Genomic comparison of two strains of Mycobacterium avium subsp. paratuberculosis with contrasting pathogenic phenotype

In a previous study, we evaluated the degree of virulence of Mycobacterium avium subsp. paratuberculosis (Map) strains isolated from cattle in Argentina in a murine model. This assay allowed us to differentiate between high-virulent MapARG1347 and low-virulent MapARG1543 strains. To corroborate whether the differences in virulence could be attributed to genetic differences between the strains, we performed Whole Genome Sequencing and compared the genomes and gene content between them and determined the differences related to the reference strain MapK10. We found 233 SNPs/INDELS in one or both strains relative to Map K10. The two strains share most of the variations, but we found 15 mutations present in only one of the strains. Considering NS-SNP/INDELS that produced a severe effect in the coding sequence, we focus the analysis on four predicted proteins, putatively related to virulence. Survival of MapARG1347 strain in bMDM was higher than MapARG1543 and was more resistant to acidic pH and H₂O₂ stresses than MapK10. The genomic differences between the two strains found in genes MAP1203 (a putative peptidoglycan hydrolase), MAP0403 (a putative serine protease) MAP1003c (a member of the PE-PPE family) and MAP4152 (a putative mycofactocin binding protein) could contribute to explain the contrasting phenotype previously observed in mice models.

AB1356 QUANTITATIVE ANALYSIS BY SODIUM AND PROTON BASED 3-TESLA MR IMAGING OF THE ACHILLES TENDON

Background

Decrease of proteoglycan is the initiating stage of post-inflammatory tissue degradation. Sodium MRI is promising great potential for identification and monitoring of proteoglycan changes in tendons and cartilage associated with inflammatory and degenerative musculoskeletal diseases, where the Achilles tendon is frequently affected.

Objectives

Proof-of-concept study to examine the usage of sodium MRI in quantifying sodium concentrations in the Achilles tendon in healthy volunteers.

Methods

Sodium (23Na) MR imaging of the Achilles tendon together with established proton (1H) MRI sequences were performed in 10 healthy volunteers (6 males, 4 females, age 29 ± 9 years) using a dual-tuned 23Na/1H surface coil (RAPID Biomedical GmbH, Würzburg-Rimpar, Germany). Imaging was performed using a 3D density adapted radial sequence [1] providing sufficient signal-to-noise ratio for sodium imaging. Reference tubes on the backside of the coil were used to enable assessment of sodium concentration from sodium signal-to-noise ratio maps. Sodium concentrations were determined for tendon insertion into calcaneus bone (INS), middle portion of the tendon (MID) and muscle-tendon junction (MTJ) and for the whole Achilles tendon. Statistical differences were analysed by Wilcoxon test.

Results

Sodium concentrations c [mM] of the Achilles tendon could be quantified in all 10 (exemplary selected volunteer is shown in Figure 1). Significantly higher sodium concentrations were obtained in INS compared to MID (p=0.002) and MTJ (p=0.002) and in MID compared to MTJ (p=0.037). The average sodium concentration of the whole Achilles tendon was 57.23±17.69 mM with only minor outliers in this healthy population.

Figure 1.

Sodium concentrations of the Achilles tendon. Highest sodium concentrations c(mM) were observed at the tendon insertion into calcaneus bone (INS), whereas lower concentrations were measured in the middle portion of the tendon (MID) and muscle-tendon junction (MTJ).

Conclusion

Performance of quantitative sodium imaging of the Achilles tendon in a high-field MRI machine is feasible for assessing sodium concentrations, a surrogate biomarker for proteoglycan content. Molecular MR studies investigating changes in the proteoglycan content of the Achilles tendon in patients with inflammatory and degenerative musculoskeletal diseases could support early diagnosis or therapy monitoring in the future.

References

[1]Nagel et al. Magn Reson Med (2009) 62(6):1565-73. DOI: 10.1002/mrm.22157

Disclosure of Interests

None declared

POS0096 SJÖGREN’S DISEASE AND SYSTEMIC LUPUS ERYTHEMATOSUS DDX6-CXCR5 RISK INTERVALS REVEAL COMMON SNPS WITH FUNCTIONAL SIGNIFICANCE IN IMMUNE AND SALIVARY GLAND CELLS

Background

Sjögren’s Disease (SjD) and Systemic Lupus Erythematosus (SLE) are autoimmune diseases with several shared characteristics and similar genome-wide significant associations with the DDX6-CXCR5 locus. DDX6 suppresses interferon-stimulated gene expression and CXCR5 regulates T cell functions implicated in autoimmunity.

