Mastodawn

Development of EST-SSR Markers Based on Transcriptome Sequencing in Kodo millet (Paspalum scrobiculatum l.) - #kodomillet #genome #transcriptome #RTPCR #cDNAlibrary #ESTSSR #cDNA #Paspalumscrobiculatum #Paspalum - https://link.springer.com/article/10.3103/S0095452725060040

Development of EST-SSR Markers Based on Transcriptome Sequencing in Kodo millet (Paspalum scrobiculatum l.) - Cytology and Genetics

Abstract Kodo millet (Paspalum scrobiculatum L.) (2n = 4x = 40) mostly found in dry and semi-arid parts of Africa and Asia, also known as miraculous millets, is a staple food and a nutrient-security crop. It’s commonly known that kodo millet has the strongest tolerance to drought. Little study was done on high throughout genomic studies in relation to the creation of millets improved by genomics. In the present investigation, 21 080 571 total reads of sequence data were included in the 6.55 gigabytes of raw sequence that was produced following the genome sequencing run. After utilizing FastQC to verify the raw data quality, a total sequence of 1 087 611 and 578 123 572 bp was obtained. Three RNA samples from mature, blooming, and vegetative specimens were gathered, and the high-throughput Ion torrent sequencing method was applied to the sequencing process. In the vegetative stage, there were 1, 34, 40, and 824 raw readings; in the reproductive and mature stages, there were 1, 66, 35, 843 reads and 97, 43, 629 bp reads, respectively. At three distinct stages, the average read length was 131.6, 137.6, and 148.8 bp, in that order. The interface modules BatchPrimer3 (version 1.0) were used to construct the SSR and EST-SSR primers. Four FASTA files including contigs from the transcriptome and genome were utilized to identify SSRs. A total of thirty SSRs were found, with GC% and Tm ranges of 40–70 and 58–62°C, respectively. Of the 30 SSR and EST-SSR primers that were used for validation, only 17 were able to amplify the DNA from 27 distinct types of Kodo millet. 24 bands were obtained from the PCR amplification of 27 distinct types. We think that these findings may be applied in the future as possible candidates to enhance this significant staple crop.

SpringerLink

Cytology and Genetics Mar 17

Comparative Analysis of the Complete Mitochondrial Genome of Apis laboriosa (Insecta: Hymenoptera: Apidae) - #Apislaboriosa #completemitogenome #phylogeneticrelationship #Apis #mitogenome #Apidae #mitochondria #mitochondrialgenome - https://link.springer.com/article/10.3103/S0095452725060076

Comparative Analysis of the Complete Mitochondrial Genome of Apis laboriosa (Insecta: Hymenoptera: Apidae) - Cytology and Genetics

Abstract Apis laboriosa Smith is the largest bee in the genus Apis, and it is mainly distributed in Yunnan and Tibet regions in China. In this study, two complete mitogenomes of A. laboriosa from Luding and Dehong were obtained through Illumina sequencing, and the phylogenetic relationship among different geographical populations of A. laboriosa was determined. The entire mitogenomes of A. laboriosa are 15 546 (Luding) and 15 239 (Dehong) bp in length, respectively. The A. laboriosa mitogenome contains 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes, and a control region rich in A + T. The maximum likelihood phylogenetic tree using 13 PCGs reveals that A. laboriosa from Dehong and Shangri-La clustered together and form a sister taxon to Luding. This study provides data for an in-depth exploration of the genetic diversity of A. laboriosa and layes a scientific foundation for the conservation of this species.

