SeedStor: A Germplasm Information Management System and Public Database

SeedStor (https://www.seedstor.ac.uk) acts as the publicly available database for the seed collections held by the Germplasm Resources Unit (GRU) based at the John Innes Centre, Norwich, UK. The GRU is a national capability supported by the Biotechnology and Biological Sciences Research Council (BBSRC). The GRU curates germplasm collections of a range of temperate cereal, legume and Brassica crops and their associated wild relatives, as well as precise genetic stocks, near-isogenic lines and mapping populations. With >35,000 accessions, the GRU forms part of the UK's plant conservation contribution to the Multilateral System (MLS) of the International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA) for wheat, barley, oat and pea. SeedStor is a fully searchable system that allows our various collections to be browsed species by species through to complicated multipart phenotype criteria-driven queries. The results from these searches can be downloaded for later analysis or used to order germplasm via our shopping cart. The user community for SeedStor is the plant science research community, plant breeders, specialist growers, hobby farmers and amateur gardeners, and educationalists. Furthermore, SeedStor is much more than a database; it has been developed to act internally as a Germplasm Information Management System that allows team members to track and process germplasm requests, determine regeneration priorities, handle cost recovery and Material Transfer Agreement paperwork, manage the Seed Store holdings and easily report on a wide range of the aforementioned tasks.

Collaborative study for the establishment of the WHO 3(rd) International Standard for Endotoxin, the Ph. Eur. endotoxin biological reference preparation batch 5 and the USP Reference Standard for Endotoxin Lot H0K354

An international collaborative study was organised jointly by the World Health Organization (WHO)/National Institute for Biological Standards and Control (NIBSC), the United States Pharmacopeia (USP) and the European Directorate for the Quality of Medicines & HealthCare (EDQM/Council of Europe) for the establishment of harmonised replacement endotoxin standards for these 3 organisations. Thirty-five laboratories worldwide, including Official Medicines Control Laboratories (OMCLs) and manufacturers enrolled in the study. Three candidate preparations (10/178, 10/190 and 10/196) were produced with the same material and same formulation as the current reference standards with the objective of generating a new (3(rd)) International Standard (IS) with the same potency (10 000 IU/vial) as the current (2(nd)) IS, as well as new European Pharmacopoeia (Ph. Eur.). and USP standards. The suitability of the candidate preparations to act as the reference standard in assays for endotoxin performed according to compendial methods was evaluated. Their potency was calibrated against the WHO 2(nd) IS for Endotoxin (94/580). Gelation and photometric methods produced similar results for each of the candidate preparations. The overall potency estimates for the 3 batches were comparable. Given the intrinsic assay precision, the observed differences between the batches may be considered unimportant for the intended use of these materials. Overall, these results were in line with those generated for the establishment of the current preparations of reference standards. Accelerated degradation testing of vials stored at elevated temperatures supported the long-term stability of the 3 candidate preparations. It was agreed between the 3 organisations that batch 10/178 be shared between WHO and EDQM and that batches 10/190 and 10/196 be allocated to USP, with a common assigned value of 10 000 IU/vial. This value maintains the continuity of the global harmonisation of reference materials and unitage for the testing of endotoxins in parenteral pharmaceutical products. Based on the results of the collaborative study, batch 10/178 was established by the European Pharmacopoeia Commission as the Ph. Eur. Endotoxin Biological Reference Preparation (BRP) batch 5. The same batch was also established by the Expert Committee on Biological Standardisation (ECBS) of WHO as the WHO 3(rd) IS for Endotoxin. Batch 10/190 was adopted as the USP Endotoxin Reference Standard, lot H0K354 and vials from this same batch (10/190) will serve as the United States Food and Drug Administration (USFDA) Endotoxin Standard, EC-7.

