Exposure of chimaeric embryos to exogenous FGF4 leads to the production of pure ESC-derived mice

Producing chimaeras constitutes the most reliable method of verifying the pluripotency of newly established cells. Moreover, forming chimaeras by injecting genetically modified embryonic stem cells (ESCs) or induced pluripotent stem cells (iPSCs) into the embryo is part of the procedure for generating transgenic mice, which are used for understanding gene function. Conventional methods for generating transgenic mice, including the breeding of chimaeras and tetraploid complementation, are time-consuming and cost-inefficient, with significant limitations that hinder their effectiveness and widespread applications. In the present study, we modified the traditional method of chimaera generation to significantly speed up this process by generating mice exclusively derived from ESCs. This study aimed to assess whether fully ESC-derived mice could be obtained by modulating fibroblast growth factor 4 (FGF4) levels in the culture medium and changing the direction of cell differentiation in the chimaeric embryo. We found that exogenous FGF4 directs all host blastomeres to the primitive endoderm fate, but does not affect the localisation of ESCs in the epiblast of the chimaeric embryos. Consequently, all FGF4-treated chimaeric embryos contained an epiblast composed exclusively of ESCs, and following transfer into recipient mice, these embryos developed into fully ESC-derived newborns. Collectively, this simple approach could accelerate the generation of ESC-derived animals and thus optimise ESC-mediated transgenesis and the verification of cell pluripotency. Compared to traditional methods, it could speed up functional studies by several weeks and significantly reduce costs related to maintaining and breeding chimaeras. Moreover, since the effect of stimulating the FGF signalling pathway is universal across different animal species, our approach can be applied not only to rodents but also to other animals, offering its utility beyond laboratory settings.

Modification of the RTX domain cap by acyl chains of adapted length rules the formation of functional hemolysin pores

The acylated pore-forming Repeats in ToXin (RTX) cytolysins α-hemolysin (HlyA) and adenylate cyclase toxin (CyaA) preferentially bind to β2 integrins of myeloid leukocytes but can also promiscuously bind and permeabilize cells lacking the β2 integrins. We constructed a HlyA1-563/CyaA860-1706 chimera that was acylated either by the toxin-activating acyltransferase CyaC, using sixteen carbon-long (C16) acyls, or by the HlyC acyltransferase using fourteen carbon-long (C14) acyls. Cytolysin assays with the C16- or C14-acylated HlyA/CyaA chimeric toxin revealed that the RTX domain of CyaA can functionally replace the RTX domain of HlyA only if it is modified by C16-acyls on the Lys983 residue of CyaA. The C16-monoacylated HlyA/CyaA chimera was as pore-forming and cytolytic as native HlyA, whereas the C14-acylated chimera exhibited very low pore-forming activity. Hence, the capacity of the RTX domain of CyaA to support the insertion of the N-terminal pore-forming domain into the target cell membrane, and promote formation of toxin pores, strictly depends on the modification of the Lys983 residue by an acyl chain of adapted length.

Aggressive systemic mastocytosis with the co-occurrence of PRKG2::PDGFRB, KAT6A::NCOA2, and RXRA::NOTCH1 fusion transcripts and a heterozygous RUNX1 frameshift mutation

Systemic mastocytosis (SM) is a myeloproliferative neoplasm displaying abnormal mast cell proliferation. It is subdivided into different forms, including aggressive systemic mastocytosis (ASM) and systemic mastocytosis with an associated hematologic neoplasm (SM-AHN). Oncogenic genetic alterations include point mutations, mainly the KIT D816V, conferring poor prognosis and therapy resistance, and fusion genes, with those involving PDGFRA/PDGFRB as the most recurrent events. We here describe an ASM case negative to the KIT D816V and JAK2 V617F alterations but showing a RUNX1 frameshift heterozygous mutation and the co-occurrence of three fusion transcripts. The first one, PRKG2::PDGFRB, was generated by a balanced t(4;5)(q24;q32) translocation as the sole abnormality. Other two novel chimeras, KAT6A::NCOA2 and RXRA::NOTCH1, originated from cryptic intra-chromosomal abnormalities. The patient rapidly evolved towards SM-AHN, characterized by the persistence of the PRKG2::PDGFRB chimera, due to the presence of an extra copy of the der(5)t(4;5)(q24;q34) chromosome and an increase in the RUNX1 mutation allelic frequency. The results indicated that the transcriptional landscape and the mutational profile of SM deserve attention to predict the evolution and prognosis of this complex disease, whose classification criteria are still a matter of debate.

Unreduced spore formation in a spontaneous chimeric pinnule in an artificially produced haploid Anisocampium niponicum (Athyriaceae, Polypodiales)

Haploid sporophytes of Anisocampium niponicum with 2n = 40, were produced artificially by induced apogamy in vitro. They were subsequently transplanted into pots and two of them have been cultivated for the investigation of sporogenesis and/or production of chimera for more than 20 years. Haploid A. niponicum is sterile, but an abnormal chimeric pinnule that developed spontaneously in a single frond produced sporangia with spores. Each sporangium bore approximately 32 spores that were almost uniform in size. Sowing of these spores resulted in 50 gametophytes. Of 20 gametophytes cultured individually, five produced sporophytes apogamously after eight months. Both the gametophytes and subsequent apogamous sporophytes showed a chromosome number of 2n = 40. Our study demonstrates that a haploid sporophyte offspring can be produced from a haploid mother sporophyte via haploid spores. Since asexual reproduction is a prominent evolutionary process in ferns, the reproduction of a haploid A. niponicum sporophyte by unreduced spore formation might help to elucidate how apogamous ferns occur and evolve.

Chimeric Amphiphilic Disinfectants: Quaternary Ammonium / Quaternary Phosphonium Hybrid Structures

Cationic biocides play a crucial role in the disinfection of domestic and healthcare surfaces. Due to the rise of bacterial resistance towards common cationic disinfectants like quaternary ammonium compounds (QACs), the development of novel actives is necessary for effective infection prevention and control.  Toward this end, a series of 15 chimeric biscationic amphiphilic compounds, bearing both ammonium and phosphonium residues, were prepared to probe the structure and efficacy of mixed cationic ammonium-phosphonium structures. Compounds were obtained in two steps and good yields, with straightforward and chromatography-free purifications. Antibacterial activity evaluation of these compounds against a panel of seven bacterial strains, including two MRSA strains as well as opportunistic pathogen A. baumannii, were encouraging, as low micromolar inhibitory activity was observed for multiple structures. Alkyl chain length on the ammonium group was, as expected, a major determinant of bioactivity. In addition, high therapeutic indexes (up to 125-fold) for triphenyl phosphonium-bearing amphiphiles were observed when comparing antimicrobial activity to mammalian cell lysis activity.

Synchronization Studies of Hindmarsh-Rose Neuron Networks: Unraveling the Influence of connection induced memristive synapse

This study focuses on the synchronization analysis of Hindmarsh-Rose neurons coupled through a common memristor (coupled mHRN). Initially, we thoroughly examine the synchronization of two mHRNs coupled via a common memristor before exploring synchronization in a network of mHRNs. The stability of the proposed model is analyzed in three cases, demonstrating the existence of a single equilibrium point whose stability is influenced by external stimuli. The stable and unstable regions are investigated using eigenvalues. Through bifurcation analysis and the determination of maximum Lyapunov exponents, we identify chaotic and hyperchaotic trajectories. Additionally, using the next-generation matrix method, we calculate the chaotic number C0, demonstrating the influence of coupling strength on the chaotic and hyperchaotic behavior of the system. The exponential stability of the synchronous mHRN is derived analytically using Lyapunov theory, and our results are verified through numerical simulations. Furthermore, we explore the impact of initial conditions and memristor synapses, as well as the coupling coefficient, on the synchronization of coupled mHRN. Finally, we investigate a network consisting of n number of mHRNs and observe various collective behaviors, including incoherent, coherent, traveling patterns, traveling wave chimeras, and imperfect chimeras, which are determined by the memristor coupling coefficient.

