Transcriptome analysis of apical meristem enriched bud samples for size dependent flowering commitment in Crocus sativus reveal role of sugar and auxin signalling.

BACKGROUND: Cultivation of Crocus sativus (saffron) faces challenges due to inconsistent flowering patterns and variations in yield. Flowering takes place in a graded way with smaller corms unable to produce flowers. Enhancing the productivity requires a comprehensive understanding of the underlying genetic mechanisms that govern this size-based flowering initiation and commitment. Therefore, samples enriched with non-flowering and flowering apical buds from small (< 6 g) and large (> 14 g) corms were sequenced. METHODS AND RESULTS: Apical bud enriched samples from small and large corms were collected immediately after dormancy break in July. RNA sequencing was performed using Illumina Novaseq 6000 to access the gene expression profiles associated with size dependent flowering. De novo transcriptome assembly and analysis using flowering committed buds from large corms at post-dormancy and their comparison with vegetative shoot primordia from small corms pointed out the major role of starch and sucrose metabolism, Auxin and ABA hormonal regulation. Many genes with known dual responses in flowering development and circadian rhythm like Flowering locus T and Cryptochrome 1 along with a transcript showing homology with small auxin upregulated RNA (SAUR) exhibited induced expression in flowering buds. Thorough prediction of Crocus sativus non-coding RNA repertoire has been carried out for the first time. Enolase was found to be acting as a major hub with protein-protein interaction analysis using Arabidopsis counterparts. CONCLUSION: Transcripts belong to key pathways including phenylpropanoid biosynthesis, hormone signaling and carbon metabolism were found significantly modulated. KEGG assessment and protein-protein interaction analysis confirm the expression data. Findings unravel the genetic determinants driving the size dependent flowering in Crocus sativus.

Comparative transcriptomic and weighted gene co-expression network analysis to identify the core genes in the cultivars of Musa acuminata under both infected and chemical perturbated conditions.

Banana is a high nutrient crop, which ranks fourth in terms of gross value production. Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense tropical race 4 (FocTR4), is considered the most destructive disease leading to the complete loss of production of the Cavendish cultivars Berangan, Brazilian and Williams, which are vulnerable to the infection of FocTR4. However, the treatment with benzothiadiazole, a synthetic salicylic analog, is aimed to induce resistance in plants. Thus, the treatments pertaining to the banana plants subjected to the Foc infection within the chosen cultivars were compared with chemically treated samples obtained at different time intervals for a short duration (0-4 days). The integrated omics analyses considering the parameters of WGCNA, functional annotation, and protein-protein interactions revealed that many pathways have been negatively influenced in Cavendish bananas under FocTR4 infections and the number of genes influenced also increased over time in Williams cultivar. Furthermore, elevation in immune response and resistance genes were also observed in the roots of the Cavendish banana.

Agronomic and Environmental Determinants of Direct Seeded Rice in South Asia.

Rice (Oryza sativa L.) is the staple food of more than 50% of the world's population. Manual puddled transplanted rice (PTR) system is still the predominant method of rice establishment. However, due to declining water tables, increasing water scarcity, water, labor- and energy-intensive nature of PTR, high labor wages, adverse effects of puddling on soil health and succeeding crops, and high methane emissions, this production system is becoming less profitable. These factors trigger the need for an alternative crop establishment method. The direct-seeded rice (DSR) technique is gaining popularity because of its low input demand compared to PTR. It is done by sowing pre-germinated seeds in puddled soil (wet-DSR), standing water (water seeding), or dry seeding on a prepared seedbed (dry-DSR). DSR requires less water and labor (12-35%), reduces methane emissions (10-90%), improves soil physical properties, involves less drudgery and production cost (US$9-125 per hectare), and gives comparable yields. Upgraded short-duration and high-yielding varieties and efficient nutrient, weed, and resource management techniques encouraged the farmers to switch to DSR culture. However, several constraints are associated with this shift: more weeds, the emergence of weedy rice, herbicide resistance, nitrous oxide emissions, nutrient disorders, primarily N and micro-nutrients, and an increase in soil-borne pathogens lodging etc. These issues can be overcome if proper weed, water, and fertilizer management strategies are adopted. Techniques like stale bed technique, mulching, crop rotation, Sesbania co-culture, seed priming, pre-emergence and post-emergence spray, and a systematic weed monitoring program will help reduce weeds. Chemical to biotechnological methods like herbicide-resistant rice varieties and more competitive allelopathic varieties will be required for sustainable rice production. In addition, strategies like nitrification inhibitors and deep urea placement can be used to reduce N2O emissions. Developing site and soil-specific integrated packages will help in the broader adoption of DSR and reduce the environmental footprint of PTR. The present paper aims to identify the gaps and develop the best-bet agronomic practices and develop an integrated package of technologies for DSR, keeping in mind the advantages and constraints associated with DSR, and suggest some prospects. Eco-friendly, cost-effective DSR package offers sustainable rice production systems with fewer resources and low emissions.

