Holomics - a user-friendly R shiny application for multi-omics data integration and analysis.

An organism's observable traits, or phenotype, result from intricate interactions among genes, proteins, metabolites and the environment. External factors, such as associated microorganisms, along with biotic and abiotic stressors, can significantly impact this complex biological system, influencing processes like growth, development and productivity. A comprehensive analysis of the entire biological system and its interactions is thus crucial to identify key components that support adaptation to stressors and to discover biomarkers applicable in breeding programs or disease diagnostics. Since the genomics era, several other 'omics' disciplines have emerged, and recent advances in high-throughput technologies have facilitated the generation of additional omics datasets. While traditionally analyzed individually, the last decade has seen an increase in multi-omics data integration and analysis strategies aimed at achieving a holistic understanding of interactions across different biological layers. Despite these advances, the analysis of multi-omics data is still challenging due to their scale, complexity, high dimensionality and multimodality. To address these challenges, a number of analytical tools and strategies have been developed, including clustering and differential equations, which require advanced knowledge in bioinformatics and statistics. Therefore, this study recognizes the need for user-friendly tools by introducing Holomics, an accessible and easy-to-use R shiny application with multi-omics functions tailored for scientists with limited bioinformatics knowledge. Holomics provides a well-defined workflow, starting with the upload and pre-filtering of single-omics data, which are then further refined by single-omics analysis focusing on key features. Subsequently, these reduced datasets are subjected to multi-omics analyses to unveil correlations between 2-n datasets. This paper concludes with a real-world case study where microbiomics, transcriptomics and metabolomics data from previous studies that elucidate factors associated with improved sugar beet storability are integrated using Holomics. The results are discussed in the context of the biological background, underscoring the importance of multi-omics insights. This example not only highlights the versatility of Holomics in handling different types of omics data, but also validates its consistency by reproducing findings from preceding single-omics studies.

Dissipation behaviours, residues, and health risk of six herbicides in sugar beets under field conditions.

This study established a residue detection method based on the QuEChERS pre-treatment method and combined it with high-performance liquid chromatography-tandem mass spectrometry to test six herbicides (metamitron, clopyralid, desmedipham, phenmedipham, ethofumesate, and haloxyfop-p-methyl) in sugar beet plants, soil, and roots. The degradation dynamics and terminal residues of each herbicide in sugar beets were analysed. Finally, the dietary risks of various herbicides in sugar beets were evaluated based on the dietary structure of Chinese people, and the risk quotient values were below 100%. Using this detection method, all reagents exhibited good linearity (0.9724 ≤ R2 ≤ 0.9998), The limit of quantification (LOQ) ranged from 0.01 to 0.05 mg/L, the matrix effect ranged from -1.2% to -50%, the addition recovery rate ranged from 77.00% to 103.48%, and the relative standard deviation ranged from 1.61% to 16.17%; therefore, all indicators of this method met the residue detection standards. Under field conditions, the half-lives (t1/2) ranged about 0.65 ∼ 2.96 d and 0.38 ∼ 27.59 d in sugar beet plants and soil, respectively. All herbicides were easily degraded in sugar beet plants and soil (t1/2 < 30 d). The terminal residue amounts in the beet plants, soil, and roots ranged from < LOQ to 0.243 mg/kg. The dietary risk assessment of each pesticide was conducted based on the residual median of the terminal residues and the highest residual values on the edible part of the beetroot. The chronic exposure risk quotient (RQc) and acute exposure risk quotient (RQa) values were < 100%, indicating that the residue of each pesticide in beetroot posed low risks to consumers in China at the recommended dosage.

Genome-wide identification, phylogenetic classification of histone acetyltransferase genes, and their expression analysis in sugar beet (Beta vulgaris L.) under salt stress.

