Genomics Proteomics Bioinformatics. 2021 Mar 16:S1672-0229(21)00059-0. doi: 10.1016/j.gpb.2021.03.001. Online ahead of print.

ABSTRACT

The aim of this study was to identify novel gene and miRNA biomarkers of risk and prognostic factors for hepatocarcinogenesis using methods in systems biology. Differentially expressed genes (DEGs), microRNAs (miRNAs), and long non-coding RNA (lncRNAs) were compared between hepatocellular carcinoma (HCC) tumour tissue and normal liver tissues in the Cancer Genome Atlas (TCGA) database. Subsequently, the prognosis-associated gene co-expression network, mRNA-miRNA, and mRNA-miRNA-lncRNA regulatory networks were constructed to identify biomarkers of risk for HCC through Cox survival analysis. Seven prognosis-associated gene co-expression modules were obtained by analyzing these DEGs. An expression module including 120 genes significantly correlated with HCC patient survival. Combined with patient survival data, several mRNAs and miRNAs, including CHST4, SLC22A8, STC2, hsa-miR-326, and hsa-miR-21 were identified from the network to predict HCC patient prognosis. Clinical significance was investigated using tissue microarray analysis of samples from 258 patients with HCC. Functional annotation of hsa-miR-326 and hsa-miR-21-5p indicated specific associations with several cancer-related pathways. The present study provides a bioinformatics method for biomarker screening, which led to the identification of an integrated mRNA-miRNA-lncRNA regulatory network and their co-expression in relation to predicting HCC patient survival.

PMID:33741523 | DOI:10.1016/j.gpb.2021.03.001

J Ethnopharmacol. 2021 Mar 16:114022. doi: 10.1016/j.jep.2021.114022. Online ahead of print.

ABSTRACT

ETHNOPHARMACOLOGICAL RELEVANCE: Semen Cuscutae and Fructus Lycii (SC-FL) is a commonly used herbal pair for male infertility treatment. Studies have found that the mechanism of SC-FL treatment may be related to repairing the blood-testis barrier (BTB). The application of network pharmacology can be used to explore the correlation between medicines and diseases and predict the potential pharmacological mechanisms of SC-FL.

AIM OF THE STUDY: This study aimed to explore the specific effects and mechanisms of SC-FL in repairing the BTB and initially revealed the mechanism of Chinese medicine treating male infertility through network pharmacology and animal experiments.

MATERIALS AND METHODS: We searched databases using the network pharmacology method and performed mass spectrometry analysis. We analyzed and predicted the active ingredients, targets and key pathways of SC-FL in male infertility treatment. Then, we designed animal experiments to verify the results. Thirty-six Sprague-Dawley rats were randomly divided into the normal control group (NC group), spermatogenic dysfunction group (SD group) and SC-FL treatment group (SCFL group). Glucosides of Tripterygium wilfordii Hook. F (GTW) (40 mg/kg/d) was administered for 4 weeks to generate a spermatogenic dysfunction model. The rats in the SCFL group were given the SC-FL suspension (6 g/kg/d) daily. After 4 weeks of treatment, we detected the sperm quality of each group of rats and observed the cell morphology. Western blotting and qRT-PCR were used to detect the expression of BTB-related proteins in testicular tissues.

RESULTS: 213 chemical ingredients of SC and FL were retrieved from the TCMSP database, and 54 effective chemical ingredients were obtained. Mass spectrometry analysis showed the above results were credible. Then, we identified 44 potential targets for the treatment of male infertility, and we plotted a network diagram of the interaction network between the core targets and a diagram of herbal medicine-active ingredient-target-disease interactions. The target genes were enriched according to biological functions, and 22 biological processes, 49 cellular components, 1487 molecular functions, and 122 signaling pathways were obtained. The results of the animal experiments showed that the sperm concentration and motility of the SCFL group were significantly improved compared with those of the SD group. Compared with those in the SD group, the structure and morphology of the Sertoli cells and seminiferous tubules of rats in the SCFL group improved, and the number of spermatogenic cells increased significantly. Western blotting and qRT-PCR results showed that compared with that in the SD group, the expression of p38 MAPK decreased significantly, and the expression of c-Jun, Occludin, ZO-1 and connexin 43 increased significantly in the SCFL group.

