Biomedical blockchain with practical implementations and quantitative evaluations: a systematic review.

OBJECTIVE: Blockchain has emerged as a potential data-sharing structure in healthcare because of its decentralization, immutability, and traceability. However, its use in the biomedical domain is yet to be investigated comprehensively, especially from the aspects of implementation and evaluation, by existing blockchain literature reviews. To address this, our review assesses blockchain applications implemented in practice and evaluated with quantitative metrics. MATERIALS AND METHODS: This systematic review adapts the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) framework to review biomedical blockchain papers published by August 2023 from 3 databases. Blockchain application, implementation, and evaluation metrics were collected and summarized. RESULTS: Following screening, 11 articles were included in this review. Articles spanned a range of biomedical applications including COVID-19 medical data sharing, decentralized internet of things (IoT) data storage, clinical trial management, biomedical certificate storage, electronic health record (EHR) data sharing, and distributed predictive model generation. Only one article demonstrated blockchain deployment at a medical facility. DISCUSSION: Ethereum was the most common blockchain platform. All but one implementation was developed with private network permissions. Also, 8 articles contained storage speed metrics and 6 contained query speed metrics. However, inconsistencies in presented metrics and the small number of articles included limit technological comparisons with each other. CONCLUSION: While blockchain demonstrates feasibility for adoption in healthcare, it is not as popular as currently existing technologies for biomedical data management. Addressing implementation and evaluation factors will better showcase blockchain's practical benefits, enabling blockchain to have a significant impact on the health sector.

Biochar-derived dissolved and particulate matter effects on the phytotoxicity of polyvinyl chloride nanoplastics.

Nanoplastics in environments are potentially detrimental to plant growth. Appropriate doses of biochar can alleviate the phytotoxicity of nanoplastics under hydroponic conditions. However, the specific mechanisms remain unknown. In this study, the effects of biochar-derived dissolved matter (BCDM) and biochar-derived particulate matter (BCPM) on the phytotoxicity of polyvinyl chloride (PVC) nanoplastics were investigated and the underlying influencing mechanisms were elucidated. The results showed that PVC nanoplastics can be adsorbed and taken up by lettuce roots, inducing oxidative damage to lettuce shoots and roots and reducing their fresh weight. BCDM can promote the aggregation and sedimentation of PVC nanoplastics, and BCPM can adsorb PVC nanoplastics and cause barrier effect, which will reduce the exposure dose of PVC nanoplastics. Furthermore, nutrients in BCDM can promote lettuce growth. As a result, the presence of both BCDM and BCPM significantly mitigated the oxidative stress of lettuce shoots and roots as demonstrated by the decrease in hydrogen peroxide and malondialdehyde levels (p < 0.05). Meanwhile, lettuce biomass was significantly increased after addition of BCDM and BCPM compared to the single PVC treatment group (p < 0.05). This study provides a theoretical basis for finding solutions to alleviate the phytotoxicity of nanoplastics.

TRAF7-targeted HOXA5 acts as a tumor suppressor in prostate cancer progression and stemness via transcriptionally activating SPRY2 and regulating MEK/ERK signaling.

Homeobox A5 (HOXA5), a homeodomain transcription factor, is considered a tumor suppressor in cancer progression; however, its function in prostate cancer (PCa) remains unclear. This study focused on the relevance of HOXA5 in PCa progression. We identified the downregulation of HOXA5 in PCa tissues based on the TCGA database and further verified in 30-paired PCa and adjacent normal tissues. Functional studies revealed that HOXA5 upregulation impaired the stem-like characteristics and malignant behaviors of PCa cells in vitro and in vivo. Mechanistically, HOXA5 was found to be regulated by tumor necrosis factor receptor-associated factor 7 (TRAF7), a putative E3-ubiquitin ligase. We observed that TRAF7 was overexpressed in PCa and subsequently enhanced the degradation of HOXA5 protein via its ubiquitin ligase activity, contributing to the acquisition of an aggressive PCa phenotype. For its downstream mechanism, we demonstrated that sprouty RTK signaling antagonist 2 (SPRY2) served as a downstream target of HOXA5. HOXA5 could directly bind to the SPRY2 promoter, thereby regulating the SPRY2-mediated MEK/ERK signaling pathway. Silencing SPRY2 largely compromised the tumor-suppressive effect of HOXA5 in PCa progression and cancer stemness. Our findings highlight the previously-underappreciated signaling axis of TRAF7-HOXA5-SPRY2, which provides a novel prognostic and therapeutic target for PCa treatment.

