Plant Physiol. 2021 Feb 25;185(1):49-66. doi: 10.1093/plphys/kiaa012.

ABSTRACT

Deciphering gene regulatory networks (GRNs) is both a promise and challenge of systems biology. The promise lies in identifying key transcription factors (TFs) that enable an organism to react to changes in its environment. The challenge lies in validating GRNs that involve hundreds of TFs with hundreds of thousands of interactions with their genome-wide targets experimentally determined by high-throughput sequencing. To address this challenge, we developed ConnecTF, a species-independent, web-based platform that integrates genome-wide studies of TF-target binding, TF-target regulation, and other TF-centric omic datasets and uses these to build and refine validated or inferred GRNs. We demonstrate the functionality of ConnecTF by showing how integration within and across TF-target datasets uncovers biological insights. Case study 1 uses integration of TF-target gene regulation and binding datasets to uncover TF mode-of-action and identify potential TF partners for 14 TFs in abscisic acid signaling. Case study 2 demonstrates how genome-wide TF-target data and automated functions in ConnecTF are used in precision/recall analysis and pruning of an inferred GRN for nitrogen signaling. Case study 3 uses ConnecTF to chart a network path from NLP7, a master TF in nitrogen signaling, to direct secondary TF2s and to its indirect targets in a Network Walking approach. The public version of ConnecTF (https://ConnecTF.org) contains 3,738,278 TF-target interactions for 423 TFs in Arabidopsis, 839,210 TF-target interactions for 139 TFs in maize (Zea mays), and 293,094 TF-target interactions for 26 TFs in rice (Oryza sativa). The database and tools in ConnecTF will advance the exploration of GRNs in plant systems biology applications for model and crop species.

PMID:33631799 | DOI:10.1093/plphys/kiaa012

Aging (Albany NY). 2021 Feb 25;13. doi: 10.18632/aging.202603. Online ahead of print.

ABSTRACT

The aim of this study is to determine the molecular functions of brain derived neurotrophic factor (BDNF) in Huntington's disease (HD). A total of 1,675 differentially expressed genes (DEGs) were overlapped from HD versus control and BDNF-low versus high groups. Five co-expression modules were constructed using weight gene correlation network analysis, among which the blue and turquoise modules were most strongly correlated with HD and low BDNF. Functional enrichment analyses revealed DEGs in these modules significantly enriched in GABAergic synapse, phagosome, cyclic adenosine monophosphate (cAMP), mitogen-activated protein kinase (MAPK), renin-angiotensin system (Ras), Ras-associated protein-1 and retrograde endocannabinoid signaling pathways. The intersection pathways of BDNF, such as cAMP, MAPK and Ras signaling pathways, were identified in global regulatory network. Further performance evaluation of low BDNF accurately predicted HD occurrence according to the area under the curve of 82.4%. In aggregate, our findings highlighted the involvement of low BDNF expression in HD pathogenesis, potentially mediated by cAMP, MAPK and Ras signaling pathways.

PMID:33631722 | DOI:10.18632/aging.202603

Biochem Biophys Res Commun. 2021 Feb 22;548:20-26. doi: 10.1016/j.bbrc.2021.02.045. Online ahead of print.

ABSTRACT

Autophagy and apoptosis are essential physiological pathways that are required to maintain cellular homeostasis. Therefore, it is suggested that dysregulation in both pathways is linked to several disease states. Moreover, the crosstalk between autophagy and apoptosis plays an important role in pathophysiological processes associated with several neurodegenerative disorders. We have previously reported that 6-hydroxydopamine (6-OHDA)-triggered reactive oxygen species (ROS) induces dysregulated autophagy, and that a dysregulated autophagic flux contributes to caspase-dependent neuronal apoptosis. Based on our previous findings, we specifically aimed to elucidate the molecular mechanisms underlying the potential role of dysregulated autophagy in apoptotic neurodegeneration. The disuccinimidyl suberate (DSS) cross-linking assay and immunological analyses indicated that exposure of several types of cells to 6-OHDA resulted in BAX activation and subsequent oligomerization. Pharmacological inhibition and genetic perturbation of autophagy prevented 6-OHDA-induced BAX oligomerization and subsequent release of mitochondrial cytochrome c into the cytosol and caspase activation. These events were independent of expression levels of XIAP. Taken together, our results suggest that BAX oligomerization comprises a critical step by which 6-OHDA-induced dysregulated autophagy mediates neuronal apoptosis.

