Effects of clonal fragmentation on Pyrrosia nuda depend on growth stages in a rubber plantation.

Introduction: Clonal fragmentation helps to assess clonal plants' growth resilience to human and environmental disturbance. Although clonal integration in epiphytes in tropical rubber plantations is important to understand their role in enhancing biodiversity and ecosystem services, research on this subject is limited. These plantations are typically monospecific economic forests that face increased anthropogenic disturbances. Methods: In this study, we selected the clonal fern Pyrrosia nuda to study its survival status, biomass, maximum quantum yield of photosystem II (Fv/Fm), and frond length in response to the level of clonal fragmentation in a tropical rubber plantation. Results and discussion: The results showed that (1) clonal fragmentation significantly negatively affected the survival rate, biomass, and frond length of clonal plants, but with minimal effects on Fv/Fm at different growth stages; (2) the performance of a ramet (e.g., biomass or frond length) increased with ramet developmental ages and decreased with the number of ramets in a clonal fragment. The age-dependent impacts of clonal fragmentation provide insights into the biodiversity conservation of epiphytes and forest management in man-made plantations. Therefore, to better conserve the biodiversity in tropical forests, especially in environment-friendly rubber plantations, there is a need to reduce anthropogenic disturbances and alleviate the level of fragmentation.

From 2D to 3D: automatic measurement of the Cobb angle in adolescent idiopathic scoliosis with the weight-bearing 3D imaging.

BACKGROUND CONTEXT: Adolescent idiopathic scoliosis (AIS) necessitates accurate spinal curvature assessment for effective clinical management. Traditional two-dimensional (2D) Cobb angle measurements have been the standard, but the emergence of three-dimensional (3D) automatic measurement techniques, such as those using weight-bearing 3D imaging (WR3D), presents an opportunity to enhance the accuracy and comprehensiveness of AIS evaluation. PURPOSE: This study aimed to compare traditional 2D Cobb angle measurements with 3D automatic measurements utilizing the WR3D imaging technique in patients with AIS. STUDY DESIGN/SETTING: A cohort of 53 AIS patients was recruited, encompassing 88 spinal curves, for comparative analysis. PATIENT SAMPLE: The patient sample consisted of 53 individuals diagnosed with AIS. OUTCOME MEASURES: Cobb angles were calculated using the conventional 2D method and three different 3D methods: the Analytical Method (AM), the Plane Intersecting Method (PIM), and the Plane Projection Method (PPM). METHODS: The 2D cobb angle was manually measured by 3 experienced clinicians with 2D frontal whole-spine radiographs. For 3D cobb angle measurements, the spine and femoral heads were segmented from the WR3D images using a 3D-UNet deep-learning model, and the automatic calculations of the angles were performed with the 3D slicer software. RESULTS: AM and PIM estimates were found to be significantly larger than 2D measurements. Conversely, PPM results showed no statistical difference compared to the 2D method. These findings were consistent in a subgroup analysis based on 2D Cobb angles. CONCLUSION: Each 3D measurement method provides a unique assessment of spinal curvature, with PPM offering values closely resembling 2D measurements, while AM and PIM yield larger estimations. The utilization of WR3D technology alongside deep learning segmentation ensures accuracy and efficiency in comparative analyses. However, additional studies, particularly involving patients with severe curves, are required to validate and expand on these results. This study emphasizes the importance of selecting an appropriate measurement method considering the imaging modality and clinical context when assessing AIS, and it also underlines the need for continuous refinement of these techniques for optimal use in clinical decision-making and patient management.

Vertical variation in leaf functional traits of Parashorea chinensis with different canopy layers.

Introduction: Canopy species need to shift their ecological adaptation to improve light and water resources utilization, and the study of intraspecific variations in plant leaf functional traits based at individual scale is of great significance for evaluating plant adaptability to climate change. Methods: In this study, we evaluate how leaf functional traits of giant trees relate to spatial niche specialization along a vertical gradient. We sampled the tropical flagship species of Parashorea chinensis around 60 meters tall and divided their crowns into three vertical layers. Fourteen key leaf functional traits including leaf morphology, photosynthetic, hydraulic and chemical physiology were measured at each canopy layer to investigate the intraspecific variation of leaf traits and the interrelationships between different functional traits. Additionally, due to the potential impact of different measurement methods (in-situ and ex-situ branch) on photosynthetic physiological parameters, we also compared the effects of these two gas exchange measurements. Results and discussion: In-situ measurements revealed that most leaf functional traits of individual-to-individual P. chinensis varied significantly at different canopy heights. Leaf hydraulic traits such as midday leaf water potential (MWP) and leaf osmotic potential (OP) were insignificantly correlated with leaf photosynthetic physiological traits such as maximal net assimilation rate per mass (A mass). In addition, great discrepancies were found between in-situ and ex-situ measurements of photosynthetic parameters. The ex-situ measurements caused a decrease by 53.63%, 27.86%, and 38.05% in A mass, and a decrease of 50.00%, 19.21%, and 27.90% in light saturation point compared to the in-situ measurements. These findings provided insights into our understanding of the response mechanisms of P. chinensis to micro-habitat in Xishuangbanna tropical seasonal rainforests and the fine scale adaption of different resultant of decoupled traits, which have implications for understanding ecological adaption strategies of P. chinensis under environmental changes.

