Mol Microbiol. 2021 Mar 18. doi: 10.1111/mmi.14717. Online ahead of print.

ABSTRACT

Chitin utilization by microbes plays a significant role in biosphere carbon and nitrogen cycling, and studying the microbial approaches used to degrade chitin will facilitate our understanding of bacterial strategies to degrade a broad range of recalcitrant polysaccharides. The early stages of chitin depolymerization by the bacterium Cellvibrio japonicus have been characterized and are dependent on one chitin-specific lytic polysaccharide monooxygenase and non-redundant glycoside hydrolases from the family GH18 to generate chito-oligosaccharides for entry into metabolism. Here, we describe the mechanisms for the latter stages of chitin utilization by C. japonicus with an emphasis on the fate of chito-oligosaccharides. Our systems biology approach combined transcriptomics and bacterial genetics using ecologically relevant substrates to determine the essential mechanisms for chito-oligosaccharide transport and catabolism in Cellvibrio japonicus. Using RNAseq analysis we found a coordinated expression of genes that encode polysaccharide-degrading enzymes. Mutational analysis determined that the hex20B gene product, predicted to encode a hexosaminidase, was required for efficient utilization of chito-oligosaccharides. Furthermore, two gene loci (CJA_0353 and CJA_1157), which encode putative TonB-dependent transporters, were also essential for chito-oligosaccharides utilization. This study further develops our model of C. japonicus chitin metabolism and may be predictive for other environmentally or industrially important bacteria.

PMID:33735458 | DOI:10.1111/mmi.14717

Ocul Immunol Inflamm. 2021 Mar 18:1-13. doi: 10.1080/09273948.2020.1870148. Online ahead of print.

ABSTRACT

Aim: Chemical injuries can potentially lead to the necrosis anterior segment of the eye, and cornea in particular. Inflammatory cytokines are the first factors produced after chemical ocular injuries. Inflammation via promoting the angiogenesis factor tries to implement the wound healing mechanism in the epithelial and stromal layer of the cornea. Methods: Narrative review.Results: In our review, we described the patterns of chemical injuries in the cornea and their molecular mechanisms associated with the expression of inflammatory cytokines. Moreover, the effects of inflammation signals on angiogenesis factors and CNV were explained. Conclusion: The contribution of inflammation and angiogenesis causes de novo formation of blood vessels that is known as the corneal neovascularization (CNV). The new vascularity interrupts cornea clarity and visual acuity. Inflammation also depleted the Limbal stem cells (LSCs) in the limbus causing the failure of normal corneal epithelial healing and conjunctivalization of the cornea.

PMID:33734925 | DOI:10.1080/09273948.2020.1870148

Mol Syst Biol. 2021 Mar;17(3):e10116. doi: 10.15252/msb.202010116.

ABSTRACT

Broad-spectrum antibiotics target multiple gram-positive and gram-negative bacteria, and can collaterally damage the gut microbiota. Yet, our knowledge of the extent of damage, the antibiotic activity spectra, and the resistance mechanisms of gut microbes is sparse. This limits our ability to mitigate microbiome-facilitated spread of antibiotic resistance. In addition to antibiotics, non-antibiotic drugs affect the human microbiome, as shown by metagenomics as well as in vitro studies. Microbiome-drug interactions are bidirectional, as microbes can also modulate drugs. Chemical modifications of antibiotics mostly function as antimicrobial resistance mechanisms, while metabolism of non-antibiotics can also change the drugs' pharmacodynamic, pharmacokinetic, and toxic properties. Recent studies have started to unravel the extensive capacity of gut microbes to metabolize drugs, the mechanisms, and the relevance of such events for drug treatment. These findings raise the question whether and to which degree these reciprocal drug-microbiome interactions will differ across individuals, and how to take them into account in drug discovery and precision medicine. This review describes recent developments in the field and discusses future study areas that will benefit from systems biology approaches to better understand the mechanistic role of the human gut microbiota in drug actions.