Objectives

To identify and characterize functional SNPs in the DDX6-CXCR5 interval.

Methods

ImmunoChip data from European populations (3785 SLE cases; 1916 SjD cases; 6893 controls) were imputed and SNP-trait associations tested. Bayesian statistics defined a credible SNP set that was refined using bioinformatic analyses (RegulomeDB, Haploreg, ENCODE, promoter capture Hi-C, eQTLs, etc.). Electrophoretic mobility shift assays (EMSAs) and luciferase expression assays were used to test allele-specific SNP function in EBV-transformed B (EBV B) cells, Daudi B cells, Jurkat T cells, THP1 monocytes, and A253 salivary gland cell lines. Chromatin conformation capture with quantitative PCR (3C-qPCR) was used to assess long-range chromatin interactions.

Results

Fine mapping of the SjD and SLE associations found similar SNP associations. Bioinformatic analyses identified 5 common SNPs with strong evidence of functionality in immune cell types: rs57494551 in an intron of DDX6, and rs4938572, rs4936443, rs7117261, and rs4938573 in the promoter/enhancer region of DDX6 and CXCR5. EMSAs and luciferase experiments showed cell type-specific differences in protein binding and promoter or enhancer activity, respectively, at each SNP. Risk allele of rs57494551 increased enhancer activity in B cells and A253 cells (p<0.001), but decreased promoter activity in T cells and A253 cells (p<0.01). SNP rs4938572 is an eQTL of DDX6 in T cells, and the risk allele significantly increased protein binding, promoter and enhancer activity in T cells (p<0.01). Risk allele of rs4938572 also increased promoter activity in A253 cells (p<0.001), but had no effect on promoter or enhancer activity in B cells. SNP rs4936443 showed no promoter or enhancer activity in immune cells, but the risk allele showed significant promoter and enhancer (p<0.001) activity in A253 cells. SNP rs7117261 showed decreased enhancer activity in EBV B cells, T cells, and A253 cells (p<0.05) and increased promoter activity in A253 cells (p<0.001). SNP rs4938573 showed decreased promoter activity in EBV B cells, T cell and A253 cells (p<0.05), decreased promoter activity in EBV B cells (p<0.05), and increased enhancer activity in A253 cells (p<0.0001). Overall, A253 cells exhibited more allele-specific effects on promoter and enhancer activity across the five SNPs compared to tested immune cells. In addition to DDX6 and CXCR5, rs57494551 and/or rs4938572 are reported eQTLs for several other genes of interest in the local chromatin regulatory network: IL10RA in T cells, TRAPPC4 in salivary gland and activated macrophages, and long non-coding (lnc)RNA AP002954.1 in T cells and whole blood. 3C-qPCR in EBV B and A253 cells showed that the two regulatory regions carrying rs4938572 or rs57494551 interacted with a region upstream of DDX6 that includes AP002954.1. Hi-C data showed looping between AP002954.1 and the regulatory region carrying rs4938572 and rs57494551 in T cells.

Conclusion

SjD and SLE share similar genomic architecture across the DDX6-CXCR5 risk interval with several common SNPs showing immune and salivary gland cell type-specific allelic effects on protein binding and/or enhancer/promoter activity. Extensive bioinformatic analyses suggest that the SNPs likely work within the local chromatin regulatory network to regulate cell type-specific expression of several genes on the interval. Ongoing studies will use 3C-qPCR to assess allele-specific chromatin interactions between the SNPs and these genes in different cells types, and CRISPR to determine how the risk alleles alters expression.