Effects of biochar on the phytotoxicity of polyvinyl chloride microplastics.

Polyvinyl chloride microplastics (PVC-MPs) are toxic to crops, resulting in economic losses during agricultural production. Owing to its strong adsorption capacity, biochar can effectively remove MPs from water. It is presumed that biochar can alleviate the phytotoxicity of PVC-MPs. To verify this hypothesis, the effects of different concentrations of corncob biochar (CCBC) on the phytotoxicity of PVC-MPs were investigated using hydroponic experiments. The results showed that PVC-MPs attached to lettuce roots substantially inhibited the growth and quality of lettuce. The tested CCBC adsorbed the PVC-MPs. At appropriate concentrations, CCBC alleviated the inhibitory effect of PVC-MPs on lettuce yield; however, it decreased some quality indicators. The single PVC-MPs induced oxidative damage to lettuce, as demonstrated by the increased hydrogen peroxide (H2O2) and malondialdehyde (MDA) content. Addition of CCBC considerably decreased the contents of H2O2 and MDA in the lettuce shoots but increased the H2O2 content in the roots. These findings indicate that CCBC may alleviate the adverse effects caused by PVC-MPs to the lettuce shoots but aggravate the toxic effects on the lettuce roots. This study provides a basis for understanding the removal of the phytotoxicity of MPs.

Responses of cherry radish to different types of microplastics in the presence of oxytetracycline.

Croplands have become a hotspot for antibiotic and microplastic (MP) pollution. However, little is known regarding their combined effects on crops. In this study, the individual and combined effects of oxytetracycline (OTC) and three MPs (i.e., polypropylene (PP), polyamide (PA), and polyvinylchloride (PVC)) on cherry radish were investigated using pot experiments. Individually, OTC (50 mg kg-1), PA (2%, w/w), and PP (2%, w/w) induced negligible effects on cherry radish biomass and the root/shoot ratio. However, PVC (2%, w/w) significantly inhibited cherry radish growth; that is, its shoot and root fresh weight decreased by 46.2% and 81.1%, respectively. In the combined exposure groups, OTC alleviated the adverse effects of PVC on the cherry radish leaf number and shoot fresh weight. This was linked to that OTC increased the content of photosynthetic pigments. Superoxide dismutase activity in cherry radish roots was inhibited to different extents in all treatment groups except for the PA and PVC treatments. Malondialdehyde (MDA) content in cherry radish roots increased in all treatment groups, suggesting that both OTC and MPs caused oxidative damage to cherry radish root cells, therefore inhibiting cherry radish root growth. However, the presence of OTC non-significantly changed the effects of MPs on cherry radish roots. Irrespective of OTC presence, MPs induced a reduction in the root/shoot ratio of cherry radish, suggesting that the inhibitory effect of MPs on cherry radish roots was stronger than that on shoots. These findings contribute to the evaluation of the phytotoxicity of antibiotics and MPs in soil-vegetable systems.

A Method for Variant Agnostic Detection of SARS-CoV-2, Rapid Monitoring of Circulating Variants, and Early Detection of Emergent Variants Such as Omicron.

The rapid emergence of SARS-CoV-2 variants raised public health questions concerning the capability of diagnostic tests to detect new strains, the efficacy of vaccines, and how to map the geographical distribution of variants to understand transmission patterns and loads on healthcare resources. Next-generation sequencing (NGS) is the primary method for detecting and tracing new variants, but it is expensive, and it can take weeks before sequence data are available in public repositories. This article describes a customizable reverse transcription PCR (RT-PCR)-based genotyping approach which is significantly less expensive, accelerates reporting, and can be implemented in any lab that performs RT-PCR. Specific single-nucleotide polymorphisms (SNPs) and indels were identified which had high positive-percent agreement (PPA) and negative-percent agreement (NPA) compared to NGS for the major genotypes that circulated through September 11, 2021. Using a 48-marker panel, testing on 1,031 retrospective SARS-CoV-2 positive samples yielded a PPA and NPA ranging from 96.3 to 100% and 99.2 to 100%, respectively, for the top 10 most prevalent World Health Organization (WHO) lineages during that time. The effect of reducing the quantity of panel markers was explored, and a 16-marker panel was determined to be nearly as effective as the 48-marker panel at lineage assignment. Responding to the emergence of Omicron, a genotyping panel was developed which distinguishes Delta and Omicron using four highly specific SNPs. The results demonstrate the utility of the condensed panel to rapidly track the growing prevalence of Omicron across the US in December 2021 and January 2022.

