Triazole antifungal drug interactions-practical considerations for excellent prescribing.

Systemic antifungal therapy is critical for reducing the mortality from many invasive and chronic fungal infections. Triazole antifungals are the most frequently prescribed antifungals but require attention to dosing and drug interactions. Nearly 600 severe drug-drug interactions and over 1100 moderate interactions requiring dose modifications are described or anticipated with systemic antifungal agents (see https://www.aspergillus.org.uk/antifungal-drug-interactions/). In this article, we address the common and less common, but serious, drug interactions observed in clinical practice with triazole antifungals, including a group of drugs that cannot be prescribed with all or most triazole antifungals (ivabradine, ranolazine, eplerenone, fentanyl, apomorphine, quetiapine, bedaquiline, rifampicin, rifabutin, sirolimus, phenytoin and carbamazepine). We highlight interactions with drugs used in children and new agents introduced for the treatment of haematological malignancies or graft versus host disease (midostaurin, ibrutinib, ruxolitinib and venetoclax). We also summarize the multiple interactions between oral and inhaled corticosteroids and triazole antifungals, and the strategies needed to optimize the therapeutic benefits of triazole antifungal therapy while minimizing potential harm to patients.

Phylogenetic and Evolutionary Analysis of Plant Small RNA 2'-O-Methyltransferase (HEN1) Protein Family.

HUA ENHANCER 1 (HEN1) is a pivotal mediator in protecting sRNAs from 3'-end uridylation and 3' to 5' exonuclease-mediated degradation in plants. Here, we investigated the pattern of the HEN1 protein family evolutionary history and possible relationships in the plant lineages using protein sequence analyses and conserved motifs composition, functional domain identification, architecture, and phylogenetic tree reconstruction and evolutionary history inference. According to our results, HEN1 protein sequences bear several highly conserved motifs in plant species retained during the evolution from their ancestor. However, several motifs are present only in Gymnosperms and Angiosperms. A similar trend showed for their domain architecture. At the same time, phylogenetic analysis revealed the grouping of the HEN1 proteins in the three main super clads. In addition, the Neighbor-net network analysis result provides some nodes have multiple parents indicating a few conflicting signals in the data, which is not the consequence of sampling error, the effect of the selected model, or the estimation method. By reconciling the protein and species tree, we considered the gene duplications in several given species and found 170 duplication events in the evolution of HEN1 in the plant lineages. According to our analysis, the main HEN1 superclass mostly showed orthologous sequences that illustrate the vertically transmitting of HEN1 to the main lines. However, in both orthologous and paralogs, we predicted insignificant structural deviations. Our analysis implies that small local structural changes that occur continuously during the folds can moderate the changes created in the sequence. According to our results, we proposed a hypothetical model and evolutionary trajectory for the HEN1 protein family in the plant kingdom.

Comparative phylogenetic analysis of SARS-CoV-2 spike protein-possibility effect on virus spillover.

Coronavirus disease 2019 has developed into a dramatic pandemic with tremendous global impact. The receptor-binding motif (RBM) region of the causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), binds to host angiotensin-converting enzyme 2 (ACE2) receptors for infection. As ACE2 receptors are highly conserved within vertebrate species, SARS-CoV-2 can infect significant animal species as well as human populations. An analysis of SARS-CoV-2 genotypes isolated from human and significant animal species was conducted to compare and identify mutation and adaptation patterns across different animal species. The phylogenetic data revealed seven distinct phylogenetic clades with no significant relationship between the clades and geographical locations. A high rate of variation within SARS-CoV-2 mink isolates implies that mink populations were infected before human populations. Positions of most single-nucleotide polymorphisms (SNPs) within the spike (S) protein of SARS-CoV-2 genotypes from the different hosts are mostly accumulated in the RBM region and highlight the pronounced accumulation of variants with mutations in the RBM region in comparison with other variants. These SNPs play a crucial role in viral transmission and pathogenicity and are keys in identifying other animal species as potential intermediate hosts of SARS-CoV-2. The possible roles in the emergence of new viral strains and the possible implications of these changes, in compromising vaccine effectiveness, deserve urgent considerations.

Purification of an antiviral protein from the seeds of quinoa (Chenopodium quinoa Willd.) and characterization of its antiviral properties.

