Immune expression in children with Wilms tumor: a pilot study.

BACKGROUND: Given improvements in multimodality therapy, survival among children with Wilms tumor (WT) exceeds 90%. However, 15% of children with favorable histology and 50% of children with anaplastic WT experience recurrence or progression. Of patients with advanced disease, only 50% survive to adulthood. In adult malignancies (including renal tumors), patient survival has improved with the advent of immunotherapy. However, little is known about the immune microenvironment of WT, making the potential role of immunotherapy unclear. OBJECTIVE: The objective of the study is to perform an exploratory, descriptive analysis of the immune milieu in WT. STUDY DESIGN: Between 2016 and 2017, all pediatric patients with WT, some of whom received neoadjuvant chemotherapy, underwent ex vivo wedge biopsy at the time of nephrectomy. The fresh tumor tissue and peripheral blood samples were analyzed for infiltrating immune infiltrate and effector cells using flow cytometry. Immunohistochemistry was performed for CD4, CD8, and PD-L1 expression. Matched blood samples were obtained for each patient, and circulating immune cells were analyzed by flow cytometry. RESULTS: A total of six patients were enrolled. One patient with neuroblastoma was excluded. The remaining five patients included the following: two with unilateral WT (resected before chemotherapy), two with bilateral WT (resected after neoadjuvant chemotherapy), and one with Denys-Drash syndrome, end-stage renal disease, and history of WT in the contralateral kidney. Immune analysis showed that WT were infiltrated by immune cells regardless of chemotherapy status. CD8 and CD4 T cells were present in the tumor tissue and exhibited an activated phenotype. Elevated levels of natural killer (NK) cells were observed in the tumors (Figure). Immune checkpoint PD-L1 was also found expressed in one of the tumors stained. DISCUSSION: In this pilot study, it was found that WTs were infiltrated by immune cells (CD45+) both before and after chemotherapy. Elevated levels of NK cells infiltrating the tumor specimens, which were quantitatively increased compared with levels of NK cells circulating in the blood, were noted. T cells, particularly CD4+ and CD8+ T cells, were present in tumor specimens. Tumor-infiltrating CD4 and CD8 T cells displayed an activated phenotype as defined by increased expression of human leukocyte antigen-DR isotype (HLA-DR), programmed cell death protein 1 (PD1), and CD57. Together, these findings suggest that WT microenvironment is immune engaged and may be susceptible to immunotherapy similar to other malignancies. CONCLUSIONS: These pilot data suggest an immune-engaged tumor microenvironment is present within WT. This implies that WT may be susceptible to immunotherapy similar to adult renal tumors and other adult malignancies. Follow-up studies are currently underway.

The dddP gene, encoding a novel enzyme that converts dimethylsulfoniopropionate into dimethyl sulfide, is widespread in ocean metagenomes and marine bacteria and also occurs in some Ascomycete fungi.

The marine alphaproteobacterium Roseovarius nubinhibens ISM can produce the gas dimethyl sulfide (DMS) from dimethylsulfoniopropionate (DMSP), a widespread secondary metabolite that occurs in many phytoplankton. Roseovarius possesses a novel gene, termed dddP, which when cloned, confers on Escherichia coli the ability to produce DMS. The DddP polypeptide is in the large family of M24 metallopeptidases and is wholly different from two other enzymes, DddD and DddL, which were previously shown to generate DMS from dimethylsulfoniopropionate. Close homologues of DddP occur in other alphaproteobacteria and more surprisingly, in some Ascomycete fungi. These were the biotechnologically important Aspergillus oryzae and the plant pathogen, Fusarium graminearum. The dddP gene is abundant in the bacterial metagenomic sequences in the Global Ocean Sampling Expedition. Thus, dddP has several novel features and is widely dispersed, both taxonomically and geographically.

Molecular genetic analysis of a dimethylsulfoniopropionate lyase that liberates the climate-changing gas dimethylsulfide in several marine alpha-proteobacteria and Rhodobacter sphaeroides.

