The phytophagous insect pests were vectors and could transmit the majority of the phytoviruses to their host plants. The orders of Hemiptera and Thysanoptera were the most common vectors of phytoviruses. The orders Orthoptera, Dermaptera, Coleoptera, Lepidoptera, Diptera, Thysanoptera, and Hemiptera were also the vectors of phytoviruses. Furthermore, aphids, whiteflies, cicadas, spittlebugs, leafhoppers, planthoppers, assassin bugs, plant bugs, stink bugs, lygaeid bugs, and thrips were among the most phytophagous insects that vector and transmit phytoviruses to healthy plants. The occurrence of a single species of these phytophagous insects resulted in one or more phytoviruses in general, and the Hemipteran order, in particular, vectored a lot of phytoviruses species. This review manuscript is focused on vectors of phytoviruses, techniques for their detection, and future directions. It will play a vital role in exploring scientific information concerning the interactions of phytoviruses and vector insects, the effect of phytoviruses on host behavior, mediators of phytoviruses transmission, persistent phytoviruses, some other insect vectors of the phytopathogen, mechanisms of host plant resistance against phytoviruses, and techniques of phytoviruses detection, as well as some important points to be considered in the future sustainably.

This paper explores if plants are capable of responding to human movement by changes in their electrical signals. Towards that goal we conducted a series of experiments, where humans over a period of 6 months were performing different types of eurythmic gestures in proximity of garden plants, namely salad, basil, and tomatoes. To measure plant perception, we used the plant spikerbox, a device that measures changes in voltage differentials of plants between roots and leaves. Using machine learning, we find that the voltage differentials over time of the plant predict if (a) eurythmy has been performed, and (b) which kind of eurythmy gestures has been performed. We also find that the signals are different based on the species of the plant. In other words, the perception of a salad, tomato, or basil might differ just as perception of different species of animals differ. This opens new ways of studying plant ecosystems, while also paving the way to use plants as biosensors for analyzing human movement.

Abstract Plant uptake and assimilation of essential nitrogen compounds from the soil are mainly in the form of nitrate and ammonium ions. Plant nitrate transporters (NRTs) play a crucial role in nitrate uptake from the soil into the roots. NRT structural analysis reveals the mechanisms by which these transporters function. Similarly, plant ammonium transporters (AMTs) mediate the uptake of ammonium ions, and their structural analysis has provided valuable information on their mechanisms. After nitrogen uptake by plant roots, the nitrogen metabolism pathway involves the incorporation of nitrogen into organic compounds. Glutamine synthetase (GS) and glutamate synthase (GoGAT) are the master players in this pathway. They work together to convert ammonium ions into glutamine and glutamate, respectively. Different isoforms of GS and GoGAT exist, enabling plants to fine-tune nitrogen metabolism based on environmental cues. Under severe abiotic stress conditions, nitric oxide (NO) has been found to enhance plant survival under drought. Furthermore, the interaction between salinity stress and nitrogen availability in plants has been studied, with NO identified as a potential mediator of responses to salt stress. On the other hand, excessive use of nitrate fertilizers can lead to health and environmental issues. Therefore, alternative strategies, such as establishing nitrogen fixation in plants through diazotrophic microbiota, have been explored to reduce reliance on synthetic fertilizers. Ultimately, genomics can identify new genes related to nitrogen fixation, which could be harnessed to improve plant productivity. By deciphering the genetic basis of nitrogen-fixing traits, researchers aim to develop crops that efficiently utilize nitrogen from the environment.

Long noncoding RNAs (lncRNAs) of virus origin accumulate in cells infected by many positive strand (+) RNA viruses to bolster viral infectivity. Their biogenesis mostly utilizes exoribonucleases of host cells that degrade viral genomic or subgenomic RNAs in the 5’-to-3’ direction until being stalled by well-defined RNA structures. Here we report a viral lncRNA that is produced by a novel replication-dependent mechanism. This lncRNA corresponds to the last 283 nucleotides of the turnip crinkle virus (TCV) genome, hence is designated tiny TCV subgenomic RNA (ttsgR). ttsgR accumulated to high levels in TCV-infected Nicotiana benthamiana cells when the TCV-encoded RNA-dependent RNA polymerase (RdRp), also known as p88, was overexpressed. Both (+) and (-) strand forms of ttsgR were produced in these cells in a manner dependent on the RdRp functionality. Strikingly, templates as short as ttsgR itself were sufficient to program ttsgR amplification, as long as the TCV-encoded replication proteins, p28 and p88, were provided in trans. Consistent with its replicational origin, ttsgR accumulation required a 5’ terminal G₃(A/U)₄ motif shown by others to be crucial for the replication of a TCV satellite RNA. More importantly, introducing a new G₃(A/U)₄ motif elsewhere in the TCV genome was alone sufficient to cause the emergence of another lncRNA. Collectively our results unveil a replication-dependent mechanism for the biogenesis of viral lncRNAs, thus suggesting that multiple mechanisms, individually or in combination, may be responsible for viral lncRNA production.

The interaction of human immunodeficiency virus with human cells is responsible for all stages of the viral life cycle, from the infection of CD4+ cells to reverse transcription, integration, and the assembly of new viral particles. To date, a large amount of OMICs data as well as information from functional genomics screenings regarding the HIV-1-host interaction has been accumulated in the literature and in public databases. We processed databases containing HIV-host interactions and found 2910 HIV-1-human protein-protein interactions, mostly related to viral group M subtype B, 137 interactions between human and HIV-1 coding and non-coding RNAs, essential for viral lifecycle and cell defense mechanisms, 232 transcriptomics, 27 proteomics, and 34 epigenomics HIV-related experiments. Numerous studies regarding network-based analysis of corresponding OMICs data have been published in recent years. We overview various types of molecular networks, which can be created using OMICs data, including HIV-human protein-protein interaction networks, co-expression networks, gene regulatory and signaling networks, and approaches for the analysis of their topology and dynamics. The network-based analysis can be used to determine the critical pathways and key proteins involved in the HIV life cycle, cellular and immune responses to infection, viral escape from host defense mechanisms, and mechanisms mediating different susceptibility of humans to infection. The proteins and pathways identified in these studies may represent a basis for developing new anti-HIV therapeutic strategies such as new small-molecule drugs preventing infection of CD4+ cells and viral replication, effective vaccines, "shock and kill" and "block and lock" approaches to cure latent infection.

Background: Every year, millions of people are hospitalized, and thousands die from influenza A virus (FLUAV) infection. Most cases of hospitalizations and death occur among elderly. Many of these elderly patients are reliant on medical treatment of underlying chronic diseases, such as arthritis, diabetes, and hypertension. We hypothesized that the commonly prescribed medicines for treatment of underlying chronic diseases can affect host responses to FLUAV infection, and thus contribute to morbidity and mortality associated with influenza. Therefore, the aim of this study was to examine whether commonly prescribed medicines could affect host responses to virus infection in vitro. Methods: We first identified 45 active compounds of medicines commonly prescribed in Central Norway. Then we constructed a drug-target interaction network and identified potential implication of these interactions for FLUAV-host cell interplay. Finally, we tested the effect of 45 drugs on viability, transcription and metabolism of mock- and A/WSN/33(H1N1)-infected human retinal pigment epithelial (RPE) cells. Results: In silico drug-target interaction analysis revealed that many drugs, such as acetylsalicylic acid, atorvastatin, candesartan, and hydroxocobalam, could target and modulate FLUAV-host cell interaction. In vitro experiments showed that these and other compounds at non-cytotoxic concentrations differently affected transcription and metabolism of mock- and FLUAV-infected cells. Conclusion: Many commonly prescribed drugs modulate FLUAV-host cell interactions in vitro and therefore could affect their interplay in vivo, thus, contributing to morbidity and mortality of patients with influenza virus infections.

Understanding biological mechanisms that regulate emergence of viral diseases, in particular those events engaging cross-species pathogens spillover, are becoming increasingly important in Virology. Species barrier jumping has been extensively studied in animal viruses, and the critical role of a suitable intermediate host in animal viruses-generated human pandemics is highly topical. However, studies on host jumping involving plant viruses have been focused on shifting intra-species, leaving aside the putative role of “bridge hosts” in facilitating interspecies crossing. Here, we take advantage of several VPg mutants, derived from a chimeric construct of the potyvirus Plum pox virus (PPV), analysing its differential behaviour in three herbaceous species. Our results showed that two VPg mutations in a Nicotiana clevelandii-adapted virus, emerged during adaptation to the bridge-host Arabidopsis thaliana, drastically prompted partial adaptation to Chenopodium foetidum. Although, both changes are expected to facilitate productive interactions with eIF(iso)4E, polymorphims detected in PPV VPg and the three eIF(iso)4E studied, extrapolated to a recent VPg:eIF4E structural model, suggested that two adaptation ways can be operating. Remarkably, we found that VPg mutations driving host-range expansion in two non-related species, not only are not associated with cost trade-off constraints in the original host, but also improve fitness on it.

Anthracnose, caused by the fungus Colletotrichum lindemuthianum, poses a significant and widespread threat to the common bean crop. The use of plant genetic resistance has proven to be the most effective strategy for managing anthracnose disease. The Amendoim Cavalo (AC) Andean cultivar has resistance against multiple races of C. lindemuthianum, which is conferred by the Co-AC gene. Fine mapping of this resistance gene to common bean chromosome Pv01 enabled the identification of Phvul.001G244300, Phvul.001G244400, and Phvul.001G244500 candidate genes for further validation. In this study, we assessed the relative expression of Co-AC candidate genes, as well as other putative genes in vicinity of this locus and known resistance genes, in the AC cultivar following inoculation with the race 73 of C. lindemuthianum. Gene expression analysis revealed significantly higher expression levels of Phvul.001G244500. Notably, Phvul.001G244500 encodes a putative Basic Helix-Loop-Helix transcription factor, suggesting its involvement in the regulation of defense responses. Furthermore, we observed a significant modulation of the expression of defense related genes PR1a, PR1b, and PR2, in a time-course experiment. These findings contribute to the development of improved strategies for breeding anthracnose-resistant common bean cultivars, thereby mitigating the impact of this pathogen on crop yields and ensuring sustainable bean production.

Human influenza A viruses (IAVs) cause global pandemics and epidemics. These viruses evolve rapidly, making current treatment options ineffective. To identify novel modulators of IAV-host interactions, we re-analyzed our recent transcriptomics, metabolomics, proteomics, phosphoproteomics, and genomics/virtual ligand screening data. We identified 713 potential modulators targeting 200 cellular and two viral proteins. Anti-influenza activity for 48 of them has been reported previously, whereas the antiviral efficacy of the remaining 665 is unknown. Studying anti-influenza efficacy, immuno-modulating properties and potential resistance of these compounds or their combinations may lead to the discovery of novel modulators of IAV-host interactions, which might be more effective than the currently available anti-influenza therapeutics.

Type IVc Pili (T4cP), also known as Tad or Flp pili, are long thin microbial filaments, which are made-up of small-sized pilins. These appendages serve different functions in bacteria including attachment, biofilm formation, surface sensing, motility, and host colonization. Despite their relevant role in diverse microbial lifestyles, knowledge about T4cP in bacteria that establish symbiosis with legumes, collectively referred to as rhizobia, is still limited. Sinorhizobium meliloti contains two clusters of T4cP-related genes: flp-1 and flp-2, which are located on the chromosome and pSymA megaplasmid, respectively. Bundle-forming pili associated to flp-1 have been involved in competitive nodulation of alfalfa plants but the role of flp-2 remains elusive. In this work, we have performed a comprehensive bioinformatic analyses of T4cP genes in the highly competitive S. meliloti strain GR4 and investigated the role of its flp clusters in pilus biogenesis, motility and in the interaction with alfalfa. Single and double flp cluster mutants were constructed in the wild-type genetic background as well as in a flagellaless derivative strain. Our data demonstrate that both chromosomal and pSymA flp clusters are functional in pili biogenesis, and contribute to surface translocation and nodule formation efficiency of GR4. In this strain, the presence of flp-1 in the absence of flp-2 reduces competitiveness for nodule occupation.

This article develops a multi-perspective view on motivations and methods for tobamovirus purification through the ages, and presents a novel efficient, easy-to-use approach that can be well-adapted to different species of native and functionalized virions. We survey the various driving forces prompting researchers to enrich tobamoviruses: from the search for the causative agents of mosaic diseases in plants to their increasing recognition as versatile nanocarriers in biomedical and engineering applications. Best practice and also rarely applied options for the serial processing steps required for successful isolation of tobamoviruses are then reviewed. Adaptations for distinct particle species, pitfalls and 'forgotten' or underrepresented technologies are considered as well. The article is topped off with our own development of a method for virion preparation, rooted in historical protocols. It combines selective re-solubilization of polyethylene glycol (PEG) virion raw precipitates with density step gradient centrifugation in biocompatible iodixanol formulations, yielding ready-to-use particle suspensions. This newly established protocol and some considerations for perhaps worthwile further developments could serve as putative stepping stones towards preparation procedures appropriate for routine practical uses of the multivalent soft-matter nanorods.

Plant growth-promoting rhizobacteria (PGPR) are members of the plant rhizomicrobiome that enhance plant growth and stress resistance by increasing nutrient availability to the plant, producing phytohormones or other secondary metabolites, stimulating plant defense responses against abiotic stresses and pathogens, or fixing nitrogen. The use of PGPR to increase crop yield with minimal environmental impact is a sustainable and readily applicable replacement for a portion of chemical fertilizer and pesticides required for the growth of high-yielding varieties. Increased plant health and productivity have long been gained by applying PGPR as commercial inoculants to crops, although with uneven results. The establishment of plant-PGPR relationships requires the exchange of chemical signals and nutrients between the partners, and polyamines (PAs) are an important class of compounds that act as physiological effectors and signal molecules in plant-microbe interactions. In this review we focus on the role of PAs in interactions between PGPR and plants. We describe the basic ecology of PGPR and production and function of PAs in them and in the plants with which they interact. We examine the metabolism and the roles of PAs in PGPR and plants individually and during their interaction with one another. Lastly, we describe some directions for future research.