Self-sufficient P450-reductase chimeras for biocatalysis

In recent years, cytochromes P450 have emerged as powerful, versatile biocatalysts for the site-selective functionalization of small molecules. Catalyzing an impressive range of chemical transformations, these enzymes have been widely used to effect C-H oxidation, biaryl coupling, and carbon-heteroatom bond formation, among many other reactions. However, the majority of P450s are multi-protein systems that employ secondary redox partners in key steps of the catalytic cycle, which limits their broader applicability. In response, the discovery of self-sufficient P450s, such as P450BM3 and P450RhF, has provided a template for the construction of artificial, self-sufficient P450-reductase fusions. In this chapter, we describe a procedure for the design, assembly, and application of two engineered, self-sufficient P450s of Streptomyces origin via fusion with an exogenous reductase domain. In particular, we generated artificial chimeras of P450s PtmO5 and TleB by linking them covalently with the reductase domain of P450RhF. Upon verification of their activities, both enzymes were employed in preparative-scale biocatalytic reactions. This approach can feasibly be applied to any P450 of interest, thereby laying the groundwork for the production of self-sufficient P450s for diverse chemical applications.

Single-cell transcriptomics identifies perturbed molecular pathways in midbrain organoids using α-synuclein triplication Parkinson's disease patient-derived iPSCs

Three-dimensional (3D) brain organoids provide a platform to study brain development, cellular coordination, and disease using human tissue. Here, we generate midbrain dopaminergic (mDA) organoids from induced pluripotent stem cells (iPSC) from healthy and Parkinson's Disease (PD) donors and assess them as a human PD model using single-cell RNAseq. We characterize cell types in our organoid cultures and analyze our model's Dopamine (DA) neurons using cytotoxic and genetic stressors. Our study provides the first in-depth, single-cell analysis of SNCA triplication and shows evidence for molecular dysfunction in oxidative phosphorylation, translation, and ER protein-folding in DA neurons. We perform an in-silico identification of rotenone-sensitive DA neurons and characterization of corresponding transcriptomic profiles associated with synaptic signalling and cholesterol biosynthesis. Finally, we show a novel chimera organoid model from healthy and PD iPSCs allowing the study of DA neurons from different individuals within the same tissue.

Collective dynamics of a coupled Hindmarsh-Rose neurons with locally active memristor

A Locally active memristors can mimic neural synapses, resulting in rich neuro-morphological dynamics in biological neurons. To illustrate the impact of a local active memristive synapse, we consider coupled Hindmarsh-Rose (HR) neurons. Firstly, the dynamical transitions of the proposed system are investigated using bifurcation analysis and Lyapunov exponents, and we find that the transition between periodic and chaotic states depends on the input currents and memristive coupling strength. By performing the two-parameter analysis, the existence of periodic and chaotic regions is revealed. The collective behavior is then examined by expanding the network to include memristive coupled HR neurons under different network connectivities. We show that the system achieves synchronization behavior for all network connectivities, including regular, random, and small-world, when the strength of the memristive coupling is increased.

The influence of synaptic pathways on the synchronization patterns of regularly structured mChialvo map network

Synchronization of interconnecting units is one of the hottest topics many researchers are interested in. In addition, this emerging phenomenon is responsible for many biological processes, and thus, the synchronization of interacting neurons is an important field of study in neuroscience. Employing the memristive Chialvo (mChialvo) neuron map, this paper investigates the effect of electrical, inner-linking, chemical, and hybrid coupling functions on the synchronization state of a neuronal network with regular structure. Master stability function (MSF) analysis is performed to obtain the necessary conditions for synchronizing the built networks. Afterward, the MSF-based results are confirmed by calculating the synchronization error. Besides, the dynamics of the synchronous neurons are discussed based on the bifurcation analysis. Our results suggest that, compared to the electrical and inner-linking functions, chemical synapses facilitate mChialvo neurons' synchronization since the neurons can achieve synchrony with a negligible chemical coupling strength. Further studies reveal that based on the active synapses, coupled mChialvo neurons can reach cluster synchronization, chimera state, sine-like synchronization, phase synchronization, and cluster phase synchronization.

Chimeras in Merlot grapevine revealed by phased assembly

Chimerism is the phenomenon when several genotypes coexist in a single individual. Used to understand plant ontogenesis they also have been valorised through new cultivar breeding. Viticulture has been taking economic advantage out of chimeras when the variant induced an important modification of wine type such as berry skin colour. Crucial agronomic characters may also be impacted by chimeras that aren't identified yet. Periclinal chimera where the variant has entirely colonised a cell layer is the most stable and can be propagated through cuttings. In grapevine, leaves are derived from both meristem layers, L1 and L2. However, lateral roots are formed from the L2 cell layer only. Thus, comparing DNA sequences of roots and leaves allows chimera detection. In this study we used new generation Hifi long reads sequencing, recent bioinformatics tools and trio-binning with parental sequences to detect periclinal chimeras on 'Merlot' grapevine cultivar. Sequencing of cv. 'Magdeleine Noire des Charentes' and 'Cabernet Franc', the parents of cv. 'Merlot', allowed haplotype resolved assembly. Pseudomolecules were built with a total of 33 to 47 contigs and in few occasions a unique contig for one chromosome. This high resolution allowed haplotype comparison. Annotation was transferred from PN40024 VCost.v3 to all pseudomolecules. After strong selection of variants, 51 and 53 'Merlot' specific periclinal chimeras were found on the Merlot-haplotype-CF and Merlot-haplotype-MG respectively, 9 and 7 been located in a coding region. A subset of positions was analysed using Molecular Inversion Probes (MIPseq) and 69% were unambiguously validated, 25% are doubtful because of technological noise or weak depth and 6% invalidated. These results open new perspectives on chimera detection as an important resource to improve cultivars through clonal selection or breeding.

Central IRF4/5 Signaling Are Critical for Microglial Activation and Impact on Stroke Outcomes

Microglia and monocytes play a critical role in immune responses to cerebral ischemia. Previous studies have demonstrated that interferon regulatory factor 4 (IRF4) and IRF5 direct microglial polarization after stroke and impact outcomes. However, IRF4/5 are expressed by both microglia and monocytes, and it is not clear if it is the microglial (central) or monocytic (peripheral) IRF4-IRF5 regulatory axis that functions in stroke. In this work, young (8-12 weeks) male pep boy (PB), IRF4 or IRF5 flox, and IRF4 or IRF5 conditional knockout (CKO) mice were used to generate 8 types of bone marrow chimeras, to differentiate the role of central (PB-to-IRF CKO) vs. peripheral (IRF CKO-to-PB) phagocytic IRF4-IRF5 axis in stroke. Chimeras generated from PB and flox mice were used as controls. All chimeras were subjected to 60-min middle cerebral artery occlusion (MCAO) model. Three days after the stroke, outcomes and inflammatory responses were analyzed. We found that PB-to-IRF4 CKO chimeras had more robust microglial pro-inflammatory responses than IRF4 CKO-to-PB chimeras, while ameliorated microglial response was seen in PB-to-IRF5 CKO vs. IRF5 CKO-to-PB chimeras. PB-to-IRF4 or IRF5 CKO chimeras had worse or better stroke outcomes respectively than their controls, whereas IRF4 or 5 CKO-to-PB chimeras had similar outcomes compared to controls. We conclude that the central IRF4/5 signaling is responsible for microglial activation and mediates stroke outcomes.

