Evaluation of supplemented protein-L-isoaspartate-O-methyltransferase (PIMT) gene of Carica papaya and Ricinus communis in stress survival of Escherichia coli BL21(DE3) cells.

In growing plant population, effect of stress is a perturb issue affecting its physiological, biochemical, yield loss and developmental growth. Protein-L-isoaspartate-O-methyltransferase (PIMT) is a broadly distributed protein repair enzyme which actuate under stressful environment or aging. Stress can mediate damage converting protein bound aspartate (Asp) residues to isoaspartate (iso-Asp). This spontaneous and deleterious conversion occurs at an elevated state of stress and aging. Iso-Asp formation is associated with protein inactivation and compromised cellular survival. PIMT can convert iso-Asp back to Asp, thus repairing and contributing to cellular survival. The present work describes the isolation, cloning, sequencing and expression of PIMT genes of Carica papaya (Cp pimt) and Ricinus communis (Rc pimt) Using gene specific primers, both the pimts were amplified from their respective cDNAs and subsequently cloned in prokaryotic expression vector pProEXHTa. BL21(DE3) strain of E. coli cells were used as expression host. The expression kinetics of both the PIMTs were studied with various concentrations of IPTG and at different time points. Finally, the PIMT supplemented BL21(DE3) cells were evaluated against different stresses in comparison to their counterparts with the empty vector control.

Planar hyperbolic polaritons in 2D van der Waals materials.

Anisotropic planar polaritons - hybrid electromagnetic modes mediated by phonons, plasmons, or excitons - in biaxial two-dimensional (2D) van der Waals crystals have attracted significant attention due to their fundamental physics and potential nanophotonic applications. In this Perspective, we review the properties of planar hyperbolic polaritons and the variety of methods that can be used to experimentally tune them. We argue that such natural, planar hyperbolic media should be fairly common in biaxial and uniaxial 2D and 1D van der Waals crystals, and identify the untapped opportunities they could enable for functional (i.e. ferromagnetic, ferroelectric, and piezoelectric) polaritons. Lastly, we provide our perspectives on the technological applications of such planar hyperbolic polaritons.

Novel Nano-Electroplating-Based Plasmonic Platform for Giant Emission Enhancement in Monolayer Semiconductors.

Two-dimensional semiconductors such as monolayer MoS2 have attracted considerable attention owing to their exceptional electronic and optical characteristics. However, their practical application has been hindered by the limited light absorption resulting from atomically thin thickness and low quantum yield. A highly effective approach to address these limitations is by integrating subwavelength plasmonic nanostructures with monolayer semiconductors. In this study, we employed electron beam lithography and nanoelectroplating techniques to develop a gold nanodisc (AuND) array plasmonic platform. Monolayer MoS2 transferred on top of the AuND array yields up to 150-fold photoluminescence enhancement compared to a gold film without normalization with respect to plasmonic hot spots. In addition, the unique protocol of nanoelectroplating helps to get flat-top cylindrical discs which enable less tear during the delicate wet transfer of monolayer MoS2. We explain our experimental findings based on electromagnetic simulations.

Prediction, Synthesis and Evaluation of a Synthetic Peptide as an Enzyme-Linked Immunosorbent Assay (ELISA) Candidate for Screening of Bovine Antibodies against Theileria annulata.

