Epitranscriptome insights into Riccia fluitans L. (Marchantiophyta) aquatic transition using nanopore direct RNA sequencing.

BACKGROUND: Riccia fluitans, an amphibious liverwort, exhibits a fascinating adaptation mechanism to transition between terrestrial and aquatic environments. Utilizing nanopore direct RNA sequencing, we try to capture the complex epitranscriptomic changes undergone in response to land-water transition. RESULTS: A significant finding is the identification of 45 differentially expressed genes (DEGs), with a split of 33 downregulated in terrestrial forms and 12 upregulated in aquatic forms, indicating a robust transcriptional response to environmental changes. Analysis of N6-methyladenosine (m6A) modifications revealed 173 m6A sites in aquatic and only 27 sites in the terrestrial forms, indicating a significant increase in methylation in the former, which could facilitate rapid adaptation to changing environments. The aquatic form showed a global elongation bias in poly(A) tails, which is associated with increased mRNA stability and efficient translation, enhancing the plant's resilience to water stress. Significant differences in polyadenylation signals were observed between the two forms, with nine transcripts showing notable changes in tail length, suggesting an adaptive mechanism to modulate mRNA stability and translational efficiency in response to environmental conditions. This differential methylation and polyadenylation underline a sophisticated layer of post-transcriptional regulation, enabling Riccia fluitans to fine-tune gene expression in response to its living conditions. CONCLUSIONS: These insights into transcriptome dynamics offer a deeper understanding of plant adaptation strategies at the molecular level, contributing to the broader knowledge of plant biology and evolution. These findings underscore the sophisticated post-transcriptional regulatory strategies Riccia fluitans employs to navigate the challenges of aquatic versus terrestrial living, highlighting the plant's dynamic adaptation to environmental stresses and its utility as a model for studying adaptation mechanisms in amphibious plants.

The research foundation for COVID-19 vaccine development.

The development of effective vaccines in <1 year to combat the spread of coronavirus disease 19 (COVID-19) is an example of particularly rapid progress in biomedicine. However, this was only made possible by decades of investment in scientific research. Many important research commentaries and reviews have been provided to describe the various contributions and scientific breakthroughs that led to the development of COVID-19 vaccines. In this work, we sought to complement those efforts by adding a systematic and quantitative study of the research foundations that led to these vaccines. Here, we analyzed citations from COVID-19 vaccine research articles to determine which scientific areas of study contributed the most to this research. Our findings revealed that coronavirus research was cited most often, and by a large margin. However, significant contributions were also seen from a diverse set of fields such as cancer, diabetes, and HIV/AIDS. In addition, we examined the publication history of the most prolific authors of COVID-19 vaccine research to determine their research expertise prior to the pandemic. Interestingly, although COVID-19 vaccine research relied most heavily on previous coronavirus work, we find that the most prolific authors on these publications most often had expertise in other areas including influenza, cancer, and HIV/AIDS. Finally, we used machine learning to identify and group together publications based on their major topic areas. This allowed us to elucidate the differences in citations between research areas. These findings highlight and quantify the relevance of prior research from a variety of scientific fields to the rapid development of a COVID-19 vaccine. This study also illustrates the importance of funding and sustaining a diverse research enterprise to facilitate a rapid response to future pandemics.

Revealing the transitory and local effect of zebularine on development and on proteome dynamics of Salix purpurea.

