The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5

Plant-parasitic nematodes are a major, and in some cases a dominant, threat to crop production in all agricultural systems. The relative scarcity of classical resistance genes highlights a pressing need to identify new ways to develop nematode-resistant germplasm. Here, we sequence and assemble a high-quality genome of the model cyst nematode Heterodera schachtii to provide a platform for the first system-wide dual analysis of host and parasite gene expression over time, covering all major stages of the interaction. This novel approach enabled the analysis of the hologenome of the infection site, to identify metabolic pathways that were incomplete in the parasite but complemented by the host. Using a combination of bioinformatic, genetic, and biochemical approaches, we show that the highly atypical completion of vitamin B5 biosynthesis by the parasitic animal, putatively enabled by a horizontal gene transfer from a bacterium, is critically important for parasitism. Knockout of either the plant-encoded or the now nematode-encoded steps in the pathway blocks parasitism. Our experiments establish a reference for cyst nematodes, use this platform to further our fundamental understanding of the evolution of plant-parasitism by nematodes, and show that understanding congruent differential expression of metabolic pathways represents a new way to find nematode susceptibility genes, and thereby, targets for future genome editing-mediated generation of nematode-resistant crops.

Urinary Extracellular Vesicles contain simplified transcriptomes enriched in circular & long noncoding RNAs with functional significance in prostate cancer

Long noncoding (lnc)RNAs modulate gene expression alongside presenting unexpected source of neoantigens. Despite their immense interest, their ability to be transferred and control adjacent cells is unknown. Extracellular Vesicles (EVs) offer a protective environment for nucleic acids, with pro and anti-tumorigenic functions by controlling the immune response. In contrast to extracellular non-vesicular RNA, few studies have addressed the full RNA content within human fluids’ EVs and none have compared them with their tissue of origin. Here, we performed Total RNA-Sequencing on 6 Formaldehyde-Fixed-Parafilm-Embedded (FFPE) prostate cancer (PCa) tumor tissues and their paired urinary (u)EVs to provide the first whole transcriptome comparison from the same patients. UEVs contain simplified transcriptome with intron-free cytoplasmic transcripts and specific lnc/circular (circ)RNAs, strikingly common to all patients. Our full cellular and EVs transcriptome comparison within 3 common PCa cell lines identified a set of overlapping 14 uEV-circRNAs characterized as essential for prostate cell proliferation in vitro and 15 uEV-lncRNAs that we predicted to encode 768 high-affinity neoantigens. Our dual analysis of EVs-lnc/circRNAs both in urines’ and in vitro’s EVs provides a fundamental resource for future uEV-lnc/circRNAs phenotypic characterization involved in PCa.

Prostate cancer urinary Extracellular Vesicles are enriched in cytoplasmic intron-free mRNAs and circular/long noncoding RNAs with functional significance

Long noncoding (lnc)RNAs modulate gene expression alongside presenting unexpected source of neoantigens. Despite their immense interest, their ability to be transferred and control adjacent cells is unknown. Extracellular Vesicles (EVs) offer a protective environment for nucleic acids, with pro and anti-tumorigenic functions by controlling the immune response. In contrast to extracellular non-vesicular RNA, few studies have addressed the full RNA content within human fluids’ EVs and none have compared them with their tissue of origin. Here, we performed Total RNA-Sequencing on 6 Formaldehyde-Fixed-Parafilm-Embedded (FFPE) prostate cancer (PCa) tumor tissues and their paired urinary (u)EVs to provide the first whole transcriptome comparison from the same patients. UEVs contain simplified transcriptome with intron-free cytoplasmic transcripts and specific lnc/circular (circ)RNAs, strikingly common to all patients. Our full cellular and EVs transcriptome comparison within 3 common PCa cell lines identified a set of overlapping 14 uEV-circRNAs characterized as essential for prostate cell proliferation in vitro and 15 uEV-lncRNAs that we predicted to encode 768 high-affinity neoantigens. Our dual analysis of EVs-lnc/circRNAs both in urines’ and in vitro’s EVs provides a fundamental resource for future uEV-lnc/circRNAs phenotypic characterization involved in PCa.

