Expression profiling and single nucleotide polymorphism of mitogen-activated protein kinase kinase kinase 8 MAP3K8 in white muscovy ducks (Cairina moschata).

A previous study on ovarian and hypothalami transcriptome analysis in white Muscovy duck revealed that MAP3K8 gene participated in MAPK signaling pathway that influence egg production. Additionally, MAP3K8 was predicted as a target gene of miRNA-509-3p that promotes the secretion of oestradiol which is an important hormone in egg ovulation. This suggested that MAP3K8 might have a functional role in the reproductive performance "egg production" of white Muscovy ducks. Herein, we focused on expression level of MAP3K8 in reproductive and non-reproductive tissues of highest (HP) and lowest (LP) egg producing white Muscovy ducks and identified the polymorphism in MAP3K8 and its association with three egg production traits; Age at first egg (AFE), number of eggs at 300 days (N300D) and 59 weeks (N59W). The results of expression level indicated that mRNA of MAP3K8 was significantly (p < 0.01) expressed in the oviduct than in the ovary and hypothalamus. Seven synonymous SNPs were detected, and association analysis showed that g.148303340 G>A and g.148290065 A>G were significantly (p < 0.05) associated with N300D and N59W. The results of this study might serve as molecular marker for marker-assisted selection of white Muscovy ducks for egg production.

Type III Collagen RNA Level Expression in Pelvic Organ Prolapse: A Systematic Review and Meta-Analysis.

INTRODUCTION AND HYPOTHESIS: Changes in the expression of type III collagen have been linked to women's predisposition to pelvic organ prolapse (POP); however, the findings of prior studies have been conflicting. This study was aimed at investigating whether changes in the type III collagen gene expression levels occur in POP development. METHODS: A systematic review and meta-analysis were conducted on research articles that evaluated type III collagen gene expression levels in patients with POP compared with those without the condition. The articles, published between January 2000 and February 2024, were obtained from PubMed, ScienceDirect, Semantic Scholar, and EBSCO databases. Data were analyzed using fixed-effect models, and the pooled standardized mean difference (SMD) was calculated. Cochrane's Review Manager 5.4 was used for the analysis. The aggregated SMD with 95% confidence interval (CI) regarding type III collagen gene expression levels relative to POP development was the main outcome measure. Results with p < 0.05 were considered statistically significant. RESULTS: Six studies were included in our analysis, comprising 229 POP cases and 139 non-POP cases. Our meta-analysis indicated that patients with POP had higher type III collagen gene expression levels than those without POP (SMD = 0.32; 95% CI: 0.07 to 0.56; p = 0.01). CONCLUSION: The results of this study provide evidence that a higher type III collagen gene expression levels is significantly associated with POP.

Investigation of the Expression and Regulation of SCG5 in the Context of the Chromogranin-Secretogranin Family in Malignant Tumors.

The SCG5 gene has been demonstrated to play an essential role in the development and progression of a range of malignant neoplasms. The regulation of SCG5 expression involves multiple biological pathways. According to relevant studies, SCG5 is differentially expressed in different cancers, and its up- or down-regulation may even affect tumour growth, invasion, and migration, which caught our attention. Therefore, we summarise the regulatory roles played by the SCG5 gene in a variety of cancers and the biological regulatory mechanisms associated with its possible promotion or inhibition of tumour biological behavior, to further explore the potential of SCG5 as a new tumour marker and hopefully provide theoretical guidance for subsequent disease research and treatment.

Analysis of Factors Associated With Pathological Complete Response in Patients With HER2-Positive Breast Cancer Receiving Neoadjuvant Chemotherapy.