PMID:33734582 | DOI:10.15252/msb.202010116

Environ Microbiol. 2021 Mar 18. doi: 10.1111/1462-2920.15462. Online ahead of print.

ABSTRACT

Microbial communities exhibit spatial structure at different scales, due to constant interactions with their environment and dispersal limitation. While this spatial structure is often considered in studies focusing on free-living environmental communities, it has received less attention in the context of host-associated microbial communities, or microbiota. The wider adoption of methods accounting for spatial variation in these communities will help to address open questions in basic microbial ecology as well as realize the full potential of microbiome-aided medicine. Here, we first overview known factors affecting the composition of microbiota across diverse host types and at different scales, with a focus on the human gut as one of the most actively studied microbiota. We outline a number of topical open questions in the field related to spatial variation and patterns. We then review existing methodology for the spatial modeling of microbiota. We suggest that methodology from related fields, such as systems biology and macro-organismal ecology, could be adapted to obtain more accurate models of spatial structure. We further posit that methodological developments in the spatial modeling and analysis of microbiota could in turn broadly benefit theoretical and applied ecology and contribute to the development of novel industrial and clinical applications. This article is protected by copyright. All rights reserved.

PMID:33734553 | DOI:10.1111/1462-2920.15462

Mol Reprod Dev. 2021 Mar 18. doi: 10.1002/mrd.23465. Online ahead of print.

ABSTRACT

Hanging drop (HD) three-dimensional (3D) culture model for buffalo granulosa cells (GC) was reported to mimic the preovulatory stage of ovarian follicles in our previous study. To further verify its reliability, the present study attempted a comparative transcriptome profile of buffalo GC freshly isolated from ovarian follicles (<8 mm diameter) (FC) and their cultures in normal culture dish (ND or 2D), polyHEMA coated dish (PH) and HD culture systems (3D). Out of 223 significantly (-log2 fold change: >3; p < .0005; false discovery rate [FDR]: <0.1) differentially expressed genes (SDEGs) among different culture systems, 137 were found unannotated, and 94, 29, and 66 were exclusively expressed in FC, PH, and HD, respectively. However, on eliminating the fixed points of p values and FDR from the entire raw data, only 11 genes related to long noncoding RNA, 12 genes related to luteinization, and 3 genes related to follicular maturation were exclusively expressed in FC, PH, and HD culture systems, respectively. The quantitative real time-PCR validation and the next generation sequencing data had more than 90% correlation. Bioinformatics analyses of the exclusively expressed SDEG revealed that the freshly aspirated GCs were a true representative of GCs from small follicles (<8 mm diameter), the GC spheroids under PH maintained mitochondrial function, and those cultured in HD system for 6 days simulated the inflammatory milieu required for ovulation. Therefore, the comparative transcriptome profile also reinforced that HD culture system is better in vitro culture method than the other methods analyzed in this study for buffalo GC.

PMID:33734523 | DOI:10.1002/mrd.23465

Emerg Microbes Infect. 2021 Mar 18:1-50. doi: 10.1080/22221751.2021.1905488. Online ahead of print.

ABSTRACT

Seasonal human coronaviruses (HCoVs) including HCoV-229E, -OC43, -NL63 and -HKU1 widely spread in global human populations. However, the relevance of humoral response against seasonal HCoVs to COVID-19 pathogenesis is elusive. In this study, we profiled the temporal changes of IgG antibody against spike proteins (S-IgG) of SARS-CoV-2 and seasonal HCoVs in 838 plasma samples collected from 344 COVID-19 patients. We tested the antigenic cross-reactivities of S protein between SARS-CoV-2 and seasonal HCoVs and evaluated the correlations between the levels of HCoV-OC43 S-IgG and the disease severity in COVID-19 patients. We found that SARS-CoV-2 S-IgG titers mounted until days 22-28, whereas HCoV-OC43 antibody titers increased until days 15-21 and then plateaued until day 46. However, IgG titers against HCoV-NL63, -229E, and -HKU1 showed no significant increase. A two-way cross-reactivity was identified between SARS-CoV-2 and HCoV-OC43. Neutralizing antibodies against SARS-CoV-2 were not detectable in healthy controls who were positive for HCoV-OC43 S-IgG. HCoV-OC43 S-IgG titers were significantly higher in patients with severe disease than those in mild patients at days 1-21 post symptom onset (PSO). Higher levels of HCoV-OC43 S-IgG were also observed in patients requiring mechanical ventilation. At days 1-10 PSO, HCoV-OC43 S-IgG titers correlated to disease severity in the age group over 60. Our data indicate that there is a correlation between cross-reactive antibody against HCoV-OC43 spike protein and disease severity in COVID-19 patients.