Isothermal Nucleic Acid Amplification based-Lateral Flow Testing (INAA-LFT) has emerged as a robust technique for on-site pathogen detection, providing a visible indication of pathogen nucleic acid amplification that rivals or even surpasses the sensitivity of real-time quantitative PCR. The isothermal nature of INAA-LFT ensures consistent conditions for nucleic acid amplification, establishing it as a crucial technology for rapid on-site pathogen detection. However, despite its considerable promise, the widespread application of isothermal INAA amplification-based lateral flow testing faces several challenges. This review provides an overview of the INAA-LFT procedure, highlighting its advancements in detecting plant viruses. Moreover, the review underscores the imperative to address existing limitations and emphasizes ongoing research efforts dedicated to enhancing the applicability and performance of this technology in the realm of rapid on-site testing.

Although the COVID-19 pandemic appears to be diminishing, the emergence of SARS-CoV-2 variants represents a threat to humans due to its inherent transmissibility, immunological evasion, virulence, and invulnerability to existing therapies. The previous COVID-19 pandemic affected more than 500 million people and caused over 6 million deaths. Vaccines are essential, but in circumstances when vaccination is not accessible or in individuals with compromised immune systems, drugs can give additional protection. Targeting host signaling pathways is recommended due to their genomic stability and resistance barriers. Plant-derived products, which have been used in traditional medicine for treating pathological conditions, offer structurally novel therapeutic compounds including anti-viral. In addition, plant-derived bioactive substances might serve as the ideal basis for developing sustainable/efficient/cost-effective anti-viral alternatives. Epigenetic modifications in the genome can affect gene expression without altering DNA sequence. Host cells can use epigenetic gene regulation as a mechanism to silence incoming viral DNA molecules, while viruses have recruited cellular epi transcriptomic (covalent modifications of RNAs) modifiers to increase the translational efficiency and transcript stability of viral transcripts to enhance viral gene expression and replication. Moreover, viruses manipulate host cells' epigenetic machinery to ensure productive viral infections. Environmental factors, such as natural products, may influence epigenetic modifications. In this review, we are exploring the potential of plant-derived substances as epigenetic modifiers for broad-spectrum anti-viral activity, reviewing modulation processes and anti-viral effects on DNA and RNA viruses, and addressing future research objectives in this rapidly emerging field.

Grapevine is one of the most relevant crops in the world being used for economically important products such as wine. Yet, relevant grapevine cultivars are heavily affected by diseases such as the downy mildew disease caused by Plasmopara viticola. Improvements on grapevine resistance are made mainly by breeding techniques where resistance traits are introgressed into cultivars with desired grape characteristics. However, there is still a lack of knowledge on how resistant or tolerant cultivars tackle the P. viticola pathogen. In this study, using a shotgun proteomics LC-MS/MS approach, we unravel the protein modulation of a highly tolerant grapevine cultivar, V. vinifera ‘Regent’, in the first hours post inoculation (hpi) with P. viticola. At 6 hpi, proteins related to defence and to response to stimuli are negatively modulated while at 12 hpi there is an accumulation of proteins belonging to both categories. The co-occurrence of effector-triggered susceptibility (ETS) and effector-triggered immunity (ETI) is detected at both time-points, showing that these defence processes present high plasticity. The results obtained in this study unravel the tolerant grapevine defence strategy towards P. viticola and may provide valuable insights on resistance associated candidates and mechanisms, which may play an important role in the definition of new strategies on breeding approaches.

Cotton (Gossypium spp.) is a major source of natural fiber and an important cash crop. The cotton growth habit and architecture determine its productivity and influence management strategies for commercial production. The GATA transcription factors (TFs) control various developmental processes in plants, such as flower, bract and embryo development, and petal differentiation. As stable transformation is still a bottleneck in many plant species, TRV-VIGS was used to manipulate gene expression in different plants, including Gossypium hirsutum L. In this study, we undertook the TRV-based VIGS to functionally characterize two candidate genes, Gohir.D05G103700 and Gohir.D12G153600, identified through the expression QTL analysis for five floral induction and meristem identity genes using the upland cotton mini-core collection. Virus-induced silencing of the Gohir.D05G103700 gene resulted in up to a 1.4-fold reduction in the transcript level in two inoculated plants, G3 and G4, and Gohir.D12G153600 gene resulted in up to a 2.3-fold reduction in transcript level in a single inoculated plant P05 relative to the mock-treated plant. The TRV2-Gohir.D05G103700 inoculated plants precisely G3 and G4 also exhibited loss of the supernumerary (fourth) floral bract in the squares, whereas the TRV2-Gohir.D12G153600 inoculated plants did not show any observable phenotypic change relative to the mock-treated plants.  Altogether, this study suggested that TRV-VIGS can be used to characterize genes in cotton relatively rapidly and the cotton Gohir.D05G103700 gene is a positive regulator of the indeterminate growth habit in cotton, which could be manipulated to obtain a cotton plant with architecture best suited for the cultivation area.

The PII protein is an evolutionary highly conserved regulatory protein from bacteria to higher plants. In bacteria it modulates the activity of several enzymes, transporters and regulatory factors by interacting with them and thereby regulating important metabolic hubs like carbon/nitrogen homeostasis. More than two decades ago the PII protein was characterized for the first time in plants, but its physiological role is still not sufficiently resolved. To gain more insights into the function of this protein, we investigated the interaction behaviour of AtPII with candidate proteins by BiFC and FRET/FLIM in planta and with GFP/RFP traps in vitro. In the course of these studies we found that AtPII interacts in chloroplasts with itself as well as with known interactors like NAGK in dot-like aggregates, which we named PII foci. In these novel protein aggregates AtPII interacts also with yet unknown partners, which are known to be involved in plastidic protein degradation. Further studies revealed that the C-terminal part of AtPII is crucial for the formation of PII foci. Altogether, the presented results indicate a novel mode of interaction for PII proteins with other proteins in plants, which may be a new starting point for the elucidation of physiological functions of PII proteins in plants.

In silico analysis is a promising approach for understanding biological events in complex diseases. Herein, we report an in silico analysis of the entire genome of virus ZikaSPH2015 strain, which was performed in order to identify the occurrence of specific motifs on genomic sequence of Zika Virus that is able to bind and therefore, sequester host’s Transcription Factors (TFs) as well as subsequently predict a possible interactions within host genome. Accordingly to obtained results of this original computational work-flow it is possible to hypothesize that these TFs Binding Motifs might be able to explain the complex and heterogeneous phenotype presentation in Zika Virus affected fe-tus/newborns, as well as the less severe condition in adults. Moreover, the proposed in silico protocol identified thirty three different TFs same as the distribution of TFBSs (Transcription Factor Binding Sites) on ZikaSPH2015 strain, potentially able to influence genes and pathways with biological functions confirming that this approach could find potential answers on disease pathogenesis.

Cowpea chlorotic mottle virus (CCMV) is a plant virus explored as a nanotechnological platform. The robust self-assembly mechanism of its capsid protein allows for drug encapsulation and targeted delivery. Additionally, the capsid nanoparticle can be used as a programmable platform to display different molecular moieties. In view of future applications, efficient production and purification of plant viruses is a key step. In established protocols, the need for ultracentrifugation is a significant limitation due to cost, difficult scalability, and safety issues. In addition, the purity of the final virus isolate often remains unclear. Here, an advanced protocol for the purification of CCMV from infected plant tissue was developed, focusing on efficiency, economy, and final purity. The protocol involves precipitation with PEG 8000, followed by an affinity extraction using a novel peptide aptamer. The efficiency of the protocol was validated using size exclusion chromatography, MALDI-TOF mass spectrometry, reversed-phase HPLC, and sandwich immunoassay. It was demonstrated that the final eluate of the affinity column is of exceptional purity (98.4%) determined by HPLC and detection at 220 nm. The scale-up of our proposed method seems to be straightforward, which opens the way to the large-scale production of such nanomaterials. This highly improved protocol may facilitate the use and implementation of plant viruses as nanotechnological platforms for in vitro and in vivo applications.

Herpes simplex virus type 1 (HSV-1) is among the most widely spread viruses on the planet. However, the rate of binding to the receptor is not among the greatest ones. Gibbs energy of binding, which represents the driving force for antigen-receptor binding, of HSV-1 is less negative than can be expected. Furthermore, the Gibbs energy of biosynthesis of HSV-1 is among the most negative in nature. This implies high rate of multiplication of HSV-1. Obviously, HSV-1 uses specific strategy in virus-host interaction. While most other viruses increase infectivity through a high rate of antigen-receptor binding and cell entry/ highly negative Gibbs energy of binding, HSV-1 uses another strategy. It is related to a relatively slow reaction of antigen-receptor binding, which is followed by a higher rate of multiplication, which is a consequence of a highly negative Gibbs energy of biosynthesis. We can conclude empirically that both strategies are successful.

Complex systems exhibit critical thresholds at which they transition among alternative phases. Complex systems theory has been applied to analyze disease progression, distinguishing three stages along progression: (i) a normal non-infected state, (ii) a pre-disease state in which the host is infected and responds; therapeutic interventions could still be effective, (iii) an irreversible state, where the system is seriously threatened. The Dynamical Network Biomarker (DNB) theory sought for early-warnings of the transition from health to disease. Such DNBs might range from individual genes to complex structures in transcriptional regulatory or protein-protein interaction networks. Here we revisit transcriptomic data obtained during infection of tobacco plants with tobacco etch potyvirus to identify DNBs signaling the transition from mild/reversible to severe/irreversible disease. We identified genes showing a sudden transition in expression along disease. Some of these genes cluster in modules that show the properties of DNBs. These modules contain both genes known to be involved in response to pathogens (e.g., ADH2, CYP19, ERF1, KAB1, LAP1, MBF1C, PR1, or TPS5) and other genes not previously related to biotic stress responses (e.g., ABCI6, BBX21, NAP1, OSM34, or ZPN1).

COVID-19 (2019-nCoV) is a pandemic disease with an estimated mortality rate of 3.4% (estimated by the WHO as of March 3, 2020). Until now there is no antiviral drug and vaccine for COVID-19. The current overwhelming situation by COVID-19 patients in hospitals is likely to increase in the next few months. About 15 percent of patients with serious disease in COVID-19 require immediate health services. Rather than waiting for new anti-viral drugs or vaccines that take a few months to years to develop and test, several researchers and public health agencies are attempting to repurpose medicines that are already approved for another similar disease and have proved to be fairly effective. This study aims to identify FDA approved drugs that can be used for drug repurposing and identify biomarkers among high- risk and asymptomatic groups. In this study gene-disease association related to COVID-19 reported mild, severe symptoms and clinical outcomes were determined. The high-risk group was studied related to SARS-CoV-2 viral entry and life cycle by using Disgenet and compared with curated COVID-19 gene data sets from the CTD database. The overlapped gene sets were enriched and the selected genes were constructed for protein-protein interaction networks. Through interactome, key genes were identified for COVID-19 and also for high risk and asymptomatic groups. The key hub genes involved in COVID-19 were VEGFA, TNF, IL-6, CXCL8, IL10, CCL2, IL1B, TLR4, ICAM1, MMP9. The identified key genes were used for drug-gene interaction for drug repurposing. The chloroquine, lenalidomide, pentoxifylline, thalidome, sorafenib, pacitaxel, rapamycin, cortisol, statins were proposed to be probable drug repurposing candidates for the treatment of COVID-19. However, these predicted drug candidates need to be validated through randomized clinical trials. Also, a key gene involved in high risk and the asymptomatic group were identified, which can be used as probable biomarkers for early identification.

Poplar (Populus) is a genus of woody plants of value for the pulp industry, green energy, urban landscaping, soil phytoremediation and as an ornamental plant. Due to the increasing economic importance of poplar, there is a need to ensure its stable growth by increasing its resistance to pathogens, as one of the main problems in poplar cultivation is its susceptibility to numerous diseases. Currently, breeding poplars with reduced susceptibility to infections is receiving increasing attention. Genetic engineering can produce organisms with improved traits faster than traditional methods, and with the development of CRISPR/Cas-based genome editing systems, scientists have a new highly efficient tool at their disposal to create valuable genotypes. In this review, we summarize recent research data on poplar diseases, the biology of their pathogens, and how these plants resist pathogens. In the final section, we discuss genetic engineering, genome editing, and microbiome strategies that we believe are suitable for obtaining new improved poplar lines.

Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiologic agent of Kaposi’s sarcoma, primary effusion lymphoma (PEL) and multicentric Castleman’s disease. During KSHV lytic infection, lytic-related genes, categorized as immediate-early, early, and late genes, are expressed in a temporal manner. The transcription of late genes requires the virus-specific pre-initiation complex (vPIC), which consists of viral transcription factors. However, the characterization of the protein-protein interactions of the vPIC factors has not been completely elucidated. KSHV ORF18 is one of the vPIC factors, and its interaction with other viral factors has not been sufficiently revealed. Here, we analyzed the interaction between ORF18 and another vPIC factor, ORF30, in living cells using the bimolecular fluorescence complementation (BiFC) assay. We identified four amino-acid residues (Leu29, Gln36, His41 and Trp170) on ORF18 that were responsible for its interaction with ORF30. The artificial intelligence (AI) system AlphaFold2 predicted that identified four residues are exposed to the surface of ORF18 and located in proximity to each other in the surface of ORF18. Thus, AI-predicted model supports the importance of four residues for binding of ORF18 to ORF30. Our results indicated that wet experiments in combination with AI may enhance the structural characterization of vPIC protein-protein interactions.