Effects of Microplastics on Higher Plants: A Review.

Microplastics pose great risks to terrestrial systems owing to their large quantity and strong persistence. Higher plants, an irreplaceable part of the terrestrial ecosystem, are inevitably exposed to microplastics. This review highlights the effects of microplastics on higher plant growth and performance. The tested microplastics, plant species, and cultural methods used in existing studies were summarized. We discussed the reasons why these microplastics, plants, and methods were selected. The various responses of higher plants to microplastics in both soils and waters were critically reviewed. We also highlighted the influencing mechanisms of microplastics on higher plants. Conclusively, more than 13 types of common microplastics and more than 30 species of higher plants have been selected and studied by the published literatures. Soil culture tests and hydroponic experiments are almost equally divided. The effects of microplastics on higher plants varied among microplastic properties, plant species, and environmental factors. Microplastics had no or positive effects on higher plants under certain experimental conditions. However, more studies showed that microplastics can inhibit higher plant growth and performance. We reduced the inhibitory mechanisms into direct and indirect mechanisms. The direct mechanisms include blocking pores or light, causing mechanical damage to roots, hindering genes expression, and releasing additives. The indirect mechanisms contain changing soil properties, affecting soil microbes or soil animals, and affecting bioavailability of other pollutants. This review improves the understanding of effects and influencing mechanisms of microplastics on higher plants.

Clinical heterogeneity and intrafamilial variability of Joubert syndrome in two siblings with CPLANE1 variants.

BACKGROUND: Joubert syndrome (JBTS) is a rare genetic disorder that is characterized by midbrain-hindbrain malformations. Multiple variants in genes that affect ciliary function contribute to the genetic and clinical heterogeneity of JBTS and its subtypes. However, the correlation between genotype and phenotype has not been elucidated due to the limited number of patients available. METHODS: In this study, we observed different clinical features in two siblings from the same family. The older sibling was classified as a pure JBTS patient, whereas her younger sibling displayed oral-facial-digital defects and was therefore classified as an oral-facial-digital syndrome type VI (OFD VI) patient. Next, we performed human genetic tests to identify the potential pathogenic variants in the two siblings. RESULTS: Genetic sequencing indicated that both siblings harbored compound heterozygous variants of a missense variant (c.1067C>T, p.S356F) and a frameshift variant (c.8377_8378del, p.E2793Lfs*24) in CPLANE1 (NM_023073.3). CONCLUSION: This study reports that two novel CPLANE1 variants are associated with the occurrence of JBTS and OFD VI. These results help elucidate the intrafamilial phenotypic variability associated with CPLANE1 variants.

Identification of two novel pathogenic variants of PIBF1 by whole exome sequencing in a 2-year-old boy with Joubert syndrome.

BACKGROUND: Joubert syndrome (OMIM 213300) is an autosomal recessive disorder with gene heterogeneity. Causal genes and their variants have been identified by sequencing or other technologies for Joubert syndrome subtypes. CASE PRESENTATION: A two-year-old boy was diagnosed with Joubert syndrome by global development delay and molar tooth sign of mid-brain. Whole exome sequencing was performed to detect the causative gene variants in this individual, and the candidate pathogenic variants were verified by Sanger sequencing. We identified two pathogenic variants (NM_006346.2: c.1147delC and c.1054A > G) of PIBF1 in this Joubert syndrome individual, which is consistent with the mode of autosomal recessive inheritance. CONCLUSION: In this study, we identified two novel pathogenic variants in PIBF1 in a Joubert syndrome individual using whole exome sequencing, thereby expanding the PIBF1 pathogenic variant spectrum of Joubert syndrome.

Prevention and Control of Pathogens Based on Big-Data Mining and Visualization Analysis.