Complex dynamics in a fractional order nephron pressure and flow regulation model

Cardiovascular diseases can be attributed to irregular blood pressure, which may be caused by malfunctioning kidneys that regulate blood pressure. Research has identified complex oscillations in the mechanisms used by the kidney to regulate blood pressure. This study uses established physiological knowledge and earlier autoregulation models to derive a fractional order nephron autoregulation model. The dynamical behaviour of the model is analyzed using bifurcation plots, revealing periodic oscillations, chaotic regions, and multistability. A lattice array of the model is used to study collective behaviour and demonstrates the presence of chimeras in the network. A ring network of the fractional order model is also considered, and a diffusion coupling strength is adopted. A basin of synchronization is derived, considering coupling strength, fractional order or number of neighbours as parameters, and measuring the strength of incoherence. Overall, the study provides valuable insights into the complex dynamics of the nephron autoregulation model and its potential implications for cardiovascular diseases.

Giant teratoma with isolated intestinal duplication in adult: A case report and review of literature

BACKGROUND

A combination of diseases is a rare phenomenon. Their clinical manifestations can vary, and the diagnosis can be challenging. Intestinal duplication is a rare congenital malformation, whereas retroperitoneal teratoma is a tumor in the retroperitoneal space, derived from the remaining embryonic tissue. There are relatively few clinical findings on adult retroperitoneal benign tumors. It is hard to believe that these two rare diseases can happen to the same person.

CASE SUMMARY

A 19-year-old woman complaining of abdominal pain with nausea and vomiting was admitted. Abdominal computed tomography angiography was suggested for invasive teratoma. Intraoperative exploration revealed that the giant teratoma was connected to an isolated intestinal tract in the retroperitoneum. The postoperative pathological examination revealed that mature giant teratoma was present with intestinal duplication. This was a rare intraoperative finding that was successfully treated surgically.

CONCLUSION

The clinical manifestations of intestinal duplication malformation are various, and difficult to diagnose before the operation. The possibility of intestinal replication should be considered when intraperitoneal cystic lesions are present.

Review: Progress in producing chimeric ungulate livestock for agricultural applications

The progress made in recent years in the derivation and culture of pluripotent stem cells from farm animals opens up the possibility of creating livestock chimeras. Chimeras producing gametes exclusively derived from elite donor stem cells could pass superior genetics on to the next generation and thereby reduce the genetic lag that typically exists between the elite breeding sector and the commercial production sector, especially for industries like beef and sheep where genetics is commonly disseminated through natural service mating. Chimeras carrying germ cells generated from genome-edited or genetically engineered pluripotent stem cells could further disseminate useful genomic alterations such as climate adaptation, animal welfare improvements, the repair of deleterious genetic conditions, and/or the elimination of undesired traits such as disease susceptibility to the next generation. Despite the successful production of chimeras with germ cells generated from pluripotent donor stem cells injected into preimplantation-stage blastocysts in model species, there are no documented cases of this occurring in livestock. Here, we review the literature on the derivation of pluripotent stem cells from ungulates, and progress in the production of chimeric ungulate livestock for agricultural applications, drawing on insights from studies done in model species, and discuss future possibilities of this fast-moving and developing field. Aside from the technical aspects, the consistency of the regulatory approach taken by different jurisdictions towards chimeric ungulate livestock with germ cells generated from pluripotent stem cells and their progeny will be an important determinant of breeding industry uptake and adoption in animal agriculture.

Efficient generation and characterization of chimeric dengue viral-like particles

Viral-like particles (VLPs) because of their non-infectious and high immunogenic properties have important applications in diagnostics, drug delivery, and vaccine production. They also serve as an attractive model system to study virus assembly and fusion processes. Unlike other flaviviruses, Dengue virus (DENV) is not very efficient in the production of VLPs on the expression of DENV structural proteins. On the other hand, the stem region and transmembrane region (TM) of G protein of Vesicular Stomatitis virus (VSV) alone are sufficient for budding. Here we generated chimeric VLPs replacing regions of stem and transmembrane domain (STEM) or only transmembrane domain (TM) of E protein of DENV-2 with corresponding regions of VSV G protein. Both chimeric proteins secreted VLPs at higher levels than the wild type (2-4 folds) without any significant change in the expression in the cell. Chimeric VLPs could be recognized by a conformational monoclonal antibody, 4G2. They were also found to interact with dengue-infected patient sera effectively thus implying that their antigenic determinants are preserved. In addition, they were able to bind to its putative receptor, heparin with similar affinity as the parent counterpart thus retaining its functional property. However, cell-cell fusion revealed that there is no significant increase in the fusion ability of chimeras as compared to the parent clone, whereas VSV G protein displayed high cell-cell fusion activity. Overall, this study suggests that chimeric dengue VLPs can be taken forward for their likely potential as vaccine production and serodiagnosis.

Analysing the brain networks corresponding to the facial contrast-chimeras

How humans recognise faces and objects effortlessly, has become a great point of interest. To understand the underlying process, one of the approaches is to study the facial features, in particular ordinal contrast relations around the eye region, which plays a crucial role in face recognition and perception. Recently the graph-theoretic approaches to electroencephalogram (EEG) analysis are found to be effective in understating the underlying process of human brain while performing various tasks. We have explored this approach in face recognition and perception to know the importance of contrast features around the eye region. We studied functional brain networks, formed using EEG responses, corresponding to four types of visual stimuli with varying contrast relationships: Positive faces, chimeric faces (photo-negated faces, preserving the polarity of contrast relationships around eyes), photo-negated faces and only eyes. We observed the variations in brain networks of each type of stimuli by finding the distribution of graph distances across brain networks of all subjects. Moreover, our statistical analysis shows that positive and chimeric faces are equally easy to recognise in contrast to difficult recognition of negative faces and only eyes.

Multi-factorial examination of amplicon sequencing workflows from sample preparation to bioinformatic analysis

BACKGROUND

The development of sequencing technologies to evaluate bacterial microbiota composition has allowed new insights into the importance of microbial ecology. However, the variety of methodologies used among amplicon sequencing workflows leads to uncertainty about best practices as well as reproducibility and replicability among microbiome studies. Using a bacterial mock community composed of 37 soil isolates, we performed a comprehensive methodological evaluation of workflows, each with a different combination of methodological factors spanning sample preparation to bioinformatic analysis to define sources of artifacts that affect coverage, accuracy, and biases in the resulting compositional profiles.

RESULTS

Of the workflows examined, those using the V4-V4 primer set enabled the highest level of concordance between the original mock community and resulting microbiome sequence composition. Use of a high-fidelity polymerase, or a lower-fidelity polymerase with an increased PCR elongation time, limited chimera formation. Bioinformatic pipelines presented a trade-off between the fraction of distinct community members identified (coverage) and fraction of correct sequences (accuracy). DADA2 and QIIME2 assembled V4-V4 reads amplified by Taq polymerase resulted in the highest accuracy (100%) but had a coverage of only 52%. Using mothur to assemble and denoise V4-V4 reads resulted in a coverage of 75%, albeit with marginally lower accuracy (99.5%).

CONCLUSIONS

Optimization of microbiome workflows is critical for accuracy and to support reproducibility and replicability among microbiome studies. These considerations will help reveal the guiding principles of microbial ecology and impact the translation of microbiome research to human and environmental health.

