Wood emissions and asthma development: Results from an experimental mouse model and a prospective cohort study.

Environ Int. 2021 Feb 18;151:106449

Authors: Junge KM, Buchenauer L, Elter E, Butter K, Kohajda T, Herberth G, Röder S, Borte M, Kiess W, von Bergen M, Simon JC, Rolle-Kampczyk UE, Lehmann I, Gminski R, Ohlmeyer M, Polte T

Abstract
BACKGROUND: Increased use of renewable resources like sustainably produced wood in construction or for all sorts of long-lived products is considered to contribute to reducing society's carbon footprint. However, as a natural, biological material, wood and wood products emit specific volatile organic compounds (VOCs). Therefore, the evaluation of possible health effects due to wood emissions is of major interest.
OBJECTIVES: We investigated the effects of an exposure to multiple wood-related VOCs on asthma development.
METHODS: A murine asthma model was used to evaluate possible allergic and inflammatory effects on the lung after short- or long-term and perinatal exposure to pinewood or oriented strand board (OSB). In addition, wood-related VOCs were measured within the German prospective mother-child cohort LINA and their joint effect on early wheezing or asthma development in children until the age of 10 was estimated by Bayesian kernel machine regression (BKMR) stratifying also for family history of atopy (FHA).
RESULTS: Our experimental data show that neither pinewood nor OSB emissions even at high total VOC levels and a long-lasting exposure period induce significant inflammatory or asthma-promoting effects in sensitized or non-sensitized mice. Moreover, an exposure during the vulnerable time window around birth was also without effect. Consistently, in our mother-child cohort LINA, an exposure to multiple wood-related VOCs during pregnancy or the first year of life was not associated with early wheezing or asthma development in children independent from their FHA.
CONCLUSION: Our findings indicate that emissions from wood and wood products at levels commonly occurring in the living environment do not exert adverse effects concerning wheezing or asthma development.

PMID: 33611105 [PubMed - as supplied by publisher]

Computational Screening of Biological Phase-separating Proteins.

Genomics Proteomics Bioinformatics. 2021 Feb 18;:

Authors: Shen B, Chen Z, Yu C, Chen T, Shi M, Li T

Abstract
Phase separation is an important mechanism that mediates the compartmentalization of proteins in cells. Proteins that can undergo phase separation in cells share certain typical sequence features, like intrinsically disordered regions (IDRs) and multiple modular domains. Sequence-based analysis tools are commonly used in the screening of these proteins. However, current phase separation predictors are mostly designed for IDR-containing proteins, thus inevitably overlook the phase-separating proteins with relatively low IDR content. Features other than amino acid sequence could provide crucial information for identifying possible phase-separating proteins: protein-protein interaction (PPI) networks imply multivalent interactions that underlines phase separation process; post-translational modifications (PTMs) are crucial in the regulation of phase separation behavior; spherical structures appearing on immunofluorescence (IF) images indicate condensed droplets formed by phase-separating proteins, distinguishing these proteins from non-phase-separating proteins. Here, we summarized the sequence-based tools for predicting phase-separating proteins and highlighted the importance of incorporating PPIs, PTMs, and IF images into phase separation prediction in future studies.

PMID: 33610793 [PubMed - as supplied by publisher]

An Integrated Systems Biology Approach Identifies the Proteasome as A Critical Host Machinery for ZIKV and DENV Replication.

Genomics Proteomics Bioinformatics. 2021 Feb 18;:

Authors: Song G, Lee EM, Pan J, Xu M, Rho HS, Cheng Y, Whitt N, Yang S, Kouznetsova J, Klumpp-Thomas C, Michael SG, Moore C, Yoon KJ, Christian KM, Simeonov A, Huang W, Xia M, Huang R, Lal-Nag M, Tang H, Zheng W, Qian J, Song H, Ming GL, Zhu H