Plant viral pathogens cause damaging diseases in many agriculture systems, and emerging viral infections are a serious threat for providing adequate food to a continuously growing population. Recent studies of biogenic substances have provided new opportunities for producing novel antiviral agents. The present work has been conducted to evaluate the antiviral activity of quinoa (Chenopodium quinoa Willd.) seeds crude extract. The antiviral activity was retained in different buffer solutions of various pH ranges (5.2-8.5) and remained after the diafiltration process. The putative virus inhibitor was sensitive to treatment with sodium dodecyl sulfate and trichloroacetic acid. An antiviral protein with ~ 25 kDa molecular weight was isolated from the seed quinoa extract using ammonium sulfate precipitation, anion and cation exchange chromatography. The purified protein (Quinoin-I) significantly inhibited TMV on tobacco leaves with an IC50 value at a 6.81 µg/ml concentration. Enzyme activity assay revealed the RNase activity of Quinoin-I, and this feature was retained in the presence of ß-mercaptoethanol and ethylene diamine tetraacetic acid. This antiviral protein has been shown as a promising leading molecule for further development as a novel antiviral agent.

Chimeric Hepatitis B core virus-like particles harboring SARS-CoV2 epitope elicit a humoral immune response in mice.

BACKGROUND: Virus-like particles are an interesting vector platform for vaccine development. Particularly, Hepatitis B virus core antigen has been used as a promising VLP platform. It is highly expressed in different recombinant expression systems, such as E. coli, and self-assembled in vitro. It effectively improves the immunogenicity of foreign antigenic epitopes on its surface. Various foreign antigens from bacteria, viruses, and protozoa can be genetically inserted into such nanoparticles. The effective immunogenicity due to VLP vaccines has been reported. However, no research has been performed on the SARS-CoV2 vaccine within this unique platform through genetic engineering. Considering the high yield of target proteins, low cost of production, and feasibility of scaling up, E. coli is an outstanding expression platform to develop such vaccines. Therefore, in this investigation, we planned to study and develop a unique HBc VLP-based vaccine against SARS-Cov2 utilizing the E. coli expression system due to its importance. RESULTS: Insertion of the selected epitope was done into the major immunodominant region (MIR) of truncated (149 residues) hepatitis B core capsid protein. The chimeric protein was constructed in PET28a+ and expressed through the bacterial E. coli BL21 expression system. However, the protein was expressed in inclusion body forms and extracted following urea denaturation from the insoluble phase. Following the extraction, the vaccine protein was purified using Ni2 + iminodiacetic acid (IDA) affinity chromatography. SDS-PAGE and western blotting were used to confirm the protein expression. Regarding the denaturation step, the unavoidable refolding process was carried out, so that the chimeric VLP reassembled in native conformation. Based on the transmission electron microscopy (TEM) analysis, the HBC VLP was successfully assembled. Confirming the assembled chimeric VLP, we explored the immunogenic effectivity of the vaccine through mice immunization with two-dose vaccination with and without adjuvant. The utilization of adjuvant was suggested to assess the effect of adjuvant on improving the immune elicitation of chimeric VLP-based vaccine. Immunization analysis based on anti-spike specific IgG antibody showed a significant increase in antibody production in harvested serum from immunized mice with HBc-VLP harboring antigenic epitope compared to HBc-VLP- and PBS-injected mice. CONCLUSIONS: The results approved the successful production and the effectiveness of the vaccine in terms of humoral IgG antibody production. Therefore, this platform can be considered a promising strategy for developing safe and reasonable vaccines; however, more complementary immunological evaluations are needed.

Successful use of Nicotiana tabacum hairy roots for the recombinant production of Cecropin A peptide.