Evaluation of the ability of human induced nephron progenitor cells to form chimeric renal organoids using mouse embryonic renal progenitor cells

The number of patients with end-stage renal failure is increasing annually worldwide and the problem is compounded by a shortage of renal transplantation donors. In our previous research, we have shown that transplantation of renal progenitor cells into the nephrogenic region of heterologous fetuses can induce the development of nephrons. We have also developed transgenic mice in which specific renal progenitor cells can be removed by drugs. By combining these two technologies, we have succeeded in generating human-mouse chimeric kidneys in fetal mice. We hope to apply these technologies to regenerative medicine. The quality of nephron progenitor cells (NPCs) derived from human pluripotent stem cells is important for the generation of chimeric kidneys, but there is currently no simple evaluation system for the chimerogenic potential of human NPCs. In this study, we focused on the fact that the re-aggregation of mouse renal progenitor cells can be used for nephron formation, even when merged into single cells. First, we examined the conditions under which nephron formation is likely to occur in mice during re-aggregation. Next, to improve the differentiation potential of human NPCs derived from pluripotent stem cells, NPCs were sorted using Integrin subunit alpha 8 (ITGA8). Finally, we demonstrated chimera formation between different species by mixing mouse cells with purified, selectively-induced human NPCs under optimum conditions. We observed these chimeric organoids at different time points to learn about these human-mouse chimeric structures at various stages of renal development. We found that the rate of chimera formation was affected by the purity of the human NPCs and the cell ratios used. We demonstrated that chimeric nephrons can be generated using a simple model, even between distant species. We believe that this admixture of human and mouse renal progenitor cells is a promising technology with potential application for the evaluation of the chimera formation abilities of NPCs.

Computational design and structure dynamics analysis of bifunctional chimera of endoxylanase from Clostridium thermocellum and xylosidase from Bacteroides ovatus

Development of chimeric enzymes by protein engineering can more efficiently contribute toward biomass conversion for bioenergy generation. Therefore, prior to experimental validation, a computational approach by modeling and molecular dynamic simulation can assess the structural and functional behavior of chimeric enzymes. In this study, a bifunctional chimera, CtXyn11A-BoGH43A comprising an efficient endoxylanase (CtXyn11A) from Clostridium thermocellum and xylosidase (BoGH43A) from Bacteroides ovatus was computationally designed and its binding and stability analysis with xylooligosaccharides were performed. The modeled chimera showed β-jellyroll fold for CtXyn11A and 5-bladed β-propeller fold for BoGH43A module. Stereo-chemical properties analyzed by Ramachandran plot showed 98.8% residues in allowed region, validating the modeled chimera. The catalytic residues identified by multiple sequence alignment were Glu94 and Glu184 for CtXyn11A and Asp229 and Glu384 for BoGH43A modules. CtXyn11A followed retaining-type, whereas BoGH43A enforced inverting-type of reaction mechanism during xylan hydrolysis as revealed by superposition and GH11 and GH43 familial analyses. Molecular docking studies showed binding energy, (ΔG) - 4.54 and - 4.18 kcal/mol for CtXyn11A and BoGH43A modules of chimera, respectively, with xylobiose, while - 3.94 and - 3.82 kcal/mol for CtXyn11A and BoGH43A modules of chimera, respectively, with xylotriose. MD simulation of CtXyn11A-BoGH43A complexed with xylobiose and xylotriose till 100 ns displayed stability by RMSD, compactness by R g and conformational stability by SASA analyses. The lowered values of RMSF in active-site residues, Glu94, Glu184, Asp229, Asp335 and Glu384 confirmed the efficient binding of chimera with xylobiose and xylotriose. These results were in agreement with the earlier experimental studies on CtXyn11A releasing xylooligosaccharides from xylan and BoGH43A releasing d-xylose from xylooligosaccharides and xylobiose. The chimera showed stronger affinity in terms of total short-range interaction energy; - 190 and - 121 kJ/mol for with xylobiose and xylotriose, respectively. The bifunctional chimera, CtXyn11A-BoGH43A showed stability and integrity with xylobiose and xylotriose. The designed chimera can be constructed and applied for efficient biomass conversion.

Gene Targeting in Mouse Embryonic Stem Cells via CRISPR/Cas9 Ribonucleoprotein (RNP)-Mediated Genome Editing

The CRISPR/Cas9-mediated genome-editing system enables the development of gene-modified mice using fertilized eggs. However, while the efficiency in developing gene knockout mice by inducing small indel mutations would be good enough, the successful ratio to create large side DNA knock-in (KI) by embryonic genome editing is still low. In contrast to the direct embryo KI method, gene targeting using embryonic stem cells (ESC) followed by chimeric mouse development by blastocyst injection still has several advantages, e.g., high-throughput in vitro targeting/screening or large-size DNA KI such as Cre, CreERT, TetON, and reporter fluorescent protein, or their fusion proteins can be carried out without serving animal lives. The ESC targeting can also be applied to strains such as BALB/c, of which embryos are known to be difficult to handle in vitro. This text describes the optimized method for either short- or large-size DNA KI in ESC by applying CRISPR/Cas9-mediated genome editing followed by chimera mice production to develop gene-manipulated mouse models.

Generation of Rabbit Chimeras by Eight-Cell Stage Embryo Injection

Pluripotent stem cell (PSC) injection to the blastocyst stage embryos is a widely used method to evaluate the pluripotency through chimeric contribution. It is routinely used to produce transgenic mice. However, PSC injection to the blastocyst stage embryos in rabbits is challenging. At this stage, the in vivo developed rabbit blastocysts possess a thick mucin layer that is inhibitory for microinjection, whereas in vitro developed rabbit blastocysts that lack such mucin layer often fail to implant after embryo transfer. In this chapter, we describe a detailed protocol of rabbit chimera production through mucin-free eight-cell stage embryo injection procedure.

Rat Embryonic Stem Cell Transgenesis

The availability of reliable germline competent rat embryonic stem cell (ESC) lines that can be genetically manipulated provides an important tool for generating new rat models. Here we describe the process for culturing rat ESCs, microinjecting the ESCs into rat blastocysts, and transferring the embryos to surrogate dams by either surgical or non-surgical embryo transfer techniques to produce chimeric animals with the potential to pass on the genetic modification to their offspring.

Adoptive Transfer and Bone Marrow Chimera Models to Analyze Treg Function and Differentiation

Cellular adoptive transfer and mixed bone marrow chimera are cornerstone experimental tools for immuno-biology. Here we describe protocols for adoptive transfer and bone marrow chimera to address the effect of a specific mutation on T regulatory cell (Treg) function and differentiation, respectively. Treg function can be quantitatively measured by analyzing the expansion of conventional CD4 T cells and their differentiation into helper cells. The quantitative measure of Treg differentiation is addressed by analyzing the number and phenotype of Foxp3-expressing cells. The use of congenic markers is instrumental for these approaches.

Frontloading of stress response genes enhances robustness to environmental change in chimeric corals

Background

Chimeras are genetically mixed entities resulting from the fusion of two or more conspecifics. This phenomenon is widely distributed in nature and documented in a variety of animal and plant phyla. In corals, chimerism initiates at early ontogenic states (larvae to young spat) and results from the fusion between two or more closely settled conspecifics. When compared to genetically homogenous colonies (non-chimeras), the literature has listed ecological and evolutionary benefits for traits at the chimeric state, further positioning coral chimerism as an evolutionary rescue instrument. However, the molecular mechanisms underlying this suggestion remain unknown.

