REVIEW | doi:10.20944/preprints202301.0539.v1
Subject: Biology, Plant Sciences Keywords: Medicinal plants; ethnomedicine; phytochemicals; transcriptome; metabolome
Online: 30 January 2023 (04:54:26 CET)
Indian Tribal population is known for their self-sustainability, including their robust natural health and trivial lifestyle, further traditionally relied on medicinal plants throughout history. The evolutionary history of the ethnic-medicinal bulbous geophyte has long been a contention in monocot systematics. In India, the genus is represented by a species array. Moreover, the phylogeny delimitation amongst them is poorly defined to date. Phenolics, sterols, proteins and some other phytochemicals of Drimia have also been isolated for pharmacological and clinical studies that have strongly recommended their background effect of geographical positioning. Through several in vivo and in vitro studies, extracts derived from Drimia species demonstrated biological activity, including antifungal antibacterial, antiviral, anti-inflammatory antioxidant, and insecticidal properties. This review highlights the comprehensive phylogenetic analysis of Indian spp. of Drimia and the multi-omics-based approach for species delineation, the discovery of candidate genes and the development of plant-based drugs, as well as the long-term utilisation of plant pharmaceutical resources.
SHORT NOTE | doi:10.20944/preprints202106.0117.v1
Subject: Earth Sciences, Atmospheric Science Keywords: COVID-19; Medical Waste; Sustainability; Environment.
Online: 3 June 2021 (13:22:55 CEST)
The situation in the world of pandemics is rapidly changing, and the second wave of COVID-19 has put a lot of pressure on the government and private sector, which are primarily responsible for controlling the situation. COVID-19 positive cases have increased in recent months relative to last year, and the number of patients admitted to hospitals has also increased, despite the fact that few of them were denied admission due to shortage of beds. Normal people who experience any symptoms immediately isolate themselves and begin taking the COVID medications prescribed by medical personnel and their team. During these times, all domestic people tossed the wrappers and boxes of medicines into the regular trash can, and the waste was handed over to the waste collector, who treated it like any other domestic waste and disposed of it using open dumping or other methods. The goal of this perspective is to suggest the collections of these types of waste from domestics, and protect the natural resources like water, soil, and even living beings like animals from pollution (from the effect of SARS-CoV-2). The main challenge for environmental waste management agencies is determining who has COVID positive and which houses generate these types of waste; thus, proposed strategy may be beneficial to the long-term sustainability of natural resources and animals.
ARTICLE | doi:10.20944/preprints201810.0103.v1
Subject: Life Sciences, Virology Keywords: Nipah Virus, outbreak, inhibitors, QSAR, database, prediction algorithm
Online: 5 October 2018 (15:04:23 CEST)
Nipah virus (NiV) is responsible to cause various outbreaks in Asian countries, with latest from Kerala state of India. Till date there is no drug available despite its urgent requirement. In the current study, we have provided a computational one-stop solution for NiV inhibitors. We have developed “anti-Nipah” web resource, which comprised of a data repository, prediction method, and data visualization modules. The database comprised of 313 (181 unique) inhibitors from different strains and outbreaks of NiV extracted from research articles and patents. However, the quantitative structure–activity relationship (QSAR) based predictors were accomplished using classification approach employing 10-fold cross validation through support vector machine with 120 (68p + 52n) inhibitors. The overall predictor showed the accuracy and Matthew’s correlation coefficient of 88.89% and 0.77 on training/testing dataset respectively. The independent validation dataset also performed equally well. The data visualization modules from chemical clustering and principal component analyses displayed the diversity in the NiV inhibitors. Therefore, our web platform would be of immense help to the researchers working in developing effective inhibitors against NiV. The user-friendly webserver is freely available on URL: http://bioinfo.imtech.res.in/manojk/antinipah/
ARTICLE | doi:10.20944/preprints202210.0462.v1
Subject: Mathematics & Computer Science, Numerical Analysis & Optimization Keywords: Newton’s method; normal S-iteration; weak condition; simple root
Online: 31 October 2022 (02:23:04 CET)
In the present paper, we introduced a quadratically convergent Newton’s like normal S2 iteration method free from the second derivative for the solution of nonlinear equations permitting 3 f'(x) = 0 at some points in the neighborhood of the root. Our proposed method works well 4 when the Newton method fails. Numerically it has been verified that the Newton’s like normal 5 S-iteration method converges faster than Fang et al. method [A cubically convergent Newton-type 6 method under weak conditions, J. Compute. and Appl. Math., 220 (2008), 409-412]. We studied 7 different aspects of normal S-iteration method. Lastly, fractal patterns support the numerical 8 results and explain the convergence, divergence, and stability of method.
