Unravelling enzymatic discoloration in potato through a combined approach of candidate genes, QTL, and expression analysis

Enzymatic discoloration (ED) of potato tubers was investigated in an attempt to unravel the underlying genetic factors. Both enzyme and substrate concentration have been reported to influence the degree of discoloration and as such this trait can be regarded as polygenic. The diploid mapping population C × E, consisting of 249 individuals, was assayed for the degree of ED and levels of chlorogenic acid and tyrosine. Using this data, Quantitative Trait Locus (QTL) analysis was performed. Three QTLs for ED have been found on parental chromosomes C3, C8, E1, and E8. For chlorogenic acid a QTL has been identified on C2 and for tyrosine levels, a QTL has been detected on C8. None of the QTLs overlap, indicating the absence of genetic correlations between these components underlying ED, in contrast to earlier reports in literature. An obvious candidate gene for the QTL for ED on Chromosome 8 is polyphenol oxidase (PPO), which was previously mapped on chromosome 8. With gene-specific primers for PPO gene POT32 a CAPS marker was developed. Three different alleles (POT32-1, -2, and -3) could be discriminated. The segregating POT32 alleles were used to map the POT32 CAPS marker and QTL analysis was redone, showing that POT32 coincides with the QTL peak. A clear correlation between allele combinations and degree of discoloration was observed. In addition, analysis of POT32 gene expression in a subset of genotypes indicated a correlation between the level of gene expression and allele composition. On average, genotypes having two copies of allele 1 had both the highest degree of discoloration as well as the highest level of POT32 gene expression

A limited set of starch related genes explain several interrelated traits in potato

To understand the molecular basis of potato starch related traits and the underlying starch biosynthesis and degradation, a Quantitative Trait Locus (QTL) analysis in combination with a candidate gene approach was performed. The diploid mapping population C × E, consisting of 249 individuals, was assayed over two consecutive years, for chipping colour, cold induced sweetening, starch content, starch granule size, starch gelling temperature, starch enthalpy, amylose content and degree of starch phosphorylation. QTLs were observed for all traits, except enthalpy on eight out of the twelve potato chromosomes. Several QTLs were found to be consistent over 2 years. Clustering of co-localizing QTLs was observed on some chromosomes, indicating common genetic factors for the different traits. On chromosome 2, Soluble Starch Synthase 2 mapped on the same position as QTLs for starch phosphorylation, starch gelling temperature and amylose content. a-glucan, water dikinase co-localizes on chromosome 5 together with QTLs for starch phosphorylation and cold induced sweetening. Furthermore, the genes coding for two phosphorylases (StPho1a and StPho2) coincide with QTLs for starch gelling temperature, chipping colour and starch granule size on chromosome 2 and a QTL for starch phosphorylation on chromosome 9, respectively. The results suggest allelic variation acting on the genetics of the different trait

Deterministic approach to microscopic three-phase traffic theory

Two different deterministic microscopic traffic flow models, which are in the context of the Kerner's there-phase traffic theory, are introduced. In an acceleration time delay model (ATD-model), different time delays in driver acceleration associated with driver behaviour in various local driving situations are explicitly incorporated into the model. Vehicle acceleration depends on local traffic situation, i.e., whether a driver is within the free flow, or synchronized flow, or else wide moving jam traffic phase. In a speed adaptation model (SA-model), vehicle speed adaptation occurs in synchronized flow depending on driving conditions. It is found that the ATD- and SA-models show spatiotemporal congested traffic patterns that are adequate with empirical results. In the ATD- and SA-models, the onset of congestion in free flow at a freeway bottleneck is associated with a first-order phase transition from free flow to synchronized flow; moving jams emerge spontaneously in synchronized flow only. Differences between the ATD- and SA-models are studied. A comparison of the ATD- and SA-models with stochastic models in the context of three phase traffic theory is made. A critical discussion of earlier traffic flow theories and models based on the fundamental diagram approach is presented.Comment: 40 pages, 14 figure