Cecropin A, as an antimicrobial peptide (AMP), is possible to use in medical and agricultural fields as a new and safe biocontrol agent. Therefore, it is highly necessary to find a cost-effective and scalable approach to generate a large scale of it. In this research, the Agrobacterium rhizogenes strain ATCC 15834 was used to transfer the Cecropin A gene to the Nicotiana tabacum. After confirmation of transgenic hairy roots, the antibacterial activity of purified Cecropin A peptide was measured using the agar gel diffusion method. Successful transforming of Cecropin A was confirmed at the RNA and protein levels in hairy root cells using RT-PCR and enzyme-linked immunosorbent assay (ELISA), respectively. The highest Cecropin A amount was detected in line 4 of the transgenic lines using ELISA in comparison with the nontransgenic line. Subsequently, the antimicrobial activity of Cecropin A extracted from line 4 showed the highest inhibition activity against Aspergillus niger. Besides, this activity was stable against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Candida albicans pathogens after 7 days. The recombinant production of Cecropin A AMP had a yield of 63.81 µg/g of fresh weight. According to a significant yield, this system can be used to produce the Cecropin A peptide for pharmacological and food science applications.

New insights into the evolution of SPX gene family from algae to legumes; a focus on soybean.

BACKGROUND: SPX-containing proteins have been known as key players in phosphate signaling and homeostasis. In Arabidopsis and rice, functions of some SPXs have been characterized, but little is known about their function in other plants, especially in the legumes. RESULTS: We analyzed SPX gene family evolution in legumes and in a number of key species from algae to angiosperms. We found that SPX harboring proteins showed fluctuations in domain fusions from algae to the angiosperms with, finally, four classes appearing and being retained in the land plants. Despite these fluctuations, Lysine Surface Cluster (KSC), and the third residue of Phosphate Binding Sites (PBS) showed complete conservation in almost all of SPXs except few proteins in Selaginella moellendorffii and Papaver sumniferum, suggesting they might have different ligand preferences. In addition, we found that the WGD/segmentally or dispersed duplication types were the most frequent contributors to the SPX expansion, and that there is a positive correlation between the amount of WGD contribution to the SPX expansion in individual species and its number of EXS genes. We could also reveal that except SPX class genes, other classes lost the collinearity relationships among Arabidopsis and legume genomes. The sub- or neo-functionalization of the duplicated genes in the legumes makes it difficult to find the functional orthologous genes. Therefore, we used two different methods to identify functional orthologs in soybean and Medicago. High variance in the dynamic and spatial expression pattern of GmSPXs proved the new or sub-functionalization in the paralogs. CONCLUSION: This comprehensive analysis revealed how SPX gene family evolved from algae to legumes and also discovered several new domains fused to SPX domain in algae. In addition, we hypothesized that there different phosphate sensing mechanisms might occur in S. moellendorffii and P. sumniferum. Finally, we predicted putative functional orthologs of AtSPXs in the legumes, especially, orthologs of AtPHO1, involved in long-distance Pi transportation. These findings help to understand evolution of phosphate signaling and might underpin development of new legume varieties with improved phosphate use efficiency.

A short overview of CRISPR-Cas technology and its application in viral disease control.

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) together with CRISPR-associated (Cas) proteins have catalysed a revolution in genetic engineering. Native CRISPR-Cas systems exist in many bacteria and archaea where they provide an adaptive immune response through sequence-specific degradation of an invading pathogen's genome. This system has been reconfigured for use in genome editing, drug development, gene expression regulation, diagnostics, the prevention and treatment of cancers, and the treatment of genetic and infectious diseases. In recent years, CRISPR-Cas systems have been used in the diagnosis and control of viral diseases, for example, CRISPR-Cas12/13 coupled with new amplification techniques to improve the specificity of sequence-specific fluorescent probe detection. Importantly, CRISPR applications are both sensitive and specific and usually only require commonly available lab equipment. Unlike the canonical Cas9 which is guided to double-stranded DNA sites of interest, Cas13 systems target RNA sequences and thus can be employed in strategies directed against RNA viruses or for transcriptional silencing. Many challenges remain for these approach, including issues with specificity and the requirement for better mammalian delivery systems. In this review, we summarize the applications of CRISPR-Cas systems in controlling mammalian viral infections. Following necessary improvements, it is expected that CRISPR-Cas systems will be used effectively for such applications in the future.

MAP30 transgenic tobacco lines: from silencing to inducing.

