Explore the vast range of titles available.

In Arabidopsis thaliana, small peptides (AtPeps) encoded by PROPEP genes act as damageassociated molecular patterns (DAMPs) that are perceived by two leucine-rich repeat receptor kinases, PEPR1 and PEPR2, to amplify defense responses. In particular, expression of PROPEP2 and PROPEP3 is strongly and rapidly induced by AtPeps, in response to bacterial, oomycete, and fungal pathogens, and microbe-associated molecular patterns (MAMPs). The cis-regulatory modules (CRMs) within the PROPEP2 and PROPEP3 promoters that mediate MAMP responsiveness were delineated, employing parsley (Petroselinum crispum) protoplasts and transgenic A. thaliana plants harboring promoter-reporter constructs. By chromatin immunoprecipitation in vivo, DNA interactions with a specific transcription factor were detected. Furthermore, the phastCons program was used to identify conserved regions of the PROPEP3 locus in different Brassicaceae species. The major MAMP-responsive CRM within the PROPEP2 promoter is composed of several W boxes and an as1/OCS (activation sequence-1/octopine synthase) enhancer element, while in the PROPEP3 promoter the CRM is comprised of six W boxes. The WRKY33 transcription factor binds in vivo to these promoter regions in a MAMP-dependent manner. Both the position and orientation of the six W boxes are conserved within the PROPEP3 promoters of four other Brassicaceae family members. WRKY factors are the major regulators of MAMP-induced PROPEP2 and PROPEP3 expression.

The effect of hypoxia on the level of expression of pyruvate kinase ( PKM ), octopine dehydrogenase ( OcDH ), and malate dehydrogenase ( MDH ) genes in the gill tissue of the Mediterranean mussel Mytilus galloprovincialis (L., 1819) was studied experimentally. The control group of mollusks was kept at 9–10°C, and the oxygen level in the water was 8.5 mg O 2 L –1 . The experimental levels were at 9–10°C and 2.2 mg O 2 L –1 . The exposure was 24 and 72 h. Some of the individuals were subsequently subjected to the reoxygenation procedure. Under conditions of hypoxia, the expression level of OcDH and MDH genes increased by three and two times, respectively ( p < 0.05). At the same time, OcDH expression showed sensitivity to the oxygen content in the medium. Under the conditions of reoxygenation, the process was completely suppressed. The expression of the PKM gene, on the contrary, did not depend on hypoxic effects and remained at the level of the control values.

Biotinidase deficiency is an autosomal recessive disorder that disrupts biotin recycling and multiple carboxylase-dependent pathways. Early and continuous biotin therapy prevents major clinical manifestations, but its long-term biochemical effects remain unclear. This study applied untargeted metabolomic and lipidomic profiling in 54 pediatric patients with genetically confirmed BD receiving regular biotin supplementation and 30 age- and sex-matched controls. Multivariate analyses and pathway enrichment revealed distinct biochemical signatures involving amino acid, energy, and lipid metabolism. Reduced levels of serine, glycine, threonine, and tricarboxylic acid cycle intermediates suggested modified mitochondrial flux, while octopine, exhibiting an approximately 11-fold increase, was the metabolite best able to discriminate between the groups. Lipidomic profiling indicated elevations in sphingolipids, phosphatidylcholines, long-chain fatty acids, and acylcarnitines, consistent with systemic lipid remodeling. These coordinated alterations imply metabolic adaptations to sustained biotin exposure rather than ongoing pathology. Octopine and selected lipid species may represent biochemical indicators of this adaptive state. Overall, the findings highlight that clinically stable children with Biotinidase deficiency exhibit unique metabolic and lipidomic patterns reflecting long-term compensatory mechanisms, underscoring the value of combined omics approaches for understanding disease-specific homeostasis and informing personalized follow-up strategies.

IntroductionOxygen is essential for metabolic processes and in the absence thereof alternative metabolic pathways are required for energy production, as seen in marine invertebrates like abalone. Even though hypoxia has been responsible for significant losses to the aquaculture industry, the overall metabolic adaptations of abalone in response to environmental hypoxia are as yet, not fully elucidated.ObjectiveTo use a multiplatform metabolomics approach to characterize the metabolic changes associated with energy production in abalone (Haliotis midae) when exposed to environmental hypoxia.MethodsMetabolomics analysis of abalone adductor and foot muscle, left and right gill, hemolymph, and epipodial tissue samples were conducted using a multiplatform approach, which included untargeted NMR spectroscopy, untargeted and targeted LC–MS spectrometry, and untargeted and semi-targeted GC-MS spectrometric analyses.ResultsIncreased levels of anaerobic end-products specific to marine animals were found which include alanopine, strombine, tauropine and octopine. These were accompanied by elevated lactate, succinate and arginine, of which the latter is a product of phosphoarginine breakdown in abalone. Primarily amino acid metabolism was affected, with carbohydrate and lipid metabolism assisting with anaerobic energy production to a lesser extent. Different tissues showed varied metabolic responses to hypoxia, with the largest metabolic changes in the adductor muscle.ConclusionsFrom this investigation, it becomes evident that abalone have well-developed (yet understudied) metabolic mechanisms for surviving hypoxic periods. Furthermore, metabolomics serves as a powerful tool for investigating the altered metabolic processes in abalone.

