Histological and proteome analyses of Microbacterium foliorum-mediated decrease in arsenic toxicity in Melastoma malabathricum

Arsenic (As) is an increasing threat across the globe, widely known as a non-threshold carcinogen, and it is reaching harmful values in several areas of the world. In this study, the effect of plant growth promoting bacteria (Microbacterium foliorum) on inorganic arsenic (Arsenate) phytoremediation by Melastoma malabathricum plants was investigated through histological analysis and proteome profiling of the M. malabathricum plants. Two-dimensional gel electrophoresis and transmission electron microscopy were used to conduct the proteome and histological analysis. When arsenic-treated cells were compared to untreated cells, substantial changes were found (1) severely altered the morphology of the cells, intensely disturbed; (2) the cell wall was thicker; (3) drastically changed the cytoplasm, the cells were polygonal in shape, different in size (scattered), and relatively dense. Compared to the control group, the ultra-structure of the root cells of the control group revealed intact cytoplasm, vacuole, and cell wall under exposure to As + bacteria that had a minor effect on the cell form. To further understand As + bacteria interaction, proteome profiling of the root cell was analyzed. The As-induced oxidative stress enrichment was confirmed by the up-regulation of tubulin, nucleoside diphosphate kinase, and major allergen during As + bacteria exposure It was observed that the profusion of proteins involved in defence, protein biogenesis, signaling, photosynthesis, nucleoside and energy metabolism was greater in As + bacteria as compared to the rooting out of As only. Overall, it can be obviously seen that the current study demonstrates the effectiveness of phytoremediation by M. foliorum on proteins involved and responsive pathways in dealing with As toxicity in M. malabathricum plant

The past and current updates on diagnostic aspects of osteoarthritis

Osteoarthritis (OA) is a progressive joint disease leading to the destruction of joint structures, which in turn causes severe and chronic pain to the patient. Since OA is a troubling and disruptive disease, numerous researches have been done into diagnosing this disease, both in the early and the late stages of the disease. Diagnostic modalities such as radiography, computed-tomography (CT), micro-computed tomography (μ-CT), and magnetic resonance imaging (MRI) have been used in OA research. Not only that, more advance measurements and criteria have been established to standardize OA research. Currently, the OA research has been delving into proteomic studies to search for potential disease biomarkers. Biomarkers such as urinary C-terminal telopeptide of collagen type 2 (uCTX-II) and cartilage oligometric protein (COMP) have shown potential to be both diagnostic and prognostic biomarkers. For this review paper, the developments in diagnostic modalities are discussed focusing more on proteomic and biomarker studies

Ability of endophytic fungi isolated from Nepenthes ampullaria to degrade polyurethane

Aims: Waste electric and electronic equipment (WEEE) are among the fastest growing waste products worldwide and solutions to their remediation are urgently needed. Bioremediation is a green approach that is helpful to minimize environmental pollution associated with Electronic waste (E-waste). The present study aimed at exploring the potential of endophytic fungi from Nepenthes ampullaria for bioremediation purposes of the plastic component in E-waste, polyurethane (PUR) polymers. Methodology and results: Endophytic fungal isolates were assessed for their ability to degrade PUR as well as their ability to utilise PUR as sole carbon source. Nine (9) out of 150 isolates demonstrated the ability to efficiently degrade polyurethane in solid medium and the top three (3) isolates were able to grow on PUR as the only carbon source. These three isolates were identified using ITS1 and ITS4 and found to be closely related to the genus Pestalotiopsis. The top two of the three isolates were then assessed for their esterase enzyme activity as well as changes in their proteome when grown with and without PUR. The highest enzymatic activity was found to be 1850.4 U/mL when tested using pnitrophenol acetate as the substrate. Analyses of the 2-dimensional electrophoresis profile revealed changes in the abundance of proteins when treated with polyurethane. Conclusion, significance and impact of study: This study is to our knowledge the first on endophytes isolated from N. ampullaria that can degrade PUR, and also their proteomes. Results obtained from this study can in the future help to reduce polyurethane wastes. Besides degrading PUR polymer, endophytic fungi produce potential valuable proteins that may find broad applications in bioremediation applications

Trichloroacetic acid/acetone precipitation method to optimize canine synovial fluid for one and two-dimensional gel electrophoresis studies