Chronic, increasing, and decreasing peer victimization trajectories and the development of externalizing and internalizing problems in middle childhood.

Children's peer victimization trajectories and their longitudinal associations with externalizing and internalizing problems were investigated from Grades 2 to 5. Secondary data analysis was performed with the Early Childhood Longitudinal Study (ECLS-K-2011; n = 13,860, M age = 8.1 years old in the spring of Grade 2; 51.1% male, 46.7% White, 13.2% African-American, 25.3% Hispanic or Latino, 8.5% Asian, and 6.1% other or biracial). Children who experienced high and persistent levels of peer victimization (high-chronic victims) exhibited co-occurring externalizing and internalizing problems. Moreover, among high-chronic victims, boys had a more pronounced increase in their externalizing trajectories, and girls had greater increases in their social anxiety trajectories. In contrast, those with decreasing peer victimization across time exhibited signs of recovery, particularly with respect to their social anxiety. These findings elucidated how chronic, increasing, and decreasing victims exhibited distinct patterns in the co-occurring development of their externalizing and internalizing problems, and how findings varied depending on the form of problem behavior and by child sex.

Raman Spectroscopy as a Simple yet Effective Analytical Tool for Determining Fermi Energy and Temperature Dependent Fermi Shift in Silicon.

The Fermi energy is known to be dependent on doping and temperature, but finding its value and corresponding thermal Fermi shift experimentally is not only difficult but is virtually impossible if one attempts their simultaneous determination. We report that temperature dependent Raman spectromicroscopy solves the purpose easily and proves to be a powerful technique to determine the position and temperature associated Fermi shift in an extrinsic semiconductor as demonstrated for silicon in the present study. The typical asymmetrically broadened Raman spectral line-shape from sufficiently doped n- and p-type silicon contains the information about the Fermi level position through its known association with the Fano coupling strength. Thus, Raman line-shape parameters, the terms quantify the Fano-coupling, have been used as experimental observables to reveal the value of the Fermi energy and consequent thermal Fermi shift. A simple formula has been developed based on existing established theoretical frameworks that can be used to calculate the position of the Fermi level. The proposed Raman spectroscopy-based formulation applies well for n- and p-type silicon. The calculated Fermi level position and its temperature dependent variation are consistent with the existing reports.

Pseudo-Anomalous Size-Dependent Electron-Phonon Interaction in Graded Energy Band: Solving the Fano Paradox.

Quantum size effects on interferons (electron-phonon bound states), confined in fractal silicon (Si) nanostructures (NSs), have been studied by using Raman spectromicroscopy. A paradoxical size dependence of Fano parameters, estimated from Raman spectra, has been observed as a consequence of longitudinal variation of nanocrystallite size along the Si wires leading to local variations in the dopants' density which actually starts governing the Fano coupling, thus liberating the interferons to exhibit the typical quantum size effect. These interferons are more dominated by the effective reduction in dopants' density rather than the quantum confinement effect. Detailed experimental and theoretical Raman line shape analyses have been performed to solve the paradox by establishing that the increasing size effect actually is accompanied by receding Fano coupling due to the weakened electronic continuum. The latter has been validated by observing a consequent variation in the Raman signal from dopants which was found to be consistent with the above conclusion.