Disclosure of Interests

Mandi M Wiley: None declared, Bhuwan Khatri: None declared, Kandice L Tessneer: None declared, Michelle L Joachims: None declared, Anna M Stolarczyk: None declared, Anna Nagel: None declared, Astrid Rasmussen: None declared, Simon J. Bowman Consultant of: Abbvie, Galapagos, and Novartis in 2020-2021, Lida Radfar: None declared, Roald Omdal: None declared, Marie Wahren-Herlenius: None declared, Blake M Warner: None declared, Torsten Witte: None declared, Roland Jonsson: None declared, Maureen Rischmueller: None declared, Patrick M Gaffney: None declared, Judith A. James: None declared, Lars Ronnblom: None declared, R Hal Scofield: None declared, Xavier Mariette: None declared, Wan Fai Ng: None declared, Kathy Sivils Employee of: current employee of Janssen., Gunnel Nordmark: None declared, Betty Tsao: None declared, Christopher Lessard: None declared

POS0456 AUTOPHAGY-RELATED RISK LOCI IN SLE AND THEIR ROLE IN NEUTROPHILS

Background

Systemic lupus erythematous (SLE) is an autoimmune disease with ~150 established susceptibility risk loci. Genome wide-association (GWA) studies in SLE cases and controls of Korean ancestry identified the SLE risk locus ATG16L2-P2RY2, and rs11235604 as a SLE-associated missense variant (R220W) of Autophagy Related 16 Like 2 (ATG16L2) [1]. PRDM1-ATG5 is also an SLE risk locus in European populations that is implicated in autophagy. Autophagy plays a crucial role in neutrophil extracellular trap (NET) formation, degranulation, and limiting autoantigens in blood. Dysregulated autophagy has been implicated in SLE pathology and poor disease outcomes. The function of ATG16L2 is unknown, but evidence suggests it may function as a negative regulator of autophagosome formation [2].

Objectives

To identify autophagy-related SLE risk variants shared across different ancestry populations and define the role of ATG16L2 in SLE and autophagy.

Methods

SLE case-control GWA scans from European (7568 cases; 1082 controls), African American (4336 cases; 935 controls), Hispanic (3752 cases; 1840 controls), and Korean (1173 cases; 4213 controls) populations were imputed and SNP associations tested. Meta-analysis was performed, then Bayesian statistics were used to define a credible SNP set. Bioinformatic analyses (RegulomeDB, promoter capture Hi-C, eQTLs, etc.) further prioritized SNPs based on predicted functionality. The functional significance of autophagy SLE risk genes, ATG16L1, ATG16L,2 and ATG5, were tested by CRISPR knockout (KO) in PLB-985 cell line. CRISPR-targeted single cell clones were screened for ATG16L1, ATG16L2 or ATG5 deletion using qPCR, NanoPore sequencing, and Western blotting. Changes in autophagy were assessed by Western blotting and confocal microscopy.

Results

Transracial fine-mapping of PRDM1-ATG5 locus identified two SNP associations shared across the credible sets in all populations: rs56886418 (p=1.38x10-5) located in the intron of PRDM1 and rs77791277 (p=1.38x10-5) that tagged a group of SNPs in strong linkage disequilibrium. Cross comparison of the credible SNP sets and bioinformatic analyses of shared SNPs identified rs533733 and rs9373843 as additional likely functional variants. Bioinformatic analyses prioritized rs56886418, an eQTL for ATG5 (p=0.05) and PRDM1 (p=4.75x10-7) in blood cells positioned in a topologically associated domain (TAD) that may interact with ATG5 and PRDM1 promoters in EBV-transformed B cells. SNP rs533733 is an eQTL for ATG5 in neutrophils (p=0.006) and is in a TAD 6.4kb 3’ of PRDM1 that interacts with the ATG5 promoter region where rs9373843 (eQTL of ATG5 in neutrophils (p=0.04)) is positioned. These data suggest that risk SNPs on the PRDM1-ATG5 locus may modulate ATG5 expression and autophagy in specific cell types by modulating the local chromatin regulatory network.

To assess the roles of ATG5, ATG16L1 and ATG16L2 in autophagy, PMA/I-induced hallmarks of autophagy, LC3-I and LC3-II conversion and p62 protein aggregation, were assessed in homozygous and heterozygous ATG5, ATG16L1, or ATG16L2 CRISPR KO PLB-985 cells by Western blotting and confocal microscopy. Loss of ATG5 or ATG16L1 impaired PMA/I-induced autophagosome formation in myeloid-like and differentiated neutrophil-like PLB-985 cells. In contrast, loss of ATG16L2 elevated the conversion of LC3-I to LC3-II and p62 protein aggregation in both cell types, suggesting that ATG16L2 may inhibit autophagy.

