Prediction of Body Weight by Using PCA-Supported Gradient Boosting and Random Forest Algorithms in Water Buffaloes (Bubalus bubalis) Reared in South-Eastern Mexico.

This study aims to use advanced machine learning techniques supported by Principal Component Analysis (PCA) to estimate body weight (BW) in buffalos raised in southeastern Mexico and compare their performance. The first stage of the current study consists of body measurements and the process of determining the most informative variables using PCA, a dimension reduction method. This process reduces the data size by eliminating the complex structure of the model and provides a faster and more effective learning process. As a second stage, two separate prediction models were developed with Gradient Boosting and Random Forest algorithms, using the principal components obtained from the data set reduced by PCA. The performances of both models were compared using R2, RMSE and MAE metrics, and showed that the Gradient Boosting model achieved a better prediction performance with a higher R2 value and lower error rates than the Random Forest model. In conclusion, PCA-supported modeling applications can provide more reliable results, and the Gradient Boosting algorithm is superior to Random Forest in this context. The current study demonstrates the potential use of machine learning approaches in estimating body weight in water buffalos, and will support sustainable animal husbandry by contributing to decision making processes in the field of animal science.

Anisotropic NMR data acquisition with a prototype 400 MHz cryogen-free NMR spectrometer.

High-temperature superconducting (HTS) materials have recently been incorporated into the construction of HTS cryogen-free magnets for nuclear magnetic resonance (NMR) spectroscopy. These HTS NMR spectrometers do not require liquid cryogens, thereby providing significant cost savings and facilitating easy integration into chemistry laboratories. However, the optimal performance of these HTS magnets against standard cryogen NMR magnets must be evaluated, especially with demanding modern NMR applications such as NMR in anisotropic media. The stability of the HTS magnets over time and their performance with complex pulse sequence experiments are the main unknown factors of this new technology. In this study, we evaluate the utility of our prototype 400 MHz cryogen-free power-driven HTS NMR spectrometer, installed in the fumehood of a chemistry laboratory, for stereochemical analysis of three commercial natural products (artemisinin, artemether, and dihydroartemisinin) via measurement of anisotropic NMR data, in particular, residual dipolar couplings. The accuracy of measurement of the anisotropic NMR data with the HTS magnet spectrometer is evaluated through the CASE-3D fitting protocol, as implemented in the Mestrenova-StereoFitter software program.

Phomactinine, the First Nitrogen-Bearing Phomactin, Produced by Biatriospora sp. CBMAI 1333.

Metabolomics analyses and improvement of growth conditions were applied toward diversification of phomactin terpenoids by the fungus Biatriospora sp. CBMAI 1333. Visualization of molecular networking results on Gephi assisted the observation of phomactin diversification and guided the isolation of new phomactin variants by applying a modified version of chemometrics based on a fractional factorial design. Consequentially, the first nitrogen-bearing phomactin, phomactinine (1), with a new rearranged carbon skeleton, was isolated and identified. The strategy combining metabolomics and chemometrics can be extended to include bioassay potency, structure novelty, and metabolic diversification connected or not to genomic analyses.

Life Science Research Immersion Program Improves STEM-Specific Skills and Science Attitudes among Precollege Students.

A predicted rapid growth in science, technology, engineering, and math (STEM) careers demands a vast and talented workforce, but students most commonly abandon STEM majors within the first 2 years of college. Performance in introductory courses, scientific literacy, and the ability to critically reason are main predictors of retention in STEM, highlighting the importance of precollege and early college experience. The Life Science Research Immersion Program (LSRIP) is a novel science education model that focuses on the development of scientific research skills, thus preparing students for introductory college courses and beyond. To evaluate the efficacy of the LSRIP, pre- and postprogram assessments and surveys were administered to three precollege student cohorts. Scientific reasoning assessment scores improved by 4.70% in Summer 2019 (P < 0.01), 9.44% in Fall 2019 (P < 0.05), and 0.97% in Winter 2020 cohorts, with two of five questions showing statistically significant improvement. Surveyed attitudes toward science improved in 62.9% of questions across all cohorts. These results suggest that research immersion experiences are an effective educational instrument for improving and promoting scientific reasoning and attitudes among precollege students. To better prepare students for success in STEM higher education and careers, we recommend implementing LSRIPs to complement traditional precollege science curricula.

Residual dipolar couplings as a tool for structural analysis of ionic liquids.

An acrylonitrile/dimethylacrylamide cross-linked polymer could be swollen in different imidazolium ionic liquids. Mechanical compression of the obtained polymer gels inside an NMR tube allowed the measurement of residual dipolar couplings. Conformational analysis of the 1-methyl-3-butyl-imidazolium (BMIM) cation could be performed by including the measured RDCs as restraints in time-averaged molecular dynamics.