Introduction: DNA methylation plays major roles in the epigenetic regulation of gene expression, transposon and transcriptional silencing, and DNA repair, with implications in developmental processes and phenotypic plasticity. Relevantly for woody species, DNA methylation constitutes a regulative layer in cell wall dynamics associated with xylogenesis. The use of methyltransferase and/or demethylase inhibitors has been proven informative to shed light on the methylome dynamics behind the regulation of these processes. Methods: The present work employs the cytidine analog zebularine to inhibit DNA methyltransferases and induce DNA hypomethylation in Salix purpurea plantlets grown in vitro and in soil. An integrative approach was adopted to highlight the effects of zebularine on proteomic dynamics, revealing age-specific (3 weeks of in vitro culture and 1 month of growth in soil) and tissue-specific (stem and root) effects. Results and discussion: After 3 weeks of recovery from zebularine treatment, a decrease of 5-mC levels was observed in different genomic contexts in the roots of explants that were exposed to zebularine, whereas a functionally heterogeneous subset of protein entries was differentially accumulated in stem samples, including entries related to cell wall biosynthesis, tissue morphogenesis, and hormonal regulation. Significant proteomic remodeling was revealed in the development from in vitro to in-soil culture, but no significant changes in 5-mC levels were observed. The identification of tissue-specific proteomic hallmarks in combination with hypomethylating agents provides new insights into the role of DNA methylation and proteome in early plant development in willow species. Proteomic data are available via ProteomeXchange with identifier PXD045653. WGBS data are available under BioProject accession PRJNA889596.

The impact of thermomechanical and chemical treatment of waste Brewers' spent grain and soil biodegradation of sustainable Mater-Bi-Based biocomposites.

Due to the massive plastic pollution, development of sustainable and biodegradable polymer materials is crucial to reduce environmental burdens and support climate neutrality. Application of lignocellulosic wastes as fillers for polymer composites was broadly reported, but analysis of biodegradation behavior of resulting biocomposites was rarely examined. Herein, sustainable Mater-Bi-based biocomposites filled with thermomechanically- and chemically-modified brewers' spent grain (BSG) were prepared and subjected to 12-week soil burial test simulating their biodegradation in natural environment. BSG stabilizing effect on polymer matrix affected by the content of melanoidins and antioxidant phytochemicals, along with the impact of diisocyanate applied to strengthen the interfacial adhesion. Biocomposites showed 25-35 wt% mass loss over 12 weeks resulting from swelling of BSG filler and sample microcracking, which increased surface roughness by 247-448 %. The degree of decomposition was partially reduced by BSG modifications pointing to the stabilizing effect of melanoidins and phytochemicals, and enhanced interfacial adhesion. Soil burial-induced structural changes enhanced biocomposites' thermal stability determined by thermogravimetric analysis shifting decomposition onset by 14.4-32.0 °C due to the biodegradation of lower molecular weight starch macromolecules confirmed by differential scanning calorimetry. For unfilled Mater-Bi, it caused an average 32 % reduction in complex viscosity and storage modulus captured by oscillatory rheological measurements. Nonetheless, the inverse effect was noted for biocomposites where modulus increased even by one order of magnitude due to the swelling of BSG particles and amorphous phase decomposition. Presented results indicate that BSG promotes soil degradation of Mater-Bi and its rate can be engineered by biofiller treatment elaboration.

Mater-Bi/Brewers' Spent Grain Biocomposites-Novel Approach to Plant-Based Waste Filler Treatment by Highly Efficient Thermomechanical and Chemical Methods.

Thermoplastic starch (TPS) is a homogenous material prepared from native starch and water or other plasticizers subjected to mixing at a temperature exceeding starch gelatinization temperature. It shows major drawbacks like high moisture sensitivity, poor mechanical properties, and thermal stability. To overcome these drawbacks without significant cost increase, TPS could be blended with bio-based or biodegradable polymers and filled with plant-based fillers, beneficially waste-based, like brewers' spent grain (BSG), the main brewing by-product. Filler modifications are often required to enhance the compatibility of such composites. Herein, we investigated the impact of BSG thermomechanical and chemical treatments on the structure, physical, thermal, and rheological performance of Mater-Bi-based composites. Thermomechanical modifications enhanced matrix thermal stability under oxidative conditions delaying degradation onset by 33 °C. Moreover, BSG enhanced the crystallization of the polybutylene adipate terephthalate (PBAT) fraction of Mater-Bi, potentially improving mechanical properties and shortening processing time. BSG chemical treatment with isophorone diisocyanate improved the processing properties of the composites, expressed by a 33% rise in melt flow index. Depending on the waste filler's selected treatment, processing, and rheological performance, thermal stability or interfacial adhesion of composites could be enhanced. Moreover, the appearance of the final materials could be adjusted by filler selection.