Conclusion

Functional characterization of SNPs on the PRDM1-ATG5 and ATG16L2-P2RY2 loci, and the functional characterization of ATG16L2 in myeloid and neutrophil cell lines, provide new insights into the mechanisms that regulate autophagy in health and disease. Ongoing studies will focus on in vitro validation of predicted functional SNPs and will introduce ATG16L2 rs11235604 risk variant in PLB-985 cells to assess its importance in autophagy.

References

[1]Lessard CJ, et al. Arthritis Rheumatol. 2016; 68(5):1197-1209.

[2]Wible DJ, et al. Cell Discov. 2019; 5:42.

Disclosure of Interests

None declared.

Long-term stabilized amorphous calcium carbonate-an ink for bio-inspired 3D printing

Biominerals formed by organisms in the course of biomineralization often demonstrate complex morphologies despite their single-crystalline nature. This is achieved owing to the crystallization via a predeposited amorphous calcium carbonate (ACC) phase, a precursor that is particularly widespread in biominerals. Inspired by this natural strategy, we used robocasting, an additive manufacturing three-dimensional (3D) printing technique, for printing 3D objects from novel long-term, Mg-stabilized ACC pastes with high solids loading. We demonstrated, for the first time, that the ACC remains stable for at least a couple of months, even after printing. Crystallization, if desired, occurs only after the 3D object is already formed and at temperatures significantly lower than those of common postprinting sintering. We also examined the effects different organic binders have on the crystallization, the morphology, and the final amount of incorporated Mg. This novel bio-inspired method may pave the way for a new bio-inspired route to low-temperature 3D printing of ceramic materials for a multitude of applications.

Amino acids nanocrystals for piezoelectric detection of ultra-low mechanical pressure

Developing biocompatible nano-materials with the ability to detect ultra-low mechanical pressure is promising for biomedical sensors. This paper reports the detection of pressure as low as 1 Pa in the environmental pressure of 1 atm (10^-3% pressure change) by nanocrystals of amino acids glycine and alanine through the piezoelectric effect. Piezoelectricity enables detection of pressure by a change of dielectric polarization when the material is subjected to external pressure. This work exploits the non-centro-symmetric structure of some amino acids and their weak hydrogen bonds to develop sensitive mechanical pressure sensors. The β-glycine and l-alanine nanocrystals were grown from aqueous solution inside porous alumina substrate. The nanocrystals exhibit pronounced preferred crystallographic orientation. The sensitive piezoelectric response to ultra-low mechanical pressure is discussed based on atomic and crystal symmetry considerations.

The Impact of Multimorbidity on Resting Metabolic Rate in Community-Dwelling Women over a Ten-Year Period: A Cross-Sectional and Longitudinal Study

OBJECTIVES

Ageing has been associated with increasing multimorbidity. This study investigated whether the number of diseases is a predictor of resting metabolic rate (RMR) and its long-term changes in community-dwelling elderly women.

SUBJECTS AND DESIGN

Cross-sectional and longitudinal data, obtained over ten years with repeated follow-ups, from 180 women aged 60 - 86 years and with a BMI of 18 - 43 kg/m2 at baseline were analyzed.

MEASUREMENTS

RMR was measured using indirect calorimetry and body composition by bioelectrical impedance analysis. Diagnosed diseases were assessed by a questionnaire comprising 23 disease categories. Subjects with 0 - 2 diseases were classified as relatively healthy and with > 2 diseases as multimorbid.

RESULTS

At baseline, relatively healthy (N = 75) and multimorbid (N = 105) women did not differ in RMR. During the ten-year follow-up, the median (range) number of diseases increased from 2 (0 - 2) to 4 (0 - 8) in relatively healthy and from 5 (3 - 11) to 7 (3 - 15) in multimorbid women. In the longitudinal analyses, only women who were multimorbid at baseline showed a significant increase in RMR of 31 kJ/d per additional disease (P = 0.015), adjusted for fat-free mass, fat mass, waist circumference and age.