Genome-Wide Analysis of TIR-NBS-LRR Gene Family in Potato Identified StTNLC7G2 Inducing Reactive Oxygen Species in Presence of Alternaria solani.

Resistance gene analogs (RGAs) comprising NBS-LRR gene family members are considered prominent candidates in the development of disease-resistant genotypes. NBS-LRR gene family comprised a very large number of genes; therefore, members of one subfamily TIR-NBS-LRR (TNL) are identified in the present study from Solanum tuberosum genome, followed by their bioinformatics characterization. The study identified a total of 44 genes encoding 60 TNL transcripts with two prominent clusters at chromosome 1 and chromosome 11. Expression analysis of 14 TNL genes after Alternaria solani infection at 1, 2, 3, 5, and 7 days post inoculation in two disease-tolerant varieties, Kufri Jyoti and Kufri Pukhraj, and one relatively susceptible variety, Kufri Chandramukhi, showed differential expression of many genes including a high expression (>15-fold) of StTNLC6G2T1 and StTNLC11G9T1. Functional characterization of one such gene, StTNLC7G2, reveals involvement in the generation of reactive oxygen species under A. solani attack, implicating its putative role in plant defense via hypersensitive response.

Atypical Green Luminescence from Raw Cassia Siamea Extract: A Comparison with Red Emitting Tinospora Cordifolia.

Optical and electrochemical properties from Cassia and Giloy leaves' raw extract have been studied, and they show similar properties as UV absorber but different emission properties, under UV excitation, even though they appear the same in natural light. Giloy and Cassia extracts show red and green luminescence, respectively, under UV excitation. Like the appearance, their redox properties are also similar, which shows that both can act as antioxidants. Raman spectroscopy and excitation wavelength dependent photoluminescence data have been compared. The difference in relative emission intensities have been explained based on the presence of corresponding color centers in different ratios in the two leaves.

Tracking Dynamic Doping in a Solid-State Electrochromic Device: Raman Microscopy Validates the Switching Mechanism.

Solid-state electrochromic devices often need appropriate characterization to establish the real working mechanism for optimization and diagnosis. Raman mapping has been used here to track "dynamic doping", an important concept in organic electronics and in polythiophene-based solid-state electrochromic devices to understand and validate the mechanism of bias-induced redox-driven color switching. The proposed method demonstrates the live formation and movement of polarons which is best suited for in situ solid-state Raman spectroelectrochemistry. A 2-fold approach has been adopted here for this (1) by fabricating a working device in cross bar geometry followed by in situ spectroscopy to demonstrate the device functioning and (2) by carrying out Raman mapping from a device in custom-designed thin-film-transistor-like geometry to track and actually "see" the mechanism spectroscopically.

Proniosomes: the effective and efficient drug-carrier system.

Niosomes, liposomes and proniosomes are the most abundantly used vesicular systems for the transdermal delivery of drugs. Proniosomes are nonhydrated niosomes, which, upon hydration, form niosomes. Various researches have proved the advantages of proniosomes over the other conventional dosage forms currently available in the market. Proniosomes overcome physical stability problems involved with other vesicular systems such as leaking, fusion and aggregation. The stability and shelf life of proniosomes especially have been found to be much better and prolonged in comparison to other vesicular systems such as liposomes. The present review has been written in an effort to bring yet another viewpoint from a different angle and curated to compile the latest updates in this highly attractive delivery system from today's research point.

Low density culture of mammalian primary neurons in compartmentalized microfluidic devices.

