Search Results (67)

This study analyzed the heavy metal tolerance and chromium reduction and the potential of plant growth to promote Rhizobium sp. OS-1. By genetic makeup, the Rhizobium strain is nitrogen-fixing and phosphate-solubilizing in metal-contaminated agricultural soil. Among the Rhizobium group, bacterial strain OS-1 showed a significant tolerance to heavy metals, particularly chromium (900 µg/mL), zinc (700 µg/mL), and copper. In the initial investigation, the bacteria strains were morphologically short-rod, Gram-negative, appeared as light pink colonies on media plates, and were biochemically positive for catalase reaction and the ability to ferment glucose, sucrose, and mannitol. Further, bacterial genomic DNA was isolated and amplified with the 16SrRNA gene and sequencing; the obtained 16S rRNA sequence achieved accession no. HE663761.1 from the NCBI GenBank, and it was confirmed that the strain belongs to the Rhizobium genus by phylogenetic analysis. The strain’s performance was best for high hexavalent chromium [Cr(VI)] reduction at 7–8 pH and a temperature of 30 °C, resulting in a total decrease in 96 h. Additionally, the adsorption isotherm Freundlich and Langmuir models fit best for this study, revealing a large biosorption capacity, with Cr(VI) having the highest affinity. Further bacterial chromium reduction was confirmed by an enzymatic test of nitro reductase and chromate reductase activity in bacterial extract. Further, from the metal biosorption study, an Artificial Neural Network (ANN) model was built to assess the metal reduction capability, considering the variables of pH, temperature, incubation duration, and initial metal concentration. The model attained an excellent expected accuracy (R² > 0.90). With these features, this bacterial strain is excellent for bioremediation and use for industrial purposes and agricultural sustainability in metal-contaminated agricultural fields. Full article

A novel barna-like virus was found to be associated with field-collected Afrina sporoboliae plant-parasitic nematodes. The positive-sense, single-stranded RNA genome of this virus, named Afrina barna-like virus (AfBLV), comprises 4020 nucleotides encoding four open reading frames (ORFs). ORF 1 encodes a protein product spanning a transmembrane, a peptidase, and VPg domains, whereas an overlapping ORF 2 encodes an RNA-dependent RNA polymerase (RdRP). ORF2 may be expressed via a −1 translational frameshift. In phylogenetic reconstructions, the RdRP of AfBLV was placed inside a separate clade of barna and barna-like viruses related to but distinct from the genera in the Solemoviridae and Alvernaviridae families, within the overall lineage of Sobelivirales. ORF 3 of AfBLV encodes a protein product of 206 amino acids (aa) long with homology to a putative protein encoded by a similarly positioned gene of an uncharacterized virus sequence identified previously as Barnaviridae sp. ORF 4 encodes a 161 aa protein with no significant similarities to sequences in the GenBank databases. AfBLV is the first barnavirus found in a nematode. Sequence comparisons of the AfBLV genome and genomes of other barna-like viruses suggested that a recombination event was involved in the evolution of AfBLV. Analyses of the phylogeny of RdRPs and genome organizations of barna-like and solemo-like viruses support the re-classification of Barnavirus and Dinornavirus genera as members of the Solemoviridae family. Full article

