Transcriptomic meta-analysis reveals biomarker pairs and key pathways in Tetralogy of Fallot.

Tetralogy of Fallot (TOF) is a cyanotic congenital condition contributed by genetic, epigenetic as well as environmental factors. We applied sparse machine learning algorithms to RNAseq and sRNAseq data to select the prospective biomarker candidates. Furthermore, we applied filtering techniques to identify a subset of biomarker pairs in TOF. Differential expression analysis disclosed 2757 genes and 214 miRNAs, which are dysregulated. Weighted gene co-expression network analysis on the differentially expressed genes extracted five significant modules that are enriched in GO terms, extracellular matrix, signaling and calcium ion binding. Also, voomNSC selected two genes and five miRNAs and transformed PLDA-predicted 72 genes and 38 miRNAs as prognostic biomarkers. Out of the selected biomarkers, miRNA target analysis revealed 14 miRNA-gene interactions. Also, 10 out of 14 pairs were oppositely expressed and four out of 10 oppositely expressed biomarker pairs shared common pathways of focal adhesion and P13K-Akt signaling. In conclusion, our study demonstrated the concept of biomarker pairs, which may be considered for clinical validation due to the high literature as well as experimental support.

Optimization of parameters to improve transformation efficiency of elephant foot yam (Amorphophallus paeoniifolius (Dennst.) Nicolson.

Elephant foot yam (Amorphophallus paeoniifolius (Dennst.) Nicolson), is an important edible tropical tuber crop, belonging to the family Araceae. Corms produced by this plant is very big and they are rich in starch, protein, mineral, vitamins, and dietary fiber but has acridity problem. This crop is susceptible to virus and phytoplasma diseases which affects crop growth and corm yield. Even though this crop has high commercial value, the problems like susceptibility to viral diseases, acridity problems, and lack of genetic diversity made hindrance in their exploitation. These issues can be resolved only by improving the characters through genetic transformation. To achieve genetic transformation in this important crop, a study was conducted to optimize various parameters for efficient Agrobacterium-mediated genetic transformation using embryogenic calli with vectors having gus reporter gene. Calli were developed using petiole and leaves of in vitro plantlets of elephant foot yam cultivar Gajendra and experiments were conducted to evaluate the sensitivity of calli to different doses of antibiotics viz. geneticin, hygromycin, ticarcillin. It was observed that complete death and discoloration of the calli were obtained with 25 mgl-1 geneticin and 10 mgl-1 hygromycin. The lowest lethal concentration of ticarcillin against Agrobacterium growth was found to be 500 mgl-1 which did not affect calli growth. Optimized parameters for efficient transformation in elephant foot yam include 100 µM acetosyringone concentration with 2 days of co-cultivation at temperature 22 °C using LBA4404 strain. The putative transformants were characterized for the integration of the gus gene using PCR and nucleic acid spot hybridization. The optimized protocol is simple and reproducible and may be adapted for other cultivars also. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02824-6.

Pre evaluation of cassava (Manihot esculenta Crantz) germplasm for genotypic variation in the identification of K efficient genotypes through different statistical tools.

Among the tropical tuber crops, cassava (Manihot esculenta Crantz) deserves special attention as regards to its higher biological efficiency in terms of dry matter production which incidentally implies to the higher amount of nutrient extraction from the soil resulting in better response to the application of manures and fertilizers. Among the major nutrients, Potassium (K) is considered as the key nutrient for cassava owing to its influence both in tuber yield and tuber quality. The above facts as well as the availability of sufficient cassava genotypes in the germplasm collection of ICAR-CTCRI made us to initiate research work to screen cassava germplasm including the pre breeding lines. The objective being to identify K efficient genotypes which can yield well under limited availability of K so that the external application of K can be reduced. This paper describes the wide variation noticed during the pre evaluation of 83 elite genotypes which was done as a prelude in the screening and identification of K efficient genotypes. The characters studied were tuber yield, tuber characters, plant dry matter percentage, plant K content, tuber quality (starch, cyanogenic glucosides) attributes, physiological efficiency and plant biometric characters. The variation among the genotypes for the above traits was assessed by making some yardstick for classification which in turn helped in determining the percent distribution of genotypes in each category. The variation among the genotypes were further affirmed through principal component analysis, wherein the first five components explained more than 77% of variability and the cluster analysis performed grouped these genotypes into five clusters. The biplot showed the traits which are closely linked to the genotypes. The dendrogram constructed indicated similar genotypes to that of the clusters to the extent of more than 50% revealing the association of members with similar traits in clusters and dendrograms. The study helped in establishing the drastic variation among the genotypes along with identification of six genotypes viz., Aniyoor, 7 Sahya (2), 7 III E3-5, W-19, CR 43-8, 6-6 for further detailed experimentation to identify K efficient genotypes.

Bioprospecting endophytic diazotrophic Lysinibacillus sphaericus as biocontrol agents of rice sheath blight disease.

