Sequence fingerprints distinguish erroneous from correct predictions of Intrinsically Disordered Protein Regions

More than sixty prediction methods for intrinsically disordered proteins (IDPs) have been developed over the years, many of which are accessible on the world-wide web. Nearly, all of these predictors give balanced accuracies in the ~65% to ~80% range. Since predictors are not perfect, further studies are required to uncover the role of amino acid residues in native IDP as compared to predicted IDP regions. In the present work, we make use of sequences of 100% predicted IDP regions, false positive disorder predictions, and experimentally determined IDP regions to distinguish the characteristics of native versus predicted IDP regions. A higher occurrence of asparagine is observed in sequences of native IDP regions but not in sequences of false positive predictions of IDP regions. The occurrences of certain combinations of amino acids at the pentapeptide level provide a distinguishing feature in the IDPs with respect to globular proteins. The distinguishing features presented in this paper provide insights into the sequence fingerprints of amino acid residues in experimentally-determined as compared to predicted IDP regions. These observations and additional work along these lines should enable the development of improvements in the accuracy of disorder prediction algorithm

Grey Relational Analysis and Anova to Determine the Optimum Process Parameters for Friction Stir Welding of Ti and Mg Alloys

The welding of Magnesium and Titanium and its alloys has continuously depicted a good challenge for designers and technologists. Ti and Mg alloys, particularly heat-treatable alloys, are difficult to join by fusion fastening techniques. The welding of dissimilar alloy such as Ti (Grade 2) and Mg (AZ91D) Alloy is an important problem during Friction Stir Welding (FSW). In this paper, the influence of Rotation speed (Rpm), Travel Speed (mm/min), Bottom Diameter Tool Pins (mm) and Tool Profiles of Ti and Mg alloy during FSW was investigated by Grey Relational Analysis and Anova was used to work out the foremost important Travel speed and feed rate affecting the Response. The primary and cooperation impact of the information factors on the normal reactions are examined. The expected values and measured values are genuinely close

Comparative Metabolomic Profiling of Horse Gram (Macrotyloma uniflorum (Lam.) Verdc.) Genotypes for Horse Gram Yellow Mosaic Virus Resistance

Horse gram (Macrotyloma uniflorum (Lam.) Verdc.) is an under-utilized legume grown in India. It is a good source of protein, carbohydrates, dietary fiber, minerals, and vitamins. We screened 252 horse gram germplasm accessions for horse gram yellow mosaic virus resistance using the percent disease index and scaling techniques. The percentage values of highly resistant, moderately resistant, moderately susceptible, susceptible, and highly susceptible were 0.34, 13.89, 38.89, 46.43, and 0.34, respectively. Repetitive trials confirmed the host-plant resistance levels, and yield loss was assessed. The present disease index ranged from 1.2 to 72.0 and 1.2 to 73.0 during the kharif and rabi seasons of 2018, respectively. The maximum percent yield loss was noticed in the HS (75.0 -89.4), while HR possessed the minimum (1.2-2.0). The methanolic leaf extracts of highly resistant and highly susceptible genotypes with essential controls were subjected to gas chromatography-mass spectrometry analysis. Differential accumulation of metabolites was noticed, and a total of 81 metabolites representing 26 functional groups were identified. Both highly resistant and susceptible genotypes harbored eight unique classes, while ten biomolecules were common. The hierarchical cluster analysis indicated a distinct metabolite profile. Fold change in the common metabolites revealed an enhanced accumulation of sugars, alkanes, and carboxylic acids in the highly resistant genotype. The principal component analysis plots explained 93.7% of the variation. The metabolite profile showed a significant accumulation of three anti-viral (octadecanoic acid, diphenyl sulfone, and 2-Aminooxazole), one insecticidal (9,10-Secocholesta-5,7,10(19)-triene-3,24,25-triol), one antifeedant (cucurbitacin B), and six metabolites with unknown biological function in the highly resistant genotype