Catabolite repression of SOS-dependent and SOS-independent spontaneous mutagenesis in stationary-phase Escherichia coli

Previous work in our laboratory established that a spontaneous mutagenesis process operating in stationary-phase Escherichia coli cells undergoing selection is subject to regulation by the global regulatory mechanism known as catabolite repression (formerly also called glucose-repression). Here, we set out to determine the identity of this hitherto unknown catabolite-repressible spontaneous mutation generation mechanism(s). We used two different spontaneous mutation detection assays, reversion of a Lac(-) (lacI33OmegalacZ) frameshift marker and forward mutation to valine-resistance, and tested the effects of varying the nature of the carbon source(s) present in the selective plating medium on the mutability of bacterial cells carrying known defects in the recA, umuDC and dinB genes, three well-known SOS response genes, whose products are important for mutagenesis in E. coli. Consistent with the results of our previous Lac(-)-->Lac(+) assay using otherwise SOS-proficient bacterial cells, we found that the overall numbers of spontaneous Lac(+)E. coli revertants were highest when the selective medium contained lactose and lowest when it contained lactose plus the non-utilizable but strongly catabolite-repressing glucose analogue, methyl-alpha-d-glucopyranoside (alphaMG). In contrast, we found that the numbers of Lac(+) revertants appearing on the lactose and lactose+alphaMG selection plates were greatly diminished and not significantly different when the bacterial cells concerned carried either a DeltarecA or DeltadinB mutation. Furthermore, introducing the DeltadinB mutant allele into bacterial cells over-expressing the recA gene reduced the numbers of Lac(+) mutations to those being recovered with the DeltadinB cells. These results appear to suggest that (i) the DinB-dependent mutation generation pathway is alone responsible for spontaneous reversion of the lacI33OmegalacZ frameshift marker, and (ii) the varying numbers of Lac(+) colonies that we recover on the lactose and lactose+alphaMG plates provide a direct measure of the differential effects of these particular carbon compounds on the overall expression of the dinB gene. Interestingly, the yields of spontaneous Val mutations arising in wild-type, DeltarecA, DeltadinB and DeltaumuDC cells were found to be similar, but always tended to be highest when the medium contained only a non-repressing carbon source (glycerol) and lowest when it had been supplemented with a strong catabolite repressor such as glucose or alphaMG. Together, our results would seem to establish that stationary-phase E. coli cells exposed to strong selection pressures can accumulate spontaneous mutations via SOS-dependent and SOS-independent mutation generation pathways whose levels of expression are regulated by catabolite repression.

Evaluation of academic and community surgery clerkships at a Midwestern medical school

BACKGROUND

The equivalency of surgical clerkship experience between academic and community sites is an issue that is assessed with difficulty. We examined the objective performance of 222 medical students after completion of the 8-week surgical clerkship. Six different consecutive semesters were analyzed. There were two objective examinations reviewed, the National Board of Medical Examiners' subject examination and the surgical subportion of the Objective Structured Clinical Examination (OSCE) given at the end of the third year.

METHODS

Medical students were classified into three separate groups based on the site of their surgical clerkship. The medical students were in either academic (100), community (79), or combined (academic and community) (43) locations. Medical student performance on the subject examination and OSCE was examined after completion of the general surgical clerkship. Single-factor analysis of variance testing was done to compare each of the three groups with respect to subject examination test score, or OSCE score. Significance was defined as P < 0.05.

RESULTS

The combined group scored highest on the subject examination (73.6%). The community group scored highest on the OSCE (80.7%). However, no statistical significance exists between the three groups with regard to subject examination (P = NS) or OSCE (P= NS). Subject examination scores did not correlate with OSCE scores (r = 0.095). Objective measurements of surgical subject examination and OSCE were not statistically different between academic, community, and academic and community surgical clerkship participants.

CONCLUSIONS

No statistically significant differences exist between the three groups with regards to OSCE failure rates, but the small amount of failures may have caused Type 2 error. Surgical clinical skills as tested by an OSCE and surgical knowledge as tested by a subject examination are equally attained by an academic or community surgical clerkship.

