Acid-Adapted Strains of Escherichia coli K-12 Obtained by Experimental Evolution

Enteric bacteria encounter a wide range of pHs throughout the human intestinal tract. We conducted experimental evolution of Escherichia coli K-12 to isolate clones with increased fitness during growth under acidic conditions (pH 4.5 to 4.8). Twenty-four independent populations of E. coli K-12 W3110 were evolved in LBK medium (10 g/liter tryptone, 5 g/liter yeast extract, 7.45 g/liter KCl) buffered with homopiperazine-N,N′-bis-2-(ethanosulfonic acid) and malate at pH 4.8. At generation 730, the pH was decreased to 4.6 with HCl. By 2,000 generations, all populations had achieved higher endpoint growth than the ancestor at pH 4.6 but not at pH 7.0. All evolving populations showed a progressive loss of activity of lysine decarboxylase (CadA), a major acid stress enzyme. This finding suggests a surprising association between acid adaptation and moderation of an acid stress response. At generation 2,000, eight clones were isolated from four populations, and their genomes were sequenced. Each clone showed between three and eight missense mutations, including one in a subunit of the RNA polymerase holoenzyme (rpoB, rpoC, or rpoD). Missense mutations were found in adiY, the activator of the acid-inducible arginine decarboxylase (adiA), and in gcvP (glycine decarboxylase), a possible acid stress component. For tests of fitness relative to that of the ancestor, lacZ::kan was transduced into each strain. All acid-evolved clones showed a high fitness advantage at pH 4.6. With the cytoplasmic pH depressed by benzoate (at external pH 6.5), acid-evolved clones showed decreased fitness; thus, there was no adaptation to cytoplasmic pH depression. At pH 9.0, acid-evolved clones showed no fitness advantage. Thus, our acid-evolved clones showed a fitness increase specific to low external pH.     

Criteria for assessing maturity of skulls in the common dolphin,Delphinus sp., from New Zealand waters

Knowledge about the maturity status of specimens included in evolutionary, taxonomic or life history investigations is fundamentally important. This study investigated the use of the degree of cranial suture fusion, the developmental status of cranial bones, and the degree of tooth wear as indicators for cranial maturity status in Delphinus sp. from New Zealand waters. In total, 15 sutures, one joint and three nonmetric characters were assessed on 66 skulls obtained from stranded and bycaught individuals sampled between 1932 and 2011. A suture index (SI) was computed based on 10 sutures, in which degree of fusion was correlated with age and the three misclassification indices (MI), calculated for a given suture, were <50%. In addition to these, five premaxilla‐maxilla fusion and seven tooth wear categories were assessed. Results suggest that New Zealand Delphinus sp. skulls should be regarded as cranially mature if at least two of the following criteria are met: (1) individuals assessed as sexually mature, (2) aged ≥ 11 yr, (3) SI ≥ 8, and (4) premaxilla‐maxilla fusion ≥ 75% of the length of the dorsal side of the rostrum. Presence of any number of rostral teeth worn to the gum line provided further evidence for cranial maturity.     

Periplasmic Acid Stress Increases Cell Division Asymmetry (Polar Aging) of Escherichia coli

Under certain kinds of cytoplasmic stress, Escherichia coli selectively reproduce by distributing the newer cytoplasmic components to new-pole cells while sequestering older, damaged components in cells inheriting the old pole. This phenomenon is termed polar aging or cell division asymmetry. It is unknown whether cell division asymmetry can arise from a periplasmic stress, such as the stress of extracellular acid, which is mediated by the periplasm. We tested the effect of periplasmic acid stress on growth and division of adherent single cells. We tracked individual cell lineages over five or more generations, using fluorescence microscopy with ratiometric pHluorin to measure cytoplasmic pH. Adherent colonies were perfused continually with LBK medium buffered at pH 6.00 or at pH 7.50; the external pH determines periplasmic pH. In each experiment, cell lineages were mapped to correlate division time, pole age and cell generation number. In colonies perfused at pH 6.0, the cells inheriting the oldest pole divided significantly more slowly than the cells inheriting the newest pole. In colonies perfused at pH 7.50 (near or above cytoplasmic pH), no significant cell division asymmetry was observed. Under both conditions (periplasmic pH 6.0 or pH 7.5) the cells maintained cytoplasmic pH values at 7.2–7.3. No evidence of cytoplasmic protein aggregation was seen. Thus, periplasmic acid stress leads to cell division asymmetry with minimal cytoplasmic stress.     