ARTICLE | doi:10.20944/preprints202106.0205.v1
Subject: Behavioral Sciences, Applied Psychology Keywords: Mental Health; Machine Learning; Modern Imaging Techniques; Psychogenic fever; rheumatic; Classifier
Online: 8 June 2021 (09:49:42 CEST)
Brain, the most complex object known in the universe, uses few watts of power. To mimic it a nuclear power plant will be required and this power house controls the human body, single handedly. Surprisingly, “On the left side, nothing is right and on the right side there is nothing left”. Typically, there are two lateral halves of the brain: Left hemisphere and right hemisphere working distinctly. Left hemisphere is inclined towards logic; Right hemisphere is the root cause of imagination added with critical thinking. In situations like the current pandemic, COVID-19, it is the right half which tends to dominate the processing. This gives birth to mental stress, anxiety thus, aggravating the existing medical condition. Considering this pattern, a survey was conducted in Durg district of Chhattisgarh, which is one of the most hard hit epicentre of the COVID-19 second wave in India. According to this survey, it was revealed that largely women of all age groups (10-25, 26-40, 40 above) were right brained i.e. dominance of right over left hemisphere. Being more imaginative and creative thinkers they are more likely to suffer from mental issues than males. The aim of this research is to improve the mental wellbeing of the citizens in such threatening conditions. To prevent this situation awareness is a must and some stress relieving games have also been created.
ARTICLE | doi:10.20944/preprints202009.0486.v1
Subject: Life Sciences, Immunology Keywords: COVID-19; comorbidity; SARS-CoV-2; leukemia; NAFLD; psoriasis; cancer; type II diabetes
Online: 21 September 2020 (03:32:58 CEST)
Background: Comorbidities have been frequently reported in COVID-19 patients, which often lead to more severe outcomes. The underlying molecular mechanisms behind these clinical observations have not yet been explained. Herein, we investigated the disease-specific gene expression signatures that may induce susceptibility to SARS-CoV-2 infection. Methods: We studied 30 frequently occurring acute, chronic, or infectious diseases of recent times that have shown comorbidity in one or another respiratory disease(s) caused by pathogenic human infecting coronaviruses, especially SARS-CoV-2. We retrieved array-based gene expression data for each disease and control from relevant datasets. Subsequently, all the datasets were quantile normalized, and log-2 transformed data was used for analysis. Results The expression of ACE2 receptor and host proteases, namely FURIN and TMPRSS2 that are essential for cellular entry of SARS-CoV-2, was upregulated in all six studied subtypes of leukemia (hereafter, referred as leukemia). The expression of ACE2 was also increased in psoriasis, lung cancer, Non-alcoholic fatty liver disease (NAFLD), breast cancer, and pulmonary arterial hypertension patients. The expression of FURIN was higher in psoriasis, NAFLD, lung cancer, and in type II diabetic liver, whereas it was lowered in breast cancer. Similarly, the expression of TMPRSS2 was increased during lung cancer and type II diabetes; it was decreased during psoriasis, NAFLD, lung cancer, breast cancer, and cervical cancer.Furthermore, a heightened expression of genes that are involved in immune response was observed in leukemia patients, as shown by the higher expression of IFNA2, IFNA8, IFNA10, IFNA14, IFNA16, IFNA21, IFNB1, CXCL10, and IL6. The expression of JAK1, STAT1, IL6, and CXCL10 was higher in NAFLD. Besides, JAK1 and STAT1 were upregulated in type II diabetic muscles. In addition, most of the upregulated genes in COVID-19 patients showed a similar trend in leukemia, NAFLD, and psoriasis. Furthermore, SARS-CoV-2, SARS-CoV and MERS CoV, were found to commonly alter two genes, namely, CARBONIC ANHYDRASE 11 and CLUSTERIN.Conclusions: The genes that may confer susceptibility to SARS-CoV-2 infection are mostly upregulated in leukemia patients; hence, leukemia patients are relatively more susceptible to develop COVID-19, followed by other chronic disorders, such as, NAFLD, type II diabetes, psoriasis, and hypertension. This study identifies key genes that are altered in the studied diseases types, which may aid in the infection of SARS-CoV-2 and underlie COVID-19 associated comorbidities.
ARTICLE | doi:10.20944/preprints202001.0380.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: barley; sowing date; seed rate; row spacing; yield
Online: 31 January 2020 (05:21:36 CET)
The precise information regarding the date of sowing, seed rate and row spacing is critical for achieving yield targets and better economic returns of barley. Therefore here, we determined the information regarding the optimum date of sowing, seed rate, spacing and economic aspects for barley production. This study was conducted for three years, in north Indian plains. Early sowing date of barley (last week of October) recorded higher yield in comparison to late sown crop (3rd week of November). Moreover, the higher barley production proved more remunerative when sown early in the last week of October to the first week of November as compared to late sown the late sown crop. Furthermore, the enhanced seed rate of 10% then recommended did not affect the grain yield of barley. But, the closer spacing of 20 cm (row to row) produced higher grain yield (5.45 Mg ha-1 ) than the recommended spacing of 22.5 cm (5.30 Mg ha-1). Likewise, the economical parameters (net returns) were higher with 20 cm row spacing. Overall, this study determines the optimum date of sowing, seed rate and spacing for scoring better returns of barley crop under north Indian conditions.