The promising field of low-temperature plasma treatment, known for its non-invasive and environmentally sustainable nature, is being actively investigated for its ability to enhance germination, emergence, yield, and overall plant development in a broad spectrum of crops. For gene bank requirements, low-temperature plasma technologies can also improve germination parameters and promote the development seeds suitable for long-term storage. Seeds from four selected cultivars of wheat, oats, flax, and rapeseed stored in the gene bank for 1, 10, and 20 years were subjected to plasma treatments for 20, 25, and 30 min. The study evaluated the mean root and shoot length, root–shoot ratio, and seedling vigour index. Additionally, the malondialdehyde level, total polyphenol content, total flavonoid content, and total antioxidant capacity were analysed. Plasma treatment displayed varying effects on the morphological characteristics and antioxidant activity of the tested cultivars, which were influenced by treatment duration and cultivar. A positive effect of plasma treatment on seedling length, seedling vigour index, and root–shoot ratio was observed in flax cultivar ‘N-9/62/K3/B’ in all periods and in variants T2 and T3. Conversely, the wheat cultivar ‘Granny’ showed variable results, and the oat cultivar ‘Risto’ showed variable negative results in regards to mean root length and mean shoot length after plasma treatment. The indicators of oxidative stress and antioxidant capacity were affected in all the cultivars studied. A positive effect of plasma treatment on these indicators was observed in the wheat cultivar ‘Granny’, while flax cultivar ‘N-9/62/K3/B’ exhibited inconsistent results. While in cereals, a decrease in malondialdehyde content after plasma treatment was associated with an increase in polyphenol and flavonoid content as the treatment duration increased, small-seeded species responded somewhat differently. The rapeseed cultivar ‘Skrivenskij’ and flax cultivar ‘N-9/62/K3/B’ showed an increase in polyphenol and flavonoid content following a decrease in malondialdehyde levels. This study highlights the potential of low-temperature plasma treatment for long-term-stored seeds and its applicability to plant genetic resources. The findings emphasize the need for the further optimization of low-temperature plasma treatment conditions for different plant species and cultivars. Full article

Chronobiotics represent a pharmacologically diverse group of substances, encompassing both experimental compounds and those utilized in clinical practice, which possess the capacity to modulate the parameters of circadian rhythms. These substances influence fluctuations in various physiological and biochemical processes, including the expression of core “clock” genes in model organisms and cell cultures, as well as the expression of clock-controlled genes. Despite their chemical heterogeneity, chronobiotics share the common ability to alter circadian dynamics. The concept of chronobiotic drugs has been recognized for over five decades, dating back to the discovery and detailed clinical characterization of the hormone melatonin. However, the field remains fragmented, lacking a unified classification system for these pharmacological agents. The current categorizations include natural chrononutrients, synthetic targeted circadian rhythm modulators, hypnotics, and chronobiotic hormones, yet no comprehensive repository of knowledge on chronobiotics exists. Addressing this gap, the development of the world’s first curated and continuously updated database of chronobiotic drugs—circadian rhythm modulators—accessible via the global Internet, represents a critical and timely objective for the fields of chronobiology, chronomedicine, and pharmacoinformatics/bioinformatics. The primary objective of this study is to construct a relational database, ChronobioticsDB, utilizing the Django framework and PostGreSQL as the database management system. The database will be accessible through a dedicated web interface and will be filled in with data on chronobiotics extracted and manually annotated from PubMed, Google Scholar, Scopus, and Web of Science articles. Each entry in the database will comprise a detailed compound card, featuring links to primary data sources, a molecular structure image, the compound’s chemical formula in machine-readable SMILES format, and its name according to IUPAC nomenclature. To enhance the depth and accuracy of the information, the database will be synchronized with external repositories such as ChemSpider, DrugBank, Chembl, ChEBI, Engage, UniProt, and PubChem. This integration will ensure the inclusion of up-to-date and comprehensive data on each chronobiotic. Furthermore, the biological and pharmacological relevance of the database will be augmented through synchronization with additional resources, including the FDA. In cases of overlapping data, compound cards will highlight the unique properties of each chronobiotic, thereby providing a robust and multifaceted resource for researchers and practitioners in the field. Full article

Background: Weed herbicide resistance is a serious problem in crop protection globally. Giant foxtail (Setaria faberi R.A.N. Herrm.) populations cannot be controlled by acetolactate synthase (ALS)-inhibiting herbicides in a few corn (Zea mays L.) monoculture fields. Methods: Five putative resistant giant foxtail populations, originating from corn monoculture fields in northeastern Greece, were evaluated for possible evolution of ALS-inhibitor resistance (nicosulfuron, rimsulfuron). The resistance ratio, the underlying resistance mechanism, and its impact on competitive ability against corn were studied. Results: The whole-plant rate-response assays showed that these populations were resistant (R) to the sulfonylureas nicosulfuron and rimsulfuron, but susceptible (S) to imidazolinone imazamox, triketone 4-hydroxyphenylpyruvate dioxygenase inhibitor tembotrione, and acetyl-CoA carboxylase inhibitor cycloxydim. The sequencing of the ALS gene did not reveal the presence of resistance-associated point mutations, indicating that the resistance was probably not target-site mediated. This was confirmed by the application of piperonyl butoxide two hours before nicosulfuron application, which reversed the resistance in all R giant foxtail populations, supporting the evidence of enhanced metabolism-mediated resistance. The competition study between corn and R or S giant foxtail populations indicated no stable trend reduction in corn traits, suggesting that the resistance mechanism was not associated with the competitive ability of the R populations. The novel ALS genotype in S. faberi, characterized for the first time and submitted to the GenBank database with accession number PV016837, indicated a closer genetic relationship with the S. viridis ALS gene than with S. italica. Conclusions: Five giant foxtail populations have evolved metabolism-based resistance to the ALS-inhibiting herbicides nicosulfuron and rimsulfuron. Full article