Prunus humilis Bunge (Cerasus humilis (Bunge) S. ya. Sokolov) (Rosaceae) is a small shrub native to China, highly valued for environmental protection and as a functional food. However, with the increasing scale of cultivation, crown gall disease has become a major concern. In this study, we aimed to isolate and identify the pathogenic strains causing crown gall disease in P. humilis, and investigate their physiological, phylogenetic, opine type, and biological control characteristics. We isolated 45 pathogenic strains from five regions of China. Using phenotypic and phylogenetic analysis of the 16S rRNA gene, we identified 12 strains as Rhizobium rhizogenes and 33 strains as members of the Agrobacterium tumefaciens species complex. Multi-locus sequence analysis of three housekeeping genes (rpoB, atpD, and recA) revealed that 11 strains belonged to A. fabacearum and 22 strains belonged to A. radiobacter within the A. tumefaciens species complex. Of the isolated strains, five displayed characteristics identical to the typical nopaline-type Ti plasmid, whereas the remaining 40 strains did not contain nopaline, octopine, or agropine plasmids. However, all strains possessed the trans-zeatin synthesizing gene and agrocinopine synthetase gene, with some also containing nopaline catabolism genes, suggesting the presence of a plasmid closely related to the nopaline type. Resistance to the agrocins produced by R. rhizogenes K1026 was observed in all strains. However, in a greenhouse experiment, K1026 demonstrated 100%, 100%, and 25% control efficiency against three P. humilis-derived pathogenic strains, respectively. These findings reveal unique characteristics of the pathogens responsible for crown gall disease in P. humilis.

Agrobacterium -mediated plant galls are often misdiagnosed as nematode-mediated knots, even by experts, because the gall symptoms in both conditions are very similar. In the present study, we developed biosensor strains based on agrobacterial opine metabolism that easily and simply diagnoses Agrobacterium -induced root galls. Our biosensor consists of Agrobacterium mannitol (ABM) agar medium, X-gal, and a biosensor. The working principle of the biosensor is that exogenous nopaline produced by plant root galls binds to NocR, resulting in NocR/nopaline complexes that bind to the promoter of the nopaline oxidase gene ( nox ) operon and activate the transcription of noxB - lacZY , resulting in readily visualized blue pigmentation on ABM agar medium supplemented with X-gal (ABMX-gal). Similarly, exogenous octopine binds to OccR, resulting in OoxR/octopine complexes that bind to the promoter of the octopine oxidase gene ( oox ) operon and activate the transcription of ooxB - lacZY , resulting in blue pigmentation in the presence of X-gal. Our biosensor is successfully senses opines produced by Agrobacterium -infected plant galls, and can be applied to easily distinguish Agrobacterium crown gall disease from nematode disease.

Agrobacterium-mediated transformation is a complex process that is widely utilized for generating transgenic plants. However, one of the major concerns of this process is the frequent presence of undesirable T-DNA vector backbone sequences in the transgenic plants. To mitigate this deficiency, a ternary strain of A. tumefaciens was modified to increase the precision of T-DNA border nicking such that the backbone transfer is minimized. This particular strain supplemented the native succinamopine VirD1/VirD2 of EHA105 with VirD1/VirD2 derived from an octopine source (pTi15955), the same source as the binary T-DNA borders tested here, residing on a ternary helper plasmid containing an extra copy of the succinamopine VirB/C/G operons and VirD1. Transformation of maize immature embryos was carried out with two different test constructs, pDAB101556 and pDAB111437, bearing the reporter YFP gene and insecticidal toxin Cry1Fa gene, respectively, contained in the VirD-supplemented and regular control ternary strains. Molecular analyses of ~ 700 transgenic events revealed a significant 2.6-fold decrease in events containing vector backbone sequences, from 35.7% with the control to 13.9% with the VirD-supplemented strain for pDAB101556 and from 24.9% with the control to 9.3% with the VirD-supplemented strain for pDAB111437, without compromising transformation efficiency. In addition, while the number of single copy events recovered was similar, there was a 24–26% increase in backbone-free events with the VirD-supplemented strain compared to the control strain. Thus, supplementing existing VirD1/VirD2 genes in Agrobacterium, to recognize diverse T-DNA borders, proved to be a useful tool to increase the number of high quality events in maize.