PMID:33631669 | DOI:10.1016/j.bbrc.2021.02.045

Biochim Biophys Acta Proteins Proteom. 2021 Feb 22:140631. doi: 10.1016/j.bbapap.2021.140631. Online ahead of print.

ABSTRACT

Leucine rich repeats (LRRs) with 20-30 residues form a super helix arrangement. Individual LRRs are separated into a highly conserved segment with a highly conserved (HCS) and a variable segment (VS). In LRRs short β-strands in HCS stack in parallel, while VS adopts various secondary structures. Among eleven classes recognized, only RI-like, Cysteine-containing (CC), and GALA classes adopt an α-helix. However, the repeat unit lengths are usually different from each other. We performed some analyses based on the atomic coordinates in the known LRR structures. In the VS consensuses of the three classes, position 8 in the VS part is, in common, occupied by conserved aliphatic residue adopting an α-helix. This aliphatic residue is near to the two conserved hydrophobic residues at position 4 (in the center of β-strands) in two adjacent HCS parts. The conserved aliphatic residue plays a crucial role to preserve two parallel β-strands.

PMID:33631375 | DOI:10.1016/j.bbapap.2021.140631

Exp Hematol. 2021 Feb 22:S0301-472X(21)00092-8. doi: 10.1016/j.exphem.2021.02.010. Online ahead of print.

ABSTRACT

Rpl11 haploinsufficient mice develop a macrocytic anemia similar to patients with DBA. Here, we fully characterize this model from clinical and pathophysiological perspectives. Early erythroid precursors have increased heme content and high cytoplasmic ROS, impairing erythroid differentiation at the CFU-E/proerythroblast stage and subsequently. Using single-cell analyses that link a cell's surface protein expression to its total transcriptome and unbiased analyses, we show GATA1, GATA1 target gene and mitotic spindle pathway gene transcription were the pathways most decreased. Expression of ribosome protein and globin genes were amplified. These changes, as well as the other transcriptional changes that were identified, closely resemble findings in mice that lack the heme export protein FLVCR, and thus suggest that heme excess and toxicity are the primary drivers of the macrocytic anemia. Consistent with this, treating Rpl11 haploinsufficient mice with corticosteroids increased the numbers of earliest erythroblasts but failed to overcome heme toxicities and improve the anemia. Rpl11 haploinsufficient mice uniquely upregulated mitochondrial genes, p53 and CDKN1A pathway genes, and DNA damage checkpoint genes, which should contribute further to erythroid marrow failure. Together our data establish Rpl11 haploinsufficient mice as an excellent model of DBA that can be used to study DBA pathogenesis and test novel therapies.

PMID:33631277 | DOI:10.1016/j.exphem.2021.02.010

Biophys J. 2021 Feb 22:S0006-3495(21)00160-0. doi: 10.1016/j.bpj.2021.02.022. Online ahead of print.

ABSTRACT

During actin-based cell migration, the actin cytoskeleton in the lamellipodium both generates and responds to force, which has functional consequences for the ability of the cell to extend protrusions. However, the material properties of the lamellipodial actin network and its response to stress on the timescale of motility are incompletely understood. Here we describe a dynamic wrinkling phenotype in the lamellipodium of fish keratocyes, where the actin sheet buckles upward away from the ventral membrane of the cell, forming a periodic pattern of wrinkles perpendicular to the cell's leading edge. Cells maintain an approximately constant wrinkle wavelength over time despite new wrinkle formation and the lateral movement of wrinkles in the cell frame of reference, suggesting that cells have a preferred or characteristic wrinkle wavelength. Generation of wrinkles is dependent upon myosin contractility, and their wavelength scales directly with the density of the actin network and inversely with cell adhesion. These results are consistent with a simple physical model for wrinkling in an elastic sheet under compression and suggest that the lamellipodial cytoskeleton behaves as an elastic material on the timescale of cell migration despite rapid actin turnover.