Results

To address this question, we developed field monitoring and multi-omics approaches to compare the responses of chimeric and non-chimeric colonies acclimated for 1 year at 10-m depth or exposed to a stressful environmental change (translocation from 10- to 2-m depth for 48h). We showed that chimerism in the stony coral Stylophora pistillata is associated with higher survival over a 1-year period. Transcriptomic analyses showed that chimeras lose transcriptomic plasticity and constitutively express at higher level (frontload) genes responsive to stress. This frontloading may prepare the colony to face at any time environmental stresses which explain its higher robustness.

Conclusions

These results show that chimeras are environmentally robust entities with an enhanced ability to cope with environmental stress. Results further document the potential usefulness of chimeras as a novel reef restoration tool to enhance coral adaptability to environmental change, and confirm that coral chimerism can be an evolutionary rescue instrument.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01371-7.

Cultivar-specific markers, mutations, and chimerisim of Cavendish banana somaclonal variants resistant to Fusarium oxysporum f. sp. cubense tropical race 4

Background

The selection of tissue culture–derived somaclonal variants of Giant Cavendish banana (Musa spp., Cavendish sub-group AAA) by the Taiwan Banana Research Institute (TBRI) has resulted in several cultivars resistant to Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), a destructive fungus threatening global banana production. However, the mutations in these somaclonal variants have not yet been determined. We performed an RNA-sequencing (RNA-seq) analysis of three TBRI Foc TR4–resistant cultivars: ‘Tai-Chiao No. 5’ (TC5), ‘Tai-Chiao No. 7’ (TC7), and ‘Formosana’ (FM), as well as their susceptible progenitor ‘Pei-Chiao’ (PC), to investigate the sequence variations among them and develop cultivar-specific markers.

Results

A group of single-nucleotide variants (SNVs) specific to one cultivar were identified from the analysis of RNA-seq data and validated using Sanger sequencing from genomic DNA. Several SNVs were further converted into cleaved amplified polymorphic sequence (CAPS) markers or derived CAPS markers that could identify the three Foc TR4–resistant cultivars among 6 local and 5 international Cavendish cultivars. Compared with PC, the three resistant cultivars showed a loss or alteration of heterozygosity in some chromosomal regions, which appears to be a consequence of single-copy chromosomal deletions. Notably, TC7 and FM shared a common deletion region on chromosome 5; however, different TC7 tissues displayed varying degrees of allele ratios in this region, suggesting the presence of chimerism in TC7.

Conclusions

This work demonstrates that reliable SNV markers of tissue culture–derived and propagated banana cultivars with a triploid genome can be developed through RNA-seq data analysis. Moreover, the analysis of sequence heterozygosity can uncover chromosomal deletions and chimerism in banana somaclonal variants. The markers obtained from this study will assist with the identification of TBRI Cavendish somaclonal variants for the quality control of tissue culture propagation, and the protection of breeders’ rights.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08692-5.

Biomedical application of small extracellular vesicles in cancer treatment

Extracellular vesicles (EVs) are produced by almost all cell types in vivo or in vitro. Among them, exosomes are small nanovesicles with a lipid bilayer, proteins and RNAs actively involved in cellular communication, suggesting that they may be used both as biomarkers and for therapeutic purposes in diseases such as cancer. Moreover, the idea of using them as drug delivery vehicle arises as a promising field of study. Here, we reviewed recent findings showing the importance of EVs, with special focus in exosomes as biomarkers including the most relevant proteins found in different cancer types and it is discussed the FDA approved tests which use exosomes in clinical practice. Finally, we present an overview of the different chimeric EVs developed in the last few years, demonstrating that they can be conjugate to nanoparticles, biomolecules, cancer drugs, etc., and can be developed for a specific cancer treatment. Additionally, we summarized the clinical trials where EVs are used in the treatment of several cancer types aiming to improve the prognosis of these deadly diseases.

Engineering multifunctional enzymes for agro-biomass utilization

Lignocellulosic biomass is a plentiful renewable resource that can be converted into a wide range of high-value-added industrial products. However, the complexity of its structural integrity is one of the major constraints and requires combinations of different fibrolytic enzymes for the cost-effective, industrially and environmentally feasible transformation. An interesting approach is constructing multifunctional enzymes, either in a single polypeptide or by joining multiple domains with linkers and performing diverse reactions simultaneously, in a single host. The production of such chimera proteins multiplies the advantages of different enzymatic reactions in a single setup, in lesser time, at lower production cost and with desirable and improved catalytic activities. This review embodies the various domain-tailoring and extracellular secretion strategies, possible solutions to their challenges, and efforts to experimentally connect different catalytic activities in a single host, as well as their applications.

Generation of chimeric kidneys using progenitor cell replacement: Oshima Award Address 2021

It is believed that the development of new renal replacement therapy (RRT) will increase treatment options for end-stage kidney disease and help reduce the mismatch between supply and demand. Technological advancement in the development of kidney organoids derived from pluripotent stem cells and xenotransplantation using porcine kidneys has been accelerated by a convergence of technological innovations, including the discovery of induced pluripotent stem cells and genome editing, and improvement of analysis techniques such as single-cell ribonucleic acid sequencing. Given the difficulty associated with kidney regeneration, hybrid kidneys are studied as an innovative approach that involves the use of stem cells to generate kidneys, with animal fetal kidneys used as a scaffold. Hybrid kidney technology entails the application of local chimerism for the generation of chimeric kidneys from exogenous renal progenitor cells by borrowing complex nephrogenesis programs from the developmental environment of heterologous animals. Hybrid kidneys can also utilize the urinary tract and bladder tissue of animal fetuses for urine excretion. Generating nephrons from syngeneic stem cells to increase self-cell ratio in xeno-tissues can reduce the risk of xeno-rejection. We showed that nephrons can be generated by ablation of host nephron progenitor cells (NPCs) in the nephron development region of animals and replacing them with exogenous NPCs. This progenitor cell replacement is the basis of hybrid kidney regeneration from progenitor cells using chimera technology. The goal of xeno-regenerative medicine using hybrid kidneys is to overcome serious organ shortage.

Development and validation of novel kit for quantification of SARS-CoV-2 antibodies on clinical samples

Since the pandemic occurred due to the emergence of SARS-CoV-2, there has always been a demand for a simple and sensitive diagnostic kit for detection of SARS-Cov-2 infection. In January 2020, WHO approved the Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) for detecting the presence of Covid-19 genetic material in individuals. Till date many diagnostic kits have arrived in the market for quantification of SARS-CoV-2 antibodies. In spite of being the gold standard method of Covid-19 detection, there are some drawbacks associated with RT-PCR which leads to false-negative results. Hence, in order to fulfil the need for an antibody testing kit for evaluating seroconversion and immunity acquisition in the population, an efficient, highly specific and sensitive assay, Chimera Soochak, an enzyme-linked immunoassay (ELISA) Kit has been developed. It works on the principle of detecting IgG antibodies developed specifically against the S1-RBD by employing a recombinant strain of S1-RBD produced in the HEK293 cell line. The developed kit was validated using different modes and methods to attain the utmost confidence on the samples collected from patients. The validation methodology included, validation with known samples, blind study, third-party validation, validation using WHO Reference Panel and comparison with FDA approved Surrogate virus neutralization kit. The kit was found successful in detecting IgG against the S1-RBD of SARS-CoV-2. The kit had been validated on multiple parameters. A total of 900 samples had been tested by using this kit and it has exhibited the sensitivity, specificity and accuracy for all the above-mentioned parameters.