Morbidity and mortality caused by infectious diseases rank first among all human illnesses. Many pathogenic mechanisms remain unclear, while misuse of antibiotics has led to the emergence of drug-resistant strains. Infectious diseases spread rapidly and pathogens mutate quickly, posing new threats to human health. However, with the increasing use of high-throughput screening of pathogen genomes, research based on big data mining and visualization analysis has gradually become a hot topic for studies of infectious disease prevention and control. In this paper, the framework was performed on four infectious pathogens (Fusobacterium, Streptococcus, Neisseria, and Streptococcus salivarius) through five functions: 1) genome annotation, 2) phylogeny analysis based on core genome, 3) analysis of structure differences between genomes, 4) prediction of virulence genes/factors with their pathogenic mechanisms, and 5) prediction of resistance genes/factors with their signaling pathways. The experiments were carried out from three angles: phylogeny (macro perspective), structure differences of genomes (micro perspective), and virulence and drug-resistance characteristics (prediction perspective). Therefore, the framework can not only provide evidence to support the rapid identification of new or unknown pathogens and thus plays a role in the prevention and control of infectious diseases, but also help to recommend the most appropriate strains for clinical and scientific research. This paper presented a new genome information visualization analysis process framework based on big data mining technology with the accommodation of the depth and breadth of pathogens in molecular level research.

Whole exome sequencing reveals novel CEP104 mutations in a Chinese patient with Joubert syndrome.

BACKGROUND: Joubert syndrome (JS, OMIM: 213300) is a recessive developmental disorder characterized by cerebellar vermis hypoplasia and a distinctive mid-hindbrain malformation called the "molar tooth sign" on axial magnetic resonance imaging. To date, more than 35 ciliary genes have been identified as the causative genes of JS. METHODS: Whole exome sequencing was performed to detect the causative gene mutations in a Chinese patient with JS followed by Sanger sequencing. RT-PCR and Sanger sequencing were used to confirm the abnormal transcript of centrosomal protein 104 (CEP104, OMIM: 616690). RESULTS: We identified two novel heterozygous mutations of CEP104 in the proband, which were c.2364+1G>A and c.414delC (p.Asn138Lysfs*11) (GenBank: NM_014704.3) and consistent with the autosomal recessive inheritance mode. CONCLUSION: Our study reported the fourth case of JS patients with CEP104 mutations, which expands the mutation spectrum of CEP104 and elucidates the clinical heterogeneity of JS.

Clinical Features and Long-Term Outcome of Primary Intracranial Ewing Sarcoma/Peripheral Primitive Neuroectodermal Tumors: 14 Cases From a Single Institution.

OBJECTIVE: Primary intracranial Ewing sarcoma (ES)/peripheral primitive neuroectodermal tumors (pPNETs) are extremely rare, and only a few studies have reported >4 cases of this disease. The purpose of this study was to explore the clinical features, treatment, and outcome of primary intracranial ES/pPNETs. METHODS: The clinical data of 14 patients who had been surgically treated from February 2003 to November 2017 and in whom immunohistochemical staining results had confirmed the diagnosis of primary intracranial ES/pPNETs were retrospectively analyzed. Kaplan-Meier survival analysis was used to estimate the survival rate and the median survival time (MST). RESULTS: Gross total resection (GTR) was achieved in 7 cases, and subtotal resection was performed in 7 cases. During follow-up, 10 (71.4%) patients had local recurrence and 3 (21.4%) patients had distant metastasis. The overall 1-, 2-, and 5-year survival rates were 78.6%, 47.6%, and 19.0%, respectively. Kaplan-Meier survival analysis showed that postoperative radiotherapy was a significant prognostic factor for longer MST (P = 0.034). GTR and radiotherapy with or without adjuvant chemotherapy yielded the highest 2-year survival rate (100%). Three patients who underwent GTR, radiotherapy, and chemotherapy had the highest 2-year survival rates (100%) and the longest MST (48 months). CONCLUSIONS: Primary intracranial ES/pPNETs have an aggressive clinical course, with a high tendency for local recurrence and distant metastasis. Radiotherapy plays a significant role in improving the survival of patients. GTR combined with radiotherapy and chemotherapy may be the most beneficial treatment modality.

Erratum to: Plant pattern-recognition receptors controlling innate immunity.