Habitat conditions play a crucial role in food acquisition and the energetic and physiological performance of marine organisms during seasonal changes. However, across a wide distribution, populations of the same species might face physiological constraints driven by the oceanographic and climatological characteristics of their habitats. In the context of climate change, biochemical and metabolic data may be important in identifying marine areas in which inhabiting organisms are more or less physiologically constrained. As a first step in identifying such marine areas on the Greek coast, we studied the seasonal metabolic and antioxidant responses of blue crab Callinectes sapidus, cuttlefish Sepia officinalis, sea cucumber Holothuria tubulosa and clam Venus verrucosa, collected from 3 different Greek gulfs: Thermaikos, Pagasitikos and Vistonikos. Seasonal analysis of metabolic responses was based on the activity of the following intermediary metabolic enzymes: lactate dehydrogenase (L-LDH), octopine dehydrogenase (ODH), β-hydroxyacyl-CoA dehydrogenase (HOAD) and citrate synthase (CS). Antioxidant responses were based on the activities of the following enzymes: superoxide dismutase (SOD), glutathione reductase (GR) and catalase, and on lipid peroxidation estimation. The blue crab and clam exhibited the most significant seasonal changes compared to the sea cucumber and cuttlefish, which exhibited no changes. The intermediary metabolism enzymatic activity of blue crab and clam decreased and antioxidant enzymatic activity increased during summer. Higher activity levels for all examined species were ob served in Pagasitikos and lower levels in Vistonikos Gulf, indicating corresponding oxidative stress. These results are correlated with the spatial oceanographic conditions of the habitats and are discussed based on future projections of global warming in the Mediterranean Sea.

Background Nitrogen fixing bacteria isolated from hot arid areas in Asia, Africa and America but from diverse leguminous plants have been recently identified as belonging to a possible new species of Ensifer ( Sinorhizobium ). In this study, 6 strains belonging to this new clade were compared with Ensifer species at the genome-wide level. Their capacities to utilize various carbon sources and to establish a symbiotic interaction with several leguminous plants were examined. Results Draft genomes of selected strains isolated from Morocco (Merzouga desert), Mexico (Baja California) as well as from India (Thar desert) were produced. Genome based species delineation tools demonstrated that they belong to a new species of Ensifer . Comparison of its core genome with those of E. meliloti , E. medicae and E. fredii enabled the identification of a species conserved gene set. Predicted functions of associated proteins and pathway reconstruction revealed notably the presence of transport systems for octopine/nopaline and inositol phosphates. Phenotypic characterization of this new desert rhizobium species showed that it was capable to utilize malonate, to grow at 48 °C or under high pH while NaCl tolerance levels were comparable to other Ensifer species. Analysis of accessory genomes and plasmid profiling demonstrated the presence of large plasmids that varied in size from strain to strain. As symbiotic functions were found in the accessory genomes, the differences in symbiotic interactions between strains may be well related to the difference in plasmid content that could explain the different legumes with which they can develop the symbiosis. Conclusions The genomic analysis performed here confirms that the selected rhizobial strains isolated from desert regions in three continents belong to a new species. As until now only recovered from such harsh environment, we propose to name it Ensifer aridi . The presented genomic data offers a good basis to explore adaptations and functionalities that enable them to adapt to alkalinity, low water potential, salt and high temperature stresses. Finally, given the original phylogeographic distribution and the different hosts with which it can develop a beneficial symbiotic interaction, Ensifer aridi may provide new biotechnological opportunities for degraded land restoration initiatives in the future.

Background Research on low-protein-level diets has indicated that even though the profiles of essential amino acids (EAAs) follow the recommendation for a normal-protein-level diet, broilers fed low-protein diets failed to achieve productive performance compared to those fed normal diets. Therefore, it is imperative to reassess the optimum profile of EAAs in low-protein diets and establish a new ideal pattern for amino acid balance. Furthermore, identifying novel sensitive biomarkers for assessing amino acid balance will greatly facilitate the development of amino acid nutrition and application technology. In this study, 12 dietary treatments [Con(+), Con(-), L&A(-), L&A(+), M&C(-), M&C(+), BCAA (-), BCAA(+), Thr(-), Thr(+), Trp(-) and Trp(+)] were established by combining different EAAs including lysine and arginine, methionine and cysteine, branched-chain amino acid (BCAA), threonine, and tryptophan to observe the growth and development of the broiler chickens fed with low-protein-level diets. Based on the biochemical parameters and untargeted metabolomic analysis of animals subjected to different treatments, biomarkers associated with optimal and suboptimal amino acid balance were identified. Results Growth performance, carcass characteristics, hepatic enzyme activity, serum biochemical parameters, and breast muscle mRNA expression differed significantly between male and female broilers under different dietary amino acid patterns. Male broilers exhibited higher sensitivity to the adjustment of amino acid patterns than female broilers. For the low-protein diet, the dietary concentrations of lysine, arginine, and tryptophan, but not of methionine, cystine, or threonine, needed to be increased. Therefore, further research on individual BCAA is required. For untargeted metabolomic analysis, Con(+) was selected as a normal diet (NP) while Con(-) represented a low-protein diet (LP). L&A(+) denotes a low-protein amino acid balanced diet (LPAB) and Thr(+) represents a low-protein amino acid imbalance diet (LPAI). The metabolites oxypurinol, pantothenic acid, and D-octopine in birds were significantly influenced by different dietary amino acid patterns. Conclusion Adjusting the amino acid profile of low-protein diets is required to achieve normal growth performance in broiler chickens fed normal-protein diets. Oxypurinol, pantothenic acid, and D-octopine have been identified as potentially sensitive biomarkers for assessing amino acid balance.