Resolving the bone - optimizing decalcification in spatial transcriptomics and molecular pathology.

Bone tissue poses critical roadblocks for spatial transcriptomics and molecular pathology due to a combination of its dense, calcified matrix and inadequate preservation of biomolecules in conventional decalcification. Decalcification is a complex and nuanced histological process to concomitantly preserve nucleic acids, proteins, and tissue architecture, ensuring molecular integrity for downstream assays. However, commonly used agents like formic and hydrochloric acids, while efficient, can degrade biomolecules to varying extents, complicating assays such as PCR, sequencing, immunohistochemistry, and hybridization.

FixNCut: A Practical Guide to Sample Preservation by Reversible Fixation for Single Cell Assays.

The quality of standard single-cell experiments often depends on the immediate processing of cells or tissues post-harvest to preserve fragile and vulnerable cell populations, unless the samples are adequately fixed and stored. Despite the recent rise in popularity of probe-based and aldehyde-fixed RNA assays, these methods face limitations in species and target availability and are not suitable for immunoprofiling or assessing chromatin accessibility. Recently, a reversible fixation strategy known as FixNCut has been successfully deployed to separate sampling from downstream applications in a reproducible and robust manner, avoiding stress or necrosis-related artifacts.

The RNA-binding protein RBMS3 inhibits the progression of colon cancer by regulating the stability of LIMS1 mRNA.

Background: The RNA-binding motif single-stranded interacting protein 3 (RBMS3) is a constituent of the RNA-binding motif (RBM) protein family, which assumes a pivotal role in governing cellular biogenesis processes such as the cell cycle and apoptosis. Despite an abundance of studies elucidating RBMS3's divergent roles in the genesis and advancement of various tumors, its involvement in colon cancer remains enigmatic.

Methods: The present investigation employed data analysis from TCGA and GTEx to unveil that RBMS3 expression demonstrated a diminished presence in colon cancer tissues when juxtaposed with normal colon tissues.

Relationship between motor dysfunction, the respiratory muscles and pulmonary function in stroke patients with hemiplegia: a retrospective study.

Background: The interaction between motor dysfunction and respiratory functions in stroke patients with hemiplegia are not fully understood, particularly with regard to the relationship between changes in trunk control, balance, and daily activities, and changes in respiratory muscle strength and pulmonary volume. Investigating this relationship will facilitate the optimization of stroke rehabilitation strategies.

Methods: Clinical history data were collected from 134 patients to analyze the relationship between motor function scales scores and spirometric data.

Genome-wide identification of the gene family in L. and expression analysis under abiotic and biotic stress.

Background: O-methyltransferase (OMT)-mediated O-methylation is a frequent modification that occurs during natural product biosynthesis, and it increases the diversity and stability of secondary metabolites. However, detailed genome-wide identification and expression analyses of gene family members have not been performed in melons. In this study, we aimed to perform the genome-wide identification of gene family members in melon to identify and clarify their actions during stress.

The IGF2BP3-COPS7B Axis Facilitates mRNA Translation to Drive Colorectal Cancer Progression.

Unlabelled: Many studies have provided valuable information about genomic and transcriptomic changes that occur in colorectal cancer. However, protein abundance cannot be reliably predicted by DNA alteration or mRNA expression, which can be partially attributed to posttranscriptional and/or translational regulation of gene expression. In this study, we identified increased translational efficiency (TE) as a hallmark of colorectal cancer by evaluating the transcriptomic and proteomic features of patients with colorectal cancer, along with comparative transcriptomic and ribosome-protected mRNA analysis in colon epithelial cells and colon cancer cells.

The role of alternative splicing in lung cancer.

Aberrant alternative splicing (AS) events are frequently observed in lung cancer, which can be attributed to aberrant gene AS, alterations in splicing regulatory factors, or changes in splicing regulatory mechanisms. Consequently, the dysregulation of alternative RNA splicing is the fundamental cause of lung cancer. In this review, we have summarized the pivotal role of AS in the development, progression, invasion, metastasis, angiogenesis, and drug resistance of lung cancer.

Extensible and self-recoverable proteinaceous materials derived from scallop byssal thread.