Tick-borne diseases (TBDs) of livestock are endemic across various parts of tropical countries. Theileriosis is one such economically important TBD, caused by the Theileriidae family of organisms, which is transmitted by ticks. Theileria annulata, the causative agent of tropical theileriosis, contributes a significant loss to the dairy sector by causing anorexia, high fever, anemia, inflammatory changes in vital organs and icterus, thus, a loss in milk yield. Though vaccines are available, their protective efficacy is not absolute, and treatment is limited to early diagnosis of the causative agent. Routinely, microscopic identification of piroplasms in the erythrocytes (Giemsa-stained) of infected animals or schizonts in lymph node biopsies are practiced for diagnosis. PCR-based techniques (multiplex, uniplex, nested and real-time) have been reported to perform well in diagnosing active infection. Several attempts have been made using serological assays like Dot blot, ELISA and ICT, but the results were of variable sensitivity and specificity. Recombinant proteins like the Theileria annulata merozoite surface antigen (Tams1) and Theileria annulata surface protein (TaSP) have been explored as antigenic candidates for these assays. In the present study, we predicted an immunogenic peptide, i.e., TaSP-34, from the TaSP using various computational tools. The predicted peptide was custom synthesized. The diagnostic potential of the peptide was assessed by indirect plate ELISA to detect the bovine-IgM against Theileria annulata. Alongside, a recombinant truncated TaSP (rTaSP(tr)) was expressed and purified, which was used to compare the performance of the peptide as a diagnostic candidate. The IgM-based peptide ELISA was 100% sensitive and 92.77% specific as compared to PCR (Tams1 targeting), while 98.04% sensitivity and 97.44% specificity were observed in comparison with rTaSP(tr) ELISA. Almost perfect agreement between peptide ELISA and Tams1 PCR was observed with a Cohen's kappa coefficient (κ-value) of 0.901 and agreement of 95.31%. Further, the κ-value between the peptide ELISA and rTaSP(tr) ELISA was found to be 0.95, and the agreement was 97.65%, which shows a good correlation between the two tests. The findings suggest that the TaSP-34 peptide can be an efficient and new-generation diagnostic candidate for the diagnosis of T. annulata. Furthermore, the peptide can be synthesized commercially at a larger scale and can be a cost-effective alternative for the protein-based diagnostic candidates for T. annulata.

Electron/Hole Mobilities of Periodic DNA and Nucleobase Structures from Large-Scale DFT Calculations.

Electron/hole transfer mechanisms in DNA and polynucleotide structures continue to garner considerable interest as emerging charge-transport systems and molecular electronics. To shed mechanistic insight into these electronic properties, we carried out large-scale density functional theory (DFT) calculations (up to 650 atoms) to systematically analyze the structural and electron/hole transport properties of fully periodic single- and double-stranded DNA. We examined the performance of various exchange-correlation functionals (LDA, BLYP, B3LYP, and B3LYP-D) and found that single-stranded thymine (T) and cytosine (C) are predominantly hole conductors, whereas single-stranded adenine (A) and guanine (G) are better electron conductors. For double-stranded DNA structures, the periodic A-T and G-C electronic band structures undergo a significant renormalization, which causes hole transport to only occur on the A and G nucleobases. Our calculations (1) provide new benchmarks for periodic nucleobase structures using dispersion-corrected hybrid functionals with large basis sets and (2) highlight the importance of dispersion effects for obtaining accurate geometries and electron/hole mobilities in these extended systems.

Mitochondrial DNA content as a biomarker for oral carcinogenesis: correlation with clinicopathologic parameters.

BACKGROUND: Mitochondrial genome (mtDNA) exhibits greater vulnerability to mutations and/or copy number variations than nuclear counterpart (nDNA) in both normal and cancer cells due to oxidative stress generated by inflammation, viral infections, physical, mechanical, and chemical load. The study was designed to evaluate the mtDNA content in oral potentially malignant disorders (OPMDs) and oral squamous cell carcinoma (OSCC). Various parameters were analyzed including its variation with human papillomavirus (HPV) during oral carcinogenesis. METHODS: The present cross-sectional study comprised of two hundred patients (100 OPMDs and 100 OSCCs) and 100 healthy controls. PCR amplifications were done for mtDNA content and HPV in OPMDs and OSCC using real-time and conventional PCR respectively. RESULTS: The relative mtDNA content was assessed quantitatively and it was observed that mtDNA was greater in OSCC (7.60±0.94) followed by OPMDs (5.93±0.92) and controls (5.37±0.95). It showed a positive linear correlation with habits and increasing histopathological grades. Total HPV-positive study groups showed higher mtDNA content (7.06±1.64) than HPV-negative counterparts (6.21±1.29). CONCLUSIONS: An elevated mutant mtDNA may be attributed to increased free radicals and selective cell clonal proliferation in test groups. Moreover, sustained HPV infection enhances tumorigenesis through mitochondria mediated apoptosis. Since, mtDNA content is directly linked to oxidative DNA damage, these quantifications might serve as a surrogate measure for invasiveness in dysplastic lesions and typify their malignant potential.