CONCLUSION: We predicted that the active ingredients of SC-FL can treat male infertility by interacting with the core targets JUN, IL6, MAPK1, TP53, MYC, CCND1, AR, EGF, FOS, and MAPK8, and the possible mechanism is related to the MAPK signaling pathway. SC-FL can regulate the MAPK pathway and affect the expression of Occludin, ZO-1 and connexin 43 to repair damaged BTB and improve spermatogenic dysfunction induced by GTW, which may be one of the possible mechanisms.

PMID:33741439 | DOI:10.1016/j.jep.2021.114022

Neurotoxicology. 2020 Dec;81:219-221. doi: 10.1016/j.neuro.2020.09.007. Epub 2020 Oct 12.

ABSTRACT

Environmental health research is at a promising stage for more precisely identifying gene-environment components of disease. Simplistic models and reductionist approaches that have been the norm both in toxicology and in clinical medicine are beginning to be replaced with a more holistic or systems biology approach. We are slowly moving to an understanding that the time between an exposure and its consequence as a diagnosed disease is a time during which many different biochemical changes are occurring and a time during which many biomarkers of disease progression could be identified and used. With such information in hand, clinicians would be able to intervene early in disease progression. With such information, environmental health researchers and policy makers could more reliably identify which elements in our environment need to be controlled or reduced and which populations need the most protection. With such information, the incidence of many human diseases could be dramatically reduced.

PMID:33741106 | DOI:10.1016/j.neuro.2020.09.007

Cancer Cell. 2021 Mar 8:S1535-6108(21)00120-3. doi: 10.1016/j.ccell.2021.02.018. Online ahead of print.

ABSTRACT

Using large, unbiased cohorts, two studies in The New England Journal of Medicine assessed the associations between germline variants in putative cancer susceptibility genes and the risk of breast cancer. They consistently identified a small set of genes as being the most informative for risk prediction, helping select high-risk women in the general population, and developing effective cancer prevention strategies.

PMID:33740422 | DOI:10.1016/j.ccell.2021.02.018

Glob Chang Biol. 2021 Mar 19. doi: 10.1111/gcb.15549. Online ahead of print.

ABSTRACT

Anthropogenic freshwater habitats may provide undervalued prospects for long-term conservation as part of species conservation planning. This fundamental, but overlooked, issue requires attention considering the pace that humans have been altering natural freshwater ecosystems and the accelerated levels of biodiversity decline in recent decades. We compiled 709 records of freshwater mussels (Bivalvia, Unionida) inhabiting a broad variety of anthropogenic habitat types (from small ponds to large reservoirs and canals) and reviewed their importance as refuges for this faunal group. Most records came from Europe and North America, with a clear dominance of canals and reservoirs. The dataset covered 228 species, including 34 threatened species on the IUCN Red List. We discuss the conservation importance and provide guidance on how these anthropogenic habitats could be managed to provide optimal conservation value to freshwater mussels. This review also shows that some of these habitats may function as ecological traps owing to conflicting management practices or because they act as a sink for some populations. Therefore, anthropogenic habitats should not be seen as a panacea to resolve conservation problems. More information is necessary to better understand the trade-offs between human use and the conservation of freshwater mussels (and other biota) within anthropogenic habitats, given the low number of quantitative studies and the strong biogeographic knowledge bias that persists.

PMID:33739622 | DOI:10.1111/gcb.15549

Mol Biol Evol. 2021 Mar 19:msab068. doi: 10.1093/molbev/msab068. Online ahead of print.