PMID:33631203 | DOI:10.1016/j.bpj.2021.02.022

J Phys Chem A. 2021 Feb 25. doi: 10.1021/acs.jpca.0c10147. Online ahead of print.

ABSTRACT

While many machine learning (ML) methods, particularly deep neural networks, have been trained for density functional and quantum chemical energies and properties, the vast majority of these methods focus on single-point energies. In principle, such ML methods, once trained, offer thermochemical accuracy on par with density functional and wave function methods but at speeds comparable to traditional force fields or approximate semiempirical methods. So far, most efforts have focused on optimized equilibrium single-point energies and properties. In this work, we evaluate the accuracy of several leading ML methods across a range of bond potential energy curves and torsional potentials. The methods were trained on the existing ANI-1 training set, calculated using the ωB97X/6-31G(d) single points at nonequilibrium geometries. We find that across a range of small molecules, several methods offer both qualitative accuracy (e.g., correct minima, both repulsive and attractive bond regions, anharmonic shape, and single minima) and quantitative accuracy in terms of the mean absolute percent error near the minima. At the moment, ANI-2x, FCHL, and a new libmolgrid-based convolutional neural net, the Colorful CNN, show good performance.

PMID:33630611 | DOI:10.1021/acs.jpca.0c10147

Environ Sci Pollut Res Int. 2021 Feb 25. doi: 10.1007/s11356-021-12929-3. Online ahead of print.

ABSTRACT

Underground coal fires are considered an ecological disaster. While underground coal fires are prevalent in coal-producing areas throughout the world, they are most problematic in northern China. Previous studies have shown that underground coal fires stimulate the formation of cracks or gas outlets on the surface, as well as coal fire sponges (CFS) on the soil layer surface, which collect coal-fired pollutants. Herein, ultra-high-performance liquid chromatography (UHPLC) was used in conjunction with electrospray ionization (ESI) high-resolution mass spectrometry to analyze CFS samples collected from the No. 8 fire zone, located in Wuda coalfield, Inner Mongolia, China. The results show that CFS contain 233 oxy-substituted polycyclic aromatic hydrocarbons (O-PAHs), e.g., naphthaldehyde; 40 oxapolycyclic aromatic hydrocarbons (OPAHs), e.g., dibenzofuran; 40 alkyl-substituted polycyclic aromatic hydrocarbons (R-PAHs); and 11 parent polycyclic aromatic hydrocarbons (PPAHs). Thus, CFS are primarily composed of O-PAHs, which are 25 times and 5 times more prevalent than PPAHs and R-PAHs, respectively. As such, a high relative abundance of varied O-PAHs are discharged from underground coal fires, which is significantly different from what is released during industrial coal burning. Owing to their water solubility and condensability, the new facts disclosed in this paper may provide a new perspective for understanding complex organic pollutants from underground coal fires and their environmental impacts.

PMID:33630262 | DOI:10.1007/s11356-021-12929-3

JAMA Netw Open. 2021 Feb 1;4(2):e210112. doi: 10.1001/jamanetworkopen.2021.0112.

ABSTRACT

IMPORTANCE: Genetic disorders are historically defined through phenotype-first approaches. However, risk estimates derived from phenotype-linked ascertainment may overestimate severity and penetrance. Pathogenic variants in DICER1 are associated with increased risks of rare and common neoplasms and thyroid disease in adults and children. This study explored how effectively a genome-first approach could characterize the clinical traits associated with germline DICER1 putative loss-of-function (pLOF) variants in an unselected clinical cohort.

OBJECTIVE: To examine the prevalence, penetrance, and phenotypic characteristics of carriers of germline DICER1 pLOF variants via genome-first ascertainment.

DESIGN, SETTING, AND PARTICIPANTS: This cohort study classifies DICER1 variants in germline exome sequence data from 92 296 participants of the Geisinger MyCode Community Health Initiative. Data for each MyCode participant were used from the start of the Geisinger electronic health record to February 1, 2018.

MAIN OUTCOMES AND MEASURES: Prevalence of germline DICER1 variation; penetrance of malignant tumors and thyroid disease in carriers of germline DICER1 variation; structured, manual review of electronic health records; and DICER1 sequencing of available tumors from an associated cancer registry.

