RNAi technology extends its reach: Engineering plant resistance against harmful eukaryotes

RNA interference (RNAi) is a homology-dependent gene silencing technology that is initiated by double stranded RNA (dsRNA). It has emerged as a genetic tool for engineering plants resistance against prokaryotic pathogens such as virus and bacteria. Recent studies broaden the role of RNAi, and many successful examples have described the application of RNAi for engineering plant resistance against a range of eukaryotic organisms. Expression of dsRNA directed against suitable eukaryotic pathogens target genes in transgenic plants has been shown to give protection against harmful eukaryotic species, including nematodes, herbivorous insects, parasitic weeds and fungi. This review addresses the progress of RNAi-based transgenic plant resistance against these four class eukaryotic pests, as well as future challenges and prospects.Key words: dsRNA, RNAi, crop resistance, biotechnology, nematode, insect, parasitic weed, fungus

An Update on the Evolution of Glucosyltransferase (Gtf) Genes in Streptococcus

In many caries-promoting Streptococcus species, glucosyltransferases (Gtfs) are recognized as key enzymes contributing to the modification of biofilm structures, disruption of homeostasis of healthy microbiota community and induction of caries development. It is therefore of great interest to investigate how Gtf genes have evolved in Streptococcus. In this study, we conducted a comprehensive survey of Gtf genes among 872 streptococci genomes of 37 species and identified Gtf genes from 364 genomes of 18 species. To clarify the relationships of these Gtf genes, 45 representative sequences were used for phylogenic analysis, which revealed two clear clades. Clade I included 12 Gtf genes from nine caries-promoting species of the Mutans and Downei groups, which produce enzymes known to synthesize sticky, water-insoluble glucans (WIG) that are critical for modifying biofilm structures. Clade II primarily contained Gtf genes responsible for synthesizing water-soluble glucans (WSG) from all 18 species, and this clade further diverged into three subclades (IIA, IIB, and IIC). An analysis of 16 pairs of duplicated Gtf genes revealed high divergence levels at the C-terminal repeat regions, with ratios of the non-synonymous substitution rate (dN) to synonymous substitution rate (dS) ranging from 0.60 to 1.03, indicating an overall relaxed constraint in this region. However, among the clade I Gtf genes, some individual repeat units possessed strong functional constraints by the same criterion. Structural variations in the repeat regions were also observed, with detection of deletions or recent duplications of individual repeat units. Overall, by establishing an updated phylogeny and further elucidating their evolutionary patterns, this work enabled us to gain a greater understanding of the origination and divergence of Gtf genes in Streptococcus

Factors that contribute to trait mindfulness level among hospitalized patients with major depressive disorder

Mindfulness training among patients with major depressive disorder (MDD) reduces symptoms, prevents relapse, improves prognosis, and is more efficient for those with a high level of trait mindfulness. Upon hospital admission, 126 MDD patients completed the Beck Depression Inventory (BDI), World Health Organization Quality of Life Brief, Five-Factor Mindfulness Questionnaire (FFMQ), and the Rumination Response Scale (RRS). The 65 patients that scored less than the median of all subjects on the FFMQ were placed into the low mindfulness level (LML) group. The other 61 patients were placed in the high mindfulness level (HML) group. All facet scores were statistically different between the mental health assessment scores of the HML and LML groups except for RRS brooding and FFMQ nonjudgement. Trait mindfulness level exhibited a negative and bidirectional association with MDD severity primarily through the facets of description and aware actions. Trait mindfulness was also related positively with age primarily through the facets of nonreactivity and nonjudgement. Being married is positively associated with trait mindfulness levels primarily through the facet of observation and by an associated increase in perceived quality of life. Mindfulness training prior to MDD diagnosis also associates positively with trait mindfulness level. Hospitalized MDD patients should have their trait mindfulness levels characterized to predict treatment efficiency, help establish a prognosis, and identify mindfulness-related therapeutic targets

FAST observations of an extremely active episode of FRB 20201124A: III. Polarimetry

