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PubMed2025

A comparative genomic analysis of left- and right-sided colon cancer using real-world data from the AACR project GENIE BPC dataset.

Left- and Right-sided colon cancers (LCC and RCC) are increasingly recognized as distinct clinicopathological and molecular subtypes with divergent prognoses and therapeutic responses. Leveraging a large, multi-institutional cohort from the AACR Project Genomics Evidence Neoplasia Information Exchange (GENIE) Biopharma Collaborative (BPC) (n = 750; LCC: 363 vs. RCC: 387), we conducted a comprehensive analysis of mutational profiles, tumor mutation burden (TMB), and survival outcomes. Our findings revealed a markedly higher TMB in RCC compared to LCC (6.65 ± 11.3 vs. 3.17 ± 4.35; adjusted P = 3.12×10-32), suggesting greater genomic instability in RCC. After applying functional annotation filters (PolyPhen > 0.85, SIFT < 0.05), RCC tumors were significantly enriched for mutations in BRAF (23.1% vs. 6.7%), KMT2D (8.6% vs. 3.2%), and SMAD4 (13.1% vs. 7.3%), while TP53 mutations predominated in LCC (40.6% vs. 31.8%). Multivariate Cox regression analysis identified RCC as an independent predictor of poorer overall survival (OS) relative to LCC (HR: 1.30, 95% CI: 1.02-1.66, P = 0.033). Notably, KRAS mutations were associated with significantly worse OS in LCC (HR: 1.68, 95% CI: 1.06-2.70, P = 0.027), while BRAF mutations predicted adverse outcomes in RCC (HR: 1.58, 95% CI: 1.05-2.37, P = 0.028). These results underscore the prognostic value of tumor sidedness and specific genetic alterations in colon adenocarcinoma. Our study highlights the need for sidedness-specific molecular profiling to inform precision oncology strategies in colon cancer management.

BRAF↗

PubMedDate not supplied

[Perinatal mortality in Spain. The need of an epidemiologic approach].

Autonomovi Communities perinatal mortality evolution in Spain from 1975 to 1983 is studied aimed at the assessment of existing inequalities in our country concerning this important public health problem. Although a positive evolution has been reported in all of them, differences in their mortality figures have rosen, showing higher rates those communities ranking lower socioeconomic indicators. Epidemiological analysis is needed so as to planning health activities as well as to study social processes responsible for this problems. Embodiment of social services into existing medical services is proposed, especially in Communities where the "sociodemographic disadvantage" is an essential problem. An optimum action in public health throughout the perinatal period world require a comprehensive analysis of the health situation assessing the problems which produce a greater number of survivors with serious sequalae as a result of a lower mortality.

Humans↗

PubMed2026

Relationship between menopausal hormone therapy and incidence risk of breast cancer: systematic review and meta-analysis.

BACKGROUND: Menopausal hormone therapy (MHT) is widely prescribed for alleviating menopausal symptoms. Prior studies have mainly focused on individual hormone therapy formulations. This meta-analysis comprehensively synthesized evidence across various regimens to systematically evaluate the association between MHT and breast cancer risk. MATERIALS AND METHODS: We systematically searched CNKI, Wanfang, PubMed, and Web of Science from inception through August 2024. Eligible studies examining breast cancer risk following MHT were independently screened and assessed by two reviewers. The review and meta-analysis followed PRISMA guidelines. RESULTS: Thirty-four studies were included. The random-effects model showed a significant but heterogeneous overall association (OR = 1.15, 95% CI: 1.09-1.22; I² = 92.4%). Subgroup analysis identified hormone type, use status, and region as key determinants (P for interaction < 0.001). Stratification by hormone type resolved much of the heterogeneity, revealing risk confined to estrogen-progestin therapy (EPT; OR = 1.44, 95% CI: 1.26-1.64), while estrogen-only therapy (ET) showed no overall association (OR = 1.00, 95% CI: 0.91-1.10). Study type, region, and sample size were significant effect modifiers. For ET, randomized controlled trials demonstrated a protective effect (OR = 0.78, 95% CI: 0.70-0.87), contrasting with neutral findings from observational studies. CONCLUSIONS: MHT is associated with a modest but significant increase in breast cancer risk, primarily driven by EPT. This risk was not observed with ET in observational studies, though trials suggested a protective effect. Crucially, the association shows marked geographical heterogeneity, indicating risk is modified by regimen and regional factors.