PURPOSE: This study aimed to examine the impact of the level of HER2 overexpression on pathologic and clinical outcomes in HER2-positive breast cancer (BC) patients treated with neoadjuvant therapy (NAT). METHODS: Women with Stage II or III HER2-positive BC who received anthracycline-taxane-trastuzumab NAT regimens followed by curative-intent surgery were included. Patients were classified according to tumor HER2 expression into HER2-high (immunohistochemistry (IHC) 3+ or fluorescence in situ hybridization (FISH) HER2/CEP17 ratio ≥5 or HER2 copy number ≥10) and HER2-intermediate (IHC 2+ with HER2/CEP17 ratio ≥2 to <5 or copy number ≥4 to <10). Univariate and multivariate logistic regression analyses were performed using HER2 expression as a categorical variable. The primary outcome was pathological complete response (pCR). Estimated 3-year disease-free survival (DFS) and Overall Survival (OS) were secondary outcomes. RESULTS: Among 161 patients with HER2-positive BC, 139 (86%) and 22 (14%) were classified as HER2-high and HER2-intermediate, respectively; 105 (65.2%) had hormone receptor (HR)-positive tumors; 72 (45%) achieved a pCR. In the overall population, pCR rates of 18% and 49% were achieved in HER2-intermediate and HER2-high cases, respectively (odds ratio [OR] = 0.23 95% CI 0.07-0.72; P = .007). No pCRs were observed among HR-positive, HER2-intermediate cases. Estimated 3-year DFS was 97.1% versus 89.3% for patients achieving a pCR versus those with residual disease, respectively (P = .0011). CONCLUSION: We found that patients with HER2-high disease were more likely to achieve pCR after NAT compared to patients with HER2-intermediate BC, a subgroup of patients that may benefit from more personalized NAT strategies.

Transcriptome-Based Screening of Candidate Low-Temperature-Associated Genes and Analysis of the BocARR-B Transcription Factor Gene Family in Kohlrabi (Brassica oleracea L. var. caulorapa L.).

Low temperature is a significant abiotic stress factor that not only impacts plant growth, development, yield, and quality but also constrains the geographical distribution of numerous wild plants. Kohlrabi (Brassica oleracea L. var. caulorapa L.) belongs to the Brassicaceae family and has a short growing period. In this study, a total of 196,642 unigenes were obtained from kohlrabi seedlings at low temperatures; of these, 52,836 unigenes were identified as differentially expressed genes. Transcription factor family members ARR-B, C3H, B3-ARF, etc. that had a high correlation with biochemical indicators related to low temperature were identified. A total of nineteen BocARR-B genes (named BocARR-B1-BocARR-B19) were obtained, and these genes were distributed unevenly across seven chromosomes. Nineteen BocARR-B genes searched four conserved motifs and were divided into three groups. The relative expression level analysis of 19 BocARR-B genes of kohlrabi showed obvious specificity in different tissues. This study lays a foundation and provides new insight to explain the low-temperature resistance mechanism and response pathways of kohlrabi. It also provides a theoretical basis for the functional analysis of 19 BocARR-B transcription factor gene family members.

Repeated release of cerium oxide nanoparticles altered algal responses: Growth, photosynthesis, and photosynthetic gene expression.

The expanding production of engineered nanomaterials (ENMs) can eventually cause their increased release into and presence in aquatic ecosystems, potentially threatening the health of aquatic organisms and the stability of the ecological environment. Generally, ENMs are repeatedly released into real-world aquatic environments in relatively low concentrations, potentially affecting photosynthesis in primary producers such as algae. However, knowledge regarding the effects of repeated exposure to ENMs on algal photosynthesis is still lacking. Herein, the physiological responses of the freshwater algae Chlorella vulgaris following single and repeated exposures to cerium oxide nanoparticles (CeO2 NPs) were investigated at 10 mg/L, with a focus on photosynthesis. The results showed that repeated exposures triggered increased photosynthetic pigment contents, oxidative stress levels, decreased photosynthetic performance, and lower biomass in C. vulgaris compared to a single exposure. Photosynthesis-related genes (i.e., petA, petB, psaA, atpB, and rbcL) were found to be upregulated following repeated exposures. Particularly for petB, repeated rather than single exposure treatment significantly upregulated its expression levels by 2.92-10.24-fold compared to unexposed controls. Furthermore, increased exposure times could aggravate the interaction between CeO2 NPs and algae, elevating 8.13%, 12.13%, and 20.51% Ce distribution on the algal cell surface or intracellularly, compared to a single exposure. This study is the first to investigate the effects of ENM exposure times on algal photosynthesis, providing new insights into the assessment of the risks these materials pose to real-world aquatic environments.

Discovery and demonstration of the temperature stress response functions of Dermatophagoides farinae proteins 1 and 2.