Altered static and dynamic intrinsic brain activity in unilateral sudden sensorineural hearing loss.

Introduction: Sudden sensorineural hearing loss (SSHL) is a critical otologic emergency characterized by a rapid decline of at least 30 dB across three consecutive frequencies in the pure-tone audiogram within a 72-hour period. This audiological condition has been associated with alterations in brain cortical and subcortical structures, as well as changes in brain functional activities involving multiple networks. However, the extent of cerebral intrinsic brain activity disruption in SSHL remains poorly understood. The aimed of this study is to investigate intrinsic brain activity alterations in SSHL using static and dynamic fractional amplitude of low-frequency fluctuation (fALFF) analysis. Methods: Resting-state functional magnetic resonance imaging (fMRI) data were acquired from a cohort of SSHL patients (unilateral, n = 102) and healthy controls (n = 73). Static and dynamic fALFF methods were employed to analyze the acquired fMRI data, enabling a comprehensive examination of intrinsic brain activity changes in SSHL. Results: Our analysis revealed significant differences in static fALFF patterns between SSHL patients and healthy controls. SSHL patients exhibited decreased fALFF in the left fusiform gyrus, left precentral gyrus, and right inferior frontal gyrus, alongside increased fALFF in the left inferior frontal gyrus, left superior frontal gyrus, and right middle temporal gyrus. Additionally, dynamic fALFF analysis demonstrated elevated fALFF in the right superior frontal gyrus and right middle frontal gyrus among SSHL patients. Intriguingly, we observed a positive correlation between static fALFF in the left fusiform gyrus and the duration of hearing loss, shedding light on potential temporal dynamics associated with intrinsic brain activity changes. Discussion: The observed disruptions in intrinsic brain activity and temporal dynamics among SSHL patients provide valuable insights into the functional reorganization and potential compensatory mechanisms linked to hearing loss. These findings underscore the importance of understanding the underlying neural alterations in SSHL, which could pave the way for the development of targeted interventions and rehabilitation strategies aimed at optimizing SSHL management.

Binary classification of non-specific low back pain condition based on the combination of B-mode ultrasound and shear wave elastography at multiple sites.

Introduction: Low back pain (LBP) is a prevalent and complex condition that poses significant medical, social, and economic burdens worldwide. The accurate and timely assessment and diagnosis of LBP, particularly non-specific LBP (NSLBP), are crucial to developing effective interventions and treatments for LBP patients. In this study, we aimed to investigate the potential of combining B-mode ultrasound image features with shear wave elastography (SWE) features to improve the classification of NSLBP patients. Methods: We recruited 52 subjects with NSLBP from the University of Hong Kong-Shenzhen Hospital and collected B-mode ultrasound images and SWE data from multiple sites. The Visual Analogue Scale (VAS) was used as the ground truth to classify NSLBP patients. We extracted and selected features from the data and employed a support vector machine (SVM) model to classify NSLBP patients. The performance of the SVM model was evaluated using five-fold cross-validation and the accuracy, precision, and sensitivity were calculated. Results: We obtained an optimal feature set of 48 features, among which the SWE elasticity feature had the most significant contribution to the classification task. The SVM model achieved an accuracy, precision, and sensitivity of 0.85, 0.89, and 0.86, respectively, which were higher than the previously reported values of MRI. Discussion: In this study, we aimed to investigate the potential of combining B-mode ultrasound image features with shear wave elastography (SWE) features to improve the classification of non-specific low back pain (NSLBP) patients. Our results showed that combining B-mode ultrasound image features with SWE features and employing an SVM model can improve the automatic classification of NSLBP patients. Our findings also suggest that the SWE elasticity feature is a crucial factor in classifying NSLBP patients, and the proposed method can identify the important site and position of the muscle in the NSLBP classification task.

Paired Medicago receptors mediate broad-spectrum resistance to nodulation by Sinorhizobium meliloti carrying a species-specific gene.