Biologically derived and biologically inspired fibers with outstanding mechanical properties have found attractive technical applications across diverse fields. Despite recent advances, few fibers can simultaneously possess high-extensibility and self-recovery properties especially under wet conditions. Here, we report protein-based fibers made from recombinant scallop byssal proteins with outstanding extensibility and self-recovery properties.

A ratiometric and two-photon fluorescent probe for imaging hydrogen peroxide in living cells.

As an important reactive oxygen species (ROS), hydrogen peroxide plays a significant role in the life activity system, and its abnormal levels are closely related to many diseases. Developing effective fluorescent probes for detecting hydrogen peroxide is very urgent. Therefore, we constructed a probe Z that can detect hydrogen peroxide in ratio.

Elevated expression of the rhythm gene NFIL3 promotes the progression of TNBC by activating NF-κB signaling through suppression of NFKBIA transcription.

Background: Epidemiological studies have confirmed that abnormal circadian rhythms are associated with tumorigenesis in breast cancer. However, few studies have investigated the pathological roles of rhythm genes in breast cancer progression. In this study, we aimed to evaluate the aberrant expression of 32 rhythm genes in breast cancer and detect the pathological roles and molecular mechanisms of the altered rhythm gene in regulating the progression of triple negative breast cancer (TNBC).

Comprehensive Analysis of Subtype-Specific Molecular Characteristics of Colon Cancer: Specific Genes, Driver Genes, Signaling Pathways, and Immunotherapy Responses.

Colon cancer is a complex, heterogeneous disease. The Colorectal Cancer Subtyping Consortium reported a novel classification system for colon cancer in 2015 to better understand its heterogeneity. This molecular classification system divided colon cancer into four distinct consensus molecular subtypes (CMS 1, 2, 3, and 4).

Single-cell transcriptomics identifies Gadd45b as a regulator of herpesvirus-reactivating neurons.

Single-cell RNA sequencing (scRNA-seq) is a powerful technique for dissecting the complexity of normal and diseased tissues, enabling characterization of cell diversity and heterogeneous phenotypic states in unprecedented detail. However, this technology has been underutilized for exploring the interactions between the host cell and viral pathogens in latently infected cells. Herein, we use scRNA-seq and single-molecule sensitivity fluorescent in situ hybridization (smFISH) technologies to investigate host single-cell transcriptome changes upon the reactivation of a human neurotropic virus, herpes simplex virus-1 (HSV-1).

Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice.

Background: Soil salinization represents a serious threat to global rice production. Although significant research has been conducted to understand salt stress at the genomic, transcriptomic and proteomic levels, few studies have focused on the translatomic responses to this stress. Recent studies have suggested that transcriptional and translational responses to salt stress can often operate independently.

Uncovering the Subtype-Specific Molecular Characteristics of Breast Cancer by Multiomics Analysis of Prognosis-Associated Genes, Driver Genes, Signaling Pathways, and Immune Activity.

Breast cancer is a heterogeneous malignant disease with different prognoses and has been divided into four molecular subtypes. It is believed that molecular events occurring in breast stem/progenitor cells contribute to the carcinogenesis and development of different breast cancer subtypes. However, these subtype-specific molecular characteristics are largely unknown.

The promising outcome with simultaneous integrated boost intensity modulated radiotherapy in confined nasal extranodal NK/T-cell lymphoma.

The study aimed to retrospectively analyze the prognosis of patients with stage IE nasal extranodal natural killer/T-cell lymphoma (ENKTL) with dose reduction to clinical target volume (CTV) by using simultaneous integrated boost intensity-modulated radiotherapy (SIB-IMRT). Forty-four patients were reviewed retrospectively. The prescribed dose was 45 Gy/25 fractions for extended involved-field site and 50-55 Gy/25 fractions for primary tumor site by using SIB-IMRT.

New strategy for detection of hydrogen peroxide based on bi-nucleophilic reaction.

Two novel fluorescent probes based on 7-hydroxy-4-methyl-coumarin, FAA-MC-OH (2-fluoro-4-nitro-phenylacetyl hydroxyl coumarin) and FBA-MC-OH (2-fluoro-4-nitro-benzoyl hydroxyl coumarin) are first synthesized, and spectral studies confirm that both the probes display highly selective and sensitive to HO, especially FBA-MC-OH has a shorter response time. Moreover, it is worth noting that the reaction mechanism is based on bi-nucleophilic substitution instead of oxidation or hydrolysis, which is different from previous reported probes'.

