Predictive value of α-synuclein expression in peripheral blood of multiple sclerosis patients: A two-dimensional assessment of a selected biomarker

INTRODUCTION

Our study aimed to evaluate whether assessing α-synuclein expression levels in blood samples could provide a reliable and straightforward alternative to existing diagnostic and prognostic methods for neurodegenerative disorders, including multiple sclerosis (MS). We specifically investigated if α-synuclein and IL-6 expression levels from serum and peripheral blood mononuclear cells (PBMCs) could accurately predict MS severity in patients using a two-dimensional approach.

METHODS

We designed a case-control study to analyze the expression of α-synuclein and IL-6 in the peripheral blood of an MS patient group (n = 51) and a control group (n = 51). We statistically evaluated the PBMCs and serum profiles of α-synuclein and IL-6 in MS patients, along with their age of onset, disease duration, tobacco exposure, and Expanded Disability Status Scale (EDSS) score, using SPSS V22.0 software and GraphPad Prism V9.0.

RESULTS

Our findings indicate that α-synuclein production was significantly downregulated in MS patients. Principal component analysis also revealed distinct profiles between MS patients and controls. PBMCs and serum profiles of α-synuclein correlated with the EDSS score, suggesting that disease severity can be predicted using α-synuclein profiles. Moreover, α-synuclein showed a significant correlation with IL-6 and age of onset. Lastly, receiver operating characteristic curves of PBMCs and serum activity of α-synuclein profiles displayed discrimination with area under the curve values of 0.856 and 0.705, respectively.

CONCLUSION

Our results imply that measuring α-synuclein levels in both serum and PBMCs could be a valuable method for diagnosing and predicting MS severity, potentially serving as a non-invasive biomarker for the disease.

The analysis of dynamic gene expression patterns in peripheral blood of multiple sclerosis patients indicates possible diagnostic and prognostic biomarkers

INTRODUCTION

Among numerous invasive procedures for the research of biomarkers, blood-based indicators are regarded as marginally non-invasive procedures in the diagnosis and prognosis of demyelinating disorders, including multiple sclerosis (MS). In this study, we looked into the blood-derived gene expression profiles of patients with multiple sclerosis to investigate their clinical traits and linked them with dysregulated gene expressions to establish diagnostic and prognostic indicators.

METHODS

We included 51 patients with relapsing-remitting MS (RRMS, n = 31), clinically isolated syndrome (CIS, n = 12), primary progressive MS (PPMS, n = 8) and a control group (n = 51). Using correlational analysis, the transcriptional patterns of chosen gene panels were examined and subsequently related with disease duration and the expanded disease disability score (EDSS). In addition, principal component analysis, univariate regression, and logistic regression analysis were employed to highlight distinct profiles of genes and prognosticate the excellent biomarkers of this illness.

RESULTS

Our findings demonstrated that neurofilament light (NEFL), tumor necrosis factor α (TNF-α), Tau, and clusterin (CLU) were revealed to be increased in recruited patients, whereas the presenilin-1 (PSEN1) and cell-surface glycoprotein-44 (CD44) were downregulated. Principal Component Analysis revealed distinct patterns between the MS and control groups. Correlation analysis indicated co-dependent dysregulated genes and their differential expression with clinical findings. Furthermore, logistic regression demonstrated that Clusterin (AUC=0.940), NEFL (AUC=0.775), TNF-α (AUC=0.817), Tau (AUC=0.749), PSEN1 (AUC=0.6913), and CD44 (AUC=0.832) had diagnostic relevance. Following the univariate linear regression, a significant regression equation was found between EDSS and IGF-1 (R² adj = 0.10844; p= 0.0060), APP (R² adj = 0.1107; p= 0.0098), and PSEN1 (R² adj = 0.1266; p=0.0102).

CONCLUSION

This study exhibits dynamic gene expression patterns that represent the significance of specified genes that are prospective diagnostic and prognostic biomarkers for multiple sclerosis.