Humans↗

PubMed2026

Circle-seq analysis reveals the involvement of eccDNAs in salt stress response of bermudagrass (Cynodon dactylon).

Extrachromosomal circular DNAs (eccDNAs) have been identified in a wide variety of plant species and play a pivotal role in genomic plasticity, emerging as key drivers of stress adaptation. However, the putative roles of eccDNAs under environmental stress remain largely unexplored in plants. As a high-quality turfgrass, bermudagrass (Cynodon dactylon L.) is a pivotal species for the reclamation and improvement of saline-alkali soils. Therefore, we performed a comprehensive analysis of the eccDNA profiles in bermudagrass under salt stress. A total of 1,068 eccDNAs were identified across all chromosomes. These eccDNAs were characterized by short lengths (ranging from 100 bp to 1 kb) and low GC content. Their genomic distribution was not entirely random but rather exhibited a certain preference for intergenic regions and coding sequences (CDS). Crucially, null model analysis of A/T-rich junction sites revealed that these eccDNAs primarily originate from physically unstable scaffold/matrix attachment regions (S/MARs) via stochastic fragmentation, followed by opportunistic circularization predominantly mediated by the non-homologous end joining (NHEJ) pathway. Notably, salt stress specifically enriched eccDNAs derived from DNA transposons, including the Tc1/Mariner, CACTA and MITE superfamilies. Overall, our findings reveal complex extrachromosomal structural dynamics in bermudagrass, offering novel insights into its genomic adaptation under environmental stress.

Cynodon↗

PubMed1989

Analysis of consecutive pseudo-first-order reactions. II: Calculation of the rate constants from the co-product or co-reactant data.

The co-product or co-reactant data for a two-step pseudo-first-order consecutive reaction gives unique shape profiles for the natural logarithm of the concentration versus time plots, based on the ratio of two rate constants (k2/k1), for theoretical data without error. But, in the presence of a +/- 2.0% random error in the simulated data, the ability to distinguish between different shapes disappears. A comprehensive analysis shows that accurate rate constants can be obtained only in a limited range of k2/k1 ratios. Reliable rate constants can be obtained when k2/k1 less than 0.5. Two special cases, k1 approximately 2k2 and k2 much greater than k1, cannot be distinguished from each other and could lead to erroneous conclusions if additional information is not used to identify the correct ratio. When k2/k1 greater than 0.5, the calculated parameters are extremely sensitive to experimental errors, and other techniques involving the concentrations of starting material and intermediate should be used to obtain the rate constants.

Chemistry, Pharmaceutical↗

PubMed2026

Proteomic analysis of ammonia-induced stress in Chinese hamster ovary (CHO) cell cultures.

Ammonia (NH₃) and its ionic form ammonium (NH₄+) are both metabolic waste products and essential nitrogen sources within Chinese hamster ovary (CHO) cell cultures. Although necessary for amino acid synthesis, excessive accumulation in the extracellular environment can exert stress, reducing cell proliferation and impairing the efficiency of recombinant protein production. Proper endoplasmic reticulum (ER) function is critical for CHO cells as biotherapeutic producers. Previous work has linked elevated ammonia concentrations to reduced productivity via altered N-glycosylation pathways, but its broader effects on ER biology remain unclear. In this study, we applied high-resolution mass spectrometry to perform a comprehensive analysis of changes in the ER proteome in CHO cells exposed to two ammonia concentrations, 10 mM and 30 mM, 48 and 120 h after supplementation. Both conditions suppressed cell growth and reduced product titre; however, the 10 mM supplementation resulted in a minor increase in specific cell productivity. Gene Ontology analysis revealed that ammonia strongly affected the tricarboxylic acid cycle, as well as key metabolic, catabolic and biogenetic processes. Several ER membrane proteins, including HMGCR and PREB, were consistently downregulated. In extended cultures, transmembrane proteins linked to Golgi-transport were upregulated, while vesicle transport associated proteins were downregulated, indicating altered intracellular trafficking. SIGNIFICANCE: This study provides a novel perspective on CHO cell biology under environmental stress by investigating the impact of ammonia accumulation in culture. Despite its presence in CHO culture, ammonia has been relatively under-investigated, compared to other culture conditions. Using high-throughput mass spectrometry for comprehensive proteomic profiling, we characterise the cellular response to ammonia build-up with a level of depth not previously applied to the study of this biological stressor. By specifically analysing proteins localised to the ER, we identify candidate pathways and molecular mechanisms that contribute to reduced CHO cell growth and productivity, offering insights directly relevant to industrial bioprocessing conditions. The link between ammonia concentration and a decrease in productivity has previously been linked to genes involved in N-glycosylation of the recombinant biotherapeutic, but the full extent of ammonia stress on ER function has not yet been investigated. These methods were applied to two IgG producing CHO cell lines to allow for comparison of cell line specific stress adaptations, as well as comparing the short- and long-term effects of excess ammonia.

