Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes.

MOTIVATION: The functional complexity of biochemical processes is strongly related to the interplay of proteins and their assembly into protein complexes. In recent years, the discovery and characterization of protein complexes have substantially progressed through advances in cryo-electron microscopy, proteomics, and computational structure prediction. This development results in a strong need for computational approaches to analyse the data of large protein complexes for structural and functional characterization. Here, we aim to provide a suitable approach, which processes the growing number of large protein complexes, to obtain biologically meaningful information on the hierarchical organization of the structures of protein complexes. RESULTS: We modelled the quaternary structure of protein complexes as undirected, labelled graphs called complex graphs. In complex graphs, the vertices represent protein chains and the edges spatial chain-chain contacts. We hypothesized that clusters based on the complex graph correspond to functional biological modules. To compute the clusters, we applied the Leiden clustering algorithm. To evaluate our approach, we chose the human respiratory complex I, which has been extensively investigated and exhibits a known biological module structure experimentally validated. Additionally, we characterized a eukaryotic group II chaperonin TRiC/CCT and the head of the bacteriophage Φ29. The analysis of the protein complexes correlated with experimental findings and indicated known functional, biological modules. Using our approach enables not only to predict functional biological modules in large protein complexes with characteristic features but also to investigate the flexibility of specific regions and coformational changes. The predicted modules can aid in the planning and analysis of experiments. AVAILABILITY AND IMPLEMENTATION: Jupyter notebooks to reproduce the examples are available on our public GitHub repository: https://github.com/MolBIFFM/PTGLtools/tree/main/PTGLmodulePrediction.

Rapid desorption and analysis for illicit drugs and chemical profiling of fingerprints by SICRIT ion source.

Forensic analysis can encompass a wide variety of analytes from biological samples including DNA, blood, serum, and fingerprints to synthetic samples like drugs and explosives. In order to analyze this variety, there are various sample preparation techniques, which can be time-consuming and require multiple analytical instruments. With recent advancements in ambient ionization mass spectrometry (MS), plasma-based dielectric barrier discharge ionization (DBDI) sources have demonstrated to cover a wide range of these analytes. The flow-through design of this source also allows for easy connection to a thermal desorption type of sample introduction. We present an in-house built thermal desorption device where the sample is introduced via a glass slide, which gets heated and transferred to the DBDI-MS with nitrogen for identification and semi-quantification. Using a glass slide as an inexpensive sampling device, detection limits as low as 20 pg for fentanyl are demonstrated. Additionally, a very precise (>96% accuracy) identification of persons based on the chemical profile of their fingerprints is possible, establishing a direct analytical link of the drug trace to the individual in one measurement. We compared the DAG, TAG, sterol, and (semi-)volatile region of the averaged fingerprint spectra over multiple days, showing the best model accuracy for identification based on the DAG region. The combination of thermal desorption and DBDI-MS minimized sample preparation, leading to an ultrasensitive and rapid analysis of illicit drug traces and the identification of underlying personas based on fingerprints.

An Efficient Triplex TaqMan Quantitative PCR to Detect a Blackleg-Causing Lineage of Pectobacterium brasiliense in Potato Based on a Pangenome Analysis.

P. brasiliense is an important bacterial pathogen causing blackleg (BL) in potatoes. Nevertheless, P. brasiliense is often detected in seed lots that do not develop any of the typical blackleg symptoms in the potato crop when planted. Field bioassays identified that P. brasiliense strains can be categorized into two distinct classes, some able to cause blackleg symptoms and some unable to do it. A comparative pangenomic approach was performed on 116 P. brasiliense strains, of which 15 were characterized as BL-causing strains and 25 as non-causative. In a genetically homogeneous clade comprising all BL-causing P. brasiliense strains, two genes only present in the BL-causing strains were identified, one encoding a predicted lysozyme inhibitor Lprl (LZI) and one encoding a putative Toll/interleukin-1 receptor (TIR) domain-containing protein. TaqMan assays for the specific detection of BL-causing P. brasiliense were developed and integrated with the previously developed generic P. brasiliense assay into a triplex TaqMan assay. This simultaneous detection makes the scoring more efficient as only a single tube is needed, and it is more robust as BL-causing strains of P. brasiliense should be positive for all three assays. Individual P. brasiliense strains were found to be either positive for all three assays or only for the P. brasiliense assay. In potato samples, the mixed presence of BL-causing and not BL-causing P. brasiliense strains was observed as shown by the difference in Ct value of the TaqMan assays. However, upon extension of the number of strains, it became clear that in recent years additional BL-causing lineages of P. brasiliense were detected for which additional assays must be developed.