The clinical specialist in community health nursing: a solution for the 21st century

The clinical specialist (CS) in community health nursing (CHN) addresses health problems in populations and communities in ways that are different from and complimentary to strategies used by practitioners of individualized patient care. Four programs based on comprehensive assessments, systematic program planning, deliberate implementation, and both formative and summative evaluation are presented. The programs were developed by graduate students in the CHN clinical specialization major at the Frances Payne Bolton School of Nursing. With expert faculty guidance and a competency-driven program of study, strategies were implemented to promote the health of community-dwelling well elderly people, home health care nurses who provide service to patients with respiratory problems, and high school students in a private religious school. Experienced parish nurses also benefited from a program designed to enhance their skills in theological reflection. This article also describes the curricular design developed to educate this clinician for the 21st century. Lastly, continued attention to the dynamic criteria of the American Nurses Association Standards of Community Health Nursing Practice is recommended as crucial to the further development of this clinical specialization.

Glucose and related catabolite repressors are powerful inhibitors of pKM101-enhanced UV mutagenesis in Escherichia coli

When stationary phase Escherichia coli K12 trp (amber) cells were exposed to UV doses ranging from 180-540 J m(-2), we found that we could not recover any induced Trp+ revertants unless the irradiated cultures were first supplied with the Muc+ mutation-enhancing IncP plasmid pKM101 (by conjugation). We also found that the numbers of UV-induced Trp+ revertants recovered from pKM101+ cultures varied quite dramatically depending upon which of several commonly-used carbon sources were present in the post-irradiation plating medium, e.g., there were always significantly fewer revertants on minimal glucose plates than on minimal glycerol plates. More importantly, there were also fewer UV-induced revertants on glycerol + glucose plates than on 'glycerol-only' plates. We then tested two glucose-related compounds which are known to depress intracellular cyclic AMP (cAMP) levels even more effectively than glucose (glucose-6-phosphate and the non-utilisable methyl-alpha-D-glucopyranoside) and found that they too were able to exert powerfully antimutagenic effects in UV-treated pKM101-containing bacteria. Taken together, these results provide strong additional support for our working hypothesis that at least one component of the mutational pathway which operates in UV-irradiated pKM101-containing cells is extremely sensitive to classical cAMP-mediated catabolite repression.

Catabolite repressors are potent antimutagens in Escherichia coli plate incorporation assays: experiments with glucose, glucose-6-phosphate and methyl-alpha-D-glucopyranoside

Having previously found that the yields of spontaneous valine-resistant (Val(r)) Escherichia coli mutants which appeared on plates containing 40 microg/ml of valine were always much lower when glucose was present in the glycerol-containing defined medium normally used to select them, we now sought to determine whether or not the global regulatory mechanism known as catabolite repression (formerly also called glucose repression) might be involved. We therefore tested glucose (the archetypal catabolite repressor), glycerol (a non catabolite-repressing substrate), glucose-6-phosphate (G6P, an exceptionally powerful catabolite repressor) and methyl-alpha-D-glucopyranoside (alphaMG, a strongly catabolite-repressing but non-utilisable glucose analogue), as potential inhibitors of spontaneous mutagenesis in plate incorporation assays, using three distinct mutation detection systems. We found that the numbers of spontaneous Val(r) and Lac+ mutations appearing on the selective plates tended to be highest when the medium contained only a non-repressing primary carbon source (glycerol in the Val(s) --> Val(r) system, lactose in the Lac- --> Lac+ system) and lowest when it had been supplemented with a strongly catabolite-repressing compound such as alphaMG, G6P or glucose. These results would seem to establish that catabolite repression is an important factor in determining the outcome of the spontaneous mutation generation process in E. coli and hence that the numbers of spontaneous mutations which can be expected to arise in any given set of mutation assay conditions may often be dependent upon the levels of catabolite repression which prevail during the course of the assay. The implications of these results for conventional plate-incorporation mutation assays are discussed.

UNIFOLIATA regulates leaf and flower morphogenesis in pea

BACKGROUND

The vegetative phenotype of the pea mutant unifoliata (uni) is a simplification of the wild-type compound leaf to a single leaflet. Mutant uni plants are also self-sterile and the flowers resemble known floral meristem and organ identity mutants. In Antirrhinum and Arabidopsis, mutations in the floral meristem identity gene FLORICAULA/LEAFY (FLO/LFY) affect flower development alone, whereas the tobacco FLO/LFY homologue, NFL, is expressed in vegetative tissues, suggesting that NFL specifies determinacy in the progenitor cells for both flowers and leaves. In this paper, we characterised the pea homologue of FLO/LFY.