Tapping panel dryness (TPD) syndrome is a complex disease of Rubber tree (Hevea brasiliensis L.) which causes cessation of latex drainage upon tapping of rubber tree. Rubber tree virus (RTV1) was identified as a novel pathogen associated with rubber tree and a potential causal agent of TPD. RTV1 is a monopartite RNA virus that is linear, non-enveloped and has a single-stranded (ss) positive RNA genome of approximately 6081 nucleotides and is composed of two major open reading frames (ORFs), ORF1 (polyprotein), and ORF2 (movement protein. This study aimed to investigate the possibility of rubber genome encoded tree microRNAs (miRNAs) as novel therapeutic targets against RTV1 using in silico algorithms. Mature rubber tree miRNAs are retrieved from the miRBase database and are used for hybridization of RTV1 using five different five different computational algorithms including miRanda, RNA22, RNAhybrid and psRNATarget. A total of eleven common rubber tree miRNAs were identified based on consensus genomic positions. The consensus of four algorithms predicted the hybridization sites of hbr-miR396a and hbr-miR398 at common locus positions 6676, 1840 respectively. To validate the prediction, secondary structures of the consensual rubber tree miRNAs and free energy of duplex binding were calculated using the RNAfold and RNAcofold algorithms respectively. We created a plot between rubber tree miRNAs and RTV1 ORFs by using Circos algorithm. In this study, we predicted eleven consensual rubber tree miRNAs. Among these miRNAs, hbr-miR398 was identified as the most effectual miRNA that may target the ORF1 gene of the RTV1 genome. The predicted data will be important in the development of rubber trees resistant to RTV1.

Since 1998, when Jim van Etten’s team initiated its characterization, Paramecium bursaria Chlorella virus 1 (PBCV-1) had been the largest known DNA virus, both in terms particle size and genome complexity. In 2003, The Acanthamoeba-infecting Mimivirus unexpectedly superseded PBCV-1, opening the era of giant viruses, i.e. with virions large enough to be visible by light microscopy and genomes encoding more proteins than many bacteria. During the 15 following years, the isolation of many Mimivirus-relatives, have made the Mimiviridae one of the largest and most diverse family of eukaryotic viruses isolated from aquatic environments. Metagenomic studies keep suggesting that many more remain to be isolated. As Mimiviridae members are found to infect an increasing range of phytoplanckton species, their taxonomic position compared to the traditional Phycodnaviridae (i.e. etymologically “algal viruses”) became a source of confusion in the literature. Following a rapid history of the key discoveries that established the Mimiviridae family, we describe its current taxonomic structure and propose a set of operational criteria to help in the classification of future isolates.

Black Knot (BK) is a deadly disease of European (Prunus domestics) and Japanese (Prunus salicina) plums caused by the hemibiotrophic fungus Apiosporina morbosa. After infection, the appearance of warty black knots indicates a phytohormonal imbalance in infected tissues. Based on this hypothesis, we quantified phytohormones such as indole-3-acetic acid, tryptophan, indoleamines (N-acetylserotonin, serotonin, and melatonin), and cytokinins (zeatin, 6-benzyladenine, and 2-isopentenyladenine) in temporally collected tissues of susceptible and resistant genotypes belonging to European and Japanese plums during of BK progression. The results suggested auxin-cytokinins interplay driven by A. morbosa appears to be vital in disease progression by hampering the plant defense system. Taken together, our results indicate the possibility of using the phytohormone profile as a biomarker for BK resistance in plums.

The order Mononegavirales harbors numerous viruses of significant relevance for human health, including both established and emerging infections. Currently, vaccines are only available for a small subset of these viruses and antiviral therapies remain limited. Being obligate cellular parasites, viruses must utilize the cellular machinery for their replication and spread. Therefore, targeting cellular pathways used by viruses can provide novel therapeutic approaches. One of the key challenges confronted by both hosts and viruses alike is the successful folding and maturation of proteins. In cells, this task is faced by cellular molecular chaperones, a group of conserved and abundant proteins that oversee protein folding and help maintain protein homeostasis. In this review, we summarize the current knowledge of how the mononegavirales interact with cellular chaperones, highlight key gaps in our knowledge, and discuss the potential of chaperone inhibitors as antivirals.

Rice grassy stunt virus (RGSV) a member of Tenuivirus family, is very potent and destructive which effects rice crop in many countries, particularly China. Non coding RNAs have important functions in development and epigenetic regulation of gene expression in numerous organsisms. There is three type of small non coding RNAs have been found in eukaryotes, which are small interferring RNAs (siRNAs), microRNAs (miRNAs) and piwi interacting RNAs (piRNAs). Small RNAs (sRNAs) origination is from the infecting virus which is known as virus-derived small interfering RNAs (vsiRNAs), has responsibility for RNA silencing in plants. Virus-induced gene silencing (VIGS) is mainly dependent on RNA silencing (RNAi). Interestingly, RNA silencing happens in plants during viral infections. RNAi technique showed significant results in Nephotettix cincticeps. RNAi technique demonstrated the gene silencing of planthopper Nilaparvata lugens. The proteins P5, pcf4, Dnj, psn5, and pn6 act as potential movement proteins and serve as silencing suppressors for RGSV. VsiRNAs originate from dsRNA molecules which require Dicer-like (DCL) proteins, RNA dependent RNA polymerase (RdRP) proteins, and Argonaute (AGO) proteins. RdRP uses ssRNA for perfect RNA amplification process and can also be used for DCL dependent secondary vsiRNA formation. VSRs interfere with the movement of signals during silencing mechanism. Moreover, intercellular movement of viruses is facilitated by virus-encoded movement protein. RNAi is found in many eukaryotes which are related to transcriptional or post-transcriptional regulation by gene suppression. Transcription is bidirectional in ssDNA viruses which are originated from dsRNA molecules. In this review, we highlighted the biology of Rice grassy stunt virus and its insect vector and its silencing suppressors. This work will be helpful for plant virologists to understand the whole biogenesis mechanism for rice viruses especially RGSV.

We investigated the interaction between the insect-specific virus, Piura virus (PIUV) and the arbovirus Zika virus (ZIKV) in Aedes albopictus cells. We performed coinfection experiments in C6/36 cells. Piura virus (Cor 33 strain, Colombia) and ZIKV (PRVABC58 strain, Puerto Rico) were co-inoculated into C6/36 cells using two MOI combinations: 0.1 for both viruses and 1.0 for ZIKV, 0.1 for PIUV. Wells were infected in triplicate with either PIUV and ZIKV coinfection, ZIKV-only, or PIUV-only. Mock infected cells served as control wells. The cell suspension was collected daily through 7 days post-infection. Zika virus load was titrated by TCID50 on Vero 76 cells. The ZIKV-only infection and PIUV and ZIKV coinfection experiments were also quantified by RT-qPCR. We also investigated whether ZIKV interfered in the PIUV replication. PIUV suppressed the replication of ZIKV resulting in a 10,000-fold reduction in ZIKV titers within 3 days post-infection. PIUV viral loads were not reduced in the presence of ZIKV. We conclude that, when concurrently infected, PIUV suppresses ZIKV in C6/36 cells while ZIKV does not interfere in PIUV replication.

Flaviviruses are a group of positive sense single-stranded RNA viruses predominantly transmitted by arthropods (mainly mos-quitoes), that cause severe endemic infections and epidemics on a global scale. It represents a major cause of systemic morbidity and death that are expanding worldwide. Among this group, Dengue fever, West Nile virus, Yellow Fever, Japanese Encephalitis, and recently Zika virus have been linked to a spectrum of ocular manifestations. The latter encompass subconjunctival hemor-rhage and conjunctivitis, anterior and posterior uveitis (inclusive of vitritis, chorioretinitis, and retinal vasculitis), maculopathy, retinal hemorrhages, and optic neuritis. Clinical diagnosis of these infectious diseases is primarily based on epidemiological data, history, systemic symptoms and signs, and the pattern of ocular involvement. Diagnosis confirmation relies on laboratory testing, including RT-PCR and serological testing. Ocular involvement typically follows a self-limited course but can result in irreversible visual impairment. Effective treatment for flavivirus infections is currently unavailable. Prevention remains the mainstay for arthropod vector and zoonotic disease control. Effective vaccines are available only for Yellow Fever virus, Dengue virus and Japanese Encephalitis virus. This review comprehensively summarizes the current knowledge regarding the ophthalmic mani-festations of the foremost flavivirus-associated human diseases.

We developed a honey bee RNA-virus vector based on the genome of a picorna-like Deformed wing virus (DWV), the main viral pathogen of the honey bee (Apis mellifera). To test the potential of DWV to be utilized as a vector, the 717 nt sequence coding for the enhanced green fluorescent protein (eGFP), flanked by the peptides targeted by viral protease, was inserted into an infectious cDNA clone of DWV in-frame between the leader protein and the virus structural protein VP2 genes. The in vitro RNA transcripts from egfp-tagged DWV cDNA clones were infectious when injected into honey bee pupae. Stable DWV particles containing genomic RNA of the recovered DWV with egfp inserts were produced, as evidenced by cesium chloride density gradient centrifugation. These particles were infectious to honey bee pupae when injected intra-abdominally. Fluorescent microscopy showed GFP expression in the infected cells and Western blot analysis demonstrated accumulation of free eGFP rather than its fusions with DWV LP and/or VP2 proteins. Analysis of the progeny egfp-tagged DWV showed gradual accumulation of genome deletions for egfp, providing estimates for the rate of loss of a non-essential gene an insect RNA virus genome during natural infection.

Finding a suitable support is a key process in the life history of climbing plants. Climbers that find a suitable support have greater performance and fitness than those that remain prostrate. Numerous studies on climbing plant behavior have elucidated the mechanistic details of support searching and attachment. Far fewer studies have addressed the ecological significance of support-searching behavior and the factors that affect it. Among these, the diameter of supports influences their suitability for twining plants. When support diameter increases beyond some point climbing plants are unable to maintain tensional forces and therefore lose attachment to the trellis. Here we further investigate this issue by putting pea plants in the situation to choose between supports of different diameters while their movement was recorded by means of a three-dimensional motion analysis system. The results indicate that the way climbing plants move can vary depending on whether they are presented with one or two potential supports. Furthermore, when presented with a choice between a thin and a thick support, the plants showed a distinct preference for the former than the latter. The present findings shed further light on how climbers make decisions as far as support search is concerned, and provide evidence that plants adopt one of several alternative plastic responses in a way that optimally corresponds to environmental scenarios.

AMF (Arbuscular Mychorhizal Fungi) are very well known due to their importance in promoting growth and developments of plants especially vegetables. These fungi can be grown easily, stored and multiplied with simple means, also the application of these fungi is generally on the layer of the soil or near the roots in the inner layers of the soils. The growth of the amf fungi is very easy and they are highly adjustable to any soil and environmental conditions. In this review our main focus is on the use of amf for production of vegetables and also the effect of amf against insects and pests. The amf is known to reduce several symptoms caused by different insect pests and also plant diseases thereby promoting healthy growth of the plants. Also use of this amf will increase the uptake of nutrient from the soils through symbiotic relationships between plants and fungi. The uptake of important minerals which are drawn from deeper layers of soils is observed with the help pf amf. This study reveals the benefits of the use of amf under severe disease and pest incidences thereby known as an alternate for harmful chemical pesticides and fungicides.

Flaviviruses cause a significant amount of mortality and morbidity, especially in the area where they are endemic. A recent example is the outbreak of Zika virus though out the world. Development of antiviral drugs against different viral targets is as important as development of vaccine. During viral replication, the flavivirus genome is translated as a single polyprotein precursor, which must be cleaved into individual proteins by a complex of the viral protease, NS3, and its cofactor, NS2B. Flavivirus protease is the most attractive target for development of therapeutic antivirals because it is essential for processing of viral polyprotein precursor and generation of functional viral proteins. In this review, we have summarized recent development in drug discovery targeting NS3-NS2B protease of flaviviruses, especially Zika, dengue and West Nile virus.

Black Knot (BK) is a deadly disease of European (Prunus domestica) and Japanese (Prunus salicina) plums caused by the hemibiotrophic fungus Apiosporina morbosa. Generally, phytopathogens hamper the balance of primary defense phytohormones such as salicylic acid (SA)-jasmonic acid (JA) balance for disease progression. Thus, we quantified the important phytohormones titers in tissues of susceptible and resistant genotypes belonging to European and Japanese plums at five different time points. The results suggested auxin-cytokinins interplay driven by A. morbosa appeared to be vital in disease progression by hampering the plant defense system via perturbance in SA, JA, and gibberellic acid. The results further point out that SA and JA in plant defense are not necessarily antagonistic always, especially in woody perennials. Results also suggest that the changes in SA and JA content following BK disease infection and progression in plums could be utilized as phytohormonal markers in the identification of BK-resistant cultivars.

The influenza virus has been the primary cause of the pandemic, posing a constant threat to human society. Due to its genetic evolution and continuous outbreak, antiviral research currently focuses on exploring a novel lead agent. A comprehensive antiviral screening discovered a marine bacterium whose extract exerted excellent efficacy against influenza viruses. Parerythrobacter sp. M20A3S10, a novel strain under the family Erythrobacteraceae, could produce carotenoids exhibiting antiviral and anticancer activity by enhancing the cellular immune system. Post-treatment of M20A3S10 extract showed outstanding therapeutic indexes: against influenza virus A/PR8 (H1N1) [selectivity index (SI) = 24.0], A/Wisconsin/15/2009 (H3N2) (SI = 30.1) and B/Florida/78/2015 (SI = 38.2). Comparably, the effectiveness was demonstrated against Zika virus (ZIKV) and dengue virus type 2 (DENV2) with an SI of 22.5 and 24.1, respectively, namely broad-spectrum activity. Of note, the antiviral responses resulted from the common replication mechanism between IAV, ZIKV, and DENV2. The stimulation of apoptosis-mediated cellular immunity prevented the viral release and protected the host, suggesting that switching from necroptosis to apoptosis is a novel antiviral target. Although the specific compound affecting the antiviral activity was not identified, its promising efficacy with broad activity will contribute to developing a strategy for preventing future pandemics.