BACKGROUND: Dermatophagoides farinae proteins (DFPs) are abundantly expressed in D. farinae; however, their functions remain unknown. Our previous transcriptome sequencing analyses revealed that the basal expression of DFP1 and DFP2 in D. farinae was high and, more importantly, upregulated under temperature stress. Therefore, DFPs were speculated to exert a temperature stress response function. RESULTS: Real-time quantitative polymerase chain reaction detection revealed that both DFP1 and DFP2 were significantly upregulated under temperature stress. Particularly, DFP1 was upregulated under cold stress. Electrophoresis of D. farinae total proteins revealed an increased abundance of DFP1 and DFP2 (40-55 kDa bands) under temperature stress, which was corroborated by the mass spectrometry results. After silencing DFP1 and DFP2 further, temperature stress led to decreases in gene expression and survival rates. Moreover, DFP1 was identified as the upstream regulator of DFP2. CONCLUSION: This study highlights the temperature stress response functions of DFP1 and DFP2 at the mRNA and protein levels. These results provide important insights for applying DFP1 and DFP2 as potential target genes for the molecular prevention and control of D. farinae to prevent allergic diseases. The newly established methods provide methodological guidance for the study of genes with unknown functions in mites.

Sex Differences in Antennal Transcriptome of Hyphantria cunea and Analysis of Odorant Receptor Expression Profiles.

Insects rely on olfaction for mating, finding oviposition sites, and locating hosts. Hyphantria cunea is a serious pest that severely damages forests. Differential expression analysis of olfactory-related genes between males and females is the basis for elucidating the functions of olfactory-related proteins in H. cunea. In this study, Illumina HiSeqTM 4000 high-throughput sequencing technology was used to perform transcriptome sequencing of the antennal tissues of adult male and female H. cunea. Functional annotation was conducted using the NR, Swiss-Prot, KOG, KEGG, and GO databases, and the results showed that the antennal transcriptome of adult H. cunea contained 50,158 unigenes. Differential expression analysis identified 3923 genes that were significantly differentially expressed between male and female antennae. A total of 221 olfactory-related genes were annotated, and 96 sex-biased genes were identified, including 13 odorant receptors (ORs), 48 odorant binding proteins (OBPs), 7 chemosensory proteins (CSPs), 10 ionotropic receptors (IRs), 10 sensory neuron membrane proteins (SNMPs), 2 gustatory receptors (GRs), and 6 odorant-degrading enzymes (ODEs), indicating that there were differences in olfaction between male and female H. cunea. Quantitative real-time PCR was used to verify the expression levels of 21 putative general odorant receptor genes in male and female antennae. HcunOR4 and HcunOR5 showed female-biased expression; HcunOR48, HcunOR49 and HcunOR50 showed male-biased expression. The results were consistent with the transcriptome differential analysis. The screening of male-biased odorant receptor genes might provide a theoretical basis for the functional characterization of odorant receptors for recognizing sex pheromones in H. cunea.

Homoeologs in Allopolyploids: Navigating Redundancy as Both an Evolutionary Opportunity and a Technical Challenge-A Transcriptomics Perspective.

Allopolyploidy in plants involves the merging of two or more distinct parental genomes into a single nucleus, a significant evolutionary process in the plant kingdom. Transcriptomic analysis provides invaluable insights into allopolyploid plants by elucidating the fate of duplicated genes, revealing evolutionary novelties and uncovering their environmental adaptations. By examining gene expression profiles, scientists can discern how duplicated genes have evolved to acquire new functions or regulatory roles. This process often leads to the development of novel traits and adaptive strategies that allopolyploid plants leverage to thrive in diverse ecological niches. Understanding these molecular mechanisms not only enhances our appreciation of the genetic complexity underlying allopolyploidy but also underscores their importance in agriculture and ecosystem resilience. However, transcriptome profiling is challenging due to genomic redundancy, which is further complicated by the presence of multiple chromosomes sets and the variations among homoeologs and allelic genes. Prior to transcriptome analysis, sub-genome phasing and homoeology inference are essential for obtaining a comprehensive view of gene expression. This review aims to clarify the terminology in this field, identify the most challenging aspects of transcriptome analysis, explain their inherent difficulties, and suggest reliable analytic strategies. Furthermore, bulk RNA-seq is highlighted as a primary method for studying allopolyploid gene expression, focusing on critical steps like read mapping and normalization in differential gene expression analysis. This approach effectively captures gene expression from both parental genomes, facilitating a comprehensive analysis of their combined profiles. Its sensitivity in detecting low-abundance transcripts allows for subtle differences between parental genomes to be identified, crucial for understanding regulatory dynamics and gene expression balance in allopolyploids.

Detecting differentially expressed genes from RNA-seq data using fuzzy clustering.

