Advances in proteomics analytical techniques

   Proteins are fundamental components of cells which mediate many essential biological processes. Proteomics is a rapidly growing field for the study of proteome, the protein complement expressed by the genome of an organism or cell type. The large-scale analysis of proteins leads to a more comprehensive view of molecular and cellular pathways that improves the overall understanding of the complex processes supporting the living systems. The analysis of proteome is significantly challenging due to high dynamic range and difficulties in assessment of low abundance proteins and the absence of efficient purification and identification techniques. A variety of methods have been utilized for protein studies including gel-based techniques, protein microarrays, mass spectrometry-based approaches such as MALDI and SELDI, high and ultra-performance liquid chromatography and fourier transform ion cyclotron resonance mass spectrometry. NMR spectroscopy and X-Ray crystallography methods are also used for structural study of proteins. This review aims to give a brief overview of some of the above techniques and their most recent advances. We also introduce Proteominer, a recent protein enrichment technology for the exploration of the entire proteome conten

Isolation and Identification of Fungal Endophytes of the Cowpea in Khuzestan Province

Introduction: Endophytes are microorganisms that colonize internal tissues of plants without causing obvious symptoms. This study was conducted to isolate and identify endophytic fungi of the cowpea in Khuzestan province. Materials and methods: During 2016, eight healthy samples of the cowpea plants were collected from the important areas under cultivation in the northern Khuzestan province. The small parts of the roots, stems, leaves and pods were deeply surface sterilized for each samples and plated on Potato-Dextrose-Agar. Sixty fungal isolates obtained in this study were purified by single spore method. Based on morphological characteristics, 21 out of 60 isolates were selected for molecular study. The isolates were grown in Potato-Dextrose-Broth and mycelial biomass was recovered by passing through filter paper. DNA extraction was performed using a phenol- and chloroform- based organic method. The parts of the nrRNA gene (ITS and 28S-D1/D2 regions) were amplified using appropriate primer pair and then sequenced. Results: The isolates were analyzedon the basis of morphological characteristics in combination with BlASTn search algorithm and ITS sequence-based phylogeny. Accordingly, the isolates were identified as follows: Alternaria destruens, Alternaria sp., Curvularia mosaddeghii, Curvularia sp., Fusarium chlamydosporum, F. nygamai, F. falciforme, F. proliferatum, Fusarium sp. Macrophomina phaseolina and Penicillium oxalicum. Discussion and conclusion: Alternaria, Fusarium and Curvularia genera were the most abundant fungal endophytes into cowpea plants, growing in warm climate of the Khuzestan Province. To the best of our knowledge, this is the first study to report endophytic growth of A. destruens, Alternaria sp., M. phaseolina, F. chlamydosporum, F. nygamai, F. falciforme, F. proliferatum and P. oxalicum within cowpea plants

Optimization of Invasive Weed for Optimal Dimensions of Concrete Gravity Dams

Dam construction projects among the most extensive and most expensive projects are considered. It is always appropriate and optimal for such concrete structures to reduce the volume of concrete and consequently reduce construction costs is essential. In this study, invasive weed optimization software GNU octave, dimensions of concrete gravity dam Koyna located in India optimized stability constraints. For this purpose, a cross-section with a length unit consists of eight geometric parameters as input variables, and other geometric parameters were defined using these variables. The result showed that invasive weeds are well-optimized dimensions of the dam as the volume of concrete in the construction of the dam at the current level measures 3633 cubic meters that optimal dropped 3353 cubic meters, which is a mean of 7.7% of the value of the objective function (the volume of concrete in dams) is reduced. This amount of concrete decreased the construction of the dam, saving the cost and is more economical

Metabolomics-based studies in the field of Leishmania/leishmaniasis

Leishmania is a neglected protozoan parasite which creates some problems for public health with different clinical infections in different countries around. Due to the lack of an effective drug without side effects and the emergence drug resistance, there is an urgent need to introduce the novel drug targets and new drugs and vaccines to control leishmaniasis during recent years, metabolomics and other ‘‘Omics” platforms has become an important approach to comprehensive knowledge of the Leishmania  parasites biology. The study of metabolite profiles can open the insights for discovering novel therapeutic targets in this infection in both of the parasites and human host. In addition, specifying the metabolomics profile changes among promastigotes, amastigotes and during metacyclogenesis can pay the way for achieving parasite survival parameters and the host-parasite interaction. The previous studies in this field have been extracted from the databases, literature and their detailed major concepts. The present review highlights the role of metabolomics approach in the field of Leishmania research. Also, several important metabolite signatures introduced in various aspect of leishmania parasite such as drug resistance and parasite biology which would be useful in the field of biomarker and drug discovery process. Finally, metabolomics plays a potential role in introducing metabolic pathways related to Leishmania parasite and its treatment design.Keywords:  Omics, System biology, Metabolomics, Leishmania, Parasite, Leishmaniasis, Biomarke