Three Dimensional Culture of Human Renal Cell Carcinoma Organoids

Renal cell carcinomas arise from the nephron but are heterogeneous in disease biology, clinical behavior, prognosis, and response to systemic therapy. Development of patient-specific in vitro models that efficiently and faithfully reproduce the in vivo phenotype may provide a means to develop personalized therapies for this diverse carcinoma. Studies to maintain and model tumor phenotypes in vitro were conducted with emerging three-dimensional culture techniques and natural scaffolding materials. Human renal cell carcinomas were individually characterized by histology, immunohistochemistry, and quantitative PCR to establish the characteristics of each tumor. Isolated cells were cultured on renal extracellular matrix and compared to a novel polysaccharide scaffold to assess cell-scaffold interactions, development of organoids, and maintenance of gene expression signatures over time in culture. Renal cell carcinomas cultured on renal extracellular matrix repopulated tubules or vessel lumens in renal pyramids and medullary rays, but cells were not observed in glomeruli or outer cortical regions of the scaffold. In the polysaccharide scaffold, renal cell carcinomas formed aggregates that were loosely attached to the scaffold or free-floating within the matrix. Molecular analysis of cell-scaffold constructs including immunohistochemistry and quantitative PCR demonstrated that individual tumor phenotypes could be sustained for up to 21 days in culture on both scaffolds, and in comparison to outcomes in two-dimensional monolayer cultures. The use of three-dimensional scaffolds to engineer a personalized in vitro renal cell carcinoma model provides opportunities to advance understanding of this disease.     

A bacterial metabolite induces glutathione-tractable proteostatic damage,proteasomal disturbances,and PINK1-dependent autophagy in C. elegans

Gene-by-environment interactions are thought to underlie the majority of idiopathic cases of neurodegenerative disease. Recently, we reported that an environmental metabolite extracted from Streptomyces venezuelae increases ROS and damages mitochondria, leading to eventual neurodegeneration of C. elegans dopaminergic neurons. Here we link those data to idiopathic disease models that predict loss of protein handling as a component of disorder progression. We demonstrate that the bacterial metabolite leads to proteostatic disruption in multiple protein-misfolding models and has the potential to synergistically enhance the toxicity of aggregate-prone proteins. Genetically, this metabolite is epistatically regulated by loss-of-function to pink-1, the C. elegans PARK6 homolog responsible for mitochondrial maintenance and autophagy in other animal systems. In addition, the metabolite works through a genetic pathway analogous to loss-of-function in the ubiquitin proteasome system (UPS), which we find is also epistatically regulated by loss of PINK-1 homeostasis. To determine remitting counter agents, we investigated several established antioxidants and found that glutathione (GSH) can significantly protect against metabolite-induced proteostasis disruption. In addition, GSH protects against the toxicity of MG132 and can compensate for the combined loss of both pink-1 and the E3 ligase pdr-1, a Parkin homolog. In assessing the impact of this metabolite on mitochondrial maintenance, we observe that it causes fragmentation of mitochondria that is attenuated by GSH and an initial surge in PINK-1-dependent autophagy. These studies mechanistically advance our understanding of a putative environmental contributor to neurodegeneration and factors influencing in vivo neurotoxicity.Protein homeostasis (proteostasis) encompasses the process of translation, folding, compartmentalization, and degradation of proteins to maintain the long-term survival and functionality of the cell.^{1, 2, 3} When proteins become misfolded they must be refolded or degraded to prevent disruptions to critical processes that result from proteotoxic stress.^{3, 4} Surveillance machinery that combats proteotoxic stress includes the ubiquitin proteasome system (UPS), retrograde chaperone-inducing signaling systems termed unfolded protein responses (UPR), and bulk destruction through autophagy. The cell also utilizes protein clearance machinery to induce the destruction of entire organelles, such as mitochondria, when they no longer function correctly^{5, 6} to protect the cell from reactive oxygen species (ROS). The last line of defense includes antioxidants in order to maintain a reduced intracellular state and attenuate damage to proteins.^{7, 8, 9, 10, 11} Often, these regulated mechanisms are challenged by both the environment and genetic susceptibility factors. The integration of both, via gene-by-environment interactions, has been hypothesized to underlie many idiopathic neurodegenerative disorders.^{12, 13, 14} Understanding how the environment contributes to disease pathologies is important for understanding neurodegeneration.Sources of environmental stressors are understudied and largely limited to human-derived toxicants such as pesticides like rotenone.^{14, 15} However, people living in agricultural environs are often at a greater risk of developing neurodegenerative disorders that cannot be accounted for by human-derived toxicants alone.¹⁶ Environmental contributors may come from natural sources like metabolite-producing bacteria. For instance, bacterial sources have been reported to induce DOPA-responsive movement disorders in mice.¹⁷ Mechanistically, competition strategies among bacteria that produce antibiotics and small metabolites like phenazines that limit the growth of other bacterial species may have off-target effects on mitochondrial homeostasis, leading to ROS, protein damage, and neurodegeneration.¹⁸ Indeed, proteostatic dysfunction, altered mitochondrial dynamics, and elevated ROS production are characteristics of sporadic Parkinson''s disease (PD).^{19, 20, 21}Our laboratory previously demonstrated neurodegeneration induced by unreported small compounds within the growth media of the Gram-positive soil bacterium Streptomyces venezuelae.^{22, 23, 24} These bacterial products induce neuronal death in both C. elegans and cultured human neurons,²² disrupt mitochondrial complex I, induce ROS, and decrease ATP production.²⁵ However, how these observations link to protein homeostasis has not been explored. Here we report that the active fraction of the S. venezuelae media induces disruptions in protein homeostasis, glutathione (GSH)-tractable α-synuclein toxicity, that UPS disruptions are epistatically regulated by loss-of-function to the PARK9 homolog pink-1, and that PINK1-dependent autophagy results in mitochondrial morphology disruptions. These observations indicate that pink-1 and UPS functionality are required for metabolite-induced protein toxicity in C. elegans, suggesting that these pathways may be linked and that environmental contributors to neurodegenerative disease may proceed through pathways implicated in familial forms.     

