Replicate plating: does it increase reliability?

K.K. WILLE, B.R. VOWELS, A.N. FOGLIA, C.A. BERGE, B.M. SCHNELL AND F.W. BRIESE. 1996. As a part of a clinical study to evaluate the antibacterial effect of a topically applied erythromycin gel, microbiological specimens were taken from two groups of patients : one group using 2% erythromycin gel and the other group using a placebo gel. These specimens were plated in triplicate using a common source on bacteriological media using standard procedures. After the appropriate incubation times, the numbers of aerobic and anaerobic organisms were counted separately from each of three plates. A comparison of the bacterial colony counts from the replicate plates showed a high degree of similarity for each type of organism. Tests for treatment differences in organism counts were performed based on single, double and triplicate plating. The results obtained were almost identical, suggesting that replicate plating from a common source is no more accurate than single plating. The only apparent advantage of this type of replicate plating is heightened confidence in the reliability of bacterial counts from single plates.     

Theobroma cacao L.: a genetic linkage map and quantitative trait loci analysis

A genetic linkage map of Theobroma cacao (cocoa) has been constructed from 131 backcross trees derived from a cross between a single tree of the variety Catongo and an F1 tree from the cross of Catongo by Pound 12. The map comprises 138 markers: 104 RAPD loci, 32 RFLP loci and two morphologic loci. Ten linkage groups were found which cover 1068 centimorgans (cM). Only six (4%) molecular-marker loci show a significant deviation from the expected 11 segregation ratio.The average distance between two adjacent markers is 8.3 cM. The final genome-size estimates based on two-point linkage data ranged from 1078 to 1112 cM for the cocoa genome. This backcross progeny segregates for two apparently single gene loci controlling (1) anthocyanidin synthesis (Anth) in seeds, leaves and flowers and (2) self-compatibility (Autoc). The Anth locus was found to be 25 cM from Autoc and two molecular markers co-segregate with Anth. The genetic linkage map was used to localize QTLs for early flowering, trunk diameter, jorquette height and ovule number in the BC₁ generation using both single-point ANOVA and interval mapping. A minimum number of 2–4 QTLs (P<0.01) involved in the genetic expression of the traits studied was detected. Coincident map locations of a QTL for jorquette height and trunk diameter suggests the possibility of pleiotropic effects in cocoa for these traits. The combined estimated effects of the different mapped QTLs explained between 11.2% and 25.8% of the phenotypic variance observed in the BC₁ population.     

Cytoplasmic granule formation in mouse pancreatic acinar cells. Evidence for formation of immature granules (condensing vacuoles) by aggregation and fusion of progranules of unit size,and for reductions in membrane surface area and immature granule volume during granule maturation

We used a computer-assisted morphometry approach to analyze quantitatively the process of cytoplasmic granule formation in mouse pancreatic acinar cells stimulated with pilocarpine to induce secretion. Our findings suggest that each condensing vacuole/immature granule of pancreatic acinar cells is formed by the progressive aggregation of 106 to 128 unit progranules of narrowly fixed volume, define a range of 7.7 to 9.2 for the factor of volume condensation between the largest immature granules and the mature unit granule, and predict that the formation of a single mature unit granule by the aggregation and fusion of unit progranules involves a net reduction of at least 95% in the amount of membrane surface area associated with these structures.     

Fine mapping of the Autosomal Dominant Split Hand/Split Foot Locus on Chromosome 7, Band q21.3-q22.1

Split hand/split foot (SHFD) is a human developmental defect characterized by missing digits, fusion of remaining digits, and a deep median cleft in the hands and feet. Cytogenetic studies of deletions and translocations associated with this disorder have indicated that an autosomal dominant split hand/split foot locus (gene SHFD1) maps to 7q21-q22. To characterize the SHFD1 locus, somatic cell hybrid lines were constructed from cytogenetically abnormal individuals with SHFD. Molecular analysis resulted in the localization of 93 DNA markers to one of 10 intervals surrounding the SHFD1 locus. The translocation breakpoints in four SHFD patients were encompassed by the smallest region of overlap among the SHFD-associated deletions. The order of DNA markers in the SHFD1 critical region has been defined as PON–D7S812–SHFD1–D7S811–ASNS. One DNA marker, D7S811, detected altered restriction enzyme fragments in three patients with translocations when examined by pulsed-field gel electro-phoresis (PFGE). These data map SHFD1, a gene that is crucial for human limb differentiation, to a small interval in the q21.3-q22.1 region of human chromosome 7.     