MAIN CONCLUSION: This study identified seven histone acetyltransferase-encoding genes (HATs) from Beta vulgaris L. (sugar beet) genome through bioinformatics tools and analyzed their expression profiles under salt stress. Sugar beet HATs are phylogenetically divided into four families: GNAT, MYST, CBP, and TAFII250. The BvHAT genes were differentially transcribed in leaves, stems, and roots of B. vulgaris salt-resistant (Casino) and -sensitive (Bravo) cultivars under salt stress. Histone acetylation is regulated by histone acetyltransferases (HATs), which catalyze ɛ-amino bond formation between lysine residues and acetyl groups with a cofactor, acetyl-CoA. Even though the HATs are known to participate in stress response and development in model plants, little is known about the functions of HATs in crops. In sugar beet (Beta vulgaris L.), they have not yet been identified and characterized. Here, an in silico analysis of the HAT gene family in sugar beet was performed, and their expression patterns in leaves, stems, and roots of B. vulgaris were analyzed under salt stress. Salt-resistant (Casino) and -sensitive (Bravo) beet cultivars were used for gene expression assays. Seven HATs were identified from sugar beet genome, and named BvHAG1, BvHAG2, BvHAG3, BvHAG4, BvHAC1, BvHAC2, and BvHAF1. The HAT proteins were divided into 4 groups including MYST, GNAT (GCN5, HAT1, ELP3), CBP and TAFII250. Analysis of cis-acting elements indicated that the BvHAT genes might be involved in hormonal regulation, light response, plant development, and abiotic stress response. The BvHAT genes were differentially expressed in leaves, stems, and roots under control and 300 mM NaCl. In roots of B. vulgaris cv. Bravo, the BvHAG1, BvHAG2, BvHAG4, BvHAF1, and BvHAC1 genes were dramatically expressed after 7 and 14 days of salt stress. Interestingly, the BvHAC2 gene was not expressed under both control and stress conditions. However, the expression of BvHAG2, BvHAG3, BvHAG4, BvHAC1, BvHAC2 genes showed a significant increase in response to salt stress in the roots of cv. Casino. This study provides new insights into the potential roles of histone acetyltransferases in sugar beet.

Role of pectin in the delivery of ß-carotene embedded in interpenetrating emulsion-filled gels made with soy protein isolate.

This study investigated the effects of different matrices on gel properties, lipid digestibility, ß-carotene bioaccessibility, released free amino acids and gel network degradation. Microstructure studies have proven that sugar beet pectin/soy protein isolate-based emulsion-filled gel (SBP/SPI-E) with interpenetrating networks was formed. SBP/SPI-E exhibited higher hardness (2.67 N, p < 0.05) and released lesser free amino acids (269.48-µmol/g SPI) than soy protein isolate-based emulsion-filled gel (SPI-E) in simulated intestinal fluid (SIF); however, both had similar free amino acids contents in simulated colonic fluid. SBP has the potential to delay gel network degradation in SIF, as evidenced by the sugar stain strips of SDS-PAGE and microstructure observation. Furthermore, SBP/SPI-E and SPI-E exhibited similar ß-carotene bioaccessibility in SIF, suggesting that SBP from composite gel could not affect the aforementioned bioaccessibility. The study provides useful information for the design of functional gels in the application of fat-soluble nutrient delivery.

Hot-air drying vs. lyophilization of sugar beet flakes for efficient pectin recovery and influence of extraction conditions on pectin physicochemical properties.

This study assessed the influence of drying pretreatment and extraction conditions (type of acid and particle size of plant material) on the yield and physicochemical properties of pectin from sugar beet flakes resulted as by-product of sugar beet processing in the sugar industry. The results indicated that the drying conditions (hot-air drying and lyophilization) affected the extraction yield, the chemical composition of pectin, its color, degree of methylation and acetylation, molecular weight, and its rheological and emulsifying properties. The best results for pectin yield (16.20%), galacturonic acid content (91.19 g/100 g), degree of methylation and acetylation (66.93 and 23.87%), and molecular weight (3.89 × 105 g/mol) were obtained when sugar beet flakes were pretreated by hot-air drying, and the extraction was made with citric acid using plant material with particle sizes of 125-200 µm. This pectin also had high emulsion activity (51.42%) and emulsion stability (88.03%). The FT-IR spectra were similar, while pectin thermal behavior was affected by the drying pretreatment and extraction conditions. The results of this study showed that from this by-product of the sugar industry it can be extracted high quality pectin with rheological and emulsifying properties that are superior to commercial citrus and apple pectin.