BACKGROUND: DNA methylation is one of the most important epigenetic event that regulates gene expression. In addition to DNA methylation, transgene copy number may induce gene silencing. Therefore, the study of these cases is useful for understanding of gene silencing regulation. METHODS AND RESULTS: In this study, the methylation pattern of 35S promoter was investigated in the second generation of MAP30 transgenic tobacco lines. Therefore, the genomic DNA melting curve changes were investigated before and after bisulfite treatment by real time PCR. To determine the exact position of methylation, the samples were sequenced after bisulfite treatment. Observation of decrease in DNA melting curve of expressing line in comparison with silenced line confirmed the presence of DNA methylation in silenced line. In order to induce the MAP30 expression, the silenced line was treated using different concentrations of Azacytidine and green tea extracts. The results showed that all concentrations of green tea extracts for 6 days and the concentrations of 3 and 10 µM Azacytidine for 10 and 3 days could induce the expression of MAP30 in silenced line respectively. Finally, the transgene copy number was estimated using real time PCR, as silenced line contained more than two copies while the lines expressing MAP30 contained only one or two copies. CONCLUSIONS: Finally, we found that the presence of DNA methylation and also multiple gene copy numbers in silenced line have been led to gene silencing. Moreover, the effect of green tea extract on DNA methylation showed incredible results for the first time.

Novel bioactive peptides of Achillea eriophora show anticancer and antioxidant activities.

Despite the limitations of current methods in cancer treatment, the use of bioactive peptides can be as an alternative to treat today. Therefore, isolation and relative purification of bioactive peptides was carried out form Achillea eriophora using a Sep-Pak C18 SPE cartridge and Amicon® Ultra Centrifugal Filters. The presence of desired peptides was checked using RP-HPLC and confirmed using LC-MS. The results of anticancer assay showed that the peptide mixture inhibits the growth of MCF-7 cancerous cell line with the values of IC50, GI50, and LC50 equal to 18.73 ± 0.22, 7.52 ± 0.15, and 56.73 ± 0.18 µg/mL, respectively. It also showed DPPH radical scavenging activity and cupric-ion reducing power with the IC50 value of 5.095 ± 0.23 and 63.3 ± 0.44 µg/mL, respectively. Although flavonoids were present in the sample along with the peptides, their amount was trivial (18.097 ± 1.36 µg/mL). Nevertheless, the results of the LC-MS showed mass-to-charge ratios of 301.17, 261.22, and 243.25, which was a dipeptide or tripeptide in compression to enzyme-digested BSA as a standard. In addition, SEM analysis of the purified peptide mixture showed that it kills the MCF-7 cancerous cell line by creating pores in the membrane. Therefore, it might be valuable to these peptides sequenced and be studied for physicochemical properties. Animal and clinical studies could help its application in drug development.

Identification of key genes associated with secondary metabolites biosynthesis by system network analysis in Valeriana officinalis.

Valeriana officinalis is a medicinal plant, a source of bioactive chemical compounds and secondary metabolites which are applied in pharmaceutical industries. The advent of ethnomedicine has provided alternatives for disease treatment and has increased demands for natural products and bioactive compounds. A set of preliminary steps to answers for such demands can include integrative omics for systems metabolic engineering, as an approach that contributes to the understanding of cellular metabolic status. There is a growing trend of this approach for genetically engineering metabolic pathways in plant systems, by which natural and synthetic compounds can be produced. As in the case of most medicinal plants, there are no sufficient information about molecular mechanisms involved in the regulation of metabolic pathways in V. officinalis. In this research, systems biology was performed on the RNA-seq transcriptome and metabolome data to find key genes that contribute to the synthesis of major secondary metabolites in V. officinalis. The R Package Weighted Gene Co-Expression Network Analysis (WGCNA) was employed to analyze the data. Based on the results, some major modules and hub genes were identified to be associated with the valuable secondary metabolites. In addition, some TF-encoding genes, including AP2/ERF-ERF, WRKY and NAC TF families, as well as some regulatory factors including protein kinases and transporters were identified. The results showed that several novel hub genes, such as PCMP-H24, RPS24B, ANX1 and PXL1, may play crucial roles in metabolic pathways. The current findings provide an overall insight into the metabolic pathways of V. officinalis and can expand the potential for engineering genome-scale pathways and systems metabolic engineering to increase the production of bioactive compounds by plants.

Removal of Basic Orange 2 dye and Ni2+ from aqueous solutions using alkaline-modified nanoclay.