SpringerLink

Cytology and Genetics Mar 10

Bioremediation of Ecosystems Using Microbiological Technologies - #microbiome #bioremediation #biosorption #bioaccumulation #toxicmetals #microbiology #bioremediation - https://link.springer.com/article/10.3103/S0095452725060064

Bioremediation of Ecosystems Using Microbiological Technologies - Cytology and Genetics

Abstract The disposal of toxic metals and munitions waste represents a critical component of environmental safety and ecosystem protection. Developing new methods and technologies that can rapidly and effectively mitigate contamination and diminish its impact on the environment and human health remains an urgent priority. As an alternative to conventional physicochemical approaches for decontaminating polluted sites, bioremediation has emerged as a promising method. This process involves the transformation of hazardous chemical compounds containing toxic metals into nontoxic or less toxic substances through the activity of diverse microorganisms. Understanding bioavailability is essential for assessing the potential toxicity of metallic elements and their compounds, as well as for designing effective strategies for ecological remediation of contaminated areas. The bioavailability of metals depends on their capacity to be absorbed, chemically transformed, or metabolized by microorganisms within the contaminated environment. The primary factors influencing metal bioavailability include the chemical form of the metal, the redox potential and pH of the environment, and its ecological and physicochemical characteristics such as temperature, substrate availability, moisture, and aeration. Microorganisms themselves play a significant role in enhancing metal bioavailability through environmental acidification (protonolysis), chelate formation that binds metals, and enzymatic synthesis capable of altering the chemical state of metals via oxidation or reduction. This article examines the key processes through which microorganisms achieve bioremediation of toxic metals, namely biosorption, bioaccumulation, mobilization, and immobilization.

SpringerLink

Cytology and Genetics Mar 3

Plant Systems as Platforms for the Production of Interferon Alpha and its Application - #molecularfarming #pharmaceuticalprotein #recombinanthumaninterferonα2b #oraldelivery #edibleplant #transgenicplants - https://link.springer.com/article/10.3103/S0095452725060088

Plant Systems as Platforms for the Production of Interferon Alpha and its Application - Cytology and Genetics

Abstract Interferon alpha (IFN) is a small glycosylated polypeptide used in the treatment of cancer, immune disorders, and various other related diseases. Demands for human and veterinary medicine in safe sources of this remedy motivate investigations for new interferon production systems. Plants expressing IFN can become an excellent substitution for traditional bacterial systems. Among the advantages of plant-based human IFN are correct glycosylation, lack of toxins and pathogens, and unexpansive production costs. The effectiveness of different plant-based systems for IFN production is compared. Oral administration of IFN produced in edible plants is a promising direction for the lack of demand for purification of the protein, its effective storage, and safe mode of the protein delivery to the competent tissues of a treated organism. The advantages of edible plants as fortified vectors for interferon delivery are discussed. Examples of oral administration of IFN from different production systems are compared. Oral usage of human IFN from various production systems in veterinary is viewed.

SpringerLink

Cytology and Genetics Feb 17

Nanoparticles of Different Nature in Plant Biotechnology: Effectiveness, Safety, and Prospects of Application - #metalnanoparticles #biosynthesis #fullerenes #graphene #singlewallednanotubes #plants #stress #nanoparticles #NPs #multiwallednanotubes #nanotubes #biotechnology - https://link.springer.com/article/10.3103/S009545272506009X

Nanoparticles of Different Nature in Plant Biotechnology: Effectiveness, Safety, and Prospects of Application - Cytology and Genetics

Abstract Data on the biological activity of nanoparticles of various natures—metallic (Ag, Cu, Zn, Ti), silicon (Si), and carbon nanomaterials—on plants are summarized. Their influence on the growth, development, and resistance of plants to biotic and abiotic stresses at the molecular, cellular, and organismal levels is considered. Special attention is paid to nanoparticles obtained by “green” synthesis, which are characterized by high bioactivity, biocompatibility, stability, and environmental safety. The physiological and biochemical effects of the action of nanoparticles are analyzed, in particular their influence on seed germination, photosynthetic activity, antioxidant system, expression of stress-induced genes, etc. It has been demonstrated that biosynthesized nanoparticles cause a positive effect without toxicity in most cases, while chemically synthesized analogues can cause significant negative changes in plants. The advantages of biosynthesized nanoparticles are emphasized: their high level of environmental safety, fungicidal, antibacterial, and antiviral activity. The need for further research to optimize dosage, methods of application, and assessment of long-term effects of nanomaterials, taking into account the balance between efficiency and environmental safety, is emphasized. The obtained results demonstrate the prospects for the use of nanomaterials in cell biology, physiology, and biotechnology of plants.