Electroplating-based engineering of plasmonic nanorod metamaterials for biosensing applications.

Sensing lower molecular weight in a diluted solution using a label-free biosensor is challenging and requires a miniaturized plasmonic structure, e.g. a vertical Au nanorod (AuNR) array-based metamaterials. The sensitivity of a sensor mainly depends on transducer properties and hence for instance, the AuNR array geometry requires optimization. Physical vapour deposition methods (e.g. sputtering and e-beam evaporation) require a vacuum environment to deposit Au, which is costly, time-consuming, and thickness-limited. On the other hand, chemical deposition, i.e. electroplating deposit higher thickness in less time and at lower cost, becomes an alternative method for Au deposition. In this work, we present a detailed optimization for the electroplating-based fabrication of these metamaterials. We find that slightly acidic (6.0 < pH < 7.0) gold sulfite solution supports immersion deposition, which should be minimized to avoid uncontrolled Au deposition. Immersion deposition leads to plate-like (for smaller radius AuNR) or capped-like, i.e. mushroom (for higher radius AuNR) structure formation. The electroplating time and DC supply are the tuning parameters that decide the geometry of the vertically aligned AuNR array in area-dependent electroplating deposition. This work will have implications for developing plasmonic metamaterial-based sensors.

GPU-Enhanced DFTB Metadynamics for Efficiently Predicting Free Energies of Biochemical Systems.

Metadynamics calculations of large chemical systems with ab initio methods are computationally prohibitive due to the extensive sampling required to simulate the large degrees of freedom in these systems. To address this computational bottleneck, we utilized a GPU-enhanced density functional tight binding (DFTB) approach on a massively parallelized cloud computing platform to efficiently calculate the thermodynamics and metadynamics of biochemical systems. To first validate our approach, we calculated the free-energy surfaces of alanine dipeptide and showed that our GPU-enhanced DFTB calculations qualitatively agree with computationally-intensive hybrid DFT benchmarks, whereas classical force fields give significant errors. Most importantly, we show that our GPU-accelerated DFTB calculations are significantly faster than previous approaches by up to two orders of magnitude. To further extend our GPU-enhanced DFTB approach, we also carried out a 10 ns metadynamics simulation of remdesivir, which is prohibitively out of reach for routine DFT-based metadynamics calculations. We find that the free-energy surfaces of remdesivir obtained from DFTB and classical force fields differ significantly, where the latter overestimates the internal energy contribution of high free-energy states. Taken together, our benchmark tests, analyses, and extensions to large biochemical systems highlight the use of GPU-enhanced DFTB simulations for efficiently predicting the free-energy surfaces/thermodynamics of large biochemical systems.

Effect of non-genetic factors on linear type traits in Karan fries (Bos taurus × Bos indicus) and Sahiwal (Bos indicus) cows in sub-tropical climatic conditions of India.

The focus of present study was to find out the effect of non-genetic factors on linear type traits in Karan Fries and Sahiwal cows reared at an organized farm of northern India. The present study was conducted on Lactating Karan Fries (N = 123) and Sahiwal (N = 133) cows maintained at Livestock Research Center of ICAR- National Dairy Research Institute, Karnal, India during the period of 2017-2019. Total eight udder morphometric traits and seven teat morphometric traits were measured. The linear model including fixed effects of season, parity and stage of lactation was used for the analysis. In Karan Fries cows, linear type traits were significantly affected by parity and stage of lactation, while in Sahiwal cows linear type traits were significantly affected by season, parity and stage of lactation. Udder depth (UD) and udder circumference (UC) were significantly (p < 0.05) affected by season, parity and stage of lactation in Sahiwal cattle, while in Karan Fries cattle udder length (UL) and shortest distance from rear teat ends to floor (SDR) were significantly (p < 0.01) affected by parity and stage of lactation. The results pertaining to present study indicated that season, parity and stages of lactation were important sources of variation for most of linear type traits. Adjustment of data for these effects is necessary to reduce known differences between animals and to obtain reliable estimates of the traits.

