Host Modification Research Articles

A fine‐scale analysis reveals microgeographic hotspots maximizing infection rate between a parasite and its fish host

Abstract For parasites, finding their hosts in vast and heterogeneous environments is a task that can be complex. Some parasite species rely on elaborate strategies to increase encounter rate with their hosts (e.g. behavioural modification of host), but others do not. For these parasites, a key issue is to reveal the processes that enable them to successfully find their hosts and complete their life cycles. Here, we tested the hypothesis that infective larvae of the freshwater ectoparasite Tracheliastes polycolpus are not homogeneously distributed along the river and preferentially occur in very specific microhabitats that maximize encounter rate, and hence infection rate, with their host fish. To do this, we combined an in situ experiment (caging) with an empirical survey carried out on the same sites to identify potential ‘hotspots’ of infection at the microgeographic scale and their environmental characteristics. Experimental and empirical results demonstrated that infections were not evenly distributed among microhabitats, and that infections were spatially aggregated in hotspots at a very fine spatial grain. We further found that certain combinations of environmental variables were consistently and nonlinearly associated with higher infection rate for both caged and wild‐caught fish. Microhabitats characterized by very low or high stream velocities, associated with medium or very small substrate, respectively, and a deep water column were strongly and repeatedly associated with higher infection rates. These microhabitats could concentrate parasites and/or promote physical contact with the hosts. We conclude that the characteristics of some microhabitats could facilitate contact between hosts and parasites and explain how some parasites manage to find their hosts in complex environments. A free Plain Language Summary can be found within the Supporting Information of this article.

Impact of O-Acetylation on S. flexneri 1b and 2a O-Antigen Immunogenicity in Mice.

Shigellosis is a diarrheal disease caused prevalently by Shigella flexneri and S. sonnei and representing a major global health risk, particularly in developing countries. Bacterial O-antigen (OAg) is the primary target of the host immune response and modifications of its oligosaccharide units, including O-acetylation, are responsible for the variability among the circulating S. flexneri serotypes. No vaccines are widely available against shigellosis and the understanding of the immunogenicity induced by the OAg is fundamental for the design of a vaccine that could cover the most prevalent Shigella serotypes. To understand whether a different O-acetylation pattern could influence the immune response elicited by S. flexneri OAg, we employed as a vaccine technology GMMA purified from S. flexneri 2a and 1b strains that were easily engineered to obtain differently O-acetylated OAg. Resulting GMMA were tested in mice, demonstrating not only no major impact of O-acetyl decorations on the immune response elicited by the two OAg against the homologous strains, but also that the O-acetylation of the Rhamnose III residue (O-factor 9), shared among serotypes 1b, 2a and 6, does not induce cross-reactive antibodies against these serotypes. This work contributes to the optimization of vaccine design against Shigella, providing indication about the ability of shared epitopes to elicit broad protection against S. flexneri serotypes and supporting the identification of critical quality attributes of OAg-based vaccines.

Epigenetic modifications in host-bacterial dialogues: more than meets the eye.

Epigenetic modifications in host-bacterial dialogues: more than meets the eye.

Guiding Uniform Sodium Deposition through Host Modification for Sodium Metal Batteries

AbstractRoom‐temperature Na metal batteries represent an emerging energy storage technology beyond Li‐ion batteries, owing to the high specific capacity and high natural abundance of Na. However, Na metal anodes are plagued with multiple challenges including unstable solid electrolyte interphase, undesirable dendrite growth, and large volumetric expansion, leading to low Coulombic efficiency during Na plating and stripping. To this end, mechanically stable and sodiophilic hosts with nano‐ or micro‐structured materials have been investigated to accommodate Na in the structured spacing or gaps for enhanced cyclability. In this concept, we will discuss the key concepts and latest developments in guiding uniform Na deposition through host modification, especially carbon, inorganic and polymeric materials. Future prospects and outlook will also be provided, including artificial interphase design, solid‐state electrolytes, and precise nanoscale characterization to improve our fundamental understanding of Na deposition and spur this burgeoning field in Na metal batteries.

Commensals make the most of their hosts

In this issue of Cell Host & Microbe, Brown etal. reveal a large group of genes within the human microbiome that code for ADP-ribosyltransferases that are predicted to manipulate host cells. Previously studied for pathogens, these host modification mechanisms may also be common properties of commensals.