The alpha-proteobacterium Sulfitobacter EE-36 makes the gas dimethylsulfide (DMS) from dimethylsulfoniopropionate (DMSP), an abundant antistress molecule made by many marine phytoplankton. We screened a cosmid library of Sulfitobacter for clones that conferred to other bacteria the ability to make DMS. One gene, termed dddL, was sufficient for this phenotype when cloned in pET21a and introduced into Escherichia coli. Close DddL homologues exist in the marine alpha-proteobacteria Fulvimarina, Loktanella Oceanicola and Stappia, all of which made DMS when grown on DMSP. There was also a dddL homologue in Rhodobacter sphaeroides strain 2.4.1, but not in strain ATCC 17025; significantly, the former, but not the latter, emits DMS when grown with DMSP. Escherichia coli containing the cloned, overexpressed dddL genes of R. sphaeroides 2.4.1 and Sulfitobacter could convert DMSP to acrylate plus DMS. This is the first identification of such a 'DMSP lyase'. Thus, DMS can be made either by this DddL lyase or by a DMSP acyl CoA transferase, specified by dddD, a gene that we had identified in several other marine bacteria.

Evidence that the Rhizobium regulatory protein RirA binds to cis-acting iron-responsive operators (IROs) at promoters of some Fe-regulated genes.

Mutations in rirA of Rhizobium have been shown to deregulate expression of several genes that are normally repressed by iron. A conserved sequence, the iron-responsive operator (IRO), was identified near promoters of vbsC (involved in the synthesis of the siderophore vicibactin), rpoI (specifies an ECF sigma factor needed for vicibactin synthesis) and the two fhuA genes (encoding vicibactin receptor). Removal of these IRO sequences abolished Fe-responsive repression. Most of these genes were constitutively expressed in the heterologous host, Paracoccus denitrificans, but introduction of the cloned rirA gene repressed expression of these Rhizobium genes in this heterologous host if the corresponding IRO sequences were also intact. These observations are the first to examine the mechanisms of RirA, which has no sequence similarity to well-known iron-responsive regulators such as Fur or DtxR. They provide strong circumstantial evidence that RirA is a transcriptional regulator that binds to cis-acting regulatory sequences near the promoters of at least some of the genes whose expression it controls in response to Fe availability.

The Fur-like protein Mur of Rhizobium leguminosarum is a Mn(2+)-responsive transcriptional regulator.

In wild-type Rhizobium leguminosarum, the sitABCD operon specifies a Mn(2+) transporter whose expression is severely reduced in cells grown in the presence of this metal. Mutations in the R. leguminosarum gene, mur (manganese uptake regulator), whose product resembles the Fur transcriptional regulator, cause high-level expression of sitABCD in the presence of Mn(2+). In gel-shift mobility assays, purified R. leguminosarum Mur protein bound to at least two regions near the sitABCD promoter region, although this DNA has no conventional consensus Fur-binding sequences (fur boxes). Thus, in contrast to gamma-proteobacteria, where Fur binds Fe(2+), the R. leguminosarum Fur homologue, Mur, act as a Mn(2)-responsive transcriptional regulator.

The Grampian Senior House Officer scheme in medicine -- the early years and now.

A rotational scheme for Senior House Officers in medicine is described. Although it was introduced more than 30 years ago its effectiveness is such that it has remained the basis of training. Details of the original scheme are given together with the underpinning principles. The modifications leading to the current scheme are noted.

Fur is not the global regulator of iron uptake genes in Rhizobium leguminosarum.

Rhizobium leguminosarum fur mutants were unaffected in Fe-dependent regulation of several operons that specify different Fe uptake systems, yet cloned R. leguminosarum fur partially corrected an Escherichia coli fur mutant and R. leguminosarum Fur protein bound to canonical fur boxes. The lack of a phenotype in fur mutants is not due to functional redundancy with Irr, another member of the Fur superfamily found in the rhizobia, since irr fur double mutants are also unaffected in Fe-responsive regulation of several operons involved in Fe uptake. Neither Irr nor Fur is needed for symbiotic N(2) fixation on peas. As in Bradyrhizobium japonicum, irr mutants accumulated protoporphyrin IX. R. leguminosarum irr is not regulated by Fur and its Irr protein lacks the motif needed for haem-dependent post-translational modification that occurs in B. japonicum Irr. The similarities and differences in the Fur superfamily in the rhizobia and other Gram-negative bacteria are discussed.

Structural studies of the Fur protein from Rhizobium leguminosarum.

The X-ray crystal structure of the apo-form of the Fur protein from Rhizobium leguminosarum has been solved at 2.7 A resolution. Small-angle X-ray scattering was used to give information on the solution conformation of the protein. The Fur homodimer folds into two domains. The N-terminal domain is formed from the packing of two helix-turn-helix motifs while the C-terminal domain appears primarily to stabilize the dimeric state of the protein.

The vbs genes that direct synthesis of the siderophore vicibactin in Rhizobium leguminosarum: their expression in other genera requires ECF sigma factor RpoI.