The pale grass blue butterfly Zizeeria maha has been used to evaluate the biological effects of the Fukushima nuclear accident in 2011. Here, we examined the DNA sequences of the mitochondrial gene cytochrome oxidase subunit I (COI) of Z. maha using the field samples collected in 2011–2014 and 2021. Among 641 individuals from 44 localities in Northeastern Japan, we detected a heteroplasmic nonsynonymous nucleotide substitution in one out of three 2012 individuals from Hirono, Fukushima Prefecture, where the biological impact of radioactive pollution was the highest among the localities surveyed in 2012, suggesting DNA damage via initial exposure to short-lived radionuclides. An additional 80 individuals from Hirono in 2021 did not show any substitution, suggesting the extinction of the Hirono mutant by 2021. We also detected another heteroplasmic and homoplasmic nonsynonymous substitution in four out of five 2014 individuals from Shibata, Niigata Prefecture, where radioactive pollution was low. These substitutions were not present in the GenBank records of Z. maha and its sister species Z. karsandra, indicating that intraspecific variation may exceed interspecific variation in Z. maha. These results highlight not only the possible impact of the initial exposure in Fukushima but also real-time molecular evolution of butterflies in the field. Full article

Recently, Fusarium root rot (FRR)-like symptoms were observed in Uganda’s agroecology zones, prompting the National Agricultural Organisation (NARO) to conduct a disease survey. The survey reports indicated FRR as the second most prevalent root rot disease of common bean in Uganda after Southern blight. Ninety nine Fusarium spp. strains were obtained from samples collected during the surveys. The strains were morphologically and pathogenically characterised and confirmed to cause Fusarium root rot as observed in the field. However, molecular characterization of the strains was not conducted. In this study, therefore, 80 of the strains were characterized using partial sequences of translation elongation factor 1-alpha (TEF-1α) gene, beta tubulin (β tubulin) gene and internal transcribed spacers (ITS) region of ribosomal RNA to determine species diversity. High-quality Sanger sequences from the target genes were compared to the sequences from Fusarium species available in the National Centre for Biotechnology Information coding sequences (NCBI-CDS) database to determine the most likely species the strains belonged. The sequences from our strains were deposited into the NCBI gene bank under ID#288420, 2883276, 2873058 for TEF-1α, β tubulin and ITS respectively. The Fusarium species identified included; F. oxysporum, F. solani, F. equiseti F. delphinoides, F. commune, F. subflagellisporum, F. fabacearum, F. falciforme, F. brevicaudatum, F. serpentimum, F. fredkrugeri and F. brachygibbosum. The diversity of these Fusarium species needs to be taken into consideration when developing breeding programs for management of the disease since currently there is no variety of common bean resistant to FRR in Uganda. Full article