Plants have evolved the ability to distinguish between symbiotic and pathogenic microbial signals. However, potentially cooperative plant-microbe interactions often abort due to incompatible signaling. The Nodulation Specificity 1 (NS1) locus in the legume Medicago truncatula blocks tissue invasion and root nodule induction by many strains of the nitrogen-fixing symbiont Sinorhizobium meliloti. Controlling this strain-specific nodulation blockade are two genes at the NS1 locus, designated NS1a and NS1b, which encode malectin-like leucine-rich repeat receptor kinases. Expression of NS1a and NS1b is induced upon inoculation by both compatible and incompatible Sinorhizobium strains and is dependent on host perception of bacterial nodulation (Nod) factors. Both presence/absence and sequence polymorphisms of the paired receptors contribute to the evolution and functional diversification of the NS1 locus. A bacterial gene, designated rns1, is required for activation of NS1-mediated nodulation restriction. rns1 encodes a type I-secreted protein and is present in approximately 50% of the nearly 250 sequenced S. meliloti strains but not found in over 60 sequenced strains from the closely related species Sinorhizobium medicae. S. meliloti strains lacking functional rns1 are able to evade NS1-mediated nodulation blockade.

The Impacts of Domestication and Breeding on Nitrogen Fixation Symbiosis in Legumes.

Legumes are the second most important family of crop plants. One defining feature of legumes is their unique ability to establish a nitrogen-fixing root nodule symbiosis with soil bacteria known as rhizobia. Since domestication from their wild relatives, crop legumes have been under intensive breeding to improve yield and other agronomic traits but with little attention paid to the belowground symbiosis traits. Theoretical models predict that domestication and breeding processes, coupled with high-input agricultural practices, might have reduced the capacity of crop legumes to achieve their full potential of nitrogen fixation symbiosis. Testing this prediction requires characterizing symbiosis traits in wild and breeding populations under both natural and cultivated environments using genetic, genomic, and ecological approaches. However, very few experimental studies have been dedicated to this area of research. Here, we review how legumes regulate their interactions with soil rhizobia and how domestication, breeding and agricultural practices might have affected nodulation capacity, nitrogen fixation efficiency, and the composition and function of rhizobial community. We also provide a perspective on how to improve legume-rhizobial symbiosis in sustainable agricultural systems.

Genetic and Physical Localization of the Gene Controlling Leaf Pigmentation Pattern in Medicago truncatula.

In Medicago truncatula, some ecotypes form a black or purple stain in the middle of adaxial leaf surface due to accumulation of anthocyanins. However, this morphological marker is missing in some other ecotypes, although anthocyanin biosynthesis pathway is not disrupted. Genetic analysis indicated that the lack of the leaf spot of anthocyanins accumulation is a dominant trait, which is controlled by a single gene, LPP1 Genetic mapping indicated that the LPP1 gene was delimited to a 280 kb-region on Chromosome 7. A total of 8 protein-coding genes were identified in the LPP1 locus through gene annotation and sequence analysis. Of those, two genes, putatively encoding MYB-transcriptional suppressors, were selected as candidates for functional validation.

Identification of plasma hsa_circ_0008673 expression as a potential biomarker and tumor regulator of breast cancer.

OBJECTIVE: Cell-free circular RNAs (circRNAs) are stable and abundantly exist in body fluids. In this study, we aimed to investigate plasma cell-free circRNAs as a novel class of biomarkers for the diagnosis of breast cancer (BC). METHODS: Differentially expressed circRNAs from 6 normal and 6 BC plasma samples were detected by microarray. Hsa_circ_0008673 was then screened and validated in the plasma of 102 normal and 378 BC samples. A receiver operating characteristic (ROC) curve was used to evaluate the diagnostic value. The correlations between hsa_circ_0008673 expression and demographic characteristics, tumor features, and prognosis were analyzed. The effects of hsa_circ_0008673 on BC cell proliferation and metastasis were also measured. RESULTS: Of the top ten up-regulated (hsa_circ_0008673, hsa_circ_0008500, hsa_circ_0005260, hsa_circ_0003423, hsa_circ_0119881, hsa_circ_0000987, hsa_circ_0007386, hsa_circ_0000091, hsa_circ_0016601, and hsa_circ_0008549) and top ten down-regulated (hsa_circ_0000826, hsa_circ_0072697, hsa_circ_0004587, hsa_circ_0000471, hsa_circ_0007786, hsa_circ_0001417, hsa_circ_0005982, hsa_circ_0001566, hsa_circ_0003823, and hsa_circ_0003823) circRNAs from microarray, hsa_circ_0008673 was the most significantly up-regulated circRNA in BC, and represented a good diagnostic value. Hsa_circ_0008673 was remarkably down-regulated after breast mastectomy. Hsa_circ_0008673 expression was associated with larger tumor size, distant metastasis, positive estrogen receptor (ER) status, and positive progesterone receptor (PR) status. Additionally, hsa_circ_0008673 could serve as a prognostic predicator of overall survival (OS) and disease-specific survival (DSS). Cell assays proved that hsa_circ_0008673 knockdown contributed to inhibition of tumor cell proliferation and migration. CONCLUSION: Plasma cell-free hsa_circ_0008673 was up-regulated in BC, which was associated with poorer prognosis and promoted tumor proliferation and metastasis. Hsa_circ_0008673 is a promising biomarker for tumor diagnosis and prognostic assessment of BC patients.

