Host-mediated gene engineering and microbiome-based technology optimization for sustainable agriculture and environment.

The agricultural sector and environmental safety both work hand in hand to promote sustainability in important issues like soil health, plant nutrition, food safety, and security. The conventional methods have greatly harmed the environment and people's health and caused soil fertility and quality to decline as well as deteriorate. Keeping in view the excessive exploitation and cascade of degradation events due to unsustainable farming practices, the need of the hour demands choosing an appropriate, eco-friendly strategy to restore soil health, plant nutrition, and environmental aspects. The priority highlights a need for a sustainable and environment-friendly upgradation of the present agricultural systems to utilize the beneficial aspects related to harnessing the gene-microbiome strategies which would help in the restoration and replenishment of the microbial pool. Thus, exploring the microbiome is the utmost priority which gives a deep insight into the different aspects related to soil and plant and stands out as an important contributor to plant health and productivity. "Microbes" are important drivers for the biogeochemical cycles and targets like sustainability and safety. This essential microbial bulk (soil microbiome) is greatly influenced by agricultural/farming practices. Therefore, with the help of microbiome engineering technologies like meta-transcriptomics, meta-proteomics, metabolomics, and novel gene-altering techniques, we can easily screen out the highly diverse and balanced microbial population in the bulk of soil, enhancing the soil's health and productivity. Importantly, we need to change our cultivation strategies to attain such sustainability. There is an urgent need to revert to natural/organic systems of cultivation patterns where the microbiome hub can be properly utilized to strengthen soil health, decrease insect pest and disease incidence, reduce greenhouse gas emissions, and ultimately prevent environmental degradation. Through this article, we wish to propose a shift in the cultivation pattern from chemical to the novel, upgraded gene-assisted designed eco-friendly methodologies which can help in incorporating, exploring, and harnessing the right microbiome consortium and can further help in the progression of environmentally friendly microbiome technologies for agricultural safety and productivity.

MRF: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus.

BACKGROUND: The genome of the largest known animal virus, the white spot syndrome virus (WSSV) responsible for huge economic losses and loss of employment in aquaculture, suffers from inconsistent annotation nomenclature. Novel genome sequence, circular genome and variable genome length led to nomenclature inconsistencies. Since vast knowledge has already accumulated in the past two decades with inconsistent nomenclature, the insights gained on a genome could not be easily extendable to other genomes. Therefore, the present study aims to perform comparative genomics studies in WSSV on uniform nomenclature. METHODS: We have combined the standard mummer tool with custom scripts to develop missing regions finder (MRF) that documents the missing genome regions and coding sequences in virus genomes in comparison to a reference genome and in its annotation nomenclature. The procedure was implemented as web tool and in command-line interface. Using MRF, we have documented the missing coding sequences in WSSV and explored their role in virulence through application of phylogenomics, machine learning models and homologous genes. RESULTS: We have tabulated and depicted the missing genome regions, missing coding sequences and deletion hotspots in WSSV on a common annotation nomenclature and attempted to link them to virus virulence. It was observed that the ubiquitination, transcription regulation and nucleotide metabolism might be essentially required for WSSV pathogenesis; and the structural proteins, VP19, VP26 and VP28 are essential for virus assembly. Few minor structural proteins in WSSV would act as envelope glycoproteins. We have also demonstrated the advantage of MRF in providing detailed graphic/tabular output in less time and also in handling of low-complexity, repeat-rich and highly similar regions of the genomes using other virus cases. CONCLUSIONS: Pathogenic virus research benefits from tools that could directly indicate the missing genomic regions and coding sequences between isolates/strains. In virus research, the analyses performed in this study provides an advancement to find the differences between genomes and to quickly identify the important coding sequences/genomes that require early attention from researchers. To conclude, the approach implemented in MRF complements similarity-based tools in comparative genomics involving large, highly-similar, length-varying and/or inconsistently annotated viral genomes.