SpringerLink

Cytology and Genetics Jan 29

NOS2 and PTGS2 Genes’ Expression during Oxidative Stress in the Blood of Patients with Osteoarthritis after SARS-CoV-2 Infection - #SARSCoV2 #osteoarthritis #inflammation #oxidativestress #NOS2 #PTGS2 #geneexpression - https://link.springer.com/article/10.3103/S0095452725060039

NOS2 and PTGS2 Genes’ Expression during Oxidative Stress in the Blood of Patients with Osteoarthritis after SARS-CoV-2 Infection - Cytology and Genetics

Abstract It is known that, aside from lung parenchyma damage, the SARS-CoV-2 virus can compromise other organ systems and complicate the condition of pati ents with comorbid pathologies. A special group of such patients consists of people suffering from chronic illnesses, namely osteoarthritis. An important role in osteoarthritis pathogenesis is played by oxidative stress developed due to oxidant–antioxidant equilibrium disturbance and inflammation induction. The aim of the presented work was the estimation of several parameters of free radical process intensity and to analyze NOS2 and PTGS2 genes’ expression in blood of patients with osteoarthritis after beating the SARS-CoV2 infection. All participants were divided into three experimental groups with the same average age in every group. The first group (n = 25) included conditionally healthy people. The second group (n = 25) consisted of patients with II–III-degree knee joint osteoarthritis with the exclusion of possible concomitant coronavirus infection presence by performing epidemiological anamnesis of every patient as well as contacts with people having active COVID-19 disease. The third group (n = 25) were II–III-degree knee joint osteoarthritis patients, having already beaten COVID-19 illness of light or medium severity 6–9 months ago. The following parameters were elucidated: in blood plasma—superoxide radical and hydrogen peroxide content and concentration of lipid peroxidation products; in whole blood—nitrogen oxide synthase (NOS2) and cyclooxygenase (PTGS2) gene expression. The results showed the increase in active oxygen radical content and lipid peroxidation product concentration in blood plasma from knee joint osteoarthritic patients also having active SARS-CoV-2 infection, and these increases were more pronounced compared to the patient group with knee joint osteoarthritis only. In blood, it was shown that the expression of the NOS2 gene increased (by 2.5 times in patients with osteoarthritis of the knee joints compared to healthy donors and by 1.3 times in patients with osteoarthritis who had COVID-19, compared to the group of patients with osteoarthritis only) and the PTGS2 gene (by 2.3 times in patients with osteoarthritis compared to healthy volunteers and by 1.3 times in patients with osteoarthritis after SARS-CoV2 infection compared to the group of patients with osteoarthritis), which is associated with the development of oxidative stress and inflammation. The shown research parameter changes indicate more active intensification of free radical processes in blood of osteoarthritis patients that had beaten SARS-CoV2. Taking into consideration the obtained results, the assumption can be made about more severe disease progress and possibility of complications in osteoarthritis patients after SARS-CoV-2. Hence, these patients require a personalized approach in both COVID-19 and further osteoarthritis treatment after recovering from coronavirus infection.

SpringerLink

Cytology and Genetics Jan 15

Involvement of Nitric Oxide in γ-Aminobutyric Acid-Induced Cellular Mechanisms of Wheat Seedling Adaptation to Water Deficit - #γaminobutyricacid #nitricoxide #oxidativestress #antioxidantsystem #osmolytes #amylase #droughtresistance #Triticumaestivum #Triticum #wheat #waterdeficit #GABA - https://link.springer.com/article/10.3103/S0095452725060106

Involvement of Nitric Oxide in γ-Aminobutyric Acid-Induced Cellular Mechanisms of Wheat Seedling Adaptation to Water Deficit - Cytology and Genetics