The coconut (Cocos nucifera L.), a valuable tropical crop, is rapidly declining in genetic diversity due to natural disasters, pest and disease attack, and land clearing for other crops. Seed banking is impractical for coconut conservation due to its large, recalcitrant seed, and maintaining field gene bank collections is costly and vulnerable to environmental pressures. Cryopreservation offers a promising alternative method for conserving coconut genetic diversity, but the success in recovering cryopreserved materials remains limited, with few studies consistently reporting high rates of recovery. This highlights the need for improved cryopreservation protocols, particularly in tissue dehydration, which is one of the critical steps in the process of cryopreservation and plant recovery. A desiccator was developed that enabled rapid embryo dehydration with ultra-dry airflow. The desiccator reduced embryo moisture content to 20% (the predetermined viability threshold) within 6 h representing a 2-h improvement when compared to a previous dehydration approach, while maintaining a high germination rate (71%). Smaller embryos (500 to 550 mg fresh weight) desiccated faster than larger embryos (800 to 900 mg fresh weight) but germination was reduced (30%), making small embryos unsuitable for cryopreservation. A 5-day sucrose (0.4 M) pre-treatment further reduced the dehydration time to 4 h, while maintaining a high germination rate (70%). These advances in the use of a sucrose pre-treatment, the rapid embryo dehydration, and selection of large embryos size will help to enhance the success of coconut embryo cryopreservation and recovery. Full article

Fowl adenovirus D is the main cause of inclusion body hepatitis in chickens. Whole genome sequencing was carried out to enrich the genomic sequence database using field isolates of FAdV-D. Out of 44 newly determined genomes, 43 were classified into FAdV-2/-11 and 2 into FAdV-3; no FAdV-9 was identified. Whole-genome based phylogeny showed that FAdV-3 was more distantly related to FAdV 9 and FAdV-2/-11 than FAdV-9 and FAdV-2/-11 to each other. Whole-genome sequence homology analysis revealed that the full-length FAdV-3 genome harbored a ~12 kbp fragment of the genome that shared moderate sequence homology with representative strains of other FAdV-D serotypes but high relatedness with only the FAdV-3 strain whose full-genome is available in GenBank. A closer look onto the fiber and the penton genes of our FAdV-3 isolate identified putative recombination events; both the fiber and the penton coding genes shared fragments originating from FAdV-9. Of interest, ORF19 displayed a close relationship with the homologous genomic region of some FAdV-E strains (amino acid sequence homology, up to 82%). Thus, although FAdV-3 is classified into FAdV-D, the genomic structure of FAdV-3 appears to result from multiple heterotypic and heterologous recombination events. This study highlights the unique origin of FAdV-3. Full article

Feline infectious peritonitis virus (FIPV) remains as one of the leading causes of morbidity and mortality in young cats from shelters and catteries worldwide. Since little is known about the molecular characteristics of currently circulating FIPV strains in Long Island, New York, samples from two shelter cats submitted to the Pathology Diagnostic Services of the Long Island University College of Veterinary Medicine, with gross and microscopic lesions consistent with those of FIP were processed for virus isolation, molecular characterization and full-length genome decoding. The younger shelter cat, a 1-year-old male (A15) was found dead without previous signs of illness. Postmortem examination revealed gross and microscopic lesions characterized by vasculitis, necrosis, hemorrhage, and pyogranulomatous inflammation confined to the colon and associated lymph nodes. The second cat, a 7-year-old spayed female (A37) had an identical clinical history and similar but widespread lesions, including fibrinous peritoneal effusion, cecal, colonic, renal, and hepatic involvement. The gross and microscopic diagnosis of FIP in these cats was confirmed by immunohistochemistry (IHC) demonstration of feline coronavirus antigen using mouse anti-FIPV3-70 monoclonal antibody. Virus isolation from saved frozen kidney and colon tissue was performed through several subsequent blind passages in MDCK and Vero cell lines. Confirmation of the FIPV isolation was done through qRT-PCR, IFA, western blot using N protein antibodies, and NGS of the full-length genome sequencing. The full-length genome sequences of the virus isolate from the two cats were decoded using next-generation sequencing (NGS) and deposited in the GenBank as accession numbers PQ192636 and PQ202302. The genome size of these isolates was (29355 and 29321) nucleotides (nt) in length, respectively. While their genome organization was consistent with other FIPV genomes as follows (5’UTR-ORF1ab-S-3abc-M-E-7b-3’UTR-3’), marked differential mutations were observed in the ORF1a/b, S, 3Abc, and 7b protein genes of the two FIPV isolates. One notable deletion of 34 nucleotides was observed in the 7b genes of one of these isolates but was absent in the other. We confirmed the potential recombination events during the evolution of those two FIPV field isolates with the potential parent virus as FECoV-US isolated in 1970 and the potential minor parent as the Canine coronavirus. Our results provide a comprehensive molecular analysis of two novel FIPV isolates causing fatal disease in shelter cats from Long Island. Diagnostic surveillance with molecular characterization and sequencing analysis of circulating FIPV strains within animal shelters may help early detect unique emerging clinical and pathological manifestations of the disease and develop more targeted prophylactic and therapeutic approaches to control it. Full article

