Untargeted metabolomics analysis of probiotic jujube juice and its anti-obesity effects on high-fat-diet-induced obese mice.

BACKGROUND: Dietary intervention, including polyphenol consumption, is recognized as an effective strategy to prevent obesity. Although fermented jujube juice (FJJ) with lactic acid bacteria has been shown to be rich in polyphenols and have strong antioxidant properties, little is known about its anti-obesity properties. RESULTS: Untargeted metabolomics was employed to identify and analyze the differential metabolites between FJJ and raw jujube juice. A total of 431 metabolites belonging to diverse classes and with various functional active ingredients were quantitatively identified. The animal experiments results showed that FJJ administration for 13 weeks significantly inhibited high-fat-diet-induced body and epididymal adipose weight gain, and improved the serum lipid parameters in obese mice. Additionally, DNA-sequencing results revealed that FJJ treatment increased Akkermansia abundance in the gut and changed the composition of fecal microbiota by decreasing the Firmicutes/Bacteroidota ratio and Helicobacter pylori abundance. CONCLUSION: These findings suggest that FJJ contributes to regulating lipid accumulation and gut microbiota composition in high-fat-diet-induced obese mice, which helps to prevent obesity. Hence, FJJ has the potential to be a beneficial beverage for controlling obesity. © 2024 Society of Chemical Industry.

A novel electrolytic gas lift reactor for efficient microbial electrosynthesis of acetate from carbon dioxide.

The low current density impedes the practical application of microbial electrosynthesis for CO2 fixation. Engineering the reactor design is an effective way to increase the current density, especially for H2-mediated microbial electrosynthesis reactors. The electrolytic bubble column microbial electrosynthesis reactor has shown great potential for scaling up, but the mixing and gas mass transfer still need to be enhanced to further increase the current density. Here, we introduced an inner draft tube to the bubble column to tackle the problem. The addition of draft tube resulted in a 76.6% increase in the volumetric mass transfer coefficient (kLa) of H2, a 40% increase in the maximum current density (337 A/m2) and a 72% increase in average acetate production rate (3.1 g/L/d). The computational fluid dynamics simulations showed that the addition of draft tube enhanced mixing efficiency by enabling a more ordered cyclic flow pattern and a more uniform gas/liquid distribution. These results indicate that the electro-bubble column reactor with draft tube holds great potential for industrial implementation.

Utilization of two plant polysaccharides to improve fresh goat milk cheese: Texture, rheological properties, and microstructure characterization.

This study aimed to evaluate the effects of added jujube polysaccharide (JP) and Lycium barbarum polysaccharide (LBP) on the texture, rheological properties, and microstructure of goat milk cheese. Seven groups of fresh goat milk cheese were produced with 4 levels (0, 0.2, 0.6, and 1%, wt/wt) of JP and LBP. The goat milk cheese containing 1% JP showed the highest water-holding capacity, hardness, and the strongest rheological properties by creating a denser and more stable casein network structure. In addition, the yield of goat milk cheese was substantially improved as a result of JP incorporation. Cheeses containing LBP expressed lower fat content, higher moisture, and softer texture compared with the control cheese. Fourier-transform infrared spectroscopy and low-field nuclear magnetic resonance analysis demonstrated that the addition of JP improved the stability of the secondary protein structure in cheese and significantly enhanced the binding capacity of the casein matrix to water molecules due to strengthened intermolecular interactions. The current research demonstrated the potential feasibility of modifying the texture of goat milk cheese by JP or LBP, available for developing tunable goat milk cheese to satisfy consumer preferences and production needs.

A label-free electrochemical aptasensor based on a gold nanoparticle/carbon nanotube/metal-organic framework nanohybrid for ultrasensitive detection of streptomycin in milk samples.

In this work, a novel electrochemical aptasensor was designed for the sensitive and specific detection of STR in milk samples. First, a gold nanoparticle@poly(diallyldimethylammonium chloride) nitrogen-doped carbon nanotube/polyethyleneimine-functionalized metal-organic framework (MOF) (Au@P-N-CNT/PEI-MIL-101(Cr)) composite was synthesized and characterized by various technique. The Au@P-N-CNT/PEI-MIL-101(Cr) composite was then modified on a bare glassy carbon electrode (GCE) surface, providing a favorable platform (Au@P-N-CNT/PEI-MIL-101(Cr)/GCE) for aptamer immobilization and current signal amplification. The STR aptamer was grafted to the Au@P-N-CNT/PEI-MIL-101(Cr)/GCE through the formation of Au-S bonds and π-π stacking interactions. The immobilized STR aptamer binds specifically STR, resulting in an obvious decrease in the current signal. Under the optimal experimental conditions, the linear range of the electrochemical aptasensor for STR detection was 0.01-250 nM which the detection limit (LOD) was calculate as 2.31 nM. This strategy is expected to be a novel platform for the rapid and sensitive detection of STR.