Sodium voltage-gated channel alpha subunit 9 mutation in epilepsy

In humans, gene mutations in voltage-gated sodium channels can cause a range of epileptic symptoms, including genetic (generalized) epilepsy with febrile seizures plus (GEFS+) and Dravet syndrome (DS). The SCN9A is a member of the SCN9 gene family that encodes sodium transporter proteins. In the current case report, we delineate a 12-year-old patient who was referred to a pediatric neurology clinic for infantile-onset generalized epileptic seizures and progressive neurodevelopmental delay. Novel heterozygous mutations c.4702A>C (p.Asn1568His) in the SCN9A gene, and c.65G>A (p.Arg22Gln) in the MLC1 gene were detected using targeted next-generation gene sequencing. The replacement of Histidine (His) with Asparagine (Asn) at position 1568 in the topological domain of SCN9A channel protein provides new insights into the impaired excitation and inactivation patterns of sodium channels. The case report adds this new patient with genetic link of SCN9A variants with progressive myoclonic epilepsy and cognitive difficulties.

Whole genome analysis of Gluconacetobacter azotocaptans DS1 and its beneficial effects on plant growth

Plant-associated bacteria play an important role in the enhancement of plant growth and productivity. Gluconacetobacter azotocaptans is an exceptional bacterium considering that till today it has been isolated and reported only from Mexico and Canada. It is a plant growth-promoting bacterium and can be used as biofertilizer for different crops and vegetables. The objective of the current study was to evaluate the inoculation effect of Gluconacetobacter azotocaptans DS1, Pseudomonas putida CQ179, Azosprillium zeae N7, Azosprillium brasilense N8, and Azosprillium canadense DS2, on the growth of vegetables including cucumber, sweet pepper, radish, and tomato. All strains increased the vegetables' growth; however, G. azotocaptans DS1 showed better results as compared to other inoculated and control plants and significantly increased the plant biomass of all vegetables. Therefore, the whole genome sequence of G. azotocaptans DS1 was analyzed to predict genes involved in plant growth promotion, secondary metabolism, antibiotics resistance, and bioremediation of heavy metals. Results of genome analysis revealed that G. azotocaptans DS1 has a circular chromosome with a size of 4.3 Mbp and total 3898 protein-coding sequences. Based on functional analysis, genes for nitrogen fixation, phosphate solubilization, indole acetic acid, phenazine, siderophore production, antibiotic resistance, and bioremediation of heavy metals including copper, zinc, cobalt, and cadmium were identified. Collectively, our findings indicated that G. azotocaptans DS1 can be used as a biofertilizer and biocontrol agent for growth enhancement of different crops and vegetables.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02996-1.

Profilin 3 genetic architecture in glioma formalin fixed paraffin embedded (FFPE) archive

Pfn3 is an intron-less gene, encoding actin binding protein that affects structure of cytoskeleton. Although, Pfn3 is mentioned in Allen Brain Atlas and in adult and prenatal Human Brain Tissue Gene Expression Profiles dataset, however, no report on brain and/or brain tumor associated Pfn3 nucleotide sequences are available in the databases. Moreover, pfn3 and pfn4 are always considered as testicular specific genes. The current study explored transcriptional expression profile and genetic architecture of pfn3 in a cohort of fifty formalin fixed paraffin embedded (FFPE) human glioma archive tissues. Results of designed study highlighted the significant dysregulated transcriptional pattern of pfn3. Molecular similarity index indicated 97% in nucleotide and 93% homology in protein sequences (with clear differences in nine amino acid residues). Thus, molecular variations in the pfn3 may be corelated with the malignancy of brain tumors, as previously, pfn1 and pfn2 were reported as tumor suppressor genes in other types of cancer.