Elective Neck Dissection Versus Therapeutic Neck Dissection in Clinically Node-Negative Early Stage Oral Cancer: A Meta-analysis of Randomized Controlled Trials.

Introduction: Oral squamous cell carcinoma (OSCC) is characterized by a high risk of cervical lymph node metastasis; however, it is still not clear whether patients with early stage OSCC with clinical N0 neck should undergo elective neck dissection (END) at the time of primary tumor removal, or they should undergo a conservative approach of observation (OBS), with therapeutic neck dissection at the time of lymph nodal recurrence. We conducted a meta-analysis of randomized controlled trials (RCTs) that compared these two approaches. Methods: PubMed and Scopus databases were searched for RCTs published in English language related to END and OBS in patients with early stage OSCC with clinical N0 neck. A meta-analysis was performed using random effects model with hazard ratio (HR) as the effect size for survival parameters and odds ratio (OR) as the effect size for lymph nodal recurrence. Results: A total of 7 RCTs, comprising 1250 patients were included in the meta-analysis. Results of the meta-analyses showed that as compared to OBS approach, END could significantly improve overall survival (HR 0.67; 95% CI 0.53, 0.86) and disease-free survival (HR 0.64; 95% CI 0.46, 0.89), and significantly reduce lymph nodal recurrence (OR 0.28; 95% CI 0.12, 0.66). After correcting for heterogeneity, the disease specific survival was also found to be improved by the END approach (HR 0.53; 95% CI 0.29, 0.98). Conclusion: The results of this meta-analysis suggest that elective neck dissection at the time of resection of the primary tumor not only leads to a reduced chance of nodal recurrence, but also confers a survival benefit in patients with clinically node-negative early stage oral cancer.

Plunging Ranula: A Case Report of a Rare Late Complication After Tongue Cancer Surgery.

A plunging ranula is a benign cystic lesion in the neck formed due to mucin extravasated from a salivary gland, most commonly the sublingual gland. Ranulas have been described in association with congenital anomalies, trauma, diseases of the sublingual gland, and HIV; however, rarely, they may result as a complication of various oral and neck surgeries. Here, we report a rare case of plunging ranula that developed in an elderly male as a sequalae to surgery for tongue cancer. The patient had undergone a partial glossectomy with supra-omohyoid neck dissection for tongue carcinoma and nine months later presented with cystic swelling on the floor of the mouth that was followed by neck swelling. It was treated successfully by excision, and the histopathology confirmed the diagnosis of ranula. We postulate that the tongue cancer surgery could have caused an inadvertent injury to the ducts of the sublingual salivary gland and mylohyoid muscle, leading to the development of a plunging ranula. Our case reiterates that surgeons need to be aware of the anatomy of the submandibular and submental region to avoid any surgical trauma to the sublingual and submandibular glands and their ducts along with the associated mylohyoid muscle.

Boosting quantum yields in two-dimensional semiconductors via proximal metal plates.

Monolayer transition metal dichalcogenides (1L-TMDs) have tremendous potential as atomically thin, direct bandgap semiconductors that can be used as convenient building blocks for quantum photonic devices. However, the short exciton lifetime due to the defect traps and the strong exciton-exciton interaction in TMDs has significantly limited the efficiency of exciton emission from this class of materials. Here, we show that exciton-exciton interaction in 1L-WS2 can be effectively screened using an ultra-flat Au film substrate separated by multilayers of hexagonal boron nitride. Under this geometry, induced dipolar exciton-exciton interaction becomes quadrupole-quadrupole interaction because of effective image dipoles formed within the metal. The suppressed exciton-exciton interaction leads to a significantly improved quantum yield by an order of magnitude, which is also accompanied by a reduction in the exciton-exciton annihilation (EEA) rate, as confirmed by time-resolved optical measurements. A theoretical model accounting for the screening of the dipole-dipole interaction is in a good agreement with the dependence of EEA on exciton densities. Our results suggest that fundamental EEA processes in the TMD can be engineered through proximal metallic screening, which represents a practical approach towards high-efficiency 2D light emitters.

Casein (CSN) gene variants and parity affect the milk protein traits in crossbred (Bos taurus x Bos indicus) cows in sub-tropical climate.