An ultrasensitive sandwich-type electrochemical aptasensor using silver nanoparticle/titanium carbide nanocomposites for the determination of Staphylococcus aureus in milk.

A novel sandwich-type electrochemical aptasensor for the detection of Staphylococcus aureus (S. aureus) was developed. S. aureus aptamers were self-assembled onto the surface of a glassy carbon electrode (GCE) modified with nanocomposites comprising titanium carbide embedded with silver nanoparticles (AgNPs@Ti3C2) through hydrogen bonds and the chelation interaction between phosphate groups and Ti ions. In addition, the self-assembled aptamers were immobilized on CuO/graphene (GR) nanocomposites via π-π stacking interactions to serve as a signal probe. In the presence of the target S. aureus, the sandwich-type recognition system reacted on the surface of GCE, and the CuO/GR nanocomposites catalyzed the hydrogen peroxide + hydroquinone reaction producing a strong current response. Under the optimal experimental conditions, the current response of the aptasensor was linearly correlated with the concentration of S. aureus (52-5.2 × 107 CFU mL-1) with a low detection limit of 1 CFU mL-1. The aptasensor displayed good repeatability and excellent selectivity for S. aureus detection. Moreover, this aptasensor was applied to the detection of S. aureus in cow, sheep, and goat milk samples, affording recoveries ranging from 92.64 to 109.58%. This research provides a new platform for the detection of pathogenic bacteria and other toxic and harmful substances in food.

A novel electrochemical aptasensor based on layer-by-layer assembly of DNA-Au@Ag conjugates for rapid detection of aflatoxin M1 in milk samples.

Aflatoxin M1 (AFM1) is a common toxin in dairy products that causes acute and chronic human health disorders. Thus, the development of a rapid and accurate AFM1 detection method is of vital importance for food safety monitoring. This work was to develop a novel electrochemical aptasensor for sensitive and specific determination of AFM1. The dendritic-like nanostructure was formed on the gold electrode surface by layer-by-layer assembly of gold-silver core-shell nanoparticles modified with DNA conjugates. In the presence of AFM1, the specific recognition between AFM1 and Apt caused the disassociation of the DNA controlled dual Au@Ag conjugates from the surface of the electrode, causing less methylene blue to bind to the surface and weakening the electrochemical signal. The more AFM1 there is, the weaker the electrochemical signal. Transmission electron microscope results showed that the successfully synthesized Au@Ag nanoparticles exhibited a core-shell structure with Au as core and Ag as shell, and their average diameter was about 30 nm. Under optimal conditions, the electrochemical aptasensor showed a wide detection ranging from 0.05 ng mL-1 to 200 ng mL-1, and a low detection limit of 0.02 ng mL-1. Moreover, the proposed strategy has been successfully applied to the detection of AFM1 in cow, goat, and sheep milk samples with satisfactory recoveries ranging from 91.10% to 104.05%. This work can provide a novel rapid detection method for AFM1, and also provide a new sensing platform for the detection of other toxins.

Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution.

The ultimate goal of genome assembly is a high-accuracy gapless genome. Here, we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui 63. The resulting 397.71-Mb final assembly is composed of 12 contigs with a contig N50 size of 31.93 Mb. Each chromosome is represented by a single contig and the genomic sequences of all chromosomes are gapless. Quality evaluation of this gapless genome assembly showed that gene regions in our assembly have the highest completeness compared with the other 15 reported high-quality rice genomes. Further comparison with the japonica rice genome revealed that the gapless indica genome assembly contains more transposable elements (TEs) and segmental duplications (SDs), the latter of which produce many duplicated genes that can affect agronomic traits through dose effect or sub-/neo-functionalization. The insertion of TEs can also affect the expression of duplicated genes, which may drive the evolution of these genes. Furthermore, we found the expansion of nucleotide-binding site with leucine-rich repeat disease-resistance genes and cis-zeatin-O-glucosyltransferase growth-related genes in SDs in the gapless indica genome assembly, suggesting that SDs contribute to the adaptive evolution of rice disease resistance and developmental processes. Collectively, our findings suggest that active TEs and SDs synergistically contribute to rice genome evolution.

Physicochemical and textural characteristics and volatile compounds of semihard goat cheese as affected by starter cultures.

