Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative chloroplast genome and transcriptome analysis on the ancient genus Isoetes from China

Isoetes is a famous living fossil that plays a significant role in the evolutionary studies of the plant kingdom. To explore the adaptive evolution of the ancient genus Isoetes from China, we focused on Isoetes yunguiensis (Q.F. Wang and W.C. Taylor), I. shangrilaensis (X. Li, Y.Q. Huang, X.K. Dai & X. Liu), I. taiwanensis (DeVol), I. sinensis (T.C. Palmer), I. hypsophila_GHC (Handel-Mazzetti), and I. hypsophila_HZS in this study. We sequenced, assembled, and annotated six individuals’ chloroplast genomes and transcriptomes, and performed a series of analyses to investigate their chloroplast genome structures, RNA editing events, and adaptive evolution. The six chloroplast genomes of Isoetes exhibited a typical quadripartite structure with conserved genome sequence and structure. Comparative analyses of Isoetes species demonstrated that the gene organization, genome size, and GC contents of the chloroplast genome are highly conserved across the genus. Besides, our positive selection analyses suggested that one positively selected gene was statistically supported in Isoetes chloroplast genomes using the likelihood ratio test (LRT) based on branch-site models. Moreover, we detected positive selection signals using transcriptome data, suggesting that nuclear-encoded genes involved in the adaption of Isoetes species to the extreme environment of the Qinghai-Tibetan Plateau (QTP). In addition, we identified 291–579 RNA editing sites in the chloroplast genomes of six Isoetes based on transcriptome data, well above the average of angiosperms. RNA editing in protein-coding transcripts results from amino acid changes to increase their hydrophobicity and conservation in Isoetes, which may help proteins form functional three-dimensional structure. Overall, the results of this study provide comprehensive transcriptome and chloroplast genome resources and contribute to a better understanding of adaptive evolutionary and molecular biology in Isoetes.
Adjusting CA19-9 values with clinical stage and bilirubin to better predict survival of resectable pancreatic cancer patients: 5-year-follow-up of a single center

Background Pancreatic cancer mortality is growing every year, and radical resection is the most essential therapy strategy. It is critical to evaluate the long-term prognosis of individuals receiving radical surgery. CA19-9 is a biomarker for patient recurrence and survival, however obstructive jaundice has a significant impact on this index. Researchers have attempted to modify the index using various modification methods, but the results have been unsatisfactory. In this study, we adjusted CA19-9 values based on clinical stage and bilirubin and found that it provided better prediction than CA19-9 alone in assessing patients. Methods We analyzed over 5 years follow-up records of patients who underwent radical pancreatic cancer surgery between August 2009 and May 2017 in a single center. We investigated the association of risk factors with overall survival (OS) as well as disease-free survival (DFS) after surgery. Threshold values for high-risk features associated with poor prognosis in resectable pancreatic cancer were determined. The hazard ratios of the indicators were eventually examined under the stratification of patients’ clinical stages. Results A total of 202 patients were involved in the study. The optimum cut-off values for CA19-9 and CA19-9/TB for predicting overall survival were 219.4 (p = 0.0075) and 18.8 (p = 0.0353), respectively. CA19-9>219.4 increased the risk of patient mortality by 1.70 times (95% CI 1.217-2.377, p = 0.002), and tumor poor differentiation raised the risk by 1.66 times (95% CI 1.083-2.553, P = 0.02). Based on clinical stage stratification, we found discrepancies in the predictive efficacy of CA19-9 and CA19-9/TB. CA19-9 was a better predictor in clinical stage 1 (HR = 2.056[CI 95%1.169-3.616], P = 0.012), whereas CA19-9/TB indications were better in stages 2 (HR = 1.650[CI 95%1.023-2.662], P = 0.040) and 3 (HR = 3.989[CI95%1.145-13.896], P = 0.030). Conclusions CA19-9, CEA, and tumor differentiation are predictors for patients with resectable PDAC. CA19-9 values can be adjusted based on clinical stage and bilirubin levels to better predict overall survival in patients with resectable PDAC. CA19-9>219.4 predicted poor survival in individuals in clinical stage 1, whereas CA19-9/TB>18.8 predicted poor survival for individuals in stages 2 and 3.
Development of an artificial synovial fluid useful for studying Staphylococcus epidermidis joint infections