Identification of Quantitative Trait Loci Conditioning the Main Biomass Yield Components and Resistance to Melampsora spp. in Salix viminalis × Salix schwerinii Hybrids.

The biomass of Salix viminalis is the most highly valued source of green energy, followed by S. schwerinii, S. dasyclados and other species. Significant variability in productivity and leaf rust resistance are noted both within and among willow species, which creates new opportunities for improving willow yield parameters through selection of desirable recombinants supported with molecular markers. The aim of this study was to identify quantitative trait loci (QTLs) linked with biomass yield-related traits and the resistance/susceptibility of Salix mapping population to leaf rust. The experimental material comprised a mapping population developed based on S. viminalis × S. schwerinii hybrids. Phenotyping was performed on plants grown in a field experiment that had a balanced incomplete block design with 10 replications. Based on a genetic map, 11 QTLs were identified for plant height, 9 for shoot diameter, 3 for number of shoots and 11 for resistance/susceptibility to leaf rust. The QTLs identified in our study explained 3%-16% of variability in the analyzed traits. Our findings make significant contributions to the development of willow breeding programs and research into shrubby willow crops grown for energy.

Variations in the chemical composition and content of salicylic glycosides in the bark of Salix purpurea from natural locations and their significance for breeding.

Willow bark is one of the few plant raw materials which contain natural active substances that have analgesic, fever-reducing, anti-inflammatory and anti-rheumatic effects. Salix purpurea, listed as widespread and common in many countries, belongs to the willow species with the highest content of salicylic compounds. The chemical composition and content of major salicylic glycosides (SGs) in the bark of S. purpurea genotypes from natural locations were investigated in this study to evaluate their applicability for pharmaceutical processing and creative breeding. Secondary metabolites were analyzed in bark extracts from 91 genotypes of S. purpurea selected from natural locations. The bark of all analyzed genotypes contained salicylic glycosides: salicin, salicortin and tremulacin; flavanones: naringenin 5-O-glucoside, naringenin 7-O-glucoside, naringenin, chalcone isosalipurposide and flavan-3-ol: catechin. Picein and populin were detected in 10% of the studied genotypes. The SG content of purple willow bark ranged from 3.04 to 10.96, pointing to high variations between S. purpurea genotypes. This study provides valuable breeding material and offers attractive prospects for the breeding of new and improved willow varieties. Varieties with the most desirable traits, grown under controlled conditions, can supply high-quality herbal materials for the pharmaceutical industry.

Genetic Diversity and Genetic Relationships of Purple Willow (Salix purpurea L.) from Natural Locations.

In this study, the genetic diversity and structure of 13 natural locations of Salix purpurea were determined with the use of AFLP (amplified length polymorphism), RAPD (randomly amplified polymorphic DNA) and ISSR (inter-simple sequence repeats). The genetic relationships between 91 examined S. purpurea genotypes were evaluated by analyses of molecular variance (AMOVA), principal coordinates analyses (PCoA) and UPGMA (unweighted pair group method with arithmetic mean) dendrograms for both single marker types and a combination of all marker systems. The locations were assigned to distinct regions and the analysis of AMOVA (analysis of molecular variance) revealed a high genetic diversity within locations. The genetic diversity between both regions and locations was relatively low, but typical for many woody plant species. The results noted for the analyzed marker types were generally comparable with few differences in the genetic relationships among S. purpurea locations. A combination of several marker systems could thus be ideally suited to understand genetic diversity patterns of the species. This study makes the first attempt to broaden our knowledge of the genetic parameters of the purple willow (S. purpurea) from natural location for research and several applications, inter alia breeding purposes.

Phylogenetic relationships between four Salix L. species based on DArT markers.