Genotypes at four casein (CSN) loci-A26181G of CSN1S1, C6227T of CSN1S2, A8101C of CSN2, and A13104C of CSN3-along with non-genetic factors were studied for their effects on various milk protein traits in 100 crossbred cows with major inheritance of Holstein Frisian (Bos taurus) and Tharparkar (Bos indicus). Results demonstrated the presence of all CSN genotypes with a predominance of heterozygotes. At CSN2 (A8101C; His67Pro) locus, the A2 allele, desirable for human health, was present in 62% as heterozygous and 29% in homozygous condition. Among non-genetic factors, parity of the cows had a significant influence on the milk protein traits in these crossbreds. The genotypes at CSN1S1, CSN2, and CSN3 loci were found to influence (p<0.05 to 0.01) the casein and whey protein yields and composition traits. The casein index and total milk yield were most influenced by the CSN1S2 locus. The AA (A1 milk) genotype of CSN2 had significantly higher yields and percentages of casein and whey proteins. Positive influence of CC genotype of CSNS3 on milk proteins of was observed similar to Bos taurus cows; however, such influence of AA genotype of CSN2 locus may be distinctive to the crossbred cows maintained in subtropical condition. Overall, the results revealed the diverse effects of CSN genotypes on milk proteins in crossbred cattle.

Mid infrared polarization engineering via sub-wavelength biaxial hyperbolic van der Waals crystals.

Mid-infrared (IR) spectral region is of immense importance for astronomy, medical diagnosis, security and imaging due to the existence of the vibrational modes of many important molecules in this spectral range. Therefore, there is a particular interest in miniaturization and integration of IR optical components. To this end, 2D van der Waals (vdW) crystals have shown great potential owing to their ease of integration with other optoelectronic platforms and room temperature operation. Recently, 2D vdW crystals of [Formula: see text]-[Formula: see text] and [Formula: see text]-[Formula: see text] have been shown to possess the unique phenomenon of natural in-plane biaxial hyperbolicity in the mid-infrared frequency regime at room temperature. Here, we report a unique application of this in-plane hyperbolicity for designing highly efficient, lithography free and extremely subwavelength mid-IR photonic devices for polarization engineering. In particular, we show the possibility of a significant reduction in the device footprint while maintaining an enormous extinction ratio from [Formula: see text]-[Formula: see text] and [Formula: see text]-[Formula: see text] [Formula: see text] based mid-IR polarizers. Furthermore, we investigate the application of sub-wavelength thin films of these vdW crystals towards engineering the polarization state of incident mid-IR light via precise control of polarization rotation, ellipticity and relative phase. We explain our results using natural in-plane hyperbolic anisotropy of [Formula: see text]-[Formula: see text] and [Formula: see text]-[Formula: see text] [Formula: see text] via both analytical and full-wave electromagnetic simulations. This work provides a lithography free alternative for miniaturized mid-infrared photonic devices using the hyperbolic anisotropy of [Formula: see text]-[Formula: see text] and [Formula: see text]-[Formula: see text] [Formula: see text].

Semen quality and total microbial load: An association study in important Indian Goat breeds during different seasons.

The invasion of the male urogenital tract by microorganisms, and its subsequent effects on sperm fertilising ability, has not been well discussed in bucks. The present study was conducted to assess the bacterial load in fresh semen of the 2-6 years old bucks. For conducting the experiment, semen ejaculates from 18 bucks (6 from each breed namely Jakhrana, Jamunapari and Barbari) were used. We collected 5 ejaculates from each buck in each season (Summer-April to June, Rainy-July to Sept and Winter-November to January). Semen was collected with the artificial vagina (AV) method, and separate AV was used for each buck every time. The semen collection frequency was once in a week. Immediately after initial evaluation, collected semen samples were transferred to the microbiology laboratory of the institute. Thereafter, the semen samples were subjected to bacteriological examination to assess the microbial load. The results of the current study indicate that the microbial load in the semen was significantly (p < 0.05) higher in the Jamunapari bucks and in aged bucks. Bacteriospermia in different seasons was not significantly varied; however, nonsignificant increase in microbial load during the rainy season was observed. Overall, the average bacterial load in the semen of Jamunapari, Barbari and Jakhrana bucks was found 540.50 ± 55.88 CFU/ml, 391.81 ± 46.33CFU/ml and 388.93 ± 44.71 CFU/ml respectively. No significant difference in bacterial counts in the subsequent ejaculates among bucks was observed. Moreover, correlation analysis revealed that the proportions of motility, viability, plasma membrane integrity and acrosomal integrity were negatively influenced by the increased bacterial contamination of buck semen.