RESULTS: A total of 92 296 adults (mean [SD] age, 59 [18] years; 98% white; 60% female) participated in the study. Germline DICER1 pLOF variants were observed in 1 in 3700 to 1 in 4600 participants, more than double the expected prevalence. Malignant tumors (primarily thyroid carcinoma) were observed in 4 of 25 participants (16%) with DICER1 pLOF variants, which is comparable (by 50 years of age) to the frequency of neoplasms in the largest registry- and clinic-based (phenotype-first) DICER1 studies published to date. DICER1 pLOF variants were significantly associated with risks of thyroidectomy (odds ratio [OR], 6.0; 95% CI, 2.2-16.3; P = .007) and thyroid cancer (OR, 9.2; 95% CI, 2.1-34.7; P = .02) compared with controls, but there was not a significant increase in the risk of goiter (OR, 1.8; 95% CI, 0.7-4.9). A female patient in her 80s who was a carrier of a germline DICER1 hotspot variant was apparently healthy on electronic health record review. The term DICER1 did not appear in any of the medical records of the 25 participants with a pLOF DICER1 variant, even in those affected with a known DICER1-associated tumor or thyroid phenotype.

CONCLUSIONS AND RELEVANCE: This cohort study was able to ascertain individuals with germline DICER1 variants based on a genome-first approach rather than through a previously established DICER1-related phenotype. Use of the genome-first approach may complement more traditional approaches to syndrome delineation and may be an efficient approach for risk estimation.

PMID:33630087 | DOI:10.1001/jamanetworkopen.2021.0112

Biomed Res Int. 2021 Feb 13;2021:2989213. doi: 10.1155/2021/2989213. eCollection 2021.

ABSTRACT

BACKGROUND: Standardization of clinical practices is an essential part of continuing education of newly registered nurses in the intensive care unit (ICU). The development of educational standards based on evidence can help improve the quality of educational programs and ultimately clinical skills and practices.

OBJECTIVES: The objectives of the study were to develop a standardized learning curve of arterial blood gas (ABG) sampling competency, to design a checklist for the assessment of competency, to assess the relative importance of predictors and learning patterns of competency, and to determine how many times it is essential to reach a specific level of ABG sampling competency according to the learning curve.

DESIGN: A quasi-experimental, nonrandomized, single-group trial with time series design. Participants. All newly registered nurses in the ICU of a teaching hospital of Tehran University of Medical Sciences were selected from July 2016 to April 2018. Altogether, 65 nurses participated in the study; however, at the end, only nine nurses had dropped out due to shift displacement.

METHODS: At first, the primary checklist was prepared to assess the nurses' ABG sampling practices and it was finalized after three sessions of the expert panel. The checklist had three domains, including presampling, during sampling, and postsampling of ABG competency. Then, 56 nurses practiced ABG sampling step by step under the supervision of three observers who controlled the processes and they filled the checklists. The endpoint was considered reaching a 95 score on the learning curve. The Poisson regression model was used in order to verify the effective factors of ABG sampling competency. The importance of variables in the prediction of practice scores had been calculated in a linear regression of R software by using the relaimpo package.

RESULTS: According to the results, in order to reach a skill level of 55, 65, 75, 85, and 95, nurses, respectively, would need average ABG practice times of 6, 6, 7, 7, and 7. In the linear regression model, demographic variables predict 47.65 percent of changes related to scores in practices but the extent of prediction of these variables totally decreased till 7 practice times, and in each practice, nurses who had the higher primary skill levels gained 1 to 2 skill scores more than those with low primary skills.

CONCLUSIONS: Utilization of the learning curve could be helpful in the standardization of clinical practices in nursing training and optimization of the frequency of skills training, thus improving the training quality in this field. This trial is registered with NCT02830971.

PMID:33628776 | PMC:PMC7899780 | DOI:10.1155/2021/2989213

Clin Exp Vaccine Res. 2021 Jan;10(1):24-34. doi: 10.7774/cevr.2021.10.1.24. Epub 2021 Jan 31.