Profiling of antimicrobial metabolites of plant growth promoting Pseudomonas spp. isolated from different plant hosts

In this study, nine strains of Pseudomonas au rantiaca and P. chlororaphis, and two isolates of Pseudomonas sp.: At1RP4 and RS-1, were characterized for the in-vitro production of secondary metabolites in LB, DMB, and King's B media, and of the genes responsible for the production of antagonistic metabolites. Based on 16S rRNA gene sequence, isolates At1RP4 and RS-1 were identified as strains of P. aeruginosa and P. fluorescens. Five phenazine derivatives comprising phenazine, phenazine-1-carboxylic acid (PCA), 2-hydroxyphenazine-1-carboxylic acid (2-OH-Phz-1-COOH), phenazine-1,6-dicarboxylic acid (Phz-1,6-di-COOH), and 2-hydroxyphenazine (2-OH-Phz) were produced by all strains in all three culture media including DMB, King's B and LB. However, 2,8-dihydroxyphenazine, 6-methylphenazine-1-carboxylic acid, pyrrolnitrin, and the ortho-dialkyl-aromatic acids, were produced by the P. aurantiaca and P. chlororaphis strains. In addition, all strains produced 2-acetamidophenol, pyochelin, and diketopiperazine derivatives in variable amounts in all three culture media used. Highest levels of quorum-sensing signal molecules including PQS, 2-Octyl-3-hydroxy-4(1H)-quinolone, and hexahydro-quinoxaline-1,4-dioxide were recorded for P. aeruginosa At1RP4. Moreover, all strains produced volatile hydrogen cyanide (0.95-6.68 µg/L) and the phytohormone indole-3-acetic acid (0.42-13.9 µM). Production of extracellular lipase and protease was recorded in all pseudomonads, whereas, cellulase production and phosphate solubilization were variable. Genes for hydrogen cyanide and phenazine-1-carboxylic acid were detected in all eleven strains while the gene for pyrrolnitrin biosynthesis was amplified in P. aurantiaca and P. chlororaphis strains. Comparative metabolomic analysis provided detailed insights about the strain-specific metabolites in pseudomonads, and their pseudo-relative quantification in different bacterial growth media to be used as single-strain biofertilizer and biocontrol inoculums.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02585-8.

DNA repair protein RAD51 enhances the CRISPR/Cas9-mediated knock-in efficiency in brain neurons

Gene knock-in using the CRISPR/Cas9 system can be achieved in a specific population of neurons in the mouse brain, by using in utero electroporation to introduce DNA fragments into neural progenitor cells. Using this strategy, we previously knocked-in the EGFP coding sequence into the N-terminal region of the β-actin gene specifically in the pyramidal neurons in layer 2/3 of the somatosensory cortex. However, the knock-in efficiency was less than 2% of the transfected neurons. In this study, we sought to improve the knock-in efficiency using this system. First, we varied the length of the homology arms of the β-actin donor template DNA, and found that the knock-in efficiency was increased to ∼14% by extending the length of the 5' and 3' homology arms to 1.6 kb and 2.0 kb, respectively. We then tested the effect of the DNA repair protein RAD51 and the knock-in efficiency was increased up to 2.5-fold when co-transfecting with two different β-actin and a camk2a targeting EGFP knock-in modules. The RAD51 overexpression did not alter the migration of developing neurons, density or morphology of the dendritic spines compared to those in neurons not transfected with RAD51. RAD51 expression will be useful for increasing the knock-in efficiency in neurons in vivo by CRISPR/Cas9-mediated homology directed repair (HDR).

