Enhanced Transport at High Plasma Pressure and Subthreshold Kinetic Ballooning Modes in Wendelstein 7-X.

High-performance fusion plasmas, requiring high pressure ß, are not well understood in stellarator-type experiments. Here, the effect of ß on ion-temperature-gradient-driven (ITG) turbulence is studied in Wendelstein 7-X (W7-X), showing that subdominant kinetic ballooning modes (KBMs) are unstable well below the ideal MHD threshold and get strongly excited in the turbulence. By zonal-flow erosion, these subthreshold KBMs (stKBMs) affect ITG saturation and enable higher heat fluxes. Controlling stKBMs will be essential to allow W7-X and future stellarators to achieve maximum performance.

Erratum: Available Energy of Trapped Electrons and Its Relation to Turbulent Transport [Phys. Rev. Lett. 128, 175001 (2022)].

This corrects the article DOI: 10.1103/PhysRevLett.128.175001.

Available Energy of Trapped Electrons and Its Relation to Turbulent Transport.

Any collisionless plasma possesses some "available energy" (AE), defined as that part of the thermal energy that can be converted into instabilities and turbulence. Here, we present a calculation of the AE carried by magnetically trapped electrons in a flux tube of collisionless plasma. The AE is compared with nonlinear simulations of the energy flux resulting from collisionless turbulence driven by trapped-electron modes in various magnetic geometries. The numerical calculation of AE is rapid and shows a strong correlation with the simulated energy fluxes, which can be expressed as a power law and understood in terms of a simple model.

Turbulence Mechanisms of Enhanced Performance Stellarator Plasmas.

We theoretically assess two mechanisms thought to be responsible for the enhanced performance observed in plasma discharges of the Wendelstein 7-X stellarator experiment fueled by pellet injection. The effects of the ambipolar radial electric field and the electron density peaking on the turbulent ion heat transport are separately evaluated using large-scale gyrokinetic simulations. The essential role of the stellarator magnetic geometry is demonstrated, by comparison with a tokamak.

Controlling turbulence in present and future stellarators.

Turbulence is widely expected to limit the confinement and, thus, the overall performance of modern neoclassically optimized stellarators. We employ novel petaflop-scale gyrokinetic simulations to predict the distribution of turbulence fluctuations and the related transport scaling on entire stellarator magnetic surfaces and reveal striking differences to tokamaks. Using a stochastic global-search optimization method, we derive the first turbulence-optimized stellarator configuration stemming from an existing quasiomnigenous design.

Rapid identification of compound mutations in patients with Philadelphia-positive leukaemias by long-range next generation sequencing.

An emerging problem in patients with Philadelphia (Ph)-positive leukaemias is the occurrence of cells with multiple mutations in the BCR-ABL1 tyrosine kinase domain (TKD) associated with high resistance to different tyrosine kinase inhibitors. Rapid and sensitive detection of leukaemic subclones carrying such changes, referred to as compound mutations, is therefore of increasing clinical relevance. However, current diagnostic methods including next generation sequencing (NGS) of short fragments do not optimally meet these requirements. We have therefore established a long-range (LR) NGS approach permitting massively parallel sequencing of the entire TKD length of 933bp in a single read using 454 sequencing with the GS FLX+ instrument (454 Life Sciences). By testing a series of individual and consecutive specimens derived from six patients with chronic myeloid leukaemia, we demonstrate that long-range NGS analysis permits sensitive identification of mutations and their assignment to the same or to separate subclones. This approach also facilitates readily interpretable documentation of insertions and deletions in the entire BCR-ABL1 TKD. The long-range NGS findings were reevaluated by an independent technical approach in select cases. Polymerase chain reaction (PCR) amplicons of the BCR-ABL1 TKD derived from individual specimens were subcloned into pGEM®-T plasmids, and >100 individual clones were subjected to analysis by Sanger sequencing. The NGS results were confirmed, thus documenting the reliability of the new technology. Long-range NGS analysis therefore provides an economic approach to the identification of compound mutations and other genetic alterations in the entire BCR-ABL1 TKD, and represents an important advancement of the diagnostic armamentarium for rapid assessment of impending resistant disease.