Characterization and emulsifying ability evaluation of whey protein-pectin conjugates formed by glycosylation.

Glycosylation is a method that enhances the functional properties of proteins by covalently attaching sugars to them. This study aimed at preparing three conjugates (WP-HG, WP-SBP, and WP-RGI) by dry heating method to research the influence of different pectin structures on the functional properties of WP and characterize properties and structures of these conjugates. The research results manifested that the degree of glycosylation (DG) of HG, SBP and RGI were 13.13 % ± 0.07 %, 23.27 % ± 0.3 % and 36.39 % ± 0.3 % respectively, suggesting that the increase of the number of branch chains promoted the glycosylation reaction. The formation of the conjugate was identified by the FT-IR spectroscopy technique. And SEM showed that WP could covalently bind to pectin, resulting in a smoother and denser surface of the conjugates. The circular dichroism analysis exhibited that the glycosylation reaction altered the secondary structure of WP and decreased the α-Helix content. This structural change in the protein spatial conformation led to a decrease in the hydrophobicity of protein surface. But the addition of pectin further regulated the hydrophilic-hydrophobic ratio on the surface of the protein, thus improving the emulsification properties of WP. In addition, the glycosylation could improve the stability of the emulsion, giving it a smaller droplet size, higher Zeta-potential and more stable properties. In a word, this study pointed out the direction for the application of different pectin structures in the development of functional properties of glycosylation products in food ingredients.

The Effects of DNA Methylation on Cytoplasmic Male Sterility in Sugar Beet.

DNA methylation is widely found in higher plants and can control gene expression by regulation without changing the DNA sequence. In this study, the whole-genome methylation map of sugar beet was constructed by WGBS (whole-genome bisulfite sequencing) technology, and the results of WGBS were verified by bisulfite transformation, indicating that the results of WGBS technology were reliable. In addition, 12 differential methylation genes (DMGs) were identified, which were related to carbohydrate and energy metabolism, pollen wall development, and endogenous hormone regulation. Quantitative real-time PCR (qRT-PCR) showed that 75% of DMG expression levels showed negative feedback with methylation level, indicating that DNA methylation can affect gene expression to a certain extent. In addition, we found hypermethylation inhibited gene expression, which laid a foundation for further study on the molecular mechanism of DNA methylation at the epigenetic level in sugar beet male sterility.

Indigenous Populations of a Biological Control Agent in Agricultural Field Soils Predicted Suppression of a Plant Pathogen.

The nematophagous fungus Hyalorbilia oviparasitica and relatives (Hyalorbilia spp.) are known to parasitize several endoparasitic nematodes. In this project, we hypothesized that indigenous populations of this fungus could be used to predict nematode suppression in agricultural field soils. We quantified Hyalorbilia spp. in soil samples from 44 different sugar beet fields in the Imperial Valley of California. Seven soils harboring Hyalorbilia spp. and two that tested negative for the fungi were examined for nematode suppressive activity. Untreated and autoclaved portions of each soil were planted with cabbage and infested with sugar beet cyst nematode (Heterodera schachtii) juveniles. Females and cysts of H. schachtii were enumerated after 12 weeks. In the seven soils harboring Hyalorbilia spp., females and cysts in the untreated soils were reduced by 61 to 82% compared with the autoclaved controls. Soils with no detectable Hyalorbilia spp. exhibited no nematode suppression. Two novel Hyalorbilia strains, HsImV25 and HsImV27, were isolated from H. schachtii females reared in field soil using an enrichment and double-baiting cultivation technique. Both strains suppressed H. schachtii populations by more than 80% in soil-based assays, confirming that Hyalorbilia spp. are the likely causal agents of the nematode suppression in these soils. This study demonstrated that indigenous populations of a hyperparasite (Hyalorbilia spp.) in agricultural field soils predicted suppressive activity against a soilborne plant pathogen (H. schachtii). To our knowledge, this is the first report to demonstrate this capability. We anticipate that this research will provide a blueprint for other similar studies, thereby advancing the field of soilborne biological control.