Aqueous Molecular Dynamics for Understanding Glycosaminoglycan Recognition by Proteins

Glycosaminoglycans (GAGs) are biopolymers that exist in most organisms. GAGs are known to bind to hundreds of proteins and partake in multiple biological processes such as growth, morphogenesis, inflammation, infection, and others. Their intrinsic structural heterogeneity and conformational variability introduce major challenges in experimental studies. On the other hand, recent advances in force field development and computational technology have yielded phenomenal opportunity to study thousands of GAG sequences simultaneously to understand recognition of target protein(s). Here, we describe experimental setup for conventional molecular dynamics simulations of GAGs to position an experimental biologist favorably in performance, analysis and interpretation of stability, specificity, and conformational properties of GAGs, while also elucidating their interactions with amino acid residues of a protein at an atomistic level in presence of water.

In Silico Design of Recombinant Chimera T Cell Peptide Epitope Vaccines for Visceral Leishmaniasis

Visceral leishmaniasis (VL) is a neglected tropical disease caused by protozoan parasites of the genus Leishmania. Systemic VL is fatal if untreated and there are no prophylactic human vaccines available. Several studies suggest that Th1 cell-mediated immunity plays a major role in protecting against VL. In this chapter we describe a method for designing recombinant chimera vaccines in silico based on the prediction of T cell epitopes within protein antigens identified as potential protective immunogens. Development of a recombinant chimera protein (RCP) vaccine using T cell epitope peptides identified from four Leishmania proteins is used as an exemplar of this method.

Sensitive and specific serodiagnosis of tegumentary leishmaniasis using a new chimeric protein based on specific B-cell epitopes of Leishmania antigenic proteins

Serological tests used for the diagnosis of tegumentary leishmaniasis (TL) presents problems, mainly related to their variable sensitivity and/or specificity, which can be caused by low levels of antileishmanial antibodies or by presence of cross-reactive diseases, respectively. In this context, the search for new antigenic candidates presenting higher sensitivity and specificity is urgently required. In the present study, the amino acid sequences of the LiHyT, LiHyD, LiHyV, and LiHyP proteins, which were previously showed to be antigenic in the visceral leishmaniasis (VL), were evaluated and eight B-cell epitopes were predicted and used for construction of gene codifying a chimeric protein called ChimLeish. The protein was expressed, purified and evaluated as a recombinant antigen in ELISA (Enzyme-Linked Immunosorbent Assay) for the diagnosis of TL. The own B cell epitopes used to construct the chimera were synthetized and also evaluated as antigens, as well as a soluble Leishmania braziliensis antigenic extract (SLA). Results showed that ChimLeish presented 100% sensitivity and specificity to diagnose TL, while synthetic peptides showed sensitivity varying from 9.1% to 90.9%, while specificity reached from 98.3% to 99.1%. SLA showed sensitivity and specificity of 18.2% and 98.3%, respectively. A preliminary prognostic evaluation showed that anti-ChimLeish IgG antibodies declined in significant levels, when serological reactivity was compared before and six months after treatment, suggesting also a possible prognostic role of this antigen for TL.

In silico analyses and design of a chimeric protein containing epitopes of SpaC, PknG, NanH, and SodC proteins for the control of caseous lymphadenitis

Abstract

Caseous lymphadenitis (CLA) is an infectious disease that affects goats and sheep causing drastic impacts on milk and meat production and is caused by Corynebacterium pseudotuberculosis. The disease can be prevented through vaccination but currently, vaccines demonstrate limited efficacy consequently leading to a need for the development of new ones. Here, we described the in silico development of a new chimeric protein constructed with epitopes identified from the sequences of the genes nanH, pknG, spaC, and sodC, previously described as potential vaccinal targets against C. pseudotuberculosis. The chimera was expressed, purified, and its immunogenicity was evaluated using sera of immunized mice. Results indicate the chimeric protein was able to stimulate antibody production. Additionally, analysis using serum from naturally infected goats showed that the protein is recognized by sera from these animals, indicating the possibility for using this chimera in new diagnostic methods.

Key points

• The chimera was expressed with 52 kDa and a yield of 7 mg/L after purification.

• The chimera was recognized by the sera of animals immunized with this formulation.

• Chimera reacted with the serum of goats naturally infected with C. pseudotuberculosis.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11619-x.

Nanobodies as sensors of GPCR activation and signaling

Nanobodies have emerged as useful tools to study G protein-coupled receptor (GPCR) structure, dynamic, and subcellular localization. Initially, several nanobodies have been developed as chaperones to facilitate GPCR crystallization. To explore their potential as biosensors to monitor receptor activation and dynamics, we here described protocols to characterize nanobody's interaction with GPCRs and their application as probes for protein identification and visualization on the cellular level. We also introduced a chimeric approach to enable a kappa-opioid receptor derived nanobody to bind to other GPCRs, including orphan GPCRs whose endogenous ligand or intracellular transducers are unknown. This approach provides a reporter assay to identify tool molecules to study the function of orphan GPCRs.

Chimeric human opsins as optogenetic light sensitisers

Human opsin-based photopigments have great potential as light-sensitisers, but their requirement for phototransduction cascade-specific second messenger proteins may restrict their functionality in non-native cell types. In this study, eight chimeric human opsins were generated consisting of a backbone of either a rhodopsin (RHO) or long-wavelength-sensitive (LWS) opsin and intracellular domains from G_q/11-coupled human melanopsin. Rhodopsin/melanopsin chimeric opsins coupled to both G_i and G_q/11 pathways. Greater substitution of the intracellular surface with corresponding melanopsin domains generally showed greater G_q/11 activity with a decrease in G_i activation. Unlike melanopsin, rhodopsin and rhodopsin/melanopsin chimeras were dependent upon exogenous chromophore to function. By contrast, wild-type LWS opsin and LWS opsin/melanopsin chimeras showed only weak G_i activation in response to light, whilst G_q/11 pathway activation was not detected. Immunocytochemistry (ICC) demonstrated that chimeric opsins with more intracellular domains of melanopsin were less likely to be trafficked to the plasma membrane. This study demonstrates the importance of G_α coupling efficiency to the speed of cellular responses and created human opsins with a unique combination of properties to expand the range of customised optogenetic biotools for basic research and translational therapies.

Summary: Combining different domains of human visual opsins and melanopsin creates functionally unique chimeric opsins with potential optogenetic applications.

Generation of phytase chimeras with low sequence identities and improved thermal stability

Being able to recombine more than two genes with four or more crossover points in a sequence independent manner is still a challenge in protein engineering and limits our capabilities in tailoring enzymes for industrial applications. By computational analysis employing multiple sequence alignments and homology modeling, five fragments of six phytase genes (sequence identities 31-64 %) were identified and efficiently recombined through phosphorothioate-based cloning using the PTRec method. By combinatorial recombination, functional phytase chimeras containing fragments of up to four phytases were obtained. Two variants (PTRec 74 and PTRec 77) with up to 32 % improved residual activity (90 °C, 60 min) and retained specific activities of > 1100 U/mg were identified. Both variants are composed of fragments from the phytases of Citrobacter braakii, Hafnia alvei and Yersinia mollaretii. They exhibit sequence identities of ≤ 80 % to their parental enzymes, highlighting the great potential of DNA recombination strategies to generate new enzymes with low sequences identities that offer opportunities for property right claims.

Interspecies chimeras as a platform for exogenic organ production and transplantation

Chronic diseases are associated with considerable morbidity and mortality. Therefore, new therapeutic strategies are warranted. Here, we provide a brief review outlining the rationale and feasibility for the generation of intraspecies and interspecies chimeras, which one day may serve as a platform for organ transplantation. These strategies are further associated with consideration of scientific and ethical issues.