Genetic localization of the SPC gene controlling pod coiling direction in Medicago truncatula.

BACKGROUND: Handedness in plants introduced by helical growth of organs is frequently observed, and it has fascinated plant scientists for decades. However, the genetic control of natural handedness has not been revealed. In the model legume Medicago truncatula, pods can be coiled in a clockwise or anti-clockwise manner, providing a model for genetic analysis of plant handedness. OBJECTIVE: We aimed to localize the Sense of Pod Coiling (SPC) gene controlling pod coiling direction in M. truncatula. METHODS: Linkage analysis was used with a biparental population for fine mapping of the SPC gene. The genome sequence of M. truncatula Mt4.0 was used for marker identification and physical mapping. Single nucleotide polymorphisms (SNPs) between the parental lines were converted to CAPS (cleaved amplified polymorphic sequences) markers. Genetic map was constructed using the software JoinMap version 3.0. Gene predication and annotation provided by the M. truncatula genome database (http://www.medicagogenome.org) was confirmed with the programs of FGENESH and Pfam 32.0, respectively. Quantitative reverse transcription PCR (qRT-PCR) was used to analyze the relative expression levels of candidate genes. RESULTS: The genetic analysis indicated that the anti-clockwise coiling is dominant to clockwise and is controlled by the single gene, SPC. The SPC gene was delimited to a 250 kb-region on Chromosome 7. Total of 15 protein-coding genes were identified in the SPC locus through gene annotation and sequence analysis. Of those, two genes, potentially encoding a receptor-like kinase and a vacuolar cation/proton exchanger respectively, were selected as candidates for the SPC gene. CONCLUSIONS: The result presented here lay a foundation for gene cloning of SPC, which will help us to understand the molecular mechanisms underlying helical growth in plant organs.

An aptamer-based new method for competitive fluorescence detection of exosomes.

Exosomes have been recognized as promising sources of biomarkers for early cancer diagnosis due to their important role in the occurrence and metastasis of cancer, and so the development of a sensitive low-cost detection method for exosomes is highly desirable. In this paper, we report a fluorescence method for the competitive detection of exosomes based on an aptamer specific to CD63 (an exosome transmembrane protein). Aptamer-modified magnetic beads were hybridized with a Cy3-labeled short sequence complementary to a region of the aptamer. In the presence of exosomes, the CD63 on the exosomes bound to the aptamer, resulting in the shedding of the short sequence into the supernatant. The quantity of the exosomes could be estimated by detecting the fluorescence intensity in the supernatant. This method could detect exosomes at a concentration as low as 1.0 × 105 particles per µL under optimal conditions, and the feasibility of the method for exosome detection in complex clinical samples was also proved using simulated serum samples. The detection cost and difficulty are significantly reduced compared to conventional methods, while ensuring sensitivity, and so this method provides a basis for subsequent exosome detection in specific cancer cells.

Reduction in milk fat globule-EGF factor 8 inhibits triple-negative breast cancer cell viability and migration.

Milk fat globule-EGF factor 8 (MFG-E8) has been demonstrated to be associated with the progression and metastasis of breast cancer, although the underlying mechanisms remain undefined. The aim of the present study was to explore the role of MFG-E8 in human breast cancer and examine the underlying molecular mechanisms. Reverse transcription-quantitative polymerase chain reaction analysis was used to evaluate the expression levels of MFG-E8 in human breast carcinoma cell lines. An MFG-E8 small interfering RNA lentiviral vector was constructed and transfected into MDA-MB-231 cells. The results indicated that the in vitro silencing of MFG-E8 significantly inhibited the viability, invasion and migration of breast cancer cells. By using a flow cytometric approach, the knockdown of MFG-E8 was revealed to significantly induce cell cycle arrest at the G2/M phase and cell apoptosis. Furthermore, the downregulation of MFG-E8 induced the activation of apoptosis-associated proteins, and inhibited the expression of matrix metalloproteinase and epithelial-mesenchymal transition-associated proteins. Collectively, the results of the present study emphasize the importance of MFG-E8 deregulation in mammary carcinogenesis and its potential use as a biomarker for the diagnosis of breast carcinomas.