Integrin-interleukin-4 mechanotransduction pathways in human chondrocytes

INTRODUCTION Low intensity ultrasound (LIUS) is a special type of sonic pressure that can generate radiation forces, shear stresses and cavitation MATERIALS AND METHODS C-28/I2 cells (human chondrocyte cell line) were cultured in monolayer and treated with LIUS at an intensity of 200 mW/cm 2 using Noblelife TM (Duplogen Inc., Suwon, Korea). The role of stretchactivated channels (SAC) and integrins was first examined in mediating the LIUS effects on the expression of type II collagen and aggrecan by RT-PCR and Western blot analysis. Inhibitors for SACs (gadolinium) and integrins (GRGDSP peptide or anti-integrin α1 antibody) were used to confirm their specificity. The involvement of three MPAKs signal pathways in the LIUS-mediated phenotypic changes of chondrocytes and its mechanotrnsduction pathways was also investigated using the phospho-specific antibodies. Similar approaches are currently undergoing using rabbit primary chondrocytes in three-dimensional alginate culture. RESULTS Effect of LIUS on the expression of cartilage matrix proteins C-28/I2 cells were stimulated with LIUS, and the optimal conditions for incubation and treatment times were examined in terms of type II collagen and aggrecan expression by RT-PCR. The mRNA level of type II collagen was the highest after 3 hr and that of aggrecan was gradually increasing by time, when cells were treated with LIUS for 15 min. Role of SACs in the LIUS signal When examined at 1, 3 and 6 hr after stimulation by RT-PCR, the LIUS effects on the mRNA levels of type II collagen and aggrecan were reduced by gadolinium treatment depending on time Role of integrins in the LIUS signal C-28/I2 cells were pre-incubated with the inhibitor (GRGDSP) or a control peptide (GRADSP) for 10 min before LIUS treatment. The mRNA levels of type II collagen and aggrecan were clearly induced by LIUS in the presence of GRADSP but were lower than the untreated control (0 hr) when GRGDSP was co-treated. MAPKs as downstream mediators of LIUS signal The phosphorylation of ERK and JNK was induced by LIUS but that of p38 kinase was not CONCLUSION These results suggest that the LIUS signal might be mediated via canonical mechanoreceptors of SACs and integrins and subsequently through JNK and ERK pathways. Further studies are necessary to understand more details of the LIUS signaling network and regulation mechanisms. In addition, our ongoing studies in a 3-D culture of chondrocytes would give more important information about the cellular and molecular mechanism(s) of LIUS effects on development of chondrogenic phenotypes. REFERENCES 1. Feril, L.B. Jr. and Kondo, T. Biological effects of low intensity ultrasound: the mechanism involved and its implications on therapy and on biosafety of ultrasound

A remote secondary binding pocket promotes heteromultivalent targeting of DC-SIGN

Dendritic cells (DC) are antigen-presenting cells coordinating the interplay of the innate and the adaptive immune response. The endocytic C-type lectin receptors DC-SIGN and Langerin display expression profiles restricted to distinct DC subtypes and have emerged as prime targets for next-generation immunotherapies and anti-infectives. Using heteromultivalent liposomes copresenting mannosides bearing aromatic aglycones with natural glycan ligands, we serendipitously discovered striking cooperativity effects for DC-SIGN+ but not for Langerin+ cell lines. Mechanistic investigations combining NMR spectroscopy with molecular docking and molecular dynamics simulations led to the identification of a secondary binding pocket for the glycomimetics. This pocket, located remotely of DC-SIGN’s carbohydrate bindings site, can be leveraged by heteromultivalent avidity enhancement. We further present preliminary evidence that the aglycone allosterically activates glycan recognition and thereby contributes to DC-SIGN-specific cell targeting. Our findings have important implications for both translational and basic glycoscience, showcasing heteromultivalent targeting of DCs to improve specificity and supporting potential allosteric regulation of DC-SIGN and CLRs in general

The Ukraine-Russia war : a symptoms network of complex posttraumatic stress disorder during continuous traumatic stress

Objective: This study is aimed to test the symptoms network of ICD-11 Complex Post-traumatic Stress Disorder (CPTSD) symptoms, using data collected from Ukrainian civilians during the 2022 Russia-Ukraine war. Findings can inform our understanding of the stress response in individuals exposed to continuous trauma and give insight into the nature of CPTSD during war. Methods: A network analysis was conducted on CPTSD symptoms as assessed by the International Trauma Questionnaire using data from a nationally representative sample of 2000 Ukrainians. Results: While Post-traumatic Stress Disorder (PTSD) and Disturbances in Self Organization (DSO) clusters did not enmesh, several communities within these clusters were merged. Results highlight that in terms of strength centrality, emotional dysregulation (emotional numbing) and a heightened sense of threat were most prominent. Conclusion: The results confirm the ICD-11 structure of CPTSD but suggest that continuous traumatic stress manifests in more condensed associations between CPTSD symptoms and that emotional regulation may play a vital role in activating the CPTSD network. War-exposed populations could be provided with scalable, brief self-help materials focused on fostering emotion regulation and sense of threat