A cluster of eight genes, vbsGSO, vbsADL, vbsC and vbsP, are involved in the synthesis of vicibactin, a cyclic, trihydroxamate siderophore made by the symbiotic bacterium Rhizobium leguminosarum. None of these vbs genes was required for symbiotic N2 fixation on peas or Vicia. Transcription of vbsC, vbsGSO and vbsADL (but not vbsP) was enhanced by growth in low levels of Fe. Transcription of vbsGSO and vbsADL, but not vbsP or vbsC, required the closely linked gene rpoI, which encodes an ECF sigma factor of RNA polymerase. Transfer of the cloned vbs genes, plus rpoI, to Rhodobacter, Paracoccus and Sinorhizobium conferred the ability to make vicibactin on these other genera. We present a biochemical genetic model of vicibactin synthesis, which accommodates the phenotypes of different vbs mutants and the homologies of the vbs gene products. In this model, VbsS, which is similar to many non-ribosomal peptide synthetase multienzymes, has a central role. It is proposed that VbsS activates L-N5-hydroxyornithine via covalent attachment as an acyl thioester to a peptidyl carrier protein domain. Subsequent VbsA-catalysed acylation of the hydroxyornithine, followed by VbsL-mediated epimerization and acetylation catalysed by VbsC, yields the vicibactin subunit, which is then trimerized and cyclized by the thioesterase domain of VbsS to give the completed siderophore.

dpp genes of Rhizobium leguminosarum specify uptake of delta-aminolevulinic acid.

An operon with homology to the dppABCDF genes required to transport dipeptides in bacteria was identified in the N2-fixing symbiont, Rhizobium leguminosarum. As in other bacteria, dpp mutants were severely affected in the import of delta-aminolevulinic acid (ALA), a heme precursor. ALA uptake was antagonized by adding dipeptides, indicating that these two classes of molecule share the same transporter. Mutations in dppABCDF did not affect symbiotic N2 fixation on peas, suggesting that the ALA needed for heme synthesis is not supplied by the plant or that another uptake system functions in the bacteroids. The dppABCDF operon of R. leguminosarum resembles that in other bacteria, with a gap between dppA and dppB containing inverted repeats that may stabilize mRNA and may explain why transcription of dppA alone was higher than that of dppBCDF. The dppABCDF promoter was mapped and is most likely recognized by sigma70.

The Rhizobium leguminosarum tonB gene is required for the uptake of siderophore and haem as sources of iron.

In the N2-fixing bacterium Rhizobium leguminosarum, mutations in a homologue of tonB (tonB(Rl)) block the import of vicibactin and haem as iron sources in free-living bacteria. TonB(Rl) mutants were normal for growth with ferric dicitrate and slightly reduced for growth with haemoglobin as sole iron sources. The deduced TonB(Rl) product is larger than that of (for example) Escherichia coli, on account of an extended N-terminal domain. Transcription of tonB(Rl) was enhanced in low-Fe growth conditions; this was not controlled by Fur, nor RpoI, an Fe-regulated extracytoplasmic sigma factor. Upstream of tonB(Rl) and transcribed divergently is an operon, hmuPSTUV, whose products are homologous to ABC transporters involved in haem uptake in pathogenic bacteria. Expression of hmuPSTUV was enhanced in low-Fe conditions, and hmu mutants show slightly diminished growth on haem as sole Fe source, suggesting that there is more than one system for the uptake of this molecule. hmuPSTUV expression appears to be from three closely linked promoters. Downstream of hmuPSTUV, a gene that may encode an extracytoplasmic sigma factor was identified, but this gene, rpoZ, did not affect the transcription of tonB(Rl) or hmuPSTUV. Mutations in tonB(Rl), hmu genes and rpoZ did not affect symbiotic N(2) fixation in peas.

A weighted version of the Melbourne Low-Vision ADL Index: a measure of disability impact.

