The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors

The function of proteins can often be inferred from their three-dimensional structures. Experimental structural biologists spent decades studying these structures, but the accelerated pace of protein sequencing continuously increases the gaps between sequences and structures. The early 2020s saw the advent of a new generation of deep learning-based protein structure prediction tools that offer the potential to predict structures based on any number of protein sequences. In this review, we give an overview of the impact of this new generation of structure prediction tools, with examples of the impacted field in the life sciences. We discuss the novel opportunities and new scientific and technical challenges these tools present to the broader scientific community. Finally, we highlight some potential directions for the future of computational protein structure prediction

THE EFFECT OF APPLIED NITROGEN FERTILIZER AND PLANT GROWTH REGULATORS ON WINTER WHEAT (TRITICUM AESTIVUM L.) YIELD AND GRAIN QUALITY

The rate of nitrogen fertilization is the most important factor for plant growth and development which can increase yield and grain quality assurance. But the high rates of applied nitrogen fertilizer combined with high precipitations favor stem elongation and increase risk of cereal lodging. Lodging is a common phenomenon that occurs near harvest time, which can significant decrease both quantity and quality of the yield. Plant growth regulators (PGRs) are widely used for lodging control in winter wheat grown at high nitrogen rates. The present study investigated the effect of PGR and nitrogen fertilization rates on wintet wheat yield and grain protein content.  The field study was conducted at the Agricultural Research and Development Station Turda in 2016 involving eight winter wheat genotypes tested at different rates of applied nitrogen fertilizer, in combination with foliar treatment with trinexapac-ethyl- based plant growth regulator sprayed over the foliage

Phosphonopeptides Revisited, in an Era of Increasing Antimicrobial Resistance

Given the increase in resistance to antibacterial agents, there is an urgent need for the development of new agents with novel modes of action. As an interim solution, it is also prudent to reinvestigate old or abandoned antibacterial compounds to assess their efficacy in the context of widespread resistance to conventional agents. In the 1970s, much work was performed on the development of peptide mimetics, exemplified by the phosphonopeptide, alafosfalin. We investigated the activity of alafosfalin, di-alanyl fosfalin and β-chloro-L-alanyl-β-chloro-L-alanine against 297 bacterial isolates, including carbapenemase-producing Enterobacterales (CPE) (n = 128), methicillin-resistant Staphylococcus aureus (MRSA) (n = 37) and glycopeptide-resistant enterococci (GRE) (n = 43). The interaction of alafosfalin with meropenem was also examined against 20 isolates of CPE. The MIC50 and MIC90 of alafosfalin for CPE were 1 mg/L and 4 mg/L, respectively and alafosfalin acted synergistically when combined with meropenem against 16 of 20 isolates of CPE. Di-alanyl fosfalin showed potent activity against glycopeptide-resistant isolates of Enterococcus faecalis (MIC90; 0.5 mg/L) and Enterococcus faecium (MIC90; 2 mg/L). Alafosfalin was only moderately active against MRSA (MIC90; 8 mg/L), whereas β-chloro-L-alanyl-β-chloro-L-alanine was slightly more active (MIC90; 4 mg/L). This study shows that phosphonopeptides, including alafosfalin, may have a therapeutic role to play in an era of increasing antibacterial resistance

MORPHO-PHYSIOLOGICAL RESPONSES OF WINTER WHEAT (TRITICUM AESTIVUM L.) TO PLANT GROWTH REGULATORS AND NITROGEN APPLICATIONS

Wheat lodging is a serious problem in cereal production in many areas. Grain yield reductions almost always accompany lodging, with the magnitude of loss dependent on the cultivar, growth stage and severity of lodging. The synthetic plant growth regulators (PGRs) such as chlormequat chloride (CC),  trinexepac-ethyl (TE)  can prevent lodging by reducing stem elongation and improving mechanical strength of the stem. A field experiment was conducted during the 2018-2019 growing season at the experimental field of the Agricultural Research and Development Station, located at Turda, to evaluate the effect of TE and CC on winter wheat morpho-physiological traits such as plant height, LAI, numbers of spikes m-2, lodging and grain yield of three winter wheat genotypes that are tall and with a high lodging susceptibility Arieşan, Apullum and Bezostaia, tested at different rates of applied nitrogen fertilizer in combination with foliar treatment with trinexapac-ethyl and chlorocholine chloride sprayed over the foliage. The influence of the TE treatment and CC treatment on the morpho-physiological traits studied in this experience was not the same for all the genotypes. Both PGR decreased plant height, more TE treatment than CC treatment. CC treatment influenced more than TE the increase of LAI and number of spikes m-2, witch leaded to the increase of grain yield where CC treatment was applied