Quantum Current Algebra Symmetry and Description of Boltzmann Type Kinetic Equations in Statistical Physics

We review a non-relativistic current algebra symmetry approach to constructing the Bogolubov generating functional of many-particle distribution functions and apply it to description of invariantly reduced Hamiltonian systems of the Boltzmann type kinetic equations, related to naturally imposed constraints on many-particle correlation functions. As an interesting example of deriving Vlasov type kinetic equations, we considered a quantum-mechanical model of spinless particles with delta-type interaction, having applications for describing so called Benney-type hydrodynamical praticle flows. We also review new results on a special class of dynamical systems of Boltzmann–Bogolubov and Boltzmann–Vlasov type on infinite dimensional functional manifolds modeling kinetic processes in many-particle media. Based on algebraic properties of the canonical quantum symmetry current algebra and its functional representations, we succeeded in dual analysis of the infinite Bogolubov hierarchy of many-particle distribution functions and their Hamiltonian structure. Moreover, we proposed a new approach to invariant reduction of the Bogolubov hierarchy on a suitably chosen correlation function constraint and deduction of the related modified Boltzmann–Bogolubov kinetic equations on a finite set of multi-particle distribution functions. There are also presented results of application of devised methods to describing kinetic properties of a many-particle system with an adsorbent surface, in particular, the corresponding kinetic equation for the occupation density distribution function is derived.

Harnessing E-Collaboration for Rural Tourism Recovery after COVID-19: Dual Analysis using SWOT and Porter’s Diamond Model

IT for rural tourism was in place before the COVID-19 pandemic emerged; however, the initiatives were intermittent and isolated. The effects of the pandemic encourage e-collaboration to accelerate the recovery of tourism. This study explores the opportunities, strategies and barriers to e-collaboration in tourism business activities. Systematic literature studies were carried out by the PRISMA approach and analyzed with the fuzzy Delphi method (FDM). Meta-analysis results are mapped in a matrix combination of SWOT and Porter’s Diamond Model. This matrix was discussed with experts selected based on their experience in IT-based collaborative activities through FDG. This study’s driving factors are management commitment, culture, trust, citizens, and local community involvement. Inhibiting factors are a lack of IT, the risk of conflict, and particular parties’ domination. Several strategies to increase e-collaboration opportunities are empowering local entrepreneurship, encouraging continuous innovation, and sharing knowledge. Conflict management and increasing trust between members need to be considered to overcome barriers to e-collaboration. This study provides a novel overview of the main issues discussed in previous tourism research regarding the importance of IT to accelerate economic recovery in the face of disruption, such as a pandemic. The study examines the case of Indonesia and hopes to become a reference for optimizing IT for the recovery of rural tourism in developing countries with similar characteristics. Doi: 10.28991/esj-2021-01297 Full Text: PDF

Spectrum of end of the world branes in holographic BCFTs

We study overlaps between two regularized boundary states in conformal field theories. Regularized boundary states are dual to end of the world branes in an AdS black hole via the AdS/BCFT. Thus they can be regarded as microstates of a single sided black hole. Owing to the open-closed duality, such an overlap between two different regularized boundary states is exponentially suppressed as $$ \left\langle \left.{\psi}_a\right|{\psi}_b\right\rangle \sim {e}^{-O\left({h}_{ab}^{\left(\min \right)}\right)} $$ ψ a ψ b ∼ e − O h ab min , where $$ {h}_{ab}^{\left(\min \right)} $$ h ab min is the lowest energy of open strings which connect two different boundaries a and b. Our gravity dual analysis leads to $$ {h}_{ab}^{\left(\min \right)} $$ h ab min = c/24 for a pure AdS3 gravity. This shows that a holographic boundary state is a random vector among all left-right symmetric states, whose number is given by a square root of the number of all black hole microstates. We also perform a similar computation in higher dimensions, and find that $$ {h}_{ab}^{\left(\min \right)} $$ h ab min depends on the tensions of the branes. In our analysis of holographic boundary states, the off diagonal elements of the inner products can be computed directly from on-shell gravity actions, as opposed to earlier calculations of inner products of microstates in two dimensional gravity.