REVIEW | doi:10.20944/preprints202107.0193.v1
Subject: Life Sciences, Biochemistry Keywords: metabolomics; plant biology; metabolomics databases; data analysis; metabolomics software tools; mass spectrometry; omics
Online: 8 July 2021 (10:46:55 CEST)
Metabolomics is now considered to be a wide-ranging, sensitive and practical approach to acquire useful information on the composition of a metabolite pool present in any organism, including plants. Investigating metabolomic regulation in plants is essential to understand their adaptation, acclimation and defense response to environmental stresses through the production of numerous metabolites. Moreover, metabolomics can be easily applied for the phenotyping of plants; and thus, it has great potential to be used in molecular breeding and genome editing programs to develop superior next generation crops. This review describes the recent analytical tools and techniques available to study plants metabolome, along with their significance of sample preparation using targeted and non-targeted method. Advanced analytical tools, like gas chromatography-mass spectrometry (GC-MS), liquid chromatography mass-spectroscopy (LC-MS), capillary electrophoresis-mass spectrometry (CE-MS), fourier transform ion cyclotron resonance-mass spectrometry (FTICR-MS) and matrix-assisted laser desorption/ionization (MALDI) have speed up metabolic profiling in plants. Further, we deliver a complete overview of bioinformatics tools and plant metabolome database that can be utilized to advance our knowledge to plant biology.
REVIEW | doi:10.20944/preprints202209.0117.v1
Subject: Life Sciences, Biotechnology Keywords: abiotic stress tolerance; base editing; CRISPR/Cas9; crop production; gene editing; prime editing
Online: 8 September 2022 (03:31:39 CEST)
Abiotic stresses, including drought, salinity, cold, heat, and heavy metals, extensively reduce global agricultural production. Approaches such as conventional breeding and transgenic breeding have been widely used to cope with these environmental stresses. The clustered regularly interspaced short palindromic repeat- Cas (CRISPR/Cas) based gene-editing tool has revolutionized due to its simplicity, accessibility, adaptability, flexibility, and wide applicability. This system has a great potential to build up crop varieties with enhanced tolerance against abiotic stresses. In this review, we summarize the most recent findings on understanding the mechanism of abiotic stress response in plants and the application of CRISPR/Cas mediated gene-editing system towards enhanced tolerance to drought, salinity, cold, heat, and heavy metals stresses. Furthermore, in this review, we highlighted the recent advancements in prime editing and base editing tools for crop improvement.
ARTICLE | doi:10.20944/preprints201810.0382.v1
Subject: Biology, Agricultural Sciences & Agronomy Keywords: intercropping; microbial community; high throughput sequencing; nifH gene; sugarcane
Online: 17 October 2018 (10:20:19 CEST)
Intercropping significantly improves land use efficiency and soil fertility. This study examines the impact of three cultivation systems (monoculture sugarcane, peanut-sugarcane and soybean-sugarcane intercropping) on soil properties and diazotrophs. Sugarcane rhizosphere soil was sampled from the farmers’ field. Soil properties and nifH gene abundance were analyzed by high throughput sequencing. Moreover, a total of 436,458 nifH gene sequences were obtained and classified into the 3201 unique operational taxonomic units (OTUs). Maximum unique OTUs resulted with soybean-sugarcane intercropping (<375). The dominant groups across all cultivation were Alpha-proteobacteria and Beta-proteobacteria. On the basis of microbial community structure, intercropping systems were more diverse than monoculture sugarcane. In the genus level, Bradyrhizobium, Burkholderia, Pelomonas, and Sphingomonas were predominant in the intercropping systems. Moreover, diazotrophic bacterial communities of these cultivation systems were positively correlated to the soil pH and soil enzyme protease. Moreover, low available P recovered from intercropping system showed a strong correlation with higher nutrient uptake activity of soil microbes. Based on the results, our investigation concluded that intercropping system caused a positive effect on the growth of diazotrophic bacterial communities and it might boost the soil fertility and this kind of study helps to develop an eco-friendly technology for sustainable sugarcane production.
REVIEW | doi:10.20944/preprints202205.0399.v1
Subject: Physical Sciences, Optics Keywords: Holography; computational imaging; non-linear reconstruction; Fresnel incoherent correlation holography; coded aperture imaging; rotating point spread function; diffractive optics; scattering.
Online: 30 May 2022 (11:37:04 CEST)
Indirect imaging methods involve at least two steps, namely optical recording, and computational reconstruction. The optical recording process uses an optical modulator that transforms the light from the object into a typical intensity distribution. This distribution is numerically processed to reconstruct the object’s image corresponding to different spatial and spectral dimensions. There have been numerous optical modulation functions and reconstruction methods developed in the past years for different applications. In most cases, a compatible pair of optical modulation function and reconstruction method gives optimal performance. A new reconstruction method termed non-linear reconstruction (NLR) was developed in 2017 to reconstruct the object image in the case of optical scattering modulators. During the years, it was revealed that the NLR could reconstruct an object’s image modulated by an axicons, bifocal lenses and even exotic spiral diffractive elements, which generate deterministic optical fields. Apparently, NLR seems to be a universal reconstruction method for indirect imaging. In this review, the performance of NLR has been investigated for many deterministic and stochastic optical fields. Simulation and experimental results for different cases are presented and discussed.