In the present research, the removal of Basic Orange 2 (BO2) dye using alkaline-modified clay nanoparticles was studied. To characterize the adsorbent, XRD, FTIR, FESEM, EDX, BET and BJH analyses were performed. The effect of the variables influencing the dye adsorption process such as adsorbent dose, contact time, pH, stirring rate, temperature, and initial dye concentration was investigated. Furthermore, the high efficiency of Ni2+ removal indicated that it is possible to remove both dye and metal cation under the same optimum conditions. The experimental data were analyzed by Langmuir and Freundlich isotherm models. Fitting the experimental data to Langmuir isotherm indicated that the monolayer adsorption of dye occurred at homogeneous sites. Experimental data were also analyzed with pseudo-first-order, pseudo-second-order, and intra-particle diffusion kinetic equations for kinetic modeling of the dye removal process. The adsorption results indicated that the process follows a pseudo-second-order kinetic model. The thermodynamic parameters of the dye adsorption process such as enthalpy, entropy, and Gibbs free energy changes were calculated and revealed that the adsorption process was spontaneous and endothermic in nature. The results presented the high potential of the modified nanoclay as a cost-effective adsorbent for the removal of BO2 dye and Ni2+ from aqueous medium.

The congenital cataract-causing mutations P20R and A171T are associated with important changes in the amyloidogenic feature, structure and chaperone-like activity of human αB-crystallin.

Cataract is the major reason for human blindness worldwide. α-Crystallin, as a key chaperone of eye lenses, keeps the lenticular tissues in its transparent state over time. In this study, cataract-causing familial mutations, P20R and A171T, were introduced in CRYАB gene. After successful expression in Escherichia coli and subsequent purification, the recombinant proteins were subjected to extensive structural and functional analyses using various spectroscopic techniques, gel electrophoresis, and electron microscopy. The results of fluorescence and Raman assessments suggest important but discreet conformational changes in human αB-Cry upon these cataractogenic mutations. Furthermore, the mutant proteins exhibited significant secondary structural alteration as revealed by FTIR and Raman spectroscopy. An increase in conformational stability was seen in the human αB-Cry bearing these congenital cataractogenic mutations. The oligomeric size distribution and chaperone-like activity of human αB-Cry were significantly altered by these mutations. The P20R mutant protein was observed to loose most of the chaperone-like activity. Finally, these cataractogenic mutant proteins exhibited an increased propensity to form the amyloid fibrils when incubated under environmental stress. Overall, the structural and functional changes in mutated human αB-Cry proteins can shed light on the pathogenic development of congenital cataracts.

Chemical- and microbial-enhanced phytoremediation of cadmium-contaminated calcareous soil by maize.

Phytoremediation is an appropriate technology used to remove pollutants from environment components. A greenhouse trial was conducted to test the hypothesis that application of surfactant levels and inoculation with Pseudomonas fluorescens bacterium and/or Piriformospora indica fungus enhances the phytoremediation of cadmium (Cd). Maize seeds were sown in Cd-polluted soil, and after 2 months Cd status in plant tissues and Cd phytoremediation criteria was determined. Results showed that application of surfactant increased root and shoot dry weight. Mean Cd uptake in roots and shoots increased following the application of 2 and 4 mmol kg-1 Tween 80, respectively. Application of 2 mmol kg-1 Tween 80 increased mean Cd uptake efficiency, while application of 4 mmol kg-1 Tween 80 increased phytoextraction and translocation efficiencies. Inoculation with P. indica and P. fluorescens was mostly effective in increasing Cd uptake and Cd phytoextraction efficiency, respectively. Co-inoculation with P. indica and P. fluorescens had no superiority to application of each inoculant alone. Since most of the Cd remained in roots, phytostabilization is probably the main mechanism controlling Cd phytoremediation by maize. According to the results, application of Tween 80 and inoculation with P. indica and P. fluorescens effectively enhanced phytoremediation of Cd-contaminated soil by maize.

Disruption of the Pathogenicity and Sex Ratio of the Beet Cyst Nematode Heterodera schachtii by Host-Delivered RNA Interference.

