Impact of biotic stresses on the Brassicaceae family and opportunities for crop improvement by exploiting genotyping traits.

MAIN CONCLUSION: Utilizing RNAi, miRNA, siRNA, lncRNA and exploiting genotyping traits can help safeguard the food supply from illnesses and pest damage to Brassicas, as well as reduce yield losses caused by plant pathogens and insect pests. In the natural environment, plants face significant challenges in the form of biotic stress, due to various living organisms, leading to biological stress and a sharp decline in crop yields. To cope with these effects, plants have evolved specialized mechanisms to mitigate these challenges. Plant stress tolerance and resistance are influenced by genes associated with stress-responsive pathogens that interact with various stress-related signaling pathway components. Plants employ diverse strategies and mechanisms to combat biological stress, involving a complex network of transcription factors that interact with specific cis-elements to regulate gene expression. Understanding both plant developmental and pathogenic disease resistance mechanisms can allow us to develop stress-tolerant and -resistant crops. Brassica genus includes commercially important crops, e.g., broccoli, cabbage, cauliflower, kale, and rapeseed, cultivated worldwide, with several applications, e.g., oil production, consumption, condiments, fodder, as well as medicinal ones. Indeed, in 2020, global production of vegetable Brassica reached 96.4 million tones, a 10.6% rise from the previous decade. Taking into account their commercial importance, coupled to the impact that pathogens can have in Brassica productivity, yield losses up to 60%, this work complies the major diseases caused due to fungal, bacterial, viral, and insects in Brassica species. The review is structured into three parts. In the first part, an overview is provided of the various pathogens affecting Brassica species, including fungi, bacteria, viruses, and insects. The second part delves into the exploration of defense mechanisms that Brassica plants encounter against these pathogens including secondary metabolites, duplicated genes, RNA interference (RNAi), miRNA (micro-RNA), siRNA (small interfering RNA), and lncRNA (long non-coding RNA). The final part comprehensively outlines the current applications of CRISPR/Cas9 technology aimed at enhancing crop quality. Taken collectively, this review will contribute to our enhanced understanding of these mechanisms and their role in the development of resistance in Brassica plants, thus supporting strategies to protect this crucial crop.

Mechano-regulation by clathrin pit-formation and passive cholesterol-dependent tubules during de-adhesion.

Adherent cells ensure membrane homeostasis during de-adhesion by various mechanisms, including endocytosis. Although mechano-chemical feedbacks involved in this process have been studied, the step-by-step build-up and resolution of the mechanical changes by endocytosis are poorly understood. To investigate this, we studied the de-adhesion of HeLa cells using a combination of interference reflection microscopy, optical trapping and fluorescence experiments. We found that de-adhesion enhanced membrane height fluctuations of the basal membrane in the presence of an intact cortex. A reduction in the tether force was also noted at the apical side. However, membrane fluctuations reveal phases of an initial drop in effective tension followed by saturation. The area fractions of early (Rab5-labelled) and recycling (Rab4-labelled) endosomes, as well as transferrin-labelled pits close to the basal plasma membrane, also transiently increased. On blocking dynamin-dependent scission of endocytic pits, the regulation of fluctuations was not blocked, but knocking down AP2-dependent pit formation stopped the tension recovery. Interestingly, the regulation could not be suppressed by ATP or cholesterol depletion individually but was arrested by depleting both. The data strongly supports Clathrin and AP2-dependent pit-formation to be central to the reduction in fluctuations confirmed by super-resolution microscopy. Furthermore, we propose that cholesterol-dependent pits spontaneously regulate tension under ATP-depleted conditions.

A Real-World Observational Study to Evaluate the Safety and Effectiveness of Fluticasone Furoate-Oxymetazoline Fixed Dose Combination Nasal Spray in Patients with Allergic Rhinitis.