Proteomics↗

PubMed2025

The landscape of structural variation in pediatric cancer.

Structural variants (SVs) account for over 60% of the driver variants in pediatric cancer, and in many cases act as the cancer initiating event. To study SVs from a pan-cancer perspective, we analyzed 1,616 pediatric cancer genomes in 16 major cancer types of hematological malignancies (n = 908), brain tumors (n = 183), and solid tumors (n = 525) and compared their profiles to those of 2,203 adult cancers. The SV burden varied ~100-fold across pediatric cancer types and demonstrated an 8- to 16-fold reduction compared to adult brain and solid tumors but was comparable in pediatric versus adult hematological malignancies. Recurrent SV hotspots occurred uniquely in pediatric acute lymphoblastic leukemias (ALLs) in proximity to RAG-mediated recombination signal sequences (RSS) and disrupted multiple immune-related loci as well as 69 genes, which often involved cryptic RSS sites. By contrast, such hotspots affected only immune-related loci but not driver genes in adult lymphoid cancers. Eight SV signatures extracted from the cohort had varying distributions across cancer types, with clustered translocations reflecting templated insertions in osteosarcoma, and medium-sized deletions (10 kb to 1 Mb) enriched in cancers with RAG-mediated deletions. Intra-patient evolutionary analysis in 13 patients with multiple spatiotemporally distinct samples revealed that RAG-mediated recombination in leukemia and complex rearrangements in solid tumors occurred both early in disease initiation and continuously during later diversification, contributing to clonal heterogeneity. Finally, we found that both driver genes and fragile sites were the two genomic regions most frequently disrupted by SVs. The unique and diverse SV landscapes that emerged from this comprehensive analysis expand the scope of RSS-mediated mutagenesis in pediatric ALL and will be a valuable resource for guiding future functional studies and the design of clinical genomic testing in pediatric cancer.

Journal Article↗

PubMed1990

Cementless total joint arthroplasty prostheses with titanium-alloy articular surfaces. A human retrieval analysis.