Today, cheese is valued because of its high nutritional value and unique characteristics. Improving the texture and flavor of cheese by selecting suitable starter cultures is an important way to promote the development of cheese industry. The effect of starter cultures on the physicochemical and textural properties and volatile compounds during the ripening of semihard goat cheese were investigated in this work. Different starter cultures-mesophilic (M) and thermophilic starters (T), Lactobacillus plantarum ssp. plantarum ATCC 14917 (Lp), a mix of the M and T starters (M1), and mix of the M, T, and Lp starters (M2)-were used in the production of the goat cheeses. Volatile compounds were determined by a solid-phase microextraction/gas chromatography-mass spectrometric (SPME/GC-MS) method. The results showed that the moisture content of cheeses produced with the 5 kinds of starter cultures decreased after maturation, whereas ash content increased. The pH values of goat cheeses decreased first and then increased during maturity, and the pH value of M2 cheese was the lowest among the cheeses. The hardness and chewiness of the cheeses increased with increasing maturity, whereas cohesiveness, springiness, and resilience showed the opposite tendency. The 60-d-old cheese made with Lp had the highest chewiness, cohesiveness, springiness, and resilience, whereas the 60-d-old cheese made with M2 had the highest hardness. A total of 53 volatile components were identified by SPME/GC-MS, and carboxylic acids, alcohols, ketones, and esters were the 4 major contributors to the characteristic flavors of the cheeses. Volatile components and their contents differed greatly among the produced cheeses. The M2 cheese contained the highest relative content of the main volatile compounds (90.10%), especially butanoic acid and acetoin. Through a comprehensive comparison of the results, we concluded that M2 cheese had a dense texture and milky flavor, and M2 is a potential starter culture candidate for the production of goat cheese.

A draft genome for Spatholobus suberectus.

Spatholobus suberectus Dunn (S. suberectus), which belongs to the Leguminosae, is an important medicinal plant in China. Owing to its long growth cycle and increased use in human medicine, wild resources of S. suberectus have decreased rapidly and may be on the verge of extinction. De novo assembly of the whole S. suberectus genome provides us a critical potential resource towards biosynthesis of the main bioactive components and seed development regulation mechanism of this plant. Utilizing several sequencing technologies such as Illumina HiSeq X Ten, single-molecule real-time sequencing, 10x Genomics, as well as new assembly techniques such as FALCON and chromatin interaction mapping (Hi-C), we assembled a chromosome-scale genome about 798 Mb in size. In total, 748 Mb (93.73%) of the contig sequences were anchored onto nine chromosomes with the longest scaffold being 103.57 Mb. Further annotation analyses predicted 31,634 protein-coding genes, of which 93.9% have been functionally annotated. All data generated in this study is available in public databases.

Optimized Extraction of Phenolics from Jujube Peel and Their Anti-inflammatory Effects in LPS-Stimulated Murine Macrophages.

The extraction of phenolics from jujube peel (PJP) was optimized using response surface methodology (RSM). A Box-Behnken design was utilized to analyze the effects of NaOH concentration, temperature, and extraction time on the total phenolic content (TPC). The results showed that RSM could be an adequate approach for modeling the extraction of PJP. The optimal extraction condition for the highest TPC was obtained with 3.4 M NaOH concentration for 67 min at 50 °C. Not only PJP but also phenolics from the jujube seed (PJS) contain considerable amounts of phenolics, particularly flavonoids. Quercetin and galangin were found to be the predominant phenolics. PJP markedly down-regulated the levels iNOS and COX-2 proteins in macrophages by inhibiting the activation of NF-κB through interfering with the MAPK signaling pathways. Compared to PJS, PJP presented higher anti-inflammatory activities, reflecting increased amounts of TPC and total flavonoid content (TFC). These findings suggest that PJP could be a potential source of anti-inflammatory agents.

Scallop genome provides insights into evolution of bilaterian karyotype and development.

Reconstructing the genomes of bilaterian ancestors is central to our understanding of animal evolution, where knowledge from ancient and/or slow-evolving bilaterian lineages is critical. Here we report a high-quality, chromosome-anchored reference genome for the scallop Patinopecten yessoensis, a bivalve mollusc that has a slow-evolving genome with many ancestral features. Chromosome-based macrosynteny analysis reveals a striking correspondence between the 19 scallop chromosomes and the 17 presumed ancestral bilaterian linkage groups at a level of conservation previously unseen, suggesting that the scallop may have a karyotype close to that of the bilaterian ancestor. Scallop Hox gene expression follows a new mode of subcluster temporal co-linearity that is possibly ancestral and may provide great potential in supporting diverse bilaterian body plans. Transcriptome analysis of scallop mantle eyes finds unexpected diversity in phototransduction cascades and a potentially ancient Pax2/5/8-dependent pathway for noncephalic eyes. The outstanding preservation of ancestral karyotype and developmental control makes the scallop genome a valuable resource for understanding early bilaterian evolution and biology.

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement.