A two-group comparison test is generally performed on RNA sequencing data to detect differentially expressed genes (DEGs). However, the accuracy of this method is low due to the small sample size. To address this, we propose a method using fuzzy clustering that artificially generates data with expression patterns similar to those of DEGs to identify genes that are highly likely to be classified into the same cluster as the initial cluster data. The proposed method is advantageous in that it does not perform any test. Furthermore, a certain level of accuracy can be maintained even when the sample size is biased, and we show that such a situation may improve the accuracy of the proposed method. We compared the proposed method with the conventional method using simulations. In the simulations, we changed the sample size and difference between the expression levels of group 1 and group 2 in the DEGs to obtain the desired accuracy of the proposed method. The results show that the proposed method is superior in all cases under the conditions simulated. We also show that the effect of the difference between group 1 and group 2 on the accuracy is more prominent when the sample size is biased.

Genome-wide identification, abiotic stress, and expression analysis of PYL family in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) during grain development.

BACKGROUND: Abscisic acid (ABA) is a plant hormone that plays an important role in plant resistance to drought, salinity, cold, and pathogens. It is also important for regulating plant growth and development. Pyrabactin resistance/pyr1-like/regulatory components of the ABA receptor (PYL/RCAR) are ABA receptor proteins in plants and the core of ABA signal transduction pathways in plant regulatory factors. At present, there are no reports on the PYL family of Tartary buckwheat. RESULTS: In this study, 19 paralogous form PYL genes in buckwheat were identified at the whole-genome level and named FtPYL1-FtPYL19 according to their positions on chromosomes. We further analyzed the gene structure, conserved motifs, cis-acting elements, gene duplication, phylogenetic relationships, and expression patterns under different stress treatments and during grain development of the 19 paralogous form PYL genes in Tartary buckwheat. The FtPYL gene exhibits a single exonic gene structure for about 68.4% of the duplicated forms from the total paralogous forms. The remaining subfamilies, such as I and II, contain three exons and two exons (e.g., FtPYL19), respectively. Nineteen FtPYL genes were evenly distributed across the eight chromosomes, with at least one FtPYL gene on each chromosome. In the FtPYL gene family, there was one tandem repeat event and five gene duplication events. We investigated the gene expression levels of FtPYL gene under four abiotic stresses and different stages of grain development. Under drought stress (PEG6000), the relative expression levels of FtPYL14 and FtPYL15 increased by fourfold. Under high temperature stress (38℃), the relative expression level of FtPYL16 dropped to 0.12, and that of FtPYL17 fell to 0.22. At different stages of grain development, the gene expression level of FtPY15 is extremely high at 19 D. The relative expression level of FtPYL7 in roots and stems reaches up to approximately 450, and the relative expression level of FtPYL10 in 13 D also reaches up to 248. In this study, the PYL gene family of Tartary buckwheat was identified and analyzed based on the whole genome, and 19 paralogous form FtPYL genes of Tartary buckwheat were bioinformatically analyzed. The expression patterns of 19 paralogous form FtPYL genes in Tartary buckwheat cultivars under different stress treatments and during grain development were analyzed. It was found that the FtPYL gene played an important role in grain development.

Transforming growth factor-ß1 and vascular endothelial growth factor levels in senile acute myeloid leukemia and correlation with prognosis.

BACKGROUND: Acute myeloid leukemia (AML) is a disease in which immature hematopoietic cells accumulate in the bone marrow and continuously expand, inhibiting hematopoiesis. The treatment and prognosis of this disease have always been unsatisfactory. AIM: To investigate the correlation between vascular endothelial growth factor (VEGF) and transforming growth factor-ß1 (TGFß1) expression and prognosis in older adults with AML. METHODS: This study enrolled 80 patients with AML (AML group), including 36 with complete response (AML-CR), 23 with partial response (AML-PR), and 21 with no response (AML-NR). The expression levels of VEGF and TGFß1 were detected by reverse transcription polymerase chain reaction in bone marrow mononuclear cells isolated from 56 healthy controls. Kaplan-Meier analysis was performed to assess overall survival (OS) and progression- or disease-free survival (DFS). Prognostic risk factors were analyzed using a Cox proportional hazards model. RESULTS: The AML group showed a VEGF level of 2.68 ± 0.16. VEGF expression was lower in patients with AML-CR than those with AML-PR or AML-NR (P < 0.05). TGFß1 expression in the AML group was 0.33 ± 0.05. Patients with AML-CR showed a higher TGFß1 expression than those with AML-PR or AML-NR (P < 0.05). VEGF and TGFß1 expression in patients with AML was significantly correlated with the counts of leukocytes, platelets, hemoglobin, and peripheral blood immature cells (P < 0.05); Kaplan-Meier survival analysis revealed that patients with high TGFß1 expression had better OS and DFS than those with low TGFß1 expression (P < 0.05), whereas patients with low VEGF levels showed better OS and DFS than those with high VEGF levels (P < 0.05). VEGF, TGFß1, and platelet count were identified by the Cox proportional hazards model as independent risk factors for OS (P < 0.05), while VEGF, TGFß1, and white blood cell count were independent risk factors for DFS (P < 0.05). CONCLUSION: Decreased VEGF expression and increased TGFß1 expression in patients with AML provide valuable references for determining and individualizing clinical treatment strategies.