CONCLUSION

Increasing multimorbidity in community-dwelling women is associated with an increase in RMR independently of body composition and age.

Improved Brain Tumor Classification by Sodium MR Imaging: Prediction of IDH Mutation Status and Tumor Progression

BACKGROUND AND PURPOSE

MR imaging in neuro-oncology is challenging due to inherent ambiguities in proton signal behavior. Sodium-MR imaging may substantially contribute to the characterization of tumors because it reflects the functional status of the sodium-potassium pump and sodium channels.

MATERIALS AND METHODS

Sodium-MR imaging data of patients with treatment-naïve glioma WHO grades I-IV (n = 34; mean age, 51.29 ± 17.77 years) were acquired by using a 7T MR system. For acquisition of sodium-MR images, we applied density-adapted 3D radial projection reconstruction pulse sequences. Proton-MR imaging data were acquired by using a 3T whole-body system.

RESULTS

We demonstrated that the initial sodium signal of a treatment-naïve brain tumor is a significant predictor of isocitrate dehydrogenase (IDH) mutation status (P < .001). Moreover, independent of this correlation, the Cox proportional hazards model confirmed the sodium signal of treatment-naïve brain tumors as a predictor of progression (P = .003). Compared with the molecular signature of IDH mutation status, information criteria of model comparison revealed that the sodium signal is even superior to IDH in progression prediction. In addition, sodium-MR imaging provides a new approach to noninvasive tumor classification. The sodium signal of contrast-enhancing tumor portions facilitates differentiation among most glioma types (P < .001).

CONCLUSIONS

The information of sodium-MR imaging may help to classify neoplasias at an early stage, to reduce invasive tissue characterization such as stereotactic biopsy specimens, and overall to promote improved and individualized patient management in neuro-oncology by novel imaging signatures of brain tumors.

[Streptococcus suis meningitis in an immunocompetent patient]

A case of Streptococcus suis meningitis is described in an immunocompetent patient presenting asthenia, general weakness, fever, vomiting, sensory deterioration and temporospatial disorder. The cerebrospinal fluid and two blood cultures (2/2 bottles) were positive. The isolate was preliminary identified by conventional biochemical tests, and the identification was completed at the Special Bacteriology Service of INEI-ANLIS "Dr. Carlos G. Malbrán". Ampicillin and ceftriaxone treatment was initiated. The isolate was susceptible to ampicillin, cefotaxime and vancomycin. The patient experienced a good outcome but suffered hearing loss. However, after four months he returned with walking ataxia, deafness in his left ear, and hearing loss in the right ear. The patient's retrospective exposure to pigs had been verified. It is important to evaluate predisposing and epidemiologic factors in order to alert about the possible presence of this etiological agent in cases of meningitis or bacteremia.

[Evaluation of cefoxitin and cefotaxime screening plates for the detection of methicillin-resistance in Staphylococcus aureus]

Detection of methicillin-resistant Staphylococcus aureus (MRSA) isolates represents a serious problem to low and media level microbiology labs. In this work cefoxitin (FOX) and cefotaxime (CTX) screen plates (AS) (8-16 microg/ml) with and without 4% of NaCl were evaluated to detect MRSA. Sensitivity, specificity, positive and negative predictive values were determined. The AS oxacillin and the agglutination test MRSA-Screen Latex for the detection of PLP2a were used as reference methods for the evaluation of the different studied screening plates. The 100% (94 strains) PLP2a positive were detected as MRSA with FOX (8 microg/ml), and CTX (8 microg/ml with 4% NaCl) AS. The advantage of FOX AS (8 microg/ml) is that it does not need the addition of NaCl, and CTX AS (8 microg/ml with 4% NaCl) is that cefotaxime is an antimicrobial easily accessible in our country.