Naked barley (Hordeum vulgare var. nudum) is a staple food crop, contributing significantly to global food security. Understanding genetic diversity will facilitate its effective conservation and utilization. To determine genetic diversity and its distribution within and among varieties, we characterized 30 naked barley varieties from Tibet, representing the traditional, modern, and germplasm-resources-bank gene pools, by analyzing SSR molecular fingerprints. The results demonstrate abundant genetic diversity in Tibetan naked barley varieties, particularly those in the traditional gene pool that holds much more private (unique) alleles. Principal coordinates and STRUCTURE analyses indicate substantial deviation of the modern varieties from the traditional and germplasm-resources-bank varieties. A considerable amount of seed mixture is detected in the modern varieties, suggesting the practices of using mixed seeds in modern-variety cultivation. Cluster analyses further indicate the narrow genetic background of the modern varieties, likely due to the limited number of traditional/germplasm-resources-bank varieties applied in breeding. Relationships between increases in genetic diversity and sample sizes within naked barley varieties highlight the importance of effective sampling strategies for field collections. The findings from this study have important implications for the sustainable utilization and effective conservation of different types of naked barley germplasm, both in Tibet and in other regions around the world. Full article

Specialized botanical gardens such as a rose garden, or rosarium, play a significant role due to their multifunctional nature surpassing simple gene bank assembly. Thus, this study conducted a detailed analysis of a rose garden through field and desk research, SWOT analysis, and ecosystem services assessment, aiming to determine the major strengths and opportunities, as well as weaknesses and threats that can promote or constrain the establishment of the first national rosarium in Serbia. After the analysis, the need for complete green area reconstruction arose to achieve both attractiveness and usefulness. Featuring old varieties, wild species, and companies’ own specific rose collections, the proposed garden has the potential to contribute major ecosystem services reflected in environmental, societal, and economic purposes. Owing to the uniqueness of the breeding program and collections created in the past decade, specific thematic parts—open field or greenhouse classroom, ‘roses under the glass bell’, abundant river flow, pollinators’ shelter, taste garden, and scent garden—are envisaged in the future exemplary rosarium that would not be only a classroom but a showroom for interested nurseries, small-scale functional food producers, flower shops, or amateur gardeners that would become aware of new cultivars and expand their marketing and utilization. Full article

Myrteae is the most species-rich tribe in the Myrtaceae family, represented by a range of socioeconomically and ecologically significant species. Many of these species, including commercially relevant ones, have become increasingly threatened in the wild, and now require conservation actions. Tissue culture presents an appropriate in vitro tool to facilitate medium-term and long-term wild germplasm conservation, as well as for commercial propagation to maintain desirable traits of commercial cultivars. So far, tissue culture has not been extensively achieved for Myrteae. Here, tissue culture for Eugenia, one of the most species-rich genera in Myrteae, is reviewed, giving directions for other related Myrteae. This review also focuses on ex situ conservation of Australian Myrteae, including using seed banking and field banking. Despite some progress, challenges to conserve these species remain, mostly due to the increasing threats in the wild and limited research. Research into in vitro methods (tissue culture and cryopreservation) is paramount given that at least some of the species are ‘non-orthodox’. There is an urgent need to develop long-term in vitro conservation for capturing the remaining germplasm of threatened Myrteae. Full article