Genome-wide characterization of the xyloglucan endotransglucosylase/hydrolase family genes and their response to plant hormone in sugar beet.

Xyloglucan endotransglucosylase/hydrolases (XTHs) play a crucial role in plant growth and development. However, their functional response to phytohormone in sugar beet still remains obscure. In this study, we identified 30 putative BvXTH genes in the sugar beet genome. Phylogenetic and evolutionary relationship analysis revealed that they were clustered into three groups and have gone through eight tandem duplication events under purifying selection. Gene structure and motif composition analysis demonstrated that they were highly conserved and all contained one conserved glycoside hydrolase family 16 domain (Glyco_hydro_16) and one xyloglucan endotransglycosylase C-terminus (XET_C) domain. Transcriptional expression analysis exhibited that all BvXTHs were ubiquitously expressed in leaves, root hairs and tuberous roots, and most of them were up-regulated by brassinolide (BR), jasmonic acid (JA), abscisic acid (ABA) and gibberellic acid (GA3). Further mutant complementary experiment demonstrated that expression of BvXTH17 rescued the retarded growth phenotype of xth22, an Arabidopsis knock out mutant of AtXTH22. The findings in our work provide fundamental information on the structure and evolutionary relationship of the XTH family genes in sugar beet, and reveal the potential function of BvXTH17 in plant growth and hormone response.

Foliar zinc spraying improves assimilative capacity of sugar beet leaves by promoting magnesium and calcium uptake and enhancing photochemical performance.

Sugar beet, a zinc-loving crop, is increasingly limited by zinc deficiency worldwide. Foliar zinc application is an effective and convenient way to supplement zinc fertilizer. However, the regulatory mechanism of foliar zinc spraying on sugar beet leaf photosynthetic characteristics remains unclear. Therefore, we investigated the effects of foliar ZnSO4·7H2O application (0, 0.1%, 0.2%, and 0.4%) on the photosynthetic performance of sugar beet leaves under controlled hydroponic conditions. The results indicated that a foliar spray of 0.2% Zn fertilizer was optimal for promoting sugar beet leaf growth. This concentration significantly reduced the leaf shape index of sugar beet, notably increasing leaf area, leaf mass ratio, and specific leaf weight. Foliar spraying of Zn (0.2%) substantially elevated the Zn content in sugar beet leaves, along with calcium (Ca) and magnesium (Mg) contents. Consequently, this led to an increase in the potential photochemical activity of PSII (Fv/Fo) (by 6.74%), net photosynthetic rate (Pn) (11.39%), apparent electron transport rate (ETR) (11.43%), actual photochemical efficiency of PSⅡ (Y (Ⅱ)) (11.46%), photochemical quenching coefficient (qP) (15.49%), and total chlorophyll content (25.17%). Ultimately, this increased sugar beet leaf dry matter weight (11.30%). In the cultivation and management of sugar beet, the application of 0.2% Zn fertilizer (2.88 mg plant-1) exhibited the potential to enhance Zn and Mg contents in sugar beet, improve photochemical properties, stimulate leaf growth, and boost light assimilation capacity. Our result suggested the foliar application of Zn might be a useful strategy for sugar beet crop management.

Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets.

Sugar beet and its wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNAs are among the fastest evolving parts of the genome, we investigated, if repeatome innovations and losses are linked to chromosomal differentiation and speciation. We traced genome and chromosome-wide evolution across 13 beet species comprising all sections of the genera Beta and Patellifolia. For this, we combined short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive framework that spans the complete scale from DNA to chromosome to genome. Genome sizes and repeat profiles reflect the separation into three gene pools with contrasting evolutionary patterns. Among all repeats, satellite DNAs harbor most genomic variability, leading to fundamentally different centromere architectures, ranging from chromosomal uniformity in Beta and Patellifolia to the formation of patchwork chromosomes in Corollinae/Nanae. We show that repetitive DNAs are causal for the genome expansions and contractions across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably between beet genomes, leading to the evolution of distinct chromosomal setups in the three gene pools, likely contributing to the barriers in beet breeding. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genomic variability, and chromosomal differentiation and provide a theoretical fundament for understanding barriers in any crop breeding effort.