Surgical implants of titanium alloy (Ti-6Al-4V) have been found to be susceptible to abrasive wear, resulting in the well-known phenomenon of metallosis. In the presence of the acrylic debris generated by loose joint arthroplasty prostheses, this abrasive wear is greatly increased. However, the bone loss seen in these cases has generally been presumed to be due to the osteolytic effects of particulate acrylic, not the alloy debris, which has generally been assumed to be biocompatible. To examine the in vivo effects of titanium-alloy wear without the added presence of acrylic debris, a comprehensive analysis was made of cementless human joint arthroplasty prostheses with Ti-6Al-4V alloy surfaces articulating on ultra-high molecular weight polyethylene (UHMWPE). Specimens, including the prostheses, synovium, pseudocapsule and additional soft tissues, and periarticular bone, were retrieved from 22 hips and two knees. Specimens were examined by histologic techniques, energy-dispersive X-ray analysis, and electron microscopy. Serial sections of the implants were evaluated for tissue ingrowth. Tissues surrounding all joints implanted more than one year showed some degree of discoloration indicative of metallosis, whereas after two years the synovium was hypertrophic and villiform. Histologic evaluation showed good fixation by bony ingrowth in the vast majority of cases, although location and extent of ingrowth was dependent on numerous factors. Viability of ingrowth bone was established by fluorochrome labeling. However, despite good biologic fixation, cavitary osteolysis of the bone surrounding the implants was frequently identified. These lesions were filled with sheets of aggressive macrophages within a matrix of fibrous tissue and necrotic debris. Under polarized light the macrophages were found to be filled with alloy and polyethylene fragments of a characteristic size. Osteoblast-mediated remodeling of bone was infrequently observed. Instead, the bone was resorbed along a front in contact with the granulomatous tissues filling the cystic lesions. Visible burnishing was observed on every articular surface, with a linear relationship between wear and time implanted. By one year the surfaces were covered with a characteristic "scratch and gouge" pattern, similar on all sizes of femoral heads as well as the total knee prostheses. This study demonstrates that the combination of Ti-6Al-4V alloy and UHMWPE, when used as a bearing surface combination in total joint arthroplasty prostheses, results in excessive wear of both metal and polymer.(ABSTRACT TRUNCATED AT 400 WORDS)

Adolescent↗

PubMed2025

Host clustering of Campylobacter species and enteric pathogens in a longitudinal cohort of infants, family members and livestock in rural Eastern Ethiopia.

BACKGROUND: Livestock are recognized as major reservoirs for Campylobacter species and other enteric pathogens, posing infection risks to humans. High prevalence of Campylobacter during early childhood has been linked to environmental enteric dysfunction and stunting, particularly in low-resource settings. METHODS: A total of 280 samples from Campylobacter positive households with complete metadata were analyzed by shotgun metagenomic sequencing followed by bioinformatic analysis via the CZ-ID metagenomic pipeline (Illumina mNGS Pipeline v7.1). Further statistical analyses in JMP PRO 16 explored the microbiome, emphasizing Campylobacter and other enteric pathogens. Two-way hierarchical clustering and split k-mer analysis examined host structuring, patterns of co-infections and genetic relationships. Principal component analysis was used to characterize microbiome composition across the seven sample types. RESULTS: The study identified that microbiome composition was strongly host-driven, with more than 3844 genera detected, and two principal components explaining 62% of the total variation. Twenty-one dominant (based on relative abundance) Campylobacter species showed distinct clustering patterns for humans, ruminants, and broad hosts. The broad-host cluster included the most prevalent species, C. jejuni, C. concisus, and C. coli, present across sample types and a sub-cluster within C. jejuni involving humans, chickens, and ruminants. Campylobacter species from chickens showed strong positive correlations with mothers (r = 0.76), siblings (r = 0.61) and infants (r = 0.54), while co-occurrence analysis found a higher likelihood (Pr > 0.5) of pairs such as C. jejuni with C. coli, C. concisus, and C. showae. Analysis of the top 50 most abundant microbial taxa showed a distinct cluster uniquely present in human stool and absent in all livestock. The study also found frequent co-occurrence of C. jejuni with other enteric pathogens such as Salmonella, and Shigella, particularly in human and chicken. Additionally, instances of Candidatus Campylobacter infans (C. infans) were identified co-occurring with Salmonella and Shigella species in stool samples from infants, mothers, and siblings. CONCLUSIONS: A comprehensive analysis of Campylobacter diversity in humans and livestock in a low-resource setting revealed that infants can be exposed to multiple Campylobacter species early in life. C. jejuni is the dominant species with a propensity for co-occurrence with other notable enteric bacterial pathogens, including Salmonella, and Shigella, especially among infants. Video Abstract.

Animals↗

PubMed1988

[Near heterophoria with a description of the heterometer].