Techniques of Using Peripheral Blood Mononuclear Cells as the Cellular System to Investigate How of the Bovine Species (Indian Zebu-Jersey Crossbreds) Responds to <em>in vitro</em> Thermal Stress Stimulation (Thermal Assault/Heat Shock)

Animal production is negatively impacted by global warming and is subject to serious consequences for livestock production systems. In order to understand how PBMCs of Indian Zebu-Jersey crossbreds respond to various levels and durations of thermal assault and heat shock, in this chapter we will discuss techniques involving in vitro thermal stress stimulation (TSS) to stimulate bovine peripheral blood mononuclear cells (PBMCs) under various thermal assault conditions (TACs), including normal to extreme temperatures and varying durations of thermal exposure (DTEs). The consequences of thermal stress on bovine species can be lessened and managed with an understanding of how PBMCs as a cellular system respond to in vitro heat shock and thermal assault. To learn more about how Indian Zebu-Jersey crossbreds respond to in vitro thermal conditions, it may also be possible to explore the relationship between the decrease in PBMCs count during in vitro TSS and the expression of the heat shock protein genes (HSPs) such as HSPs 70 and 90 genes. This will be exploited to discover how Indian Zebu-Jersey crossbreds respond in vivo to diverse environmental thermal conditions and will further enable in vivo understanding of the potential for thermotolerance in bovine species for better adaptability, survival, and production performance

An investigation into the age and origin of Suranga in the foothills of the Western Ghats of India

This document is the Accepted Manuscript version. The final publication is available at Springer via: https://doi.org/10.1007/s12685-015-0125-yThis paper presents the evidence for determining the age and origin of suranga irrigation found mainly in southern Karnataka and northern Kerala in the foothills of the Western Ghats of south India. It draws on on-going research that has attempted to use an interdisciplinary approach to date the system using Indian Archives, British and Portuguese colonial archives, etymology, oral testimony archaeology, phenology and palaeo dating techniques. The results from this study put the origins of the system at around 1900–1940 CE. These results are compared with the current academic discourse that supports the view that the system originates from ancient Persia and qanat technology, because of the long established trade links with Persia and the Arabian Peninsula in the Malabar region. We argue that a new ‘origin discourse’ should be framed around these much more recent dates. The methodological constraints behind both theories are discussed throughout to enable the reader to appreciate the limitations of both arguments.Peer reviewedFinal Accepted Versio

Characteristic Investigation of Macro Fiber Composite Structure Using FE Model

In this investigation, the effective mechanical, coupling and dielectric properties of Macro-fiber-composites (MFCs) consisting of piezorod-element constituents are determined using representative volume element method combined with finite element analysis. Experiments are conducted on piezo-bar-element MFCs to understand the applicability of the proposed approach which would later be extended to composites with modified geometric pattern. The longitudinal strains with respect to static deflections of beam and forced displacements under varying electrical loads are measured for the MFCs, and compared with the numerical simulations. Based on the good agreement from the result comparisons of piezo-bar-element MFCs, the effective material properties of piezo-rod-element MFCs are numerically determined based on the RVE approach

Sequence fingerprints distinguish erroneous from correct predictions of intrinsically disordered protein regions

<p>More than 60 prediction methods for intrinsically disordered proteins (IDPs) have been developed over the years, many of which are accessible on the World Wide Web. Nearly, all of these predictors give balanced accuracies in the ~65%–~80% range. Since predictors are not perfect, further studies are required to uncover the role of amino acid residues in native IDP as compared to predicted IDP regions. In the present work, we make use of sequences of 100% predicted IDP regions, false positive disorder predictions, and experimentally determined IDP regions to distinguish the characteristics of native versus predicted IDP regions. A higher occurrence of asparagine is observed in sequences of native IDP regions but not in sequences of false positive predictions of IDP regions. The occurrences of certain combinations of amino acids at the pentapeptide level provide a distinguishing feature in the IDPs with respect to globular proteins. The distinguishing features presented in this paper provide insights into the sequence fingerprints of amino acid residues in experimentally determined as compared to predicted IDP regions. These observations and additional work along these lines should enable the development of improvements in the accuracy of disorder prediction algorithm.</p