A chimeric vaccine combined with adjuvant system induces immunogenicity and protection against visceral leishmaniasis in BALB/c mice

In Brazil, canine visceral leishmaniasis is an important public health problem due to its alarming growth. The high prevalence of infected dogs reinforces the need for a vaccine for use in prophylactic vaccination campaigns. In the present study, we evaluate the immunogenicity and protection of the best dose of Chimera A selected through the screening of cytokines production important in disease. BALB/c mice were vaccinated subcutaneously with three doses and challenged intravenously with 1 × 10⁷L. infantum promastigotes. Spleen samples were collected to assess the intracellular cytokine profile production, T cell proliferation and parasite load. At first, three different doses of Chimera A (5 μg, 10 μg and 20 μg) were evaluated through the production of IFN-γ and IL-10 cytokines. Since the dose of 20 μg showed the best results, it was chosen to continue the study. Secondarily, Chimera A at dose of 20 μg was formulated with Saponin plus Monophosphoryl lipid A. Vaccination with Chimera A alone and formulated with SM adjuvant system was able to increase the percentage of the proliferation of specific T lymphocytes and stimulated a Th1 response with increased levels of IFN-γ, TNF-α and IL-2, and decreased of IL-4 and IL-10. The vaccine efficacy through real-time PCR demonstrated a reduction in the splenic parasite load in animals that received Chimera A formulated with the SM adjuvant system (92%). Additionally, we observed increased levels of nitric oxide in stimulated-culture supernatants. The Chimera A formulated with the SM adjuvant system was potentially immunogenic, being able to induce immunoprotective mechanisms and reduce parasite load. Therefore, the use of T-cell multi-epitope vaccine is promising against visceral leishmaniasis.

Intradermal co-inoculation of codon pair deoptimization (CPD)-attenuated chimeric porcine reproductive and respiratory syndrome virus (PRRSV) with Toll like receptor (TLR) agonists enhanced the protective effects in pigs against heterologous challenge

The objective of this study was to assess protective efficacy of vaccination using CPD-attenuated chimeric PRRSV and Toll like receptor (TLR) agonists (HSP70 c-terminal domain and HSPX) as adjuvants through different inoculation routes. In this study, a chimeric PRRSV composed of two field isolates was synthesized and attenuated by CPD in NSP1 as described in the previous study. The infection of the CPD-attenuated chimeric PRRSV to pigs of 3 weeks-old showed no clinical signs without pathological lesions in necropsy, while it induced improved cross immunity between its parent strains. The TLR agonists were expressed in E. coli and purified to be used. In challenge experiment, pigs of 3 weeks-old were vaccinated using the CPD-attenuated chimeric virus with the prepared TLR agonists through intramuscular or intradermal route, following heterologous challenge after 4 weeks of vaccination. In results, intramuscular or intradermal inoculation of the CPD-attenuated chimeric virus demonstrated excellent protective efficacy against heterologous challenges. Importantly, intradermal inoculation with the TLR agonists enhanced protective effects as shown in the significantly increased level of PRRSV-specific IFN-γ-SCs and cytokines in sera, and the significant reduction of pathological lesion and viral load in lung. This study suggested that the intradermal inoculation of CPD-attenuated chimeric PRRSV plus TLR agonists should be more effective for protection of pigs against diverse PRRS field viruses.

Misclassifications in human papillomavirus databases

We assessed the quality of human papillomavirus (HPV) sequences in GenBank by analyzing the possible presence of chimeras, "wrong-assembled" contigs and errors in taxonomy using an open-source script (HPVChimera_Gb) that compared 25 638 HPV-related nucleotide sequences in GenBank with the 221 numbered HPV types and another 220 complete HPV sequences. There were 110 sequences with taxonomy/naming errors (sequences reported as another HPV type than the one they corresponded to) and 1318 possibly chimeric sequences. Manual analysis found plausible explanations for most of them (e.g. sequence covering an integration site) but 114 sequences appeared to be chimeras (96/114 were already flagged as "unverified" by GenBank) and 13 had taxonomy/naming errors. When comparing all correct HPV sequences in GenBank, there appeared to exist about 800 unique putative HPV types. Systematic and regular work towards eliminating chimeric sequences and taxonomy/naming errors could increase the quality and order in HPV research.

Perspectives of pluripotent stem cells in livestock

The recent progress in derivation of pluripotent stem cells (PSCs) from farm animals opens new approaches not only for reproduction, genetic engineering, treatment and conservation of these species, but also for screening novel drugs for their efficacy and toxicity, and modelling of human diseases. Initial attempts to derive PSCs from the inner cell mass of blastocyst stages in farm animals were largely unsuccessful as either the cells survived for only a few passages, or lost their cellular potency; indicating that the protocols which allowed the derivation of murine or human embryonic stem (ES) cells were not sufficient to support the maintenance of ES cells from farm animals. This scenario changed by the innovation of induced pluripotency and by the development of the 3 inhibitor culture conditions to support naïve pluripotency in ES cells from livestock species. However, the long-term culture of livestock PSCs while maintaining the full pluripotency is still challenging, and requires further refinements. Here, we review the current achievements in the derivation of PSCs from farm animals, and discuss the potential application areas.

A chimeric porcine reproductive and respiratory syndrome virus (PRRSV)-2 vaccine is safe under international guidelines and effective both in experimental and field conditions

Vaccination is currently the most effective strategy to control porcine reproductive and respiratory syndrome (PRRS). New-generation PRRS vaccines are required to be safe and broadly cross-protective. We have recently created the chimeric PRRS virus K418DM which proved to be a good vaccine candidate under field conditions. In the present study, we designed safety and efficacy tests under experimental and field conditions for further evaluation of K418DM1.1, a plaque-purified K418DM. In the homologous challenge study, K418DM1.1 induced high serum virus neutralization (SVN) antibody titers (i.e., 4.2 log₂ ± 1.7) at 21 days post-challenge (dpc) and provided protection as demonstrated by the significantly lower levels of viremia at 3 and 7 dpc and significantly lower microscopic lung lesion scores compared to the unvaccinated group. K418DM1.1 was also protective in the heterologous challenge study, with vaccinated pigs showing significantly lower levels of viremia at 14 dpc compared to the unvaccinated pigs. A field study was performed to evaluate the efficacy of K418DM1.1 against heterologous exposure and vaccinated pigs presented significantly lower viremia than unvaccinated pigs. According to the safety test for the examination of virulence reversion, no infectivity was observed in tissue homogenate filtrate both in the vaccinated and comingled groups. Thus, the risk of virulence, as well as transmission, appeared negligible. These overall results indicate that K418DM1.1 is a good vaccine candidate based on its safety and protective efficacy.

Measuring In Vivo Neutrophil Trafficking Responses During Fungal Infection Using Mixed Bone Marrow Chimeras

Neutrophil migration to the site of infection is an essential process for the control and clearance of microbial growth within the host. Identifying the molecular factors that mediate neutrophil chemotaxis is therefore critical for our understanding of disease pathogenesis and the mechanisms underlying protective immunity. Here, we describe a protocol that enables analysis of neutrophil recruitment from the blood into fungal-infected organs in vivo, using mixed bone marrow chimeras and flow cytometry. This method directly assesses the relative contribution of a receptor or intracellular molecule in controlling neutrophil chemotaxis during fungal infection and can be adapted to a variety of other non-fungal infection experimental settings.