QMRA of Ralstonia solanacearum in potato cultivation: Risks associated with irrigation water recycled through managed aquifer recharge.

Agricultural aquifer storage recovery and transfer (ASTR) stores excess fresh water for later reuse in irrigation. Moreover, water quality improves because chemical pollutants and pathogens will be removed by degradation and attachment to the aquifer material. The source water may contain the bacterial plant pathogen Ralstonia solanacearum which causes plant infections and high yield losses. We used quantitative microbial risk assessment (QMRA) to investigate the removal of R. solanacearum during ASTR to predict infection risks of potato plants after irrigation with the recovered water. Laboratory experiments analyzed the ASTR treatment by investigating the bacterial die-off in the water phase and the removal by attachment to the aquifer sediment. Die-off in the water phase depends on the residence time and ranged between 1.3 and 2.7 log10 after 10 or 60 days water storage, respectively. A subpopulation of the bacteria persisted for a prolonged time at low concentrations which may pose a risk if the water is recovered too early. However, the natural aquifer sand filtration proofed to be highly effective in removing R. solanacearum by attachment which depends on the distance between injection and abstraction well. The high removal by attachment alone (18 log10 after 1 m) would reduce bacterial concentrations to negligible numbers. Upscaling to longer soil passages is discussed in the paper. Infection risks of potato plants were calculated using a dose-response model and ASTR treatment resulted in negligible infection risks of a single plant, but also when simulating the irrigation of a 5 ha potato field. This is the first QMRA that analyzed an agricultural ASTR and the fate of a plant pathogen focusing on plant health. QMRA is a useful (water) management tool to evaluate the treatment steps of water reclamation technologies with the aim to provide safe irrigation water and reduce risks disseminating plant diseases.

Proof-of-concept and Randomized, Placebo-controlled Trials of an FcRn Inhibitor, Batoclimab, for Thyroid Eye Disease.

CONTEXT: Inhibition of the neonatal fragment crystallizable receptor (FcRn) reduces pathogenic thyrotropin receptor antibodies (TSH-R-Ab) that drive pathology in thyroid eye disease (TED). OBJECTIVE: We report the first clinical studies of an FcRn inhibitor, batoclimab, in TED. DESIGN: Proof-of-concept (POC) and randomized, double-blind placebo-controlled trials. SETTING: Multicenter. PARTICIPANTS: Patients with moderate-to-severe, active TED. INTERVENTION: In the POC trial, patients received weekly subcutaneous injections of batoclimab 680 mg for 2 weeks, followed by 340 mg for 4 weeks. In the double-blind trial, patients were randomized 2:2:1:2 to weekly batoclimab (680 mg, 340 mg, 255 mg) or placebo for 12 weeks. MAIN OUTCOME: Change from baseline in serum anti-TSH-R-Ab and total IgG (POC); 12-week proptosis response (randomized trial). RESULTS: The randomized trial was terminated because of an unanticipated increase in serum cholesterol; therefore, data from 65 of the planned 77 patients were analyzed. Both trials showed marked decreases in pathogenic anti-TSH-R-Ab and total IgG serum levels (P < .001) with batoclimab. In the randomized trial, there was no statistically significant difference with batoclimab vs placebo in proptosis response at 12 weeks, although significant differences were observed at several earlier timepoints. In addition, orbital muscle volume decreased (P < .03) at 12 weeks, whereas quality of life (appearance subscale) improved (P < .03) at 19 weeks in the 680-mg group. Batoclimab was generally well tolerated, with albumin reductions and increases in lipids that reversed upon discontinuation. CONCLUSIONS: These results provide insight into the efficacy and safety of batoclimab and support its further investigation as a potential therapy for TED.