An Aptamer-Based Probe for Molecular Subtyping of Breast Cancer.

Molecular subtyping of breast cancer is of considerable interest owing to its potential for personalized therapy and prognosis. However, current methodologies cannot be used for precise subtyping, thereby posing a challenge in clinical practice. The aim of the present study is to develop a cell-specific single-stranded DNA (ssDNA) aptamer-based fluorescence probe for molecular subtyping of breast cancer. Methods: Cell-SELEX method was utilized to select DNA aptamers. Flow cytometry and confocal microscopy were used to study the specificity, binding affinity, temperature effect on the binding ability and target type analysis of the aptamers. In vitro and in vivo fluorescence imaging were used to distinguish the molecular subtypes of breast cancer cells, tissue sections and tumor-bearing mice. Results: Six SK-BR-3 breast cancer cell-specific ssDNA aptamers were evolved after successive in vitro selection over 21 rounds by Cell-SELEX. The Kd values of the selected aptamers were all in the low-nanomolar range, among which aptamer sk6 showed the lowest Kd of 0.61 ± 0.14 nM. Then, a truncated aptamer-based probe, sk6Ea, with only 53 nt and high specificity and binding affinity to the target cells was obtained. This aptamer-based probe was able to 1) differentiate SK-BR-3, MDA-MB-231, and MCF-7 breast cancer cells, as well as distinguish breast cancer cells from MCF-10A normal human mammary epithelial cells; 2) distinguish HER2-enriched breast cancer tissues from Luminal A, Luminal B, triple-negative breast cancer tissues, and adjacent normal breast tissues (ANBTs) in vitro; and 3) distinguish xenografts of SK-BR-3 tumor-bearing mice from those of MDA-MB-231 and MCF-7 tumor-bearing mice within 30 min in vivo. Conclusion: The results suggest that the aptamer-based probe is a powerful tool for fast and highly sensitive subtyping of breast cancer both in vitro and in vivo and is also very promising for the identification, diagnosis, and targeted therapy of breast cancer molecular subtypes.

Aptamer selection and applications for breast cancer diagnostics and therapy.

Aptamers are short non-coding, single-stranded oligonucleotides (RNA or DNA) developed through Systematic Evolution of Ligands by Exponential enrichment (SELEX) in vitro. Similar to antibodies, aptamers can bind to specific targets with high affinity, and are considered promising therapeutic agents as they have several advantages over antibodies, including high specificity, stability, and non-immunogenicity. Furthermore, aptamers can be produced at a low cost and easily modified, and are, therefore, called "chemical antibodies". In the past years, a variety of aptamers specifically bound to both breast cancer biomarkers and cells had been selected. Besides, taking advantage of nanomaterials, there were a number of aptamer-nanomaterial conjugates been developed and widely investigated for diagnostics and targeted therapy of breast cancer. In this short review, we first present a systematical review of various aptamer selection methods. Then, various aptamer-based diagnostic and therapeutic strategies of breast cancer were provided. Finally, the current problems, challenges, and future perspectives in the field were thoroughly discussed.

TPX2 promotes migration and invasion of human breast cancer cells.

OBJECTIVE: To investigate the expression of targeting protein for Xenopus kinesin-like protein 2 (TPX2) in breast cancer tissue and to explore its role in proliferation, migration and invasion of breast cancer cells. METHODS: The mRNA and protein expressions of TPX2 in breast cancer tissue and cell lines were assessed by quantitative RT-PCR and Western blot. The effect of TPX2 with RNA interference on proliferation, invasion and migration of breast cancer cells was observed by MTT and Transwell assays. RESULTS: Both mRNA and protein expressions of TPX2 were upregulated in breast cancer tissues compared to tumor-adjacent tissue. TPX2 expression was also upregulated in breast cancer cell lines, and the TPX2 interfered by small interfering RNA could inhibit the proliferation, invasion and migration of breast cancer cells by inhibiting matrix metalloproteinase-2 and matrix metalloproteinase-9. CONCLUSIONS: Significantly upregulated TPX2 expression is observed in breast cancer tissue and cells, and contributes to promote the proliferation, migration and invasion of breast cancer cells.