Staphylococcus epidermidis is a major causative agent of prosthetic joint infections (PJI). The ability to form biofilms supports this highly selective pathogenic potential. In vitro studies essentially relying on phenotypic assays and genetic approaches have provided a detailed picture of the molecular events contributing to biofilm assembly. A major limitation in these studies is the use of synthetic growth media, which significantly differs from the environmental conditions S. epidermidis encounters during host invasion. Building on evidence showing that growth in serum substantially affects S. epidermidis gene expression profiles and phenotypes, the major aim of this study was to develop and characterize a growth medium mimicking synovial fluid, thereby facilitating research addressing specific aspects related to PJI. Using fresh human plasma, a protocol was established allowing for the large-scale production of a medium that by biochemical analysis matches key characteristics of synovial fluid and therefore is referred to as artificial synovial fluid (ASF). By analysis of biofilm-positive, polysaccharide intercellular adhesion (PIA)-producing S. epidermidis 1457 and its isogenic, PIA- and biofilm-negative mutant 1457-M10, evidence is provided that the presence of ASF induces cluster formation in S. epidermidis 1457 and mutant 1457-M10. Consistent with the aggregative properties, both strains formed multilayered biofilms when analyzed by confocal laser scanning microscopy. In parallel to the phenotypic findings, expression analysis after growth in ASF found upregulation of genes encoding for intercellular adhesins (icaA, aap, and embp) as well as atlE, encoding for the major cell wall autolysin being responsible for eDNA release. In contrast, growth in ASF was associated with reduced expression of the master regulator agr. Collectively, these results indicate that ASF induces expression profiles that are able to support intercellular adhesion in both PIA-positive and PIA-negative S. epidermidis. Given the observation that ASF overall induced biofilm formation in a collection of S. epidermidis isolates from PJI, the results strongly support the idea of using growth media mimicking host environments. ASF may play an important role in future studies related to the pathogenesis of S. epidermidis PJI.
The TAM receptor tyrosine kinases Axl and Mer drive the maintenance of highly phagocytic macrophages

Many apoptotic thymocytes are generated during the course of T cell selection in the thymus, yet the machinery through which these dead cells are recognized and phagocytically cleared is incompletely understood. We found that the TAM receptor tyrosine kinases Axl and Mer, which are co-expressed by a specialized set of phagocytic thymic macrophages, are essential components of this machinery. Mutant mice lacking Axl and Mer exhibited a marked accumulation of apoptotic cells during the time that autoreactive and nonreactive thymocytes normally die. Unexpectedly, these double mutants also displayed a profound deficit in the total number of highly phagocytic macrophages in the thymus, and concomitantly exhibited diminished expression of TIM-4, CD163, and other non-TAM phagocytic engulfment systems in the macrophages that remained. Importantly, these previously unrecognized deficits were not confined to the thymus, as they were also evident in the spleen and bone marrow. They had pleiotropic consequences for the double mutants, also previously unrecognized, which included dysregulation of hemoglobin turnover and iron metabolism leading to anemia.
Combined Toxicity Evaluation of Ochratoxin A and Aflatoxin B1 on Kidney and Liver Injury, Immune Inflammation, and Gut Microbiota Alteration Through Pair-Feeding Pullet Model

Ochratoxin A (OTA) and aflatoxin B1 (AFB1) are often co-contaminated, but their synergistic toxicity in poultry is limitedly described. Furthermore, the traditional ad libitum feeding model may fail to distinguish the specific impact of mycotoxins on the biomarkers and the indirect effect of mildew on the palatability of feed. A pair-feeding model was introduced to investigate the specific effect and the indirect effect of the combined toxicity of OTA and AFB1, which were independent and dependent on feed intake, respectively. A total of 180 one-day-old pullets were randomly divided into 3 groups with 6 replicates, and each replicate contained 10 chicks. The control group (Group A) and the pair-feeding group (Group B) received the basal diet without mycotoxin contamination. Group C was administrated with OTA- and AFB1-contaminated feed (101.41 μg/kg of OTA + 20.10 μg/kg of AFB1). The scale of feeding in Group B matched with the feed intake of Group C. The trial lasted 42 days. Compared with the control group, co-contamination of OTA and AFB1 in feed could adversely affect the growth performance (average daily feed intake (ADFI), body weight (BW), average daily weight gain (ADG), feed conversion ratio (FCR), and shank length (SL)), decrease the relative weight of the spleen (p < 0.01), and increase the relative weight of the kidney (p < 0.01). Moreover, the reduction of feed intake could also adversely affect the growth performance (BW, ADG, and SL), but not as severely as mycotoxins do. Apart from that, OTA and AFB1 also activated the antioxidative and inflammation reactions of chicks, increasing the level of catalase (CAT), reactive oxygen species (ROS), and interleukin-8 (IL-8) while decreasing the level of IL-10 (p < 0.01), which was weakly influenced by the feed intake reduction. In addition, OTA and AFB1 induced histopathological changes and apoptosis in the kidney and liver as well as stimulated the growth of pernicious bacteria to cause toxic effects. There were no histopathological changes and apoptosis in the kidney and liver of the pair-feeding group. The combined toxicity of OTA and AFB1 had more severe effects on pullets than merely reducing feed supply. However, the proper reduction of the feed intake could improve pullets’ physical health by enriching the bacteria Lactobacillus, Phascolarctobacterium, Bacteroides, Parabacteroides, and Barnesiella.
Management of neuropathic bladder secondary to spina bifida: Twenty years' experience with a conservative approach