Resilience of quasi-isodynamic stellarators against trapped-particle instabilities.

It is shown that in perfectly quasi-isodynamic stellarators, trapped particles with a bounce frequency much higher than the frequency of the instability are stabilizing in the electrostatic and collisionless limit. The collisionless trapped-particle instability is therefore stable as well as the ordinary electron-density-gradient-driven trapped-electron mode. This result follows from the energy balance of electrostatic instabilities and is thus independent of all other details of the magnetic geometry.

A multi-site study using high-resolution HLA genotyping by next generation sequencing.

The high degree of polymorphism at human leukocyte antigen (HLA) class I and class II loci makes high-resolution HLA typing challenging. Current typing methods, including Sanger sequencing, yield ambiguous typing results because of incomplete genomic coverage and inability to set phase for HLA allele determination. The 454 Life Sciences Genome Sequencer (GS FLX) next generation sequencing system coupled with conexio atf software can provide very high-resolution HLA genotyping. High-throughput genotyping can be achieved by use of primers with multiplex identifier (MID) tags to allow pooling of the amplicons generated from different individuals prior to sequencing. We have conducted a double-blind study in which eight laboratory sites performed amplicon sequencing using GS FLX standard chemistry and genotyped the same 20 samples for HLA-A, -B, -C, DPB1, DQA1, DQB1, DRB1, DRB3, DRB4, and DRB5 (DRB3/4/5) in a single sequencing run. The average sequence read length was 250 base pairs and the average number of sequence reads per amplicon was 672, providing confidence in the allele assignments. Of the 1280 genotypes considered, assignment was possible in 95% of the cases. Failure to assign genotypes was the result of researcher procedural error or the presence of a novel allele rather than a failure of sequencing technology. Concordance with known genotypes, in cases where assignment was possible, ranged from 95.3% to 99.4% for the eight sites, with overall concordance of 97.2%. We conclude that clonal pyrosequencing using the GS FLX platform and CONEXIO ATF software allows reliable identification of HLA genotypes at high resolution.

Overcoming methodical limits of standard RHD genotyping by next-generation sequencing.

BACKGROUND AND OBJECTIVES: Molecular variations of the RHD gene may result in the reduced expression of the D antigen and altered Rh phenotypes. In many occasions, they cannot be typed reliably by standard serological methods. Sequence-based typing is the gold standard to determine rare and unknown RHD genotypes. For this pilot study, sequence-based typing by standard Sanger sequencing was compared to a newly established next-generation sequencing approach based on pyrosequencing. MATERIALS AND METHODS: Twenty-six DNA samples were selected after primary serological testing exhibiting a weak reaction in Rh phenotype. Parallel sequence analysis of the complete coding sequence including adjacent intronic sequences allowed a comparison of the methodical potency in mutation detection of Sanger with next-generation sequencing. RESULTS: Sanger sequencing revealed 39 RHD polymorphisms in 21 of 26 samples in the RHD coding region, while pyrosequencing detected all but two alterations resulting in a concordance rate of 94·9% and clearly revealed a heterozygous compound mutation in one sample with RHDψ and Weak D type 4 alleles. The resolution of cis/trans linkage of polymorphisms and exact characterization of a 37 bp duplication was achieved by next-generation sequencing. CONCLUSION: Our data suggest that next-generation sequencing offers a new development for high-throughput and clonal sequencing for molecular RHD genotyping. However, further attempts in the methodical set-up have to be undertaken prior to validation and introduction as a routine service.

Characterisation of two novel HLA alleles, HLA-Cw*0429 and HLA-DRB3*0223.

We report here the novel human leukocyte antigens (HLA)-Cw*0429 and HLA-DRB3*0223 alleles identified during routine cord blood characterisation by sequence-based typing.

Introduction of a real-time-based blood-group genotyping approach.