Targeting Lewis Y (LeY) in small cell lung cancer (SCLC) with a humanized monoclonal antibody, hu3S193

7086

Background: LeY is a blood group antigen with dominant expression on the surface of epithelial tumors, including SCLC, making it a potential target for antibody-based immunotherapy. 3S193, an IgG3 mAb, has demonstrated superior specificity, affinity, and cytotoxicity over other anti-LeY antibodies. A phase I trial of humanized 3S193 (hu3S193) with dosing up to 40 mg/m2 demonstrated tumor targeting without serious toxicities or the development of human antihuman antibodies (Scott et al, ASCO, 2004). Methods: We tested the targeting and pharmacokinetics of hu3S193 in patients with SCLC. Eligibility required progressive SCLC treated with up to three prior chemotherapy regimens, measurable disease not previously irradiated, and tumor samples immunohistochemistry (IHC)-positive for 3S193. Patients received four weekly injections of hu3S193, 5 patients at 10mg/m2 and 5 patients at 20 mg/m2. The first and fourth injections were radiolabeled with 111Indium for gamma camera imaging. Results: Of 40 patients screened, 25/34 (74%) evaluable SCLC tumor samples were 3S193-positive by IHC: 1+ (n = 13), 2+ (n = 3), 3+ (n = 2), 4+ (n = 7). Ten patients were treated with hu3S193; eight completed all four injections (one had disease progression and one is still on treatment). At the lower dose, about 50% of lesions >2 cm diameter visualized on FDG-PET were also seen on 111In SPECT imaging. However, at the higher dose, essentially all FDG avid lesions showed targeting. The mean T1/2 for all infusions was 2.89 ± 0.84 days at 10 mg/m2 (n = 9) and 3.29 ± 0.66 days at 20 mg/m2 (n = 7). No difference was noted in imaging or pharmacokinetics between the first and fourth injections. At the 20 mg/m2 dose, patients experienced grade 2 urticaria (n = 1), grade 1 vomiting (n = 2), and grade 2 hypertension (n = 1) transiently after infusion. No other grade 2 or greater toxicities were observed. No objective responses were observed. Conclusions: SCLC has a high rate of Lewis Y expression. Given the strong tumor targeting, particularly at the higher dose, and the potential for immunomodulatory effects, administration of hu3S193 with chemotherapy would be warranted. Supported by the Ludwig Institute and the Experimental Therapeutics Committee of MSKCC.

No significant financial relationships to disclose.

Inherited cholesterol lipidosis: cerebrotendinous xanthomatosis (van Bogaert Scherer Epstein disease). A clinicopathological study

Cerebrotendinous xanthomathosis (CTX) is a rare autosomal-recessively transmitted disease of the lipid storage system with an array of general and neurological symptoms, based on the pathological storage of cholestanol and cholesterol. The histologic manifestations are foamy cell granulomata and cholesterol crystals within various tissues, associated with a loss of both nerve cells and demyelination inside the CNS. We present a case of CTX with clinical progression as well as the pathomorphologic autopsy findings. The CNS affection in our case will be demonstrated and the pathogenesis be discussed. Medical treatment of CTX is possible but with variable success. In the case shown, the patient profited only marginally from a long-term application of chenodeoxycholic acid.

[Hemithyroidectomy on principle in cases of unclear fine needle biopsy and frozen section findings]

SUMMARY

Fine needle aspiration biopsy (FNB) and frozen section (FS) may help to validate pre- and intraoperatively dignity of thyroid nodules. Credibility and clinical valuation of both methods have to be taken into consideration of surgical treatment. Between 7/96 and 6/00 82 patients were operated for thyroid lesions using both diagnostic methods to verify thyroid lesions. The sensitivity of both methods is low. With FNB only 5/11 malignancies (45.5 %) were recognized. Within the group of "suspicious" FNB findings (22/82; 26.8 %) definitive histology demonstrated another 6 carcinomas. Only 1 of these initially not recognized carcinomas was verified by FS intraoperatively whereas 5 carcinomas were judged to be benign lesions. Follicular carcinomas and follicular variants of papillary carcinomas could not be assessed by FNB in 6/8 and by FS in 8/9 cases. Only very few malignancies, which are not found by FNB, can be verified by FS. A routine use of intraoperative FS to verify FNB results is not justified, but can give additional information about tumor size, lymph node status and extra-/intrathyroid nodules, which are not examined by FNB preoperatively. Hemithyroidectomy with lymph node dissection represents the operation of choice in cases with unclear FNB results to avoid a second operation with increased risk of recurrent nerve palsy and hypoparathyroidism.

