miR-200c, miR-141, and miR-429) and miR-203 in serum samples from stage I (
n
= 12) and stage IV (
n
= 12) GC patients. The second phase involved the independent validation of candidate miRNAs in serum specimens from 130 patients with GC and 22 controls.
Results
Based on the preliminary experiments, miR-203 was selected as the candidate serum miRNA that was most closely associated with metastasis. Validation analysis revealed that serum miR-203 levels were significantly lower in stage IV than stage I–III GC patients. Serum miR-203 expression was significantly lower in GC patients with a higher T stage, vessel invasion, and lymph node, peritoneal, and distant metastases. Low expression of serum miR-203 was significantly associated with poor disease-free and overall survival. Multivariate analysis revealed that low serum miR-203 expression was an independent predictive marker for lymph node, peritoneal, and distant metastases and a poor prognosis in patients with GC.
Conclusions
Serum miR-203 has the potential to serve as a noninvasive biomarker for prognosis and to predict metastasis in patients with GC.
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