Isolation and characterization of a basic encephalitogenic protein from the central nervous system of sheep.

A basic protein has been purified from sheep brain. The purified protein sedimented in the analytical centrifuge at 56,000 r.p.m. as an homogenous product. This protein induced an allergic encephalitis when injected into guinea pigs. Some physiochemical properties of the protein were studied: the sedimentation coefficient was 1.52 and the molecular weight was 20,000 +/- 2,000, as estimated by electrophoresis in acrylamide gels containing SDS and urea; the specific extinction coefficient (see article) was 6.01 +/- 0.20. The aminoacid composition of the molecule was determined and its most prominent aspects are a high content of arginine and lysine, the presence of a single tryptophan, the total absence of cysteine and cystine and a blocked N-terminal residue. All these properties are very close to those of human and bovine encephalitogenic proteins.     

Sampling Bias in Roadsides: The Case of Galling Aphids on Pistacia Trees

Sampling along roadsides is convenient and is widely practiced in insect population researches. Ecological conditions in road verges are very different than those prevailing in natural habitats and they affect the annual growth of plants in semi-arid and arid regions. This in turn may improve development, survival and abundance of insects feeding on plants growing in roadsides. These trends may bias the results of sampling. To verify this assertion, we quantified the effects of growing in roadside on annual growth of Pistacia atlantica trees and Pistacia palaestina shrubs and compare two demographic indexes of nine gall-inducing aphid species on trees growing along roads with trees in the open landscape, in Israel. The annual growth of the two host plants was significantly more vigorous in roadsides than away from roads. Tests of Combined Probabilities showed that the likelihood of P. atlantica and P. palaestina to be parasitized by more galls of Fordini species is higher in roadsides than away from roads. Moreover, in the semi-dry regions of Israel, three aphid species on P. atlantica and five species on P. palaestina induced more galls in plants growing along roads than away from roads, while in the rainy Northern region, the difference was not significant between the two habitats. These results indicate a biased evaluation of population size in roadside habitat, which has to be accounted in insect–plant relation researches.     

Bovine skeletal muscle adenosine deaminase. Purification and some properties

A low molecular weight form of adenosine deaminase from bovine skeletal muscle was purified about 930-fold. The enzyme had a mol. wt of 31,000, a Km value for adenosine of 2.37 X 10(-5) M and a pH optimum at 7.0. This enzyme is very resistant to heat inactivation and does not require metal activators or other dialysable cofactors. A possible role in the post-mortem metabolism of adenine nucleotide in skeletal muscle is discussed.     

Diet quality and immunocompetence influence parasite load of roe deer in a fragmented landscape

The influence of landscape structure and host diet on parasite load of wildlife is still largely unknown. We studied a roe deer (Capreolus capreolus) population in a fragmented agricultural landscape in southern France to explore the relationship of gastrointestinal nematode load with spleen mass (to index immunocompetence), faecal nitrogen (to index diet quality), landscape structure and age of 33 hunt-harvested roe deer. Gastrointestinal worm counts were negatively related to faecal nitrogen and spleen mass, explaining respectively 24.7% and 9.2% of the observed variability in parasite load. Landscape structure did not appear to have a direct influence on gastrointestinal worm counts, but since animals from more open areas have a diet that is richer in nitrogen, its influence may be indirect. In conclusion, in the study area, the colonisation of the agricultural landscape does not seem to have increased the risk of gastrointestinal nematode parasitism for roe deer, possibly because access to high-quality food enhances immunocompetence.