Towards environmental toxicogenomics -- development of a flow-through, high-density DNA hybridization array and its application to ecotoxicity assessment

Assessment of the environmental hazard posed by soils/sediments containing low to moderate levels of contaminants using standard analytical chemical methods is uncertain due (in part) to a lack of information on contaminant bioavailability, the unknown interactive effects of contaminant mixtures, our inability to determine the species of a metal in an environmental matrix, and the relative sensitivity of bioassay species. Regulatory agencies compensate for this uncertainty by lowering cleanup goals, but in this process they effectively exclude otherwise attractive cleanup options (i.e. bioremediation). Direct evaluations of soil and sediment toxicity preclude uncertainty from most of these sources. However, the time and cost of chronic toxicity tests limits their general application to higher levels of tiered toxicity assessments. Transcriptional level (mRNA) toxicity assessments offer great advantages in terms of speed, cost and sample throughput. These advantages are currently offset by questions about the environmental relevance of molecular level responses. To this end a flow-through, high-density DNA hybridization array (genosensor) system specifically designed for environmental risk assessment was developed. The genosensor is based on highly regular microchannel glass wafers to which gene probes are covalently bound at discrete (200-microm diameter spot) and addressable (250-microm spot pitch) locations. The flow-through design enables hybridization and washing times to be reduced from approximately 18 h to 20 min. The genosensor was configured so that DNA from 28 environmental samples can be simultaneously hybridized with up to 64 different gene probes. The standard microscopic slide format facilitates data capture with most automated array readers and, thus high sample throughput (> 350 sample/h). In conclusion, hardware development for molecular analysis is enabling very tractable means for analyzing RNA and DNA. These developments have underscored the need for further developmental work in probe design software, and the need to relate transcriptional level data to whole-organism toxicity indicators.

Evolutionary dynamics of the SGM transposon family in the Drosophila obscura species group

SGM (Drosophila subobscura, Drosophila guanche, and Drosophila madeirensis) transposons are a family of transposable elements (TEs) in Drosophila with some functional and structural similarities to miniature inverted-repeat transposable elements (MITEs). These elements were recently active in D. subobscura and D. madeirensis (1-2 MYA), but in D. guanche (3-4 MYA), they gave rise to a species-specifically amplified satellite DNA making up approximately 10% of its genome. SGM elements were already active in the common ancestor of all three species, giving rise to the A-type specific promoter section of the P:-related neogene cluster. SGM sequences are similar to elements found in other obscura group species, such as the ISY elements in D. miranda and the ISamb elements in Drosophila ambigua. SGM elements are composed of different sequence modules, and some of them, i.e., LS and LS-core, are found throughout the Drosophila and Sophophora radiation with similarity to more distantly related TEs. The LS-core module is highly enriched in the noncoding sections of the Drosophila melanogaster genome, suggesting potential regulatory host gene functions. The SGM elements can be considered as a model system elucidating the evolutionary dynamics of mobile elements in their arms race with host-directed silencing mechanisms and their evolutionary impact on the structure and composition of their respective host genomes.

The MITE family heartbreaker (Hbr): molecular markers in maize

Transposable elements are ubiquitous in plant genomes, where they frequently comprise the majority of genomic DNA. The maize genome, which is believed to be structurally representative of large plant genomes, contains single genes or small gene islands interspersed with much longer blocks of retrotransposons. Given this organization, it would be desirable to identify molecular markers preferentially located in genic regions. In this report, the features of a newly described family of miniature inverted repeat transposable elements (MITEs) (called Heartbreaker), including high copy number and polymorphism, stability, and preference for genic regions, have been exploited in the development of a class of molecular markers for maize. To this end, a modification of the AFLP procedure called transposon display was used to generate and display hundreds of genomic fragments anchored in Hbr elements. An average of 52 markers were amplified for each primer combination tested. In all, 213 polymorphic fragments were reliably scored and mapped in 100 recombinant inbred lines derived from a cross between the maize inbreds B73 x Mo17. In this mapping population, Hbr markers are distributed evenly across the 10 maize chromosomes. This procedure should be of general use in the development of markers for other MITE families in maize and in other plant and animal species where MITEs have been identified.

