Moving a Journal Article-Based Upper-Level Microbiology Dry Lab from In-Person to Online Instruction.

During the spring semester of 2020, a journal article-based upper-level microbiology laboratory course was offered through Western New Mexico University at Glendale Community College in Glendale, AZ. Because most of the students had taken a lower-level microbiology class with a traditional wet laboratory, a dry lab format was used instead. In the first period of each 2-week cycle, a microbiology article selected by the instructor from the primary literature was discussed using a PowerPoint presentation and a detailed study sheet.

Genomic sequencing of Gracilibacillus dipsosauri reveals key properties of a salt-tolerant α-amylase.

Gracilibacillus dipsosauri is a moderately-halophilic Gram-positive bacterium which forms an extracellular α-amylase that is induced by starch, repressed by D-glucose, and active in 2.0 M KCl. Previous studies showed that while enzyme activity could be measured with the synthetic substrate 2-chloro-4-nitrophenyl-α-D-maltotrioside (CNPG3), other assays were inconsistent and the protein showed aberrant mobility during nondenaturing gel electrophoresis.

Inhibition of urease activity in the urinary tract pathogens Staphylococcus saprophyticus and Proteus mirabilis by dimethylsulfoxide (DMSO).

Aims: Urease is a virulence factor for the urinary tract pathogens Staphylococcus saprophyticus and Proteus mirabilis. Dimethylsulfoxide (DMSO) is structurally similar to urea, used as a solvent for urease inhibitors, and an effective treatment for interstitial cystitis/bladder pain syndrome (IC/BPS). The aims of this study were to test DMSO as a urease inhibitor and determine its physiological effects on S.

Biochemistry laboratory reports: Filling in the introduction and discussion.

Laboratory reports written in the style of a standard scientific article are commonly used to assess student learning in biochemistry laboratory courses. While most students can complete the Materials and Methods or Results sections successfully, many have difficulty with the Introduction and Discussion. They fail to place their data in a larger experimental context or to compare their results to those previously published.

L-Proline catabolism by the high G + C Gram-positive bacterium Paenarthrobacter aurescens strain TC1.

Paenarthrobacter aurescens (formerly called Arthrobacter aurescens) strain TC1 is a high G + C Gram-positive aerobic bacterium that can degrade the herbicide atrazine. Analysis of its genome indicated strain TC1 has the potential to form a bifunctional PutA protein containing L-proline dehydrogenase and L-glutamate-γ-semialdehyde dehydrogenase (L-Δ-pyrroline-5-carboxylate dehydrogenase) activities. P.

Browning in apples: Exploring the biochemical basis of an easily-observable phenotype.

Many fruits and vegetables undergo browning when they are cut and the tissue is exposed to the air. This is due to the activity of the enzyme polyphenol oxidase (PPO, EC 1.14.

Limited effectiveness of over-the-counter plant preparations used for the treatment of urinary tract infections as inhibitors of the urease activity from Staphylococcus saprophyticus.

Aims: Urease is a key virulence factor for the Gram-positive urinary tract pathogen Staphylococcus saprophyticus and a potential target for antimicrobial therapy. The enzyme from S. saprophyticus is unusual in that it does not contain cysteine at the active site.

Susceptibility of Escherichia coli to the toxic L-proline analogue L-selenaproline is dependent on two L-cystine transport systems.

Aims: L-Selenaproline (L-selenazolidine-4-carboxylic acid) is a toxic analogue of L-proline that inhibits the growth of the urinary tract pathogen Escherichia coli in both laboratory culture media and normal human urine. The aim of this study was to identify the transport systems involved in its uptake.

Methods And Results: Deletion mutants from the Keio collection were tested for their susceptibility to L-selenaproline (SCA) and L-selenocystine (SeCys) on minimal salts agar medium.

Analysis of strains lacking known osmolyte accumulation mechanisms reveals contributions of osmolytes and transporters to protection against abiotic stress.

Osmolyte accumulation and release can protect cells from abiotic stresses. In Escherichia coli, known mechanisms mediate osmotic stress-induced accumulation of K(+) glutamate, trehalose, or zwitterions like glycine betaine. Previous observations suggested that additional osmolyte accumulation mechanisms (OAMs) exist and their impacts may be abiotic stress specific.