PMID:33734013 | DOI:10.1080/22221751.2021.1905488

ACS Biomater Sci Eng. 2021 Mar 18. doi: 10.1021/acsbiomaterials.1c00069. Online ahead of print.

ABSTRACT

We present a collagen-mimetic protein of bacterial origin based upon a modified subdomain of the collagen-like Sc12 protein from Streptococcus pyogenes, as an alternative collagen-like biomaterial platform that is highly soluble, forms stable, homogeneous, fluid-like solutions at elevated concentrations, and that can be efficiently fabricated into hydrogel materials over a broad range of pH conditions. This extended bacterial collagen-like (eBCL) protein is expressed in a bacterial host and purified as a trimeric assembly exhibiting a triple helical secondary structure in its collagen-like subdomain that is stable near physiological solution conditions (neutral pH and 37 °C), as well as over a broad range of pH conditions. We also show how this sequence can be modified to include biofunctional attributes, in particular, the Arg-Gly-Asp (RGD) sequence to elicit integrin-specific cell binding, without loss of structural function. Furthermore, through the use of EDC-NHS chemistry, we demonstrate that members of this eBCL protein system can be covalently cross-linked to fabricate transparent hydrogels with high protein concentrations (at least to 20% w/w). These hydrogels are shown to possess material properties and resistance to enzymatic degradation that are comparable or superior to a type I collagen control. Moreover, such hydrogels containing the constructs with the RGD integrin-binding sequence are shown to promote the adhesion, spreading, and proliferation of C2C12 and 3T3 cells in vitro. Due to its enhanced solubility, structural stability, fluidity at elevated concentrations, ease of modification, and facility of cross-linking, this eBCL collagen-mimetic system has potential for numerous biomedical material applications, where the ease of processing and fabrication and the facility to tailor the sequence for specific biological functionality are desired.

PMID:33733733 | DOI:10.1021/acsbiomaterials.1c00069

J Crohns Colitis. 2021 Mar 18:jjab051. doi: 10.1093/ecco-jcc/jjab051. Online ahead of print.

ABSTRACT

Many diseases that affect modern humans fall in the category of complex diseases, thus called because they result from a combination of multiple aetiological and pathogenic factors. Regardless of the organ or system affected, complex diseases present major challenges in diagnosis, classification, and management. Current forms of therapy are usually applied in an indiscriminate fashion based on clinical information, but even the most advanced drugs only benefit a limited number of patients and to a variable and unpredictable degree. This 'one measure does not fit all' situation has spurred the notion that therapy for complex disease should be tailored to individual patients or groups of patients, giving rise to the notion of 'precision medicine' [PM]. Inflammatory bowel disease [IBD] is a prototypical complex disease where the need for PM has become increasingly clear. This prompted the European Crohn's and Colitis Organisation to focus the 7 th Scientific Workshop on this emerging theme. The articles in this special issue of the Journal address the various complementary aspects of PM in IBD, including what is PM; why it is needed and how it can be used; how PM can contribute to prediction and prevention of IBD; how IBD PM can aid in prognosis and improve response to therapy; and the challenges and future directions of PM in IBD. This first article of this series is structured on three simple concepts [what, why, and how] and addresses the definition of PM, discusses the rationale for the need of PM in IBD, and outlines the methodology required to implement PM in IBD in a correct and clinically meaningful way.