An Acrylonitrile-Based Copolymer Gel as an NMR Alignment Medium for Extraction of Residual Dipolar Couplings of Small Molecules in Aqueous Solution.

An NMR weakly-aligning polymer gel has been prepared by copolymerization of acrylonitrile and 2-acrylamide-2-methyl-1-propanesulfonic acid in the presence of 1,4-butanediol diacrylate as a cross-linker. The polymer readily swells in water in a large range of temperatures, although the swelling ratio is decreased in saline solutions. The swollen gel can be mechanically compressed, in a reversible way, generating anisotropy, as easily shown in 2 H NMR experiments, and allowing measurement of 1 DCH residual dipolar couplings (RDCs) through F1-coupled HSQC experiments. The performance of this gel as a NMR alignment medium was evaluated in several water-soluble organic molecules and, while it provided RDCs of proper size for sucrose and even such as small molecule as 5-norbornen-2-ol, in the case of azidothymidine and cefuroxime sodium salt the strong interaction of these molecules with the gel prevented successful extraction of the RDCs.

Weizhouochrones: Gorgonian-Derived Symmetric Dimers and Their Structure Elucidation Using Anisotropic NMR Combined with DP4+ Probability and CASE-3D.

Natural product dimers have intriguing structural features and often have remarkable pharmacological activities. We report here two uncommon marine gorgonian-derived symmetric dimers, weizhouochrones A (1) and B (2), with indenone-derived monomers, that were isolated from the coral Anthogorgia ochracea collected from the South China Sea. These dimers are difficult targets for structure elucidation that solely relies upon conventional NMR data such as NOEs and J-couplings. Here, to explore the application of emerging methods on the structure elucidation of challenging molecules, we explored a number of different anisotropic and computational NMR approaches. The measurements of anisotropic NMR parameters of weizhouochrone A, including residual dipolar couplings (RDCs) and residual chemical shift anisotropy (RCSA), allowed us to successfully determine the planar structure and its relative configuration. This result was corroborated by a computational NMR analysis based on DP4+ probability and computer-assisted 3D structure elucidation (CASE-3D).

Connection of Isolated Stereoclusters by Combining 13C-RCSA, RDC, and J-Based Configurational Analyses and Structural Revision of a Tetraprenyltoluquinol Chromane Meroterpenoid from Sargassum muticum.

The seaweed Sargassum muticum, collected on the southern coast of Galicia, yielded a tetraprenyltoluquinol chromane meroditerpene compound known as 1b, whose structure is revised. The relative configuration of 1b was determined by J-based configurational methodology combined with an iJ/DP4 statistical analysis and further confirmed by measuring two anisotropic properties: carbon residual chemical shift anisotropies (13C-RCSAs) and one-bond 1H-13C residual dipolar couplings (1DCH-RDCs). The absolute configuration of 1b was deduced by ECD/OR/TD-DFT methods and established as 3R,7S,11R.

Programmable alignment media from self-assembled oligopeptide amphiphiles for the measurement of independent sets of residual dipolar couplings in organic solvents.

NMR spectroscopy in anisotropic media has emerged as a powerful technique for the structural elucidation of organic molecules. Its application requires weak alignment of analytes by means of suitable alignment media. Although a number of alignment media, that are compatible with organic solvents, have been introduced in the last 20 years, acquiring a number of independent, non-linearly related sets of anisotropic NMR data from the same organic solvent system remains a formidable challenge, which is however crucial for the alignment simulations and deriving dynamic and structural information of organic molecules unambiguously. Herein, we introduce a programmable strategy to construct several distinct peptide-based alignment media by adjusting the amino acid sequence, which allows us to measure independent sets of residual dipolar couplings (RDCs) in a highly efficient and accurate manner. This study opens a new avenue for de novo structure determination of organic compounds without requiring prior structural information.

A sorghum genome-wide association study (GWAS) identifies a WRKY transcription factor as a candidate gene underlying sugarcane aphid (Melanaphis sacchari) resistance.