ABSTRACT

Many evolutionary comparative methods seek to identify associations between phenotypic traits or between traits and genotypes, often with the goal of inferring potential functional relationships between them. Comparative genomics methods aimed at this goal measure the association between evolutionary changes at the genetic level with traits evolving convergently across phylogenetic lineages. However, these methods have complex statistical behaviors that are influenced by non-trivial and oftentimes unknown confounding factors. Consequently, using standard statistical analyses in interpreting the outputs of these methods leads to potentially inaccurate conclusions. Here, we introduce phylogenetic permulations, a novel statistical strategy that combines phylogenetic simulations and permutations to calculate accurate, unbiased p-values from phylogenetic methods. Permulations construct the null expectation for p-values from a given phylogenetic method by empirically generating null phenotypes. Subsequently, empirical p-values that capture the true statistical confidence given the correlation structure in the data are directly calculated based on the empirical null expectation. We examine the performance of permulation methods by analyzing both binary and continuous phenotypes, including marine, subterranean, and long-lived large-bodied mammal phenotypes. Our results reveal that permulations improve the statistical power of phylogenetic analyses and correctly calibrate statements of confidence in rejecting complex null distributions while maintaining or improving the enrichment of known functions related to the phenotype. We also find that permulations refine pathway enrichment analyses by correcting for non-independence in gene ranks. Our results demonstrate that permulations are a powerful tool for improving statistical confidence in the conclusions of phylogenetic analysis when the parametric null is unknown.

PMID:33739420 | DOI:10.1093/molbev/msab068

Nat Cancer. 2021 Jan;2(1):66-82. doi: 10.1038/s43018-020-00148-7. Epub 2020 Dec 14.

ABSTRACT

Despite objective responses to PARP inhibition and improvements in progression-free survival compared to standard chemotherapy in patients with BRCA-associated triple-negative breast cancer (TNBC), benefits are transitory. Using high dimensional single-cell profiling of human TNBC, here we demonstrate that macrophages are the predominant infiltrating immune cell type in BRCA-associated TNBC. Through multi-omics profiling we show that PARP inhibitors enhance both anti- and pro-tumor features of macrophages through glucose and lipid metabolic reprogramming driven by the sterol regulatory element-binding protein 1 (SREBP-1) pathway. Combined PARP inhibitor therapy with CSF-1R blocking antibodies significantly enhanced innate and adaptive anti-tumor immunity and extends survival in BRCA-deficient tumors in vivo and is mediated by CD8+ T-cells. Collectively, our results uncover macrophage-mediated immune suppression as a liability of PARP inhibitor treatment and demonstrate combined PARP inhibition and macrophage targeting therapy induces a durable reprogramming of the tumor microenvironment, thus constituting a promising therapeutic strategy for TNBC.

PMID:33738458 | PMC:PMC7963404 | DOI:10.1038/s43018-020-00148-7

Front Cell Dev Biol. 2021 Mar 2;9:641618. doi: 10.3389/fcell.2021.641618. eCollection 2021.

ABSTRACT

Lung cancer is the most common cancer worldwide and the leading cause of cancer-related deaths in both men and women. Despite the development of novel therapeutic interventions, the 5-year survival rate for non-small cell lung cancer (NSCLC) patients remains low, demonstrating the necessity for novel treatments. One strategy to improve translational research is the development of surrogate models reflecting somatic mutations identified in lung cancer patients as these impact treatment responses. With the advent of CRISPR-mediated genome editing, gene deletion as well as site-directed integration of point mutations enabled us to model human malignancies in more detail than ever before. Here, we report that by using CRISPR/Cas9-mediated targeting of Trp53 and KRas, we recapitulated the classic murine NSCLC model Trp53 fl/fl :lsl-KRas G12D/wt . Developing tumors were indistinguishable from Trp53 fl/fl :lsl-KRas G12D/ wt -derived tumors with regard to morphology, marker expression, and transcriptional profiles. We demonstrate the applicability of CRISPR for tumor modeling in vivo and ameliorating the need to use conventional genetically engineered mouse models. Furthermore, tumor onset was not only achieved in constitutive Cas9 expression but also in wild-type animals via infection of lung epithelial cells with two discrete AAVs encoding different parts of the CRISPR machinery. While conventional mouse models require extensive husbandry to integrate new genetic features allowing for gene targeting, basic molecular methods suffice to inflict the desired genetic alterations in vivo. Utilizing the CRISPR toolbox, in vivo cancer research and modeling is rapidly evolving and enables researchers to swiftly develop new, clinically relevant surrogate models for translational research.

PMID:33738287 | PMC:PMC7961101 | DOI:10.3389/fcell.2021.641618

J Tissue Eng. 2021 Feb 26;12:2041731420985299. doi: 10.1177/2041731420985299. eCollection 2021 Jan-Dec.