First surveillance of pesticides in soils of the perimeter of Tadla, a Moroccan sugar beet intensive area.

With the long-term application of pesticides on sugar beet farms in the irrigated perimeter of Tadla in Morocco for over 50 years, pesticide monitoring is necessary to assess soil health. The objective of our study was to monitor multiple pesticide residues in topsoil samples collected from post-harvest sugar beet fields and verify their migration to deep soil layers. Topsoil and deep soil samples were collected from arbitrarily selected sugar beet fields in the IPT. In this study, a target-screening method was applied. All target pesticides were detected in soil samples, with tefluthrin being the most frequently detected pesticide. The residue with the highest concentration in soil samples was DDE. All the soil samples contained a mixture of pesticide residues, with a maximum of 13 residues per sample. The total pesticide content decreased toward more profound layers of soil, except in one field where it reached a concentration of 348 µg/kg at the deeper soil layer. For pesticides detected at the three soil depths, only tefluthrin concentration increased in the deep soil layer. The results provide comprehensive and precise information on the pesticide residue status in sugar beet soils warning against the multiple risks that this contamination can cause. This study indicates the need of regular monitoring of pesticides over a large area of the perimeter to enable decision-makers to pronounce the impacts of the extension and intensification of sugar beet cultivation at the irrigated perimeter of Tadla.

Genomic characterization of a nematode tolerance locus in sugar beet.

BACKGROUND: Infection by beet cyst nematodes (BCN, Heterodera schachtii) causes a serious disease of sugar beet, and climatic change is expected to improve the conditions for BCN infection. Yield and yield stability under adverse conditions are among the main breeding objectives. Breeding of BCN tolerant sugar beet cultivars offering high yield in the presence of the pathogen is therefore of high relevance. RESULTS: To identify causal genes providing tolerance against BCN infection, we combined several experimental and bioinformatic approaches. Relevant genomic regions were detected through mapping-by-sequencing using a segregating F2 population. DNA sequencing of contrasting F2 pools and analyses of allele frequencies for variant positions identified a single genomic region which confers nematode tolerance. The genomic interval was confirmed and narrowed down by genotyping with newly developed molecular markers. To pinpoint the causal genes within the potential nematode tolerance locus, we generated long read-based genome sequence assemblies of the tolerant parental breeding line Strube U2Bv and the susceptible reference line 2320Bv. We analyzed continuous sequences of the potential locus with regard to functional gene annotation and differential gene expression upon BCN infection. A cluster of genes with similarity to the Arabidopsis thaliana gene encoding nodule inception protein-like protein 7 (NLP7) was identified. Gene expression analyses confirmed transcriptional activity and revealed clear differences between susceptible and tolerant genotypes. CONCLUSIONS: Our findings provide new insights into the genomic basis of plant-nematode interactions that can be used to design and accelerate novel management strategies against BCN.

Insights into Endophytic and Rhizospheric Bacteria of Five Sugar Beet Hybrids in Terms of Their Diversity, Plant-Growth Promoting, and Biocontrol Properties.