A latent green fluorescent styrylcoumarin probe for the selective growth and detection of Gram negative bacteria

A novel, green fluorescent β-alanylstyrylcoumarin derivative was synthesized and evaluated for its performance as a fluorogenic enzyme substrate on a range of clinically relevant microorganisms. The substrate was selectively hydrolysed by β-alanyl aminopeptidase producing P. aeruginosa resulting in an on-to-off fluorescent signal. Growth inhibitory effect of the substrate was observed on Gram positive bacteria and yeasts. Meanwhile, Gram negative species, despite their extremely protective cell envelope, showed ready uptake and accumulation of the substrate within their healthy growing colonies displaying intense green fluorescence.NHMR

Learner and Teacher Roles in the Treatment of Oral Error in Group Work

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/69127/2/10.1177_003368828001100204.pd

An Exactly Conservative Integrator for the n-Body Problem

The two-dimensional n-body problem of classical mechanics is a non-integrable Hamiltonian system for n > 2. Traditional numerical integration algorithms, which are polynomials in the time step, typically lead to systematic drifts in the computed value of the total energy and angular momentum. Even symplectic integration schemes exactly conserve only an approximate Hamiltonian. We present an algorithm that conserves the true Hamiltonian and the total angular momentum to machine precision. It is derived by applying conventional discretizations in a new space obtained by transformation of the dependent variables. We develop the method first for the restricted circular three-body problem, then for the general two-dimensional three-body problem, and finally for the planar n-body problem. Jacobi coordinates are used to reduce the two-dimensional n-body problem to an (n-1)-body problem that incorporates the constant linear momentum and center of mass constraints. For a four-body choreography, we find that a larger time step can be used with our conservative algorithm than with symplectic and conventional integrators.Comment: 17 pages, 3 figures; to appear in J. Phys. A.: Math. Ge

An Overview of the 13:8 Mean Motion Resonance between Venus and Earth

It is known since the seminal study of Laskar (1989) that the inner planetary system is chaotic with respect to its orbits and even escapes are not impossible, although in time scales of billions of years. The aim of this investigation is to locate the orbits of Venus and Earth in phase space, respectively to see how close their orbits are to chaotic motion which would lead to unstable orbits for the inner planets on much shorter time scales. Therefore we did numerical experiments in different dynamical models with different initial conditions -- on one hand the couple Venus-Earth was set close to different mean motion resonances (MMR), and on the other hand Venus' orbital eccentricity (or inclination) was set to values as large as e = 0.36 (i = 40deg). The couple Venus-Earth is almost exactly in the 13:8 mean motion resonance. The stronger acting 8:5 MMR inside, and the 5:3 MMR outside the 13:8 resonance are within a small shift in the Earth's semimajor axis (only 1.5 percent). Especially Mercury is strongly affected by relatively small changes in eccentricity and/or inclination of Venus in these resonances. Even escapes for the innermost planet are possible which may happen quite rapidly.Comment: 14 pages, 11 figures, submitted to CMD

La2010: A new orbital solution for the long term motion of the Earth

We present here a new solution for the astronomical computation of the orbital motion of the Earth spanning from 0 to -250 Myr. The main improvement with respect to the previous numerical solution La2004 (Laskar et al. 2004) is an improved adjustment of the parameters and initial conditions through a fit over 1 Myr to a special version of the high accurate numerical ephemeris INPOP08 (Fienga et al. 2009). The precession equations have also been entirely revised and are no longer averaged over the orbital motion of the Earth and Moon. This new orbital solution is now valid over more than 50 Myr in the past or in the future with proper phases of the eccentricity variations. Due to chaotic behavior, the precision of the solution decreases rapidly beyond this time span, and we discuss the behavior of various solutions beyond 50 Myr. For paleoclimate calibrations, we provide several different solutions that are all compatible with the most precise planetary ephemeris. We have thus reached the time where geological data are now required to discriminate among planetary orbital solutions beyond 50 Myr.Comment: 17 pages, 14 figure