ABSTRACT

The COVID-19 pandemic has aggravated a preexisting epidemic: the opioid crisis. Much literature has shown that the circumstances imposed by COVID-19, such as social distancing regulations, medical and financial instability, and increased mental health issues, have been detrimental to those with opioid use disorder (OUD). In addition, unexpected neurological sequelae in COVID-19 patients suggest that COVID-19 compromises neuroimmunity, induces hypoxia, and causes respiratory depression, provoking similar effects as those caused by opioid exposure. Combined conditions of COVID-19 and OUD could lead to exacerbated complications. With limited human in vivo options to study these complications, we suggest that iPSC-derived brain organoid models may serve as a useful platform to investigate the physiological connection between COVID-19 and OUD. This mini-review highlights the advances of brain organoids in other neuropsychiatric and infectious diseases and suggests their potential utility for investigating OUD and COVID-19, respectively.

PMID:33738089 | PMC:PMC7934045 | DOI:10.1177/2041731420985299

Comput Struct Biotechnol J. 2021 Feb 27;19:1325-1334. doi: 10.1016/j.csbj.2021.02.013. eCollection 2021.

ABSTRACT

A protein binder with a desired epitope and binding affinity is critical to the development of therapeutic agents. Here we present computationally-guided design and affinity improvement of a protein binder recognizing a specific site on domain IV of human epidermal growth factor receptor 2 (HER2). As a model, a protein scaffold composed of Leucine-rich repeat (LRR) modules was used. We designed protein binders which appear to bind a target site on domain IV using a computational method. Top 10 designs were expressed and tested with binding assays, and a lead with a low micro-molar binding affinity was selected. Binding affinity of the selected lead was further increased by two-orders of magnitude through mutual feedback between computational and experimental methods. The utility and potential of our approach was demonstrated by determining the binding interface of the developed protein binder through its crystal structure in complex with the HER2 domain IV.

PMID:33738081 | PMC:PMC7941009 | DOI:10.1016/j.csbj.2021.02.013

Nat Genet. 2021 Mar 18. doi: 10.1038/s41588-021-00807-0. Online ahead of print.

ABSTRACT

Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.

PMID:33737754 | DOI:10.1038/s41588-021-00807-0

Science. 2021 Mar 18:eabf8003. doi: 10.1126/science.abf8003. Online ahead of print.

ABSTRACT

Understanding when SARS-CoV-2 emerged is critical to evaluating our current approach to monitoring novel zoonotic pathogens and understanding the failure of early containment and mitigation efforts for COVID-19. We employed a coalescent framework to combine retrospective molecular clock inference with forward epidemiological simulations to determine how long SARS-CoV-2 could have circulated prior to the time of the most recent common ancestor. Our results define the period between mid-October and mid-November 2019 as the plausible interval when the first case of SARS-CoV-2 emerged in Hubei province. By characterizing the likely dynamics of the virus before it was discovered, we show that over two-thirds of SARS-CoV-2-like zoonotic events would be self-limited, dying out without igniting a pandemic. Our findings highlight the shortcomings of zoonosis surveillance approaches for detecting highly contagious pathogens with moderate mortality rates.

PMID:33737402 | DOI:10.1126/science.abf8003

Proc Natl Acad Sci U S A. 2021 Mar 23;118(12):e2022598118. doi: 10.1073/pnas.2022598118.

ABSTRACT

The ability to map causal interactions underlying genetic control and cellular signaling has led to increasingly accurate models of the complex biochemical networks that regulate cellular function. These network models provide deep insights into the organization, dynamics, and function of biochemical systems: for example, by revealing genetic control pathways involved in disease. However, the traditional representation of biochemical networks as binary interaction graphs fails to accurately represent an important dynamical feature of these multivariate systems: some pathways propagate control signals much more effectively than do others. Such heterogeneity of interactions reflects canalization-the system is robust to dynamical interventions in redundant pathways but responsive to interventions in effective pathways. Here, we introduce the effective graph, a weighted graph that captures the nonlinear logical redundancy present in biochemical network regulation, signaling, and control. Using 78 experimentally validated models derived from systems biology, we demonstrate that 1) redundant pathways are prevalent in biological models of biochemical regulation, 2) the effective graph provides a probabilistic but precise characterization of multivariate dynamics in a causal graph form, and 3) the effective graph provides an accurate explanation of how dynamical perturbation and control signals, such as those induced by cancer drug therapies, propagate in biochemical pathways. Overall, our results indicate that the effective graph provides an enriched description of the structure and dynamics of networked multivariate causal interactions. We demonstrate that it improves explainability, prediction, and control of complex dynamical systems in general and biochemical regulation in particular.