Sugar beet is the most important crop for sugar production in temperate zones. The plant microbiome is considered an important factor in crop productivity and health. Here, we investigated the bacterial diversity of seeds, roots, and rhizosphere of five sugar beet hybrids named Eduarda (ED), Koala (KO), Tibor (T), Tajfun (TF), and Cercospora-resistant (C). A culture-independent next-generation sequencing approach was used for the further investigation of seed-borne endophytes. Hybrid-associated bacteria were evaluated for their plant growth-promoting (PGP) characteristics, antagonistic activity towards Cercospora beticola and several Fusarium strains in dual culture assays, and drought and salinity tolerance. High-throughput sequencing revealed that the Proteobacteria phylum was most dominant in the seeds of all hybrids, followed by Cyanobacteria and Actinobacteriota. The predominant genus in all hybrids was Pantoea, followed by Pseudomonas, Acinetobacter, Chalicogloea, Corynebacterium, Enterobacter, Enterococcus, Glutamicibacter, Kosakonia, and Marinilactibacillus. Unique genera in the hybrids were Pleurocapsa and Arthrobacter (T), Klebsiella (TF), Apibacter (ED), and Alloscardovia (KO). The genera that were most represented in one hybrid were Weissella and Staphylococcus (TF); Streptococcus (T); Gardnerella, Prevotella, and Rothia (KO); and Gilliamella, Lactobacillus, and Snodgrassella (ED). Thirty-two bacteria out of 156 isolates from the rhizosphere, roots, and seeds were selected with respect to various plant growth-promoting activities in vitro, i.e., nitrogen fixation, phosphate solubilization, siderophore production, indole-3-acetic acid production, 1-aminocyclopropane-1-carboxylic acid deaminase activity, hydrogen cyanide production, exoenzymatic activity (amylase, protease, lipase, cellulase, xylanase, mannanases, gelatinase, and pectinase), mitigation of environmental stresses, and antifungal activity. Mixta theicola KO3-44, Providencia vermicola ED3-10, Curtobacterium pusillum ED2-6, and Bacillus subtilis KO3-18 had the highest potential to promote plant growth due to their multiple abilities (nitrogen fixation, phosphate solubilization, production of siderophores, and IAA). The best antagonistic activity towards phytopathogenic fungi was found for Bacillus velezensis C3-19, Paenibacillus polymyxa C3-36 and Bacillus halotolerans C3-16/2.1. Only four isolates B. velezensis T2-23, B. subtilis T3-4, B. velezensis ED2-2, and Bacillus halotolerans C3-16/2.1 all showed enzymatic activity, with the exception of xylanase production. B. halotolerans C3-16/2.1 exhibited the greatest tolerance to salinity, while two B. subtilis strains (C3-62 and TF2-1) grew successfully at the maximum concentration of PEG. The current study demonstrates that sugar beet-associated bacteria have a wide range of beneficial traits and are therefore highly promising for the formulation of biological control and PGP agents.

Combined Omics Approaches Reveal Distinct Mechanisms of Resistance and/or Susceptibility in Sugar Beet Double Haploid Genotypes at Early Stages of Beet Curly Top Virus Infection.

Sugar beet is susceptible to Beet curly top virus (BCTV), which significantly reduces yield and sugar production in the semi-arid growing regions worldwide. Sources of genetic resistance to BCTV is limited and control depends upon insecticide seed treatments with neonicotinoids. Through double haploid production and genetic selection, BCTV resistant breeding lines have been developed. Using BCTV resistant (R) [KDH13; Line 13 and KDH4-9; Line 4] and susceptible (S) [KDH19-17; Line 19] lines, beet leafhopper mediated natural infection, mRNA/sRNA sequencing, and metabolite analyses, potential mechanisms of resistance against the virus and vector were identified. At early infection stages (2- and 6-days post inoculation), examples of differentially expressed genes highly up-regulated in the 'R' lines (vs. 'S') included EL10Ac5g10437 (inhibitor of trypsin and hageman factor), EL10Ac6g14635 (jasmonate-induced protein), EL10Ac3g06016 (ribosome related), EL10Ac2g02812 (probable prolyl 4-hydroxylase 10), etc. Pathway enrichment analysis showed differentially expressed genes were predominantly involved with peroxisome, amino acids metabolism, fatty acid degradation, amino/nucleotide sugar metabolism, etc. Metabolite analysis revealed significantly higher amounts of specific isoflavonoid O-glycosides, flavonoid 8-C glycosides, triterpenoid, and iridoid-O-glycosides in the leaves of the 'R' lines (vs. 'S'). These data suggest that a combination of transcriptional regulation and production of putative antiviral metabolites might contribute to BCTV resistance. In addition, genome divergence among BCTV strains differentially affects the production of small non-coding RNAs (sncRNAs) and small peptides which may potentially affect pathogenicity and disease symptom development.