OBJECTIVE: To develop a version of the Melbourne Low-Vision ADL Index that measures the personal impact of disability in activities of daily living (ADL's). Also, to determine the relationship between clinical measures of vision impairment and disability impact. METHODS: The Melbourne Low-Vision ADL Index (MLVAI) is a desk-based clinical assessment of disability in ADL's. Ability to perform each item is rated on a five-level descriptive scale from zero to four. In this study, the original version of the MLVAI was modified to measure disability impact. The simple modification involved weighting each item by the importance of that item to the person being tested. Importance was also rated on a five-level scale from zero to four. The validity and reliability of the Weighted Melbourne Low-Vision ADL Index (MLVAI(W)) was determined for 97 vision-impaired subjects in a cross-sectional study. RESULTS: Cronbach's alpha coefficient indicated an internal reliability of 0.94, and an intraclass correlation coefficient indicated an overall reliability of 0.88. The standard error of measurement was 24.7 points (out of a possible score of 400). There was a statistically significant difference in test scores between normal subjects and vision-impaired subjects. All vision measures had a high, statistically significant correlation with MLVAI(W) score. Near-word acuity had the strongest correlation (r(s) = 0.78, p < 0.001), followed by Melbourne Edge Test contrast sensitivity (r(s) = -0.72, p < 0.001). Visual field had the weakest correlation (r(s) = -0.52, p < 0.001). The best predictive model of MLVAI(W) score incorporated the variables age, near-word acuity, and visual field. Together, these variables accounted for 65.1% of the variance in MLVAI(W) score. CONCLUSIONS: The MLVAI is highly valid and reliable when weighted by a scale that reflects the personal importance of ADL's. The MLVAI(W) can provide information over and above that obtained with the usual clinical vision measures and may be used to assess low-vision patients and to measure low-vision rehabilitation outcomes. It is suggested that the assessment of disability using the original MLVAI and the assessment of the impact of disability using the MLVAI(W) should be kept separate to facilitate the clear interpretation of the outcomes of low-vision rehabilitation.

Preliminary investigation of the responsiveness of the Melbourne Low Vision ADL index to low-vision rehabilitation.

PURPOSE: To conduct a preliminary investigation on the ability of the Melbourne Low Vision ADL Index to detect changes in functional ability as a result of low-vision rehabilitation. METHODS: Twenty two subjects with age-related macular degeneration (ARMD) who were newly referred to the Kooyong Low Vision Clinic were recruited. The Melbourne Low Vision ADL Index was administered prerehabilitation and postrehabilitation. Changes in scores and effect size statistics were analyzed. RESULTS: The median total score for the subjects prerehabilitation was 67, and the median total score postrehabilitation was 76. The difference in prerehabilitation and postrehabilitation scores was statistically significant (Wilcoxon signed rank test = 248.5, p < 0.001). The mean change score for the total Melbourne Low Vision ADL Index was 9.3 (SD, 5.6). Thus the overall effect size statistic (mean change score divided by SD of prerehabilitation score) was 0.78. CONCLUSIONS: This preliminary investigation indicates that the Melbourne Low Vision ADL Index is responsive to a rehabilitation program for patients with ARMD. It has potential to be used as a measure of low-vision rehabilitation outcomes.

Solute-binding protein-dependent ABC transporters are responsible for solute efflux in addition to solute uptake.

The ATP-binding cassette (ABC) transporter superfamily is one of the most widespread of all gene families and currently has in excess of 1100 members in organisms ranging from the Archaea to manQ1. The movement of the diverse solutes of ABC transporters has been accepted as being strictly unidirectional, with recent models indicating that they are irreversible. However, contrary to this paradigm, we show that three solute-binding protein-dependent (SBP) ABC transporters of amino acids, i.e. the general amino acid permease (Aap) and the branched-chain amino acid permease (Bra) of Rhizobium leguminosarum and the histidine permease (His) of Salmonella typhimurium, are bidirectional, being responsible for efflux in addition to the uptake of solutes. The net solute movement measured for an ABC transporter depends on the rates of uptake and efflux, which are independent; a plateau is reached when both are saturated. SBP ABC transporters promote active uptake because, although the Vmax values for uptake and efflux are not significantly different, there is a 103-104 higher affinity for uptake of solute compared with efflux. Therefore, the SBP ABC transporters are able to support a substantial concentration gradient and provide a net uptake of solutes into bacterial cells.

Metals and the rhizobial-legume symbiosis--uptake, utilization and signalling.

In this review, we consider how the nitrogen-fixing root nodule bacteria, the 'rhizobia', acquire various metals, paying particular attention to the uptake of iron. We also review the literature pertaining to the roles of molybdenum and nickel in the symbiosis with legumes. We highlight some gaps in our knowledge, for example the lack of information on how rhizobia acquire molybdenum. We examine the means whereby different metals affect rhizobial physiology and the role of metals as signals for gene regulation. We describe the ways in which genetics has shown (or not) if, and how, particular metal uptake and/or metal-mediated signalling pathways are required for the symbiotic interaction with legumes.

The development of the Melbourne low-vision ADL index: a measure of vision disability.