Noninvasive prediction of CCL2 expression level in high-grade glioma patients.

BACKGROUND: Gliomas are recognized as the most frequent type of malignancies in the central nervous system, and efficacious prognostic indicators are essential to treat patients with gliomas and improve their clinical outcomes. The chemokine (C-C motif) ligand 2 (CCL2) is a promising predictor for glioma malignancy and progression. However, at present, the methods to evaluate CCL2 expression level are invasive and operator-dependent. OBJECTIVE: It was expected to noninvasively predict CCL2 expression levels in malignant glioma tissues by magnetic resonance imaging (MRI)-based radiomics and assess the association between the developed radiomics model and prognostic indicators and related genes. METHODS: MRI-based radiomics was used to predict CCL2 expression level using data obtained from The Cancer Imaging Archive (TCIA) and The Cancer Genome Atlas (TCGA) databases. A support vector machine (SVM)-based radiomics model and a logistic regression (LR)-based radiomics model were used to predict the radiomics score, and its correlation with CCL2 expression level was analyzed. RESULTS: The results revealed that there was an association between CCL2 expression level and the overall survival of cases with gliomas, and bioinformatics correlation analysis showed that CCL2 expression level was highly correlated with disease-related pathways, such as mTOR signaling pathway, cGMP-PKG signaling pathway, and MAPK signaling pathway. Both SVM- and LR-based radiomics data robustly predicted CCL2 expression level, and radiomics scores could also be used to predict the overall survival of patients. Moreover, the high/low radiomics scores were highly correlated with the known glioma-related genes, including CD70, CD27, and PDCD1. CONCLUSION: An MRI-based radiomics model was successfully developed, and its clinical benefits were confirmed, including the prediction of CCL2 expression level and patients' prognosis.

Preliminary Study on Clinical Characteristics and Pathogenesis of IQSEC2 Mutations Patients.

Background: The IQ motif and Sec7 domain ArfGEF 2 (IQSEC2), an X-linked gene that encodes the BRAG1 protein, is a guanine nucleotide exchange factor for the ADP ribosylation factor (ARF) protein family in the small guanosine triphosphate (GTP) binding protein. Mutations in this gene result in disorders such as intellectual disability (ID) and epilepsy. In this study, we analyze the clinical features of two patients with IQSEC2-mutation-related disease and discuss their possible pathogenesis. Methods: The two patients were diagnosed with ID and epilepsy. Genetic testing was performed using whole-exome sequencing, and the three-dimensional protein structure was analyzed. UCSC Genome Browser was used to analyze the conservation of IQSEC2 in different species. We compared IQSEC2 expression in the proband families with that in a control group, as well as the expression of the postsynaptic identity protein 95 (PSD-95), synapse-associated protein 97 (SAP97), ADP ribosylation factor 6 (ARF-6), and insulin receptor substrate 53kDa (IRSP53) genes interacting with IQSEC2. Results: We identified two semi-zygote mutations located in conserved positions in different species: an unreported de novo mutation, C.3576C>A (p. Tyr1192*), and a known mutation, c.2983C>T (p. Arg995Trp). IQSEC2 mutations resulted in significant changes in the predicted three-dimensional protein structure, while its expression in the two probands was significantly lower than that in the age-matched control group, and IQSEC2 expression in proband 1 was lower than that in his family members. The expression levels of PSD-95, ARF-6, and SAP97, IRSP 53, which interact with IQSEC2, were also significantly different from those in the family members and age-matched healthy children. Conclusion: The clinical phenotype resulting from IQSEC2 mutations can be explained by the significant decrease in its expression, loss of function of the mutant protein, and change in the expression of related genes. Our results provide novel insights into the molecular phenotype conferred by the IQSEC2 variants.