BACKGROUND AND OBJECTIVE: Genotyping may be applied for rare blood group polymorphisms in a high-throughput mode as well for the molecular determination of blood groups due to unclear serological results. MATERIAL AND METHODS: We developed and validated a DNA typing method for the determination of KEL1/2, JK1/2, FY1/2, FY0, MNS1/2, MNS3/4, DO1/2, CO1/2 and LU1/2 alleles using a melting curve analysis downstream from a fully automated DNA extraction. All assays were validated in terms of specificity, sensitivity, assay variability and robustness. The usability was proven by a batch of 200 blood samples with partially known phenotype. RESULTS: Assays for all blood groups were within the range of specificity (100%), assay variability and robustness (coefficient of variance < 3%). Genotypes of 200 random platelet donors were fully consistent with existing phenotype data. The obtained genotype distribution is in complete concordance with existing data for the European population underlined by a complete absence of CO2 homozygous donors and the FY0 allele among the cohort. CONCLUSION: We introduce an approach for blood group genotyping of particular samples or gene loci in glass capillary format and for medium-throughput analysis in 96/384-well format. The advantages of this real-time polymerase chain reaction method are its automation potential, the flexibility regarding hardware and the rapid cycling time.

Long-term high protein intake does not increase oxidative stress in rats.

The maximum dietary protein intake that does not cause adverse effects in a healthy population is uncertain. We tested whether a high protein intake enhances oxidative stress. Adult rats were adapted to different casein-based diets containing either an adequate (13.8%; AP), medium (25.7%; MP), or high (51.3%; HP) level of crude protein; a fourth group received a HP diet but no RRR-alpha-tocopherol acetate (HP-toc). After 15 wk of feeding, plasma protein carbonyl concentration, liver lipid peroxide levels [thiobarbituric acid-reacting substances (TBARS)], reduced glutathione (GSH) status and leucine kinetics ([1-(13)C]leucine) were measured. Higher concentrations of protein carbonyls and TBARS were found in rats fed the AP and the HP-toc diets compared with those fed the MP and HP diets (P: < 0.05). GSH concentrations in plasma did not differ but total blood GSH concentrations were significantly (P: < 0.05) lower in rats fed the HP-toc diet compared with those fed the AP, MP and HP diets. Liver GSH concentrations were significantly (P: < 0.01) lower in rats fed the AP diet compared with the other groups. Rates of postabsorptive leucine oxidation (LeuOX) and flux (Q(Leu)) were positively correlated with the dietary protein level (for AP, MP, and HP, respectively: LeuOX, 74.9 +/- 28.5, 109 +/- 35.2, 142.3 +/- 38.4 micromol/(kg. h); Q(Leu), 425 +/- 102, 483 +/- 82, 505 +/- 80 micromol/(kg. h). Only HP-toc resulted in a significantly greater protein breakdown (PB(Leu)) and Q(Leu). No difference was seen in nonoxidative leucine disposal. Long-term intake of high protein diets did not increase variables of oxidative stress, in contrast to our initial hypothesis. An unexpected finding was that adequate protein feeding (AP) may in fact induce oxidative stress.

The full length HLA-G1 and no other alternative form of HLA-G is expressed at the cell surface of transfected cells.

In contrast to HLA class Ia, the HLA-G class Ib transcripts can be alternativeley spliced to yield several isoforms including four potentially membrane-bound variants, namely HLA-G1, -G2, -G3 and G4. It is so far unclear whether each of these splice variants lacking one or two external domains is properly translated and expressed at the cell surface. We used targeted Enhanced Green Fluorescence Protein (EGFP)-HLA-G fusion cDNA to track HLA-G isoform expression in living murine (L-human beta2m) and human (JAR) transiently transfected cells. It was demonstrated that the four HLA-G1, -G2, -G3, and -G4 isoforms were translated in these transfectants by the means of (i) Western blotting analysis, using an anti-EGFP mAb; (ii) intracellular double labeling flow cytometry analysis, using the EGFP natural fluorescence and phycoerythrin-labeled HCA2 anti-HLA-G mAb; and (iii) immunocytochemistry on isolated acetone fixed transfectants with the use of different anti-HLA-G mAbs. Cell surface flow cytometry analysis using the HCA2 mAb revealed that only the HLA-G1 isoform was expressed as a membrane-bound protein. Two color confocal microscopy performed on fixed, permeabilized cells further showed that the EGFP green fluorescence co-localized with anti-calnexin rhodamine fluorescence in the four HLA-G isoform transfectants but only in HLA-G1 transfectant was the green EGFP fluorescence also detectable at the outer part of the cells, suggesting that the HLA-G2, -G3, and G4 were retained in the endoplasmic reticulum. Such intracellular retention of the three shorter forms of HLA-G suggest that they may play a role in regulating cell surface expression either of the full length HLA-G1 form or of HLA-E.