RESULTS

The pea cDNA homologue of FLO/LFY, PEAFLO, mapped to the uni locus in recombinant-inbred mapping populations and markers based on PEAFLO cosegregated with uni in segregating sibling populations. The characterisation of two spontaneous uni mutant alleles, one containing a deletion and the other a point mutation in the PEAFLO coding sequences, predicted that PEAFLO corresponds to UNI and that the mutant vegetative phenotype was conferred by the defective PEAFLO gene.

CONCLUSIONS

The uni mutant demonstrates that there are shared regulatory processes in the morphogenesis of leaves and flowers and that floral meristem identity genes have an extended role in plant development. Pleiotropic regulatory genes such as UNI support the hypothesis that leaves and flowers derive from a common ancestral sporophyll-like structure. The regulation of indeterminancy during leaf and flower morphogenesis by UNI may reflect a primitive function for the gene in the pre-angiosperm era.

Spontaneous mutations in bacteria: chance or necessity?

Several investigators have recently reported that significant numbers of appropriately adapted mutants can be induced in bacterial and yeast strains by exposing stationary phase cells to specific environmental challenges. The resulting mutants are said to be both selection-induced and demonstrably non-random in origin; if this interpretation is correct, it is in direct conflict with the conventional neo-Darwinian view, which is that spontaneous mutants are truly random in origin and arise without the intervention of any overtly adaptive forces. We believe that there are alternative ways of accounting for the appearance of many (and probably all) of the additional mutants which proponents of the adaptive mutation theory claim are observed only after they applied the appropriate selective pressure. Having reviewed the available evidence, we consider that most (if not all) of the sorts of mutants which are said to have been induced following exposure of stationary-phase cells to intense selective pressure are equally likely to have been generated during the operation of certain well-known, conventional (and essentially random) cellular DNA repair processes. Evidence in support of our view can be found in the mainstream literature on the origins of spontaneous mutations. We also note that some of the molecular models which have recently been proposed to explain the production of selection-induced mutations preferentially (or even only) in genes of adaptive significance may turn out to be of considerable interest in their own right, even although the mutants whose origins they were intended to explain may turn out to have arisen in a manner which is totally independent of the conditions used for their selection.

Core antigen mutations of human hepatitis B virus in hepatomas accumulate in MHC class II-restricted T cell epitopes

Despite the extensive molecular information on serum-derived human hepatitis B viruses (HBV), liver-derived replicative HBV genomes have remained largely uninvestigated. We have examined the sequences of the entire core antigen (nucleocapsid) of liver-derived HBVs in 15 different hepatoma patients. Bona fide mutations, rather than subtype polymorphism, have been identified based on the high-frequency occurrence of structural differences from wild type at the highly evolutionarily conserved positions, instead of at the positions known to contain genetic heterogeneity among different isolates from different geographic locations. The distribution of these naturally occurring mutations of HBV core gene appears to be nonrandom and is found predominantly within three major (I, IV, and V) and four minor domains (II, III, VI, and VII). In general, domain IV mutations correlate with domain V mutations. The replicative HBV DNAs tend to accumulate a higher number of mutated core domains than the integrated HBV DNAs. At the domain level, there is no significant difference in HBV core mutation frequencies between the liver tumors and the adjacent nontumorous livers. Strikingly, domains I, III, and V coincide with three major known T cell epitopes within the core protein in acute and chronic hepatitis B patients. Furthermore, these domains coincide with HLA class II-restricted T cell epitopes, rather than with the conventional HLA class I-restricted epitopes of cytotoxic T lymphocytes. Our results support the hypothesis that HBV core antigen variants can accomplish immunoevasion via accumulated escape mutations. In addition, they also provide a potential molecular explanation for the maintenance of persistent infection of human hepatitis B virus in chronic carriers.