PMID:33733656 | DOI:10.1093/ecco-jcc/jjab051

Cell Mol Life Sci. 2021 Mar 17. doi: 10.1007/s00018-021-03795-w. Online ahead of print.

ABSTRACT

Guanine (G)-rich single-stranded nucleic acids can adopt G-quadruplex structures. Accumulating evidence indicates that G-quadruplexes serve important regulatory roles in fundamental biological processes such as DNA replication, transcription, and translation, while aberrant G-quadruplex formation is linked to genome instability and cancer. Understanding the biological functions played by G-quadruplexes requires detailed knowledge of their protein interactome. Here, we report that both RNA and DNA G-quadruplexes are bound by human Dicer in vitro. Using in vitro binding assays, mutation studies, and computational modeling we demonstrate that G-quadruplexes can interact with the Platform-PAZ-Connector helix cassette of Dicer, the region responsible for anchoring microRNA precursors (pre-miRNAs). Consequently, we show that G-quadruplexes efficiently and stably inhibit the cleavage of pre-miRNA by Dicer. Our data highlight the potential of human Dicer for binding of G-quadruplexes and allow us to propose a G-quadruplex-driven sequestration mechanism of Dicer regulation.

PMID:33733306 | DOI:10.1007/s00018-021-03795-w

Front Artif Intell. 2020 Dec 23;3:524339. doi: 10.3389/frai.2020.524339. eCollection 2020.

ABSTRACT

The field artificial intelligence (AI) was founded over 65 years ago. Starting with great hopes and ambitious goals the field progressed through various stages of popularity and has recently undergone a revival through the introduction of deep neural networks. Some problems of AI are that, so far, neither the "intelligence" nor the goals of AI are formally defined causing confusion when comparing AI to other fields. In this paper, we present a perspective on the desired and current status of AI in relation to machine learning and statistics and clarify common misconceptions and myths. Our discussion is intended to lift the veil of vagueness surrounding AI to reveal its true countenance.

PMID:33733197 | PMC:PMC7944138 | DOI:10.3389/frai.2020.524339

iScience. 2021 Feb 20;24(3):102212. doi: 10.1016/j.isci.2021.102212. eCollection 2021 Mar 19.

ABSTRACT

Adenoid cystic carcinoma (ACC) is a rare cancer type that originates in the salivary glands. Tumors commonly invade along nerve tracks in the head and neck, making surgery challenging. Follow-up treatments for recurrence or metastasis including chemotherapy and targeted therapies have shown limited efficacy, emphasizing the need for new therapies. Here, we report a Drosophila-based therapeutic approach for a patient with advanced ACC disease. A patient-specific Drosophila transgenic line was developed to model the five major variants associated with the patient's disease. Robotics-based screening identified a three-drug cocktail-vorinostat, pindolol, tofacitinib-that rescued transgene-mediated lethality in the Drosophila patient-specific line. Patient treatment led to a sustained stabilization and a partial metabolic response of 12 months. Subsequent resistance was associated with new genomic amplifications and deletions. Given the lack of options for patients with ACC, our data suggest that this approach may prove useful for identifying novel therapeutic candidates.

PMID:33733072 | PMC:PMC7940980 | DOI:10.1016/j.isci.2021.102212

iScience. 2021 Feb 16;24(3):102198. doi: 10.1016/j.isci.2021.102198. eCollection 2021 Mar 19.

ABSTRACT

Alzheimer's disease (AD) is a worldwide burden. Diagnosis is complicated by the fact that AD is asymptomatic at an early stage. Studies using AD-modeled animals offer important and useful insights. Here, we classified mice with a high risk of AD at a preclinical stage by using only their behaviors. Wild-type and knock-in AD-modeled (App NL-G-F/NL-G-F ) mice were raised, and their cognitive behaviors were assessed in an automated monitoring system. The classification utilized a machine learning method, i.e., a deep neural network, together with optimized stepwise feature selection and cross-validation. The AD risk could be identified on the basis of compulsive and learning behaviors (89.3% ± 9.8% accuracy) shown by AD-modeled mice in the early age (i.e., 8-12 months old) when the AD symptomatic cognitions were relatively underdeveloped. This finding reveals the advantage of machine learning in unveiling the importance of compulsive and learning behaviors for early AD diagnosis in mice.