Tubal versus uterine placentation: similar HLA-G expressing extravillous cytotrophoblast invasion but different maternal leukocyte recruitment.

The nonclassical HLA-G class I gene is expressed by extravillous cytotrophoblast that invades decidua in uterine pregnancy, suggesting that it may contribute to the immunological mechanisms that protect the fetus against maternal alloimmune response and/or pathogen infections. We first addressed the question of whether HLA-G expression was dependent on maternal tissue environment by comparing uterine and ectopic tubal pregnancies. Using HLA-G-specific mAb on placental cryosections, we found by immunohistochemistry that all subtypes of extravillous cytotrophoblast similarly expressed HLA-G in pregnant tubes, demonstrating that its expression was independent of the site of implantation. We next compared by immunohistochemistry the phenotype of maternal leukocytes recruited in both pregnant tissues. In contrast to decidua, pregnant tubes were characterized firstly, by the lack of natural killer (NK) cells and of cells expressing CD94 receptor specific for HLA-E, secondly, by a prominent increase of CD8+ T cells, dendritic cells, and macrophages, the latter co-expressing the LIR1/ILT2 killer immunoglobulin-like receptor (KIR), and finally, by the presence of cells expressing LIR2/ILT4 KIR or BY55 NK receptors, known to bind to HLA-G. Such cell types may favor a unique innate defense in pregnant tubes. These observations also suggest that trophoblast HLA-G expression does not influence the recruitment of particular maternal leukocytes in pregnant tissues.

Placental HLA-G protein expression in vivo: where and what for?

In contrast to HLA-A and -B class Ia genes that are down-regulated in human trophoblast cells, HLA-G class Ib molecules are expressed in the placenta throughout gestation. In addition to extravillous cytotrophoblast that invade the decidua basalis essentially, HLA-G was also observed in endothelial cells of fetal vessels in the chorionic villi as well as in amnion cells and amniotic fluid. Both membrane-bound and soluble HLA-G isoforms have been detected. In view of the recently published functional data showing that HLA-G: (i) has the capability to bind and present peptides; (ii) is recognized by at least three different killing inhibitory receptors; and (iii) is a regulator of HLA-E expression, we can predict that such functions are likely to be exerted by extravillous cytotrophoblast. Of particular importance will be the anti-viral function of HLA-G at this materno-fetal interface, knowing that HLA-G was shown to be expressed by thymic medullary epithelial cells. In addition to these immunological functions, due to its presence on chorionic fetal endothelial cells, we hypothesize that HLA-G could also be a regulator of chorionic villous angiogenesis. Finally, soluble HLA-G isoforms may act as specific immunosuppressors during pregnancy.

First trimester human endovascular trophoblast cells express both HLA-C and HLA-G.

PROBLEM: In human pregnancies, trophoblasts, in contrast to placental connective tissue and the fetus itself, come into direct contact with the maternal allorecognizing system at special sites. Villous syncytiotrophoblasts washed around by maternal blood lack HLA class I proteins, whereas extravillous trophoblasts, which deeply invade maternal uterine tissues, express high amounts of HLA-G and also HLA-C, the latter to a lesser degree, however. A subpopulation of extravillous trophoblasts, the endovascular trophoblast, enters maternal spiral artery lumen and, like syncytiotrophoblast, comes into direct contact with maternal blood. Less is known about HLA class I distribution on this endovascular trophoblast subpopulation. METHOD OF STUDY: A comparative immununohistochemical analysis was done on decidual cryo-sections containing trophoblast-invaded spiral arteries using different anti-HLA class I monoclonal antibodies (mAbs) and a peroxidase-labeled streptavidinbiotin detection system. RESULTS: MAbs W6/32 (anti-HLA-A, -B, -C, -G), HCA2 (anti-HLA-A, -G) G233 and 87G (both anti-HLA-G) resulted in strong positivity on endovascular trophoblasts. L31 (anti-HLA-C) and HC10 (anti-HLA-B, -C) revealed clear positivity, whereas TU149 (anti-HLA-B, -C, some -A) produced a heterogeneous staining pattern, faintly positive on some endovascular trophoblastic cells and negative on others. MAb LA45 (anti-HLA-A, -B) did not bind to any endovascular trophoblast, neither did BFL.1 (anti-HLA-G) nor 16G1 (anti-HLA-G, soluble). CONCLUSION: This study shows that trophoblastic cells belonging to the endovascular subpopulation express considerable amounts of HLA-G and slightly less HLA-C.