Emerging role of MicroRNA-Based theranostics in Hepatocellular Carcinoma.

Hepatocellular carcinoma (HCC), with its high mortality and short survival rate, continues to be one of the deadliest malignancies despite relentless efforts and several technological advances. The poor prognosis of HCC and the few available treatments are to blame for the low survival rate, which emphasizes the importance of creating new, effective diagnostic markers and innovative therapy strategies. In-depth research is being done on the potent biomarker miRNAs, a special class of non-coding RNA and has shown encouraging results in the early identification and treatment of HCC in order to find more viable and successful therapeutics for the disease. It is beyond dispute that miRNAs control cell differentiation, proliferation, and survival and, depending on the genes they target, can either promote tumorigenesis or suppress it. Given the vital role miRNAs play in the biological system and their potential to serve as ground-breaking treatments for HCC, more study is required to fully examine their theranostic potential.

Transcriptomic variations associated with salinity stress in Penaeus indicus.

BACKGROUND: The Indian white shrimp, Penaeus indicus a native species of India, is important brackishwater aquaculture species. Shrimps are euryhaline in nature and they regulate osmotic and ionic concentrations by osmoregulatory process. However, variations in abiotic factors such as salinity result in stress to the shrimps during culture period affecting their growth and immunity. METHODS AND RESULTS: To understand the adaptive mechanism to stress in low salinity conditions, RNA-seq was used to compare the transcriptomic response of P. indicus upto 3 weeks. De novo assembly using Trinity assembler generated a total of 173,582 transcripts. The assembly had a mean length of 854 bp, N50 value of 1243 bp and GC content of 42.33%. Differential gene expression analysis, resulted in identification of 2130, 3090, and 5351 DEGs in 7 days, 14 days and 21 days respectively of salinity stress period. The pathway prediction of the assembled trinity transcripts using KEGG database showed total number of 329 pathways linking 12,430 transcripts. KEGG pathway enrichment analyses led to the identification of several enriched pathways related to lipid metabolism, amino acid metabolism, glycolysis, signalling pathways etc. Selected genes involved in osmoregulatory process and immune response in shrimps were validated and analysed for the gene expression levels by quantitative real-time PCR (qPCR). CONCLUSION: This study on the adaptive transcriptomic response of P. indicus to low salinity, will further help in our understanding of the molecular mechanisms underlying osmoregulation mechanism in shrimps.

Simultaneous imaging of sound propagations and spatial distribution of acoustic frequencies.

We propose a simultaneous imaging technique of both sound propagations and spatial distribution of acoustic frequencies. We experimentally demonstrated the proposed technique for the acoustic waves of frequencies 39,500 and 40,500 Hz, which have close sound pressure. The sounds were recorded at the framerate of 100,000 fps by parallel phase-shifting digital holography. To obtain the distribution of the acoustic frequencies, the short-time Fourier transform analysis was applied. The simultaneous imaging was carried out by assigning the frequencies and the pixel values of the phase-difference images to the components of HSL color space. The images obtained by the proposed technique represent the frequencies with the hue in addition to the sound propagations with the luminance. We succeeded in imaging the spatiotemporal evolution of the spatial frequencies of the sounds.

Ti2C-TiO2 MXene Nanocomposite-Based High-Efficiency Non-Enzymatic Glucose Sensing Platform for Diabetes Monitoring.