Newcastle disease (ND) is caused by virulent strains of avian paramyxovirus type 1, also known as Newcastle disease virus (NDV). Despite vaccination, the frequency of reported outbreaks in Ethiopia has increased. From January to June 2022, an active outbreak investigation was conducted in six commercial chicken farms across areas of central Ethiopia to identify the circulating NDV strains. Thirty pooled tissue specimens were collected from chickens suspected of being infected with NDV. A questionnaire survey of farm owners and veterinarians was also carried out to collect information on the farms and the outbreak status. NDV was isolated using specific-pathogen-free (SPF)-embryonated chicken eggs and detected using haemagglutination and the reverse transcriptase–polymerase chain reaction (RT–PCR). The genotype and virulence of field NDV isolates were determined using phylogenetic analysis of fusion (F) protein gene sequences and the mean death time (MDT) test in SPF-embryonated chicken eggs. The questionnaire results revealed that ND caused morbidity (23.1%), mortality (16.3%), case fatality (70.8%), and significant economic losses. Eleven of thirty tissue specimens tested positive for NDV using haemagglutination and RT–PCR. The MDT testing and sequence analysis revealed the presence of virulent NDV classified as genotype VII of class II velogenic pathotype and distinct from locally used vaccine strains (genotype II). The amino acid sequences of the current virulent NDV fusion protein cleavage site motif revealed ¹¹²RRQKR↓F¹¹⁷, unlike the locally used avirulent vaccine strains (¹¹²GRQGR↓L¹¹⁷). The epidemiological data, MDT results, cleavage site sequence, and phylogenetic analysis all indicated that the present NDV isolates were virulent. The four NDV sequences were deposited in GenBank with accession numbers F gene (PP726912-15) and M gene (PP726916-19). The genetic difference between avirulent vaccine strains and circulating virulent NDV could explain the low level of protection provided by locally used vaccines. Further studies are needed to better understand the circulating NDV genotypes in different production systems. Full article

The protection of biological diversity in nature and in agriculture, including the production of ornamental crops, has become increasingly important in Poland as well as worldwide. The Convention on Biological Diversity, signed in 1992 at the Earth Summit of the UN in Rio de Janeiro and ratified by the Polish government in 1995, imposed new regulations related to the protection of nature and the genetic resources of cultivated crops in Poland. The conservation of the genera, varieties and cultivars of ornamental geophytes—a group of plants of great interest from a botanical and physiological, but also a horticultural point of view—takes place in situ (both in nature and in the places of cultivation) and through the establishment of ex situ gene banks and collections. The natural genetic resources of ornamental geophytes include species from the genera Allium, Fritillaria, Gladiolus, Iris, Leucojum, Lilium and Muscari, among others, and more than a dozen species are protected by law due to varying degrees of threats. Botanical gardens play an essential role in the conservation of endangered species. Their activities focus on genus monitoring, managing ex situ gene banks (including National Collections), developing propagation methods and carrying out their reintroduction. In order to protect the national genetic resources of cultivated plants, the National Centre for Plant Genetic Resources at the Plant Breeding and Acclimatisation Institute—National Research Institute, under the auspices of the Ministry of Agriculture and Rural Development, was established. Concerning ornamental geophytes, the National Centre coordinates two field collections of cultivars of the genera Gladiolus, Lilium, Narcissus and Tulipa, which are of great economic importance and have a long tradition of breeding in Poland. The first one is located at the National Institute of Horticultural Research in Skierniewice (central Poland), and the second one is at the Experimental Substation of Variety Testing in Lisewo (northern Poland). The history of tulip collections in Poland dates back to the 1960s. At that time, the first breeding work for this species began. The collection of bulbous crops in Skierniewice is currently one of the largest in Poland, with a total of 934 accessions. Most of them are tulips (522) and lilies (222). Other plants in the collection in Skierniewice are gladiolus and narcissus. The most valuable accessions are grown under special protection (tunnels with dense nets) to guard against insects and maintain a mild climate inside. The genetic resources of the ornamental bulb plant collection in Lisewo currently consist of 611 accessions, mainly tulips (358), daffodils (121) and gladioli (132). All bulbous crops in both collections (Skierniewice and Lisewo) are grown in accordance with all principles of agrotechnics (negative field selection, fertilisation, soil maintenance). A particularly important task of botanical gardens, universities, research institutes and the National Centre is leading research on the methods of storage for survival organs, in vitro cultures and cryopreservation. We have discovered that the various activities for the species conservation of ornamental geophytes require a great deal of constantly deepening knowledge and extraordinary measures, including frequent monitoring of the effects of the applied measures. Full article