Abstract γ-Aminobutyric acid (GABA) is one of the key stress metabolites involved in the functioning of the plant cell signaling network. However, its functional relationships with main signaling molecules, particularly nitric oxide (NO), are not well understood. This study aimed to determine NO’s involvement in GABA’s stress-protective effect on wheat seedlings (Triticum aestivum L., Etana cultivar) under model drought conditions (13% PEG 6000). Priming grains with a 0.5 mM GABA solution or a 0.1 mM solution of the NO donor sodium nitroprusside (SNP) increased germination energy, seed germination, and water content in seedlings under stressful conditions. Additionally, GABA and SNP treatment mitigated the inhibitory effect of drought on the accumulation of root and shoot biomass. Osmotic stress increased NO content in shoots, and priming with GABA and SNP enhanced this effect. Treatment with the nitric oxide scavenger methylene blue (MB, 0.1 mM) eliminated the increase in NO content caused by stress or GABA action. MB also negated the positive effects of GABA on growth processes. Under the action of GABA and SNP, total amylase activity in grains and soluble carbohydrate content in shoots increased under stressful conditions; MB eliminated GABA’s effect on these parameters. Under the model drought, the content of oxidative stress markers (superoxide anion radical, hydrogen peroxide, and malondialdehyde) increased in shoots, but pretreatment of grains with GABA or SNP significantly reduced these effects. Osmotic stress caused an increase in activity of catalase and guaiacol peroxidase in shoots. Preliminary priming with GABA, SNP, and MB did not affect the nature of the changes in activity of these antioxidant enzymes caused by model drought. Meanwhile, superoxide dismutase activity remained unchanged following exposure to the model drought; however, pretreatment seeds with GABA, SNP, and MB increased the enzyme activity. Priming seeds with GABA and SNP increased the total content of phenolic compounds in shoots and preserved the anthocyanin pool under stressful conditions, while MB treatment eliminated these effects. It was concluded that the enhancement of grain germination and seedling growth induced by GABA priming under model drought conditions is largely due to NO-mediated modulation of carbohydrate and secondary compound metabolism.

SpringerLink

Cytology and Genetics Dec 16

Genome-Wide Identification and Diversity Analysis of DGAT1, DGAT2, LPAT2, WRI1, FAD2, FAD3, and FAE1 Genes in Terms of Breeding Importance in Brassica carinata - #Brassicacarinata #fattyacidbiosynthesisgenes #triacylglycerolsynthesisgenes #genomewideresearch #SSR #breeding #Brassica #fattyacids #DGAT1 #DGAT2 #LPAT2 #WRI1 #FAD2 #FAD3 #FAE1 #intron #promoter #molecularmarkers #markerassistedbreeding - https://link.springer.com/article/10.3103/S0095452725060027

Genome-Wide Identification and Diversity Analysis of DGAT1, DGAT2, LPAT2, WRI1, FAD2, FAD3, and FAE1 Genes in Terms of Breeding Importance in Brassica carinata - Cytology and Genetics

Abstract Abyssinian mustard, or carinata (Brassica carinata), is currently considered one of the most promising alternative oilseed crops, particularly for liquid biofuel production. Breeding and genetic engineering studies that enhance seed oil quality and yield have become increasingly important as the agricultural use of this crop expands. Leveraging publicly available genomic resources for carinata simplifies crop improvement and enables a targeted focus on loci or genes involved in lipid and fatty acid biosynthesis. This study aimed to conduct a genome-wide identification and comprehensive analysis of genes regulating fatty acid and neutral lipid synthesis (DGAT1, DGAT2, LPAT2, WRI1, FAD2, FAD3, and FAE1) in the allopolyploid species B. carinata. A total of 24 genes were identified, with each enzyme encoded by multiple homoeologs. These genes shared a high degree of sequence similarity but differed in noncoding regions (introns and promoter sequences), which allowed us to identify several microsatellite loci specific to each gene family. The results support the development of highly accurate molecular markers for marker-assisted breeding, which will accelerate the creation of B. carinata varieties with enhanced oil quality and increased seed oil content.