The challenge associated with the use of synovial fluid for osteoarthritic proteome studies is the optimization step, which involves the depletion of high abundant proteins from the samples. The objective of this study was to develop a cost efficient and effective method to remove albumin from canine synovial fluid for proteome studies. Pooled synovial fluid samples were obtained from clinically healthy dogs (n=5), with no radiographic features of osteoarthritis. The acetone precipitation method and 10% w/v of trichloroacetic acid/acetone were chosen to deplete the albumin from canine synovial fluid and the outcome from the different methods were compared using one dimensional and two-dimensional gel electrophoresis studies. The results showed that the 10% w/v TCA/acetone precipitation method removed highly abundant proteins from synovial fluid for gel electrophoresis studies compared to the acetone precipitation method. The 10% w/v TCA/acetone precipitation method provides an effective method to remove albumin from the synovial fluid using gel electrophoresis, especially two-dimensional gel electrophoresis. The accessibility and cost of TCA and acetone make this method of precipitation a simple and cost-effective technique in preparing a canine synovial fluid for two-dimensional gel electrophoresis analysis

Comparative proteomic analysis on fruit ripening processes in two varieties of tropical mango (Mangifera indica)

Mango (Mangifera indica L.) is an economically important fruit. However, the marketability of mango is affected by the perishable nature and short shelf-life of the fruit. Therefore, a better understanding of the mango ripening process is of great importance towards extending its postharvest shelf life. Proteomics is a powerful tool that can be used to elucidate the complex ripening process at the cellular and molecular levels. This study utilized 2-dimensional gel electrophoresis (2D-GE) coupled with MALDI-TOF/TOF to identify differentially abundant proteins during the ripening process of the two varieties of tropical mango, Mangifera indica cv. ‘Chokanan’ and Mangifera indica cv ‘Golden Phoenix’. The comparative analysis between the ripe and unripe stages of mango fruit mesocarp revealed that the differentially abundant proteins identified could be grouped into the three categories namely, ethylene synthesis and aromatic volatiles, cell wall degradation and stress-response proteins. There was an additional category for differential proteins identified from the ‘Chokanan’ variety namely, energy and carbohydrate metabolism. However, of all the differential proteins identified, only methionine gamma-lyase was found in both ‘Chokanan’ and ‘Golden Phoenix’ varieties. Six differential proteins were selected from each variety for validation by analysing their respective transcript expression using reverse transcription-quantitative PCR (RT-qPCR). The results revealed that two genes namely, glutathione S-transferase (GST) and alpha-1,4 glucan phosphorylase (AGP) were found to express in concordant with protein abundant. The findings will provide an insight into the fruit ripening process of different varieties of mango fruits, which is important for postharvest management

Differential analyses of leaf proteomes in oil palm seedlings inoculated with pathogenic and nonpathogenic species of ganoderma

Basal stem rot (BSR) is a destructive disease of oil palm caused by the basiodiomycete fungus known as Ganoderma spp. Basal stem rot disease is considered the most serious disease affecting commercial oil palm plantations in South East Asia, especially in Malaysia and Indonesia. The disease reduces the productivity and yield of infected oil palm by disrupting water and nutrient movement from the roots to the other parts of the plant. Until now, there is no protein biomarker available to detect BSR disease at early stage of infection due to the insufficient information of Ganoderma spp. and most of the analyses related to the interaction between oil palm and Ganoderma spp. were conducted using roots tissues which require destructive sampling. Therefore, the objective of this study is to search for specific responsive protein candidates for early and non-destructive protein-based disease detection method by using leaf sample. Proteomic analysis of oil palm leaf was conducted on samples collected 72 hours following introduction of oil palm seedlings onto the mycelium of G. boninense and G.tornatum in flask. It is hypothesized that specific responsive proteins related to defence mechanism will be differently expressed by the leaf protein from oil palm seedling inoculated with G. boninese compared to the uninoculated control and G.tornatum-inoculated seedlings. A total of 82 proteins were resolved by two-dimensional gel electrophoresis with significant differences in the spot abundance. From there, 24 differentially expressed proteins in response to Ganoderma spp. inoculations were successfully identified by mass spectrophotometry (MALDI TOF/TOF). The proteins are mainly involved in photosynthesis and energy metabolism, RNA and protein metabolism as well as stress/defence mechanism. Proteins related to photosynthesis and energy production such as ATP synthase and ribulose bisphosphate carboxylase (Rubisco) were downregulated while proteins such as 70kDa heat shock protein and cyclophilin which involves in protein metabolism were up-regulated in comparison to un-inoculated sample. Defence related proteins, WAK proteins was up-regulated while hyrdroxyproline-rich glycoprotein like protein (HRGP) and mannose-binding lectin were down-regulated during the mycelium attachment process. Based on predicted cellular function classification, this study managed to identify several specific responsive proteins that can be used as possible candidates for biomarker or biological indicator for BSR early detection in oil palm which is important to properly manage the disease

Comparative proteomic analysis of Ganoderma species during in vitro interaction with oil palm root