This paper demonstrates the fabrication of a compartmentalized microfluidic device with docking sites to position a single neuron or a cluster of 5-6 neurons along with varying length of microgrooves and the optimization process for culturing primary mammalian neurons at low densities. The principle of centrifugation was employed to situate cells in desired locations followed by the application of a fluid flow to remove the extra or unwanted cells lying in the vicinity of the located neurons. The neuronal cell density was optimized by seeding 103 cells and 104 cells/microfluidic device. The speed of centrifugation was optimized as 1500 rpm for 1 min and a cell density of greater than or equal to 104 cells/microfluidic device was found to be suitable for loading maximum number of docking sites. The outcomes of the simulated experiments was found to be in compliance with the experimemtal verifications. Furthermore, the cells cultured within the microfluidic device were assessed for immunocytochemical staining and the axonal growth was quantified with the help of an Axofluidic software. Although, several in vitro microfluidic platforms have been developed that facilitate the investigations where communication between neurons or between neurons and other cell types is concerned, none of the partitioned devices so far has reported the presence of docking sites along with an array of grooves of varying lengths. These physically connected but fluidically isolated compartmentalized microfluidic devices may serve us in analysing the activity of a low density of neurons and the influence of axonal length in setting up a communication with other cell type.This platform is useful to gain insights into the processes of synapse formation, axonal guidance, cell-cell interaction, to name a few.

Deconvoluting Diffuse Reflectance Spectra for Retrieving Nanostructures' Size Details: An Easy and Efficient Approach.

A new model has been reported here to estimate the mean size and size distribution in nanostructured materials by utilizing a simple and economic diffuse reflectance spectroscopy through spectral line-shape analysis. In the proposed model, a theoretical line shape has been derived by taking into account a size distribution function, which represents a variation in absorption coefficient as a function of size, which in turn depends on the band gap and thus on the excitation photon energy. A fitting of the experimental absorption spectra with the derived line-shape function yields the mean crystallite size and size distribution. The size and size distribution have been successfully estimated from two different silicon nanostructured samples, prepared by metal induced etching. The model has been validated by comparing the estimated values with the sizes estimated using Raman spectroscopy, which is a well-known technique. The two results are not only consistent with each other but are also found to be consistent with the electron microscopy's results, revealing that a technique as simple and as economic as diffuse reflectance spectroscopy can be used to estimate size distribution. In addition, the proposed model can also be used to investigate the homogeneity in the size distribution in a nanostructured sample.

Quantifying the Short-Range Order in Amorphous Silicon by Raman Scattering.

Quantification of the short-range order in amorphous silicon has been formulized using Raman scattering by taking into account established frameworks for studying the spectral line-shape and size dependent Raman peak shift. A theoretical line-shape function has been proposed for representing the observed Raman scattering spectrum from amorphous-Si-based on modified phonon confinement model framework. While analyzing modified phonon confinement model, the term "confinement size" used in the context of nanocrystalline Si was found analogous to the short-range order distance in a-Si thus enabling one to quantify the same using Raman scattering. Additionally, an empirical formula has been proposed using bond polarizability model for estimating the short-range order making one capable to quantify the distance of short-range order by looking at the Raman peak position alone. Both the proposals have been validated using three different data sets reported by three different research groups from a-Si samples prepared by three different methods making the analysis universal.

Delayed selfing ensures reproductive assurance in Utricularia praeterita and Utricularia babui in Western Ghats.

Numerous bladderwort (Utricularia) species are distributed worldwide, but their reproductive biology is rarely investigated. Bladderworts are known to depend on tiny organisms to meet a significant proportion of their energy requirement by trapping them in bladders. However, information on the extent of their reliance on insects for pollination success is limited. We examined the reproductive strategy of two Utricularia species viz. Utricularia praeterita and U. babui, endemic to Western Ghats, India. The main aspects of the investigation involved floral biology, breeding system, pollination mechanism, and reproductive success. Flowers of both the species are structured for outbreeding through entomophilous floral suites, herkogamy, protandrous dichogamy and sensitive lobes of the stigma. With nearly 65% natural fruit-set, both the species appeared to be sufficiently open-pollinated. However, pollinators failed to show in plants of U. praeterita while in U. babui there was an apparent mismatch between the extent of fruit-set and pollinator visits. The study demonstrated that in the absence/insufficient visits of pollinators, the two species resort to autonomous selfing. In U. babui, denser patches of plants appeared to be crucial for attracting the pollinators. Both species are self-compatible, and reproductive success is predominantly achieved by delayed autonomous selfing. The sensitive stigma in the species fails to prevent selfing due to diminished herkogamy during the late anthetic stages. It is inferred that in the pollinator-limited environment, delayed selfing contributes to absolute natural fecundity in U. praeterita, while it produces a mixed progeny in U. babui.