Plasma protein carbonyl concentration is not enhanced by chronic intake of high-protein diets in adult rats.

We tested the hypothesis of whether high dietary protein intake is linked to oxidative stress as measured by the concentration of reactive carbonyl residues in plasma proteins. Three groups of male Wistar rats ( approximately 230 g, n = 10) were fed either 15% (15C), 30% (30C), or 60% (60C) casein diets over a period of 18 weeks. For comparison, a vitamin E deficient diet (60C-E) based on diet 60C was given to an additional group to provoke oxidative stress. Concentrations of alpha-tocopherol in plasma and of reactive carbonyl residues in total plasma proteins were measured by high performance liquid chromatography using fluorescence and by diode array detection after 2,4-dinitrophenylhydrazine reaction, respectively. After 1 week the concentration of reactive carbonyl residues in plasma proteins was found to be significantly (P < 0.05) higher in the 60C and 60C-E groups ( approximately 2.7 nmol/mg protein) compared with the 15C and 30C groups ( approximately 1.7 nmol/mg protein). After 14 weeks the 15C (3.4 +/- 1.2 nmol/mg protein) and 60C-E groups (3.9 +/- 1.7 nmol/mg protein) showed a significantly increased concentration of reactive carbonyl residues in plasma protein compared with the 30C and 60C groups (2.5 +/- 1.0 nmol/mg protein; 2.6 +/- 0.8 nmol/mg protein). As expected, chronic vitamin E deficiency (60C-E) resulted in significantly decreased alpha-tocopherol concentrations (3.91 +/- 2.42 micromol/mL vs. 31.3 +/- 4.8 micromol/mL) and a higher concentration of reactive carbonyl residues in plasma proteins. These results do not support the hypothesis that a chronic intake of high-protein diets leads to oxidative stress in adult rats. However, in the non-adapted state (1 week) a high protein intake contributes to oxidative modifications of protein-bound amino acid residues.

Low nutritional quality of unconventional tropical crop seeds in rats.

As the search for alternative sources of food to alleviate hunger continues, this study was undertaken to determine the biological value in growing rats (BV) of proteins of some lesser known tropical seeds gathered in Nigeria. Antinutritional factors (trypsin inhibitors, phytic acid, oxalate, tannin, alkaloids) and amino acid compositions were also determined, and protein digestibility-corrected amino acid score (PDCAAS) was calculated using the amino acid requirement pattern of the preschool child and individual seed-specific correction factors for crude protein. A rat growth and balance study was conducted to determine digestibility, nitrogen-, and energy balance by feeding as the only unsupplemented protein source milled and heat-treated seeds of Adansonia digitata (Bombacaceae) and Prosopis africana, Lonchocarpus sericeus, Enterolobium cyclocarpium, Sesbania pachycarpa and Pterocarpus osun (Leguminosae) in comparison to casein fortified with methionine (control). Diets containing P. africana and L. sericeus seeds caused poor feed intake and weight loss in rats and were excluded from the nitrogen-balance test. Among the seed samples, S. pachycarpa followed by A. digitata showed the most advantageous nutritional quality [amino acid composition, digestibility, BV and net protein utilization (NPU)]. True digestibility was 82.9 and 74.5 vs. 98.5, BV was 64.6 and 70.0 vs. 90.4, and NPU was 53.5 and 52.1 vs. 89.0 for S. pachycarpa and A. digitata vs. casein (control), respectively. In terms of PDCAAS, lysine was the first limiting amino acid for S. pachycarpa (88%) and for A. digitata (58%). The PDCAAS of all essential amino acids was below 100% for E. cyclocarpium (e.g., cysteine + methionine: 37%) and for P. africana (e.g., threonine: 46%, except valine and a very high content of cysteine and methionine). In conclusion, all seeds tested in the rat balance trial were of inferior quality compared to casein. Before these tropical seeds could be used as food components or feed supplements, safety studies and proper processing to remove antinutritional factors and possible toxic constituents were required.