The objectives of this study were to evaluate the usefulness of DArT markers in genotypic identification of willow species and describe genetic relationships between four willow species: Salix viminalis, S. purpurea, S. alba and S. triandra. The experimental plant material comprised 53 willow genotypes of these four species, which are popularly grown in Poland. DArT markers seem to identify Salix species with a high degree of accuracy. As a result, the examined species were divided into four distinct groups which corresponded to the four analyzed species. In our study, we observed that S. triandra was very different genetically from the other species, including S. alba which is generally classified into the same subgenus of Salix. The above corroborates the findings of other authors who relied on molecular methods to reveal that the classification of S. triandra to the subgenus Salix was erroneous. The Principal Coordinate Analysis (PCoA) and the neighbor-joining dendrogram also confirmed the clear division of the studied willow genotypes into four clusters corresponding to individual species. This confirmed the usefulness of DArT markers in taxonomic analyses and identification of willow species.

Measuring the evolution and output of cross-disciplinary collaborations within the NCI Physical Sciences-Oncology Centers Network.

Development of effective quantitative indicators and methodologies to assess the outcomes of cross-disciplinary collaborative initiatives has the potential to improve scientific program management and scientific output. This article highlights an example of a prospective evaluation that has been developed to monitor and improve progress of the National Cancer Institute Physical Sciences-Oncology Centers (PS-OC) program. Study data, including collaboration information, was captured through progress reports and compiled using the web-based analytic database: Interdisciplinary Team Reporting, Analysis, and Query Resource. Analysis of collaborations was further supported by data from the Thomson Reuters Web of Science database, MEDLINE database, and a web-based survey. Integration of novel and standard data sources was augmented by the development of automated methods to mine investigator pre-award publications, assign investigator disciplines, and distinguish cross-disciplinary publication content. The results highlight increases in cross-disciplinary authorship collaborations from pre- to post-award years among the primary investigators and confirm that a majority of cross-disciplinary collaborations have resulted in publications with cross-disciplinary content that rank in the top third of their field. With these evaluation data, PS-OC Program officials have provided ongoing feedback to participating investigators to improve center productivity and thereby facilitate a more successful initiative. Future analysis will continue to expand these methods and metrics to adapt to new advances in research evaluation and changes in the program.

A characterization of the oral microbiome in allogeneic stem cell transplant patients.

BACKGROUND: The mouth is a complex biological structure inhabited by diverse bacterial communities. The purpose of this study is to describe the effects of allogeneic stem cell transplantation on the oral microbiota and to examine differences among those patients who acquired respiratory complications after transplantation. METHODOLOGY/PRINCIPAL FINDINGS: All patients were consented at the National Institutes of Health, Clinical Center. Bacterial DNA was analyzed from patients' oral specimens using the Human Oral Microbe Identification Microarray. The specimens were collected from four oral sites in 45 allogeneic transplantation patients. Specimens were collected at baseline prior to transplantation, after transplantation at the nadir of the neutrophil count and after myeloid engraftment. If respiratory signs and symptoms developed, additional specimens were obtained. Patients were followed for 100 days post transplantation. Eleven patients' specimens were subjected to further statistical analysis. Many common bacterial genera, such as Streptococcus, Veillonella, Gemella, Granulicatella and Camplyobacter were identified as being present before and after transplantation. Five of 11 patients developed respiratory complications following transplantation and there was preliminary evidence that the oral microbiome changed in their oral specimens. Cluster analysis and principal component analysis revealed this change in the oral microbiota. CONCLUSIONS/SIGNIFICANCE: After allogeneic transplantation, the oral bacterial community's response to a new immune system was not apparent and many of the most common core oral taxa remained unaffected. However, the oral microbiome was affected in patients who developed respiratory signs and symptoms after transplantation. The association related to the change in the oral microbiota and respiratory complications after transplantation will be validated by future studies using high throughput molecular methods.

Effects of systematic oral care in critically ill patients: a multicenter study.