The examination of near heterophoria with a heterometer using a large series of test plates presented "free-sighted" (i.e., not hindered by optical or mechanical means) enables a more comprehensive analysis to be made than has so far been achieved with other instruments. The principal components of the instruments are an angle mirror and various test panels. The selection of test panels currently available should be developed further. However, comparison with other instruments for examining near heterophoria justifies the conclusion that heterophoria or nearsightedness due to errors of refraction can be determined more easily with this instrument and hence treated more appropriately. Results of examination with the heterometer, combined with exhaustive application of comprehensive analytical test procedures, will probably help to extend our knowledge of the control sequence of binocular coordination in near vision. The instrument has already proved its value not only in orthoptic departments, clinics, and ophthalmologists' offices, but also for determining refractive indices and for screening. It can therefore be recommended for the diagnosis of near heterophoria.

Convergence, Ocular↗

PubMed1990

Mean interconversion times and distribution rate parameters for drugs undergoing reversible metabolism.

The mean interconversion time and recycling numbers are introduced as intrinsic metabolic interconversion and distribution parameters for drugs undergoing linear reversible metabolism. Equations for these parameters, the distribution clearance, and the mean transit time in the central and peripheral compartments are derived for a metabolic pair where interconversion and elimination occur in central compartments. These parameters can be calculated from plasma concentration versus time slopes and intercepts, AUC, and AUMC data of parent drug and its metabolite partner following iv administration of each compound. The mean time analysis is illustrated with disposition data obtained previously for methylprednisolone and methylprednisone in the rabbit. Examination of mean times and additional properties of the system reveals that total exposure time of methylprednisolone is weakly influenced by the metabolic interconversion process, whereas the total exposure time of methylprednisone is strongly influenced by the process. In addition, the tissue distribution process moderately influence the total exposure times of both compounds. The derived mean time parameters, along with previously evolved equations for clearances, volumes of distribution, moments, and mean residence times allow comprehensive analysis of linear, multicompartmental reversible metabolic systems.

Animals↗

PubMed1990

Tissue distribution and quantitation of the mRNAs for three rat tachykinin receptors.

The family of mammalian tachykinin receptors consists of substance P receptor (SPR), neuromedin K receptor (NKR) and substance K receptor (SKR). In this investigation, tissue and regional distributions of the mRNAs for the three rat tachykinin receptors were investigated by blot-hybridization and RNase-protection analyses using the previously cloned receptor cDNAs. SPR mRNA is widely distributed in both the nervous system and peripheral tissues and is expressed abundantly in the hypothalamus and olfactory bulb, as well as in the urinary bladder, salivary glands and small and large intestines. In contrast, NKR mRNA is predominantly expressed in the nervous system, particularly in the cortex, hypothalamus and cerebellum, whereas SKR mRNA expression is restricted to the peripheral tissues, being abundant in the urinary bladder, large intestine, stomach and adrenal gland. Thus, the mRNAs for the three tachykinin receptors show distinct patterns of expression between the nervous system and peripheral tissues. Blot-hybridization analysis in combination with S1 nuclease protection and primer-extension analyses revealed that there are two large forms of SKR mRNA expressed commonly in the peripheral tissues, and two additional small forms of the mRNA expressed specifically in the adrenal gland and eye. These analyses also showed that the multiple forms of SKR mRNA differ in the lengths of the 5' mRNA portions, and that the two small forms of the mRNA, if translated, encode a truncated SKR polypeptide lacking the first two transmembrane domains. This investigation thus provides the comprehensive analysis of the distribution and mode of expression of the mRNAs for the multiple peptide receptors and offers a new basis on which to interpret the diverse functions of multiple tachykinin peptides in the CNS and peripheral tissues.

Animals↗

PubMed2025

Whole genome sequence analysis of low-density lipoprotein cholesterol across 246 K individuals.