MAIN CONCLUSION: A WRKY transcription factor identified through forward genetics is associated with sorghum resistance to the sugarcane aphid and through heterologous expression reduces aphid populations in multiple plant species. Crop plant resistance to insect pests is based on genetically encoded traits which often display variability across diverse germplasm. In a comparatively recent event, a predominant sugarcane aphid (SCA: Melanaphis sacchari) biotype has become a significant agronomic pest of grain sorghum (Sorghum bicolor). To uncover candidate genes underlying SCA resistance, we used a forward genetics approach combining the genetic diversity present in the Sorghum Association Panel (SAP) and the Bioenergy Association Panel (BAP) for a genome-wide association study, employing an established SCA damage rating. One major association was found on Chromosome 9 within the WRKY transcription factor 86 (SbWRKY86). Transcripts encoding SbWRKY86 were previously identified as upregulated in SCA-resistant germplasm and the syntenic ortholog in maize accumulates following Rhopalosiphum maidis infestation. Analyses of SbWRKY86 transcripts displayed patterns of increased SCA-elicited accumulation in additional SCA-resistant sorghum lines. Heterologous expression of SbWRKY86 in both tobacco (Nicotiana benthamiana) and Arabidopsis resulted in reduced population growth of green peach aphid (Myzus persicae). Comparative RNA-Seq analyses of Arabidopsis lines expressing 35S:SbWRKY86-YFP identified changes in expression for a small network of genes associated with carbon-nitrogen metabolism and callose deposition, both contributing factors to defense against aphids. As a test of altered plant responses, 35S:SbWRKY86-YFP Arabidopsis lines were activated using the flagellin epitope elicitor, flg22, and displayed significant increases in callose deposition. Our findings indicate that both heterologous and increased native expression of the transcription factor SbWRKY86 contributes to reduced aphid levels in diverse plant models.

Physicochemical Characteristics of Yogurt from Sheep Fed with Moringa oleifera Leaf Extracts.

This study determined the effect of feeding Moringa oleifera (MO) leaf extracts to lactating ewes on the physicochemical composition of their milk and yogurt during storage (4 °C for 14 days) and the sensory acceptance of the yogurt. Over 45 days, 24 multiparous lactating Pelibuey and Katahdin ewes (two days in lactation) were randomly assigned to four groups: MO-0, basal diet (BD) + 0 mL MO; MO-20, BD + 20 mL MO; MO-40, BD + 40 mL MO; and MO-60, BD + 60 mL MO. In the milk, an increase of 6% in protein, 26% in leucine, 14% in ash, and 1% in the pH (6.71) was observed with MO-60. The density values decreased by 0.3% at a higher dose of MO compared to MO-0, while the nonfat solids (NFS) in the milk were similar between the treatments. In the yogurt, an increase of 5% in protein, 113% in leucine (MO-20), 9% in NFS, and a reduction of 2% in moisture with MO-60 was observed. The acidity reflected an inverse relationship to the pH, as did the moisture and NFS with MO-60. In conclusion, dietary supplementation with MO in lactating ewes did not have negative effects on the chemical composition of their yogurt during storage (14 days). Overall, feeding sheep with 20 mL of MO positively influenced the physicochemical composition of their milk and yogurt during storage.

Computational Structural Revision of a 4-Hydroxy-3-(1'-angeloyloxy-2',3'-epoxy-3'-methyl)butylacetophenone Compound from Ageratina grandifolia.

The structure of the reported compound 4-hydroxy-3-((S)-1'-angeloyloxy-(R)-2',3'-epoxy-3'-methyl)butylacetophenone (1), isolated from Ageratina grandifolia, has been revised through the use of DFT computational predictions. Re-examination of the reported experimental and DFT computed chemical shifts has led to the proposal of a chromane skeleton rather than the original epoxide derivative. Empirical predictions of the 13C and 1H NMR shifts showed a much better fit for the chromane structure than for the epoxide. The relative configuration of the molecule was established using CASE-3D methodology on the basis of new DFT chemical shielding and J-coupling predictions, allowing the proposal of a new rel-2,2-dimethyl-3R-hydroxy-4S-(1-angeloyloxy)chromane structure (2) for the isolated compound. However, DFT prediction of the optical rotation for the CASE-3D selected configuration/conformations did not provide a conclusive answer for the absolute configuration.

Karplus relationships of the 2 JHNα and 3 JΗΝß couplings in organic azides.

Density functional theory (DFT) and second-order polarization propagator approximation (SOPPA) computations in model organic azides revealed a Karplus-like dependence not only of the vicinal 3 JH-C-Nα-Nß coupling but also of the geminal 2 JH-C-Nα one, with the H-C-Nα Nß dihedral angle. Karplus equations were derived from the DFT computations on the isopropylazide model system. In light of these stablished relationships, natural abundance 1 H-15 N couplings obtained for the azide group of the zidovudine antiviral helped to probe its conformation around the C-Nα bond as being of the synclinal type.

A DFT/machine-learning hybrid method for the prediction of 3 JHCCH couplings.

A machine learning model for the prediction of vicinal proton-proton couplings has been developed based on a hybrid representation that includes geometrical and electronic parameters derived from natural bond orbital (NBO) analysis of low-level BLYP/STO-3G computations. The model can predict 3 JHH couplings with accuracy comparable or better than the well-known Altona equation, and it can provide sensible 3 JHH predictions in systems not well handled by the Altona equation such as epoxide or cyclopropane rings.