A dual target sequencing solution to assess genomic and epigenomic alterations in cell-free DNA with no sample splitting.

3043 Background: Assessing the genomic and epigenomic changes on plasma cell-free DNA (cfDNA) using next-generation sequencing (NGS) has become increasingly important for cancer detection and treatment selection guidance. However, two major hurdles of existing targeted NGS methods make them impractical for the clinical setting. First, there is no comprehensive, end to end, kit solution available for targeted methylation sequencing (TMS), let alone one that analyzes both mutation and methylation information in one assay. Second, the low yield of cfDNA from clinical blood samples presents a major challenge for conducting multi-omic analysis. Thus, an assay that is capable of both genomic and epigenomic analysis would be advantageous for clinical research and future diagnostic assays. Methods: Here, we report the performance of Point-n-SeqTM dual analysis, a kit solution that can provide in-depth DNA analysis with highly flexible and customizable focused panels to enable both genomic and epigenomic analysis without sample splitting. With custom panels of tens to thousands of markers designed with > 99% first-pass success rate, we conducted both performance validation and multi-center, multi-operator, reproducibility studies. Using spike-in titration of cancer cell-line gDNA with known mutation and methylation profiles, Point-n-Seq assay achieved a reliable detection level down to 0.003% of tumor DNA with a linear relationship between the measured and expected fractions. Benchmarked with conventional targeted sequencing and methylation sequencing, Point-n-Seq solution also demonstrated improved performance, speed and shortened hands-on time. Results: In a pilot clinical study, a colorectal cancer (CRC) TMS panel covering 560 methylation markers and a mutation panel with > 350 hotspot mutations in 22 genes were used in the dual assay. Using 1ml of plasma from late-stage CRC patients, cancer-specific methylation signals were detected in all samples tested, and oncogenic mutations. In an early-stage cohort (33 stage I/II CRC patient ), comparison of the analysis between tumor-informed, personalized-mutation panels (̃100 private SNVs) for each patient and the tumor-independent CRC methylation panels were conducted. The initial results showed that tumor-independent TMS assay achieved a comparable detection compared to the personalized tumor-informed approach. Moreover, cfDNA size information (fragmentome) is also integrated into the analysis of the same Point-n-Seq workflow to improve the assay sensitivity. Conclusions: Point-n-Seq dual analysis is poised to advance both research and clinical applications of early cancer detection, minimal residual disease (MRD), and monitoring.

Macrophage Plasticity and Function in the Lung Tumour Microenvironment Revealed in 3D Heterotypic Spheroid and Explant Models

In non-small cell lung cancer (NSCLC), stroma-resident and tumour-infiltrating macrophages may facilitate an immunosuppressive tumour microenvironment (TME) and hamper immunotherapeutic responses. Analysis of tumour-associated macrophage (TAM) plasticity in NSCLC is largely lacking. We established a novel, multi-marker, dual analysis approach for assessing monocyte-derived macrophage (Mf polarisation and M1/M2 phenotypic plasticity. We developed a flow cytometry-based, two-marker analysis (CD64 and CD206) of CD14+ cells. The phenotype and immune function of in vitro-induced TAMs was studied in a heterotypic spheroid and tumour-derived explant model of NSCLC. Heterotypic spheroids and NSCLC explants skewed Mfs from an M1- (CD206loCD64hi) to M2-like (CD206hiCD64lo) phenotype. Lipopolysaccharide (LPS) and IFNg treatment reversed M2-like Mf polarisation, indicating the plasticity of Mfs. Importantly, antigen-specific CD8+ T cell responses were reduced in the presence of tumour explant-conditioned Mfs, but not spheroid-conditioned Mfs, suggesting explants are likely a more relevant model of the immune TME than cell line-derived spheroids. Our data indicates the importance of multi-marker, functional analyses within Mf subsets and the advantages of the ex vivo NSCLC explant model in immunomodulation studies. We highlight the plasticity of the M1/M2 phenotype using the explant model and provide a tool for studying therapeutic interventions designed to reprogram M2-like Mf-induced immunosuppression.