ABSTRACT

PURPOSE: Chitosan is a natural polymer that has excellent properties include biocompatibility, biodegradability, no cytotoxicity, high charge density, low cost, mucoadhesive, permeation enhancing (ability to cross tight junction), and immunomodulating ability that makes the spectrum of its applicability much broader. This study was conducted to investigate the stabilizing, preservative and immunogenicity properties of N-trimethyl chitosan nanospheres (N-TMCNS).

MATERIALS AND METHODS: The tetanus toxoid (TT) was encapsulated into N-TMCNS and then characterized by scanning electron microscope, atomic force microscope, and dynamic light scattering. For stabilizer assay of N-TMCNS after storage of TT-N-TMCNS at different temperatures for 3 weeks, they were used for immunization of mice and different temperatures groups' anti-TT-N-TMCNS production compared with other groups. Finally, the immunized mice were challenged with tetanus toxin. The preservation activity of TT-N-TMCNS against Escherichia coli was compared with thimerosal formulated TT.

RESULTS: Our results revealed that heat-treated TT-N-TMCNS could induce higher titer of neutralizing immunoglobulin G in compared to TT vaccine and was able to protect the mice better than TT vaccine in challenge test. Furthermore, N-TMCNS as a preservative inhibited the growth of E. coli more effective than thimerosal.

CONCLUSION: Overall, the obtained results indicated that the N-TMCNS is one of the best stabilizer and preservative agent that can be used in the formulation of TT vaccine.

PMID:33628751 | PMC:PMC7892940 | DOI:10.7774/cevr.2021.10.1.24

Front Pharmacol. 2021 Jan 20;11:553404. doi: 10.3389/fphar.2020.553404. eCollection 2020.

ABSTRACT

Sinensetin, a plant-derived polymethoxylated flavonoid found in Orthosiphon aristatus var. aristatus and several citrus fruits, has been found to possess strong anticancer activities and a variety of other pharmacological benefits and promising potency in intended activities with minimal toxicity. This review aims to compile an up-to-date reports of published scientific information on sinensetin pharmacological activities, mechanisms of action and toxicity. The present findings about the compound are critically analyzed and its prospect as a lead molecule for drug discovery is highlighted. The databases employed for data collection are mainly through Google Scholar, PubMed, Scopus and Science Direct. In-vitro and in-vivo studies showed that sinensetin possessed strong anticancer activities and a wide range of pharmacological activities such as anti-inflammatory, antioxidant, antimicrobial, anti-obesity, anti-dementia and vasorelaxant activities. The studies provided some insights on its several mechanisms of action in cancer and other disease states. However, more detail mechanistic studies are needed to understand its pharmacological effects. More in vivo studies in various animal models including toxicity, pharmacokinetic, pharmacodynamic and bioavailability studies are required to assess its efficacy and safety before submission to clinical studies. In this review, an insight on sinensetin pharmacological activities and mechanisms of action serves as a useful resource for a more thorough and comprehensive understanding of sinensetin as a potential lead candidate for drug discovery.

PMID:33628166 | PMC:PMC7898666 | DOI:10.3389/fphar.2020.553404

mSphere. 2021 Feb 24;6(1):e01204-20. doi: 10.1128/mSphere.01204-20.