Basal stem rot disease caused by Ganoderma spp. is still considered a large threat to oil palm production in many countries, especially in Malaysia, which contributes to approximately 45% of the world's palm oil exports. In the last 10 years, studies on the oil palm-Ganoderma interaction have mainly focused on the response of the plant towards the fungus. In this study, a comparative proteomic analysis was conducted to investigate the change in protein expression of two Ganoderma spp., namely Ganoderma boninense, which is known as the most aggressive species and Ganoderma tornatum, previously reported as non-pathogenic. Our results showed that both species colonize and penetrate the oil palm root after only 72 h of inoculation. In addition, proteins were expressed differentially in both species that have either direct or indirect links to virulence and pathogenicity. Other proteins related to fungal growth, metabolism and stress from both species were also discussed in this study

Proteomic analysis of synovial fluid obtained from a dog diagnosed with idiopathic immune-mediated polyarthritis

This case study is to report the proteins detected by proteomic analysis of synovial fluid from a dog diagnosed with idiopathic immune-mediated polyarthritis, and to compare it with healthy dogs. Synovial fluid was collected via arthrocentesis from a dog diagnosed with immune-mediated polyarthritis. Protein precipitation was performed on the synovial fluid, followed by isoelectric focusing and 2-dimensional gel electrophoresis. The spots on the 2-dimensional gels were analyzed using MALDI-TOF/MS. The results were then analyzed against the MASCOT database. The results from the proteomic analysis revealed an abundance of several types of immunoglobulins together with the presence of complement C4b-binding protein alpha chain. Actin and keratin were also among the proteins detected. Proteomic studies, facilitate a better understanding of the different levels of proteins expressed during disease activity. Potential disease biomarkers can aid in the diagnosis of disease, as well as help in monitoring treatment efficacy and providing prognosis for the patient

LCMS-QTOF Determination of Lentinan-Like β-D-Glucan Content Isolated by Hot Water and Alkaline Solution from Tiger’s Milk Mushroom, Termite Mushroom, and Selected Local Market Mushrooms

Lentinan, 1152 Dalton β-D-glucan found in Shiitake Mushroom (Lentinus edodes), has been claimed to have anticancer and immunomodulatory activity. Several extraction methods have been used by researchers to isolate Lentinan including hot water and alkaline solution (1.25 M NaOH). In this study, hot water and alkaline solution (1.25 M NaOH) were used to extract the Lentinan-like β-D-glucan (1151 Dalton) from Tiger’s Milk Mushroom, Termite Mushroom, and selected local market mushrooms. The isolated Lentinan-like β-D-glucan from both hot water and alkaline solution was analyzed by LCMS-QTOF. Commercial Lentinan standard from Lentinus edodes was used as a reference. The results showed significant differences on chromatogram patterns of Lentinan-like β-D-glucan between both extracts. The peak of Lentinan-like β-D-glucan was only found in isolated polysaccharide glucan of hot water extracts. The isolated polysaccharide glucans from Tiger’s Milk Mushroom and Termite Mushroom were found to have 0.74±0.12 μg/mg and 0.53±0.07 μg/mg Lentinan-like β-D-glucan. Button Mushroom, Shiitake Mushroom, and Oyster Mushroom showed the presence of Lentinan-like β-D-glucan at 16.16±4.15 μg/mg, 0.22±0.04, and 0.10±0.01 μg/mg, respectively

Comparative proteomic analysis of different developmental stages of the edible mushroom Termitomyces heimii

BACKGROUND: Termitomyces heimii is a basidiomycete fungus that has a symbiotic relationship with termites, and it is an edible mushroom with a unique flavour and texture. T. heimii is also one of the most difficult mushrooms to cultivate throughout the world. Little is known about the growth and development of these mushrooms, and the available information is insufficient or poor. The purpose of this study was to provide a base of knowledge regarding the biological processes involved in the development of T. heimii. The proteomic method of 2 dimensional difference gel electrophoresis 2D-DIGE was used to determine and examine the protein profiles of each developmental stage (mycelium, primordium and fruiting body). Total proteins were extracted by TCA-acetone precipitation. RESULTS: A total of 271 protein spots were detected by electrophoresis covering pH 3 - 10 and 10 - 250 kDa. Selected protein spots were subjected to mass spectrometric analyses with matrix-assisted laser desorption/ionisation (MALDI TOF/TOF). Nineteen protein spots were identified based on peptide mass fingerprinting by matching peptide fragments to the NCBI non-redundant database using MASCOT software. The 19 protein spots were categorised into four major groups through KEGG pathway analysis, as follows: carbohydrate metabolism, energy metabolism, amino acid metabolism and response to environmental stress. CONCLUSIONS: The results from our study show that there is a clear correlation between the changes in protein expression that occur during different developmental stages. Enzymes related to cell wall synthesis were most highly expressed during fruiting body formation compared to the mycelium and primordial stages. Moreover, enzymes involved in cell wall component degradation were up-regulated in the earlier stages of mushroom development