Inhibition of urease activity in the urinary tract pathogen Staphylococcus saprophyticus.

Unlabelled: Urease is a virulence factor for the Gram-positive urinary tract pathogen Staphylococcus saprophyticus. The susceptibility of this enzyme to chemical inhibition was determined using soluble extracts of Staph. saprophyticus strain ATCC 15305.

L-Malate dehydrogenase activity in the reductive arm of the incomplete citric acid cycle of Nitrosomonas europaea.

The autotrophic nitrifying bacterium Nitrosomonas europaea does not synthesize 2-oxoglutarate (α-ketoglutarate) dehydrogenase under aerobic conditions and so has an incomplete citric acid cycle. L-malate (S-malate) dehydrogenase (MDH) from N. europaea was predicted to show similarity to the NADP(+)-dependent enzymes from chloroplasts and was separated from the NAD(+)-dependent proteins from most other bacteria or mitochondria.

L-Proline nutrition and catabolism in Staphylococcus saprophyticus.

Staphylococcus saprophyticus strains ATCC 15305, ATCC 35552, and ATCC 49907 were found to require L-proline but not L-arginine for growth in a defined culture medium. All three strains could utilize L-ornithine as a proline source and contained L-ornithine aminotransferase and Δ(1)-pyrroline-5-carboxylate reductase activities; strains ATCC 35552 and ATCC 49907 could use L-arginine as a proline source and had L-arginase activity. The proline requirement also could be met by L-prolinamide, L-proline methyl ester, and the dipeptides L-alanyl-L-proline and L-leucyl-L-proline.

Susceptibility of Escherichia coli to L-selenaproline and other L-proline analogues in laboratory culture media and normal human urine.

Aims: The aims of this study were to identify analogues of L-proline which inhibit the growth of Escherichia coli in both laboratory culture media and normal human urine and to study their mechanisms of uptake.

Methods And Results: The susceptibility of E. coli to L-proline analogues was studied by radial streak assays on agar plates and by minimal inhibitory concentration determinations in liquid media.

Oxidation of 3,4-dehydro-D-proline and other D-amino acid analogues by D-alanine dehydrogenase from Escherichia coli.

3,4-Dehydro-DL-proline is a toxic analogue of L-proline which has been useful in studying the uptake and metabolism of this key amino acid. When membrane fractions from Escherichia coli strain UMM5 (putA1::Tn5 proC24) lacking both L-proline dehydrogenase and L-Delta(1)-pyrroline-5-carboxylate reductase were incubated with 3,4-dehydro-DL-proline, pyrrole-2-carboxylate was formed. There was no enzyme activity with 3,4-dehydro-L-proline, but activity was restored after racemization of the substrate.

Characterization of a salt-tolerant extracellular a-amylase from Bacillus dipsosauri.

Aims: The aims of this study were to purify and characterize an extracellular alpha-amylase from the salt-tolerant bacterium Bacillus dipsosauri.

Methods And Results: An extracellular alpha-amylase from B. dipsosauri strain DD1 was studied using the synthetic substrate 2-chloro-4-nitrophenyl-alpha-D-maltotrioside.

Oxidation of L-thiazolidine-4-carboxylate by delta1-pyrroline-5-carboxylate reductase in Escherichia coli.

L-Thiazolidine-4-carboxylate (T4C, thiaproline) is a sulfur-containing proline analog that stimulates the immune system in aging mice and inhibits urinary tract pathogens such as Escherichia coli. A constitutive NADP+-dependent T4C dehydrogenase activity was detected in the soluble fraction of a putA::Tn5 mutant of E. coli lacking l-proline dehydrogenase and partially purified by ammonium sulfate precipitation, dye-affinity chromatography on Cibacron Blue 3GA agarose, and ion-exchange chromatography on DEAE-cellulose.

Adaptive characteristics of salt-induced myceloids of Arthrobacter globiformis.

When Arthrobacter globiformis is grown in medium containing increased concentrations of NaCl or decreased levels of cations, the bacteria grow as clusters of branching myceloid cells. The sensitivities of salt-induced and citrate-induced myceloids to several environmental stresses were compared to those of normal exponential-phase bacilli and stationary-phase cocci. Salt-induced myceloids were more resistant than normal cells to ultraviolet light or heat shock at 45 degrees C but not to osmotic upshock or pH 4.