Plants are exposed to numerous potential pathogenic microbes. To counter the threat, plants have evolved diverse patternrecognition receptors (PRRs), which are receptor kinases (RKs) and receptor proteins (RPs) specialized to detect conserved pathogen/microbe-associated molecular patterns (PAMPs/MAMPs). Although only a handful of RKs and RPs are known PRRs, they belong to the receptor-like kinase (RLK) and receptor-like protein (RLP) superfamilies that undergo lineagespecific expansion, suggesting that many of these RLKs and RLPs are potential PRRs. Analyses of existing PRRs have uncovered ligand-induced RLK-RK or RLK-RP oligomerization as a common mechanism for immune activation. PRRs can recruit additional components to form dynamic receptor complexes, which mediate specific cellular responses. Detailed analyses of these components are shedding light on molecular mechanisms underlying the regulation of PRR activity and downstream signaling.

Proline isomerization of the immune receptor-interacting protein RIN4 by a cyclophilin inhibits effector-triggered immunity in Arabidopsis.

In the absence of pathogen infection, plant effector-triggered immune (ETI) receptors are maintained in a preactivation state by intermolecular interactions with other host proteins. Pathogen effector-induced alterations activate the receptor. In Arabidopsis, the ETI receptor RPM1 is activated via bacterial effector AvrB-induced phosphorylation of the RPM1-interacting protein RIN4 at Threonine 166. We find that RIN4 also interacts with the prolyl-peptidyl isomerase (PPIase) ROC1, which is reduced upon RIN4 Thr166 phosphorylation. ROC1 suppresses RPM1 immunity in a PPIase-dependent manner. Consistent with this, RIN4 Pro149 undergoes cis/trans isomerization in the presence of ROC1. While the RIN4(P149V) mutation abolishes RPM1 resistance, the deletion of Pro149 leads to RPM1 activation in the absence of RIN4 phosphorylation. These results support a model in which RPM1 directly senses conformational changes in RIN4 surrounding Pro149 that is controlled by ROC1. RIN4 Thr166 phosphorylation indirectly regulates RPM1 resistance by modulating the ROC1-mediated RIN4 isomerization.

Genome characteristics reveal the impact of lichenization on lichen-forming fungus Endocarpon pusillum Hedwig (Verrucariales, Ascomycota).

BACKGROUND: Lichen is a classic mutualistic organism and the lichenization is one of the fungal symbioses. The lichen-forming fungus Endocarpon pusillum is living in symbiosis with the green alga Diplosphaera chodatii Bialsuknia as a lichen in the arid regions. RESULTS: 454 and Illumina technologies were used to sequence the genome of E. pusillum. A total of 9,285 genes were annotated in the 37.5 Mb genome of E. pusillum. Analyses of the genes provided direct molecular evidence for certain natural characteristics, such as homothallic reproduction and drought-tolerance. Comparative genomics analysis indicated that the expansion and contraction of some protein families in the E. pusillum genome reflect the specific relationship with its photosynthetic partner (D. chodatii). Co-culture experiments using the lichen-forming fungus E. pusillum and its algal partner allowed the functional identification of genes involved in the nitrogen and carbon transfer between both symbionts, and three lectins without signal peptide domains were found to be essential for the symbiotic recognition in the lichen; interestingly, the ratio of the biomass of both lichen-forming fungus and its photosynthetic partner and their contact time were found to be important for the interaction between these two symbionts. CONCLUSIONS: The present study lays a genomic analysis of the lichen-forming fungus E. pusillum for demonstrating its general biological features and the traits of the interaction between this fungus and its photosynthetic partner D. chodatii, and will provide research basis for investigating the nature of its drought resistance and symbiosis.

Genetic diversity and population structure of rice pathogen Ustilaginoidea virens in China.

Rice false smut caused by the fungal pathogen Ustilaginoidea virens is becoming a destructive disease throughout major rice-growing countries. Information about its genetic diversity and population structure is essential for rice breeding and efficient control of the disease. This study compared the genome sequences of two U. virens isolates. Three SNP-rich genomic regions were identified as molecular markers that could be used to analyze the genetic diversity and population structure of U. virens in China. A total of 56 multilocus sequence types (haplotypes) were identified out of 162 representative isolates from 15 provinces covering five major rice-growing areas in China. However, the phylogeny, based on sequences at individual SNP-rich regions, strongly conflicted with each other and there were significant genetic differences between different geographical populations. Gene flow between the different geographical populations and genetic differentiation within each geographical population were also detected. In addition, genetic recombination and genetic isolation resulting from geographic separation was also found.

