The road-map for establishment of a prognostic molecular marker panel in glioma using liquid biopsy: current status and future directions

Gliomas are primary intracranial tumors with defined molecular markers available for precise diagnosis. The prognosis of glioma is bleak as there is an overlook of the dynamic crosstalk between tumor cells and components of the microenvironment. Herein, different phases of gliomagenesis are presented with reference to the role and involvement of secreted proteomic markers at various stages of tumor initiation and development. The secreted markers of inflammatory response, namely interleukin-6, tumor necrosis factor-α, interferon-ϒ, and kynurenine, proliferation markers human telomerase reverse transcriptase and microtubule-associated-protein-Tau, and stemness marker human-mobility-group-AThook-1 are involved in glial tumor initiation and growth. Further, hypoxia and angiogenic factors, heat-shock-protein-70, endothelial-growth-factor-receptor-1 and vascular endothelial growth factor play a major role in promoting vascularization and tumor volume expansion. Eventually, molecules such as matrix-metalloprotease-7 and intercellular adhesion molecule-1 contribute to the degradation and remodeling of the extracellular matrix, ultimately leading to glioma progression. Our study delineates the roadmap to develop and evaluate a non-invasive panel of secreted biomarkers using liquid biopsy for precisely evaluating disease progression, to accomplish a clinical translation.

Curcumin in Combination with Other Adjunct Therapies for Brain Tumor Treatment: Existing Knowledge and Blueprint for Future Research

Malignant brain tumors proliferate aggressively and have a debilitating outcome. Surgery followed by chemo-radiotherapy has been the standard procedure of care since 2005 but issues of therapeutic toxicity and relapse still remain unaddressed. Repurposing of drugs to develop novel combinations that can augment existing treatment regimens for brain tumors is the need of the hour. Herein, we discuss studies documenting the use of curcumin as an adjuvant to conventional and alternative therapies for brain tumors. Comprehensive analysis of data suggests that curcumin together with available therapies can generate a synergistic action achieved through multiple molecular targeting, which results in simultaneous inhibition of tumor growth, and reduced treatment-induced toxicity as well as resistance. The review also highlights approaches to increase bioavailability and bioaccumulation of drugs when co-delivered with curcumin using nano-cargos. Despite substantial preclinical work on radio-chemo sensitizing effects of curcumin, to date, there is only a single clinical report on brain tumors. Based on available lab evidence, it is proposed that antibody-conjugated nano-curcumin in combination with sub-toxic doses of conventional or repurposed therapeutics should be designed and tested in clinical studies. This will increase tumor targeting, the bioavailability of the drug combination, reduce therapy resistance, and tumor recurrence through modulation of aberrant signaling cascades; thus improving clinical outcomes in brain malignancies.

Facets of rhizospheric microflora in biocontrol of phytopathogen Macrophomina phaseolina in oil crop soybean

The use of microbial bioinoculants for managing plant diseases and promoting plant growth is an effective alternative approach to integrated farming. One of the devastating phytopathogens is Macrophomina phaseolina (Tassi) Goid. It is an omnipresent fungus infecting more than 500 plant species. It causes charcoal rot disease in soybean leading to 30-50% yield loss. Soybean Glycine max (L.) oil seed crop produced globally is highly susceptible to M. phaseolina. India is the fifth largest producer of soybean in the world. Madhya Pradesh is the largest soybean-producing state in India; Around 70% yield loss of soybean is accounted to M. phaseolina infection in India. Control of charcoal rot is the requisite of the current situation. Chemical control is not feasible due to saprophytic nature and prolonged survival of Macrophomina phaseolina. Chemical fungicides are expensive, toxic, hazardous, and cause pollution. Biological control is an effective approach to control this devastating fungus. The rhizosphere of soil is rich in beneficial microflora competent to suppress plant pathogens and also promote plant growth. PGPR have well-developed mechanisms that impart antagonistic traits to them. PGPR produces various antifungal metabolites siderophores and HCN which inhibit fungal growth, and can be used as potent BCA. Pseudomonas and Bacillus species have been reported effective against M. phaseolina. The mechanisms and antifungal compounds produced by these bacteria to control charcoal rot can be studied extensively. BCA or the metabolites secreted by them have the potential to develop effective bioformulations for soybean at the commercial level for sustainable agriculture.