Zika virus (ZIKV) is a widespread mosquito-borne pathogen. Phylogenetically, two lineages of the ZIKV are distinguished: African and Asian-American. The latter became the cause of the 2015-2016 pandemic with severe defeat to newborns. In West African countries the African lineage has been found, but there is evidence of the emergence of Asian-American lineage in Cape Verde and Angola. This highlights the need not only to monitor the ZIKV, but also to sequence the isolates. In this article, we present a case report of Zika fever in a pregnant woman from Guinea, identified in 2018. Viral RNA was detected by qRT-PCR in serum sample. In addition, seroconversion of anti-Zika IgM and IgG antibodies was detected in repeated blood samples. Subsequently, the virus was isolated in C6/36 cell line. The detected ZIKV belonged to the African lineage, the Nigerian sublineage. The strains with the closest sequences were isolated from mosquitoes in Senegal in 2011 and 2015. In addition, we conducted serological screening of 116 blood samples collected from patients presenting to the hospital of Faranah with fevers during the period 2018-2021. As a result, it was found that IgM-positive patients occurred each year, seroprevalence varied between 5.6% and 17.1%.

A pandemic happens when a novel influenza A virus is able to infect and transmit efficiently to a new, distinct host species. Although the exact timing of pandemics is uncertain, it is known that both viral and host factors play a role in their emergence. Species-specific interactions between the virus and the host cell determine the virus tropism. These include binding and entering cells, replicating the viral RNA genome within the host cell nucleus, assembling, maturing, and releasing the virus to neighbouring cells, tissues, or organs before transmitting it between individuals. Influenza has a vast and antigenically varied reservoir. In wild aquatic birds, the infection is typically asymptomatic. Avian influenza virus (AIV) can cross into new species, and occasionally, it can acquire the ability to transmit from human to human. A pandemic might occur if a new influenza virus acquires enough adaptive mutations to maintain transmission between people. This review highlights the key determinants AIV must achieve to initiate a human pandemic and describes how AIV mutates to establish tropism and stable human adaptation. Understanding the tropism of AIV may be crucial in preventing virus transmission in humans and may help design vaccines, antivirals and therapeutic agents against the virus.

Marburg virus (MARV) is a lipid-enveloped negative sense single stranded RNA virus, which can cause a deadly hemorrhagic fever. MARV encodes seven proteins, including VP40 (mVP40), a matrix protein that interacts with the cytoplasmic leaflet of the host cell plasma membrane. VP40 traffics to the plasma membrane inner leaflet, where it assembles to facilitate the budding of viral particles. VP40 is a multifunctional protein that interacts with several host proteins and lipids to complete the viral replication cycle, but many of these host-interactions remain unknown or are poorly characterized. In this study, we investigated the role of a hydrophobic loop region in the carboxy-terminal domain (CTD) of mVP40 that shares sequence similarity with the CTD of Ebola virus VP40 (eVP40). These conserved hydrophobic residues in eVP40 have been previously shown to be critical to plasma membrane localization and membrane insertion. An array of cellular experiments and confirmatory in vitro work strongly suggests proper orientation and hydrophobic residues (Phe281, Leu283, and Phe286) in the mVP40 CTD are critical to plasma membrane localization. In line with the different functions proposed for eVP40 and mVP40 CTD hydrophobic residues, molecular dynamics simulations demonstrate large flexibility of residues in the EBOV CTD whereas conserved mVP40 hydrophobic residues are more restricted in their flexibility. This study sheds further light on important amino acids and structural features in mVP40 required for its plasma membrane localization as well as differences in the functional role of CTD amino acids in eVP40 and mVP40.

Common bean (Phaseolus vulgaris L.) is an important crop for food security and for national economics for several countries worlwide. One of the most important factors of risk in common bean production is the fungal disease anthracnose caused by Colletotrichum lindemuthianum, which in some cases, causes complete yield losses; this kind of plant disease is usually managed through the application of chemical products such as fungicides, that are commonly not accepted by society, this rejection is based on the relationship of pesticides with health damage and environmental contamination. In order to help in solving this drawbacks, the present work propose the use of Electrochemically Activated Salt Solutions(EASS) as a safer pathogen control agent in crops due to it have shown an elicitor and biostimulant effect on plants such as tobacco and apple. With this background, this manuscript presented in vitro results of the evaluation of the inhibitory effect for multiple bean pathogens and in vivo results of EASS in the common bean-Colletotrichum pathosystem by in vitro evaluations of the inhibitory effect for multiple bean pathogens and in vivo evaluation of the infection severity and defense activation such as secondary metabolites production and antioxidant activity. EASS presence in growth media had strong inhibitory effect, at beginning of experiment, for some of the evaluated fungi. EASS showed effect against the development of the disease when applied in specific doses to prevent distress in plants.

Fire-related cues could alter vegetation community composition by promoting or excluding different types of plants. Smoke-derived compounds have been a hot topic in plant and crop physiology. There are some fire-prone areas in Australia, both Americas, some Mediterranean countries and regions with extensive prescribed or illegal burning like central European, which are subjected to a direct impact of fire (heat, minerals accumulation from the burning matter) and/or the indirect one (smoke) and undergo compositional and structural changes. This review first updates information about the effect of the compounds on plants' kingdoms and focuses on the research advances in the field of smoke compounds and attempts to gather and summarize the recent state of research and opinions on the role of smoke-derived compounds in plants' lives. We finish our review by discussing major research gaps, which include: Why plants respond to smoke chemicals? Is the response of seeds to smoke and smoke compounds an evolutionary-driven trait allowing plants to adapt to local environment?

This study reports the design of a dielectric resonator (DR) metasurface-based terahertz biosensor for rapid and accurate detection of different kinds of viruses (H1N1, SARA-COV-2, etc.). The characterization of the sensor is done by analyzing its absorbance properties with and without the presence of the H1N1 virus layer of different concentrations and electrical properties in the frequency range of 2.4 THz to 3 THz. A full-wave EM model of the sensor is designed using CST MWS software. The geometrical parameters of the proposed biosensor, as well as its dielectric constant of the virus swab, are varied to achieve good performance with an absorption level close to 1 (100%). A significant change in the resonating pick-up frequency owing to the variation in the effective refractive index of the realized sensor ensures the detection and classification of the different concentrations of the same or different viruses. The presented design could be used for the rapid detection of viruses with the added advantages of contactless, label-free, and accurate identification of different concentrations of viruses.

Dengue has long been a serious health burden to the global community, especially for those living in the tropics. In spite of the availability of vaccines, effective treatment for the infection is still needed and currently remained absent. In the present study, antiviral properties of the KSF 103 ME which consisted of a number of potential antiviral compounds were investigated against DENV-2. The effects of this extract against DENV-2 replication were determined using the qRT-PCR. Findings from the study suggested that the KSF 103 ME showed maximum inhibitory properties toward the virus during the virus entry stage at concentrations of more than 12.5 µg/mL. Minimal antiviral activities were observed at other virus replication stages; adsorption (42% reduction at 50 µg/mL), post-adsorption (67.6% reduction at 50 µg/mL), prophylactic treatment (68.4% and 87.7% reductions at 50 µg/mL and 25 µg/mL, respectively) and direct virucidal assay (48% and 56.8% reductions at 50 µg/mL and 25 µg/mL, respectively. The KSF 103 ME inhibited dengue virus repication with an IC50 value of 20.3 µg/mL and SI value of 38.9. The KSF 103 ME showed potent antiviral properties against DENV during the entry stage. Further studies will be needed to deduce the antiviral mechanisms of the KSF 103 ME against DENV.

Survival following Ebola virus (EBOV) infection correlates with the ability to mount an early and robust interferon (IFN) response. The host IFN-induced proteins that contribute to controlling EBOV replication are not fully known. Among the top genes with the strongest early increases in expression after infection in vivo is IFN-induced HERC5. Using a transcription- and replication-competent VLP system, we showed that HERC5 inhibits EBOV virus-like particle (VLP) replication by depleting EBOV mRNAs. The HERC5 RCC1-like domain was necessary and sufficient for this inhibition and did not require zinc finger antiviral protein (ZAP). Moreover, we showed that EBOV (Zaire) glycoprotein (GP) but not Marburg virus GP antagonized HERC5 early during infection. Our data identifies a novel ‘protagonist-antagonistic’ relationship between HERC5 and GP in the early stages of EBOV infection that could be exploited for the development of novel antiviral therapeutics.

Ash trees have considerable economic, cultural and environmental value on the island of Ireland. However, European ash (Fraxinus excelsior L.) is currently under threat from the invasive ascomycete pathogen Hymenoscyphus fraxineus. This pathogen is the causal agent of ash dieback disease, which was initially reported in Poland in 1992. Hymenoscyphus fraxineus has since spread across Europe and the first recorded case of the disease on the island of Ireland was in 2012 at a forestry plantation in Co. Leitrim. The pathogen is now present in all 26 counties in Ireland and 6 counties in Northern Ireland, and it is considered unfeasible to eradicate. The spread of ash dieback disease is reflected in recent policy changes, which focus on management rather than eradication strategies. Since the first formal description of H. fraxineus in 2006, considerable research efforts have been made by the international scientific community to understand the biology of the pathogen and to develop management strategies against it. This review provides an update of current knowledge of H. fraxineus biology and infection. We then explore examples of mitigation techniques that have been trialled in Europe, in order to identify strategies that are feasible for disease management at a local level on the island of Ireland. Finally, we outline five key avenues of research that have the potential to provide breakthroughs in methods to protect valuable F. excelsior resources.

Understanding how plants change their root foraging strategy in the presence of neighbors is of paramount importance for plant ecology and agriculture. The root tragedy of the common (RToC) is a plant behavior predicted by game theory models in which competing plants forage for soil resources inefficiently. The RToC is generally assumed to be induced by non-self root recognition, and researchers consider root overproliferation and reduced fitness with respect to a plant growing solo as the trace left by plants engaging in an RToC in experiments and model results. Herein, I first challenge both notions, and argue that the RToC is a suboptimal phenotypically plastic response of plants that is based in soil resource information exclusively. Second, I discuss how this new perspective carries important implications for the design of experiments investigating the physiological mechanisms underlying observable plant root responses. Finally, I discuss why placing the RToC theory in the context of more general root research is fundamental: The RToC represents a mechanistic foundation for understanding the belowground behavior of plants interacting with neighbors, and a spatially explicit approach to RToC may produce more comprehensive results.

Reproductively lethal mutations (RLMs) are mutations that, upon expression of the encoded lethal phenotypes, cause individuals carrying them to die or to be sterile. An underappreciated fact is that loss-of-function RLMs in protein-coding genes can be phenotypically shielded by favorable environments rendering these genes conditionally non-essential, or by their sister alleles in diploid organisms. Absent of rigorous mitigation, such phenotype-shielding causes the number of genes incurring RLMs to increase over time, and simultaneously allows each RLM to reach high allele frequencies in a conspecific population. Over-accumulation of RLMs then sets the population up for eventual concurrent expression of large numbers of RLMs, and massive deaths in rapid succession, possibly even population-level extinction. This hypothetical scenario in turn predicts that organismal lineages that evolved means to minimize the allele frequencies of phenotypically shielded RLMs are favored by natural selection. We argue that bottlenecking the genome copies destined for reproduction is a universal strategy adopted by all living beings to compel phenotype-based RLM purging. We further postulate that primitive RNA replicons must first evolve bottlenecked reproduction before evolving the capacity to encode diffusible products. In more complex, multicellular organisms, RLM management through bottlenecked reproduction gains additional reinforcement through sexual reproduction. In short, the evidence chronicled in this essay strongly suggest that the Bottleneck, Isolate, Amplify, Select (BIAS) principle, originally proposed to explain intracellular evolutionary dynamics of viruses, may be universally applicable to all living beings.

A substantial amount of phosphorus (P) in soil is not readily available for plant uptake. Certain species may enhance P availability from poorly soluble P forms. This research aimed to compare the P solubilization capacity of the soil of two Lupine species, L. albus, and L. angustifolius, with a control crop of oats (Avena strigosa L.). Plants were planted in pots in four soils with varying texture, organic matter content, acidity, and P availability. Phosphorus solubilization capacity was assessed on variations of P availability (PBray1) at four points in time, comparing soils with lupine to oat-containing soils and their baseline values. At harvest, measurements of plant shoot biomass included their shoot dry weight and some nutrient concentrations such as P, nitrogen (N), manganese (Mn), and lupine nitrogen fixation. Compared to soils containing oats, lupine soils significantly increased PBray1 concentrations; increments ranged from 0.9 to 5.4 mg kg-1, depending on species, sampling time, and soil type. Lupine-induced soil acidification did not fully explain this P increase., As a proxy measurement of organic acid exudation, Manganese concentration was high in both lupine species' shoot biomass; however, these legumes had divergent Mn accumulation responses to soil acidity and P availability. Nitrogen fixed quantity varied with Lupine species (105-240 mg pot-1) and soil type (60-240 mg pot-1). Lupinus albus had a higher ability to mobilize non-labile P and provide N through biological N fixation (BNF), positioning it as a suitable crop for diversifying Uruguay's agricultural crop rotation systems.

The purpose of this investigation was to study the impact of different rates of bio fertilizer on agronomic characteristics and the relations among herbaceous plant diversity and soil properties of Aloysia citrodora in central Greece. For this aim a two – year Completely Randomized Design (CRD) field experiment was carried out in central Greece. The experiments included four biological fertilizer levels, BF0: 0 kg ha-1, BF50: 50 kg ha-1, BF100: 100 kg ha-1 and BF150: 150 kg ha-1 with 3 replication. Plant height, dry stem, dry leaves, dry total yield and Leaf Area Ιndex (LAI) were measured during the two growing years. The results showed that in the 1st studied the maximum plant height was observed in BF150 treatment while the 2nd year the BF150 level provoked a raise of 16.08% and 1.09% compared to BF50 and BF100, respectively. The 1st year the values of total dry yield were better in BF150 application. The 2nd year the total yield increased by 50.27% in BF100 and 50.09% BF150 treatments. Moreover, LAI was ameliorated by applied the BF100 and BF150 treatments both in two studied years. A key finding in this study is that Aloysia citrodora ecosystem favors herbaceous plant species richness. Also, soil factors (soil organic matter, P and K) promote positive herbaceous plant diversity within the Aloysia citrodora ecosystem. Finally, Aloysia citrodora can be a promising medicinal plant, cultivated under the Mediterranean climatic conditions.