Introduction Treatment of neuropathic bladder secondary to spina bifida is an ongoing challenge. Although different management strategies and protocols are available in the literature, reliance on expert opinion remains fundamental. A conservative approach can be utilized, but patients must be closely monitored throughout the management process. The objective of this study was to review the management and outcomes of neuropathic bladder in spina bifida by appraising long-term bladder and renal function in patients treated at a medical center utilizing a conservative management style. Methods This is a single-center retrospective review of urology care for all spina bifida patients 5–19 years of age with a neuropathic bladder who attended follow-ups between April 2000 and April 2020. Only patients with more than 5 years of follow-up were included. Renal functions, continence and results of invasive video urodynamics (IUD) and any surgical interventions were recorded. Results Seventy-one patients (mean age = 10.5 years) were identified after exclusions. Bladder compliance between first and last IUDs increased significantly (p = 0.0056). Anticholinergic treatment was started at the first outpatient appointment. Intravesical botulinum toxin injection was the second line treatment in ten patients. 94% of patients had an end fill pressure below 40 cm H2O in their last IUD. 82% were socially continent (dry or occasional damp patches) with or without catheterisations at the age of 11.5 years. One patient in the cohort had bladder augmentation. Conclusion The optimal management of neuropathic bladder secondary to spina bifida remains controversial. Bladder and renal functional outcomes can be improved with close monitoring and less invasive management.
A protocol for rapid construction of senescent cells

Aging may be the largest factor for a variety of chronic diseases that influence survival, independence, and wellbeing. Evidence suggests that aging could be thought of as the modifiable risk factor to delay or alleviate age-related conditions as a group by regulating essential aging mechanisms. One such mechanism is cellular senescence, which is a special form of most cells that are present as permanent cell cycle arrest, apoptosis resistance, expression of anti-proliferative molecules, acquisition of pro-inflammatory, senescence-associated secretory phenotype (SASP), and others. Most cells cultured in vitro or in vivo may undergo cellular senescence after accruing a set number of cell divisions or provoked by excessive endogenous and exogenous stress or damage. Senescent cells occur throughout life and play a vital role in various physiological and pathological processes such as embryogenesis, wound healing, host immunity, and tumor suppression. In contrast to the beneficial senescent processes, the accumulation of senescent also has deleterious effects. These non-proliferating cells lead to the decrease of regenerative potential or functions of tissues, inflammation, and other aging-associated diseases because of the change of tissue microenvironment with the acquisition of SASP. While it is understood that age-related diseases occur at the cellular level from the cellular senescence, the mechanisms of cellular senescence in age-related disease progression remain largely unknown. Simplified and rapid models such as in vitro models of the cellular senescence are critically needed to deconvolute mechanisms of age-related diseases. Here, we obtained replicative senescent L02 hepatocytes by culturing the cells for 20 weeks. Then, the conditioned medium containing supernatant from replicative senescent L02 hepatocytes was used to induce cellular senescence, which could rapidly induce hepatocytes into senescence. In addition, different methods were used to validate senescence, including senescence-associated β-galactosidase (SA-β-gal), the rate of DNA synthesis using 5-ethynyl-2′-deoxyuridine (EdU) incorporation assay, and senescence-related proteins. At last, we provide example results and discuss further applications of the protocol.
Editorial: Molecular interactions between crops and phytopathogens, volume II: Rice

COPYRIGHT © 2022 Li, Wang, Wang, Zhang, Chen, Wu, Gou and Ma. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Editorial: Molecular interactions between crops and phytopathogens, volume II: Rice
Linkage analysis and residual heterozygotes derived near isogenic lines reveals a novel protein quantitative trait loci from a Glycine soja accession