Inactivation of tomato WAT1 leads to reduced susceptibility to Clavibacter michiganensis through downregulation of bacterial virulence factors.

Tomato bacterial canker caused by Clavibacter michiganensis (Cm) is considered to be one of the most destructive bacterial diseases of tomato. To date, no resistance to the pathogen has been identified. While several molecular studies have identified (Cm) bacterial factors involved in disease development, the plant genes and mechanisms associated with susceptibility of tomato to the bacterium remain largely unknown. Here, we show for the first time that tomato gene SlWAT1 is a susceptibility gene to Cm. We inactivated the gene SlWAT1 through RNAi and CRISPR/Cas9 to study changes in tomato susceptibility to Cm. Furthermore, we analysed the role of the gene in the molecular interaction with the pathogen. Our findings demonstrate that SlWAT1 functions as an S gene to genetically diverse Cm strains. Inactivation of SlWAT1 reduced free auxin contents and ethylene synthesis in tomato stems and suppressed the expression of specific bacterial virulence factors. However, CRISPR/Cas9 slwat1 mutants exhibited severe growth defects. The observed reduced susceptibility is possibly a result of downregulation of bacterial virulence factors and reduced auxin contents in transgenic plants. This shows that inactivation of an S gene may affect the expression of bacterial virulence factors.

Thyrotropin Receptor Antagonism by a Novel Small Molecule: Preclinical In Vitro Observations.

Background: Treatment of Graves' hyperthyroidism (GH) and Graves' orbitopathy (GO) is far from adequate, and hence, new substances that specifically target the autoantigens in GH/GO are warranted. This study determined the preclinical in vitro efficacy of SYD5115, a novel low-molecular-weight compound that inhibits the thyrotropin receptor (TSH-R). Methods: The TSH-R inhibiting capability of SYD5115 was tested through stimulation of wild-type and chimeric TSH-R expressed in Chinese hamster ovary (CHO) cells using two functional (stimulatory and blocking) cell-based TSH-R-Ab bioassays. TSH-R expressing human orbital fibroblasts, collected from GH+GO patients (GOF), were stimulated with the monoclonal antibody M22 or with stimulatory TSH-R-Ab (TSAb)-positive sera with cyclic adenosine monophosphate (cAMP) or hyaluronic acid (HA) release as readouts. The effect of SYD5115 on the viability of GOF was tested in 4,5-dimethylthiazol-2-yl-2,5-diphenyltetrazolium bromide and scratch cell growth assays. Results: SYD5115 significantly and dose dependently inhibited the TSH-R activation through M22 or TSAb-positive sera in all performed bioassays. Inhibition showed similar levels in the TSAb reporter bioassay and in the cAMP assay with GOF. The % inhibition and compound concentration showed a sigmoidal relationship, with all seven TSAb-positive sera markedly inhibited by SYD5115. An SYD5115 dose-dependent inhibition of M22 (10 ng/mL, 6 hours)-stimulated HA and/or cAMP-release from GOF was observed. Strong SYD5115-induced inhibitions of M22-stimulated cAMP production in GOF were registered with SYD5115 concentrations of 1 (p = 0.0029), 10 (p < 0.0001), 100 (p < 0.0001), 1,000 (p < 0.0001), and 10,000 (p < 0.0001) nM, respectively. SYD5115-induced inhibition of M22-stimulated HA production was noted with SYD5115 concentrations of 100 (p = 0.0392), 1000 (p = 0.0431), and 10,000 (p = 0.0245) nM, respectively. The inhibitory activity of SYD5115 was confirmed in a human osteosarcoma U2OS cell line stably expressing human TSH-R with cAMP as readout. SYD5115 induced 100% inhibition of the M22-induced cAMP levels with a potency of 193 nM. Compared with control, SYD5115 did neither impact the growth nor the migration of cultivated GOF. In addition, SYD5115 did not alter the viability of GOF. Conclusions: SYD5115 blocked M22- and TSAb-induced TSH-R activity with a nanomolar potency in TSH-R-overexpressed CHO cells as well as primary GOF, which demonstrates the ability of this small molecule to block TSH-R overactivity.