Abstract
The zika virus (ZIKV) and dengue virus (DENV) flaviviruses exhibit similar replicative processes but have distinct clinical outcomes. A systematic understanding of virus-host protein-protein interaction networks can reveal cellular pathways critical to viral replication and disease pathogenesis. Here we employed three independent systems biology approaches toward this goal. First, protein array analysis of direct interactions between individual ZIKV/DENV viral proteins and 20,240 human proteins revealed multiple conserved cellular pathways and protein complexes, including proteasome complexes. Second, an RNAi screen of 10,415 druggable genes identified the host proteins required for ZIKV infection and uncovered that proteasome proteins were crucial in this process. Third, high-throughput screening of 6016 bioactive compounds for ZIKV inhibition yielded 134 effective compounds, including six proteasome inhibitors that suppress both ZIKV and DENV replication. Integrative analyses of these orthogonal datasets pinpoint proteasomes as critical host machinery for ZIKV/DENV replication. Our study provides multi-omics datasets for further studies of flavivirus-host interactions, disease pathogenesis, and new drug targets.

PMID: 33610792 [PubMed - as supplied by publisher]

The burden of disease of three food-associated heavy metals in clusters in the Danish population - towards targeted public health strategies.

Food Chem Toxicol. 2021 Feb 18;:112072

Authors: Romero Herrera JA, Thomsen ST, Jakobsen L, Fagt S, Banasik K, Izarzugaza JM, Brunak S, Pires SM

Abstract
Lifestyle and sociodemographics are likely to influence dietary patterns, and, as a result, human exposure to chemical contaminants in foods and their associated health impact. We aimed to characterize subgroups of the Danish population based on diet and sociodemographic indicators, and identify those bearing a higher disease burden due to exposure to methylmercury (MeHg), cadmium (Cd) and inorganic arsenic (i-As) . We collected dietary, lifestyle, and sociodemographic data on the occurrence of chemical contaminants in foods from Danish surveys. We grouped participants according to similarities in diet, lifestyle, and sociodemographics using Self-Organizing Maps (SOM), and estimated disease burden in disability-adjusted life years (DALY). SOM clustering resulted in 12 population groups with distinct characteristics. Exposure to contaminants varied between clusters and was largely driven by intake of fish, seafood and cereal products. Five clusters had an estimated annual burden > 20 DALY/100,000. The cluster with the highest burden had a high proportion of women of childbearing age, with most of the burden attributed to MeHg. Individuals belonging to the top three clusters had higher education and physical activity, were mainly non-smokers and lived in urban areas. Our findings may facilitate the development of preventive strategies targeted to the most affected subgroups.

PMID: 33610621 [PubMed - as supplied by publisher]

Direct coupling of oligomerization and oligomerization-driven endocytosis of the dopamine transporter to its conformational mechanics and activity.

J Biol Chem. 2021 Feb 18;:100430

Authors: Sorkina T, Cheng MH, Bagalkot TR, Wallace C, Watkins SC, Bahar I, Sorkin A

Abstract
Dopamine transporter (DAT) mediates the reuptake of synaptically-released dopamine, and thus controls the duration and intensity of dopamine neurotransmission. Mammalian DAT has been observed to form oligomers, although the mechanisms of oligomerization and its role in DAT activity and trafficking remain largely unknown. We discovered a series of small molecule compounds that stabilize trimers and induce high-order oligomers of DAT, and concomitantly promote its clathrin-independent endocytosis. Using a combination of chemical cross-linking, FRET microscopy, antibody-uptake endocytosis assay, live-cell lattice light sheet microscopy, ligand binding and substrate transport kinetics analyses, and molecular modeling and simulations, we investigated molecular basis of DAT oligomerization and endocytosis induced by these compounds. Our study showed that small molecule-induced DAT oligomerization and endocytosis are favored by the inward-facing DAT conformation and involve interactions of four hydrophobic residues at the interface between transmembrane helices TM4 and TM9. Surprisingly, a corresponding quadruple DAT mutant displays altered dopamine transport kinetics and increased cocaine-analog binding. The latter is shown to originate from an increased preference for outward-facing conformation and inward-to-outward transition. Taken together, our results demonstrate a direct coupling between conformational dynamics of DAT, functional activity of the transporter and its oligomerization leading to endocytosis. The high specificity of such coupling for DAT makes the TM4-9 hub a new target for pharmacological modulation of DAT activity and subcellular localization.