Secondary Metabolites Production and Plant Growth Promotion by Pseudomonas chlororaphis and P. aurantiaca Strains Isolated from Cactus, Cotton, and Para Grass

Fluorescent pseudomonads have been isolated from halophytes, mesophytes, and xerophytes of Pakistan. Among these, eight isolates, GS-1, GS-3, GS-4, GS-6, GS-7, FS-2 (cactus), ARS-38 (cotton), and RP-4 (para grass), showed antifungal activity and were selected for detailed study. Based on biochemical tests and 16S rRNA gene sequences, these were identified as strains of P. chlororaphis subsp. chlororaphis and aurantiaca. Secondary metabolites of these strains were analyzed by LC-MS. Phenazine-1-carboxylic acid (PCA), 2-hydroxy-phenazine, Cyclic Lipopeptide (white line-inducing principle (WLIP)), and lahorenoic acid A were detected in variable amounts in these strains. P. aurantiaca PB-St2 was used as a reference as it is known for the production of these compounds. The phzO and PCA genes were amplified to assure that production of these compounds is not an artifact. Indole acetic acid production was confirmed and quantified by HPLC. HCN and siderophore production by all strains was observed by plate assays. These strains did not solubilize phosphate, but five strains were positive for zinc solubilization. Wheat seedlings were inoculated with these strains to observe their effect on plant growth. P. aurantiaca strains PB-St2 and GS-6 and P. chlororaphis RP-4 significantly increased both root and shoot dry weights, as compared with uninoculated plants. However, P. aurantiaca strains FS-2 and ARS-38 significantly increased root and shoot dry weights, respectively. All strains except PB-St2 and ARS-38 significantly increased the root length. This is the first report of the isolation of P. aurantiaca from cotton and cactus, P. chlororaphis from para grass, WLIP and lahorenoic acid A production by P. chlororaphis, and zinc solubilization by P. chlororaphis and P. aurantiaca.

Distortion of the normal function of synaptic cell adhesion molecules by genetic variants as a risk for autism spectrum disorders

Synaptic cell adhesion molecules (SCAMs) are a functional category of cell adhesion molecules that connect pre- and postsynapses by the protein-protein interaction via their extracellular cell adhesion domains. Countless numbers of common genetic variants and rare mutations in SCAMs have been identified in the patients with autism spectrum disorders (ASDs). Among these, NRXN and NLGN family proteins cooperatively function at synaptic terminals both of which genes are strongly implicated as risk genes for ASDs. Knock-in mice carrying a single rare point mutation of NLGN3 (NLGN3 R451C) discovered in the patients with ASDs display a deficit in social interaction and an enhancement of spatial learning and memory ability reminiscent of the clinical phenotype of ASDs. NLGN4 knockout (KO) and NRXN2α KO mice also show a deficit in sociability as well as some specific neuropsychiatric behaviors. In this review, we selected NRXNs/NLGNs, CNTNAP2/CNTNAP4, CNTN4, ITGB3, and KIRREL3 as strong ASD risk genes based on SFARI score and summarize the protein structures, functions at synapses, representative discoveries in human genetic studies, and phenotypes of the mutant model mice in light of the pathophysiology of ASDs.

Prediction of post translation modifications at the contact site between Anaplasma phagocytophilum and human host during autophagosome induction using a bioinformatic approach

Autophagy is crucial for maintaining physiological homeostasis, but its role in infectious diseases is not yet adequately understood. The binding of Anaplasma translocated substrate-1 (ATS1) to the human Beclin1 (BECN1) protein is responsible for the modulation of autophagy pathway. ATS1-BECN1 is a novel type of interaction that facilitates Anaplasma phagocytophilum proliferation, leading to intracellular infection via autophagosome induction and segregation from the lysosome. Currently, there is no report of post translational modifications (PTMs) of BECN1 or cross-talk required for ATS-BECN1 complex formation. Prediction/modeling of the cross-talk between phosphorylation and other PTMs (O-β-glycosylation, sumoylation, methylation and palmitoylation) has been attempted in this study, which might be responsible for regulating function after the interaction of ATS1 with BECN1. PTMs were predicted computationally and mapped onto the interface of the docked ATS1-BECN1 complex. Results show that BECN1 phosphorylation at five residues (Thr91, Ser93, Ser96, Thr141 and Ser234), the interplay with O-β-glycosylation at three sites (Thr91, Ser93 and Ser96) with ATS1 may be crucial for attachment and, hence, infection. No other PTM site at the BECN1 interface was predicted to associate with ATS1. These findings may have significant clinical implications for understanding the etiology of Anaplasma infection and for therapeutic studies.