A Novel Monoclonal Antibody Degrades the Thyrotropin Receptor Autoantibodies in Graves' Disease.

OBJECTIVE: Autoantibodies against the thyrotropin receptor (TSH-R-Ab) are key mediators for the pathogenesis of Graves' disease (GD). TSH-R-Ab degradation was evaluated using several immunoassays within an exploratory, controlled trial in patients with GD receiving a monoclonal antibody (mAb) targeting the neonatal crystallizable fragment receptor (FcRn). METHODS: Serial measurements of TSH-R-Ab serum levels were performed using 3 different binding and cell-based assays in patients with GD either on medication or on placebo. RESULTS: In contrast to the placebo group, in which no changes were observed, a 12-week mAb therapy led to an early and significant decrease (>60%) in the serum TSH-R-Ab levels in patients with thyroidal and extrathyroidal GD, as unanimously shown in all 3 assays. These marked changes were noted already at week 7 post baseline (P <.0001 for the binding immunoassay and for the luciferase (readout) bioassay). The 3 TSH-R-Ab binding and bioassays were highly correlated in the samples of both study groups (binding immunoassay vs luciferase bioassay, r =.91, P <.001, binding vs cyclic adenosine monophosphate (cAMP) bioassay, r = 0.86, P <.001, and luciferase vs cAMP bioassay, r = 0.71, P =.006). The serological results correlated with the course of the extrathyroidal clinical parameters of GD, that is, clinical activity score and proptosis. CONCLUSION: Targeting the FcRn markedly reduces the disease-specific TSH-R-Ab in patients with GD. The novel and rapid TSH-R-Ab bioassay improves diagnosis and management of patients with GD.

Effect of Dopants and Gas-Phase Composition on Ionization Behavior and Efficiency in Dielectric Barrier Discharge Ionization.

Cold plasma-based ionization techniques allow for soft ionization of a wide variety of chemical compounds. In this chemical ionization mechanism, the atmosphere plays a crucial role in ionization. Knowing its influence is critical for the optimization of analysis conditions and interpretation of resulting spectra. This study uses soft ionization by chemical reaction in transfer (SICRIT), a variant of dielectric barrier discharge ionization (DBDI), that allows for a controlled atmosphere to investigate atmosphere and dopant effects. The influence of eight makeup gas compositions (dry nitrogen, room air, and nitrogen-enriched with either water, HCl, MeOH, hexane, NH3, and fluorobenzene) on the ionization with SICRIT was investigated. Fifteen compound classes, comprising alkanes, polyaromatic hydrocarbons (PAHs), terpenes, oxygen-containing terpenes, alkylphenols, chlorophenols, nitrophenols, trialkylamines, triazines, phthalates with or without ether groups, aldehydes, ketones, fatty acid methyl esters (FAMEs), and polyoxy-methylene ethers (OMEs) were measured via gas chromatography SICRIT high-resolution mass spectrometry (GC-SICRIT-HRMS). The different atmospheres were compared in terms of generated ions, ion intensities and fragmentation during ionization. Measurements of reactant ions were performed for a better understanding of the underlying mechanisms. All 15 compound classes were mostly softly ionized. For most compound classes and atmospheres, protonation is the dominant ionization mode. The highest number of compounds ionized via protonation was observed in dry nitrogen, followed by room air and humid nitrogen. The study should work as a guideline for the choice of atmosphere for specific compound classes and the interpretation of spectra generated under a specific atmosphere.

Natural Infections of Potato Plants Grown from Minitubers with Blackleg-Causing Soft Rot Pectobacteriaceae.