Investigating the Mechanism of Arsenic-induced Ferroptosis in the Skin

Background: Ferroptosis, an oxidative and iron-dependent cell death, is a new type of regulated cell death. There are few studies on the mechanisms of ferroptosis in the skin and related diseases. Arsenic is shown to induce ferroptosis cell death. This study aimed to decipher the relationship between arsenic exposure and ferroptosis cell death in the skin. Methods: Arsenic-gene interactions were obtained. Then, skin-specific arsenic-gene interactions were screened. Ferroptosis-related genes were identified. Analysis of functional and biological interactions was performed to identify possible mechanisms. Results: The arsenic-gene interactions and the ferroptosis-related genes showed an overlap of 59 genes. Functional enrichment, protein-protein interaction, and transcription factor (TF)/miRNA target gene interaction analyses were used to look into the mechanism of arsenic-induced ferroptosis in the skin. ACTB, CTNNB1, HSPA8, SRC, RACK1, CD44, and SQSTM1 were identified as key proteins. Gene ontology analysis of these proteins indicated the mitochondrial morphology and functionality changes following arsenic-induced ferroptosis in the skin. HIF1A and SP1 TFs regulate a large number of genes compared to other TFs. Ten miRNAs with high interaction with ferroptosis-associated genes were identified. Conclusion: This work investigated the mechanism of arsenic-induced ferroptosis in the skin and identified key genes and regulators, and functional analysis highlighted the role of mitochondria in this skin exposure

Effects of Imunit Insecticide on Biological Characteristics and Life Table Parameters of Spodoptera cilium (Lepidoptera: Noctuidae)

Imunit is a mixture of alpha-cypermethrin + teflubenzuron, and has been launched for controlling caterpillars. In this study, the effects of Imunit at LC50 and LC30 were investigated on parental and offspring generation of S. cilium, according to age-stage, two-sex life table. The experiments were conducted by leaf dipping method at 25 C and 60 5% relative humidity, under a cycle of 16 h fluorescent light and 8 h darkness. LC30 and LC50 concentrations of Imunit increased the immature developmental time of S. cilium in the offspring generation, while the LC50 of Imunit significantly reduced the developmental time of adults. The adult pre-oviposition period and total pre-oviposition period considerably increased when offspring were treated with LC50 of Imunit. In offspring of S. cilium exposed to LC50 and LC30 concentrations of Imunit, the gross reproductive rate (GRR), net reproduction rate (R0), the intrinsic rate of population increase (r), and the finite rate of population increase (l) significantly reduced compared to the control. This study showed that the application of Imunit at LC50 could suppress the S. cilium population and can be used in the integrated management program of this pest

Investigating the Mechanism of Arsenic-induced Ferroptosis in the Skin

Background: Ferroptosis, an oxidative and iron-dependent cell death, is a new type of regulated cell death. There are few studies on the mechanisms of ferroptosis in the skin and related diseases. Arsenic is shown to induce ferroptosis cell death. This study aimed to decipher the relationship between arsenic exposure and ferroptosis cell death in the skin. Methods: Arsenic-gene interactions were obtained. Then, skin-specific arsenic-gene interactions were screened. Ferroptosis-related genes were identified. Analysis of functional and biological interactions was performed to identify possible mechanisms. Results: The arsenic-gene interactions and the ferroptosis-related genes showed an overlap of 59 genes. Functional enrichment, protein-protein interaction, and transcription factor (TF)/miRNA target gene interaction analyses were used to look into the mechanism of arsenic-induced ferroptosis in the skin. ACTB, CTNNB1, HSPA8, SRC, RACK1, CD44, and SQSTM1 were identified as key proteins. Gene ontology analysis of these proteins indicated the mitochondrial morphology and functionality changes following arsenic-induced ferroptosis in the skin. HIF1A and SP1 TFs regulate a large number of genes compared to other TFs. Ten miRNAs with high interaction with ferroptosis-associated genes were identified. Conclusion: This work investigated the mechanism of arsenic-induced ferroptosis in the skin and identified key genes and regulators, and functional analysis highlighted the role of mitochondria in this skin exposure

Potential Molecular Mechanisms of Bisphenol A in Obesity Development

Bisphenol A (BPA), an endocrine disruptor, is associated with metabolic disorders. However, several studies have suggested that exposure to BPA can cause obesity. It has recently got more attention from scientists as a risk factor for obesity due to its ability to mimic natural estrogens and bind to their receptors. Nonetheless, the molecular mechanism underpinning the environmental etiology of metabolic disorders has not been not fully clarified. In this regard, BPA exposure directly disrupts endocrine regulation, neuroimmune and signaling pathways, and gut microbes, resulting in obesity. In addition, epidemiological studies have revealed a significant relationship between BPA exposure and the development of obesity, although conflicting results have been reported. Therefore, this review summarized the possible role and molecular mechanisms associated with BPA exposure that may lead to obesity based on in vivo and in vivo studies

Numerical investigation of ground surface settlement due to circular tunnelling influenced by variations of geometric characteristics of tunnel and mechanical properties of saturated soil and its prediction in the artificial neural network