Expression of H19 long non-coding RNA is down-regulated in oral squamous cell carcinoma

Long non-coding RNAs (lncRNAs) are a group of non-protein-coding RNAs which are longer than 200 nucleotides. LncRNAs play important roles in epigenetic modification, transcription and post-transcriptional regulation, maintenance of normal tissue development and differentiation. LncRNA could serve as a biomarker for diagnosis and prognosis as well as a molecular target for therapy in oral squamous cell carcinoma (OSCC). Therefore, we have determined the expression profile of 5-lncRNAs namely UCA1, TUG1, HOTAIR, MALAT1, and H19 by quantitative real-time PCR in tumor tissues and adjacent normal tissue of 32 OSCC patients. To determine the expression, methylation status and genomic alterations in lncRNAs across pancancer, TCGA datasets were analyzed by UALCAN, MEXPRESS and cBioPortal database. Then, we determined the association between lncRNA expression and clinicopathological attributes of patients by Spearman's rank test. Expression of UCA1 and TUG1 genes was up-regulated in 54.83 % and 53.12 % OSCC tumors, respectively. Importantly, expression of MALAT1 and H19 was down-regulated in tumor tissues of 62.5 % and 81.25 % respectively of OSCC patients. Except for MALAT1, our experimental data showed concordance with the TCGA analysis. Expression of HOTAIR in OSCC tumors was positively correlated with tumor volume, whereas MALAT1 and H19 negatively correlated with the smoking status of patients.

Emergence of antibiotic resistance Pseudomonas aeruginosa in intensive care unit; a critical review

The emergence of antibiotic resistant bacteria in the healthcare is a serious concern. In the Healthcare premises precisely intensive care unit are major sources of microbial diversity. Recent findings have demonstrated not only microbial diversity but also drug resistant microbes largely habitat in ICU. Pseudomonas aeruginosa found as a part of normal intestinal flora and a significant pathogen responsible for wide range of ICU acquired infection in critically ill patients. Nosocomial infection associated with this organism including gastrointestinal infection, urinary tract infections and blood stream infection. Infection caused by this organism are difficult to treat because of the presence of its innate resistance to many antibiotics (β-lactam and penem group of antibiotics), and its ability to acquire further resistance mechanism to multiple class of antibiotics, including Beta-lactams, aminoglycosides and fluoroquinolones. In the molecular evolution microbes adopted several mechanism to maintain genomic plasticity. The tool microbe use for its survival is mainly biofilm formation, quorum sensing, and horizontal gene transfer and enzyme promiscuity. Such genomic plasticity provide an ideal habitat to grow and survive in hearse environment mainly antibiotics pressure. This review focus on infection caused by Pseudomonas aeruginosa, its mechanisms of resistance and available treatment options. The present study provides a systemic review on major source of Pseudomonas aeruginosa in ICU. Further, study also emphasizes virulence gene/s associated with Pseudomonas aeruginosa genome for extended drug resistance. Study gives detailed overview of antibiotic drug resistance mechanism.

Effect of environmental factors on bacterial quorum sensing

Biodegradation of complex hydrocarbons usually requires the cooperation of more than a single species of microorganisms including bacteria. This is particularly true in pollutants that are made up of many different compounds such as crude oil or petroleum, and where complete mineralization to CO2 and H2O is desired. An effort has been made to form the consortium of bacterial isolates (Qs1, Qs2 and Qs5) which are isolated from oil contaminated soil, and the effects of different environmental factors on these consortium has been studied . The growth of the consortium was studied at 6.5 pH and 35°C like the individual bacterial isolates on the different hydrocarbons (xylene, toluene, hexane, diesel, benzene and petrol). These consortium of bacterial isolates, shared more efficient utilization of hydrocarbon as carbon source. This consortium shows confluent growth- at pH 6.0, 5.5, and 5.0 but survival rate decreases at pH above 6.5. Extremes in pH were shown to have a negative influence on the ability of microbial populations to degrade hydrocarbons. They also show the higher growth rate at the higher temperature range (up to 40°C) but their growth rate decreases at lower temperature range (below 25°C). It is suggested that the use of above bacterial consortium (at 35°C temperature and 6.5pH) will be an effective and eco-friendly technology for the remediation of hydrocarbons.