Upland cotton is a model for polyploid crop domestication and transgenic improvement. Here we sequenced the allotetraploid Gossypium hirsutum L. acc. TM-1 genome by integrating whole-genome shotgun reads, bacterial artificial chromosome (BAC)-end sequences and genotype-by-sequencing genetic maps. We assembled and annotated 32,032 A-subgenome genes and 34,402 D-subgenome genes. Structural rearrangements, gene loss, disrupted genes and sequence divergence were more common in the A subgenome than in the D subgenome, suggesting asymmetric evolution. However, no genome-wide expression dominance was found between the subgenomes. Genomic signatures of selection and domestication are associated with positively selected genes (PSGs) for fiber improvement in the A subgenome and for stress tolerance in the D subgenome. This draft genome sequence provides a resource for engineering superior cotton lines.

Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history.

Colobines are a unique group of Old World monkeys that principally eat leaves and seeds rather than fruits and insects. We report the sequencing at 146× coverage, de novo assembly and analyses of the genome of a male golden snub-nosed monkey (Rhinopithecus roxellana) and resequencing at 30× coverage of three related species (Rhinopithecus bieti, Rhinopithecus brelichi and Rhinopithecus strykeri). Comparative analyses showed that Asian colobines have an enhanced ability to derive energy from fatty acids and to degrade xenobiotics. We found evidence for functional evolution in the colobine RNASE1 gene, encoding a key secretory RNase that digests the high concentrations of bacterial RNA derived from symbiotic microflora. Demographic reconstructions indicated that the profile of ancient effective population sizes for R. roxellana more closely resembles that of giant panda rather than its congeners. These findings offer new insights into the dietary adaptations and evolutionary history of colobine primates.

Draft genome sequence of the Tibetan antelope.

The Tibetan antelope (Pantholops hodgsonii) is endemic to the extremely inhospitable high-altitude environment of the Qinghai-Tibetan Plateau, a region that has a low partial pressure of oxygen and high ultraviolet radiation. Here we generate a draft genome of this artiodactyl and use it to detect the potential genetic bases of highland adaptation. Compared with other plain-dwelling mammals, the genome of the Tibetan antelope shows signals of adaptive evolution and gene-family expansion in genes associated with energy metabolism and oxygen transmission. Both the highland American pika, and the Tibetan antelope have signals of positive selection for genes involved in DNA repair and the production of ATPase. Genes associated with hypoxia seem to have experienced convergent evolution. Thus, our study suggests that common genetic mechanisms might have been utilized to enable high-altitude adaptation.

Genome sequence of ground tit Pseudopodoces humilis and its adaptation to high altitude.

BACKGROUND: The mechanism of high-altitude adaptation has been studied in certain mammals. However, in avian species like the ground tit Pseudopodoces humilis, the adaptation mechanism remains unclear. The phylogeny of the ground tit is also controversial. RESULTS: Using next generation sequencing technology, we generated and assembled a draft genome sequence of the ground tit. The assembly contained 1.04 Gb of sequence that covered 95.4% of the whole genome and had higher N50 values, at the level of both scaffolds and contigs, than other sequenced avian genomes. About 1.7 million SNPs were detected, 16,998 protein-coding genes were predicted and 7% of the genome was identified as repeat sequences. Comparisons between the ground tit genome and other avian genomes revealed a conserved genome structure and confirmed the phylogeny of ground tit as not belonging to the Corvidae family. Gene family expansion and positively selected gene analysis revealed genes that were related to cardiac function. Our findings contribute to our understanding of the adaptation of this species to extreme environmental living conditions. CONCLUSIONS: Our data and analysis contribute to the study of avian evolutionary history and provide new insights into the adaptation mechanisms to extreme conditions in animals.

Coordinated regulation of gene expression for carotenoid metabolism in Chlamydomonas reinhardtii.

Carotenoids are important plant pigments for both light harvesting and photooxidation protection. Using the model system of the unicellular green alga Chlamydomonas reinhardtii, we characterized the regulation of gene expression for carotenoid metabolism by quantifying changes in the transcript abundance of dxs, dxr and ipi in the plastidic methylerythritol phosphate pathway and of ggps, psy, pds, lcyb and bchy, directly involved in carotenoid metabolism, under different photoperiod, light and metabolite treatments. The expression of these genes fluctuated with light/dark shifting. Light treatment also promoted the accumulation of transcripts of all these genes. Of the genes studied, dxs, ggps and lcyb displayed the typical circadian pattern by retaining a rhythmic fluctuation of transcript abundance under both constant light and constant dark entrainments. The expression of these genes could also be regulated by metabolic intermediates. For example, ggps was significantly suppressed by a geranylgeranyl pyrophosphate supplement and ipi was upregulated by isopentenyl pyrophosphate. Furthermore, CrOr, a C. reinhardtii homolog of the recently characterized Or gene that accounts for carotenoid accumulation, also showed co-expression with carotenoid biosynthetic genes such as pds and lcyb. Our data suggest a coordinated regulation on carotenoid metabolism in C. reinhardtii at the transcriptional level.