Comparative Metabolomic Profiling of Horse Gram (<i>Macrotyloma uniflorum</i> (Lam.) Verdc.) Genotypes for Horse Gram Yellow Mosaic Virus Resistance

Horse gram (Macrotyloma uniflorum (Lam.) Verdc.) is an under-utilized legume grown in India. It is a good source of protein, carbohydrates, dietary fiber, minerals, and vitamins. We screened 252 horse gram germplasm accessions for horse gram yellow mosaic virus resistance using the percent disease index and scaling techniques. The percentage values of highly resistant, moderately resistant, moderately susceptible, susceptible, and highly susceptible were 0.34, 13.89, 38.89, 46.43, and 0.34, respectively. Repetitive trials confirmed the host-plant resistance levels, and yield loss was assessed. The present disease index ranged from 1.2 to 72.0 and 1.2 to 73.0 during the kharif and rabi seasons of 2018, respectively. The maximum percent yield loss was noticed in the HS (75.0 –89.4), while HR possessed the minimum (1.2–2.0). The methanolic leaf extracts of highly resistant and highly susceptible genotypes with essential controls were subjected to gas chromatography–mass spectrometry analysis. Differential accumulation of metabolites was noticed, and a total of 81 metabolites representing 26 functional groups were identified. Both highly resistant and susceptible genotypes harbored eight unique classes, while ten biomolecules were common. The hierarchical cluster analysis indicated a distinct metabolite profile. Fold change in the common metabolites revealed an enhanced accumulation of sugars, alkanes, and carboxylic acids in the highly resistant genotype. The principal component analysis plots explained 93.7% of the variation. The metabolite profile showed a significant accumulation of three anti-viral (octadecanoic acid, diphenyl sulfone, and 2-Aminooxazole), one insecticidal (9,10-Secocholesta-5,7,10(19)-triene-3,24,25-triol), one antifeedant (cucurbitacin B), and six metabolites with unknown biological function in the highly resistant genotype

Not Available

Not AvailableThe development of a negative marker vaccine against the foot-and-mouth disease virus (FMDV) will enhance the capabilities to differentiate vaccinated from infected animals and move forward in the progressive control pathway for the control of FMD. Here, we report the development of mutant FMDV of Asia1 with partial deletion of non-structural proteins 3A and 3B and characterization of their infectivity and protection response in the guinea pig model. The deleted FMDV Asia1/ IND/63/1972 mutants, pAsiaΔ3A and pAsiaΔ3A3B1 were constructed from the full-length infectious clone pAsiaWT, the viable virus was rescued, and the genetic stability of the mutants was confirmed by 20 monolayer passages in BHK21 cells. The mutant Asia1 viruses showed comparable growth pattern and infectivity with that of AsiaWT in the cell culture. However, the AsiaΔ3A3B1 virus showed smaller plaque and lower virus titer with reduced infectivity in the suckling mice. In guinea pigs, the AsiaΔ3A3B1 virus failed to induce the disease, whereas the AsiaΔ3A virus induced typical secondary lesions of FMD. Vaccination with inactivated Asia1 mutant viruses induced neutralizing antibody response that was significantly lower than that of the parent virus on day 28 post-vaccination (dpv) in guinea pigs (P < 0.05). Furthermore, challenging the vaccinated guinea pigs with the homologous vaccine strain of FMDV Asia1 conferred complete protection. It is concluded that the mutant AsiaΔ3A3B1 virus has the potential to replace the wild-type virus for use as a negative marker vaccine after assessing the vaccine worth attributes in suspension cell and protective efficacy study in cattle.CAAST; ICAR-IVR