Evaluation of animal models to explore the influence of maternal genetic and maternal permanent environment effect on reproductive performance of Jersey crossbred cattle.

The present study was conducted on 1,002 reproductive records of 430 Jersey crossbred cattle, descended from 57 sires and 198 dams, maintained at the Eastern Regional Station of ICAR-National Dairy Research Institute, Kalyani, Nadia, West Bengal, India to investigate the influence of direct genetic, maternal genetic and maternal permanent environmental effect on three most important reproductive traits viz., number of service per conception (NSPC), days open (DO) and calving interval (CI) of Jersey crossbred cattle. Six single-trait animal models (including or excluding maternal genetic or permanent environmental effects) were fitted to analyse these traits, and the best model was chosen after testing the significant increase in the log-likelihood values when additional parameters were added in the model. Direct heritability estimates for NSPC, DO and CI from the best model were 0.10, 0.14 and 0.20, respectively. The maternal permanent environmental (c2 ) effects on reproductive traits accounted for almost negligible fraction of the total phenotypic variance in this study. The maternal genetic effects (m2 ) also contributed very little (0%-3%) to the total phenotypic variance except for CI where it was important and accounted for 20% of phenotypic variance. A significantly large negative genetic correlation was observed between direct and maternal genetic effects for all traits, suggesting the presence of antagonistic relationship between dam's direct additive component and daughter's additive genetic component. Results suggest that both direct and maternal effects were important only for CI but not for other traits. Therefore, both direct additive effects and maternal genetic effect need to be considered for improving this trait by selection.

Alternate PCR assays for screening of JH1 mutation associated with embryonic death in Jersey cattle.

Jersey haplotype (JH) 1, a stop-gain lethal mutation in the CWC15 gene, causes embryonic losses in Jersey cattle. Two PCR based assays using Amplification Refractory Mutation System (T-ARMS-PCR) and restriction fragment length polymorphism (PCR-RFLP) were developed for screening of the JH1 in cattle. During the screening, seven among 30 Indian Jersey bulls were identified as carriers of the mutant JH1 allele, the first time in the country. These PCR assays are economical, rapid and accurate; and can be used separately or in combination for screening and cross-validation of the JH1 carriers in Jersey cattle.

A cyclical deep learning based framework for simultaneous inverse and forward design of nanophotonic metasurfaces.

The conventional approach to nanophotonic metasurface design and optimization for a targeted electromagnetic response involves exploring large geometry and material spaces. This is a highly iterative process based on trial and error, which is computationally costly and time consuming. Moreover, the non-uniqueness of structural designs and high non-linearity between electromagnetic response and design makes this problem challenging. To model this unintuitive relationship between electromagnetic response and metasurface structural design as a probability distribution in the design space, we introduce a framework for inverse design of nanophotonic metasurfaces based on cyclical deep learning (DL). The proposed framework performs inverse design and optimization mechanism for the generation of meta-atoms and meta-molecules as metasurface units based on DL models and genetic algorithm. The framework includes consecutive DL models that emulate both numerical electromagnetic simulation and iterative processes of optimization, and generate optimized structural designs while simultaneously performing forward and inverse design tasks. A selection and evaluation of generated structural designs is performed by the genetic algorithm to construct a desired optical response and design space that mimics real world responses. Importantly, our cyclical generation framework also explores the space of new metasurface topologies. As an example application of the utility of our proposed architecture, we demonstrate the inverse design of gap-plasmon based half-wave plate metasurface for user-defined optical response. Our proposed technique can be easily generalized for designing nanophtonic metasurfaces for a wide range of targeted optical response.