The settlement of the ground surface due to tunneling are considered as tunnel instability factors, as well as the displacement of the crown of the tunnel. Considering the importance of the subject, numerous research have been discussed but not considered on the effect of shape and type of ground surface settlement and its magnitude with respect to different factors. However, there is still no accurate equation to predict ground surface settlement, considering all effective parameters, including geometrical parameters of tunnel section and soil mechanical properties. In this paper, some numerical and parametric analysis of circular tunneling in frictional-cohesive saturated soil has been investigated using 2D FEM by ABAQUS. The behavior of ground surface, considering to change the different values of depth to diameter ratio(H/D), soil cohesion, internal friction angle and permeability coefficient, and the influence of these variables on settlement of surface in each model have been separately evaluated. Then, a multi-layer perception (MLP) artificial neural network is designed to predict the ground surface settlement. MLP is a type of feedforward artificial neural network utilizing back propagation technique for training phase and the Levenberg-Marquardt method are used to reduce the errors and distance between the network outputs and finite element method results. There are four independent variables in the input layer and a dependent variable in the output layer. The middle layer consists of 7 neurons. Finally, the high potential of the artificial neural network with a correlation coefficient of 0.98 is shown in the prediction of ground surface settlement

Chaetomium albiziae M. Mehrabi-Koushki & A. Safi 2023, sp. nov.

Chaetomium albiziae M. Mehrabi-Koushki & A. Safi, sp. nov. (Fig. 1) MycoBank: MB 841114 Holotype: IRAN, Khuzestan Province, Ahvaz, isolated from a living leaf of Albizia lebbeck (Fabaceae), Oct. 2018, A. Safi (holotype, IRAN 18081F; ex-type cultures, IRAN 4137C = SCUA-Saf-B10). Etymology. Species epithet refers to the host genus Albizia from which the holotype was isolated. Sexual morph: Hyphae hyaline to pale brown, septate, branched. Ascomata perithecioid, superficial, brown to dark brown in reflected light, globose to subglobose, (79–)118–170(–184) × (71–)100–145(–158) μm, 95 % confidence limits = 134–148.5 × 112.2–124.8 μm, (± SD = 141.3 ± 25.5 × 118.5 ± 22.1 μm, n = 50). Ascomatal wall brown, textura angularis in surface view. Terminal hairs seta-like, septate, unbranched, smooth, brown, tapering towards the tips, 2.5–3.8 μm diam near the base. Lateral hairs similar but more flexuous, narrower and shorter. Asci fasciculate, clavate, spore bearing part (20–)22.5–35(–38.75) × 7.5–16.5 μm, stalks 11.25–22.5 μm long, with 8 irregularly-arranged ascospores, evanescent. Ascospores brown to olivaceous brown, ellipsoidal to ovoid, aseptate, biapiculate, bilaterally flattened, with an apical germ pore, (7.5–)10–11.25(–12.5) × 7.5–10 μm, 95 % confidence limits = 10.4–10.9 × 8.1–8.6 μm, (± SD = 10.7 ± 0.8 × 8.3 ± 0.7 μm, n = 50). Asexual morph: not observed. Culture characteristics—Colonies on OA reaching 60–66 mm after 4 d of incubation at 28 ± 0.5 °C, circular with regular margin, initially white, with age becoming creamy white or slightly pinkish, highly floccose; reverse pinkish white. Colonies on PDA reaching 40–45 mm d after 4 d of incubation at 28 ± 0.5 °C, circular with regular margin, initially pale buff with creamy margin, with age becoming buff with paler margin and sectors, floccose; reverse buff with paler sectors. Additional materials examined. IRAN, Khuzestan Province; Karoon, isolated from a living leaf of A. lebbeck, Sep 2020, A. Safi (SCUA-Saf-B10-2). Notes: In the phylogenetic tree, C. albiziae is closely related to C. cucumericola, but can be distinguished by single nucleotide polymorphism (SNP) analysis of three ITS, tub2 and rpb2 loci (Fig. 2). This new species and the extype strain of C. cucumericola (CBS 378.71) showed 1 bp difference (0.2 %) across 496 nucleotides of the ITS region, 6 bp difference (1.1 %) across 547 nucleotides of the tub2 region, and 5 bp difference (1 %) across 481 nucleotides of the rpb2 region. Chaetomium cucumericola was established by Wang et al. (2016) to accommodate two sterile strains of the genus Chaetomium (CBS 378.71 and CBS 126777), which formed a well-supported clade within phylogenetic group III, including the related species C. olivaceum Cooke & Ellis, C. subglobosum Sergeeva, and C. undulatulum Asgari & Zare. C. albiziae can be distinguished from these three species by smaller ascomata (C. olivaceum: 260–440 × 200–360 μm, C. subglobosum: 300–450 × 265–355 μm, C. undulatulum: 230–280 × 185–250 μm) (Asgari & Zare 2011, Wang et al. 2016b).Published as part of Mehrabi-Koushki, Mehdi & Safi, Atena, 2023, Chaetomium albiziae, a new endophytic species from Albizia lebbeck in Iran, pp. 137-146 in Phytotaxa 591 (2) on pages 140-142, DOI: 10.11646/phytotaxa.591.2.5, http://zenodo.org/record/779748