The molecular interaction between the nematode and the host plant cells is complex and sophisticated. Initial contact with the plant parasitic nematodes (PPNs) triggers immune response in the host plant system which includes the release of toxic molecules. To put a bridle on this immune response, PPNs trigger pivotal cytoprotective mechanisms, such as antioxidant and detoxification pathways. Mechanisms of these pathways have been studied in PPNs and the specific genes involved have been targeted for gene silencing research in view of developing novel control measures. However, one of the important group of proteins involved in detoxification pathways known as ABC-transporters are not being studied until recently in PPNs. This opinion article focusses on the current knowledge and future prospects of ABC transporters in PPNs.

The major arboviruses belong mainly to the families Bunyaviridae, Togaviridae, and Flaviviridae amongst which chikungunya virus and dengue virus have emerged as a global public health problem. The main objective of the study was to develop a specific, sensitive, and cost-effective molecular multiplex RT-PCR and RT-qPCR assay for the rapid and simultaneous detection of CHIKV and the four serotypes of DENV for arbovirus surveillance. Specific primers of all virus were designed, one step multiplex RT-PCR (mRT-PCR) and RT-qPCR (mRT-qPCR) was developed using reference strains of CHIKV and DENV serotypes. The specificity of the test for all the viruses was confirmed by sequencing. The standard curves showed a high correlation coefficient, R2= 0.99, for DENV-2 and DENV-3; R2= 0.98, for DENV-4 and CHIKV; R2= 0.93, for DENV-1. The limits of detection were calculated to be 10-2 copies/µL for all viruses. The specificity and sensitivity of the newly developed mRT-PCR and mRT-qPCR were validated using positive serum samples collected in India and Burkina Faso. The sensitivity of mRT-PCR and mRT-qPCR are 91%, and 100% respectively. The specificity of both assays was 100% specific. mRT-PCR and mRT-qPCR assays are low cost and a combination of both will be a useful tool for arbovirus surveillance.

Zika virus (ZIKV) is a mosquito-borne flavivirus, and its infection may cause severe neurodegenerative diseases. The outbreak of ZIKV in 2015 in South American has caused severe human congenital and neurologic disorders. Thus, it is vitally important to figure out inner mechanism of ZIKV infection. Here, our data suggested that the ubiquitin-specific peptidase 38 (USP38) played an important role in host resistance to ZIKV infection, during which ZIKV infection did not affect USP38 expression. Mechanistically, USP38 bound to ZIKV envelope (E) protein through its C-terminal domain and attenuated its K48-linked and K63-linked polyubiquitination, thereby repressed the infection of ZIKV. In addition, we found that the deubiquitinase activity of USP38 was essential to inhibit ZIKV infection, and the mutant that lacked the deubiquitinase activity of USP38 lost ability to inhibit the infection. In conclusion, we found a novel host protein USP38 against ZIKV infection, and this may represent a potential therapeutic target for the treatment and prevention of ZIKV infection.

Many positive sense RNA viruses, especially those infecting plants, are known to experience stringent, stochastic population bottlenecks inside the cells they invade, but exactly how and why these populations become bottlenecked are unclear. A model proposed ten years ago advocates that such bottlenecks are evolutionarily favored because they cause the isolation of individual viral variants in separate cells. Such isolation in turn allows the viral variants to manifest the phenotypic differences they encode. Recently published observations lend mechanistic support to this model, and prompt us to refine the model with novel molecular details. The refined model, designated Bottleneck, Isolate, Amplify, Select (BIAS), postulates that these viruses impose population bottlenecks on themselves by encoding bottleneck-enforcing proteins (BNEPs) that function in a concentration-dependent manner. In cells simultaneously invaded by numerous virions of the same virus, BNEPs reach the bottleneck-ready concentration sufficiently early to arrest nearly all internalized viral genomes. As a result, very few (as few as one) viral genomes stochastically escape to initiate reproduction. Repetition of this process in successively infected cells isolate viral genomes with different mutations in separate cells. This isolation prevents mutant viruses encoding defective viral proteins from hitchhiking on sister genome-encoded products, leading to the swift purging of such mutants. Importantly, genome isolation also ensures viral genomes harboring beneficial mutations accrue the cognate benefit exclusively to themselves, leading to the fixation of such beneficial mutations. Further interrogation of the BIAS hypothesis promises to deepen our understanding of virus evolution, and inspire new solutions to virus disease mitigation.

From the first isolation of the cystovirus bacteriophage Φ6 from Pseudomonas syringae 50 years ago, we have progressed to a better understanding of the structure and transformations of the many parts of the virion. The three-layered virion encapsulating the tripartite double stranded RNA (dsRNA) genome, breaches the cell envelope on infection, generates its own transcripts, and coopts the bacterial machinery to produce its proteins. The generation of new virions starts with a procapsid with a contracted shape, followed by packaging single stranded RNA segments with concurrent expansion of the capsid, and finally replication to reconstitute the dsRNA genome. The outer two layers are then added, and the fully formed virions released by cell lysis. Most of the procapsid structure composed of the proteins P1, P2, P4 and P7 is now known, as well as its transformations to the mature, packaged nucleocapsid. The outer two layers are less well studied. One additional study investigated the binding of the host protein YajQ to the infecting nucleocapsid, where it enhances the transcription of the large RNA segment that codes for the capsid proteins. Finally, we relate the structural aspects of bacteriophage Φ6 top those of other dsRNA viruses, noting the similarities and differences.

Diseases caused by arboviruses are on the increase worldwide. In addition to arthropod bites, most arboviruses can be transmitted via accessory routes. Products of human origin (labile blood products, solid organs, hematopoietic stem cells, tissues) present a risk of contamination for the recipient if the donation is made when the donor is viremic. This narrative review describes the risks of acquiring certain arboviral diseases from human products, mainly solid organs and hematopoietic stem cells, in the French context. Mainland France and its overseas territories are exposed to a complex array of imported and endemic arboviruses, which differ according to their respective location. The main risks considered in this study are infections by West Nile virus, dengue virus and tick-borne encephalitis virus. The ancillary risks represented by Usutu virus infection, chikungunya and Zika are also addressed more briefly. For each disease, the guidelines issued by the French High Council of Public Health, which is responsible for issuing guidelines to mitigate the risks associated with products of human origin and for supporting public health policy decisions, are briefly outlined. The aim of this review is also to contribute to the standardization of recommendations at international level in areas with the same viral epidemiology.

A synoptic review of plant disease epidemics and outbreaks was made using two complementary approaches. The first approach involved reviewing scientific literature published in 2021, in which quantitative data related to new plant disease epidemics or outbreaks were obtained via surveys or similar methodologies. The second approach involved retrieving new records added in 2021 to the CABI Distribution Database, which contains over a million global geographic records of organisms from over 50,000 species. The literature review retrieved 186 articles, describing studies in 62 categories (pathogen species/species complexes) across >40 host species on 6 continents. Pathogen species with >5 articles were: Bursaphelenchus xylophilus, Candidatus Liberibacter asiaticus, cassava mosaic viruses, citrus tristeza virus, Erwinia amylovora, Fusarium spp. complexes, Fusarium oxysporum f. sp. cubense, Magnaporthe oryzae, maize lethal necrosis co-infecting viruses, Meloidogyne spp. complexes, Pseudomonas syringae pvs, Puccinia striiformis f. sp. tritici, Xylella fastidiosa, and Zymoseptoria tritici. Automated searches of the CABI Distribution Database identified 617 distribution records new in 2021 of 283 plant pathogens. A further manual review of these records confirmed 15 pathogens reported in new locations: apple hammerhead viroid, apple rubbery wood viruses, Aphelenchoides besseyi, Biscogniauxia mediterranea, Ca. Liberibacter asiaticus, citrus tristeza virus, Colletotrichum siamense, cucurbit chlorotic yellows virus, Erwinia rhapontici, Erysiphe corylacearum, Fusarium oxysporum f. sp. cubense Tropical Race 4, Globodera rostochiensis, Nothophoma quercina, potato spindle tuber viroid, and tomato brown rugose fruit virus. Of these, 4 pathogens had at least 25% of all records reported in 2021. We assessed two of these pathogens – tomato brown rugose fruit virus and cucurbit chlorotic yellows virus – to be actively emerging in/spreading to new locations. Although three important pathogens – Ca. Liberibacter asiaticus, citrus tristeza virus and Fusarium oxysporum f. sp. cubense – were represented in the results of both our literature review and our interrogation of the CABI Distribution Database, in general our dual approaches revealed distinct sets of plant disease outbreaks and new records, with little overlap.

Due to the fact that to date, the question of the origin of SARS-CoV-2 has not been resolved yet, the author analyzed the main advances in the development of genetic engineering of viruses that took place before the onset of the COVID-19 pandemic. The first artificial genetically modified viruses could appear in nature in the mid-1950s. The technique of nucleic acid hybridization was developed by the end-1960s. In the late 1970s, a method called the "reverse genetics" emerged to synthesize RNA and DNA molecules. In the early 1980-s, it became possible to combine the genes of different viruses and insert the genes of one virus into the genome of another virus. Since that time, the production of vector vaccines began. Currently, by modern technologies one can assemble any virus based on the nucleotide sequence available in the virus database or designed by a computer as a virtual model.Scientists around the world are invited to answer the call of Neil Harrison and Jeffrey Sachs of Columbia University, for a thorough and independent investigation into the origin of SARS-CoV-2. Only a full understanding of the origin of the new virus can minimize the likelihood of a similar pandemic in the future.

We present the detailed calculations of social distancing requirement. A comparative study of the growth pattern and death tolls in different communities indicates that the growth pattern of infected patients and death rate follow the similar distribution with different parametrizations. Every distribution follows an exponential growth pattern curve, like other microbes, then reaches the saturation point an d eventually decay s However, the argument for the exponential function depends on several parameters unbeknownst, as of yet. However, the slope varies different ial ly for various epicenter s and seems to have a relationship with parameters such as accessibi lity to healthcare facilities, pre existing medical conditions socio economic conditions and lifestyle. The mismatch of the growth pattern is also linked with the impact of various other factors and a premature interpretation of limit ed data. Novel behavi or of the virus brought many surprises, opened up new venues for medical research, and the need for the more detailed study of pathogens in the light of the interaction of RNA and DNA The adaptability to diverse ecological condition s and the relevant modification in the structure is also worth investigation The genetic modification can be studied using quantum mechanical probabilistic approach.

Plant-microbe interactions play a crucial role in shaping plant health and survival. In recent years, the role of extracellular vesicles (EVs) in mediating intercellular communication between plants and microbes has emerged as an intriguing area of research. EVs, serve as important carriers of bioactive molecules and genetic information, facilitating communication between cells and even between different organisms. Pathogenic bacteria leverage extracellular vesicles (EVs) to amplify their virulence, exploiting their cargo rich in toxins and virulence factors. Conversely, beneficial microbes initiate EV secretion to stimulate plant immune responses and nurture symbiotic relationships. The transfer of EV-packed small RNAs (sRNAs) has been demonstrated to facilitate the modulation of immune responses. Furthermore, harnessing the potential of EVs holds promise for the development of innovative diagnostic tools and sustainable crop protection strategies. This review highlights the biogenesis and functions of EVs in bacteria, and their importance in plant defense and paves the way for future research in this exciting field.

Medicinal plants are generally defined as rare herbals with potent medicinal activities that can be used as an alternative treatment for diseases. Recent studies exploring novel medicine developments, originating from folk-medicinal practices challenges this notion and suggests that both the circumference of the term medicinal plant and their potential application covers a substantially extensive verse than previously suggested. While medicinal plants are not limited to the borders of any country, Bangladesh and its south-east Asian neighbors do boast a huge collection of potent medicinal plants with considerable folk-medicine history compared to most other countries of the world. MPDB 2.0 is the continuation of MPDB 1.0, it serves as both a data repertoire for medicinal of Bangladesh and a user-friendly interface for researchers, health practitioners, drug developers, and students who wish to study the various medicinal & nutritive plants scattered around Bangladesh and the underlying phytochemicals contributing to their efficacy in folk medicine. While in developing MPDB 2.0 human diseases have been highly focused upon, the information in this database is not limited in its application for human diseases or diseases only, as many of the plants indexed here can serve in developing biofuel or bioremediation technologies or nutritive diets or cosmetics, etc. MPDB 2.0 comprises a collection of more than five hundred medicinal plants from Bangladesh along with a record of their corresponding scientific, family, and local names together with their utilized parts, information regarding ailments, active compounds, and PubMed ID of related publications.

Segmentation of a region of interest is an important pre-processing step for many colour image analysis techniques. Similarly segmentation of plant in digital images is an important preprocessing step in phenotying plants by image analysis. In this paper we present an analytical study to statistically determine the suitability of colour space representation of an image to best detect plant pixels and separate them from background pixels. Our hypothesis is that the colour space representation in which the separation of the distributions representing plant pixels and background pixels is maximized would be the best for detection of plant pixels. The two classes of pixels are modelled as a Gaussian mixture model (GMM). In our GM modelling we don't make any prior assumption about the number of Gaussians in the model. Rather a constant bandwidth mean-shift filter is used to cluster the data and the number of clusters and hence the number of Gaussians is automatically determined. Here we have analysed following representative colour spaces like $RGB$, $rgb$, $HSV$, $Ycbcr$ and $CIE-Lab$. This is because these colour spaces represent several other similar colour spaces and also an exhaustive study of all the colour space will be too voluminous. We also analyse the colour space feature from the two-class variance ratio perspective and compare the results of our hypothesis with this metric. The dataset for this empirical study consist of 378 digital images of plants and their manual segmentation. Dataset consist of various species of plants (arabidopsi, tobacco, wheat, rye grass etc.) imaged under different lighting conditions, indoor and outdoor, controlled and uncontrolled background. In results we obtain better segmentation of the plants in $HSV$ colour space, which is supported by its Earth mover distance (EMD) on the GMM distribution of plant and background pixels.