Rapid Genome Modification in Serratia marcescens Through Red Homologous Recombination.

Despite the great potential of Serratia marcescens in industrial applications, lack of powerful genetic modification tools limits understanding of the regulatory networks of the useful metabolites and therefore restricts their mass production. To meet the urgent demand, we established a genome-editing strategy for S. marcescens based on Red recombineering in this study. Without host modification in advance, nucA and pigA were substituted by PCR-amplified resistance genes. No long homologous arms were required at the two sides of resistance genes. Using this procedure, the fragment at the S. marcescens as large as 20 kb was easily deleted. Then we constructed a counter-selection gene kil constructed under the control of inducible PBAD operon, which demonstrates obvious lethality to S. marcescens. Subsequently, GmR-kil double selection cassette was inserted into the CDS of pigA gene. Using single-stranded DNA-mediated recombination, this insertion mutation was efficiently repaired through kil counter-selection. A powerful genetic modification platform based on Red recombineering system was successfully established for S. marcescens. Multiple types of modification and multiple recombination strategies can all be performed easily in this species. We hope this study will be useful for the theoretical research and the research of metabolic engineering in S. marcescens.

Remote attestation and integrity measurements with Intel SGX for virtual machines

With response to the emerging virtualization trend, we focus on a Virtual Machine (VM) remote attestation process assuming that it is running in an uncontrolled and untrusted cloud infrastructure.We present a solution that is able to establish a chain of trust in a cloud environment. Our solution is based on a set of CPU instructions and it does not need any additional components to track host modifications. Our solution enables integrity verification of a filesystem. Additionally, it ensures trust level assessment for remote VMs during their startup or while triggered manually at any point in time afterwards.We identify security properties for our solution and show how it meets them. The security analysis shows that with necessary countermeasures, the proposed model can ensure the required level of security. Additionally, We evaluate the performance impact of the prototype and virtualization overhead for a real-life scenario. Here, we assume that small configuration files, binaries, and executables are most critical. The results show that important filesystem components can be verified with a minimum impact on a startup time. This way, the whole proposal allows for making VM a part of a trusted compute resource pool.

Interfacial modification by lithiophilic oxide facilitating uniform and thin solid electrolyte interphase towards stable lithium metal anodes

In this work, metal foam current collectors (CCs, i.e. nickel [Ni] and copper [Cu]) were treated by thermal oxidation to create a lithiophilic oxide surface that exhibited enhanced electrochemical performances of lithium anodes such as the cyclic stability of Coulombic efficiency at different current densities for various capacities compared to pristine CCs. The oxidized CCs facilitated much increased diffusivities of ions for lithium growth than pristine CCs. It was found that an inhomogeneous solid electrolyte interphase (SEI) formed on pristine CCs while a uniform SEI formed on oxidized CCs. Uniform lithium (Li) deposition can be achieved on oxidized CCs owing to the lithiophilic oxide surface containing metal nanoparticles and the ionic compound lithium oxide (Li2O) matrix that led to a uniform SEI film and many nucleation sites. In addition, the porous and non-porous composite anodes exhibited different electrochemical performances. The porous composite anodes showed initial lower voltage hysteresis but shorter lifetime with carbonate-based electrolyte than non-porous composite anodes. The porous composite anodes showed better rate performances in full-cell measurements while the non-porous composite anodes displayed better stability. The interfacial modification of porous hosts by lithiated oxides and the effects of porous structure on battery performances can be also useful for designing other electrodes (e.g. sodium [Na], potassium [K], zinc [Zn]).

Using biotechnological approaches to develop crop resistance to root parasitic weeds.

New transgenic and biotechnological approaches may serve as a key component in achieving crop resistance to root parasitic weeds. Root parasitic weeds inflict severe damage to numerous crops, reducing yield quantity and quality. A lack of new sources of resistance limits our ability to manage newly developing, more virulent races. Having no effective means to control the parasites in most crops, innovative biotechnological solutions are needed. Several novel biotechnological strategies using regulatory RNA molecules, the CRISPR/Cas9 system, and T-DNA insertions have been acknowledged for engineering resistance against parasitic weeds. Significant breakthroughs have been made over the years in deciphering the plant genome and its functions, including the genomes of parasitic weeds. However, the basis of biotechnological strategies to generate host resistance to root parasitic weeds needs to be further developed. Gene-silencing and editing tools should be used to target key processes of host-parasite interactions, such as strigolactone biosynthesis and signaling, haustorium development, and degradation and penetration of the host cell wall. In this review, we summarize and discuss the main areas of research leading to the discovery and functional analysis of genes involved in host-induced gene silencing that target key parasite genes, transgenic host modification, and host gene editing to generate sustainable resistance to root parasitic weeds.