Information on the infection incidence of blackleg-causing soft rot Pectobacteriaceae (BL-SRP) in potato crops grown from minitubers (PB1-crop) and the distribution of BL-SRP in individual plants was collected during a two-year survey conducted at five potato growers located in the Netherlands. In the last weeks before haulm destruction, leaves, stems, and tubers of 100 or 200 plants were analyzed separately for the presence of Pectobacterium parmentieri, P. brasiliense, P. atrosepticum, and Dickeya spp. Extracted plant parts enriched for BL-SRP were analyzed with TaqMan assays specific for the detection of blackleg-causing BL-SRP. In 2019, low incidences of P. parmentieri (1-6%) in leaves were found at four growing sites. At one farm, reactions were detected in TaqMan assays for D. zeae and D. chrysanthemi in leaves. In 2020, the crops of two growers were largely free from BL-SRP. At one farm, a high infection incidence (21%) was found for D. fangzhongdai in tubers. The isolated pathogen was able to cause potato blackleg. At two other farms, high infection incidences in tubers were found with P. brasiliense (35-39%) and P. parmentieri (12-19%), whereas the incidence of P. brasiliense in leaves was also high (8%). In conclusion, high infection incidences with BL-SRP in potatoes can be found in a PB1 crop at the end of the growing season. Infections in individual plants were found either in tubers or in leaves. The potential sources of initial infection are discussed.

A novel point-of-care device accurately measures thyrotropin in whole blood, capillary blood and serum.

OBJECTIVES: Point-of-care (POC) measurement of thyrotropin (TSH) may facilitate prompt diagnosis of thyroid dysfunction. We evaluated the analytical performance of a new POC TSH assay (Wondfo). METHODS: TSH measurements were made from 730 consecutive, unselected subjects in an outpatient setting, using Wondfo in whole blood, capillary blood and serum or automated reference equipment (serum only). RESULTS: TSH measurements were user-independent. Total intra-and inter-assay variation (CV%) was 12.1 and 16.2%, respectively. Total CV% was 10.6-22.6% and 14.5-21.6% in serum and whole blood, respectively. Linearity was very good. Recovery rate was 97-127%. Prolongation of incubation time increased TSH results of 12% (13%) and 33% (35%) after 2 and 5 additional minutes in serum (blood), respectively. When measured simultaneously in two Wondfo devices, the slope of the regression line was 1.03 (serum) and 1.02 (blood), with Spearman's correlation of 0.99 for both. TSH measurements between Wondfo and reference correlated strongly (r=0.93-0.96), though TSH measurements were lower with Wondfo (slopes of plots of measurements made using the two devices were 0.94 [serum vs. serum]; 0.83 [whole blood vs. serum] and 0.64 [capillary blood vs. serum]). Depending on sample material, TSH in capillary blood was lower vs. whole blood (slope: 0.82) and for whole blood vs. serum (Wondfo and reference method; slope: 0.69 and 0.83). Total haemolysis, but not elevated bilirubin or lipemia, disrupted TSH measurement. CONCLUSIONS: The Wondfo system was straightforward to use without need for specialist technicians and demonstrated analytic performance suitable for clinical use for the diagnosis of thyroid dysfunction.

Removal of bacterial plant pathogens in columns filled with quartz and natural sediments under anoxic and oxygenated conditions.

Irrigation with surface water carrying plant pathogens poses a risk for agriculture. Managed aquifer recharge enhances fresh water availability while simultaneously it may reduce the risk of plant diseases by removal of pathogens during aquifer passage. We compared the transport of three plant pathogenic bacteria with Escherichia coli WR1 as reference strain in saturated laboratory column experiments filled with quartz sand, or sandy aquifer sediments. E. coli showed the highest removal, followed by Pectobacterium carotovorum, Dickeya solani and Ralstonia solanacearum. Bacterial and non-reactive tracer breakthrough curves were fitted with Hydrus-1D and compared with colloid filtration theory (CFT). Bacterial attachment to fine and medium aquifer sand under anoxic conditions was highest with attachment rates of max. katt1 = 765 day-1 and 355 day-1, respectively. Attachment was the least to quartz sand under oxic conditions (katt1 = 61 day-1). In CFT, sticking efficiencies were higher in aquifer than in quartz sand but there was no differentiation between fine and medium aquifer sand. Overall removal ranged between < 6.8 log10 m-1 in quartz and up to 40 log10 m-1 in fine aquifer sand. Oxygenation of the anoxic aquifer sediments for two weeks with oxic influent water decreased the removal. The results highlight the potential of natural sand filtration to sufficiently remove plant pathogenic bacteria during aquifer storage.