PMID:33737396 | DOI:10.1073/pnas.2022598118

Microbiol Resour Announc. 2021 Mar 18;10(11):e00072-21. doi: 10.1128/MRA.00072-21.

ABSTRACT

The dissimilatory sulfate-reducing deltaproteobacterium Desulfovibrio vulgaris Hildenborough (ATCC 29579) was chosen by the research collaboration ENIGMA to explore tools and protocols for bringing this anaerobe to model status. Here, we describe a collection of genetic constructs generated by ENIGMA that are available to the research community.

PMID:33737356 | DOI:10.1128/MRA.00072-21

Reprod Biomed Online. 2021 Feb 8:S1472-6483(21)00058-4. doi: 10.1016/j.rbmo.2021.01.024. Online ahead of print.

ABSTRACT

RESEARCH QUESTION: Is the transcriptome of cumulus cells of infertile women with advanced endometriosis (EIII/IV), with and without endometrioma, altered?

DESIGN: In this prospective case-control study, next-generation RNA sequencing was used to compare the transcript profile of cumulus cells among infertile patients undergoing ovarian stimulation for intracytoplasmic sperm injection with EIII/IV, with (n = 9) and without endometrioma (n = 9), and controls (n = 9). An in-silico enrichment analysis was conducted to establish the possibly altered pathways in cumulus cells of patients with endometriosis.

RESULTS: Most of the differentially expressed genes (DEG) were found when cumulus cells from women with EIII/IV with endometrioma were compared with controls (DEG, n = 461). In women with EIII/IV without endometrioma, only 66 DEG were verified compared with controls. The enrichment analysis showed that some DEG in cumulus cells of endometriosis are involved in important pathways for the oocyte competence acquisition, such as oxidative phosphorylation, metabolism, mitochondrial function, acetylation and steroid biosynthesis. No DEG were found when cumulus cells from women with EIII/IV with and without endometrioma were compared.

CONCLUSION: RNA sequencing results suggest that cumulus cells of infertile women with EIII/IV have an altered transcriptome, regardless of endometrioma. The present findings offer a better understanding of the genes and molecular mechanisms that may be involved in endometriosis-related infertility, mostly in the oocyte competence acquisition process.

PMID:33736992 | DOI:10.1016/j.rbmo.2021.01.024

Ann Oncol. 2021 Mar 10:S0923-7534(21)00123-X. doi: 10.1016/j.annonc.2021.02.006. Online ahead of print.

ABSTRACT

BACKGROUND: High tumor mutation burden (TMB-H) has been proposed as a predictive biomarker for response to immune checkpoint blockade (ICB), largely due to the potential for tumor mutations to generate immunogenic neoantigens. Despite recent pan-cancer approval of ICB treatment for any TMB-H tumor, as assessed by the targeted FoundationOne CDx assay in nine tumor types, the utility of this biomarker has not been fully demonstrated across all cancers.

PATIENTS AND METHODS: Data from over 10 000 patient tumors included in The Cancer Genome Atlas were used to compare approaches to determine TMB and identify the correlation between predicted neoantigen load and CD8 T cells. Association of TMB with ICB treatment outcomes was analyzed by both objective response rates (ORRs, N = 1551) and overall survival (OS, N = 1936).

RESULTS: In cancer types where CD8 T-cell levels positively correlated with neoantigen load, such as melanoma, lung, and bladder cancers, TMB-H tumors exhibited a 39.8% ORR to ICB [95% confidence interval (CI) 34.9-44.8], which was significantly higher than that observed in low TMB (TMB-L) tumors [odds ratio (OR) = 4.1, 95% CI 2.9-5.8, P < 2 × 10-16]. In cancer types that showed no relationship between CD8 T-cell levels and neoantigen load, such as breast cancer, prostate cancer, and glioma, TMB-H tumors failed to achieve a 20% ORR (ORR = 15.3%, 95% CI 9.2-23.4, P = 0.95), and exhibited a significantly lower ORR relative to TMB-L tumors (OR = 0.46, 95% CI 0.24-0.88, P = 0.02). Bulk ORRs were not significantly different between the two categories of tumors (P = 0.10) for patient cohorts assessed. Equivalent results were obtained by analyzing OS and by treating TMB as a continuous variable.