PMID:33733064 | PMC:PMC7937558 | DOI:10.1016/j.isci.2021.102198

Front Oncol. 2021 Feb 23;11:622244. doi: 10.3389/fonc.2021.622244. eCollection 2021.

ABSTRACT

Effective radiation treatment (RT) for recurrent nasopharyngeal cancers (NPC), featuring an intrinsic hypoxic sub-volume, remains a clinical challenge. Lack of disease-specific in-vitro models of NPC, together with difficulties in establishing patient derived xenograft (PDX) models, have further hindered development of personalized therapeutic options. Herein, we established two NPC organoid lines from recurrent NPC PDX models and further characterized and compared these models with original patient tumors using RNA sequencing analysis. Organoids were cultured in hypoxic conditions to examine the effects of hypoxia and radioresistance. These models were then utilized to determine the radiobiological parameters, such as α/β ratio and oxygen enhancement ratio (OER), characteristic to radiosensitive normoxic and radioresistant hypoxic NPC, using simple dose-survival data analytic tools. The results were further validated in-vitro and in-vivo, to determine the optimal boost dose and fractionation regimen required to achieve effective NPC tumor regression. Despite the differences in tumor microenvironment due to the lack of human stroma, RNA sequencing analysis revealed good correlation of NPC PDX and organoid models with patient tumors. Additionally, the established models also mimicked inter-tumoral heterogeneity. Hypoxic NPC organoids were highly radioresistant and had high α/β ratio compared to its normoxic counterparts. In-vitro and in-vivo fractionation studies showed that hypoxic NPC was less sensitive to RT fractionation scheme and required a large bolus dose or 1.4 times of the fractionated dose that was effective against normoxic cells in order to compensate for oxygen deficiency. This study is the first direct experimental evidence to predict optimal RT boost dose required to cause sufficient damage to recurrent hypoxic NPC tumor cells, which can be further used to develop dose-painting algorithms in clinical practice.

PMID:33732646 | PMC:PMC7959730 | DOI:10.3389/fonc.2021.622244

Virus Evol. 2021 Mar 2;7(1):veab018. doi: 10.1093/ve/veab018. eCollection 2021 Jan.

ABSTRACT

In 2017, a survey of the molecular epidemiology of human adenovirus (HAdV) infections in Southern China based on hexon and fiber genotype demonstrated that the most prevalent genotypes of HAdV were HAdV-3 (n = 62), HAdV-2 (n = 21), and HAdV-7 (n = 16). In addition, two patients were co-infected with two genotypes of HAdV. Interestingly, a novel human adenovirus C recombinant genotype strain was isolated from one of the pneumonia patients in this survey. Phylogenetic, recombination, and proteotyping analysis showed that this novel pathogen originated from the recombination of parental viruses harboring the HAdV-1 penton and hexon gene, and the HAdV-2 fiber gene. It was named 'P1H1F2' and was assigned as HAdV-C104 based on the nomenclature protocol of using three major capsid proteins for characterization. Subsequent in vitro experiments demonstrated that HAdV-C104 had comparable proliferation capacity to HAdV-1, HAdV-2, and another recombination genotype P1H2F2. In addition, the HAdV-C104 infected patient was diagnosed with pneumonia and recovered after antiviral therapy. This report strengthens the hypothesis of recombination as a major pathway for the molecular evolution of HAdV-C species.

PMID:33732504 | PMC:PMC7953211 | DOI:10.1093/ve/veab018

Nat Genet. 2021 Mar 17. doi: 10.1038/s41588-021-00804-3. Online ahead of print.