SpringerLink

Cytology and Genetics Dec 11

Identification of New Gliadin Alleles of Mutant, Recombinant, and Introgressive Origin in Bread Wheat Varieties - #prolamin #diversity #Triticumaestivum #Triticumdicoccum #GliA1 #GliB1 #GliA3 #GliD1 #APAGE #gliadinblock #cultivar #commonwheat #glutenproteins #Triticum #wheat #gluten #mutant #breadwheat - https://link.springer.com/article/10.3103/S0095452725060052

Identification of New Gliadin Alleles of Mutant, Recombinant, and Introgressive Origin in Bread Wheat Varieties - Cytology and Genetics

Abstract A special feature of the major gliadin loci in wheat is multiple allelism. Catalogs of gliadin blocks encoded by alleles at the gliadin loci in bread wheat were compiled and are regularly updated. When analyzing gliadin patterns of Ukrainian bread wheat varieties and F2 seeds, the authors identified new alleles at the Gli-A1, Gli-B1, and Gli-A3 loci that had not been previously described in the literature. Gliadin blocks encoded by alleles at the Gli-D1 locus that were described previously but are absent in the latest published catalogues are also presented. Acid polyacrylamide gel electrophoresis of gliadins was performed by the procedure developed by the authors. New alleles were given temporary designations. At the Gli-B1 locus, new alleles of recombinant origin, Gli-B1fg* and Gli-B1eg*, and of mutant origin, Gli-B1ba*, were identified, and alleles of introgressive origin were also detected: Gli-B1xm* (also identified in T. dicoccum accessions), Gli-B1bl* (Gli-B1b with two linked genes, probably from Ae. variabilis, according to the variety Lastivka Odeska pedigree), and Gli-B1wb* (1BL.1RS with a block of ω-secalins as in the variety Amigo). The patterns of Gli-D1 alleles that are not present in the published catalogue of gliadin alleles are also given: Gli-D1ct* from Ae. tauschii and Gli-D1x, apparently of mutant origin, corresponding to the GLD 1D10 block, which was previously identified in some Odessa varieties, in particular Olvia and Prokofievka. At Gli-A1, two new alleles, Gli-A1ag* and Gli-A1ah*, were identified, which were formed via combination with certain alleles at the minor locus Gli-A6. The allele Gli-A3e, which encodes two ω-gliadins, was identified at the minor locus Gli-A3. This allele, which is widespread among spring bread wheat varieties, seems to be extant as it was also identified in T. dicoccum.

SpringerLink

Cytology and Genetics Dec 4

Mutations in Rye (Secale cereale L.) - #ryemutantvariety #selffertilitygenes #meiotic #chlorophyllmutants #anthocyaninless #morphologicalmutations #rye #selffertility #dwarfmutants #Secalecereale #Secale - https://link.springer.com/article/10.3103/S0095452725050044

Mutations in Rye (Secale cereale L.) - Cytology and Genetics

Abstract Mutations found in cultivated rye were grouped as follows: self-fertility genes, meiotic mutants, embryo lethality and enzyme-specific deficiency genes, chlorophyll mutants, dwarf mutants, morphological mutations, anthocyaninless and seed color genes. The traits in the mutants were controlled by recessive genes excepted for the dominant dwarfs, self-fertile genes and some morphological mutations. All the meiotic mutations caused partial or complete spike sterility and were maintained in a heterozygous state. Chlorophyll mutants were divided into lethal and semi-lethal, with the difference that the latter usually reach maturity. Dwarf mutants formed one of the largest groups, in which the dwarfism character of 15 numbers was determined by a single recessive gene. The response to gibberellic acid was found in fourteen mutants, including the dominant dwarfs. Mutations in morphological traits were also governed by recessive genes excepted for the hairy leaf sheath, spring growth habit and waxy endosperm. The use of self-fertile mutants in rye allowed to study the genetics of inbred lines with different seed color (yellow, green, brown, and violet) depending mainly on the combination of the recessive alleles of Vi, C and Vs genes. The production of more inbred lines led to the identification of various mutations and their subsequent detailed research for enhancing germplasm diversity in cultivated rye.

SpringerLink