CONCLUSIONS: Our analysis failed to support application of TMB-H as a biomarker for treatment with ICB in all solid cancer types. Further tumor type-specific studies are warranted.

PMID:33736924 | DOI:10.1016/j.annonc.2021.02.006

BMC Genomics. 2021 Mar 18;22(1):195. doi: 10.1186/s12864-021-07469-6.

ABSTRACT

BACKGROUND: The technology of single cell RNA sequencing (scRNA-seq) has gained massively in popularity as it allows unprecedented insights into cellular heterogeneity as well as identification and characterization of (sub-)cellular populations. Furthermore, scRNA-seq is almost ubiquitously applicable in medical and biological research. However, these new opportunities are accompanied by additional challenges for researchers regarding data analysis, as advanced technical expertise is required in using bioinformatic software.

RESULTS: Here we present WASP, a software for the processing of Drop-Seq-based scRNA-Seq data. Our software facilitates the initial processing of raw reads generated with the ddSEQ or 10x protocol and generates demultiplexed gene expression matrices including quality metrics. The processing pipeline is realized as a Snakemake workflow, while an R Shiny application is provided for interactive result visualization. WASP supports comprehensive analysis of gene expression matrices, including detection of differentially expressed genes, clustering of cellular populations and interactive graphical visualization of the results. The R Shiny application can be used with gene expression matrices generated by the WASP pipeline, as well as with externally provided data from other sources.

CONCLUSIONS: With WASP we provide an intuitive and easy-to-use tool to process and explore scRNA-seq data. To the best of our knowledge, it is currently the only freely available software package that combines pre- and post-processing of ddSEQ- and 10x-based data. Due to its modular design, it is possible to use any gene expression matrix with WASP's post-processing R Shiny application. To simplify usage, WASP is provided as a Docker container. Alternatively, pre-processing can be accomplished via Conda, and a standalone version for Windows is available for post-processing, requiring only a web browser.

PMID:33736596 | DOI:10.1186/s12864-021-07469-6

Sci Total Environ. 2021 May 15;769:144648. doi: 10.1016/j.scitotenv.2020.144648. Epub 2021 Jan 18.

ABSTRACT

Arsenic (As)-reducing bacteria are able to influence As-speciation and, in this way, change As bio-availability. In consequence, this has an impact on As uptake by plants growing on polluted soil and on the effectiveness of the phytoremediation process. To be able to efficiently utilize these bacteria for As-phytoremediation in the field, a better understanding of the plant-bacterial interactions involved in As-tolerance or toxicity is needed. In this work, seedlings of a clone of Salix atrocinerea derived from a specimen naturally growing on an As-polluted brownfield were grown under gnotobiotic conditions exposed to As, and in the presence or absence of two of its field-associated and in vitro characterized plant growth-promoting (PGP) bacteria. The inoculation with Pantoea sp., induced a moderate reduction of AsV to AsIII in the exposure medium that, together with a coordinated plant response of As uptake, chelation and sequestration, increased As accumulation in roots; which is reflected into a higher phytostabilization. However, inoculation with Rhodococcus erythropolis due to a higher disproportionate reduction of AsV to AsIII in the medium caused less As accumulation in roots that non-bioaugmented plants and despite the lower As content, the concentrations of AsIII present in the medium and the damage suffered in roots and leaves, indicated that As tolerance mechanisms (such as prevention of AsIII uptake and efflux) did not occur in time to avoid physical disturbance and plants growth reduction. Interestingly, by two different metabolic pathways -coordinated by different key transporters mediating As uptake, tolerance, distribution and vacuolar accumulation at the roots- both bacteria limited As accumulation in Salix shoots. Our results provide for the first time a detailed insight in the plant-bacterial responses and physiological changes contributing to As tolerance in S. atrocinerea, that will facilitate the design of effective strategies for exploitation of plant-associated microorganisms for phytoremediation.