Effect of the solvent on the conformation of monocrotaline as determined by isotropic and anisotropic NMR parameters.

The conformation in solution of monocrotaline, a pyrrolizidine alkaloid presenting an eleven-membered macrocyclic diester ring, has been investigated using a combination of isotropic and anisotropic nuclear magnetic resonance parameters measured in four solvents of different polarity (D2 O, DMSO-d6 , CDCl3 , and C6 D6 ). Anisotropic nuclear magnetic resonance parameters were measured in different alignment media, based on their compatibility with the solvent of interest: cromoglycate liquid crystal solution was used for D2 O, whereas a poly (methyl methacrylate) polymer gel was chosen for CDCl3 and C6 D6 , and a poly (hydroxyethyl methacrylate) gel for DMSO-d6 . Whereas the pyrrolizidine ring shows an E6 exo-puckered conformation in all of the solvents, the macrocyclic eleven-membered ring adopts different populations of syn-parallel and anti-parallel relative orientation of the carbonyl groups according to the polarity of the solvent.

Single experiment measurement of residual dipolar couplings in aqueous solution using a biphasic bisperylene imide chromonic liquid crystal.

The use of the biphasic isotropic/nematic region in a bisperylene imide-based lyotropic liquid crystal system allows the extraction of proton-carbon 1 DCH residual dipolar couplings in aqueous solution from a single F1-coupled HSQC experiment. The method was successfully applied to the RDC-based conformational analysis of sucrose.

NMR spectral fingerprint patterns as diagnostics for the unambiguous configurational analysis of the classic organo-gelator 1,3:2,4-dibenzylidene-d-sorbitol (DBS) and its derivatives.

On the basis of experimental data and density functional theory (DFT) chemical shift and scalar coupling predictions, simple spectral nuclear magnetic resonance (NMR) fingerprint patterns have been established for the determination of the configuration in 1,3:2,4-dibenzylidene-d-sorbitol (DBS), a classic low molecular weight gelator, and its derivatives. The results rigorously prove the orientation of the phenyl rings in DBS that had been previously assumed in the literature on the basis of thermodynamic arguments.

Author Correction: Relative configuration of micrograms of natural compounds using proton residual chemical shift anisotropy.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Relative configuration of micrograms of natural compounds using proton residual chemical shift anisotropy.

3D molecular structure determination is a challenge for organic compounds or natural products available in minute amounts. Proton/proton and proton/carbon correlations yield the constitution. J couplings and NOEs oftentimes supported by one-bond 1H,13C residual dipolar couplings (RDCs) or by 13C residual chemical shift anisotropies (RCSAs) provide the relative configuration. However, these RDCs or carbon RCSAs rely on 1% natural abundance of 13C preventing their use for compounds available only in quantities of a few 10's of µgs. By contrast, 1H RCSAs provide similar information on spatial orientation of structural moieties within a molecule, while using the abundant 1H spin. Herein, 1H RCSAs are accurately measured using constrained aligning gels or liquid crystals and applied to the 3D structural determination of molecules with varying complexities. Even more, deuterated alignment media allow the elucidation of the relative configuration of around 35 µg of a briarane compound isolated from Briareum asbestinum.

Deuterium Residual Quadrupolar Couplings: Crossing the Current Frontiers in the Relative Configuration Analysis of Natural Products.

The determination of the 3D structure (configuration and preferred conformation) of complex natural and synthetic organic molecules is a long-standing but still challenging task for chemists, with various implications in pharmaceutical sciences whether or not these substances have specific bioactivities. Nuclear magnetic resonance (NMR) in aligning media, either lyotropic liquid crystals (LLCs) or polymer gels, in combination with molecular modeling is a unique framework for solving complex structural problems whose analytical wealth lies in the establishment of nonlocal structural correlations. As an alternative to the already well-established anisotropic NMR parameters, such as RDCs (residual dipolar couplings) and RCSAs (residual chemical shift anisotropies), it is shown here that deuterium residual quadrupolar couplings (2H-RQCs) can be extracted from 2H 2D-NMR spectra recorded at the natural abundance level in samples oriented in a homopolypeptide LLCs (poly-γ-benzyl-l-glutamate (PBLG)). These 2H-RQCs were successfully used to address nontrivial structural problems in organic molecules. The performance and scope of this new tool is examined for two natural chiral compounds of pharmaceutical interest (strychnine and artemisinin). This is the first report in which the 3D structure/relative configuration of complex bioactive molecules is unambiguously determined using only 2H-RQCs, which, in this case, are at 2H natural abundance.