BACKGROUND: Rare genetic variation provided by whole genome sequence datasets has been relatively less explored for its contributions to human traits. Meta-analysis of sequencing data offers advantages by integrating larger sample sizes from diverse cohorts, thereby increasing the likelihood of discovering novel insights into complex traits. Furthermore, emerging methods in genome-wide rare variant association testing further improve power and interpretability. RESULTS: Here, we conduct the largest meta-analysis of whole genome sequencing for low-density lipoprotein cholesterol (LDL-C), a therapeutic target for coronary artery disease, analyzing data from 246 K participants and integrating 1.23B variants from the UK Biobank and the Trans-Omics for Precision Medicine (TOPMed) program. We identify numerous rare coding and non-coding gene associations related to LDL-C, with replication across 86 K participants in All of Us. Our findings are based on single-variant analyses, rare coding and non-coding variant aggregation tests, and sliding window approaches. Through this comprehensive analysis, we identify 704 novel single-variant associations, 25 novel rare coding variant aggregates, 28 novel rare non-coding variant aggregates, and one novel sliding window aggregate. CONCLUSIONS: This study provides a meta-analysis framework for large-scale whole genome sequence association analyses from diverse population groups, yielding novel rare non-coding variant associations.

Humans↗

PubMed1991

Characterization of ligand-binding properties and selectivities of three rat tachykinin receptors by transfection and functional expression of their cloned cDNAs in mammalian cells.

We investigated the ligand-binding properties and selectivities of rat substance P, substance K and neuromedin K receptors by transfection and functional expressions of the cDNAs for these receptor subtypes in monkey kidney COS cells. Selective radioligand binding analysis of both substance P and substance K receptors revealed the presence of high-affinity and low-affinity components which are governed primarily by the difference in rates of dissociation of the ligand-receptor complex. The two affinity components were interconvertible by the presence and absence of a guanine nucleotide, suggesting the involvement of a G protein in the two affinity states. The ligand bindings of the three receptors were inhibited in different potencies by naturally occurring tachykinins and a series of carboxyl-terminal fragments containing a common tachykinin sequence, and this comprehensive analysis indicated that a high and selective affinity of each of the tachykinin receptors is governed by interaction with several key amino acids under recognition of the fundamental core sequence of the tachykinin peptides. The potencies and selectivities of several synthetic agonists and an antagonist for the three receptors were also examined, and senktide was found to be a highly selective and potent agonist for neuromedin K receptor. This investigation thus indicates the detailed properties and binding selectivities characteristic of the three tachykinin receptors and also the usefulness of this receptor expression system for examination and development of a new receptor agonist or antagonist.

Animals↗

PubMedDate not supplied

[Quantitative analysis of individual RNA in preparations of poly(A)+-RNA mammalian cells].

A new method of simultaneous analysis of the relative abundance of the most abundant individual mRNA's in poly(A)(+)-RNA preparations is described. The method is based on the synthesis of short (10-20 nucleotides) cDNA products by reverse transcription of poly(A)(+)-RNA primed with 5'-labeled oligonucleotides of 9 nucleotide lengths. Three natural nucleotides and one terminator nucleotide are used as substrates for reverse transcriptase. The numbers, lengths and sequence of the oligonucleotides used as primers were chosen to provide more than a 90% probability that synthesis would be initiated from any individual RNA present in the poly(A)(+)-RNA, thus assuring comprehensive analysis of RNA with abundance higher than 0.01%. Each primer produces about 20-60 bands per track following polyacrylamide electrophoresis under denaturing conditions. A full set of 30 oligonucleotides used to analyze a poly(A)(+)-RNA preparation produces an electrophoretic pattern with information capacity similar to that obtained from high resolution 2-dimensional electrophoresis of protein. Using this method we show that the patterns of poly(A)(+)-RNA differ from tissue to tissue, from normal tissues to neoplastic tissue (human myoma of uterus) and during differentiation of a F9 embryonic carcinoma cell line.

Base Sequence↗

PubMed2025

Rehabilomics Strategies Enabled by Cloud-Based Rehabilitation: Scoping Review.