ABSTRACT

Unlike most other eukaryotes, Leishmania and other trypanosomatid protozoa have largely eschewed transcriptional control of gene expression, relying instead on posttranscriptional regulation of mRNAs derived from polycistronic transcription units (PTUs). In these parasites, a novel modified nucleotide base (β-d-glucopyranosyloxymethyluracil) known as J plays a critical role in ensuring that transcription termination occurs only at the end of each PTU, rather than at the polyadenylation sites of individual genes. To further understand the biology of J-associated processes, we used tandem affinity purification (TAP) tagging and mass spectrometry to reveal proteins that interact with the glucosyltransferase performing the final step in J synthesis. These studies identified four proteins reminiscent of subunits in the PTW/PP1 complex that controls transcription termination in higher eukaryotes. Moreover, bioinformatic analyses identified the DNA-binding subunit of Leishmania PTW/PP1 as a novel J-binding protein (JBP3), which is also part of another complex containing proteins with domains suggestive of a role in chromatin modification/remodeling. Additionally, JBP3 associates (albeit transiently and/or indirectly) with the trypanosomatid equivalent of the PAF1 complex involved in the regulation of transcription in other eukaryotes. The downregulation of JBP3 expression levels in Leishmania resulted in a substantial increase in transcriptional readthrough at the 3' end of most PTUs. We propose that JBP3 recruits one or more of these complexes to the J-containing regions at the end of PTUs, where they halt the progression of the RNA polymerase. This decoupling of transcription termination from the splicing of individual genes enables the parasites' unique reliance on polycistronic transcription and posttranscriptional regulation of gene expression.IMPORTANCE Leishmania parasites cause a variety of serious human diseases, with no effective vaccine and emerging resistance to current drug therapy. We have previously shown that a novel DNA base called J is critical for transcription termination at the ends of the polycistronic gene clusters that are a hallmark of Leishmania and related trypanosomatids. Here, we describe a new J-binding protein (JBP3) associated with three different protein complexes that are reminiscent of those involved in the control of transcription in other eukaryotes. However, the parasite complexes have been reprogrammed to regulate transcription and gene expression in trypanosomatids differently than in the mammalian hosts, providing new opportunities to develop novel chemotherapeutic treatments against these important pathogens.

PMID:33627513 | DOI:10.1128/mSphere.01204-20

mSphere. 2021 Feb 24;6(1):e01202-20. doi: 10.1128/mSphere.01202-20.

ABSTRACT

Short-amplicon 16S rRNA gene sequencing is currently the method of choice for studies investigating microbiomes. However, comparative studies on differences in procedures are scarce. We sequenced human stool samples and mock communities with increasing complexity using a variety of commonly used protocols. Short amplicons targeting different variable regions (V-regions) or ranges thereof (V1-V2, V1-V3, V3-V4, V4, V4-V5, V6-V8, and V7-V9) were investigated for differences in the composition outcome due to primer choices. Next, the influence of clustering (operational taxonomic units [OTUs], zero-radius OTUs [zOTUs], and amplicon sequence variants [ASVs]), different databases (GreenGenes, the Ribosomal Database Project, Silva, the genomic-based 16S rRNA Database, and The All-Species Living Tree), and bioinformatic settings on taxonomic assignment were also investigated. We present a systematic comparison across all typically used V-regions using well-established primers. While it is known that the primer choice has a significant influence on the resulting microbial composition, we show that microbial profiles generated using different primer pairs need independent validation of performance. Further, comparing data sets across V-regions using different databases might be misleading due to differences in nomenclature (e.g., Enterorhabdus versus Adlercreutzia) and varying precisions in classification down to genus level. Overall, specific but important taxa are not picked up by certain primer pairs (e.g., Bacteroidetes is missed using primers 515F-944R) or due to the database used (e.g., Acetatifactor in GreenGenes and the genomic-based 16S rRNA Database). We found that appropriate truncation of amplicons is essential and different truncated-length combinations should be tested for each study. Finally, specific mock communities of sufficient and adequate complexity are highly recommended.IMPORTANCE In 16S rRNA gene sequencing, certain bacterial genera were found to be underrepresented or even missing in taxonomic profiles when using unsuitable primer combinations, outdated reference databases, or inadequate pipeline settings. Concerning the last, quality thresholds as well as bioinformatic settings (i.e., clustering approach, analysis pipeline, and specific adjustments such as truncation) are responsible for a number of observed differences between studies. Conclusions drawn by comparing one data set to another (e.g., between publications) appear to be problematic and require independent cross-validation using matching V-regions and uniform data processing. Therefore, we highlight the importance of a thought-out study design including sufficiently complex mock standards and appropriate V-region choice for the sample of interest. The use of processing pipelines and parameters must be tested beforehand.

PMID:33627512 | DOI:10.1128/mSphere.01202-20

J Virol. 2021 Feb 24:JVI.00140-21. doi: 10.1128/JVI.00140-21. Online ahead of print.