The influence of cell adsorbent interactions on protein adsorption in expanded beds

Expanded bed adsorption (EBA) is a primary recovery operation allowing the adsorption of proteins directly from unclarified feedstock, e.g. culture suspensions, homogenates or crude extracts. Thus solid-liquid separation is combined with adsorptive purification in a single step. The concept of integration requires that the solid components of the feed solution are regarded as a part of the process, which influences stability, reproducibility, and overall performance. This aspect is investigated here at the example of the influence of presence and concentration of intact yeast cells (S. cerevisiae) on the adsorption of model proteins (hen egg white lysozyme and bovine serum albumin) to various stationary phases (cation and anion-exchange, hydrophobic interaction, immobilised metal affinity). The interaction of the cells with the adsorbents is determined qualitatively and quantitatively by a pulse response method as well as by a finite bath technique under different operating conditions. The consequence of these interactions for the stability of expanded beds in suspensions of varying cell concentration is measured by residence time distributions (RTDs) after tracer pulse injection (NaBr, LiCl). Analysis of the measured RTD by the PDE model allows the calculation of the fraction of perfectly fluidised bed (phi), a parameter which may be regarded as a critical quantity for the estimation of the quality of fluidisation of adsorbents in cell containing suspensions. The correlation between bed stability and performance is made by analysing the breakthrough of model proteins during adsorption from unclarified yeast culture broth. A clear relationship is found between the degree of cell/adsorbent interaction, bed stability in terms of the phi parameter, and the sorption efficiency. Only beds characterised by a phi value larger than 0.8 in the presence of cells will show a conserved performance compared to adsorption from cell free solutions. A drop in phi, which is due to interactions of the fluidised adsorbent particles with cells from the feed, will directly result in a reduced breakthrough efficiency. The data presented highlight the importance of including the potential interaction of solid feedstock components and the expanded adsorbents into the design of EBA processes, as the interrelation found here is a key factor for the overall performance of EBA as a truly integrated operation.

Membrane-based cell culture systems--an alternative to in vivo production of monoclonal antibodies

A new generation of membrane-based cell culture devices especially designed for small scale production of monoclonal antibodies (mabs) has entered the market in the last few years. In contrast to conventional perfusion hollow fibre bioreactors, these devices contain two functionally different membranes--one ultrafiltration membrane for nutrient supply and one gas-permeable membrane for direct oxygenation of cells. The latest systems of this generation are static culture systems which are of moderate cost and either better than, or equal to, the ascites mice in terms of quality and quantity of produced monoclonal antibodies. We have investigated the advantages of the perfused Tecnomouse bioreactor and the static CELLine culture flasks in comparison to ascites production and conventional roller bottle cultures.

Genetic basis of enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprint pattern in Sinorhizobium meliloti and identification of S. meliloti employing PCR primers derived from an ERIC-PCR fragment

The enterobacterial repetitive intergenic consensus (ERIC)-PCR method was employed to generate genomic amplification products of Sinorhizobium meliloti strain 2011. Eleven distinctive PCR fragments obtained in PCR reactions by using the ERIC2 primer were cloned and their partial or complete nucleotide sequences established. DNA sequences that extended past the ERIC2 primer region were not conserved among the 11 PCR fragments and showed no sequence similarity to the enterobacterial ERIC consensus sequence. Thus, repetitive ERIC or ERIC-like sequences seem not to be an integral part of the S. meliloti genome. An amplification product of S. meliloti 2011 was identified which was present in S. meliloti strains but absent in other rhizobial species. Based on the nucleotide sequence information, a pair of PCR primers was designed and used for PCR amplification of sequences of S. meliloti laboratory strains 2011, L5-30, AK631 and 102F34. Nucleotide sequence analysis of the amplification products revealed a 100% DNA sequence conservation. Database searches showed that the DNA fragment putatively encodes the C-terminal part of a protein displaying similarity to 2-hydroxyacid dehydrogenases of various organisms. The newly designed PCR primers should be useful for the rapid identification of S. meliloti isolates.