PMID: 33610553 [PubMed - as supplied by publisher]

Self-Sufficient Class VII Cytochromes P450: From Full-Length Structure to Synthetic Biology Applications.

Trends Biotechnol. 2021 Feb 18;:

Authors: Correddu D, Di Nardo G, Gilardi G

Abstract
Members of class VII cytochromes P450 are catalytically self-sufficient enzymes containing a phthalate dioxygenase reductase-like domain fused to the P450 catalytic domain. Among these, CYP116B46 is the first enzyme for which the 3D structure of the whole polypeptide chain has been solved, shedding light on the interaction between its domains, which is crucial for catalysis. Most of these enzymes have been isolated from extremophiles or detoxifying bacteria that can carry out regio- and enantioselective oxidation of compounds of biotechnological interest. Protein engineering has generated mutants that can perform challenging organic reactions such as the anti-Markovnikov alkene oxidation. This potential, combined with the detailed 3D structure, forms the basis for further directed evolution studies aimed at widening their biotechnological exploitation.

PMID: 33610332 [PubMed - as supplied by publisher]

Plant Cell Environ. 2021 Feb 22. doi: 10.1111/pce.14007. Online ahead of print.

ABSTRACT

The elucidation of plant health status requires quantifying multiple molecular metabolism markers. Until now, the extraction of these biomarkers is performed independently, with different extractions and protocols. This approach is inefficient, since it increases laboratory time, amount of sample, and could introduce biases or difficulties when comparing data. To limit these drawbacks, we introduce a versatile protocol for quantifying seven of the most commonly analysed biomarkers (photosynthetic pigments, free amino acids, soluble sugars, starch, phenolic compounds, flavonoids and malondialdehyde) covering substantial parts of plant metabolism, requiring only a minimum sample amount and common laboratory instrumentation. The procedures of this protocol rely on classic methods that have been updated to allow their sequential use, increasing reproducibility, sensibility and easiness to obtain quantitative results. Our method has been tested and validated over an extended diversity of organisms (Arabidopsis thaliana, Solanum lycopersicum, Olea europaea, Quercus ilex, Pinus pinaster and Chlamydomonas reinhardtii), tissues (leaves, roots and seeds) and stresses (cold, drought, heat, ultraviolet B and nutrient deficiency). Its application will allow increasing the number of parameters that can be monitored at once while decreasing sample handling and consequently, increasing the capacity of the laboratory.

PMID:33618425 | DOI:10.1111/pce.14007

Biochem Pharmacol. 2021 Feb 19:114482. doi: 10.1016/j.bcp.2021.114482. Online ahead of print.

ABSTRACT

We present ten insights that can be gained from computational models based on molecular mechanisms for the mammalian circadian clock. These insights range from the conditions in which circadian rhythms occur spontaneously to their entrainment by the light-dark (LD) cycle and to clock-related disorders of the sleep-wake cycle. Endogenous oscillations originate spontaneously from transcription-translation feedback loops involving clock proteins such as PER, CRY, CLOCK and BMAL1. Circadian oscillations occur in a parameter domain bounded by critical values. Outside this domain the circadian network ceases to oscillate and evolves to a stable steady state. This conclusion bears on the nature of arrhythmic behavior of the circadian clock, which may not necessarily be due to mutations in clock genes. Entrainment by the LD cycle occurs in a certain range of parameter values, with a phase that depends on the endogenous period of the circadian clock. A decrease in PER phosphorylation is accompanied by a decrease in endogenous period and a phase advance of the clock; this situation accounts for the familial, advanced sleep phase syndrome (FASPS). The mirror delayed sleep phase syndrome (DSPS) can be accounted for, similarly, by an increase in PER phosphorylation and a rise in autonomous period. Failure of entrainment by the LD cycle in the model corresponds to the non-24h sleep-wake cycle syndrome, in which the phase of the circadian clock drifts in the course of time. Quasi-periodic oscillations that develop in these conditions sometimes correspond to long-period patterns in which the circadian clock is nearly entrained for long bouts of time before its phase rapidly drifts until a new regime of quasi-entrainment is re-established. In regard to jet lag, the computational approach accounts for the two modes of re-entrainment observed after an advance or delay which correspond, respectively, to an eastward or westward flight: the clock adjusts in a direction similar (orthodromic) or opposite (antidromic) to that of the shift in the LD cycle. Computational modeling predicts that in the vicinity of the switch between orthodromic and antidromic re-entrainment the circadian clock may take a very long time to resynchronize with the LD cycle. Repetitive perturbations of the circadian clock due, for example, to chronic jet lag -a situation somewhat reminiscent of shift work- may lead to quasi-periodic or chaotic oscillations. The latter irregular oscillations can sometimes be observed in normal LD cycles, raising the question of their possible relevance to fragmented sleep patterns observed in narcolepsy. The latter condition, however, appears to originate from disorders in the orexin neural circuit, which promotes wakefulness, rather than from an irregular operation of the circadian clock.