PURPOSE: To develop a new test of activities of daily living (ADLs) appropriate for the low-vision population: the Melbourne Low-Vision ADL Index (MLVAI). METHODS: The MLVAI was designed as a desk-based clinical assessment, comprising 18 observed items on complex ADLs in part (a) and 9 questions on broad self-care ADLs in part (b). Each item was rated on a five-level descriptive scale from 0 to 4, based on independence, speed, and accuracy of performance. It was designed to be administered under standardized conditions with regard to the instructions, illumination, and working distances. The validity and reliability of the new MLVAI was determined for 122 subjects who were representative of the general low-vision population, in a cross-sectional study. RESULTS: Two items were found to be redundant and were eliminated from the test. Thus, the final test comprised 25 items, with 100 being the highest possible score. Cronbach's alpha indicated an internal reliability of 0.96, and an intraclass correlation coefficient indicated an overall reliability of 0.95. The SE of measurement was 4.5. According to Spearman's correlation coefficient, the test-retest reliability was 0.94 (P < 0.001), and the interpractitioner reliability for five different pairs of practitioners was 0.90 or higher (P < 0.001). With regard to validity, there was a moderately high correlation with vision impairment (r = -0.68, P < 0.001). Using Rasch analysis, content validity was also demonstrated by good separation indexes (4.70 and 9.88) and high reliability scores (0.96 and 0.99) for the person and items parameters, respectively. Separate calculation of indexes and reliability scores for parts (a) and (b) indicated high content validity and reliability of each part. However, the separation indexes and reliability scores were higher for part (a) than for part (b). The correlation coefficient for part (a) and part (b) was 0.68. CONCLUSIONS: The MLVAI is a highly valid and reliable standardized test of ADL performance for the general low-vision population. It may be used to assess patients with low vision and has the potential to be used as a measure of low-vision rehabilitation outcomes.

The purMN genes of Rhizobium leguminosarum and a superficial link with siderophore production.

We isolated a mutant of R. leguminosarum initially on the basis of reduced production of the siderophore vicibactin on chrome azurol sulfonate (CAS)/agar indicator plates. The mutation was in the purMN operon and the mutant was shown to be an adenine auxotroph and defective for nodulation of peas. The siderophore defect appears to be trivial, being due to diminished growth of the auxotroph on agar-based minimal medium, which contains unknown contaminant(s) that allow it grow poorly. Transcriptional fusions showed that purMN was transcribed at relatively high levels in media containing purines. Expression was enhanced, approximately twofold, if purines were omitted.

A putative ECF sigma factor gene, rpol, regulates siderophore production in Rhizobium leguminosarum.

A cloned Rhizobium leguminosarum gene, termed rpoI, when transferred to wild-type strains, caused overproduction of the siderophore vicibactin. An rpoI mutant was defective in Fe uptake but was unaffected in symbiotic N2 fixation. The RpoI gene product was similar in sequence to extra-cytoplasmic sigma factors of RNA polymerase. Transcription of rpoI was reduced in cells grown in medium that was replete with Fe.

Is the fur gene of Rhizobium leguminosarum essential?

Using primers corresponding to conserved regions of the bacterial regulatory gene fur, a homologue of this gene from the genome of Rhizobium leguminosarum biovar viciae, the nitrogen-fixing symbiont of peas, was isolated and sequenced. The fur gene is normally expressed constitutively, independent of the presence of Fe in the medium, but in one Rhizobium strain it was transcribed at a low level. Attempts to isolate a fur knockout mutant failed, suggesting that the gene is essential for free-living growth. In other bacteria, certain fur mutations confer manganese resistance; however, none of the manganese-resistant mutants of R. leguminosarum which we isolated was corrected by the cloned fur gene. When the cloned R. leguminosarum fur gene was introduced into a fur mutant of Escherichia coli, it caused some Fe-dependent reduction in the amount of siderophore, indicating that it can function heterologously.

Iron-dependent transcription of the regulatory gene ros of Agrobacterium radiobacter.

Transcription of the regulatory gene ros of Agrobacterium radiobacter requires growth in the presence of Fe although this regulation was not mediated by ros itself. The ros gene repressed its own transcription, independently of the Fe status of the growth media. It was shown that the two cysteine residues in the Ros protein were essential for the complementation of the exopolysaccharide synthesis defect of ros mutant strains. It was found that the mutation in one exo mutant strain that was complemented both by ros and by the "structural" exoY gene was not, in fact, in ros but is in some other, unknown gene. The two cysteines were also essential for the correction of this mutant. This mutant affected the expression of exoY but not of ros.