BACKGROUND: No standard oral assessment tools are available for determining frequency of oral care in critical care patients, and the method of providing oral care is controversial. OBJECTIVES: To examine the effects of a systematic program of oral care on oral assessment scores in critically ill intubated and nonintubated, patients. METHODS: Clinical data were collected 3 times during critical care admissions before and after institution of a systematic program of oral care in 3 different medical centers. The oral care education program consisted of instruction from a dentist or dental hygienist and a clear procedure outlining systematic oral care. The Beck Oral Assessment Scale and the mucosal-plaque score were used to assess the oral cavity. Data were analyzed by using linear mixed modeling with controls for severity of illness. RESULTS: Scores on the Beck Scale differed significantly (F = 4.79, P = .01) in the pattern of scores across the 3 days and between the control group (before oral education) and the systematic oral care group. Unlike the control group, the treatment group had decreasing scores on the Beck Scale from day 1 to day 5. The mucosal-plaque score and the Beck Scale scores had strong correlations throughout the study; the highest correlation was on day 5 (r = 0.798, P < .001, n = 43). CONCLUSIONS: Oral assessment scores improved after nurses implemented a protocol for systematic oral care. Use of the Beck Scale and the mucosal-plaque score could standardize oral assessment and guide nurses in providing oral interventions.

The PDGF-C regulatory region SNP rs28999109 decreases promoter transcriptional activity and is associated with CL/P.

Human linkage and association studies suggest a gene(s) for nonsyndromic cleft lip with or without cleft palate (CL/P) on chromosome 4q31-q32 at or near the platelet-derived growth factor-C (PDGF-C) locus. The mouse Pdgfc(-/-) knockout shows that PDGF-C is essential for palatogenesis. To evaluate the role of PDGF-C in human clefting, we performed sequence analysis and SNP genotyping using 1048 multiplex CL/P families and 1000 case-control samples from multiple geographic origins. No coding region mutations were identified, but a novel -986 C>T SNP (rs28999109) was significantly associated with CL/P (P=0.01) in cases from Chinese families yielding evidence of linkage to 4q31-q32. Significant or near-significant association was also seen for this and several other PDGF-C SNPs in families from the United States, Spain, India, Turkey, China, and Colombia, whereas no association was seen in families from the Philippines, and Guatemala, and case-controls from Brazil. The -986T allele abolished six overlapping potential transcription regulatory motifs. Transfection assays of PDGF-C promoter reporter constructs show that the -986T allele is associated with a significant decrease (up to 80%) of PDGF-C gene promoter activity. This functional polymorphism acting on a susceptible genetic background may represent a component of human CL/P etiology.

[Evaluation of usefulness of different methods for detection of Cryptosporidium in human and animal stool samples]. / Ocena uzytecznosci metod wykrywania Cryptosporidium w kale ludzi i zwierzat.

There are many methods for detection of Cryptosporidium oocysts. Most of them (more than 20) enable the microscopic detection of Cryptosporidium oocysts in faecal smears. Such a great variability of diagnostic methods may lead to confusion as far as the choice of an appropriate technique by a given laboratory is concerned. This study evaluated the diagnostic usefulness of Cryptosporidium oocysts and coproantigen detection methods in the diagnosis of cryptosporidiosis in human (266 stool specimen) and animals (205 from cattle, 160 from sheep, 30 from horses, 80 from cats, 227 from dogs and 11 from wild animals). The total number of human and animal stool specimens processed was 266 and 713, respectively. In this study the usefulness of several diagnostic methods was compared. The following techniques were taken into account: wet mounts, hematoxylin staining, four different specific methods (modified Zeihl-Neelsen, Kinyoun's, safranin-methylene blue, as well as carbol-methyl violet and tartrazyne) and commercially available kit based on enzyme-linked immunoassay (ProspecT(r) Cryptosporidium Microplate Assay). The final number of positive specimens was 123. Out of them 77 were positive in all specific methods. The oocysts found in stool specimens were measured. Humans were infected with C. parvum and animals with C. parvum, C. andersoni or C. felis. The statistical analysis has shown that EIA test was a better than microscopy method for identification of Cryptosporidium in faecal samples in human and wild animal. Sensitivity and specificity are important factors for the choice of a proper diagnostic method for Cryptosporidium detection, however other factors such as cost, simplicity and ease of interpretation of results are also important considerations.