PMID:33617843 | DOI:10.1016/j.bcp.2021.114482

Cell Mol Gastroenterol Hepatol. 2021 Feb 19:S2352-345X(21)00027-8. doi: 10.1016/j.jcmgh.2021.01.021. Online ahead of print.

NO ABSTRACT

PMID:33617792 | DOI:10.1016/j.jcmgh.2021.01.021

PLoS One. 2021 Feb 22;16(2):e0247294. doi: 10.1371/journal.pone.0247294. eCollection 2021.

ABSTRACT

Honeybees (Apis mellifera) play a significant role in the pollination of various food crops and plants. In the past decades, honeybee management has been challenged with increased pathogen and environmental pressure associating with increased beekeeping costs, having a marked economic impact on the beekeeping industry. Pathogens have been identified as a contributing cause of colony losses. Evidence suggested a possible route of pathogen transmission among bees via oral-oral contacts through trophallaxis. Here we propose a model that describes the transmission of an infection within a colony when bee members engage in the trophallactic activity to distribute nectar. In addition, we examine two important features of social immunity, defined as collective disease defenses organized by honeybee society. First, our model considers the social segregation of worker bees. The segregation limits foragers, which are highly exposed to pathogens during foraging outside the nest, from interacting with bees residing in the inner parts of the nest. Second, our model includes a hygienic response, by which healthy nurse bees exterminate infected bees to mitigate horizontal transmission of the infection to other bee members. We propose that the social segregation forms the first line of defense in reducing the uptake of pathogens into the colony. If the first line of defense fails, the hygienic behavior provides a second mechanism in preventing disease spread. Our study identifies the rate of egg-laying as a critical factor in maintaining the colony's health against an infection. We propose that winter conditions which cease or reduce the egg-laying activity combined with an infection in early spring can compromise the social immunity defenses and potentially cause colony losses.

PMID:33617598 | DOI:10.1371/journal.pone.0247294

PLoS Genet. 2021 Feb 22;17(2):e1009396. doi: 10.1371/journal.pgen.1009396. Online ahead of print.

ABSTRACT

How to respond to starvation determines fitness. One prominent behavioral response is increased locomotor activities upon starvation, also known as Starvation-Induced Hyperactivity (SIH). SIH is paradoxical as it promotes food seeking but also increases energy expenditure. Despite its importance in fitness, the genetic contributions to SIH as a behavioral trait remains unexplored. Here, we examined SIH in the Drosophila melanogaster Genetic Reference Panel (DGRP) and performed genome-wide association studies. We identified 23 significant loci, corresponding to 14 genes, significantly associated with SIH in adult Drosophila. Gene enrichment analyses indicated that genes encoding ion channels and mRNA binding proteins (RBPs) were most enriched in SIH. We are especially interested in RBPs because they provide a potential mechanism to quickly change protein expression in response to environmental challenges. Using RNA interference, we validated the role of syp in regulating SIH. syp encodes Syncrip (Syp), an RBP. While ubiquitous knockdown of syp led to semi-lethality in adult flies, adult flies with neuron-specific syp knockdown were viable and exhibited decreased SIH. Using the Temporal and Regional Gene Expression Targeting (TARGET) system, we further confirmed the role of Syp in adult neurons in regulating SIH. To determine how syp is regulated by starvation, we performed RNA-seq using the heads of flies maintained under either food or starvation conditions. RNA-seq analyses revealed that syp was alternatively spliced under starvation while its expression level was unchanged. We further generated an alternatively-spliced-exon-specific knockout (KO) line and found that KO flies showed reduced SIH. Together, this study demonstrates a significant genetic contribution to SIH as a behavioral trait, identifies syp as a SIH gene, and highlights the significance of RBPs and post-transcriptional processes in the brain in regulating behavioral responses to starvation.