Diabetes is a major health challenge, and it is linked to a number of serious health issues, including cardiovascular disease (heart attack and stroke), diabetic nephropathy (kidney damage or failure), and birth defects. The detection of glucose has a direct and significant clinical importance in the management of diabetes. Herein, we demonstrate the application of in-situ synthesized Ti2C-TiO2 MXene nanocomposite for high throughput non-enzymatic electrochemical sensing of glucose. The nanocomposite was synthesized by controlled oxidation of Ti2C-MXene nanosheets using H2O2 at room temperature. The oxidation results in the opening up of Ti2C-MXene nanosheets and the formation of TiO2 nanocrystals on their surfaces as revealed in microscopic and spectroscopic analysis. Nanocomposite exhibited considerably high electrochemical response than parent Ti2C MXene, and hence utilized as a novel electrode material for enzyme-free sensitive and specific detection of glucose. Developed nanocomposite-based non-enzymatic glucose sensor (NEGS) displays a wide linearity range (0.1 µM-200 µM, R2 = 0.992), high sensitivity of 75.32 µA mM-1 cm-2, a low limit of detection (0.12 µM) and a rapid response time (~3s). NEGS has further shown a high level of repeatability and selectivity for glucose in serum spiked samples. The unveiled excellent sensing performance of NEGS is credited to synergistically improved electrochemical response of Ti2C MXene and TiO2 nanoparticles. All of these attributes highlight the potential of MXene nanocomposite as a next-generation NEGS for on the spot mass screening of diabetic patients.

Single-shot common-path off-axis digital holography: applications in bioimaging and optical metrology [Invited].

The demand for single-shot and common-path holographic systems has become increasingly important in recent years, as such systems offer various advantages compared to their counterparts. Single-shot holographic systems, for example, reduce computational complexity as only a single hologram with the object information required to process, making them more suitable for the investigation of dynamic events; and common-path holographic systems are less vibration-sensitive, compact, inexpensive, and high in temporal phase stability. We have developed a single-shot common-path off-axis digital holographic setup based on a beam splitter and pinhole. In this paper, we present a concise review of the proposed digital holographic system for several applications, including the quantitative phase imaging to investigate the morphological and quantitative parameters, as a metrological tool for testing of micro-optics, industrial inspection and measurement, and sound field imaging and visualization.

Multimodal sound field imaging using digital holography [Invited].

Sound is an important invisible physical phenomenon that needs to be explained in several physical and biological processes, along with visual phenomena. For this purpose, multiparameter digital holography (DH) has been proposed to visualize both features simultaneously due to the phase and amplitude reconstruction properties of DH. In this paper, we present a brief review on sound field imaging techniques with special focus on the multiparameter imaging capability of DH for visualizing sound and visual features. The basic theory and several experimental results with very high-speed recordings are also presented to demonstrate sound field imaging for the audible range as well as in the ultrasound range.

High-speed imaging of the sound field by parallel phase-shifting digital holography.

Sound field imaging techniques have been found very useful for acoustic designs. Building on this idea, innovative techniques are needed and presented in this paper, where we report on developed imaging of the sound field radiated from speakers by parallel phase-shifting digital holography. We adopted an ultrasonic wave radiated from a speaker for an object. The phase distribution of the light wave was modulated by the sound field radiated from the speaker. The modulated phase distribution was recorded in the form of multiplexed phase-shifted holograms at the frame rate of 100,000 fps. A 40,000 Hz sound field radiated from a speaker is used as an observation target. Our proposed method can implement the imaging of the sound field successfully. Also, in order to demonstrate the digital refocusing capability of digital holography, we set two speakers, whose difference in depth positions was 6.6 cm, as a long-depth object. We demonstrated the digital refocusing on the two speakers along with the capability of measuring the positions of the objects. Furthermore, we succeeded in imaging of 40,000 Hz and 41,000 Hz sound fields radiated from the two speakers. The presented experimental results showed that parallel phase-shifting digital holography is very useful and suitable for sound field imaging.

Point of care detection of COVID-19: Advancement in biosensing and diagnostic methods.

The recent outbreak of COVID-19 has created much inconvenience and fear that the virus can seriously affect humans, causing health hazards and death. This pandemic has created much worry and as per the report by World Health Organization (WHO), more than 43 million individuals in 215 countries and territories were affected. People around the world are still struggling to overcome the problems associated with this pandemic. Of all the available methods, reverse-transcriptase polymerase chain reaction (RT-PCR) has been widely practiced for the pandemic detection even though several diagnostic tools are available having varying accuracy and sensitivity. The method offers many advantages making it a life-saving tool, but the method has the limitation of transporting to the nearest pathology lab, thus limiting its application in resource limited settings. This has a risen a crucial need for point-of-care devices for on-site detection. In this venture, biosensors have been used, since they can be applied immediately at the point-of-care. This review will discuss about the available diagnostic methods and biosensors for COVID-19 detection.