The beet cyst nematode (BCN) Heterodera schachtii causes serious damage and yield losses in numerous important crops worldwide. This study examines the efficacy of three types of transgenic Arabidopsis RNA interference (RNAi) lines to decrease the biological activity of this devastating nematode. The first RNAi construct (E1E2-RNAi) targets two nematode endoglucanase genes, which are involved in BCN pathogenicity, the second construct (MSP-RNAi) contains a fragment corresponding to the major sperm protein transcript necessary for BCN development and reproduction, and the third construct (E1E2MSP-RNAi) comprises all three target fragments. Transcript expression profiles of the target genes in all biological stages of the nematode were determined for the initial inoculated population and the resulting progeny. Bioassay data under indoor aseptic cultivation indicated that feeding on these RNAi lines did not affect pathogenic activity and reproductive capacity of the initial population, whereas inoculating the progeny into new transgenic plants corresponding with the lines from which they were recovered reduced the nematode penetration and the number of eggs per cyst. In addition, the male/female ratio increased more than the double, and the effects of RNAi continued in the second generation of the nematodes, because the progeny derived from E1E2-RNAi and E1E2MSP-RNAi lines showed an impaired ability to infect wild-type plants.

Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil.

One of the main challenges in elimination of oil contamination from polluted environments is improvement of biodegradation by highly efficient microorganisms. Bacillus subtilis MJ01 has been evaluated as a new resource for producing biosurfactant compounds. This bacterium, which produces surfactin, is able to enhance bio-accessibility to oil hydrocarbons in contaminated soils. The genome of B. subtilis MJ01 was sequenced and assembled by PacBio RS sequencing technology. One big contig with a length of 4,108,293 bp without any gap was assembled. Genome annotation and prediction of gene showed that MJ01 genome is very similar to B. subtilis spizizenii TU-B-10 (95% similarity). The comparison and analysis of orthologous genes carried out between B. subtilis MJ01, reference strain B. subtilis subsp. subtilis str. 168, and close relative spizizenii TU-B-10 by microscope platform and various bioinformatics tools. More than 88% of 4269 predicted coding sequences in MJ01 had at least one similar sequence in genome of reference strain and spizizenii TU-B-10. Despite this high similarity, some differences were detected among encoding sequences of non-ribosome protein and bacteriocins in MJ01 and spizizenii TU-B-10. MJ01 has unique nucleotide sequences and a novel predicted lasso-peptide bacteriocin; it also has not any similar nucleotide sequence in non-redundant nucleotide data base.

Molecular characterization of Brassica napus stress related transcription factors, BnMYB44 and BnVIP1, selected based on comparative analysis of Arabidopsis thaliana and Eutrema salsugineum transcriptomes.

Many studies have been performed to identify regulatory circuit underlying plant stress tolerance. However, the reliability of some findings has been criticized because of exclusive use of stress sensitive plant species such as Arabidopsis thaliana. Sensitive plant species often harbor narrow defensive mechanisms and have relatively low capacity for adaptive responses. Therefore, it is useful to employ tolerant model plants, such as Eutrema salsugineum, to provide comprehensive insights into various mechanisms involved in response to abiotic stresses. In this study, comparative transcriptome and regulatory network analysis of stress-sensitive (A. thaliana) and -tolerant (E. salsugineum) model plants uncovered regulatory hierarchies underlying response to abiotic stresses and suggested the transcription factor genes, MYB44 and VIP1 as the candidate hub genes to perform molecular analyses on their Brassica napus homologs, BnMYB44 and BnVIP1. The full-length coding sequence of BnMYB44 and BnVIP1 with 891 and 969 bp long were cloned and sequenced. They shared high similarity with their counterparts in other plants at nucleotide and amino acid levels. The expression patterns of BnMYB44 and BnVIP1 genes of the two B. napus cultivars under drought and salt stress conditions coupled with the data obtained from the physiological measurements as well as analysis of the BnMYB44 and BnVIP1 promoters suggested that BnMYB44 and BnVIP1 genes may contribute to responses to drought and salt stresses in B. napus.

Expression of recombinant Arabian camel lactoferricin-related peptide in Pichia pastoris and its antimicrobial identification.

