Effects of Transglutaminase on Myofibrillar Protein Composite Gels with Addition of Non-Meat Protein Emulsion.

The emulsions prepared by three non-meat proteins, sodium caseinate (SC), soy protein isolate (SPI) and egg white protein (EPI), were individually added to the continuous phase of myofibrillar protein (MP) sol to form MP composite gels to simulate meat products. The research aimed to investigate the effects of Transglutaminase (TGase) on the physicochemical properties, microstructure and water phase distribution of non-meat protein emulsion MP composite gels. The results of this study revealed that TGase played a crucial role in forming a tight gel network structure in the composite gels. This enhanced their ability to retain water and improved their overall gel strength. Additionally, TGase increased the gel formation temperature of myofibrillar proteins. Electrophoresis analysis showed that when catalyzed by TGase, there was a lighter band compared to those not catalyzed by TGase. This indicated that the addition of TGase facilitated cross-linking interactions between meat proteins and non-meat proteins in the composite gels. Furthermore, microscopy observations demonstrated that composite gels treated with TGase exhibited a more uniform microstructure. This could be attributed to an acceleration in relaxation time T2. The uniform network structure restricted the movement of water molecules in the gel matrix, thereby improving its water-holding capacity. Overall, these findings highlight how incorporating non-meat proteins into myofibrillar systems can be effectively achieved through enzymatic treatment with TGase. Such modifications not only enhanced important functional properties but also contributed towards developing alternative meat products with improved texture and moisture retention abilities.

Applications of machine learning in pine nuts classification.

Pine nuts are not only the important agent of pine reproduction and afforestation, but also the commonly consumed nut with high nutritive values. However, it is difficult to distinguish among pine nuts due to the morphological similarity among species. Therefore, it is important to improve the quality of pine nuts and solve the adulteration problem quickly and non-destructively. In this study, seven pine nuts (Pinus bungeana, Pinus yunnanensis, Pinus thunbergii, Pinus armandii, Pinus massoniana, Pinus elliottii and Pinus taiwanensis) were used as study species. 210 near-infrared (NIR) spectra were collected from the seven species of pine nuts, five machine learning methods (Decision Tree (DT), Random Forest (RF), Multilayer Perceptron (MLP), Support Vector Machine (SVM) and Naive Bayes (NB)) were used to identify species of pine nuts. 303 images were used to collect morphological data to construct a classification model based on five convolutional neural network (CNN) models (VGG16, VGG19, Xception, InceptionV3 and ResNet50). The experimental results of NIR spectroscopy show the best classification model is MLP and the accuracy is closed to 0.99. Another experimental result of images shows the best classification model is InceptionV3 and the accuracy is closed to 0.964. Four important range of wavebands, 951-957 nm, 1,147-1,154 nm, 1,907-1,927 nm, 2,227-2,254 nm, were found to be highly related to the classification of pine nuts. This study shows that machine learning is effective for the classification of pine nuts, providing solutions and scientific methods for rapid, non-destructive and accurate classification of different species of pine nuts.

Improved hybrid de novo genome assembly and annotation of African wild rice, Oryza longistaminata, from Illumina and PacBio sequencing reads.

African wild rice Oryza longistaminata, one of the eight AA- genome species in the genus Oryza, possesses highly valued traits, such as the rhizomatousness for perennial rice breeding, strong tolerance to biotic and abiotic stresses, and high biomass production on poor soils. To obtain the high-quality reference genome for O. longistaminata we employed a hybrid assembly approach through incorporating Illumina and PacBio sequencing datasets. The final genome assembly comprised only 107 scaffolds and was approximately ∼363.5 Mb, representing ∼92.7% of the estimated African wild rice genome (∼392 Mb). The N50 lengths of the assembled contigs and scaffolds were ∼46.49 Kb and ∼6.83 Mb, indicating ∼3.72-fold and ∼18.8-fold improvement in length compared to the earlier released assembly (∼12.5 Kb and 364 Kb, respectively). Aided with Hi-C data and syntenic relationship with O. sativa, these assembled scaffolds were anchored into 12 pseudo-chromosomes. Genome annotation and comparative genomic analysis reveal that lineage-specific expansion of gene families that respond to biotic- and abiotic stresses are of great potential for mining novel alleles to overcome major diseases and abiotic adaptation in rice breeding programs. This reference genome of African wild rice will greatly enlarge the existing database of rice genome resources and unquestionably form a solid base to understand genomic basis underlying highly valued phenotypic traits and search for novel gene sources in O. longistaminata for the future rice breeding programs.

Draft genomes of two outcrossing wild rice, Oryza rufipogon and O. longistaminata, reveal genomic features associated with mating-system evolution.

Oryza rufipogon and O. longistaminata are important wild relatives of cultivated rice, harboring a promising source of novel genes for rice breeding programs. Here, we present de novo assembled draft genomes and annotation of O. rufipogon and O. longistaminata. Our analysis reveals a considerable number of lineage-specific gene families associated with the self-incompatibility (SI) and formation of reproductive separation. We show how lineage-specific expansion or contraction of gene families with functional enrichment of the recognition of pollen, thus enlightening their reproductive diversification. We documented a large number of lineage-specific gene families enriched in salt stress, antifungal response, and disease resistance. Our comparative analysis further shows a genome-wide expansion of genes encoding NBS-LRR proteins in these two outcrossing wild species in contrast to six other selfing rice species. Conserved noncoding sequences (CNSs) in the two wild rice genomes rapidly evolve relative to selfing rice species, resulting in the reduction of genomic variation owing to shifts of mating systems. We find that numerous genes related to these rapidly evolving CNSs are enriched in reproductive structure development, flower development, and postembryonic development, which may associate with SI in O. rufipogon and O. longistaminata.