The Effects of Nisin-Producing Lactococcus lactis Strain Used as Probiotic on Gilthead Sea Bream (Sparus aurata) Growth, Gut Microbiota, and Transcriptional Response

The present research tested the effects of dietary nisin-producingLactococcus lactison growth performance, feed utilization, intestinal morphology, transcriptional response, and microbiota in gilthead sea bream (Sparus aurata). A feeding trial was conducted with fish weighting 70–90 g. Fish were tagged with passive, integrated transponders and distributed in nine 500 L tanks with 40 fish each. Fish were fed for 12 weeks with either a control (diet A) or experimental diets (diets B and C) in triplicate (3 tanks/diet). Extruded pellets of diets B and C were supplemented with a low (2 × 109CFU/kg) and a high (5 × 109CFU/kg) dose of probiotic, respectively. No significant differences were found between groups for the feed conversion ratio or specific growth rates. However, the final body weight of fish fed diet C was significantly higher than the control group with intermediate values for fish fed diet B. Histological analysis conducted using a semi-quantitative scoring system showed that probiotic did not alter the morphology of the intestine and did not trigger inflammation. With regard to the transcriptomic response, a customized PCR array layout was designed to simultaneously profile a panel of 44 selected genes. Significant differences in the expression of key genes involved in innate and acquired immunity were detected between fish fed probiotic and control diets. To analyze the microbiota associated to the feeds and the gut autochthonous microbial communities, we used the Illumina MiSeq platform for sequencing the 16S rRNA gene and a metagenomics pipeline based on VSEARCH and RDP databases. The analysis of gut microbiota revealed a lack of colonization of the probiotic in the host’s intestinal mucosa. However, probiotic did modulate the fish gut microbiota, confirming that colonization is not always necessary to induce host modification. In fact, diets B and C were enriched with Actinomycetales, as compared to diet A, which instead showed a higher percentage ofPseudomonas,Sphyngomonas, andLactobacillusgenera. These results were confirmed by the clear separation of gut bacterial community of fish fed with the probiotic from the bacterial community of control fish group in the beta-diversity and PLS-DA (supervised partial least-squares discriminant analysis) analyses.

Host Modification of Layered Double Hydroxide Electrocatalyst to Boost the Thermodynamic and Kinetic Activity of Oxygen Evolution Reaction

AbstractLayered double hydroxides (LDHs) are regarded as an earth‐abundant and highly efficient electrocatalyst for oxygen evolution reaction (OER). In this work, a systematic strategy is demonstrated to simultaneously optimize the OER thermodynamic and kinetic activity via introducing a series of transition and main group metal atoms into the NiFe‐LDH host layers. Typically, V, Co, and Cr dopants largely promote the intrinsic activity of NiFe‐LDH through the effective electron transfer from Fe3+ in NiFe‐LDH laminate to the doping metals, while the introduction of V, Ti, and Mn into NiFe‐LDH facilitates the kinetics of water oxidation due to the increased conductivity induced by dopants. Furthermore, the detailed experiments and density functional theory calculations illustrate that the presence of suitable heteroatoms (V) lowers the activation energy barrier for OER rate‐limiting step as well as promotes the electron transfers by effective electronic modification. This work provides an effective strategy to modulate the OER activity of LDHs and determine their performance trends for a more rational design of high‐performed OER electrocatalysts.