Ern?hrungsphysiologie des Blaunackenmausvogels (Urocolius macrourus pulcher)

Zusammenfassung Beim Blaunackenmausvogel (Urocolius macrourus pulcher) wurde die Ausnutzung der verschiedenen Nährstoffe (Fette, Eiweiße, Kohlenhydrate) und die Assimilationseffizienz des Gesamtfutters untersucht. Mausvögel sind Vegetarier und hauptsächlich frugivor. Im Versuch erhielten die Vögel vier Diäten: I. Mischfutter (Bananen, Salat, gekochtes Ei, gekochter Reis, Apfel); II. Bananen; III. Fruchtfutter (Pfirsiche und Birnen); IV. Eiweißfutter (Quark und gekochtes Weißei). Die minimalen Darmpassagezeiten betrugen für alle vier Diäten zusammengefaßt zwischen 6 und 18 min. Damit kommen die Mausvögel an die Werte für Nektarfresser heran (unter 15 min). Der Darmtrakt ist mit 19,0 ±2,4 cm (n = 16) für einen Vogel dieser Körpermasse ( 56,4 ±2,7 g; 49,2 ±2,9 g) extrem kurz und zeigt den für Fruchtfresser typischen einfachen Bau. Blinddärme fehlen. Die mittlere Gesamteffizienz für die vier Diäten liegt bei 71,0 %. Die Werte variieren in einem relativ engen Bereich zwischen 65,9 % (Banane) und 74,0 % (Mischfutter). Damit sind Blaunackenmausvögel innerhalb der Vögel als relativ schlechte Nahrungsverwerter zu bezeichnen. Für Fruchtfresser allgemein werden allerdings noch niedrigere Werte zwischen 30 % und 70 % angegeben. Die Assimilationsrate der einzelnen Nährstoffe hängt in starkem Maße vom Angebot im Futter ab. Die Zusammensetzung der assimilierten Nahrung zeigt, daß Kohlenhydrate mit 89,0–91,1 % den weitaus größten Anteil am Energiestoffwechsel haben. Vermutlich werden nur gelöste oder leicht verdauliche Einfachzucker bzw. Stärken verwertet. Zellulose wird praktisch ungenutzt ausgeschieden. Fette und Proteine spielen unter Normalbedingungen nur eine untergeordnete Rolle. Der Energieumsatz ist nahrungsabhängig und beträgt 62,5 J/g·h bei der Bananendiät, 69,2 J/g·h bei der Fruchtdiät, 87,3 J/g·h bei der Eiweißdiät und 99,6 J/g·h beim Mischfutter.

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Nutrient physiology of the Blue-naped Mousebird (Urocolius macrourus pulcher)

Blue-naped Mousebirds were fed with four different diets: I. mixed food (bananas, salad, boiled eggs, boiled rice, apples); II. bananas only; III. soft fruits (pears and peaches); and IV. food enriched with protein (curd cheese and egg-white). The minimal times for food passage through the digestive tract were 6–18 min altogether. This is similar to the data known from nectarivorous birds (<15 min). The intestines are extremely short (19,0 ±2,4 cm; n = 16) and simple-structured, without specialization and without any caeca. The overall efficiency for the diets with 71,0 %, ranging between 65,9 % (bananas) and 74,0 % (mixed food), is relatively low. However, for frugivorous birds in general, far lower efficiencies are recorded (30–70 %). The assimilation efficiencies of nutrients depend on their amount in food and the physiological and seasonal requirements. The composition of the assimilated food shows that carbohydrates, having the largest part with 89,0–91,1 %, are most important for energy supply. Presumably, the birds utilize only sugars being easy to digest, because cellulose is removed. Fat and protein are playing a subordinate role in metabolism. The metabolic turnover differs with the diet and ranges between 62,5 J/g·h (bananas), 69,2 J/g·h (fruits), 87,3 J/g·h (protein food) and 99,6 J/g·h (mixed food).