ABSTRACT

Human coronaviruses (HCoV) are respiratory pathogens which have been known since the 1960's. In December 2019, a new betacoronavirus, SARS-CoV-2, was reported and is responsible for one of the biggest pandemics of the last two centuries. Similar to the HCoV-OC43 strain, available evidence suggests SARS-CoV-2 neuroinvasion associated with potential neurological disorders. Coronavirus infection of the central nervous system (CNS) is largely controlled by a viral factor, the spike glycoprotein (S) and a host factor, innate immunity. However, the interaction between these two factors remains elusive. Proteolytic cleavage of the S protein can occur at the interface between receptor binding (S1) and fusion (S2) domains (S1/S2), as well as in a position adjacent to a fusion peptide within S2 (S2'). Herein, using HCoV-OC43 as a surrogate for SARS-CoV-2, we report that both S protein sites are involved in neurovirulence and are required for optimal CNS infection. Whereas efficient cleavage at S1/S2 is associated with decreased virulence, the potentially cleavable putative S2' site is essential for efficient viral infection. Furthermore, type 1 interferon (IFN 1)-related innate immunity also plays an important role in the control of viral spread towards the spinal cord, by preventing infection of ependymal cells. Our results underline the link between the differential S cleavage and IFN 1 in the prevention of viral spread, to control the severity of infection and pathology in both immunocompetent and immunodeficient mice. Taken together, these results point towards two potential therapeutic anti-viral targets: cleavage of the S protein in conjunction with efficient IFN 1-related innate immunity to prevent or at least reduce neuroinvasion, neural spread, and potential associated neurovirulence of human coronaviruses.ImportanceHuman coronaviruses (HCoV) are recognized respiratory pathogens. The emergence of the novel pathogenic member of this family in December 2019 (SARS-CoV-2, which causes COVID-19) poses a global health emergency. As with other coronaviruses reported previously, invasion of the human central nervous system (CNS), associated with diverse neurological disorders, was suggested for SARS-CoV-2. Herein, using the related HCoV-OC43 strain, we show that the viral spike protein constitutes a major neurovirulence factor and that type 1 interferon (IFN 1), in conjunction with cleavage of S protein by host proteases, represent important host factors that participate in the control of CNS infection.To our knowledge, this is the first demonstration of a direct link between cleavage of the S protein, innate immunity and neurovirulence. Understanding mechanisms of viral infection and spread in neuronal cells is essential to better design therapeutic strategies, and to prevent infection by human coronaviruses such as SARS-CoV-2 in human CNS especially in the vulnerable populations such as the elderly and immune-compromised individuals.

PMID:33627397 | DOI:10.1128/JVI.00140-21

Diabetes. 2021 Feb 24:db200572. doi: 10.2337/db20-0572. Online ahead of print.

ABSTRACT

Obesity-induced white adipose tissue (WAT) hypertrophy is associated with elevated adipose tissue macrophage (ATM) content. Overexpression of the triggering receptor expressed on myeloid cells 2 (TREM2) reportedly increases adiposity, worsening health. Paradoxically, using insulin resistance, elevated fat mass and hypercholesterolemia as hallmarks of unhealthy obesity, a recent report demonstrated ATM-expressed TREM2 promoted health. Here, we identified that in mice TREM2 deficiency aggravated diet-induced insulin resistance and hepatic steatosis independently of fat and cholesterol levels. Metabolomics linked TREM2 deficiency with elevated obesity-instigated serum ceramides that correlated with impaired insulin sensitivity. Remarkably, while inhibiting ceramide synthesis exerted no influences on TREM2-dependent ATM remodeling, inflammation or lipid load, it restored insulin tolerance, reversing adipose hypertrophy and secondary hepatic steatosis of TREM2-deficient animals. Bone marrow transplantation experiments revealed unremarkable influences of immune cell-expressed TREM2 on health instead demonstrating that WAT-intrinsic mechanisms impinging on sphingolipid metabolism dominate in TREM2's systemic protective effects on metabolic health.

PMID:33627323 | DOI:10.2337/db20-0572

Cell Rep. 2021 Feb 23;34(8):108771. doi: 10.1016/j.celrep.2021.108771.