Phylogenetic characterization of a novel salt-tolerant Bacillus species: description of Bacillus dipsosauri sp. nov.

The taxonomic position of a novel halophilic endospore-forming bacterium previously isolated from a desert iguana was investigated by 16S rRNA gene sequencing. Comparative sequence analyses showed the unidentified bacterium to be phylogenetically loosely associated with some other spore-forming (Bacillus pantothenticus, Sporosarcina halophila) and non-spore-forming (Marinococcus albus) halotolerant bacteria. Based on the phenotypic and phylogenetic distinctiveness of the unidentified bacterium, it is proposed that it is classified in the genus Bacillus as a new species, Bacillus dipsosauri.

Sensitivity of Escherichia coli to proline analogues during osmotic stress and anaerobiosis.

The sensitivity of wild-type Escherichia coli K-12 to a series of proline analogues was determined in cultures containing increasing concentrations of NaCl under both aerobic and anaerobic conditions. The bacteria were most sensitive to L-azetidine-2-carboxylate and L-thiazolidine-4-carboxylate. The minimum inhibitory concentrations for these compounds decreased progressively during osmotic stress, but the bacteria were much more sensitive to these proline analogues under aerobic conditions than during anaerobiosis.

Post-transcriptional regulation of a salt-inducible alfalfa gene encoding a putative chimeric proline-rich cell wall protein.

A cDNA previously shown to identify a salt-inducible root-specific transcript in Medicago sativa was used to screen an alfalfa library for the corresponding genomic sequence. One positive clone was recovered. The nucleotide sequence of a subclone contained a 329 bp 5' region upstream of the first ATG codon, a 1143 bp coding segment, and a 447 bp 3'-untranslated region interrupted by a single 475 bp intron.

Oxidation of L-thiazolidine-4-carboxylate by L-proline dehydrogenase in Escherichia coli.

L-Thiazolidine-4-carboxylate (T4C, gamma-thioproline) is a toxic analogue of L-proline. T4C can be oxidized by Escherichia coli to form N-formylcysteine, which is hydrolysed to yield formate and cysteine. To determine if L-proline dehydrogenase (EC 1.

Myceloid cell formation in Arthrobacter globiformis during osmotic stress.

Arthrobacter globiformis was grown in a semi-defined liquid medium containing added solutes to determine the effects of osmotic stress on its reproduction and cell morphology. There was a progressive reduction in the specific growth rate during exponential phase as the concentration of NaCl was increased, although the final yields of the cultures during stationary phase were not affected. Clusters of branching myceloid cells rather than the typical bacillary forms predominated during exponential phase.

Interictal spikes and hippocampal somatostatin levels in temporal lobe epilepsy.

We investigated the relationship between somatostatin-like immunoreactivity (SSLI) and interictal spikes (IIS) in human temporal lobe epileptic tissue. IIS counted manually from depth electrode recordings obtained preoperatively were expressed as spike frequency in anterior, middle, and posterior portions of hippocampus. SSLI was determined by radioimmunoassay (RIA).

Nonspecific inhibition of proline dehydrogenase synthesis in Escherichia coli during osmotic stress.

L-Proline, which is accumulated by Escherichia coli during growth in media of high osmolality, also induces the synthesis of the enzyme degrading it to glutamate. To determine if proline catabolism is inhibited during osmotic stress, proline utilization and the formation of proline dehydrogenase were examined in varying concentrations of NaCl and sucrose. Although the specific growth rate of E.

Identification of a trans-dominant mutation affecting proline dehydrogenase in Escherichia coli.

L-Proline dehydrogenase catalyzes the oxidation of L-proline to delta 1-pyrroline-5-carboxylate, a reaction that is an important step in the utilization of proline as a carbon or nitrogen source by bacteria. A mutant of Escherichia coli K-12 lacking L-leucyl-tRNA:protein transferase had been found previously to contain about five times as much proline dehydrogenase activity as its parent strain. This difference has now been shown to be due to the presence in the parent strain of a previously unrecognized mutation.