Two new species of Sphaeronemoura (Plecoptera: Nemouridae) from Yunnan Province of China.

Two new species of the nemourid genus Sphaeronemoura are described based on males and females collected from Yunnan Province of southwestern China. The new taxa include S. kunmingensis Qian Du sp. nov. and S. campylura Qian Du sp. nov.. The new species are compared to related taxa.

A new species of Agnetina from China with redescription of Paragnetina indentata Wu amp; Claassen, 1934 (Plecoptera: Perlidae).

A new species of genus Agnetina (Plecoptera: Perlidae), Agnetina donans Qian Du sp. nov. from Xinjiang Uygur Autonomous Region of China is described from males and females. Additionally, Paragnetina indentata Wu Claassen, 1934 is redescribed from two males and a female collected from Mt. Gaoligong, Yunnan Province in southwestern China.

Evolution of Oryza chloroplast genomes promoted adaptation to diverse ecological habitats.

The course, tempo and mode of chloroplast genome evolution remain largely unknown, resulting in limited knowledge about how plant plastome gene and genome evolve during the process of recent plant speciation. Here, we report the complete plastomes of 22 closely related Oryza species in chronologically ordered stages and generate the first precise map of genomic structural variation, to our knowledge. The occurrence rapidity was estimated on average to be ~7 insertions and ~15 deletions per Myr. Relatively fewer deletions than insertions result in an increased repeat density that causes the observed growth of Oryza chloroplast genome sizes. Genome-wide scanning identified 14 positively selected genes that are relevant to photosynthesis system, eight of which were found independently in shade-tolerant or sun-loving rice species. psaA seemed positively selected in both shade-tolerant and sun-loving rice species. The results show that adaptive evolution of chloroplast genes makes rice species adapt to diverse ecological habitats related to sunlight preferences.

Effects of graft copolymer of chitosan and salicylic acid on reducing rot of postharvest fruit and retarding cell wall degradation in grapefruit during storage.

This study was to evaluate the effect of graft copolymer (CTS-g-SA) of chitosan (CTS) and salicylic acid (SA) on the storability of grapefruit fruits during postharvest storage. Results indicate that the graft copolymer treatment significantly depressed green mold caused by Penicillium digitatum. The graft copolymer application kept fruit firmness without impairing the fruit quality. Moreover, the graft copolymer treatment inhibited the activity and gene expression of cell wall-modifying enzymes such as polygalacturonase, cellulase, pectin methylesterase, α-l-arabinofuranosidase, ß-galactosidase, and suppressed the modification of cell wall components including covalently bound polysaccharide (sodium carbonate soluble pectin, 24% KOH-soluble fraction), which were associated with fruit softening. These results suggested that graft copolymer application can be recognized as a postharvest technique to suppress rotting and delay softening through inhibiting solubilization of cell wall polysaccharides.

The Tea Tree Genome Provides Insights into Tea Flavor and Independent Evolution of Caffeine Biosynthesis.

Tea is the world's oldest and most popular caffeine-containing beverage with immense economic, medicinal, and cultural importance. Here, we present the first high-quality nucleotide sequence of the repeat-rich (80.9%), 3.02-Gb genome of the cultivated tea tree Camellia sinensis. We show that an extraordinarily large genome size of tea tree is resulted from the slow, steady, and long-term amplification of a few LTR retrotransposon families. In addition to a recent whole-genome duplication event, lineage-specific expansions of genes associated with flavonoid metabolic biosynthesis were discovered, which enhance catechin production, terpene enzyme activation, and stress tolerance, important features for tea flavor and adaptation. We demonstrate an independent and rapid evolution of the tea caffeine synthesis pathway relative to cacao and coffee. A comparative study among 25 Camellia species revealed that higher expression levels of most flavonoid- and caffeine- but not theanine-related genes contribute to the increased production of catechins and caffeine and thus enhance tea-processing suitability and tea quality. These novel findings pave the way for further metabolomic and functional genomic refinement of characteristic biosynthesis pathways and will help develop a more diversified set of tea flavors that would eventually satisfy and attract more tea drinkers worldwide.

Synthesis of 2-Sulfenylindenones via One-Pot Tandem Meyer-Schuster Rearrangement and Radical Cyclization of Arylpropynols with Disulfides.

A tandem annulation of arylpropynols with disulfides has been developed for the synthesis of 2-sulfenylindenone derivatives. The reaction pathway involves one-pot tandem Meyer-Schuster rearrangement of arylpropynols and successive radical cyclization with disulfides. Various arylpropynols and disulfides with a number of functional groups are compatible in this reaction that affords the corresponding 2-sulfenylindenones in moderate to good yields.

Rapid diversification of five Oryza AA genomes associated with rice adaptation.

Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.