Development of a marker-free mutagenesis system using CRISPR-Cas9 in the pathogenic mould Aspergillus fumigatus

Aspergillus fumigatus is a saprophytic fungal pathogen that is the cause of more than 300,000 life-threatening infections annually. Our understanding of pathogenesis and factors contributing to disease progression are limited. Development of rapid and versatile gene editing methodologies for A. fumigatus is essential. CRISPR-Cas9 mediated transformation has been widely used as a novel genome editing tool and has been used for a variety of editing techniques, such as protein tagging, gene deletions and site-directed mutagenesis in A. fumigatus. However, successful genome editing relies on time consuming, multi-step cloning procedures paired with the use of selection markers, which can result in a metabolic burden for the host and/or unintended transcriptional modifications at the site of integration. We have used an in vitro CRISPR-Cas9 assembly methodology to perform selection-free genome editing, including epitope tagging of proteins and site-directed mutagenesis. The repair template used during this transformation use 50 bp micro-homology arms and can be generated with a single PCR reaction or by purchasing synthesised single stranded oligonucleotides, decreasing the time required for complex construct synthesis.

ZenoFishDb v1.1: A Database for Xenotransplantation Studies in Zebrafish.

Rapidly accumulating literature has proven feasibility of the zebrafish xenograft models in cancer research. Nevertheless, online databases for searching the current zebrafish xenograft literature are in great demand. Herein, we have developed a manually curated database, called ZenoFishDb v1.1 (https://konulab.shinyapps.io/zenofishdb), based on R Shiny platform aiming to provide searchable information on ever increasing collection of zebrafish studies for cancer cell line transplantation and patient-derived xenografts (PDXs). ZenoFishDb v1.1 user interface contains four modules: DataTable, Visualization, PDX Details, and PDX Charts. The DataTable and Visualization pages represent xenograft study details, including injected cell lines, PDX injections, molecular modifications of cell lines, zebrafish strains, as well as technical aspects of the xenotransplantation procedures in table, bar, and/or pie chart formats. The PDX Details module provides comprehensive information on the patient details in table format and can be searched and visualized. Overall, ZenoFishDb v1.1 enables researchers to effectively search, list, and visualize different technical and biological attributes of zebrafish xenotransplantation studies particularly focusing on the new trends that make use of reporters, RNA interference, overexpression, or mutant gene constructs of transplanted cancer cells, stem cells, and PDXs, as well as distinguished host modifications.

In-situ anchoring sulfiphilic silica nanoparticles onto macro-mesoporous carbon framework for cost-effective Li-S cathodes

Porous carbons have been the leading conductive hosts for constructing cathodes of lithium-sulfur batteries but are currently challenged by the weak polar surface and cost-effective synthesis. Herein, a 3D hierarchical macro-mesoporous carbon with in-situ silica anchoring (SMC) is prepared via an economical and high-throughput sol-gel approach, followed by the ambient pressure drying and carbonization. The resultant carbons possess developed porosity with bi-continuous macro-mesoporous network. Moreover, the ultrathin silica nanoparticles are homogeneously anchored onto surface of macro-mesoporous carbon framework, which can greatly enhance the polar of carbon surface, thus improving the wettability and dispersion of sulfur during melt impregnation process. In addition, the polysulfides mobilization is also dramatically restrained through chemical binding between silica nanoparticles and polysulfides. Combined with the 3D conductive macro-mesoporous network, the resultant sulfur cathode could deliver a high reversible capacity of 969.7 mAh g−1 and enhanced capacity of 625.5 mAh g−1 with a capacity fading rate of only 0.088% per cycle after 400 cycles at 0.2 C. The present work may provide a direct and cost-effective approach to surface chemistry modification of carbon-based sulfur hosts to ultimately advance energy conversion and storage system.

Cytoskeleton-a crucial key in host cell for coronavirus infection.

The emerging coronavirus (CoV) pandemic is threatening the public health all over the world. Cytoskeleton is an intricate network involved in controlling cell shape, cargo transport, signal transduction, and cell division. Infection biology studies have illuminated essential roles for cytoskeleton in mediating the outcome of host‒virus interactions. In this review, we discuss the dynamic interactions between actin filaments, microtubules, intermediate filaments, and CoVs. In one round of viral life cycle, CoVs surf along filopodia on the host membrane to the entry sites, utilize specific intermediate filament protein as co-receptor to enter target cells, hijack microtubules for transportation to replication and assembly sites, and promote actin filaments polymerization to provide forces for egress. During CoV infection, disruption of host cytoskeleton homeostasis and modification state is tightly connected to pathological processes, such as defective cytokinesis, demyelinating, cilia loss, and neuron necrosis. There are increasing mechanistic studies on cytoskeleton upon CoV infection, such as viral protein‒cytoskeleton interaction, changes in the expression and post-translation modification, related signaling pathways, and incorporation with other host factors. Collectively, these insights provide new concepts for fundamental virology and the control of CoV infection.