BACKGROUND: Allergic rhinitis (AR) has shown an increasing prevalence leading to a considerable medical and social burden. Nasal congestion is the cardinal symptom of AR, and the upper respiratory tract is most affected by this long-lasting ailment. Intranasal corticosteroids alleviate nasal congestion, along with other symptoms of AR, but their effect is not evident immediately. Oxymetazoline has a rapid onset of action, but its use should be limited to 3-5 days. OBJECTIVE: The study aimed to evaluate the safety and effectiveness of the fixed-dose combination nasal spray containing fluticasone furoate and oxymetazoline hydrochloride (FF + OXY) 27.5/50 mcg once daily in patients with AR in a real-world clinical setting. METHODS: The study was a prospective, open-label, single-arm, multicenter, real-world observational study conducted in patients with AR for a period of 28 days. Patients (n = 388) with a diagnosis of AR were treated with a combination of FF + OXY nasal spray. Total nasal symptom score (TNSS), total ocular symptom score (TOSS) and total symptom score (TSS) were documented at baseline and at the end of study period. The overall effectiveness of treatment with FF + OXY was rated by the investigators as very good/good/satisfactory/poor (4-point Likert scale) for each patient. RESULTS: Treatment with FF + OXY resulted in significant reduction in the TNSS, TOSS and TSS, from 7.18 ± 3.38 at baseline to 0.20 ± 0.84 (p < 0.001), from 2.34 ± 2.29 at baseline to 0.09 ± 0.53 (p < 0.001), from 9.51 ± 4.94 at baseline to 0.29 ± 1.32 (p < 0.001) at 28 days respectively. With respect to effectiveness, the investigators reported very good effectiveness in 52.12% of patients. No serious adverse events were reported. CONCLUSION: The fixed-dose combination of once-daily fluticasone furoate and oxymetazoline hydrochloride nasal spray 27.5/50 mcg was effective in relieving the nasal congestion and reduction of TNSS, TOSS and TSS in patients suffering from AR. The combination was safe and well tolerated with no rebound congestion throughout the treatment period.

Experimental verification of arcsine laws in mesoscopic nonequilibrium systems.

A large number of processes in the mesoscopic world occur out of equilibrium, where the time evolution of a system becomes immensely important since it is driven principally by dissipative effects. Nonequilibrium steady states (NESS) represent a crucial category in such systems, where relaxation timescales are comparable to the operational timescales. In this study, we employ a model NESS stochastic system, which is comprised of a colloidal microparticle optically trapped in a viscous fluid, externally driven by a temporally correlated noise, and show that time-integrated observables such as the entropic current, the work done on the system or the work dissipated by it, follow the three Lévy arcsine laws [A. C. Barato et al., Phys. Rev. Lett. 121, 090601 (2018)0031-900710.1103/PhysRevLett.121.090601], in the large time limit. We discover that cumulative distributions converge faster to arcsine distributions when it is near equilibrium and the rate of entropy production is small, because in that case the entropic current has weaker temporal autocorrelation. We study this phenomenon by changing the strength of the added noise as well as by perturbing our system with a flow field produced by a microbubble at close proximity to the trapped particle. We confirm our experimental findings with theoretical simulations of the systems. Our work provides an interesting insight into the NESS statistics of the meso-regime, where stochastic fluctuations play a pivotal role.

Single-shot phase-sensitive wideband active microrheology of viscoelastic fluids using pulse-scanned optical tweezers.

We present a fast phase sensitive active microrheology technique exploring the phase response of a microscopic probe particle trapped in a linear viscoelastic fluid using optical tweezers under an external perturbation. Thus, we experimentally determine the cumulative response of the probe to an entire repertoire of sinusoidal excitations simultaneously by applying a spatial square pulse as an excitation to the trapped probe. The square pulse naturally contains the fundamental sinusoidal frequency component and higher odd harmonics, so that we measure the phase response of the probe over a wide frequency band in a single shot, with the band being tunable over the spectrum by choosing suitable experimental parameters. We then determine the responses to individual harmonics using a lock-in algorithm, and compare the phase shifts to those obtained theoretically by solving the equation of motion of the probe particle confined in a harmonic potential in the fluid in the presence of a sinusoidal perturbation. We go on to relate the phase response of the probe to the complex shear modulus [Formula: see text], and proceed to verify our technique in a mixture of polyacrylamide and water, which we compare with known values in literature and obtain very good agreement. Our method increases the robustness of active microrheology in general and ensures that any drifts in time are almost entirely ruled out from the data, with the added advantage of high speed and ease of use.

Resolving population structure and genetic differentiation associated with RAD-SNP loci under selection in tossa jute (Corchorus olitorius L.).