As the third paper in the multiple-part series, we report the statistical properties of radio bursts detected from the repeating fast radio burst (FRB) source FRB 20201124A with the Five-hundred-meter Aperture Spherical radio telescope (FAST) during an extremely active episode between the 25th and the 28th of September 2021 (UT). We focus on the polarisation properties of 536 bright bursts with $\mathrm{S/N}>50$. We found that the Faraday rotation measures (RMs) monotonically dropped from $-579 \ {\rm rad \ m^{-2}}$ to $-605 \ {\rm rad \ m^{-2}}$ in the 4-day window. The RM values were compatible with the values ($-300$ to $-900\ {\rm rad \ m^{-2}}$ ) reported 4 month ago (Xu et al. 2022). However, the RM evolution rate in the current observation window was at least an order of magnitude smaller than the one ($\sim 500\ {\rm rad \ m^{-2}\, day^{-1}}$) previously reported during the rapid RM-variation phase, but is still higher than the one ($\le 1\ {\rm rad \ m^{-2} day^{-1}}$) during the later RM no-evolution phase. The bursts of FRB 20201124A were highly polarised with the total degree of polarisation (circular plus linear) greater than 90polarisation position angles (PAs), degree of linear polarisation ($L/I$), and degree of circular polarisation ($V/I$) can be characterised with unimodal distribution functions. During the observation window, the distributions became wider with time, i.e. with larger scatter, but the centroids of the distribution functions remained nearly constant. For individual bursts, significant PA variations (confidence level 5-$\sigma$) were observed in 33% of all bursts. The polarisation of single pulses seems to follow certain complex trajectories on the Poincar\'e sphere, which may shed light on the radiation mechanism at the source or the plasma properties along the path of FRB propagation.Comment: 25 pages, 16 figures. Accepted by Research in Astronomy and Astrophysics (RAA

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Optimasi Portofolio Resiko Menggunakan Model Markowitz MVO Dikaitkan dengan Keterbatasan Manusia dalam Memprediksi Masa Depan dalam Perspektif Al-Qur`an

Risk portfolio on modern finance has become increasingly technical, requiring the use of sophisticated mathematical tools in both research and practice. Since companies cannot insure themselves completely against risk, as human incompetence in predicting the future precisely that written in Al-Quran surah Luqman verse 34, they have to manage it to yield an optimal portfolio. The objective here is to minimize the variance among all portfolios, or alternatively, to maximize expected return among all portfolios that has at least a certain expected return. Furthermore, this study focuses on optimizing risk portfolio so called Markowitz MVO (Mean-Variance Optimization). Some theoretical frameworks for analysis are arithmetic mean, geometric mean, variance, covariance, linear programming, and quadratic programming. Moreover, finding a minimum variance portfolio produces a convex quadratic programming, that is minimizing the objective function ðð¥with constraintsð ð 𥠥 ðandð´ð¥ = ð. The outcome of this research is the solution of optimal risk portofolio in some investments that could be finished smoothly using MATLAB R2007b software together with its graphic analysis

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Measurement of the top quark forward-backward production asymmetry and the anomalous chromoelectric and chromomagnetic moments in pp collisions at √s = 13 TeV

Abstract The parton-level top quark (t) forward-backward asymmetry and the anomalous chromoelectric (d̂ t) and chromomagnetic (μ̂ t) moments have been measured using LHC pp collisions at a center-of-mass energy of 13 TeV, collected in the CMS detector in a data sample corresponding to an integrated luminosity of 35.9 fb−1. The linearized variable AFB(1) is used to approximate the asymmetry. Candidate t t ¯ events decaying to a muon or electron and jets in final states with low and high Lorentz boosts are selected and reconstructed using a fit of the kinematic distributions of the decay products to those expected for t t ¯ final states. The values found for the parameters are AFB(1)=0.048−0.087+0.095(stat)−0.029+0.020(syst),μ̂t=−0.024−0.009+0.013(stat)−0.011+0.016(syst), and a limit is placed on the magnitude of | d̂ t| < 0.03 at 95% confidence level. [Figure not available: see fulltext.