Distribution analysis of profilin isoforms at transcript resolution with mRNA-seq and secondary structure in various organs of Rattus norvegicus

Profilin (Pfn) is an actin binding protein, ubiquitously found in mammals and is essential for the actin polymerization in cells. In brain, it plays a pivotal role in neurogenesis and synapse formation by interacting with various proteins. Four Pfn isoforms have been identified in mammals. This study presents the identification and transcriptional expression of various Pfn isoforms (Pfn1, Pfn2, Pfn3 and Pfn4) in brain, heart, kidney, liver, and muscle and testis of Rattus norvegicus. Organs have been classified into groups based on some similarities. Group I includes brain and testis, Group II includes skeletal muscle and heart, while Group III includes kidney and liver. Pfn1 has been identified in all groups, Pfn2 and Pfn3 have been identified in group I, group III and in one organ (skeletal muscle) of group II. To the best of the authors knowledge, no report of Pfn1 and Pfn2 presence in testis, Pfn3 in brain, liver and skeletal muscle, Pfn4 in kidney and skeletal muscle exists to date. Transcriptional expression showed variations among expression level of different Pfn isoforms in various organs with respect to the control gene GADPH. We hypothesize that this could be attributed to profilin isoform specific mRNA structure and corresponding motifs, which generally contribute to similar or varied decay rates, cellular localization, post transcriptional regulation pattern and ligand binding.

Genetic and phenotypic diversity of plant growth promoting rhizobacteria isolated from sugarcane plants growing in pakistan

Bacteria were isolated from roots of sugarcane varieties grown in the fields of Punjab. They were identified by using API20E/NE bacterial identification kits and from sequences of 16S rRNA and amplicons of the cpn60 gene. The majority of bacteria were found to belong to the genera of Enterobacter, Pseudomonas, and Klebsiella, but members of genera Azospirillum, Rhizobium, Rahnella, Delftia, Caulobacter, Pannonibacter, Xanthomonas, and Stenotrophomonas were also found. The community, however, was dominated by members of the Pseudomonadaceae and Enterobacteriaceae, as representatives of these genera were found in samples from every variety and location examined. All isolates were tested for the presence of five enzymes and seven factors known to be associated with plant growth promotion. Ten isolates showed lipase activity and eight were positive for protease activity. Cellulase, chitinase, and pectinase were not detected in any strain. Nine strains showed nitrogen fixing ability (acetylene reduction assay) and 26 were capable of solubilizing phosphate. In the presence of 100 mg/l tryptophan, all strains except one produced indole acetic acid in the growth medium. All isolates were positive for ACC deaminase activity. Six strains produced homoserine lactones and three produced HCN and hexamate type siderophores. One isolate was capable of inhibiting the growth of 24 pathogenic fungal strains of Colletotrichum, Fusarium, Pythium, and Rhizoctonia spp. In tests of their abilities to grow under a range of temperature, pH, and NaCl concentrations, all isolates grew well on plates with 3% NaCl and most of them grew well at 4 to 41degrees C and at pH 11.

Cry genes profiling and the toxicity of isolates of Bacillus thuringiensis from soil samples against American bollworm, Helicoverpa armigera

AIMS

 The aim of this study was to search for Bacillus thuringiensis (Bt) harbouring cry1A gene which could effectively control cotton pest, American bollworm, Helicoverpa armigera.