The genetic basis of selection for geographic adaptation and how it has contributed to population structure are unknown in tossa jute (Corchorus olitorius), an important bast fibre crop. We performed restriction site-associated DNA (RAD) sequencing-based (1115 RAD-SNPs) population genomic analyses to investigate genetic differentiation and population structure within a collection of 221 fibre-type lines from across nine geographic regions of the world. Indian populations, with relatively higher overall diversity, were significantly differentiated (based on FST and PCA) from the African and the other Asian populations. There is strong evidence that African C. olitorius was first introduced in peninsular India that could perhaps be its secondary centre of origin. However, multiple later introductions have occurred in central, eastern and northern India. Based on four assignment tests with different statistical bases, we infer that two ancestral subpopulations (African and Indian) structure the C. olitorius populations, but not in accordance with their geographic origins and patterns of diversity. Our results advocate recent migration of C. olitorius through introduction and germplasm exchange across geographical boundaries. We argue that high intraspecific genetic admixture could be associated with increased genetic variance within Indian populations. Employing both subpopulation (FST/GST-outlier) and individual-based (PCAdapt) tests, we detected putative RAD-SNP loci under selection and demonstrated that bast fibre production was an artificial, while abiotic and biotic stresses were natural selection pressures in C. olitorius adaptation. By reinferring the population structure without outlier loci, we propose ad interim that C. olitorius was possibly domesticated as a fibre crop in the Indian subcontinent.

The draft genome of Corchorus olitorius cv. JRO-524 (Navin).

Here, we present the draft genome (377.3 Mbp) of Corchorus olitorious cv. JRO-524 (Navin), which is a leading dark jute variety developed from a cross between African (cv. Sudan Green) and indigenous (cv. JRO-632) types. We predicted from the draft genome a total of 57,087 protein-coding genes with annotated functions. We identified a large number of 1765 disease resistance-like and defense response genes in the jute genome. The annotated genes showed the highest sequence similarities with that of Theobroma cacao followed by Gossypium raimondii. Seven chromosome-scale genetically anchored pseudomolecules were constructed with a total size of 8.53 Mbp and used for synteny analyses with the cocoa and cotton genomes. Like other plant species, gypsy and copia retrotransposons were the most abundant classes of repeat elements in jute. The raw data of our study are available in SRA database of NCBI with accession number SRX1506532. The genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession LLWS00000000, and the version described in this paper will be the first version (LLWS01000000).

Fast Bayesian inference of optical trap stiffness and particle diffusion.

Bayesian inference provides a principled way of estimating the parameters of a stochastic process that is observed discretely in time. The overdamped Brownian motion of a particle confined in an optical trap is generally modelled by the Ornstein-Uhlenbeck process and can be observed directly in experiment. Here we present Bayesian methods for inferring the parameters of this process, the trap stiffness and the particle diffusion coefficient, that use exact likelihoods and sufficient statistics to arrive at simple expressions for the maximum a posteriori estimates. This obviates the need for Monte Carlo sampling and yields methods that are both fast and accurate. We apply these to experimental data and demonstrate their advantage over commonly used non-Bayesian fitting methods.

Development of SSR markers and construction of a linkage map in jute.

Jute is an important natural fibre crop, which is only second to cotton in its importance at the global level. It is mostly grown in Indian subcontinent and has been recently used for the development of genomics resources.We recently initiated a programme to develop simple sequence repeat markers and reported a set of 2469 SSR that were developed using four SSR-enriched libraries (Mir et al. 2009). In this communication, we report an additional set of 607 novel SSR in 393 SSR containing sequences. However, primers could be designed for only 417 potentially useful SSR. Polymorphism survey was carried out for 374 primer pairs using two parental genotypes (JRO 524 and PPO4) of a mapping population developed for fibre fineness; only 66 SSR were polymorphic. Owing to a low level of polymorphism between the parental genotypes and a high degree of segregation distortion in recombinant inbred lines, genotypic data of only 53 polymorphic SSR on the mapping population consisting of 120 RIL could be used for the construction of a linkage map; 36 SSR loci were mapped on six linkage groups that covered a total genetic distance of 784.3 cM. Hopefully, this map will be enriched with more SSR loci in future and will prove useful for identification of quantitative trait loci/genes for molecular breeding involving improvement of fibre fineness and other related traits in jute.

A simple ethanol wash of the tissue homogenates recovers high-quality genomic DNA from Corchorus species characterized by highly acidic and proteinaceous mucilages

A simple miniprep based on early elimination of highly acidic and proteinaceous mucilages through ethanol washing of the tissue homogenates has been developed for the extraction of genomic DNA from mature leaves and seeds of Corchorus spp. As compared to high cetyltrimethylammonium bromide (CTAB)-NaCl DNA extraction followed by ethanol-based removal of remnant mucilages from the DNA pellet, this simple miniprep consistently and reproducibly recovers high amounts of DNA with good spectral qualities at A260/A280 and A260/A230. The purified DNA is efficiently digested by restriction endonucleases, and is suitable for PCR amplification of nuclear microsatellites with expected allele sizes.