Modern soybean [Glycine max (L.) Merr] cultivars have low overall genetic variation due to repeated bottleneck events that arose during domestication and from selection strategies typical of many soybean breeding programs. In both public and private soybean breeding programs, the introgression of wild soybean (Glycine soja Siebold and Zucc.) alleles is a viable option to increase genetic diversity and identify new sources for traits of value. The objectives of our study were to examine the genetic architecture responsible for seed protein and oil using a recombinant inbred line (RIL) population derived from hybridizing a G. max line (‘Osage’) with a G. soja accession (PI 593983). Linkage mapping identified a total of seven significant quantitative trait loci on chromosomes 14 and 20 for seed protein and on chromosome 8 for seed oil with LOD scores ranging from 5.3 to 31.7 for seed protein content and from 9.8 to 25.9 for seed oil content. We analyzed 3,015 single F4:9 soybean plants to develop two residual heterozygotes derived near isogenic lines (RHD-NIL) populations by targeting nine SNP markers from genotype-by-sequencing, which corresponded to two novel quantitative trait loci (QTL) derived from G. soja: one for a novel seed oil QTL on chromosome 8 and another for a novel protein QTL on chromosome 14. Single marker analysis and linkage analysis using 50 RHD-NILs validated the chromosome 14 protein QTL, and whole genome sequencing of RHD-NILs allowed us to reduce the QTL interval from ∼16.5 to ∼4.6 Mbp. We identified two genomic regions based on recombination events which had significant increases of 0.65 and 0.72% in seed protein content without a significant decrease in seed oil content. A new Kompetitive allele-specific polymerase chain reaction (KASP) assay, which will be useful for introgression of this trait into modern elite G. max cultivars, was developed in one region. Within the significantly associated genomic regions, a total of eight genes are considered as candidate genes, based on the presence of gene annotations associated with the protein or amino acid metabolism/movement. Our results provide better insights into utilizing wild soybean as a source of genetic diversity for soybean cultivar improvement utilizing native traits.
Attitudes toward finitude in the cinema of Federico Fellini: Light on older adults

COPYRIGHT © 2022 Coelho-Junior and Marzetti. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Attitudes toward finitude in the cinema of Federico Fellini: Light on older adults
One or many? Multi-species livestock grazing influences soil microbiome community structure and antibiotic resistance potential

Soil health has been highlighted as a key dimension of regenerative agriculture, given its critical importance for food production, carbon sequestration, water filtration, and nutrient cycling. Microorganisms are critical components of soil health, as they are responsible for mediating 90% of soil functions. Multi-species rotational grazing (MSRG) is a promising strategy for maintaining and improving soil health, yet the potential effects of MSRG on soil microbiomes are poorly understood. To address this knowledge gap, we collected soil microbial samples at three timepoints during the 2020 grazing season for 12 total paddocks, which were equally split into four different grazing treatments—cattle only, sheep only, swine only, or multi-species. Shallow shotgun metagenomic sequencing was used to characterize soil microbial community taxonomy and antibiotic resistome. Results demonstrated broad microbial diversity in all paddock soil microbiomes. Samples collected early in the season tended to have greater archaeal and bacterial alpha diversity than samples collected later for all grazing treatments, while no effect was observed for fungi or viruses. Beta diversity, however, was strongly influenced by both grazing treatment and month for all microbial kingdoms, suggesting a pronounced effect of different livestock on microbial composition. Cattle-only and swine-only paddocks were more dissimilar from multi-species paddocks than those grazed by sheep. We identified a large number of differentially abundant taxa driving community dissimilarities, including Methanosarcina spp. , Candidatus Nitrocosmicus oleophilus, Streptomyces spp. , Pyricularia spp. , Fusarium spp. , and Tunggulvirus Pseudomonas virus ϕ-2. In addition, a wide variety of antibiotic resistance genes (ARGs) were present in all samples, regardless of grazing treatment; the majority of these encoded efflux pumps and antibiotic modification enzymes (e.g., transferases). This novel study demonstrates that grazing different species of livestock, either separately or together, can impact soil microbial community structure and antibiotic resistance capacity, though further research is needed to fully characterize these impacts. Increasing the knowledge base about soil microbial community structure and function under real-world grazing conditions will help to construct metrics that can be incorporated into traditional soil health tests and allow producers to manage livestock operations for optimal soil microbiomes.
Chromatin Dynamics in Digestive System Cancer: Commander and Regulator

Digestive system tumors have a poor prognosis due to complex anatomy, insidious onset, challenges in early diagnosis, and chemoresistance. Epidemiological statistics has verified that digestive system tumors rank first in tumor-related death. Although a great number of studies are devoted to the molecular biological mechanism, early diagnostic markers, and application of new targeted drugs in digestive system tumors, the therapeutic effect is still not satisfactory. Epigenomic alterations including histone modification and chromatin remodeling are present in human cancers and are now known to cooperate with genetic changes to drive the cancer phenotype. Chromatin is the carrier of genetic information and consists of DNA, histones, non-histone proteins, and a small amount of RNA. Chromatin and nucleosomes control the stability of the eukaryotic genome and regulate DNA processes such as transcription, replication, and repair. The dynamic structure of chromatin plays a key role in this regulatory function. Structural fluctuations expose internal DNA and thus provide access to the nuclear machinery. The dynamic changes are affected by various complexes and epigenetic modifications. Variation of chromatin dynamics produces early and superior regulation of the expression of related genes and downstream pathways, thereby controlling tumor development. Intervention at the chromatin level can change the process of cancer earlier and is a feasible option for future tumor diagnosis and treatment. In this review, we introduced chromatin dynamics including chromatin remodeling, histone modifications, and chromatin accessibility, and current research on chromatin regulation in digestive system tumors was also summarized.