Many protein expression systems are primary utilised to produce a single, specific recombinant protein. In contrast, most biological processes such as virus assembly rely upon a complex of several interacting proteins rather than the activity of a sole protein. The high complexity of the baculovirus genome, coupled with a multiphase replication cycle incorporating distinct transcriptional steps, made it the ideal system to manipulate for high-level expression of a single or co-expression of multiple foreign proteins within a single cell. We have developed and utilised a series of recombinant baculovirus systems to unravel the sequential assembly process of a complex non-enveloped model virus, Bluetongue virus (BTV). The high protein yields expressed by the baculovirus system not only facilitated structure-function analysis of each viral proteins but were also advantageous to crystallography studies and supported the first atomic level resolution of a recombinant viral protein, the major BTV capsid protein. Further, the formation of recombinant double-shelled virus-like particles (VLPs) provided insights into the structure-function relationships among the four major structural proteins of the BTV whilst also representing a potential candidate for a viral vaccine. The baculovirus multi-gene expression system facilitated the study of structurally complex viruses (both non-enveloped and enveloped viruses) and heralded in a new generation of viral vaccines.

Tick-borne encephalitis virus (TBEV) is one of the most threatening pathogens which affects the human central nervous system (CNS). TBEV circulates widely in Northern Eurasia. According to ECDC the number of TBE cases increase annually. There is no specific treatment for the TBEV infection, thus vaccination is the main preventive measure. Despite the existence of several inactivated vaccines currently being licensed, the development of new TBEV vaccines remains a leading priority in countries endemic to this pathogen. Here we report new recombinant virus made by infectious subgenomic amplicon (ISA) approach using TBEV and yellow fever virus vaccine strain (YF17DD-UN) as a genetic backbone. The recombinant virus is capable of effective replication in mammalian cells and induce TBEV-neutralizing antibodies in mice. Unlike the original vector based on the yellow fever vaccine strain chimeric virus became neuroinvasive in doses of 107-106 PFU and can be used as a model of Flavivirus neuroinvasiveness, neurotropism and neurovirulence. These properties of hybrid structures are the main factors limiting their practical use as vaccines platforms.

Ecologists use the net biotic interactions among plants to predict fundamental ecosystem features. Following this approach, ecologists have built a giant body of theory founded on observational evidence. However, due to the limitations that a phenomenological approach raises both in empirical and theoretical studies, an increasing number of scientists claim the need for a mechanistic understanding of plant interaction outcomes, and a few studies have taken such a mechanistic approach. In this synthesis, we propose a modeling framework to study the plant interaction mechanistically. We first establish a conceptual ground to frame plant-plant interactions, and then, we propose to formalize this research line theoretically developing a family of individual-based, spatially-explicit models in which biotic interactions are an emergent property mediated by the interaction between plants’ functional traits and the environment. These models allow researchers to evaluate the strength and sign of biotic interactions under different environmental scenarios and thus constitute a powerful tool to investigate the mechanisms underlying facilitation, species coexistence, or the formation of vegetation spatial patterns.

It is important to be able to detect and differentiate between distinct porcine enteric coronaviruses that can cause similar diseases. However, the existence of naturally occurring recombinant coronaviruses such as swine enteric coronavirus (SeCoV) can give misleading results with currently used diagnostic methods. Therefore, we have developed and validated three duplex real-time quantitative RT-PCR assays for the simultaneous detection of, and differentiation between, porcine epidemic diarrhea virus (PEDV) and SeCoV. Transmissible gastroenteritis virus (TGEV) is also detected by two out of these three assays. In addition, a novel triplex assay was set up that was able to detect and differentiate between these alphacoronaviruses and the porcine deltacoronavirus (PDCoV). The validated assays have low limits of detection, close to 100% efficiency and were able to correctly identify the presence of PEDV and SeCoV in 55 field samples, while 20 samples of other pathogens did not give a positive result. Implementing one or more of these multiplex assays into the routine diagnostic surveillance for PEDV will ensure that the presence of SeCoV, TGEV and PDCoV will not go unnoticed.

The induction of acoustic-mechanical oscillations to virus particles by illuminating them with microwave signals is analyzed theoretically. Assuming the virus particle being of spherical shape, its capsid consisting primarily of glycoproteins, a viscous fluid model is adopted while the outside medium of the sphere is taken to be ideal fluid. The electrical charge distribution of virus particle is assumed to be spherically symmetric with a variation along the radius. The generated acoustic-mechanical oscillations are computed by solving a boundary value problem analytically, making use of the Green’s function approach. Resonance conditions to achieve maximum energy transfer from microwave radiation to acoustic oscillation to the particle is investigated. Estimation of the feasibility of the technique to compete virus epidemics either for sterilization of spaces and/or use for future therapeutic applications is examined briefly.

The production and N-glycosylation of recombinant human butyrylcholinesterase (BChE), a model highly glycosylated therapeutic protein, in a transgenic rice cell suspension culture treated with kifunensine, a strong α-mannosidase I inhibitor, was studied in a 5 L bioreactor. A media exchange was performed at day 7 of cultivation by removing spent sugar rich media (NB+S) and adding fresh sugar free (NB-S) media to induce the rice α-amylase 3D (RAmy3D) promoter to produce rice recombinant human BChE (rrBChE). Using a 1.25X concentrated sugar-free medium together with an 80% reduced working volume during the media exchange lead to a total active rrBChE production level of 79 ± 2 µg (g FW)^-1 or 7.5 ± 0.4 mg L^-1 in the presence of kifunensine, which is 1.5-times higher than our previous bioreactor runs using normal sugar free medium with no kifunensine treatment. Importantly, the amount of secreted active rrBChE in culture medium was enhanced in the presence of kifunensine, comprising 44% of the total active rrBChE at day 5 post-induction. Coomassie stained SDS-PAGE gel and Western blot analyses reveal different electrophoretic migration of purified rrBChE bands with and without kifunensine treatment, which is attributed to different N-glycoforms. N-Glycosylation analysis shows substantial increase of oligomannose glycans (Man5/6/7/8) in rrBChE treated with kifunensine compared to controls. However, mass transfer limitation of kifunensine is likely the major reason for incomplete inhibition of α-mannosidase I in this bioreactor study.

Evolution remains an incessant process in viruses, allowing them to elude host immune response and induce severe diseases, impacting the diagnostic and vaccine effectiveness. Predicting emerging viral genomes is crucial, particularly in diseases like dengue, where viruses disrupt host cells, leading to fatal outcomes. Deep learning has been applied to predict dengue fever cases; there has been relatively less emphasis on its significance in forecasting emerging Dengue Virus (DENV) serotype. While Recurrent Neural Networks (RNN) were originally designed for modeling temporal sequences, our proposed DL-DVE generative and classification model, trained on complete genome data of DENV, transcends traditional approaches by learning semantic relationships between nucleotides in a continuous vector space instead of representing contextual meaning of nucleotide characters. Leveraging 2000 publicly available DENV complete genome sequences, our Long Short-Term Memory (LSTM) based generative and Feedforward Neural Network (FNN) based classification DL-DVE model showcases proficiency in learning intricate patterns and generating sequences for emerging serotype of DENV. The generative model showed accuracy of 93% and the classification model provided insight into the specific serotype label, corroborated by BLAST search verification. Evaluation metrics such as ROC-AUC value 0.818, accuracy, precision, recall and F1 score all to be around 99.00%, demonstrated the classification model’s reliability.  Our model classified the generated sequences as DENV-4, exhibiting 65.99% similarity to DENV-4 and around 63-65% similarity with other serotypes, indicating notable distinction from other serotypes. Moreover, the intra-serotype divergence of sequences with a minimum 90% similarity underscored their uniqueness. We analyzed the conserved motifs in the genome through MEME Suite (version 5.5.5). Our research strives to contribute to the ongoing fight against the Dengue virus by offering predictive insights into its genomic evolution. Looking ahead, proactive predictive modeling before mutations occur holds potential for guiding vaccine design and diagnostic kit development.

Medicinal plants are being tested as options to prevent infectious diseases in many countries. Baccharis crispa Spreng. (Asteraceae), is a native medicinal species widely used throughout South America. Our objective was to evaluate the antiviral activity of four wild populations of B. crispa from the province of Córdoba (Argentina) and determine if there is variability between them. The cytotoxicity of the extracts (chlorofom, ethanol and aquose) was evaluated by the neutral red uptake method. Using the plaque-forming unit reduction assay, virucidal and antiviral activity against Herpes Simplex type 1 and Chikungunya viruses were tested. Phytochemical screening of each extract was also performed. Puesto Pedernera (PP) population showed the best antiviral and virucidal effect, standing out the ethanolic extract as the least toxic and with the best inhibitory activity against both viral models. Villa del Parque (VP) population was inactive, regardless of the extract and the virus tested. The results revealed that extracts bioactivities vary significantly depending on the geographic area of collection, with PP and VP populations showing the most significant variability, not only in activity but also in chemical composition. These findings support the potential use of extracts as a source of therapeutic agents against different viruses.

Tilapia lake virus (TiLV) is the main tilapia-infecting virus worldwide, causing serious economic losses. However, there is no vaccine for this viral disease. Here, TiLV ORF10 (TiLV-ORF10) encoding a protein with abundant epitopes was constructed into the eukaryotic expression vector pcDNA3.1, and used to evaluate the immune protective effects in Nile tilapia (Oreochromis niloticus). RT-PCR and western blot analyses confirmed vaccine plasmid expression in tilapia muscle tissues. Moreover, the transcription levels of immunoglobulin M, toll-like receptor 2, myeloid differentiation factor 88, interleukin 8, tumor necrosis factor alpha, gamma-IFN, and nuclear factor κB immune-related genes were statistically significantly upregulated in the spleen, liver, and kidney of vaccinated tilapias (P < 0.05). TiLV challenge experiments showed that relative percent survival (RPS) was significantly enhanced in fish by this DNA vaccine. Moreover, RPS was enhanced further when using a higher amount of the DNA vaccine (85.72% RPS at a DNA dose of 45 μg pcDNA3.1–ORF10). Vaccination with pcDNA3.1–ORF10 significantly reduced virus replication, as evidenced by the low amount of virus in the spleen, liver, and kidney of vaccinated tilapias after TiLV challenge. Thus, pcDNA3.1–ORF10 could induce protective immunity in tilapia and may be a potential vaccine candidate for controlling diseases caused by TiLV.

Arthropod-borne viruses belonging to the flavivirus genus possess an enormous relevance in public health. Neotropical non-human primates (NPs) have been proposed to be infected more frequently with flaviviruses due to their arboreal and diurnal habits, their genetic similarity to humans and their relative closeness to humans. However, the only known flavivirus in America that is maintained by sylvatic cycles involving NPs is Yellow Fever virus (YFV), and the NPs role as potential hosts of flaviviruses is still unknown. Here, we examined flavivirus exposure in 86 free range and captive NPs of Costa Rica to evaluate their involvement in flavivirus transmission cycles and their potential as flavivirus hosts. We used a highly-specific micro plaque reduction neutralization test (micro-PRNT) to determine the presence of antibodies against YFV, Dengue virus 1-4 (DENV), Zika virus, West Nile Virus (WNV) and Saint Louis Encephalitis virus (SLEV). We found evidence of seropositive NPs to DENV-1 8.2% (homotypic –3/86, heterotypic – 4/86), SLEV 15.1% (homotypic – 10/86, heterotypic – 2/86), WNV 2.3% (homotypic – 2/86) and 8.1% (7/86) undetermined Flavivirus species. No antibodies against YFV or ZIKV were found. This work provides compelling serological evidence of exposure in NPs of flaviviruses associated with urban cycles, i.e. DENV, and confirms decades of circulation of SLEV in the same environments. Also, the range of years of sampling and the socioeconomic region was statistically significant for the presence of Dengue and Flavivirus undetermined seropositive individuals, respectively. Both the years and socioeconomic regions with greater seroprevalence coincide with the years and socioeconomic regions with high numbers of Dengue human cases for the country. Our work suggests bidirectional? circulation of different flaviviruses between humans and wildlife with public health importance and underscores the necessity of further surveillance for flaviviruses in the humans/wildlife interface in Central America.

Bovine Respiratory Disease Complex, a complex respiratory ailment in cattle, results from a combination of viral and bacterial factors, compounded by environmental stressors such as overcrowding, transportation, and adverse weather conditions. Its impact extends beyond mere health concerns, posing significant economic threats to the cattle industry. This study presents an extensive investigation into viral pathogens associated with BRDC in Serbian cattle, utilizing serum samples and nasal swabs. A cross-sectional study was conducted in 2024 across 65 randomly selected dairy farms in Serbia, excluding vaccinated farms. Farms were categorized by livestock count: small (≤50 animals), medium-sized (51-200 animals), and large (&gt;200 animals). Serum samples from adult cattle older than 24 months were tested for antibodies against BVDV, BHV-1, BRSV, and BPIV3. Nasal swab samples from animals with respiratory signs were tested using PCR for viral genome detection. Results showed seropositivity for all four viruses across all farms, with BPIV3 exhibiting universal seropositivity. Medium-sized and large farms demonstrated higher seropositivity for BRSV and BHV-1 compared to small farms (p&lt;.05). True seroprevalence estimates at the animal level were 84.29% for BRSV, 54.08% for BVDV, 90.61% for BHV-1, and 84.59% for BPIV3. PCR analysis of nasal swabs revealed positive detections for BRSV (20%), BHV-1 (1.7%), BVDV (8%), and BPIV3 (10.9%). Influenza D virus was not found in any of samples. This study provides critical insights into the prevalence and circulation of viral pathogens associated with BRDC in Serbian cattle, emphasizing the importance of surveillance and control measures to mitigate the impact of respiratory diseases in cattle populations.