METHODS AND RESULTS

 cry gene profiling of 50 Bt isolates showed the presence of cry1, cry2, cry3, cry4, cry7, cry8 and cry9 genes. None of the isolates harboured cry1 gene alone. It was always found in combination with cry3. There was no isolate positive for cry10 gene. Considering isolates with single cry genes, the frequency of cry4 was predominant (22%) followed cry2 (6%), cry3 (4%) and cry8 (2%). Isolates having two cry genes in combination had 14% incidence for cry2 + cry4, 12% for cry3 + cry4 and 10% for cry1 + cry3. The most dominant three gene linkage was cry1 + cry3 + cry4. Further profiling of cry1 gene showed that cry1K gene was abundantly present in all combinations such as cry1A, cry1D, cry1F and cry1I. However, cry1C existed independent of other subtypes. Finally, the Bt isolates with cry1A were analyzed for 16S rRNA gene, which showed two distinct groups of isolates on the basis of sequence homology. Bioassays of spore-crystal mixtures of SBS-Bt4, 8, 17, 21 and 26 harbouring cry1 against neonate larvae of H. armigera showed LC(50) 1288, 1202, 467·7, 524·8 and 108·5 μg ml(-1) . The SBS-Bt26 showed fourfold higher toxicity than the cry 1Ac harbouring positive control, HD-73.

CONCLUSIONS

  None of the isolates harboured single cry 1 gene. They were always in combination of two or three genes. A Bt isolate (Bt26) had fourfold higher toxicity against H. armigera larvae compared with the positive control HD 73 and hence can be commercially exploited to control insect pest.

SIGNIFICANCE AND IMPACT OF THE STUDY

  The inter relationship between the cry genes content and the toxicity may allow better understanding of Bt ecology.

Characterization of a phenazine and hexanoyl homoserine lactone producing Pseudomonas aurantiaca strain PB-St2, isolated from sugarcane stem

A novel strain of fluorescent pseudomonad (PB-St2) was isolated from surface-sterilized stems of sugarcane grown in Pakistan. The bacterium was identified as Pseudomonas aurantiaca on the basis of 16S rRNA gene sequence analysis and results from physiological and biochemical characteristics carried out with API50 CH and QTS 24 bacterial identification kits. Assays using substrate specific media for enzymes revealed lipase and protease activities but cellulase, chitinase, or pectinase were not detected. The bacterium was unable to solubilize phosphate or produce indole acetic acid. However, it did produce HCN, siderophores, and homoserine lactones. In dual culture assays on agar, the bacterium showed antifungal activity against an important pathogen of sugarcane in Pakistan, namely Colletotrichum falcatum, as well as for pathogenic isolates of Fusarium oxysporium, F. lateritium but not against F. solani. The antifungal metabolites were identified using thin-layer chromatography, UV-spectra, and MALDI-TOFF spectra and shown to be phenazine-1-carboxylic acid (PCA), 2-hydroxyphenazine (2-OH-PHZ), and N-hexanoyl homoserine lactone (HHL) (assessed using only TLC data). The capacity of this bacterium to produce HCN and 2-OH-PHZ, as well as to inhibit the growth of C. falcatum, has not been previously reported.

Determination and distribution of cry-type genes in halophilc Bacillus thuringiensis isolates of Arabian Sea sedimentary rocks

Bacillus thuringiensis produces insecticidal crystal during its sporulation phase. In this study, marine sediments from Arabian Sea along coastal area of Pakistan were examined for the occurrence of B. thuringiensis. On the basis of morphological and biochemical properties, 31 out of 200 colonies were assigned to B. thuringiensis. Isolated strains were characterized on the basis of cry genes profile. PCR approach was used to analyze the presence of different crystal toxin encoding genes with six pairs of universal primers that could detect the cry1, cry4, cry7, cry8, cry9, and cry10 genes. Strains containing cry1 genes were the most abundant in our collection (49.5%). Seventeen different profiles of cry genes were identified, i.e., twelve harboring two cry genes while five profiles of more than two cry genes. The characterization of these strains provided useful information on the ecological patterns of distribution of B. thuringiensis and opportunities for the selection of new strains to develop novel bio-insecticidal products.