PMID:33617535 | DOI:10.1371/journal.pgen.1009396

J Proteome Res. 2021 Feb 22. doi: 10.1021/acs.jproteome.0c00734. Online ahead of print.

ABSTRACT

Since the outset of COVID-19, the pandemic has prompted immediate global efforts to sequence SARS-CoV-2, and over 450 000 complete genomes have been publicly deposited over the course of 12 months. Despite this, comparative nucleotide and amino acid sequence analyses often fall short in answering key questions in vaccine design. For example, the binding affinity between different ACE2 receptors and SARS-COV-2 spike protein cannot be fully explained by amino acid similarity at ACE2 contact sites because protein structure similarities are not fully reflected by amino acid sequence similarities. To comprehensively compare protein homology, secondary structure (SS) analysis is required. While protein structure is slow and difficult to obtain, SS predictions can be made rapidly, and a well-predicted SS structure may serve as a viable proxy to gain biological insight. Here we review algorithms and information used in predicting protein SS to highlight its potential application in pandemics research. We also showed examples of how SS predictions can be used to compare ACE2 proteins and to evaluate the zoonotic origins of viruses. As computational tools are much faster than wet-lab experiments, these applications can be important for research especially in times when quickly obtained biological insights can help in speeding up response to pandemics.

PMID:33617253 | DOI:10.1021/acs.jproteome.0c00734

iScience. 2021 Jan 27;24(2):102101. doi: 10.1016/j.isci.2021.102101. eCollection 2021 Feb 19.

ABSTRACT

A virtual metabolic human model is a valuable complement to experimental biology and clinical studies, because in vivo research involves serious ethical and technical problems. I have proposed a multi-organ and multi-scale kinetic model that formulates the reactions of enzymes and transporters with the regulation of hormonal actions at postprandial and postabsorptive states. The computational model consists of 202 ordinary differential equations for metabolites with 217 reaction rates and 1,140 kinetic parameter constants. It is the most comprehensive, largest, and highly predictive model of the whole-body metabolism. Use of the model revealed the mechanisms by which individual disorders, such as steatosis, β cell dysfunction, and insulin resistance, were combined to cause diabetes. The model predicted a glycerol kinase inhibitor to be an effective medicine for type 2 diabetes, which not only decreased hepatic triglyceride but also reduced plasma glucose. The model also enabled us to rationally design combination therapy.

PMID:33615200 | PMC:PMC7878987 | DOI:10.1016/j.isci.2021.102101

iScience. 2021 Jan 22;24(2):102089. doi: 10.1016/j.isci.2021.102089. eCollection 2021 Feb 19.

ABSTRACT

The anti-CD20 monoclonal antibodies rituximab and obinutuzumab differ in their mechanisms of action, with obinutuzumab evoking greater direct B cell death. To characterize the signaling processes responsible for improved B cell killing by obinutuzumab, we undertook a phosphoproteomics approach and demonstrate that rituximab and obinutuzumab differentially activate pathways downstream of the B cell receptor. Although both antibodies induce strong ERK and MYC activation sufficient to promote cell-cycle arrest and B cell death, obinutuzumab exceeds rituximab in supporting apoptosis induction by means of aberrant SYK phosphorylation. In contrast, rituximab elicits stronger anti-apoptotic signals by activating AKT, by impairing pro-apoptotic BAD, and by releasing membrane-bound NOTCH1 to up-regulate pro-survival target genes. As a consequence, rituximab appears to reinforce BCL2-mediated apoptosis resistance. The unexpected complexity and differences by which rituximab and obinutuzumab interfere with signaling pathways essential for lymphoma pathogenesis and treatment provide important impetus to optimize and personalize the application of different anti-CD20 treatments.