This review examines the categorization of Essentially Derived Varieties (EDV) introduced in the 1991 revision of the Convention of the Union internationale pour la protection des obtentions végétales (UPOV). Challenges in the implementation of the concept and progress made on a crop-by-crop basis to provide greater clarity and more efficient implementation are reviewed. The current approach to EDV remains valid provided i) clarity on thresholds can be achieved including through resource intensive research on an individual crop species basis and ii) that threshold clarity does not lead to perverse incentives to avoid detection of essential derivation. However, technological advances leading to new varieties resulting from the simultaneous introduction or change in expression of more than “a few” genes will so challenge the concept to require a new Convention. Revision could include deletion of the concept of essential derivation and revision on a crop-by-crop basis of the breeder exception. Countries that allow utility patents for individual plant varieties per se should consider removing that possibility unless plant breeders utilize those encouragements for risk taking and investment to broaden the germplasm base upon which the long-term sustainability of plant breeding resides.

A striking aspect of COVID-19 is the difference in the outcome of the infection between different countries, and different ethnic groups within one country. We surveyed the literature on SARS-CoV-2 complemented with comparative publications on SARS-CoV and other coronaviruses to capture the current understanding of virus – host interactions including virus subtypes, transmission, zoonotic aspects, and potential host determinants.

Plant transcriptomes are an extremely dynamic entities shaped spatially and temporally by many intracellular and environmental cues. In this review, we first summarize the complexity and diversity of plant genomes and transcriptomes as a start point for the multitude of transcriptomic responses. Numerous alterations within various tissue and organ-specific transcriptomes as well as the most relevant transcriptomic responses associated with plant acclimation to selected abiotic and biotic stress conditions, from the current studies employing high-throughput transcriptomic analysis are widely discussed. Understanding changes within plant transcriptomes, revealed by in silico functional analysis, allows for the characterization of stress-affected genes and stress acclimatory mechanisms, as well as allows to perform plant metabolic engineering. The latter allow cultivars to produce more secondary metabolites in the future, which are often desirable substances in the biomedical industry. Accordingly, in this review special attention was also paid to characterize the potential of transcriptomic analyses of medicinal species, particularly to search for new cultivars. Extensive characterization of transcriptomic responses in stress would also result in the development of new cultivars that display physiological and molecular mechanisms that allow them to cope with adverse environmental conditions more adequately.

Abstract: Brassinosteroids (BR) are essential plant hormones that play a crucial role in regulating plant growth and development, as well as their resistance to abiotic and biotic stresses, including pathogen infections. In the context of plant im-munity, BR influence various processes such as the expression of genes related to pathogen defense, the production of antimicrobial compounds, and the re-inforcement of the plant cell structure. The aim of work is understand the role of BR in plant defense against abiotic and biotic stresses. BR are involved in the regulation of metabolic processes, water economy, and photosynthesis, contributing to increased plant resistance to abiotic stresses. The study discusses various mechanisms of BR action on plant immunity, including the regulation of gene expression related to defense, activation of the plant defense system, in-teraction with other plant hormones, regulation of water and salt balance, and influence on photosynthetic processes. In the context of plant immunity, BR influence various processes, including the expression of genes related to pathogen defense, the production of antimicrobial compounds, and the reinforcement of the plant cell structure. Additionally, BR are involved in the regulation of metabolic processes, water economy, and photosynthesis, con-tributing to increased plant resistance to abiotic and biotic stresses. The paper emphasizes the importance of further research on the role and mechanisms of action of BR in plant immunity, which may contribute to the development of more effective strategies for the use of BR in agriculture, horticulture, and plant protection.

A layout of urban waste fired zero emission power plant is described in this paper. The principle of layout, which comes from similar coal-fired plants retrieved from the literature, integrates gasification with a power generation section, and implements two parallel conversion processes, one supplied by the heat of the gasifier consisting of a thermoacousticmagnetohydrodynamic (TAMHD) generator, while in the second one the syngas is treated in order to obtain almost pure hydrogen, which is fed to fuel cells. The CO2 deriving from the oxidation of Carbon base is stocked in liquid form. The novelty of the proposed layout lies in the fact that the entire conversion is performed without solid moving parts. The resulting plant avoids any type of emissions in the atmosphere, increases mechanical efficiency as compared to traditional plants, thanks to the absence of moving parts, nonetheless, resolving at its root the ever-increasing waste-related pollution problems.

In sustainable agriculture, plant nutrients are the most important elements. Biofertilizers introduce microorganisms that improve the soil nutrients and increase their accessibility to crops. In order to meet the demands of a growing population, healthy crops need to be produced using the right type of fertilizers to provide them with all the major nutrients they require. However, an increasing dependency on chemical fertilizers is destroying the environment and negatively af-fecting the health of humans. Thus, using microbes as bioinoculants as the best replacement of chemical fertilizers as eco-friendly way for plant growth and soil fertility is believed to be the best method for improving plant growth and soil fertility. In sustainable agriculture, these microbes provide significant benefits to crops. In addition to colonizing plant systems (epiphytic, endo-phytic, and rhizospheric), beneficial microbes play a key role in absorbing nutrients from surrounding ecosystems. Plant associate microbes can promote plant growth regardless of natural and extreme conditions. Plant growth promoting microbes promote plant growth through a variety of direct and indirect methods, such as nitrogen fixation, plant growth hormone production, siderophores, HCN, several hydrolytic enzymes, and potassium, zinc, and phosphorus solubilization. Research on biofertilizers has been extensive and even available, which demonstrates how these microbes can deliver nutrients to crops in sufficient quantities to enhance their yield. This review examines in detail the direct and indirect mechanisms of PGPR action and their interaction in plant growth and resistance.

Background: Fusarium head blight (FHB) is a serious fungal disease of crop plants due to substantial yield reduction and production of mycotoxins in the infected grains. The breeding progress in increasing resistance with maintaining a high yield is not possible without a thorough examination of the molecular basis of plant immunity responses; Methods: LC-MS based metabolomics approaches powered by three-way ANOVA and differentially accumulated metabolites (DAMs) selection, correlation network and functional enrichment were conducted on grains of resistant and susceptible to FHB genotypes of barley and wheat as well as model grass Brachypodium distachyon (Bd) still poorly known at metabolomic level; Results: We selected common and genotype-specific DAMs in response to F. culmorum inoculation. Immunological reaction at metabolomic level was strongly diversified between resistant and susceptible genotypes. DAMs common for all tested species from porphyrins, flavonoids and phenylpropanoids metabolic pathways were highly correlated and reflects conservativeness in FHB response in Poaceae family. Resistant related DAMs belonged to different structural classes including tryptophan derived metabolites, pirimidines, amino acids proline and serine as well as phenylpropanoids and flavonoids. Physiological response to F. culmorum of Bd was close to barley and wheat genotypes however, metabolomic changes were strongly diversified. Conclusions: Combined targeted and untargeted metabolomics provides comprehensive knowledge about significant elements of plant immunity with potential of being molecular biomarkers of enhance resistance to FHB in grass family. Thorough examination of Bd21 metabolome in juxtaposition with barley and wheat diversified genotypes facilitate their setting as model grass for plant-microbe interaction.

Eysenhardtia platycarpa (Fabaceae) is a medicinal plant used in México and it lacks biotechnological studies for its use. The aim of this work was to establish a cell suspension cultures (CSC) of E. platycarpa, determine the phytochemical profile, and evaluate its antifungal activity. Friable callus and CSC were established with 2 mg/L 1-naphthaleneacetic acid plus 0.1 mg/L kinetin. The highest total phenolics of CSC was 15.6 mg GAE/g dry weight and the total flavonoids content ranged from 56.2 to 104.1 µg QE/g dry weight. CG‒MS analysis showed that the dichloromethane extracts of CSC, sapwood and heartwood have a high amount of hexadecanoic acid (22.3 ‒ 35.3 %) and steroids (13.5 ‒ 14.7%). Heartwood and sapwood defatted hexane extracts have the highest amount of stigmasterol (≈ 23.4%) and β-sitosterol (≈ 43%), and leaf extracts presented β-amyrin (16.3%). Methanolic leaves extracts showed mostly sugars and some polyols, mainly D-pinitol (74.3%). Dichloromethane and fatty hexane extracts of CSC exhibited the percentages inhibition higher for Sclerotium cepivorum with 71.5 and 62.0%, respectively. The maximum inhibition for Rhizoctonia solani was with fatty hexane extracts of the sapwood (51.4%). Our study suggest that CSC extracts could be used as a possible complementary alternative to synthetic fungicides.

Indirect effects of global change via changing species interactions have been largely ignored in studies predicting global change impacts on ecosystems. Antagonistic biotic interactions, however, can strongly affect ecosystems and are likely to be affected by global change drivers themselves. We synthesize current knowledge on the impact of invertebrate herbivores and pathogens on plant productivity, diversity and community composition, and outline theory and expectations on how important global change drivers – nitrogen enrichment, climate change and elevated CO², and plant and insect diversity loss, may affect enemy impact on plant communities. We illustrate that our ability to predict global change impact requires a holistic perspective, taking into account direct as well as indirect effects via the biotic component of ecosystems.

The vascular flora of Sardinia has been investigated for more than 250 years, with particular attention to the endemic component, due to their phylogeographic and conservation interest. However, continuous changes in the floristic composition through natural processes, anthropogenic drivers or modified taxonomical attributions require constant updating. We checked all available literature, web sources, field and unpublished data from authors and acknowledged external experts to compile an updated checklist of vascular plants endemic to Sardinia. Life and chorological forms, and the conservation status of the updated taxa list were reported. Sardinia hosts 340 taxa (15% of the total native flora) endemic to the Tyrrhenian islands and other limited continental territories; 195 of these are exclusive to Sardinia. Asteraceae (50 taxa) and Plumbaginaceae (42 taxa) are the most representative families, while the most frequent life forms are hemicryptophytes (118 taxa) and chamaephytes (105 taxa). The global conservation status, available for 200 taxa, indicates that most endemics are under the ‘Critically Endangered’ (25 taxa), ‘Endangered’ (31 taxa) or ‘Least Concern’ (90 taxa) IUCN categories. This research provides an updated basis for future biosystematics, taxonomic, biogeographical and ecological studies, and for supporting more integrated and efficient policy tools.

This paper describes new horizons in the diversity and taxonomy of negev-like viruses encoding the membrane-embedded SP24 protein. First, our data extend the known host range of SP24-encoding negev-like viruses to include brown algae, fungi, green plants, the phylum Entoprocta, the phylum Mollusca, and vertebrates. Second, our phylogenetic analysis suggests that the evolution of the SP24 gene family may have involved frequent events of inter-order virus genome shuffling. Third, the identification of 2-3 copies of SP24 protein genes in some virus RNAs shows that virus genomes may have acquired additional SP24 genes during the evolutionary process due to duplications or new acquisition steps. Forth, the broad host specificity of some SP24-encoded viruses may be related to an important adaptive role of SP24. Fifth, insect and nematode genomes may acquire viral SP24 genes by putative horizontal transfer from negev-like viruses known to infect species of both taxa.

Infection with Ebola virus (EBOV) is responsible for haemorrhagic fever in humans with a high mortality rate. Combined efforts of prevention and therapeutic intervention are required to tackle highly variable RNA viruses, whose infections often lead to outbreaks. Here, we have screened the 2P2I3D chemical library using a nanoluc-based protein complementation assay (NPCA) and isolated two compounds disrupting the interaction of the EBOV protein fragment VP35IID with the N terminus of the dsRNA-binding proteins PKR and PACT, involved in IFN response and/or intrinsic immunity, respectively. The two compounds inhibited EBOV infection in cell culture as well as infection by measles virus (MV) independently of IFN induction. Consequently, we propose the compounds are antiviral by restoring intrinsic immunity driven by PACT. Given that PACT is highly conserved across mammals, we support further testing of the compounds in other species, as well as against further negative sense RNA viruses.

Herpes simplex virus 1 (HSV-1) expresses a large number of miRNAs, and their function is still not completely understood. In addition, HSV-1 has been found to deregulate host miRNAs, which adds to the complexity of regulation of efficient virus replication. In this study, we comprehen-sively addressed the deregulation of host miRNAs by massive-parallel sequencing. We found that only miRNAs expressed from a single cluster, miR-183/96/182 are reproducibly deregulated dur-ing productive infection. These miRNAs are predicted to regulate a great number of potential tar-gets involved in different cellular processes and have only 33 shared targets. Among these, mem-bers of the FoxO family of proteins were identified as potential targets for all three miRNAs. However, our study shows that the upregulated miRNAs do not affect the expression of FoxO proteins, moreover these proteins were upregulated in HSV-1 infection. Furthermore, we show that the individual FoxO proteins are not required for efficient HSV-1 replication. Taken together, our results indicate a complex and redundant response of infected cells to the virus infection that is efficiently inhibited by the virus.

It remains poorly understood how the life history strategies and transmission ecologies of viruses of plants, arthropods, and vertebrates are interrelated. The present analysis hinges on the virus transmission success. Virus transmission reflects where in the host-body viruses are retained or replicating. Plants, arthropods, and vertebrates share a protective outer-layer, a circulatory system, and reproductive organs. The latter enables vertical virus transmission and associates with virus-host mutualism. Two broadly opposing virus life history strategies are considered. Acute viruses tend to be replicative and are swiftly transmitted to the next host. Instead, persistent viruses keep virus replicating costs and host damage to a minimum. The intertwined life histories and transmission ecologies are accordingly pieced together, based on the virus mono- or instead dual-host tropism, the location of virus retention or replication on or in the host-body, the presence of cyclical or mechanical transmission by arthropods, and of horizontal and vertical host-to-host transmission modes. It is shown that in the arthropod and in the vertebrate animal host, virus circulation in the hemocoel or blood circulation goes hand-in-hand with vertical transmission. Instead, plant phloem viruses do not transmit via seed. The latter is the rule for the plant-only viruses. The risk management implications are discussed in brief.