Holographic multi-parameter imaging of dynamic phenomena with visual and audio features.

In this Letter, a concept of new multi-parameter imaging that can acquire visual and audio data of dynamic object phenomena simultaneously by a holographic technique is proposed. Temporal intensity distributions give us visual information of the dynamic events. The temporal profile of the phase distribution can give different information of the dynamic events, such as audio data. These two physical data can express the dynamic events with multi-parameters in various dimensions. The proposed imaging approach has potential in several applications in physics and life science research. Two experimental demonstrations such as static object and broken glass with visual and sound features are provided to show the effectiveness of the proposed concept.

Security-enhanced optical voice encryption in various domains and comparative analysis.

Optical voice encryption based on digital holography (DH), which uses the double random phase encoding (DRPE) in the Fourier transform domain, has been proposed [Opt. Lett.42, 4619 (2017)OPLEDP0146-959210.1364/OL.42.004619]. In the present work, we propose optical voice encryption in other optical domains such as fractional Fourier, Fresnel, and gyrator transform, which convert input information into different mixed space-frequency domains. We also analyze the recording conditions of human voice and some security aspects of the scheme. An optical setup based on off-axis DH is used to record the time-series of holograms, and these holograms can visualize the sound wave propagation. Then, the different encryption domains in double random phase encoding (DRPE) are used to encrypt voice information with enhanced security. With the numerical reconstruction and decryption procedure of DRPE with all correct keys and correct orders of optical domains, the original voice information can be retrieved. The extension of voice encryption in different domains will enhance the security level and analysis of recording, and security aspects will explore the possibilities and challenges of the optical voice encryption scheme. We present simulation results for encryption of an experimentally recorded human voice in various domains.

Space-variant video compression and processing in digital holographic microscopy sensor networks with application to potable water monitoring.

Water-related diseases affect societies in all parts of the world. Online sensors are considered a solution to the problems associated with laboratory testing in potable water. One of the most active research areas of such online sensors has been within optics. Digital holographic microscopy (DHM) has the potential to rival state-of-the-art techniques such as advanced turbidity measurement. However, its use as an online sensor is limited by the large data requirements typical for digital holographic video. In this paper, we provide a solution that permits DHM to be applied to a whole class of online remote sensor networks, of which potable water analysis is one example. The designed sensors incorporate a novel space-variant quantization algorithm to preprocess each frame of a video sequence before transmission over a network. The system satisfies the generally accepted requirements of an online system: automated, near real-time, and operating in a real environment. To verify the effectiveness of the design, we implemented and evaluated it in an active potable water facility.

Optical voice encryption based on digital holography.

We propose an optical voice encryption scheme based on digital holography (DH). An off-axis DH is employed to acquire voice information by obtaining phase retardation occurring in the object wave due to sound wave propagation. The acquired hologram, including voice information, is encrypted using optical image encryption. The DH reconstruction and decryption with all the correct parameters can retrieve an original voice. The scheme has the capability to record the human voice in holograms and encrypt it directly. These aspects make the scheme suitable for other security applications and help to use the voice as a potential security tool. We present experimental and some part of simulation results.

THE EFFECT OF A SINGLE DOSE OF MAGNESIUM SULPHATE AS AN ADJUVANT TO EPIDURAL BUPIVACAINE FOR INFRAUMBILICAL SURGERIES: A PROSPECTIVE DOUBLE-BLIND, RANDOMIZED CONTROL TRIAL.