PMID:33615197 | PMC:PMC7878992 | DOI:10.1016/j.isci.2021.102089

Pept Sci (Hoboken). 2021 Jan 8:e24217. doi: 10.1002/pep2.24217. Online ahead of print.

ABSTRACT

COVID-19 is caused by a novel coronavirus called severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). Virus cell entry is mediated through a protein-protein interaction (PPI) between the SARS-CoV-2 spike protein and angiotensin-converting enzyme 2 (ACE2). A series of stapled peptide ACE2 peptidomimetics based on the ACE2 interaction motif were designed to bind the coronavirus S-protein RBD and inhibit binding to the human ACE2 receptor. The peptidomimetics were assessed for antiviral activity in an array of assays including a neutralization pseudovirus assay, immunofluorescence (IF) assay and in-vitro fluorescence polarization (FP) assay. However, none of the peptidomimetics showed activity in these assays, suggesting that an enhanced binding interface is required to outcompete ACE2 for S-protein RBD binding and prevent virus internalization.

PMID:33615115 | PMC:PMC7883042 | DOI:10.1002/pep2.24217

ERJ Open Res. 2021 Feb 15;7(1):00723-2020. doi: 10.1183/23120541.00723-2020. eCollection 2021 Jan.

ABSTRACT

For individuals with high risk of exposure and thereafter developing and transmitting active tuberculosis, conditional post-exposure prophylaxis might be a potential tool for tuberculosis control https://bit.ly/39qHHh4.

PMID:33614775 | PMC:PMC7882782 | DOI:10.1183/23120541.00723-2020

Front Cardiovasc Med. 2021 Feb 3;7:617277. doi: 10.3389/fcvm.2020.617277. eCollection 2020.

ABSTRACT

The incidence of myocardial infarction (MI) increases every year worldwide. Better diagnostic and prognostic biomarkers for clinical applications are the consistent pursuit of MI research. In addition to electrocardiogram, echocardiography, coronary angiography, etc., circulating biomarkers are essential for the diagnosis, prognosis, and treatment effect monitoring of MI patients. In this review, we assessed both strength and weakness of MI circulating biomarkers including: (1) originated from damaged myocardial tissues including current golden standard cardiac troponin, (2) released from non-myocardial tissues due to MI-induced systems reactions, and (3) preexisted in blood circulation before the occurrence of MI event. We also summarized newly reported MI biomarkers. We proposed that the biomarkers preexisting in blood circulation before MI incidents should be emphasized in research and development for MI prevention in near future.

PMID:33614740 | PMC:PMC7886815 | DOI:10.3389/fcvm.2020.617277

Oncol Lett. 2021 Mar;21(3):222. doi: 10.3892/ol.2021.12483. Epub 2021 Jan 21.