The P450-Monooxygenase Activity and CYP6D1 Expression in the Chlorfenapyr-Resistant Strain of Musca domestica L.

The house fly Musca domestica L. is one of the most common insects of veterinary and medical importance worldwide; its ability to develop resistance to a large number of insecticides is well known. Many studies support the involvement of cytochrome P-450-dependent monooxygenases (P450) in the development of resistance to pyrethroids, neonicotinoids, carbamates, and organophosphates among insects. In this paper, the monooxygenase activity and expression level of CYP6D1 were studied for the first time in a chlorfenapyr-resistant strain of house fly. Our studies demonstrated that P450 activity in adults of the susceptible strain (Lab TY) and chlorfenapyr-resistant strain (ChlA) was 1.56-4.05-fold higher than that in larvae. In females of the Lab TY and ChlA strains, this activity was 1.53- and 1.57-fold higher, respectively (p < 0.05), than that in males, and in contrast, the expression level of CYP6D1 was 21- and 8-fold lower, respectively. The monooxygenase activity did not vary between larvae of the susceptible strain Lab TY and the chlorfenapyr-resistant strain ChlA. Activity in females and males of the ChlA strain exceeded that in the Lab TY strain specimens by 1.54 (p = 0.08) and 1.83 (p < 0.05) times, respectively, with the same level of CYP6D1 expression. PCR-RFLP analysis revealed a previously undescribed mutation in the promoter region of the CYP6D1 gene in adults of the Lab TY and ChlA strains, and it did not affect the gene expression level. The obtained results show that the development of resistance to chlorfenapyr in M. domestica is accompanied by an increase in P450-monooxygenase activity without changes in CYP6D1 expression.

Mechanisms and clinical landscape of N6-methyladenosine (m6A) RNA modification in gastrointestinal tract cancers.

Epigenetics encompasses reversible and heritable chemical modifications of non-nuclear DNA sequences, including DNA and RNA methylation, histone modifications, non-coding RNA modifications, and chromatin rearrangements. In addition to well-studied DNA and histone methylation, RNA methylation has emerged as a hot topic in biological sciences over the past decade. N6-methyladenosine (m6A) is the most common and abundant modification in eukaryotic mRNA, affecting all RNA stages, including transcription, translation, and degradation. Advances in high-throughput sequencing technologies made it feasible to identify the chemical basis and biological functions of m6A RNA. Dysregulation of m6A levels and associated modifying proteins can both inhibit and promote cancer, highlighting the importance of the tumor microenvironment in diverse biological processes. Gastrointestinal tract cancers, including gastric, colorectal, and pancreatic cancers, are among the most common and deadly malignancies in humans. Growing evidence suggests a close association between m6A levels and the progression of gastrointestinal tumors. Global m6A modification levels are substantially modified in gastrointestinal tumor tissues and cell lines compared to healthy tissues and cells, possibly influencing various biological behaviors such as tumor cell proliferation, invasion, metastasis, and drug resistance. Exploring the diagnostic and therapeutic potential of m6A-related proteins is critical from a clinical standpoint. Developing more specific and effective m6A modulators offers new options for treating these tumors and deeper insights into gastrointestinal tract cancers.

Circulating miR-16 and miR-21 Levels in Multiple Myeloma: Prognostic Significance of Survival and Response to Lenalidomide Treatment.

MicroRNAs (miRNAs), particularly miR-16 and miR-21, play a crucial role in multiple myeloma (MM) pathogenesis by regulating gene expression. This study evaluated the prognostic significance of circulating miR-16 and miR-21 expression levels in 48 patients with MM at diagnosis treated with lenalidomide-dexamethasone (LD) compared with 15 healthy individuals (HI). All patients were treated with LD, 13 at first line and 35 at relapse, of whom 21 were tested twice at diagnosis and before LD initiation. The results revealed significantly lower levels of miR-16 and miR-21 in patients than in HIs, both at diagnosis and relapse, with decreased miR-16 levels at diagnosis, indicating improved overall survival (OS) (p value 0.024). Furthermore, miR-16 and miR-21 levels were associated with disease markers, while both correlated with the depth of response and mir-16 with sustained response to LD treatment. Ratios of both miR-16 and miR-21 expression levels (prior to LD treatment/diagnosis) below two predicted a shorter time to response (p = 0.027) and a longer time to next treatment (p = 0.042), respectively. These findings suggested a prognostic value for serum miR-16 and miR-21 levels in MM, as their expression levels correlated with disease variables and treatment outcomes.