CONTEXT: Epidural anesthesia provides the advantage of segmental blockade and many adjuvants have been added to shorten the onset of action, improve the quality of analgesia and prolong the duration of analgesia. Magnesium sulphate(MgSO4) by virtue of its anti-iociceptive property has been administered by various routes. AIM: To assess the effect of MgSO4 on the duration of onset of action of injection bupivacaine for epidural anesthesia in infraumbilical surgeries. MATERIALS AND METHODS: A prospective, double-blind, randomized control study was conducted in 40 patients. Group M received 15 ml of bupivacaine 0.5% + 1 ml of 50 mg MgSO4 and Group C received 15 ml of bupivacaine 0.5% + 1 ml of normal saline via epidural route. Onset time of the sensory and motor blockade were the primary outcomes studied. Highest level of sensory block, time for two segment regression, hemodynamic parameters, side effects were the secondary parameters. RESULTS: There was a significant difference between the groups in the mean onset time of sensory blockade at T8, 12.85 ± 2.32 min in Group M and 16.75 ± 1.74 min in Group C. Median level of sensory blockade was comparable. Mean onset time of motor blockade was 13.85 ± 3.28 min in Group M and 23.25 ± 3.35 min in Group C which was clinically and statistically significant. Time for two segment regression of sensory blockade was 95.75 ± 11.84 min in Group M and 55.5 ± 8.57 min in Group C which was significant. Hemodynamic parameters and side effects were comparable. CONCLUSION: Magnesium sulphate as an adjuvant provides rapid onset of epidural anesthesia and prolongs the duration of analgesia with minimal side effects.

EFFECT OF DEXMEDETOMIDINE ON HEMODYNAMIC PARAMETERS DURING EXTUBATION. A PROSPECTIVE RANDOMIZED DOUBLE BLIND STUDY.

BACKGROUND: Extubation is known to produce significant hemodynamic disturbances. There is a need to avoid increase in heart rate and blood pressure in hypertensive and cardiac patients and in vascular, neuro and intraocular surgeries. AIMS: To study the ability of dexmedetomidine to attenuate the hemodynamic responses during extubation. MATERIALS AND METHODS: 80 patients of ASA Grade I-II aged 18-50 years received standard anesthesia. At the closure of skin incision, patients were randomly allocated to receive either dexmedetomidine 0.5 µg/kg (Group D) or saline placebo (Group C) intravenously over 10 minutes in a double-blind design. Heart rate (HR), systolic, diastolic and mean arterial pressures (SBP, DBP, MAP) were assessed before, during- and after extubation. Time to eye opening and extubation, sedation, complications such as coughing, laryngospasm, bronchospasm and desaturation were recorded. RESULTS: HR, SBP, DBP and MAP were comparable to basal values in group D at extubation and lower than baseline values post-extubation but significant increase was noted in group C (P <0.001). Time to extubation and eye opening were prolonged in Group D (P <0.001). Incidence of hypotension was more in group D (22%) but was transient. Incidence of coughing was lower in Group D than in group C (P <0.001). Patients in group D were more sedated for 30 minutes post extubation. CONCLUSION: Dexmedetomidine 0.5 µg/kg given before extubation attenuates hemodynamic reflexes during emergence from anesthesia without causing undue sedation, but prolongs time to extubation.

Cholesterol Oxidase Functionalised Polyaniline/Carbon Nanotube Hybrids for an Amperometric Biosensor.

Functional carbon nanotubes (CNT) have attracted much attention for analytical and biomedical applications. This paper describes the fabrication of a cholesterol oxidase (ChOx) immobilised polyaniline (PANI)/CNT composite electrode for the amperometric detection of cholesterol. The prepared ChOx/PANI/CNT/Au bioelectrode bound ChOx via the available functionalties of PANI (-NH2) and CNT (-COOH). Moreover, the CNT creates a network inside the matrix that strengthens the mechanical property of the bioelectrode. The multifunctional matrix is presumed to provide a 3D-mesoporous surface, which substantially enhances enzyme activity. The linear range of the biosensor for cholesterol oleate was 30-280 µM with a response time of 10 sec.