Sequencing the Potato Genome: Outline and First Results to Come from the Elucidation of the Sequence of the World’s Third Most Important Food Crop

Potato is a member of the Solanaceae, a plant family that includes several other economically important species, such as tomato, eggplant, petunia, tobacco and pepper. The Potato Genome Sequencing Consortium (PGSC) aims to elucidate the complete genome sequence of potato, the third most important food crop in the world. The PGSC is a collaboration between 13 research groups from China, India, Poland, Russia, the Netherlands, Ireland, Argentina, Brazil, Chile, Peru, USA, New Zealand and the UK. The potato genome consists of 12 chromosomes and has a (haploid) length of approximately 840 million base pairs, making it a medium-sized plant genome. The sequencing project builds on a diploid potato genomic bacterial artificial chromosome (BAC) clone library of 78000 clones, which has been fingerprinted and aligned into ~7000 physical map contigs. In addition, the BAC-ends have been sequenced and are publicly available. Approximately 30000 BACs are anchored to the Ultra High Density genetic map of potato, composed of 10000 unique AFLPTM markers. From this integrated genetic-physical map, between 50 to 150 seed BACs have currently been identified for every chromosome. Fluorescent in situ hybridization experiments on selected BAC clones confirm these anchor points. The seed clones provide the starting point for a BAC-by-BAC sequencing strategy. This strategy is being complemented by whole genome shotgun sequencing approaches using both 454 GS FLX and Illumina GA2 instruments. Assembly and annotation of the sequence data will be performed using publicly available and tailor-made tools. The availability of the annotated data will help to characterize germplasm collections based on allelic variance and to assist potato breeders to more fully exploit the genetic potential of potat

Chronic hyperglycemia induces trans-differentiation of human pancreatic stellate cells and enhances the malignant molecular communication with human pancreatic cancer cells

BACKGROUND: Diabetes mellitus is linked to pancreatic cancer. We hypothesized a role for pancreatic stellate cells (PSC) in the hyperglycemia induced deterioration of pancreatic cancer and therefore studied two human cell lines (RLT-PSC, T3M4) in hyperglycemic environment. METHODOLOGY/PRINCIPAL FINDINGS: The effect of chronic hyperglycemia (CHG) on PSCs was studied using mRNA expression array with real-time PCR validation and bioinformatic pathway analysis, and confirmatory protein studies. The stress fiber formation (IC: αSMA) indicated that PSCs tend to transdifferentiate to a myofibroblast-like state after exposure to CHG. The phosphorylation of p38 and ERK1/2 was increased with a consecutive upregulation of CDC25, SP1, cFOS and p21, and with downregulation of PPARγ after PSCs were exposed to chronic hyperglycemia. CXCL12 levels increased significantly in PSC supernatant after CHG exposure independently from TGF-β1 treatment (3.09-fold with a 2.73-fold without TGF-β1, p<0.05). The upregualtion of the SP1 transcription factor in PSCs after CHG exposure may be implicated in the increased CXCL12 and IGFBP2 production. In cancer cells, hyperglycemia induced an increased expression of CXCR4, a CXCL12 receptor that was also induced by PSC's conditioned medium. The receptor-ligand interaction increased the phosphorylation of ERK1/2 and p38 resulting in activation of MAP kinase pathway, one of the most powerful stimuli for cell proliferation. Certainly, conditioned medium of PSC increased pancreatic cancer cell proliferation and this effect could be partially inhibited by a CXCR4 inhibitor. As the PSC conditioned medium (normal glucose concentration) increased the ERK1/2 and p38 phosphorylation, we concluded that PSCs produce other factor(s) that influence(s) pancreatic cancer behaviour. CONCLUSIONS: Hyperglycemia induces increased CXCL12 production by the PSCs, and its receptor, CXCR4 on cancer cells. The ligand-receptor interaction activates MAP kinase signaling that causes increased cancer cell proliferation and migration