Effects of sugar beet pectin on the pasting, rheological, thermal, and microstructural properties of wheat starch.

The effects of addition of sugar beet pectin (SBP) on the pasting, rheological, thermal, and microstructural properties of wheat starch (WS) were investigated. Results revealed that SBP addition significantly increased the peak viscosity, trough viscosity, breakdown value, final viscosity, and setback value of WS, whereas decreased the pasting temperature. SBP raised the swelling power (from 13.44 to 21.32 g/g) and endothermic enthalpy (ΔH, from 8.17 to 8.98 J/g), but decreased the transparency (from 9.70 % to 1.37 %). Regarding rheological properties, WS-SBP mixtures exhibited a pseudo-plastic behavior, and SBP enhanced the viscoelasticity, but decreased the deformability. Particle size distribution analysis confirmed that SBP promoted the swelling of WS granules. Fourier-transform infrared spectroscopy results suggested that the interactions between SBP and WS did not involve covalent bonding, and the formation of ordered structure was inhibited by SBP addition. Additionally, scanning electron microscopy observation found that the gel network of WS-SBP mixtures became more irregular, pore size gradually decreased, and the wall became thinner as the SBP concentration increased. These results indicated that SBP is a promising non-starch polysaccharide that can enhance the processing properties of WS.

Biochemical characterisation of cellulose and cell-wall-matrix polysaccharides in variously oxidised sugar-beet pulp preparations differing in viscosity.

Sugar-beet pulp (SBP) is an abundant, cellulose-rich, non-food by-product of agriculture. Oxidised SBP (oP) has valuable viscosity attributes, and different oxidation protocols yield higher- or lower-viscosity oP. We investigated how SBP polysaccharides change during oxidation, since these changes must define oP quality. Oxidation solubilised much pectin and hemicellulose; however, most cellulose stayed insoluble. Fresh SBP contains negligible 'hemicellulose a' (=alkali-extractable polysaccharides that precipitate upon acidification), but oxidation created abundant glucose-rich 'hemicellulose a' from SBP cellulose. We propose that the cellulose acquired COOH groups, conferring alkali-extractability and admitting more water, thereby augmenting viscosity. The pectin and hemicellulose molecules that were retained during oxidation had been partially depolymerised, and their median Mr correlated negatively with oP viscosity. We developed a novel procedure to explore cellulose's permeability by measuring the ingress of tritium from [3H]water into microfibrils and its retention during desiccation. In high-crystallinity Avicel, 75 % of the cellulose's OH groups were inaccessible to [3H]water, whereas filter-paper cellulose acquired the theoretical maximum 3H, indicating an open structure. Retention of 3H by oP preparations correlated positively with viscosity, indicating that increased cellulose accessibility generates a viscous oP. In conclusion, depolymerisation and solubilisation of matrix polysaccharides, accompanied by increasing water-accessibility of cellulose, enhanced SBP's viscosity.

Assessment of co-infection with BNYVV and BSCTV on resistance against Rhizomania disease in transgenic sugar beet plants.

Sugar beet is an economically important crop and one of the major sources of sucrose around the world. Beet necrotic yellow vein virus (BNYVV) and Beet severe curly top virus (BSCTV) are two widespread viruses in sugar beet that cause severe damage to its performance. Previously, we have successfully produced resistance to BNYVV based on RNA silencing in sugar beet by introducing constructs carrying the viral coat-protein-encoding DNA sequence, CP21, in sense and anti-sense orientations. Yet, the RNA silencing-mediated resistance to a specific virus could be affected by other ones as a part of synergistic interactions. In this study, we assayed the specificity of the induced resistance against BNYVV in two sets of transgenic events, S3 and S6 carrying 5'-UTR with or without CP21-coding sequences, respectively. These events were subjected to viral challenges with either BNYVV, an Iranian isolate of BSCTV (BSCTV-Ir) or both. All the plants inoculated with just BSCTV-Ir displayed curly-leaf symptoms. However, partial resistance was evident in S3 events as shown by mild symptoms and reduced PCR amplification of the BSCTV-Ir coat protein encoding sequence. Based on the presented data, resistance to BNYVV was stable in almost all the transgenic plants co-infected with BSCTV-Ir, except for one event, S3-229. In general, it seems that the co-infection does not affect the resistance to BNYVV in transgenic plants. These findings demonstrated that the introduced RNA silencing-mediated resistance against BNYVV in transgenic sugar beets is specific and is not suppressed after co-infection with a heterologous virus.