Transcriptome and anatomical analysis of Stipa breviflora in response to different grazing intensities in desert steppe.

Stipa breviflora is a dominant species in the desert steppe of Northern China. Grazing is the main land use pattern of grassland, which could cause a variety of adaptive evolutionary mechanisms in plant community composition as well as individual plant growth and morphological characteristics. However, very little is known about the morphological structure and transcriptional regulation response to different grazing intensities in S. breviflora. In this study, transcriptome and anatomical analyses of S. breviflora under different grazing intensities, including no grazing, moderate grazing, and heavy grazing, were performed. The anatomical analysis results showed that epidermis cells and xylems significantly thicken with grazing intensity, suggesting that grazing results in increasing lignification. Furthermore, the components of cell walls such as lignin, cellulose, hemicellulose, and pectin were all increased dramatically and significantly under both moderate and heavy grazing. Transcriptome analysis showed that the differentially expressed genes related to different grazing intensities were also engaged in plant cell wall formation and in photosynthesis and respiration. In addition, the activities of ATP synthase and Rubisco-activating enzyme increased significantly with enhanced grazing intensity and differed significantly between moderate and heavy grazing intensities. The trends in transcriptome and plant phenotype changes are consistent. Taken together, these results indicated that S. breviflora has evolved a grazing tolerance strategy under long-term grazing conditions, influencing photosynthesis and respiration in terms of its own structure and enzyme activities in the body, to maintain normal life activities under different grazing conditions.

hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors.

Hybridization, the process of crossing individuals from diverse genetic backgrounds, plays a pivotal role in evolution, biological invasiveness, and crop breeding. At the transcriptional level, hybridization often leads to complex nonadditive effects, presenting challenges for understanding its consequences. Although standard transcriptomic analyses exist to compare hybrids to their progenitors, such analyses have not been implemented in a software package, hindering reproducibility. We introduce hybridexpress, an R/Bioconductor package designed to facilitate the analysis, visualization, and comparison of gene expression patterns in hybrid triplets (hybrids and their progenitors). hybridexpress provides users with a user-friendly and comprehensive workflow that includes all standard comparative analyses steps, including data normalization, calculation of midparent expression values, sample clustering, expression-based gene classification into categories and classes, and overrepresentation analysis for functional terms. We illustrate the utility of hybridexpress through comparative transcriptomic analyses of cotton allopolyploidization and rice root trait heterosis. hybridexpress is designed to streamline comparative transcriptomic studies of hybrid triplets, advancing our understanding of evolutionary dynamics in allopolyploids, and enhancing plant breeding strategies. hybridexpress is freely accessible from Bioconductor (https://bioconductor.org/packages/HybridExpress) and its source code is available on GitHub (https://github.com/almeidasilvaf/HybridExpress).

Expression responses of XTH genes in tomato and potato to environmental mechanical forces: focus on behavior in response to rainfall, wind and touch.

Rainfall, wind and touch, as mechanical forces, were mimicked on 6-week-old soil-grown tomato and potato under controlled conditions. Expression level changes of xyloglucan endotransglucosylase/hydrolase genes (XTHs) of tomato (Solanum lycopersicum L. cv. Micro Tom; SlXTHs) and potato (Solanum tuberosum L. cv. Desirée; StXTHs) were analyzed in response to these mechanical forces. Transcription intensity of every SlXTHs of tomato was altered in response to rainfall, while the expression intensity of 72% and 64% of SlXTHs was modified by wind and touch, respectively. Ninety-one percent of StXTHs (32 out of 35) in potato responded to the rainfall, while 49% and 66% of the StXTHs were responsive to the wind and touch treatments, respectively. As previously demonstrated, all StXTHs were responsive to ultrasound treatment, and all were sensitive to one or more of the environmental mechanical factors examined in the current study. To our best knowledge, this is the first study to demonstrate that these ubiquitous mechanical environmental cues, such as rainfall, wind and touch, influence the transcription of most XTHs examined in both species.