BACKGROUND: Lactoferricin (LFcin) is a strong cationic peptide released from the N-terminus of lactoferrin by gastric pepsin digestion. LFcin has some important properties, including high antimicrobial activity. To date, lactoferricins have been isolated and characterised from various animal species, but not from camel. The aim of this study was to characterise and express recombinant camel lactoferricin (LFcinC) in Pichia pastoris and investigate its antimicrobial activity. RESULTS: After methanol induction, LFcinC was expressed and secreted into a culture broth medium and the results determined by concentrated supernatant culture medium showed high antimicrobial activity against the following microorganisms: Escherichia coli PTCC 1330 (ATCC 8739), Staphylococcus aureus PTCC 1112 (ATCC 6538), Pseudomonas aeruginosa PTCC 1074 (ATCC 9027), Bacillus subtilis PTCC 1023 (ATCC 6633), and Candida albicans PTCC 5027 (ATCC 10231). Thermal stability was clarified with antibacterial activity against Escherichia coli PTCC 1330 (ATCC 8739). CONCLUSION: Results confirmed that camel lactoferricin had suitable antimicrobial activity and its production by Pichia pastoris can be used for recombinant production.

Temporal characterization of 2-phenylethanol in strongly and weakly scented genotypes of damask rose.

The molecular and physiological properties of 2-phenylethanol (2-PE) in the strongly scented genotype (SSG) and a weakly scented genotype (WSG) of damask rose at six floral developmental stages were investigated. The chemical compositions of volatile emissions were determined by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) analysis of the floral headspace. In both genotypes, the relative percentage of 2-PE increased more in SSG than WSG, as flowers developed. In the petals of damask rose the relative transcript levels of phenyl acetaldehyde reductase (PAR) were higher at stages 3 and 4 in SSG and WSG, respectively. Also, the expression pattern of PAR indicated a significant difference between two genotypes during flower developmental stages. In this study, enzymatic activity leading to the synthesis of 2-PE from the phenyl acetaldehyde (PAld) moderately increased during flower development up to stage 5 in SSG. However, high level of PAR enzymatic activity was observed in stage 3 of WSG. These results indicated that the pattern activity of PAR was different in two used genotypes of damask rose. For SSG, PAR activities were low in early stage of flower development and then gradually increased reaching its highest value at full bloom stage. In WSG, no significant change in enzyme activity was seen after stage 3.

Uncovering waterlogging-responsive genes in cucumber through machine learning and differential gene correlation analysis.

As climate change intensifies, the frequency and severity of waterlogging are expected to increase, necessitating a deeper understanding of the cucumber response to this stress. In this study, three public RNA-seq datasets (PRJNA799460, PRJNA844418, and PRJNA678740) comprising 36 samples were analyzed. Various feature selection algorithms including Uncertainty, Relief, SVM (Support Vector Machine), Correlation, and logistic least absolute shrinkage, and selection operator (LASSO) were performed to identify the most significant genes related to the waterlogging stress response. These feature selection techniques, which have different characteristics, were used to reduce the complexity of the data and thereby identify the most significant genes related to the waterlogging stress response. Uncertainty, Relief, SVM, Correlation, and LASSO identified 4, 4, 10, 21, and 13 genes, respectively. Differential gene correlation analysis (DGCA) focusing on the 36 selected genes identified changes in correlation patterns between the selected genes under waterlogged versus control conditions, providing deeper insights into the regulatory networks and interactions among the selected genes. DGCA revealed significant changes in the correlation of 13 genes between control and waterlogging conditions. Finally, we validated 13 genes using the Random Forest (RF) classifier, which achieved 100% accuracy and a 1.0 Area Under the Curve (AUC) score. The SHapley Additive exPlanations (SHAP) values clearly showed the significant impact of LOC101209599, LOC101217277, and LOC101216320 on the model's predictive power. In addition, we employed the Boruta as a wrapper feature selection method to further validate our gene selection strategy. Eight of the 13 genes were common across the four feature weighting algorithms, LASSO, DGCA, and Boruta, underscoring the robustness and reliability of our gene selection strategy. Notably, the genes LOC101209599, LOC101217277, and LOC101216320 were among genes identified by multiple feature selection methods from different categories (filtering, wrapper, and embedded). Pathways associated with these specific genes play a pivotal role in regulating stress tolerance, root development, nutrient absorption, sugar metabolism, gene expression, protein degradation, and calcium signaling. These intricate regulatory mechanisms are crucial for cucumbers to adapt effectively to waterlogging conditions. These findings provide valuable insights for uncovering targets in breeding new cucumber varieties with enhanced stress tolerance.