BACKGROUND: Rehabilomics, or the integration of rehabilitation with genomics, proteomics, metabolomics, and other "-omics" fields, aims to promote personalized approaches to rehabilitation care. Cloud-based rehabilitation offers streamlined patient data management and sharing and could potentially play a significant role in advancing rehabilomics research. This study explored the current status and potential benefits of implementing rehabilomics strategies through cloud-based rehabilitation. OBJECTIVE: This scoping review aimed to investigate the implementation of rehabilomics strategies through cloud-based rehabilitation and summarize the current state of knowledge within the research domain. This analysis aims to understand the impact of cloud platforms on the field of rehabilomics and provide insights into future research directions. METHODS: In this scoping review, we systematically searched major academic databases, including CINAHL, Embase, Google Scholar, PubMed, MEDLINE, ScienceDirect, Scopus, and Web of Science to identify relevant studies and apply predefined inclusion criteria to select appropriate studies. Subsequently, we analyzed 28 selected papers to identify trends and insights regarding cloud-based rehabilitation and rehabilomics within this study's landscape. RESULTS: This study reports the various applications and outcomes of implementing rehabilomics strategies through cloud-based rehabilitation. In particular, a comprehensive analysis was conducted on 28 studies, including 16 (57%) focused on personalized rehabilitation and 12 (43%) on data security and privacy. The distribution of articles among the 28 studies based on specific keywords included 3 (11%) on the cloud, 4 (14%) on platforms, 4 (14%) on hospitals and rehabilitation centers, 5 (18%) on telehealth, 5 (18%) on home and community, and 7 (25%) on disease and disability. Cloud platforms offer new possibilities for data sharing and collaboration in rehabilomics research, underpinning a patient-centered approach and enhancing the development of personalized therapeutic strategies. CONCLUSIONS: This scoping review highlights the potential significance of cloud-based rehabilomics strategies in the field of rehabilitation. The use of cloud platforms is expected to strengthen patient-centered data management and collaboration, contributing to the advancement of innovative strategies and therapeutic developments in rehabilomics.

Cloud Computing↗

PubMed2025

Large-scale analysis of MYB genes in Cucurbitaceae identifies a novel gene regulating plant height.

The MYB transcription factor (TF) family, which is involved in plant growth and development, is large and diverse. Previous studies on MYB family in Cucurbitaceae were mostly based on a single genome or focused on the R2R3 subfamily. Here, we analyzed 91 genomes of 11 Cucurbitaceae species and identified a total of 15 858 MYB genes. According to phylogenetic relationships, these genes were divided into 27 subgroups. The identified MYB genes were further classified into 121 MYB orthologous gene groups (OGGs), including 25 core, 57 softcore, 19 shell and 20 line-specific/cloud groups. Whole-genome duplication was the most common mechanism of MYB genes expansion. In core group, the higher proportions of MYB genes were found to be in the coexpression network constructed by the RNA-seq data. Through the comprehensive analysis including phylogeny and gene expression profile of cucumber MYB genes, as well as genetic variations in 103 cucumber germplasms, we identified a MYB gene CsRAX5, which may be related to cucumber plant height. We used gene editing technology to knockout and overexpress CsRAX5. In the knockout lines, Csrax5, the height was significantly increased compared with wild type (WT), whereas after overexpression the height of CsRAX5-OE plants was significantly decreased compared with WT. These results indicated that MYB gene CsRAX5 negatively regulated cucumber plant height. The large-scale analysis of MYB genes in Cucurbitaceae in this study provides insights for further investigating the evolution and function of MYB genes in Cucurbitaceae crops.

Journal Article↗

PubMed2024

Small noncoding RNAs and sperm nuclear basic proteins reflect the environmental impact on germ cells.

BACKGROUND: Molecular techniques can complement conventional spermiogram analyses to provide new information on the fertilizing potential of spermatozoa and to identify early alterations due to environmental pollution. METHODS: Here, we present a multilevel molecular profiling by small RNA sequencing and sperm nuclear basic protein analysis of male germ cells from 33 healthy young subjects residing in low and high-polluted areas. RESULTS: Although sperm motility and sperm concentration were comparable between samples from the two sites, those from the high-pollution area had a higher concentration of immature/immune cells, a lower protamine/histone ratio, a reduced ability of sperm nuclear basic proteins to protect DNA from oxidative damage, and an altered copper/zinc ratio in sperm. Sperm levels of 32 microRNAs involved in intraflagellar transport, oxidative stress response, and spermatogenesis were different between the two areas. In parallel, a decrease of Piwi-interacting RNA levels was observed in samples from the high-polluted area. CONCLUSIONS: This comprehensive analysis provides new insights into pollution-driven epigenetic alterations in sperm not detectable by spermiogram.

Male↗