A comparison of the variation in Indian populations of pigeonpea cyst nematode, Heterodera cajani revealed by morphometric and AFLP analysis

The cyst nematode Heterodera cajani is one of the major endemic diseases of pigeonpea, an important legume for food security and protein nutrition in India. It occurs in several pulse crops grown over a range of Indian agro climatic conditions but the extent of its intraspecific variation is inadequately defined. In view of this, 11 populations of Heterodera cajani were analyzed using morphometrics and the results correlated with those obtained from an AFLP approach using 24 primer pair combinations that amplified a total of 1278 AFLP markers. The cluster solution from this binary data indicated similarities for five populations that differed from those suggested by morphometrics. The differences obtained could not be related to geographic distance between populations. The data suggests that recent and long distance dispersal has occurred whose causes need to be defined to restrict further field introductions. Four AFLP primer pairs clustered the populations similarly to that generated using all 24 primer pairs. This simplified approach may provide a rapid basis for discriminating populations for their future management and help to check further distribution in agricultural trade. It may also have potential to determine differences in populations that relate to host range or virulence to resistance genes.

Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.)

This study reports generation of large-scale genomic resources for pigeonpea, a so-called 'orphan crop species' of the semi-arid tropic regions. FLX/454 sequencing carried out on a normalized cDNA pool prepared from 31 tissues produced 494 353 short transcript reads (STRs). Cluster analysis of these STRs, together with 10 817 Sanger ESTs, resulted in a pigeonpea trancriptome assembly (CcTA) comprising of 127 754 tentative unique sequences (TUSs). Functional analysis of these TUSs highlights several active pathways and processes in the sampled tissues. Comparison of the CcTA with the soybean genome showed similarity to 10 857 and 16 367 soybean gene models (depending on alignment methods). Additionally, Illumina 1G sequencing was performed on Fusarium wilt (FW)- and sterility mosaic disease (SMD)-challenged root tissues of 10 resistant and susceptible genotypes. More than 160 million sequence tags were used to identify FW- and SMD-responsive genes. Sequence analysis of CcTA and the Illumina tags identified a large new set of markers for use in genetics and breeding, including 8137 simple sequence repeats, 12 141 single-nucleotide polymorphisms and 5845 intron-spanning regions. Genomic resources developed in this study should be useful for basic and applied research, not only for pigeonpea improvement but also for other related, agronomically important legumes.

Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.)

BACKGROUND

Pigeonpea [Cajanus cajan (L.) Millsp.] is an important legume crop of rainfed agriculture. Despite of concerted research efforts directed to pigeonpea improvement, stagnated productivity of pigeonpea during last several decades may be accounted to prevalence of various biotic and abiotic constraints and the situation is exacerbated by availability of inadequate genomic resources to undertake any molecular breeding programme for accelerated crop improvement. With the objective of enhancing genomic resources for pigeonpea, this study reports for the first time, large scale development of SSR markers from BAC-end sequences and their subsequent use for genetic mapping and hybridity testing in pigeonpea.

RESULTS

A set of 88,860 BAC (bacterial artificial chromosome)-end sequences (BESs) were generated after constructing two BAC libraries by using HindIII (34,560 clones) and BamHI (34,560 clones) restriction enzymes. Clustering based on sequence identity of BESs yielded a set of >52K non-redundant sequences, comprising 35 Mbp or >4% of the pigeonpea genome. These sequences were analyzed to develop annotation lists and subdivide the BESs into genome fractions (e.g., genes, retroelements, transpons and non-annotated sequences). Parallel analysis of BESs for microsatellites or simple sequence repeats (SSRs) identified 18,149 SSRs, from which a set of 6,212 SSRs were selected for further analysis. A total of 3,072 novel SSR primer pairs were synthesized and tested for length polymorphism on a set of 22 parental genotypes of 13 mapping populations segregating for traits of interest. In total, we identified 842 polymorphic SSR markers that will have utility in pigeonpea improvement. Based on these markers, the first SSR-based genetic map comprising of 239 loci was developed for this previously uncharacterized genome. Utility of developed SSR markers was also demonstrated by identifying a set of 42 markers each for two hybrids (ICPH 2671 and ICPH 2438) for genetic purity assessment in commercial hybrid breeding programme.

CONCLUSION

In summary, while BAC libraries and BESs should be useful for genomics studies, BES-SSR markers, and the genetic map should be very useful for linking the genetic map with a future physical map as well as for molecular breeding in pigeonpea.

Isolation and physiological characterization of Synechococcus cedrorum 1191 strain tolerant to heavy metals and pesticides

The toxicity of heavy metals (Hg2+, Zn2+) and pesticides has been investigated by comparing the physiological properties in wild and tolerant strains of Synechococcus cedrorum 1191. The differential pattern of growth, absorption spectra of pigments and nutrient uptake was observed in tolerant strain.