The success of many viruses depends upon cooperative interactions between viral genomes. For example, viruses that coinfect the same cell can share essential gene products, such as replicase, the enzyme that replicates the viral genome. However, when cooperation occurs, there is the potential for ‘cheats’ to exploit that cooperation. We suggest that: (1) the biology of viruses makes viral cooperation particularly susceptible to cheating; (2) cheats are common across a wide range of viruses, including viral entities that are already well studied, such as defective interfering genomes, and satellite viruses. Consequently, evolutionary theory developed to explain cheating offers a conceptual framework for understanding and manipulating viral dynamics. At the same time, viruses offer unique opportunities to study how cheats evolve, because cheating is relatively common in viruses, compared with taxa where cooperation is more usually studied, such as animals.

Novel segmented tick-borne RNA viruses belonging to the group of Jingmenviruses (JMVs) are widespread across Africa, Asia, Europe, and America. In this work, we obtained whole-genome sequences of two Kindia tick virus (KITV) isolates and performed modeling and functional annotation of the secondary structure of 5’ and 3’ UTRs from JMV and KITV viruses. UTRs of various KITV segments are characterized by: (1) polyadenylated 3’ UTRs; (2) 5’ DAR and 3’ DAR motifs; (3) a highly conserved 5’-CACAG-3’ pentanucleotide; (4) a La protein binding site; (5) multiple UAG sites providing interactions with the MSI1 protein; (6) three homologous sequences in the 5’ UTR and 3’ UTR of segment 2; (7) the segment 2 3’ UTR of a KITV/2017/1 isolate comprises two consecutive 40 nucleotide repeats forming a Y-3 structure; (8) a 35-nucleotide deletion in the second repeat of the segment 2 3’ UTR of KITV/2018/1 and KITV/2018/2 isolates, leading to a modification of the Y-3 structure; (9) two pseudoknots in the segment 2 3’ UTR; (10) the 5’ UTR and 3’ UTR are represented by patterns of conserved motifs; (11) the 5’-CAAGUG-3’ sequence occurs in early UTR hairpins. Thus, we identified regulatory elements in the UTRs of KITV, which are characteristic of orthoflaviviruses. This suggests their functional significance for the replication of JMVs and the evolutionary similarity between orthoflaviviruses and segmented flavi-like viruses.

Invasive weeds cause significant crop yield and economic losses in agriculture. The highest in-direct impact may be attributed to the role of invasive weeds as virus reservoirs especially within the commercial growing areas. The new tobamovirus tomato brown rugose fruit virus (ToBRFV), recently identified in the Middle-East, overcomes the Tm-22 resistance allele in the cultivated tomato varieties grown in greenhouses. In this study, we determined the role of invasive weed species as potential hosts for ToBRFV and pepino mosaic virus (PepMV). Out of all tested weed species, the invasive species So-lanum elaeagnifolium and S. rostratum, mechanically inoculated with ToBRFV, were positive for To-BRFV in both enzyme linked immunosorbent assay (ELISA) and RT-PCR tests. S. rostratum was also positive for PepMV. No conspicuous phenotype was observed on ToBRFV infected S. elaeagnifolium plants suggesting a hostplant associated defense response. S. rostratum plants inoculated with either ToBRFV alone or a mixture of ToBRFV and PepMV-IL, contained high ToBRFV levels. In addition, when inoculated with ToBRFV or PepMV-IL disease symptom manifestations were observed in S. rostratum plants and the symptoms were exacerbated upon mixed infections with both viruses. The distribution and abundance of both Solanaceae species increase the risks of virus transmission between species.

The taxonomic identity and phylogenetic relationships of several southern African perennial taxa related to Frankenia repens are discussed. In particular, F. nodiflora Lam., a misunderstood species described from the Cape region and synonymised to F. pulverulenta, is restored for plants endemic to salt-pans and riverbeds in the coastal lowlands across the Cape plains (Western Cape Province, South Africa). Further, a revision of morphologically close plants, usually identified as F. pulverulenta or F. repens, also occurring in similar saline ecosystems of the inland western South Africa revealed the existence of two distinct new entities not matching any described taxa of the genus. Molecular analyses of nuclear ribosomal (ITS1-5.8S-ITS2 region) DNA sequence data together with morphological divergence allow recognition of those taxa at species rank, within an independent lineage close to F. repens. In consequence, two new species are described in the so-called “F. repens group”: F. nummularia from the Nama-Karoo Biome (Western Cape and Northern Cape Provinces), and F. namaquana from the Succulent Karoo Biome (Northern Cape Province). Full morphological description and type designation are reported for each accepted species, as well as data on ecology, habitat, distribution and taxonomic relationships to other close relatives are given. Further, an identification key is presented to facilitate recognition of the southern African taxa of Frankenia.

The effects of methyl jasmonate (MeJ) on growth and taxoid formation in the cell culture of Himalayan yew was investigated for elucidate the specifics of the action of phytohormones on dedifferentiated plant cells in vitro. The characteristics of the same suspension culture of Taxus wallichiana was compared in 2017 ("young culture") and in 2022 ("old culture") - 1.5 or 6 years after culture induction, respectively. Cells were grown in flasks and bioreactors, MeJ (100 µM) was added at the exponential growth phase. It was found that cell culture demonstrated good growth (dry weight (DW) accumulation 10–18 g/l, specific growth rate µ = 0.15–0.35 day-1) regardless of "age", cultivation system and MeJ addition. UPLC–ESI-MS analysis showed the presence of C14-hydroxylated taxoids (yunnanxane, taxuyunnanine C, sinenxane C, sinenxane B) in cell biomass in the amounts comparable to plants. The content of C14-OH taxoids during 5 years of cultivation increased by 3-5 times. It was 0.2–1.6 mg/g DW for "young culture” and 0.6-10.1 mg/g for “old culture” depending on cultivation conditions. The ratio of individual compounds changed also: in the "young culture" was predominant yunnanxane, in the "old culture" - sinenxane C. Important that C13-hydroxylated taxoids were found in trace amounts only in the "young culture” (below 0.05 mg/g DW) and were not detected in the "old culture”. The response to MeJ was radically different depending on culture’s «age». In the “young culture”, exogenous MeJ had no effect on the content of C14-OH com-pounds, but significantly (almost 10 times) increased the content of C13-OH compounds. In particular, paclitaxel concentration was elevated up to 0.12–0.19 mg/g DW, which is comparable to its content in the bark of yew trees. By contrast, MeJ added to the "old culture” had minor effect on the synthesis of C13-OH toxoids that appeared in trace amounts only (below 3.5 µg/g DW for paclitaxel) but notably increased the content of C14-OH compounds (1.5–2.0 times in flasks and 5–8 times in bioreactors). These findings suggest that hormonal signaling in dedifferentiated yew cells grown in vitro is different from that in plants and change with culture age. This might be a result of the high level of heterogeneity of cells in vitro and their constant auto-selection for proliferate intensity which leads to predominant formation of C14-OH taxoids versus C13-OH taxoids and modified cell response to exogenous MeJ treatment. These results have both fundamental and practical biotechnological application.

Plants harbor a large diversity of endophytic microbes. Meadow fescue (Festuca pratensis) is a cool-season grass known for its symbiotic relationship to the systemic and vertically- via seeds - transmitted fungal endophyte Epichloë uncinata but the effect of the endophyte on the microbial endophyte community and phytohormones is largely unexplored. Here, we sequenced the endophytic bacterial and fungal communities in the leaves and roots, analyzed phytohormone concentrations and plant performance parameters in Epichloë-symbiotic (E+) and Epichloë-free (E-) individuals of two meadow fescue cultivars. The endophytic leaf microbial community differed between leaf and root tissues independent of endophyte symbiosis while the fungal community was different in leaves of Epichloë-symbiotic and Epichloë-free plants in both cultivars. At the same time, endophyte symbiosis decreased salicylic acid and increased auxin concentrations in leaves. Epichloë-symbiotic plants showed a higher biomass, chlorophyll content (SPAD) and higher seed mass at the end of the season. Our results demonstrate that Epichloë-symbiosis alters the leaf fungal microbiome, which coincides with changes in phytohormone concentrations, indicating that Epichloë endophytes affect both, plant immune responses and other fungal endophytes. Whether the effect of Epichloë endophytes on other fungal endophytes is connected to changes in the phytohormone concentrations remains to be elucidated.

In the Agriculture sector, control of plant leaf diseases is crucial as it influences the quality and production of plant species with an impact on the economy of any country. Therefore, automated identification and classification of plant leaf disease at an early stage is essential to reduce economic loss and to conserve the specific species. Previously, to detect and classify plant leaf disease, various Machine Learning models have been proposed; however, they lack usability due to hardware incompatibility, limited scalability and inefficiency in practical usage. Our proposed DeepLens Classification and Detection Model (DCDM) approach deal with such limitations by introducing automated detection and classification of the leaf diseases in fruits (apple, grapes, peach and strawberry) and vegetables (potato and tomato) via scalable transfer learning on A.W.S. SageMaker and importing it on AWS DeepLens for real-time practical usability. Cloud integration provides scalability and ubiquitous access to our approach. Our experiments on extensive image data set of healthy and unhealthy leaves of fruits and vegetables showed an accuracy of 98.78% with a real-time diagnosis of plant leaves diseases. We used forty thousand images for the training of deep learning model and then evaluated it on ten thousand images. The process of testing an image for disease diagnosis and classification using AWS DeepLens on average took 0.349s, providing disease information to the user in less than a second.

The research objectives was to determine the plants vegetation profile in forest revegetation and Mount Arjuna springs. The method used was descriptive method. While based on the techniques and tools used to research, the author uses the survey method to obtain facts that occur in the research area, namely in the area around the springs of Arjuna mount, Pasuruan, East Java, Indonesia. Data obtained in the field are then processed and analyzed using GIS, ArcView 3.3 and Google Earth programs. The results of the study explain the profile of plant vegetation, namely plant stratification, bird wealth, taxonomic wealth and plant density have a significant effect on forest revegetation and springs in Arjuna mount. The forest vegetation profile has a positive and significant effect on the preservation of springs. The better the profile of forest vegetation, the preservation of springs will be better, and vice versa.

Human papillomavirus (HPV) uses the cellular trafficking machinery to reach the cell nucleus and initiate a successful infection. The HPV capsid consists of two proteins: L1 (the major capsid protein) and L2 (minor capsid protein), and L2 is known to be responsible for trafficking the viral genome to the nucleus. From previous studies, we know that many cellular proteins interact with L2 and are involved in the trafficking process at different stages of the infectious entry process. To further investigate how HPV-16 achieves successful viral entry, we have performed a mass spectrometry analysis to identify novel interacting proteins that associate with incoming HPV-16 virions. We show that HPV-16 pseudovirions interact with a group of cellular cargo proteins (COPI), and here we confirm that this is mediated by the direct binding of L2, but not L1, to the COPB1 subunit. We also show that the ability of L2 to interact with COPB1 is conserved in both low- and high-risk HPV types. Furthermore, we also show that the interaction is essential for successful infection entry of multiple HPV types, thereby identifying a novel constituent of the infectious entry pathway of the HPV.

Canine distemper virus (CDV) is a serious contagious disease of canines, cats and sometimes ra-coons. The study included seven raccoons from Timisoara Zoo. The detection of CDV in all raccoons was accomplished using qRT-PCR, but several other exams were also conducted. Clinically, severe digestive disorders were observed, characterized by diarrhea and repeated hematemesis. Pseudomembranous gastroenteritis, congestion and pulmonary edema were found during the ne-cropsy of two racoons. Immunohistochemically, the brown color was highlighted in the examined sectionsand it was present in the cytoplasm of the cells from the germinal centers of the medullary area. Histopathological examination revealed lymphocyte depletion and intranuclear and intracy-toplasmic inclusions in the intestine. Based on the qRT-PCR assay, laboratory tests and lesions ob-served, it was established that the raccoons got infected with CDV, and two of them died as a result. The necropsy, histological lesions and immunohistochemical results are comparable between dogs and racoons. Through the results obtained, it was concluded that the interspecific infection is possible and the epidemiological risk of infection transmitted by racoons to domestic animals, such as dogs and cats, needs to be examined in the future.

"Medusaviridae" is a proposed family of large DNA viruses so far represented by a sole virus isolated from a hot spring. In the present study, we report the isolation and genome sequencing of a new member of this family, medusavirus stheno, discovered from a freshwater sample with Acanthamoeba castellanii coculture.

BK polyomavirus (BKPyV) causes a lifelong chronic infection and is associated with debilitating disease in kidney transplant recipients. Despite its importance, aspects of the virus life cycle remain poorly understood. In addition to the structural proteins, the late region of the BK genome encodes for an auxiliary protein called agnoprotein. Studies on other polyomavirus agnoproteins have suggested that the protein may contribute to virion infectivity. Here, we demonstrate an essential role for agnoprotein in BK virus release. Viruses lacking agnoprotein do not propagate to wild-type levels and fail to release from host cells. Despite this, loss of agnoprotein does not impair virion infectivity or morphogenesis. Instead, agnoprotein expression correlates with nuclear egress of BK virions. We demonstrate that the agnoprotein binding partner α-SNAP is necessary for BK virion release, and siRNA knockdown of α-SNAP prevents nuclear release of wild-type BK virions. These data highlight a novel role for agnoprotein and begin to reveal the mechanism by which polyomaviruses leave an infected cell.

The recently discovered Jingmenvirus group includes viruses with a segmented genome, RNA of a positive polarity, and several proteins with distant homology to the proteins of the members of the genus Flavivirus. Some Jingmenvirus group members, namely Alongshan virus (ALSV) and Jingmen tick virus, are reported to be tick-borne human pathogens, causing a wide variety of symptoms. ALSV is widely distributed in Eurasia, yet there is no reliable assay for its detection. Here, we describe a qPCR system for the detection of ALSV. Our data show that this system can detect as low as 10⁴ copies of ALSV in the probe. It shows no amplification with common tick-borne viruses circulating in Eurasia, Yanggou tick virus—another member of the Jingmenvirus group—or some known members of the genus Flavivirus. The qPCR system was tested have no non-specific signal for Ixodes ricinus, I. persulcatus, Dermacentor reticulatus, D. marginatus, Haemaphysalis concinna, and H. japonica ticks. Overall, the qPCR system described here can be used for reliable and quantitative ALSV detection.