ABSTRACT

Gene regulatory divergence is thought to play a central role in determining human-specific traits. However, our ability to link divergent regulation to divergent phenotypes is limited. Here, we utilized human-chimpanzee hybrid induced pluripotent stem cells to study gene expression separating these species. The tetraploid hybrid cells allowed us to separate cis- from trans-regulatory effects, and to control for nongenetic confounding factors. We differentiated these cells into cranial neural crest cells, the primary cell type giving rise to the face. We discovered evidence of lineage-specific selection on the hedgehog signaling pathway, including a human-specific sixfold down-regulation of EVC2 (LIMBIN), a key hedgehog gene. Inducing a similar down-regulation of EVC2 substantially reduced hedgehog signaling output. Mice and humans lacking functional EVC2 show striking phenotypic parallels to human-chimpanzee craniofacial differences, suggesting that the regulatory divergence of hedgehog signaling may have contributed to the unique craniofacial morphology of humans.

PMID:33731941 | DOI:10.1038/s41588-021-00804-3

Nature. 2021 Mar 17. doi: 10.1038/s41586-021-03287-8. Online ahead of print.

NO ABSTRACT

PMID:33731935 | DOI:10.1038/s41586-021-03287-8

Nat Metab. 2021 Mar 18. doi: 10.1038/s42255-021-00377-9. Online ahead of print.

NO ABSTRACT

PMID:33731896 | DOI:10.1038/s42255-021-00377-9

Sci Adv. 2021 Mar 17;7(12):eabf1380. doi: 10.1126/sciadv.abf1380. Print 2021 Mar.

ABSTRACT

For the two proteins myoglobin and fluoroacetate dehalogenase, we present a systematic comparison of crystallographic diffraction data collected by serial femtosecond (SFX) and serial synchrotron crystallography (SSX). To maximize comparability, we used the same batch of micron-sized crystals, the same sample delivery device, and the same data analysis software. Overall figures of merit indicate that the data of both radiation sources are of equivalent quality. For both proteins, reasonable data statistics can be obtained with approximately 5000 room-temperature diffraction images irrespective of the radiation source. The direct comparability of SSX and SFX data indicates that the quality of diffraction data obtained from these samples is linked to the properties of the crystals rather than to the radiation source. Therefore, for other systems with similar properties, time-resolved experiments can be conducted at the radiation source that best matches the desired time resolution.

PMID:33731353 | DOI:10.1126/sciadv.abf1380

Cell Rep. 2021 Mar 16;34(11):108854. doi: 10.1016/j.celrep.2021.108854.

ABSTRACT

A near-constant feature of stress responses is a downregulation or arrest of the cell cycle, resulting in transient growth slowdown. To investigate the role of growth slowdown in the hyperosmotic shock response of S. cerevisiae, we perturbed the G1/S checkpoint protein Sic1 to enable osmo-stress response activation with diminished growth slowdown. We document that in this mutant, adaptation to stress is accelerated rather than delayed. This accelerated recovery of the mutant proceeds by liquidation of internal glycogen stores, which are then shunted into the osmo-shock response. Therefore, osmo-adaptation in wild-type cells is delayed because growth slowdown prevents full accessibility to cellular glycogen stores. However, faster adaptation comes at the cost of acute sensitivity to subsequent osmo-stresses. We suggest that stress-induced growth slowdown acts as an arbiter to regulate the resources devoted to osmo-shock, balancing short-term adaptation with long-term robustness.

PMID:33730573 | DOI:10.1016/j.celrep.2021.108854

Annu Rev Plant Biol. 2021 Mar 17. doi: 10.1146/annurev-arplant-081720-010120. Online ahead of print.

ABSTRACT

Single-cell approaches are quickly changing our view on biological systems by increasing the spatiotemporal resolution of our analyses to the level of the individual cell. The field of plant biology has fully embraced single-cell transcriptomics and is rapidly expanding the portfolio of available technologies and applications. In this review, we give an overview of the main advances in plant single-cell transcriptomics over the past few years and provide the reader with an accessible guideline covering all steps, from sample preparation to data analysis. We end by offering a glimpse of how these technologies will shape and accelerate plant-specific research in the near future. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

PMID:33730513 | DOI:10.1146/annurev-arplant-081720-010120