PMID:33736260 | DOI:10.1016/j.scitotenv.2020.144648

Environ Pollut. 2021 Mar 9;278:116863. doi: 10.1016/j.envpol.2021.116863. Online ahead of print.

ABSTRACT

Inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4) is a type II acute-phase protein; however, the role of pulmonary ITIH4 after exposure to air pollution remains unclear. In this study, we investigated the role of ITIH4 in the lungs in response to air pollution. ITIH4 expression in bronchoalveolar lavage fluid (BAL) of 47 healthy human subjects and of Sprague-Dawley rats whole-body exposed to air pollution was determined, and the underlying antiapoptotic and matrix-stabilizing pathways in alveolar epithelial A549 cells induced by diesel exhaust particles (DEPs) as well as ITIH4-knockdown were investigated. We found that an interquartile range (IQR) increase in PM2.5 was associated with a decrease of 2.673 ng/mL in ITIH4, an increase of 1.104 pg/mL of 8-isoprostane, and an increase of 6.918 pg/mL of interleukin (IL)-6 in human BAL. In rats, increases in 8-isoprostane, IL-6, and p53 and a decrease in sirtuin-1 (Sirt1) in the lungs and decreases in ITIH4 in the BAL, lungs, and serum were observed after PM2.5 and gaseous exposure. ITIH4 levels in lung lysates were correlated with levels in BAL samples (r = 0.377, p < 0.01), whereas ITIH4 levels in BAL were correlated with IL-6 levels (r = -0.420, p < 0.01). ITIH4 expression was significantly reduced in alveolar epithelial A549 cells by DEP in a dose-dependent manner. A decrease in Sirt1 and increases in phosphorylated extracellular signal-regulated kinase (p-ERK) and caspase-3 were observed after DEP exposure and ITIH4-knockdown. In conclusion, air pollution decreased ITIH4 expression in the lungs, which was associated with alveolar epithelial cell senescence and apoptosis. ITIH4 could be a vital protein in regulating alveolar cell destruction and its inhibition after exposure to air pollution.

PMID:33735794 | DOI:10.1016/j.envpol.2021.116863

Int Immunopharmacol. 2021 Mar 11;95:107522. doi: 10.1016/j.intimp.2021.107522. Online ahead of print.

ABSTRACT

BACKGROUND: We examined the safety and efficacy of a treatment protocol containing Favipiravir for the treatment of SARS-CoV-2.

METHODS: We did a multicenter randomized open-labeled clinical trial on moderate to severe cases infections of SARS-CoV-2. Patients with typical ground glass appearance on chest computerized tomography scan (CT scan) and oxygen saturation (SpO2) of less than 93% were enrolled. They were randomly allocated into Favipiravir (1.6 gr loading, 1.8 gr daily) and Lopinavir/Ritonavir (800/200 mg daily) treatment regimens in addition to standard care. In-hospital mortality, ICU admission, intubation, time to clinical recovery, changes in daily SpO2 after 5 min discontinuation of supplemental oxygen, and length of hospital stay were quantified and compared in the two groups.

RESULTS: 380 patients were randomly allocated into Favipiravir (193) and Lopinavir/Ritonavir (187) groups in 13 centers. The number of deaths, intubations, and ICU admissions were not significantly different (26, 27, 31 and 21, 17, 25 respectively). Mean hospital stay was also not different (7.9 days [SD = 6] in the Favipiravir and 8.1 [SD = 6.5] days in Lopinavir/Ritonavir groups) (p = 0.61). Time to clinical recovery in the Favipiravir group was similar to Lopinavir/Ritonavir group (HR = 0.94, 95% CI 0.75 - 1.17) and likewise the changes in the daily SpO2 after discontinuation of supplemental oxygen (p = 0.46) CONCLUSION: Adding Favipiravir to the treatment protocol did not reduce the number of ICU admissions or intubations or In-hospital mortality compared to Lopinavir/Ritonavir regimen. It also did not shorten time to clinical recovery and length of hospital stay.

PMID:33735712 | DOI:10.1016/j.intimp.2021.107522