TMT-based quantitative proteomics analysis reveals the attenuated replication mechanism of Newcastle disease virus caused by nuclear localization signal mutation in viral matrix protein

ABSTRACT Nuclear localization of cytoplasmic RNA virus proteins mediated by intrinsic nuclear localization signal (NLS) plays essential roles in successful virus replication. We previously reported that NLS mutation in the matrix (M) protein obviously attenuates the replication and pathogenicity of Newcastle disease virus (NDV), but the attenuated replication mechanism remains unclear. In this study, we showed that M/NLS mutation not only disrupted M’s nucleocytoplasmic trafficking characteristic but also impaired viral RNA synthesis and transcription. Using TMT-based quantitative proteomics analysis of BSR-T7/5 cells infected with the parental NDV rSS1GFP and the mutant NDV rSS1GFP-M/NLSm harboring M/NLS mutation, we found that rSS1GFP infection stimulated much greater quantities and more expression changes of differentially expressed proteins involved in host cell transcription, ribosomal structure, posttranslational modification, and intracellular trafficking than rSS1GFP-M/NLSm infection. Further in-depth analysis revealed that the dominant nuclear accumulation of M protein inhibited host cell transcription, RNA processing and modification, protein synthesis, posttranscriptional modification and transport; and this kind of inhibition could be weakened when most of M protein was confined outside the nucleus. More importantly, we found that the function of M protein in the cytoplasm effected the inhibition of TIFA expression in a dose-dependent manner, and promoted NDV replication by down-regulating TIFA/TRAF6/NF-κB-mediated production of cytokines. It was the first report about the involvement of M protein in NDV immune evasion. Taken together, our findings demonstrate that NDV replication is closely related to the nucleocytoplasmic trafficking of M protein, which accelerates our understanding of the molecular functions of NDV M protein.

Developmental immaturity of sialic acid recognition mediates neonatal susceptibility to GBS pneumonia

Abstract Group B Streptococcus (GBS) is a major neonatal pathogen but rarely causes disease in adults. We previously showed in mice that GBS escapes killing in the neonatal lung via its heavily sialylated capsule. Immune cells detect sialic acid moieties via expression of a repertoire of Siglec receptors. Combinatory expression of proinflammatory and anti-inflammatory Siglec receptors allows differentiation between host and pathogenic microbial sialic acid modifications. We test here the hypothesis that neonatal alveolar macrophages (AMs) fail to detect and kill GBS due to developmental immaturity of Siglec receptor expression. Adult AMs express the proinflammatory sialic acid receptor Sialoadhesin (Sn, Siglec-1) and the anti-inflammatory receptors Siglec-E and Siglec-F. However, real time PCR, immunofluorescence, and FACS detected only Siglec-E in neonatal lung macrophage populations. Sn expression increased soon after birth and was restricted to AMs. The timing of increased Sn expression in newborn mice correlated with susceptibility to GBS. Mice infected with GBS on day 1 suffered early onset mortality, while mice infected on day 2 displayed late onset disease. Mice infected on day 3 survived GBS infection. Further implicating AM immaturity, Csf2−/− mice, which have defects in AM differentiation, lacked Sn expression and had reduced GBS clearance following infection. The presence of Siglec-E but absence of Sn in newborn AMs appeared to promote tolerance to GBS. Newborn SigE−/− mice had increased GBS phagocytosis and killing compared to WT controls. We therefore conclude that GBS exploits developmental immaturity of Siglec expression in AMs via its sialic acid capsule in causing neonatal disease.