Exploring the antibacterial potential of plant extracts and essential oils against Bacillus thermophilus in beet sugar for enhanced sucrose retention: a comparative assessment and implications.

Sugar beet is one of the greatest sources for producing sugar worldwide. However, a group of bacteria grows on beets during the storage process, leading to a reduction in sucrose yield. Our study focused on identifying common bacterial species that grow on beets during manufacturing and contribute to sucrose loss. The ultimate goal was to find a potential antibacterial agent from various plant extracts and oils to inhibit the growth of these harmful bacteria and reduce sucrose losses. The screening of bacterial species that grow on beet revealed that a large group of mesophilic bacteria, such as Bacillus subtilis, Leuconostoc mesenteroides, Pseudomonas fluorescens, Escherichia coli, Acinetobacter baumannii, Staphylococcus xylosus, Enterobacter amnigenus, and Aeromonas species, in addition to a dominant thermophilic species called Bacillus thermophilus, were found to be present during the manufacturing of beets. The application of 20 plant extracts and 13 different oils indicated that the extracts of Geranium gruinum, Datura stramonium, and Mentha spicata were the best antibacterials to reduce the growth of B. thermophilus with inhibition zones equal to 40, 39, and 35 mm, respectively. In contrast, the best active oils for inhibiting the growth of B. thermophilus were Mentha spicata and Ocimum bacilicum, with an inhibitory effect of 50 and 45 mm, respectively. RAPD-PCR with different primers indicated that treating sugar juice with the most effective oils against bacteria resulted in new recombinant microorganisms, confirming their roles as strong antibacterial products. The characterization of Mentha spicata and Ocimum bacilicum oils using GC/MS analysis identified cis-iso pulegone and hexadecanoic acid as the two main bioactive compounds with potential antibacterial activity. An analysis of five genes using DD-PCR that have been affected due to antibacterial activity from the highly effective oil from Mentha spicata concluded that all belonged to the family of protein defense. Our findings indicate that the application of these pure antibacterial plant extracts and oils would minimize the reduction of sucrose during sugar production.

Alternative methods for RuBisCO extraction from sugar beet waste: A comparative approach of ultrasound and high voltage electrical discharge.

Ultrasound (US) and high voltage electric discharge (HVED) with water as a green solvent represent promising novel non-thermal techniques for protein extraction from sugar beet (Beta vulgaris subsp. vulgaris var. altissima) leaves. Compared to HVED, US proved to be a better alternative method for total soluble protein extraction with the aim of obtaining high yield of ribulose-1,5-bisphosphate carboxylase-oxygenase enzyme (RuBisCO). Regardless of the solvent temperature, the highest protein yields were observed at 100% amplitude and 9 min treatment time (84.60 ± 3.98 mg/gd.m. with cold and 96.75 ± 4.30 mg/gd.m. with room temperature deionized water). US treatments at 75% amplitude and 9 min treatment time showed the highest abundance of RuBisCO obtained by immunoblotting assay. The highest protein yields recorded among HVED-treated samples were observed at a voltage of 20 kV and a treatment time of 3 min, disregarding the used gas (33.33 ± 1.06 mg/gd.m. with argon and 34.89 ± 1.59 mg/gd.m. with nitrogen as injected gas), while the highest abundance of the RuBisCO among HVED-treated samples was noticed at 25 kV voltage and 3 min treatment time. By optimizing the US and HVED parameters, it is possible to affect the solubility and improve the isolation of RuBisCO, which could then be purified and implemented into new or already existing functional products.