The Broad Host Range Plant Pathogen Dickeya dianthicola Shows a High Genetic Diversity.

The wide host range phytopathogen D. dianthicola, first described in ornamentals in the 1950s, rapidly became a threat for potato production in Europe and, more recently, worldwide. Previous genomic analyses, mainly of strains isolated from potato, revealed little sequence diversity. To further analyse D. dianthicola genomic diversity, we used a larger genome panel of 41 isolates encompassing more strains isolated from potato over a wide time scale and more strains isolated from other hosts. The phylogenetic and pan-genomic trees revealed a large cluster of highly related genomes but also the divergence of two more distant strains, IPO 256 and 67.19, isolated from potato and impatiens, respectively, and the clustering of the three strains isolated from Kalanchoe with one more distinct potato strain. An SNP-based minimal spanning tree highlighted both diverse clusters of (nearly) clonal strains and several strains scattered in the MST, irrespective of country or date of isolation, that differ by several thousand SNPs. This study reveals a higher diversity in D. dianthicola than previously described. It indicates the clonal spread of this pathogen over long distances, as suspected from worldwide seed trading, and possible multiple introductions of D. dianthicola from alternative sources of contaminations.

Drug safety in thyroid eye disease - a systematic review.

INTRODUCTION: The autoimmune-induced thyroid eye disease (TED) is a frequent extrathyroidal manifestation of Graves' disease and less frequently of Hashimoto's thyroiditis. Pathognomonic clinical signs, i.e. exophthalmos, double vision, and inflammation of the orbital tissue cause physical, ophthalmic, and socio-psychological limitations. AREAS COVERED: PubMed and MeSH database were searched for specific guidelines, randomized controlled trials, prospective clinical studies, systematic reviews, and meta-analyses pertaining to the safety profile of currently administered immunosuppressive agents for the treatment of TED. Occurred adverse events (AE), severe AE (SAE), side effects (SE), and severe SE (SSE) were classified according to the standardized medical dictionary for regulatory activities (MedDRA). EXPERT OPINION: This novel systematic analysis offers an overview of potential AE, SAE, and SE for currently recommended immunosuppressive drugs for the treatment of TED. Nonspecific, anti-inflammatory drugs and more specific, targeted biologicals are treatment options for active and severe TED. Critical evaluation of the pertinent literature confirms an evidence-based, beneficial efficacy/risk ratio of the current first-line and second-line treatment recommendations endorsed by the European Society of Endocrinology. However, further large, well-conceived trials are mandatory to enhance our knowledge and experience with novel specific small molecules and/or monoclonal antibodies targeting the key autoantigens in TED.

Bacterial ring rot of potato caused by Clavibacter sepedonicus: A successful example of defeating the enemy under international regulations.