Analysis of the role of transcription factor VAD-5 in conidiation of Neurospora crassa.

Conidiation is the major mode of reproduction in many filamentous fungi. The Neurospora crassa gene vad-5, which encodes a GAL4-like Zn2Cys6 transcription factor, was suggested to contribute to conidiation in a previous study using a knockout mutant. In this study, we confirmed the positive contribution of vad-5 to conidiation by gene complementation. To understand the role of vad-5 in conidiation, transcriptomic profiles generated by digital gene expression profiling from the vad-5 deletion mutant and the wild-type strain were compared. Among 7559 detected genes, 176 genes were found to be transcriptionally down-regulated and 277 genes transcriptionally upregulated in the vad-5 deletion mutant, using ≥1-fold change as a cutoff threshold. Among the down-regulated genes, four which were already known to be involved in conidiation -fluffy, ada-6, rca-1, and eas - were examined further in a time course experiment. Transcription of each of the four genes in the vad-5 deletion mutant was lower than in the wild-type strain during conidial development. Phenotypic observation of deletion mutants for 132 genes down-regulated by vad-5 deletion revealed that deletion mutants for 17 genes, including fluffy, ada-6, and eas, produced fewer conidia than the wild type. By phenotypic observation of deletion mutants for 211 genes upregulated in the vad-5 deletion mutant, two types of deletion mutants were found. One type, which produced more conidia than the wild-type strain, includes deletion mutants for previously characterized genes cat-2, cat-3, and sah-1 and for a non-characterized gene NCU07221. Deletion mutants of NCU06302 and NCU11090, representing the second type, produced conidia earlier than the wild-type strain. Based on these conidiation phenotypes, we designated NCU07221 as high conidial production-1 (hcp-1) and named NCU06302 and NCU11090 as early conidial development-1 (ecd-1) and ecd-2, respectively. Given the collective results from this study, we propose that vad-5 exerts an effect on conidiation by activating genes that positively contribute to conidiation as well as by repressing genes that negatively influence conidial development.

Reentrant spiral waves of spreading depression cause macular degeneration in hypoglycemic chicken retina.

Spreading depression (SD), a slow diffusion-mediated self-sustained wave of depolarization that severely disrupts neuronal function, has been implicated as a cause of cellular injury in a number of central nervous system pathologies, including blind spots in the retina. Here we show that in the hypoglycemic chicken retina, spontaneous episodes of SD can occur, resulting in irreversible punctate lesions in the macula, the region of highest visual acuity in the central region of the retina. These lesions in turn can act as sites of origin for secondary self-sustained reentrant spiral waves of SD that progressively enlarge the lesions. Furthermore, we show that the degeneration of the macula under hypoglycemic conditions can be prevented by blocking reentrant spiral SDs or by blocking caspases. The observation that spontaneous formation of reentrant spiral SD waves leads to the development of progressive retinal lesions under conditions of hypoglycemia establishes a potential role of SD in initiation and progression of macular degeneration, one of the leading causes of visual disability worldwide.

Receptor-mediated glutamate release from volume sensitive channels in astrocytes.

Several lines of work have shown that astrocytes release glutamate in response to receptor activation, which results in a modulation of local synaptic activity. Astrocytic glutamate release is Ca(2+)-dependent and occurs in conjunction with exocytosis of glutamate containing vesicles. However, astrocytes contain a millimolar concentration of cytosolic glutamate and express channels permeable to small anions, such as glutamate. Here, we tested the idea that astrocytes respond to receptor stimulation by dynamic changes in cell volume, resulting in volume-sensitive channel activation, and efflux of cytosolic glutamate. Confocal imaging and whole-cell recordings demonstrated that astrocytes exhibited a transient Ca(2+)-dependent cell volume increase, which activated glutamate permeable channels. HPLC analysis revealed that glutamate was released in conjunction with other amino acid osmolytes. Our observations indicate that volume-sensitive channel may constitute a previously uncharacterized target for modulation of astrocyte-neuronal interactions.