"ANESTHETIC SPARING EFFECT OF INTRAOPERATIVE LIGNOCAINE OR DEXMEDETOMIDINE INFUSION ON SEVOFLURANE DURING GENERAL ANESTHESIA".

BACKGROUND: Lidocaine and Dexmedetomidine are known to blunt the stress response to surgery, and have anesthetic sparing activity. This study was designed to evaluate and compare the anesthetic sparing effect of intravenous lidocaine with Dexmedetomidine infusion during sevoflurane based general anesthesia and also to assess their effects on hemodynamic parameters. METHODS: Forty-eight ASA I-II patients aged between 18-55 yr, scheduled for abdominal surgery lasting less than 2 h, performed under general anesthesia were enrolled and they were randomly allocated to Lidocaine(L), Dexmedetomidine (D) and Saline (S) groups of 16 each. Group L received Inj. Lidocaine at 1.5 mg/kg bolus over 10 min followed by infusion at 1.5 mg/ kg/hr, and Group D received Inj. Dexmedetomidine at 1 µg/kg over 10 min, followed by 0.5 µg/ kg/hr infusion till the end of surgery. Group S received similar volume of normal saline. Anesthesia was induced with Inj. Propofol and maintained with N2O in O2 and sevoflurane, keeping entropy between 40-60. The hourly sevoflurane requirements and hemodynamic parameters were recorded. Results: Demographic parameters, entropy and duration of surgery were comparable. Mean sevoflurane requirement at 1st h in group L and D were 11.6 ± 1.5 ml, and 10.2 ± 1.3 ml respectively, while it was 16.7 ± 4.1 ml in Saline group (P < 0.001). Sevoflurane requirements were significantly lesser in group D compared to group L (P = 0.009). The Mean ET(sevo) concentrations in Group L, D and S were 0.8 ± 0.3, 0.8 ± 0.4 and 1.2 ± 0.5 (P = 0.021), respectively. CONCLUSIONS: Both drugs produce significant anesthetic sparing effect during sevoflurane based general anesthesia, but dexmedetomidine has better sparing effect than lignocaine.

Source investigation of the tar balls deposited along the Gujarat coast, India, using chemical fingerprinting and transport modeling techniques.

Deposition of tar balls (TBs) along the south Gujarat coast, situated on the west coast of India (WCI), commonly occurs during the southwest monsoon season. Several offshore oil fields off the Mumbai-Gujarat coast, and refineries along the coast might be sources of oil spills/leakages and lead to the formation of TBs. To identify the sources, we collected 12 TB samples from the beaches of Gujarat (Tithal, Maroli, Umbergam, and Nargol) during 15-17 July 2012 as well as samples of crude oils, namely, Cairn, NIKO, MSC Chitra, and two at Bombay High (BH). These TBs were subject to the following multimarker approach for source identification: Diagnostic Ratios of n-alkanes, polycyclic aromatic hydrocarbons, pentacyclic triterpanes, compound specific isotope analysis, Principle Component Analysis and numerical simulations (hydrodynamic model coupled with particle trajectories). The chemical fingerprint results reveal that the source of the TBs is BH crude oils, and the model results confirm that the source location is BH north oil fields. This is the first study of its kind in India to use fingerprinting and transport modeling techniques for source identification of TBs.

An optical encryption and authentication scheme using asymmetric keys.

We propose a novel optical information encryption and authentication scheme that uses asymmetric keys generated by the phase-truncation approach and the phase-retrieval algorithm. Multiple images bonded with random phase masks are Fourier transformed, and obtained spectra are amplitude- and phase-truncated. The phase-truncated spectra are encoded into a single random intensity image using the phase-retrieval algorithm. Unlike most of the authentication schemes, in this study, only one encrypted reference image is required for verification of multiple secured images. The conventional double random phase encoding and correlation techniques are employed for authentication verification. Computer simulation results and theoretical explanation prove the effectiveness of the proposed scheme.