The present study tried to explore the possible in vitro biocontrol mechanisms of Lysinibacillus sphaericus, a diazotrophic endophyte from rice against the rice sheath blight pathogen Rhizoctonia solani. The in vivo biocontrol potential of the isolate and the induction of systemic resistance under greenhouse conditions have also been experimented employing different treatments with positive control carbendazim, the chemical fungicide. The endophytic isolate showed 100% growth inhibition of the fungal pathogen via volatile organic compound production and was positive for the production of siderophores, biosurfactants, HCN, and ammonia. Under greenhouse conditions, foliar and soil application of L. sphaericus significantly decreased the percentage of disease incidence. All bacterized treatments are superior to chemical fungicide treatment. Application of L. sphaericus in single and combination treatments induces systemic resistance as evident from the significant accumulation of defense enzymes such as peroxides, polyphenol oxides and phenylalanine ammonia in addition to the increase of phenolic compounds. The results biologically prospect endophytic diazotroph L. sphaericus as a potent plant growth promoter with excellent biocontrol efficiency.

Diagnosis of Helicobacter pylori by carbon-13 urea breath test using a portable mass spectrometer.

CONTEXT: In the non-invasive detection of markers of disease, mass spectrometry is able to detect small quantities of volatile markers in exhaled air. However, the problem of size, expense and immobility of conventional mass spectrometry equipment has restricted its use. Now, a smaller, less expensive, portable quadrupole mass spectrometer system has been developed. Helicobacter pylori has been implicated in the development of chronic gastritis, gastric and duodenal ulcers and gastric cancer. OBJECTIVES: To compare the results obtained from the presence of H. pylori by a carbon-13 urea test using a portable quadrupole mass spectrometer system with those from a fixed mass spectrometer in a hospital-based clinical trial. METHODS: Following ethical approval, 45 patients attending a gastroenterology clinic at the Royal Liverpool University Hospital exhaled a breath sample into a Tedlar gas sampling bag. They then drank an orange juice containing urea radiolabelled with carbon and 30 min later gave a second breath sample. The carbon-13 content of both samples was measured using both quadrupole mass spectrometer systems. If the post-drink level exceeded the pre-drink level by 3% or more, a positive diagnosis for the presence of H. pylori was made. RESULTS: The findings were compared to the results using conventional isotope ratio mass spectrometry using a laboratory-based magnetic sector instrument off-site. The results showed agreement in 39 of the 45 patients. CONCLUSIONS: This study suggests that a portable quadrupole mass spectrometer is a potential alternative to the conventional centralised testing equipment. Future development of the portable quadrupole mass spectrometer to reduce further its size and cost is indicated, together with further work to validate this new equipment and to enhance its use in mass spectrometry diagnosis of other medical conditions.

Kinetics of thermal softening of cassava tubers and rheological modeling of the starch.

Cassava or tapioca (Manihot esculenta Crantz) tubers having high amount of carbohydrate are utilized after boiling or processing into starch and flour. Textural properties of raw and cooked tubers depend on variety, maturity, growing environment, physico-chemical and starch properties. Starch is used in food preparations as gelling and thickening agent, stabilizer and texture modifier. This study aims at analyzing and modeling the textural, dynamic rheological and gelatinization properties of selected cassava varieties. The thermal softening behavior was analyzed by linear regression and fractional conversion techniques, rheological properties of the gelated starch by Maxwell and power law models. The varieties were classified based on their physico-chemical, texture profile, rheological and gelatinization properties by multivariate analysis. The textural, rheological and gelatinization properties were significantly affected by the varieties (p < 0.05). Thermal softening of tubers was modeled by dual mechanism first order kinetic model with rate constant values ranging from 0.081 to 0.105 min(-1). Linear regression models with extremely good fit were obtained to explain the relationship between the degree of cooking and relative firmness. The dynamic spectra of the gelated starch showed the characteristics of concentrated biopolymer dispersion and described using Maxwell and power law model. The results showed that textural, rheological and gelatinization properties varied considerably among the varieties and besides the physico-chemical properties, interaction between them and structural make up of the tuber parenchyma had a great influence on cooking quality and rheological properties.

Diadochokinesimetry: a study of patients with Parkinson's disease and manganese exposed workers.

Diadochokinesia, the ability to perform rapid alternating movements is often impaired in patients with extrapyramidal disease. It is a common sign among patients with Parkinsonism or manganism. In the present study we compare patients with Parkinson's disease (n = 11), workers formerly exposed to manganese (n = 10) and control subjects (n = 11) performing rapid alternating hand movements for 5 s under four conditions repeated twice (natural cadence and maximal speed with one or two hands). Data recorded using a diadochokinesimeter built in our laboratory and connected to a 486/33 microcomputer were digitized in real time while subjects rotated back and forth hand held foam spheres connected to flexible rods articulated with optical encoders. Significant differences were found between control subjects and patients with Parkinson's disease, but not with manganese exposed workers, in most variables examined. However, trajectory length (a combination of movement amplitude and velocity) indicated that manganese exposed workers and patients with Parkinson's disease were significantly different from the controls in functional asymmetries between right and left hand. In addition, workers and patients tend to have marked differences between the performance of right and left hands. Improved quantitative measurement of rapid alternating movements may prove to be an important tool in early and differential diagnosis of Parkinson's disease and manganese exposure.