Sulfur double encapsulated in a porous hollow carbon aerogel with interconnected micropores for advanced lithium-sulfur batteries

Abstract Due to high theoretical specific capacity, energy density, and low-cost lithium-sulfur (Li-S) batteries became the most potential energy storage devices for the next generation. The harsh shuttling effect, poor electroconductibility of sulfur, and volume change affect the Li-S battery’s practical application. Herein, the rational design of porous hollow carbon aerogel (PHCA) with an ultra-high specific surface area of 2054.5 m2 g−1 and outstanding adsorption ability is firstly fabricated to restrict the shuttling effect of lithium polysulfides (LiPSs) by using commercialized nano-CaCO3 as a template. As a sulfur host, the S/PHCA cathode delivers initially discharge specific capacity of 992.7 mAh g−1 with an average Coulombic efficiency of 97.6%. After 200 cycles, it obtains the reversible specific capacities of 600.1 mAh g−1 for S/PHCA cathode at 0.1C (2.2 mg cm−2) corresponding to 60.45% of their initial discharge specific capacity. As a PHCA interlayer, the Li-S battery with the PHCA interlayer exhibits initially discharge specific capacity of 1267.7 mAh g−1 with an average Coulombic efficiency of 99.36% at 0.1C (3.2 mg cm−2) and maintains at 863.3 mAh g−1 with the discharge specific capacity retention rate of 69.2%. This is an effective strategy to improve the outstanding electrochemical performance which is beyond reported carbon materials, which is attributed to stronger adsorption of LiPSs by the micropore. This work provides a new direction for the modification of a sulfur host and interlayer and simultaneously reveals the relationship between the heteroatom distribution and LiPSs.

Novel in vivo mouse model of shoulder implant infection

Animal models are used to guide management of periprosthetic implant infections. No adequate model exists for periprosthetic shoulder infections, and clinicians thus have no preclinical tools to assess potential therapeutics. We hypothesize that it is possible to establish a mouse model of shoulder implant infection (SII) that allows noninvasive, longitudinal tracking of biofilm and host response through invivo optical imaging. The model may then be employed to validate a targeting probe (1D9-680) with clinical translation potential for diagnosing infection and image-guided débridement. A surgical implant was press-fit into the proximal humerus of c57BL/6J mice and inoculated with 2 μL of 1 × 103 (e3), or 1 × 104 (e4), colony-forming units (CFUs) of bioluminescent Staphylococcus aureus Xen-36. The control group received 2 μL sterile saline. Bacterial activity was monitored invivo over 42 days, directly (bioluminescence) and indirectly (targeting probe). Weekly radiographs assessed implant loosening. CFU harvests, confocal microscopy, and histology were performed. Both inoculated groups established chronic infections. CFUs on postoperative day (POD) 42 were increased in the infected groups compared with the sterile group (P < .001). By POD 14, osteolysis was visualized in both infected groups. The e4 group developed catastrophic bone destruction by POD 42. The e3 group maintained a congruent shoulder joint. Targeting probes helped to visualize low-grade infections via fluorescence. Given bone destruction in the e4 group, a longitudinal, noninvasive mouse model of SII and chronic osteolysis was produced using e3 of S aureus Xen-36, mimicking clinical presentations of chronic SII. The development of this model provides a foundation to study new therapeutics, interventions, and host modifications.

Intracellular proliferation of Anaplasma phagocytophilum is promoted via modulation of endoplasmic reticulum stress signaling in host cells.

Anaplasma phagocytophilum, an obligate intracellular bacterium that propagates within host granulocytes, is considered to modify the host intracellular environment for pathogenesis. However, the mechanism(s) underlying such host modifications remain unclear. Here, we aimed to investigate the relation between A. phagocytophilum and endoplasmic reticulum (ER) stress in THP-1 cells. A. phagocytophilum activated the three ER stress sensors: inositol-requiring enzyme-1 (IRE1), protein kinase RNA-like endoplasmic reticulum kinase (PERK), and activating transcription factor-6 (ATF6). IRE1 activation occurred immediately after host cell invasion by A. phagocytophilum; however, the activated IRE1-induced splicing of X-box-binding protein 1 was not promoted during A. phagocytophilum infection. This suppression was sustained even after the doxycycline-mediated elimination of intracellular A. phagocytophilum. IRE1 knockdown accelerated A. phagocytophilum-induced apoptosis and decreased intracellular A. phagocytophilum. These data suggest that A. phagocytophilum utilizes IRE1 activation to promote its own intracellular proliferation. Moreover, PERK and ATF6 partially mediated A. phagocytophilum-induced apoptosis by promoting the expression of CCAAT/enhancer-binding protein homologous protein, which induces the transcription of several proapoptotic genes. Thus, A. phagocytophilum possibly manipulates the host ER stress signals to facilitate intracellular proliferation and infection of surrounding cells before/after host cell apoptosis.