ABSTRACT

Glypican-3 (GPC3) is a cell membrane glycoprotein that regulates cell growth and proliferation. Aberrant expression or distribution of GPC3 underlies developmental abnormalities and the development of solid tumours. The strongest evidence for the participation of GPC3 in carcinogenesis stems from studies on hepatocellular carcinoma and lung squamous cell carcinoma. To the best of our knowledge, the role of the GPC3 protein and its potential therapeutic application have never been studied in small cell lung carcinoma (SCLC), despite the known involvement of associated pathways and the high mortality caused by this disease. Therefore, the aim of the present study was to examine GPC3 targeting for SCLC immunotherapy. An immunotoxin carrying an anti-GPC3 antibody (hGC33) and Pseudomonas aeruginosa exotoxin A 38 (PE38) was generated. This hGC33-PE38 protein was overexpressed in E. coli and purified. ADP-ribosylation activity was tested in vitro against eukaryotic translation elongation factor 2. Cell internalisation ability was confirmed by confocal microscopy. Cytotoxicity was analysed by treating liver cancer (HepG2, SNU-398 and SNU-449) and lung cancer (NCI-H510A, NCI-H446, A549 and SK-MES1) cell lines with hGC33-PE38 and estimating viable cells number. A BrdU assay was employed to verify anti-proliferative activity of hGC33-PE38 on treated cells. Fluorescence-activated cell sorting was used for the detection of cell membrane-bound GPC3. The hGC33-PE38 immunotoxin displayed enzymatic activity comparable to native PE38. The protein was efficiently internalised by GPC3-positive cells. Moreover, hGC33-PE38 was cytotoxic to HepG2 cells but had no effect on known GPC3-negative cell lines. The H446 cells were sensitive to hGC33-PE38 (IC50, 70.6±4.6 ng/ml), whereas H510A cells were resistant. Cell surface-bound GPC3 was abundant on the membranes of H446 cells, but absent on H510A. Altogether, the present findings suggested that GPC3 could be considered as a potential therapeutic target for SCLC immunotherapy.

PMID:33613711 | PMC:PMC7859473 | DOI:10.3892/ol.2021.12483

Front Plant Sci. 2021 Feb 4;11:602313. doi: 10.3389/fpls.2020.602313. eCollection 2020.

ABSTRACT

Molecular characterization of genetically modified plants can provide crucial information for the development of detection and identification methods, to comply with traceability, and labeling requirements prior to commercialization. Detailed description of the genetic modification was previously a challenging step in the safety assessment, since it required the use of laborious and time-consuming techniques. In this study an accurate, simple, and fast method was developed for molecular characterization of genetically modified (GM) plants, following a user-friendly workflow for researchers with limited bioinformatic capabilities. Three GM events from a diverse array of crop species-perennial ryegrass, white clover, and canola-were used to test the approach that exploits long-read sequencing by the MinION device, from Oxford Nanopore Technologies. The method delivered a higher degree of resolution of the transgenic events within the host genome than has previously been possible with the standard Illumina short-range sequencing strategies. The flanking sequences, copy number, and presence of backbone sequences, and overall transgene insertion structure were determined for each of the plant genomes, with the additional identification of moderate-sized secondary insertions that would have previously been missed. The proposed workflow takes only about 1 week from DNA extraction to analyzed result, and the method will complement the existing approaches for molecular characterization of GM plants, since it makes the process faster, simpler, and more cost-effective.

PMID:33613582 | PMC:PMC7889508 | DOI:10.3389/fpls.2020.602313

Front Immunol. 2021 Feb 5;11:620716. doi: 10.3389/fimmu.2020.620716. eCollection 2020.

ABSTRACT

Germinal centers play a key role in the adaptive immune system since they are able to produce memory B cells and plasma cells that produce high affinity antibodies for an effective immune protection. The mechanisms underlying cell-fate decisions are not well understood but asymmetric division of antigen, B-cell receptor affinity, interactions between B-cells and T follicular helper cells (triggering CD40 signaling), and regulatory interactions of transcription factors have all been proposed to play a role. In addition, a temporal switch from memory B-cell to plasma cell differentiation during the germinal center reaction has been shown. To investigate if antigen affinity-based Tfh cell help recapitulates the temporal switch we implemented a multiscale model that integrates cellular interactions with a core gene regulatory network comprising BCL6, IRF4, and BLIMP1. Using this model we show that affinity-based CD40 signaling in combination with asymmetric division of B-cells result in switch from memory B-cell to plasma cell generation during the course of the germinal center reaction. We also show that cell fate division is unlikely to be (solely) based on asymmetric division of Ag but that BLIMP1 is a more important factor. Altogether, our model enables to test the influence of molecular modulations of the CD40 signaling pathway on the production of germinal center output cells.

PMID:33613551 | PMC:PMC7892951 | DOI:10.3389/fimmu.2020.620716