     

Two distinct P element subfamilies in the genome of Drosophila bifasciata

The genome of Drosophila bifasciata harbours two distinct subfamilies of P-homologous sequences, designated M-type and O-type elements based on similarities to P element sequences from other species. Both subfamilies have some general features in common: they are of similar length (M-type: 2935 bp, O-type: 2986 bp), are flanked by direct repeats of 8 by (the presumptive target sequence), contain terminal inverted repeats, and have a coding region consisting of four exons. The splice sites are at homologous positions and the exons have the coding capacity for proteins of 753 amino acids (M-type) and 757 amino acids (O-type). It seems likely that both types of element represent functional transposons. The nucleotide divergence of the two P element subfamilies is high (31%). The main structural difference is observed in the terminal inverted repeats. Whereas the termini of M-type elements consist of 31 by inverted repeats, the inverted repeats of the O-type elements are interrupted by non-complementary stretches of DNA, 12 by at the 5 end and 14 by at the 3 end. This peculiarity is shared by all members of the O-type subfamily. Comparison with other P element sequences indicates incongruities between the phylogenies of the species and the P transposons. M-type and O-type elements apparently have no common origin in the D. bifasciata lineage. The M-type sequence seems to be most closely related to the P element from Scaptomyza pallida and thus could be considered as a more recent invader of the D. bifasciata gene pool. The origin of the O-type elements cannot be unequivocally deduced from the present data. The sequence comparison also provides new insights into conserved domains with possible implications for the function of P transposons.     

Genetic and biochemical properties of an extracellular neutral metalloprotease from Staphylococcus hyicus subsp. hyicus

The gene encoding the extracellular neutral metalloprotease ShpI from Staphylococcus hyicus subsp. hyicus was cloned. DNA sequencing revealed an ORF of 1317 nucleotides encoding a 438 amino acid protein with Mr of 49698. When the cloned gene was expressed in Staphylococcus carnosus, a 42 kDa protease was found in the culture medium. The protease was purified from both S. carnosus (pCAshp1) and S. hyicus subsp. hyicus. The N-terminal amino acid sequences of the two proteases revealed that ShpI is organized as a pre-pro-enzyme with a proposed 26 amino acid signal peptide, a 75 amino acid hydrophilic pro-region, and a 337 amino acid extracellular mature form with a calculated Mr of 38394. The N-termini showed microheterogeneity in both host strains. ShpI had a maximum proteolytic activity at 55°C and pH 7.4–8.5. The protease, which had a low substrate specificity, could be inhibited by metal- and zinc-specific inhibitors, such as EDTA and 1,10-phenanthroline. Insensitivity to phosphoramidon separates ShpI from the thermolysin-like family. The conserved Zn²⁺ binding motif, the only homology to other proteases, and the reactivation of the apoenzyme by Zn²⁺, indicated that Zn²⁺ is the catalytic ion. Ca²⁺ very probably acts as a stabilizer. We also demonstrated the presence of a second extracellular protease in S. hyicus subsp. hyicus.     

Identification and Cloning of Genes Involved in Specific Desulfurization of Dibenzothiophene by Rhodococcus sp. Strain IGTS8

The gram-positive bacterium Rhodococcus sp. strain IGTS8 is able to remove sulfur from certain aromatic compounds without breaking carbon-carbon bonds. In particular, sulfur is removed from dibenzothiophene (DBT) to give the final product, 2-hydroxybiphenyl. A genomic library of IGTS8 was constructed in the cosmid vector pLAFR5, but no desulfurization phenotype was imparted to Escherichia coli. Therefore, IGTS8 was mutagenized, and a new strain (UV1) was selected that had lost the ability to desulfurize DBT. The genomic library was transferred into UV1, and several colonies that had regained the desulfurization phenotype were isolated, though free plasmid could not be isolated. Instead, vector DNA had integrated into either the chromosome or a large resident plasmid. DNA on either side of the inserted vector sequences was cloned and used to probe the original genomic library in E. coli. This procedure identified individual cosmid clones that, when electroporated into strain UV1, restored desulfurization. When the origin of replication from a Rhodococcus plasmid was inserted, the efficiency with which these clones transformed UV1 increased 20- to 50-fold and they could be retrieved as free plasmids. Restriction mapping and subcloning indicated that the desulfurization genes reside on a 4.0-kb DNA fragment. Finally, the phenotype was transferred to Rhodococcus fascians D188-5, a species normally incapable of desulfurizing DBT. The mutant strain, UV1, and R. fascians produced 2-hydroxybiphenyl from DBT when they contained appropriate clones, indicating that the genes for the entire pathway have been isolated.