Dietary guar gum and pectin stimulate intestinal microbial polyamine synthesis in rats.

The effects of two highly fermentable dietary fibers (guar gum and pectin) on the type and concentrations of cecal polyamines as affected by the intestinal microflora were studied in groups of germ-free (n = 10/group) and conventional rats (n = 6/group). Both germ-free and conventional rats were randomly assigned to one of three treatments as follows: 1) fiber-free control diet, 2) control diet + 10% guar gum and 3) control diet + 10% pectin. In germ-free rats, guar gum and pectin had no effect on cecal polyamine concentrations. Putrescine was confirmed to be the major endogenous polyamine within the gut lumen. In cecal contents of conventional rats, both guar gum and pectin led to the appearance of cadaverine and to elevated putrescine concentrations in comparison with the fiber-free control diet (1.35 +/- 0.15 and 2.27 +/- 0.32, respectively, vs. 0.20 +/- 0.03 micromol/g dry weight, P < 0.05). The cecal cadaverine concentration was higher in pectin- than in guar-fed rats (8.20 +/- 0.89 vs. 1.92 +/- 0.27 micromol/g dry weight, P < 0.05). Counts of total bacteria, bacteroides, fusobacteria and enterobacteria were higher (P < 0.05) in rats fed guar gum and pectin. Bifidobacteria were found exclusively in guar-fed rats. In vitro studies on selected species representing the numerically dominant population groups of the human gut flora (bacteroides, fusobacteria, anaerobic cocci and bifidobacteria) were examined for their ability to synthesize intracellular polyamines. These experiments demonstrated the ability of bacteroides, fusobacteria and anaerobic cocci to synthesize high amounts of putrescine and spermidine. Calculations based on these results suggest that the intestinal microflora are a major source of polyamines in the contents of the large intestine.

Feeding resistant starch affects fecal and cecal microflora and short-chain fatty acids in rats.

The effects of different forms of resistant potato starch (RS) on the major microbial population groups and short-chain fatty acids (SCFA) in the cecum and feces of rats were studied over a 5-mo feeding period. Thirty 8-wk-old male Wistar rats, averaging 210 g initial body weight, were adapted for 7 d to a balanced basal diet containing 60% waxy maize starch devoid of any RS. On d 8, three groups of 10 rats each were fed diets containing the following forms of starch: 1) rapidly digestible waxy maize starch (basal diet), 2) a mixture of 83.3% waxy maize starch and 16.7% native granular potato starch (RS 1), or 3) a mixture of 33.3% waxy maize starch and 66.7% modified potato starch (RS 2). The final RS content in RS 1 and RS 2 was 10%. Fecal samples were collected at d 8 and 1, 3, and 5 mo after the start of the experiment. Cecal contents were taken after 5 mo. The colony counts of microbial groups did not vary with time in the control or the RS 1 group (P > .05). Only the number of Bacteroides/fusobacteria decreased between mo 1 and 5 in rats fed RS 1 (P < .05). The RS 2 diet led to a significant increase in total culturable bacteria, lactobacilli, streptococci, and enterobacteria between mo 1 and 5. The RS 1 and RS 2 diets stimulated the growth of bifidobacteria. Cecal numbers of lactobacilli, streptococci, and enterobacteria were higher in rats fed RS 2 than in rats fed RS 1 or control diet (P < .05). Lactobacillus cellobiosus occurred only in rats fed RS 1 or RS 2. Acetate increased in mo 3 compared with d 8 in all groups (P < .05). The fecal and cecal SCFA displayed higher concentrations of acetate and propionate and a higher molar proportion of propionate in RS 2 than in RS 1 or control rats (P < .05). Stimulation of bifidobacteria, lactobacilli, and SCFA may be useful for the suppression of pathogenic organisms in the colon.