BACKGROUND: Bacterial ring rot of potato (Solanum tuberosum) caused by the gram-positive coryneform bacterium Clavibacter sepedonicus is an important quarantine disease threatening the potato industry around the globe. Since its original description in 1906 in Germany, management of ring rot has been a major problem due to the seedborne nature (via seed tubers not true seeds) of the pathogen allowing the bacterium to be transmitted long distances via infected tubers. DISEASE SYMPTOMS: On growing potato plants: interveinal chlorosis on leaflets leading to necrotic areas and systemic wilt. On infected tubers: vascular tissues become yellowish brown with a cheesy texture due to bacterial colonization and decay. HOST RANGE: Potato is the main host of the pathogen, but natural infection also occurs on eggplant, tomato, and sugar beet. TAXONOMIC STATUS OF THE PATHOGEN: Class: Actinobacteria; Order: Actinomycetales; Family: Microbacteriaceae; Genus: Clavibacter; Species: Clavibacter sepedonicus (Spieckermann and Kotthoff 1914) Li et al. 2018. SYNONYMS (NONPREFERRED SCIENTIFIC NAMES): Aplanobacter sepedonicus; Bacterium sepedonicum; Corynebacterium sepedonicum; Corynebacterium michiganense pv. sepedonicum; Clavibacter michiganensis subsp. sepedonicus. MICROBIOLOGICAL PROPERTIES: Gram-positive, club-shaped cells with creamy to yellowish-cream colonies for which the optimal growth temperature is 20-23°C. DISTRIBUTION: Asia (China, Japan, Kazakhstan, Nepal, North Korea, Pakistan, South Korea, Uzbekistan, the Asian part of Russia), Europe (Belarus, Bulgaria, Czech Republic, Estonia, Finland, Georgia, Germany, Greece, Hungary, Latvia, Lithuania, Norway, Poland, Romania, European part of Russia, Slovakia, Spain, Sweden, Turkey, Ukraine), and North America (Canada, Mexico, USA). PHYTOSANITARY CATEGORIZATION: CORBSE: EPPO A2 list no. 51. EU; Annex designation I/A2.

Dose-response relationship of Ralstonia solanacearum and potato in greenhouse and in vitro experiments.

Ralstonia solanacearum is the causative agent of bacterial wilt of potato and other vegetable crops. Contaminated irrigation water contributes to the dissemination of this pathogen but the exact concentration or biological threshold to cause an infection is unknown. In two greenhouse experiments, potted potato plants (Solanum tuberosum) were exposed to a single irrigation with 50 mL water (non-invasive soil-soak inoculation) containing no or 102 - 108 CFU/mL R. solanacearum. The disease response of two cultivars, Kondor and HB, were compared. Disease development was monitored over a three-month period after which stems, roots and tubers of asymptomatic plants were analyzed for latent infections. First wilting symptoms were observed 15 days post inoculation in a plant inoculated with 5x109 CFU and a mean disease index was used to monitor disease development over time. An inoculum of 5x105 CFU per pot (1.3x102 CFU/g soil) was the minimum dose required to cause wilting symptoms, while one latent infection was detected at the lowest dose of 5x102 CFU per pot (0.13 CFU/g). In a second set of experiments, stem-inoculated potato plants grown in vitro were used to investigate the dose-response relationship under optimal conditions for pathogen growth and disease development. Plants were inoculated with doses between 0.5 and 5x105 CFU/plant which resulted in visible symptoms at all doses. The results led to a dose-response model describing the relationship between R. solanacearum exposure and probability of infection or illness of potato plants. Cultivar Kondor was more susceptible to brown-rot infections than HB in greenhouse experiments while there was no significant difference between the dose-response models of both cultivars in in vitro experiments. The ED50 for infection of cv Kondor was 1.1x107 CFU. Results can be used in management strategies aimed to reduce or eliminate the risk of bacterial wilt infection when using treated water in irrigation.

Susceptibility reversed: modified plant susceptibility genes for resistance to bacteria.

Plants have evolved complex defence mechanisms to avoid invasion of potential pathogens. Despite this, adapted pathogens deploy effector proteins to manipulate host susceptibility (S) genes, rendering plant defences ineffective. The identification and mutation of plant S genes exploited by bacterial pathogens are important for the generation of crops with durable and broad-spectrum resistance. Application of mutant S genes in the breeding of resistant crops is limited because of potential pleiotropy. New genome editing techniques open up new possibilities for the modification of S genes. In this review, we focus on S genes manipulated by bacteria and propose ways for their identification and precise modification. Finally, we propose that genes coding for transporter proteins represent a new group of S genes.

Three-Dimensional Quantification of Facial Asymmetry in Children with Positional Cranial Deformity.