Prophylactic cranial irradiation confers favourable prognosis for patients with limited-stage small cell lung cancer in the era of MRI: A propensity score-matched analysis.

Introduction: Prophylactic cranial irradiation (PCI) is recommended for patients with limited-stage small cell lung cancer (LS-SCLC) who achieve good response after chemoradiotherapy. But PCI is neurotoxic. Magnetic resonance imaging (MRI) is the standard tool for evaluating brain metastasis (BM).

Comparative methylome reveals regulatory roles of DNA methylation in melon resistance to Podosphaera xanthii.

Powdery mildew caused by Podosphaera xanthii (P. xanthii) severely endangers melon (Cucumis melo L.) production, while the mechanistic understanding about its resistance to powdery mildew remains largely limited.

Single cell RNA sequencing for breast cancer: present and future.

Breast cancer is one of the most common malignant tumors in women. It is a heterogeneous disease related to genetic and environmental factors. Presently, the treatment of breast cancer still faces challenges due to recurrence and metastasis.

Neoadjuvant chemoradiotherapy improves survival in locally advanced adenocarcinoma of esophagogastric junction compared with neoadjuvant chemotherapy: a propensity score matching analysis.

Background: To analyze whether neoadjuvant chemoradiotherapy (nCRT) could improve the survival for patients with adenocarcinoma of the esophagogastric junction compared with neoadjuvant chemotherapy (nCT). Both neoadjuvant chemotherapy alone and chemoradiotherapy before surgery have been shown to improve overall long-term survival for patients with adenocarcinoma in the esophagus or esophagogastric junction compared to surgery alone. It remains controversial whether nCRT is superior to nCT.

Alternative splicing: An important regulatory mechanism in colorectal carcinoma.

Alternative splicing (AS) is a process that produces various mRNA splicing isoforms via different splicing patterns of mRNA precursors (pre-mRNAs). AS is the primary mechanism for increasing the types and quantities of proteins to improve biodiversity and influence multiple biological processes, including chromatin modification, signal transduction, and protein expression. It has been reported that AS is involved in the tumorigenesis and development of colorectal carcinoma (CRC).

Multidimensional factors affecting care needs in daily living among community-dwelling older adults: A structural equation modelling approach.

Aims: To develop a model illustrating the factors that can influence care needs in daily living (CNDL) of older adults and the pathways between these.

Background: The care needs in community-dwelling older adults have increased sharply. A better understanding of the elderly's CNDL would thus help policymakers define which types of support and services should be given.

Genome-wide characterization of two-component system (TCS) genes in melon (Cucumis melo L.).

To better understand cytokinin signaling in melon (Cucumis melo L.), one of the most important fruit crops in the Cucurbitaceae family, we identified and characterized melon two-component system (TCS) genes in this study. The results showed that there were 51 genes encoding putative TCS proteins in melon, and these TCS genes were classified into 3 subgroups, with 17 HK(L)s (histidine kinase/histidine-kinase like; 9 HKs and 8 HKLs), 9 HPs (histidine phosphotransfer proteins; 6 authentic and 3 pseudo), and 25 RRs (response regulators; 8 Type-A, 11 Type-B and 6 pseudo).

The discovered chimeric protein plays the cohesive role to maintain scallop byssal root structural integrity.

Adhesion is essential for many marine sessile organisms. Unraveling the compositions and assembly of marine bioadheisves is the fundamental to understand their physiological roles. Despite the remarkable diversity of animal bioadhesion, our understanding of this biological process remains limited to only a few animal lineages, leaving the majority of lineages remain enigmatic.

Ma2/d promotes myonuclear positioning and association with the sarcoplasmic reticulum.

The cytoplasm of striated myofibers contains a large number of membrane organelles, including sarcoplasmic reticulum (SR), T-tubules and the nuclear membrane. These organelles maintain a characteristic juxtaposition that appears to be essential for efficient inter-membranous exchange of RNA, proteins and ions. We found that the membrane-associated Muscle-specific α2/δ (Ma2/d) subunit of the Ca channel complex localizes to the SR and T-tubules, and accumulates at the myonuclear surfaces.