Pericyte Ontogeny: The Use of Chimeras to Track a Cell Lineage of Diverse Germ Line Origins

The goal of lineage tracing is to understand body formation over time by discovering which cells are the progeny of a specific, identified, ancestral progenitor. Subsidiary questions include unequivocal identification of what they have become, how many descendants develop, whether they live or die, and where they are located in the tissue or body at the end of the window examined. A classical approach in experimental embryology, lineage tracing continues to be used in developmental biology and stem cell and cancer research, wherever cellular potential and behavior need to be studied in multiple dimensions, of which one is time. Each technical approach has its advantages and drawbacks. This chapter, with some previously unpublished data, will concentrate nonexclusively on the use of interspecies chimeras to explore the origins of perivascular (or mural) cells, of which those adjacent to the vascular endothelium are termed pericytes for this purpose. These studies laid the groundwork for our understanding that pericytes derive from progenitor mesenchymal pools of multiple origins in the vertebrate embryo, some of which persist into adulthood. The results obtained through xenografting, like in the methodology described here, complement those obtained through genetic lineage-tracing techniques within a given species.

Somatic embryogenesis is an effective strategy for dissecting chimerism phenomena in Vitis vinifera cv Nebbiolo

The tendency of somatic embryogenesis to regenerate plants only from the L1 layer, associated with the spread of chimerism in grapevine, must be carefully considered in the framework of biotechnological improvement programmes. Grapevine is an important fruit crop with a high economic value linked to traditional genotypes that have been multiplied for centuries by vegetative propagation. In this way, somatic variations that can spontaneously occur within the shoot apical meristem are fixed in the whole plant and represent a source of intra-varietal variability. Previously identified inconsistencies in the allelic calls of single nucleotide variants (SNVs) suggested that the Vitis vinifera 'Nebbiolo' CVT185 clone is a potential periclinal chimera. We adopted the somatic embryogenesis technique to separate the two genotypes putatively associated with the L1 and L2 layers of CVT185 into different somaclones. Despite the recalcitrance of 'Nebbiolo' to the embryogenic process, 58 somaclones were regenerated and SNV genotyping assays attested that the genotype of all them differed from that of the mother plant and was only attributable to L1. The results confirmed that L2 has low or no competence for differentiating somatic embryos. After one year in the greenhouse, the somaclones showed no phenotypic alterations in comparison with the mother plant; however further analyses are needed to identify potential endogenous sources of variation. The tendency of somatic embryogenesis to regenerate plants only from L1 must be carefully considered in the framework of biotechnological improvement programmes in this species.

Protection against leptospirosis conferred by Mycobacterium bovis BCG expressing antigens from Leptospira interrogans

Leptospirosis is a zoonotic disease worldwide and caused by the pathogenic spirochetes of the genus Leptospira. Bacterins make up the vaccines used against leptospirosis, but they only succeed in providing short-term and serovar-specific protection. The use of Mycobacterium bovis BCG as a live vaccine vector expressing leptospiral antigens is a promising alternative, particularly due to its adjuvant properties. Four distinct portions P₁ (lipL32), P₂ (ligAni), P₃ (lemA:ligAni) and P₄ (lipL32:lemA) of a recombinant chimera composed of the lipL32, lemA and ligANI genes from Leptospira interrogans were cloned individually according to the BioBricks® strategy in the plasmid pUP500/P_pAN. These constructs were individually transformed into a BCG Pasteur strain, and protein expression was detected by Western blot. For vaccination, 5 groups of 10 Golden Syrian hamsters were used, aged 4-6 weeks - group 1, rBCG (LipL32); group 2, rBCG (LigAni); group 3, rBCG (LemA:LigAni); group 4, (LipL32:LemA); group 5, wild-type BCG Pasteur (negative control). Two doses containing 10⁶ CFU of rBCG were administered subcutaneously, the challenge was performed with 5 × LD₅₀ of Leptospira interrogans serovar Copenhageni L1-130, and the animals were observed for a 30-day period until the endpoint was reached. Humoral immunity was assessed via indirect ELISA, while renal colonisation was assessed by culture and quantitative real-time PCR. All vaccinated groups were protected against lethal challenge and renal colonisation, in comparison with negative control group (P < 0.05). Recombinant vaccines were not effective at inducing significant humoral immunity, which suggests the induction of cellular immunity - a characteristic of M. bovis BCG. In conclusion, all formulations provide 100% significant protection against leptospirosis in hamsters with no renal colonisation. The use of rBCG as a vaccine vector represents a promising alternative for the control of animal leptospirosis, allowing for protection against clinical signs of leptospirosis and renal colonisation.

Individuals, Boundaries, and Graft-versus-Host Disease

Hematopoietic cell transplantation generates new individuals, transplant chimeras, composed of 2 genetic partners-the patient and donor-derived cells-no longer restricted by their original genomes. Interactions of donor-derived and recipient cells occur prominently at the boundary of the recipient with a third partner, the microbiome, in particular skin and intestinal tract, leading to disruption of microbiome homeostasis. These interactions of donor and patient cells at the boundary set the stage for the development of graft-versus-host disease, an expression of the defense of individuality by recipient and donor. Establishment of tolerance and return of homeostasis at the boundary will allow for the survival of the new integrated, physiologic individual.

Effects of graphene oxide on PCR amplification for microbial community survey

BACKGROUND

Graphene oxide (GO) has been suggested as an efficient assistant additive to eliminate non-specific amplification of the polymerase chain reaction (PCR). Although many studies have focused on exploring its molecular mechanism, the practice of GO on the quantitation of microbial community has not been implemented yet. In this study, GO was added in PCR system to explore the changes on removing typical amplification errors, such as chimera and mismatches on two kinds of mock communities (an evenly mixed and a staggered mock communities) and environmental samples.

RESULTS

High-throughput sequencing of bacterial and fungal communities, based on 16S rRNA genes and internal transcribed spacers (ITS) respectively, showed that GO could significantly increase large segmental error (chimeric sequence) in PCR procedure while had no specific effect on point error (mismatched sequence). Besides, GO reduced the α-diversity of community, and changed the composition of fungal community more obviously than bacterial community.

CONCLUSIONS

Our study provides the first quantitative data on microbial community level to prove the negative effect of GO, and also indicates that there may be a more complex interaction between GO and comprehensive DNA fragments in PCR process.

Developmental potential of somatic and germ cells of hybrids between Carassius auratus females and Hemigrammocypris rasborella males

The cause of hybrid sterility and inviability has not been analyzed in the fin-fish hybrid, although large numbers of hybridizations have been carried out. In this study, we produced allo-diploid hybrids by cross-fertilization between female goldfish (Carassius auratus) and male golden venus chub (Hemigrammocypris rasborella). Inviability of these hybrids was due to breakage of the enveloping layer during epiboly or due to malformation with serious cardiac oedema around the hatching stage. Spontaneous allo-triploid hybrids with two sets of the goldfish genome and one set of the golden venus chub genome developed normally and survived beyond the feeding stage. This improved survival was confirmed by generating heat-shock-induced allo-triploid hybrids that possessed an extra goldfish genome. When inviable allo-diploid hybrid cells were transplanted into goldfish host embryos at the blastula stage, these embryos hatched normally, incorporating the allo-diploid cells. These allo-diploid hybrid cells persisted, and were genetically detected in a 6-month-old fish. In contrast, primordial germ cells taken from allo-diploid hybrids and transplanted into goldfish hosts at the blastula stage had disappeared by 10 days post-fertilization, even under chimeric conditions. In allo-triploid hybrid embryos, germ cells proliferated in the gonad, but had disappeared by 10 weeks post-fertilization. These results showed that while hybrid germ cells are inviable even in chimeric conditions, hybrid somatic cells remain viable.