ABSTRACT

Mass spectrometry (MS)-based phosphoproteomics has revolutionized our ability to profile phosphorylation-based signaling in cells and tissues on a global scale. To infer the action of kinases and signaling pathways in phosphoproteomic experiments, we present PhosR, a set of tools and methodologies implemented in a suite of R packages facilitating comprehensive analysis of phosphoproteomic data. By applying PhosR to both published and new phosphoproteomic datasets, we demonstrate capabilities in data imputation and normalization by using a set of "stably phosphorylated sites" and in functional analysis for inferring active kinases and signaling pathways. In particular, we introduce a "signalome" construction method for identifying a collection of signaling modules to summarize and visualize the interaction of kinases and their collective actions on signal transduction. Together, our data and findings demonstrate the utility of PhosR in processing and generating biological knowledge from MS-based phosphoproteomic data.

PMID:33626354 | DOI:10.1016/j.celrep.2021.108771

Adv Nutr. 2021 Feb 24:nmab014. doi: 10.1093/advances/nmab014. Online ahead of print.

ABSTRACT

The comprehensive characterization of probiotic action has flourished during the past few decades, alongside the evolution of high-throughput, multiomics platforms. The integration of these platforms into probiotic animal and human studies has provided valuable insights into the holistic effects of probiotic supplementation on intestinal and extraintestinal diseases. Indeed, these methodologies have informed about global molecular changes induced in the host and residing commensals at multiple levels, providing a bulk of metagenomic, transcriptomic, proteomic, and metabolomic data. The meaningful interpretation of generated data remains a challenge; however, the maturation of the field of systems biology and artificial intelligence has supported analysis of results. In this review article, we present current literature on the use of multiomics approaches in probiotic studies, we discuss current trends in probiotic research, and examine the possibility of tailor-made probiotic supplementation. Lastly, we delve deeper into newer technologies that have been developed in the last few years, such as single-cell multiomics analyses, and provide future directions for the maximization of probiotic efficacy.

PMID:33626128 | DOI:10.1093/advances/nmab014

Curr Microbiol. 2021 Feb 24. doi: 10.1007/s00284-021-02389-w. Online ahead of print.

ABSTRACT

Selection and dissemination of resistant bacteria and antibiotic resistance genes (ARGs) require a deeper understanding since antibiotics are permanently released to the environment. The objective of this paper was to evaluate the phenotypic resistance of 499 isolates of Pseudomonas spp. from urban water sources, and the prevalence of 20 ARGs within those isolates. Resistance to penicillins, cephalosporins, carbapenems, quinolones, macrolides, and tetracyclines was mainly observed in the hospital effluent, municipal wastewater and river water downstream the city. Resistant strains were frequently identified as P. aeruginosa and P. putida. P. aeruginosa isolates were mostly resistant to cefepime, ceftazidime, imipenem, and gentamycin, while P. putida strains were especially resistant to piperacillin-tazobactam. ARGs such as blaTEM-1, blaSHV-1, blaPER-1, blaAmpC, blaVIM-1, PstS, qnrA, qnrB, ermB, tetA, tetB and tetC have been detected. The blaAmpC gene was found in P. aeruginosa, while blaTEM-1 and blaPER-1 genes were found in P. putida. Class 1 integron integrase gene was found in 6.81% of the Pseudomonas isolates.

PMID:33625570 | DOI:10.1007/s00284-021-02389-w

Elife. 2021 Feb 24;10:e60321. doi: 10.7554/eLife.60321. Online ahead of print.

ABSTRACT

Although identifying cell names in dense image stacks is critical in analyzing functional whole-brain data enabling comparison across experiments, unbiased identification is very difficult, and relies heavily on researchers' experiences. Here we present a probabilistic-graphical-model framework, CRF_ID, based on Conditional Random Fields, for unbiased and automated cell identification. CRF_ID focuses on maximizing intrinsic similarity between shapes. Compared to existing methods, CRF_ID achieves higher accuracy on simulated and ground-truth experimental datasets, and better robustness against challenging noise conditions common in experimental data. CRF_ID can further boost accuracy by building atlases from annotated data in highly computationally efficient manner, and by easily adding new features (e.g. from new strains). We demonstrate cell annotation in C. elegans images across strains, animal orientations, and tasks including gene-expression localization, multi-cellular and whole-brain functional imaging experiments. Together, these successes demonstrate that unbiased cell annotation can facilitate biological discovery, and this approach may be valuable to annotation tasks for other systems.

PMID:33625357 | DOI:10.7554/eLife.60321