BACKGROUND: The extent of facial involvement in positional plagiocephaly is only little investigated so far. Investigation methods that take into account the challenging anatomical conditions and growth of infants' faces are desirable. In this study, the authors established a new three-dimensional photogrammetry quantification method evaluating pretherapeutic and posttherapeutic facial asymmetry in positional plagiocephaly. Furthermore, a facial asymmetry index was established and evaluated. METHODS: Three-dimensional photographs of 100 children undergoing treatment with head orthoses were analyzed by constructing a standardized interindividual coordinate system. Defining landmarks, section planes, and point coordinates with a computer-aided design software, both sides of the faces were compared. Facial asymmetry was quantified by measuring differences between left and right sides and pretherapeutic and posttherapeutic changes in each patient. The facial asymmetry index was calculated by putting the absolute differences in relation with the coordinates of the nonaffected side. RESULTS: Present results indicate that positional plagiocephaly results in a distinct facial asymmetry (range, -3.8 to 9.6 mm) in nearly all spatial directions and facial regions. Helmet therapy led to a significant reduction (p < 0.05) of intraindividual facial asymmetry (median change in facial asymmetry index, -1.9 to 3.1 percent). However, no correlation of the Cranial Vault Asymmetry Index and facial asymmetry (Spearman rank correlation coefficient, ρ = -0.09 to 0.47) has been seen. According to these results, severe occipital deformation does not necessarily provoke distinct facial asymmetry. CONCLUSIONS: Present three-dimensional photogrammetry method allows the longitudinal quantification of facial involvement in positional plagiocephaly. Asymmetry has been determined in all facial regions. The facial asymmetry decreased through helmet therapy but was not eliminated completely.

Plug-and-play laser ablation-mass spectrometry for molecular imaging by means of dielectric barrier discharge ionization.

The plug-and-play hyphenation of UV-laser ablation (LA) and mass spectrometry is presented, using dielectric barrier discharge ionization (DBDI). The DBDI source employed here is characterized by its unique geometry, being directly mounted onto the inlet capillary of a mass spectrometer. In the literature, this particular kind of DBDI source is also referred to as active capillary plasma ionization. It has been commercialized as soft ionization by chemical reaction in transfer (SICRIT) and will be addressed as DBDI in this study. LA-DBDI-MS was used for the direct, molecule-specific and spatially resolved analysis of various solid samples, such as coffee beans and pain killer tablets without extensive sample preparation. The combination of fast washout UV-laser ablation and the principle of the DBDI source used here allowed for highly efficient soft ionization as well as high spatial resolution down to 10 µm for molecular imaging.

Gas Chromatography-Atmospheric Pressure Inlet-Mass Spectrometer Utilizing Plasma-Based Soft Ionization for the Analysis of Saturated, Aliphatic Hydrocarbons.

Soft ionization by a chemical reaction in transfer (SICRIT) is applied to couple gas chromatography (GC) to a high-resolution atmospheric pressure inlet mass spectrometer. These instruments are generally used in combination with liquid chromatography systems (LC-MS). Ionization of alkanes is not possible here with conventional electrospray ionization. Alternatively, separate GC-electron ionization (EI)-MS is employed for the analysis of nonpolar substances like alkanes, however, with the inherent challenge of strong fragmentation. In the case of alkanes, the determination of molecular masses becomes nearly impossible in complex hydrocarbon mixtures because of the wealth of similar fragment ions and the absence of the molecular ion signal. SICRIT, a soft ionization technique based on dielectric barrier discharge (DBDI), produces characteristic oxidized cations from alkanes that can be directly correlated to their molecular mass. Isotope labeling experiments reveal an ionization mechanism via hydride abstraction and reaction with water. Soft ionization can be achieved for iso- and n-alkanes, with very little fragmentation, enabling the determination of their molecular mass. Calibrations for n-alkanes from C10 to C30 were performed exhibiting high linearity, reproducibility, and sensitivity with an average LOD of 69 pg (on column). Measurements of diesel fuel samples are compared to traditional GC-EI-MS. The presented method combines sensitivity and easy handling of a GC-EI-MS with the determination of molecular mass commonly only achieved with field ionization (FI)-MS, while using existing and highly optimized mass spectrometers commonly coupled with LC. Additionally, many other analytes such as (alkylated-) PAHs could be detected simultaneously in the diesel sample.