The challenge of translating ischemic conditioning from animal models to humans: the role of comorbidities

Following a period of ischemia (local restriction of blood supply to a tissue), the restoration of blood supply to the affected area causes significant tissue damage. This is known as ischemia-reperfusion injury (IRI) and is a central pathological mechanism contributing to many common disease states. The medical complications caused by IRI in individuals with cerebrovascular or heart disease are a leading cause of death in developed countries. IRI is also of crucial importance in fields as diverse as solid organ transplantation, acute kidney injury and following major surgery, where post-operative organ dysfunction is a major cause of morbidity and mortality. Given its clinical impact, novel interventions are urgently needed to minimize the effects of IRI, not least to save lives but also to reduce healthcare costs. In this Review, we examine the experimental technique of ischemic conditioning, which entails exposing organs or tissues to brief sub-lethal episodes of ischemia and reperfusion, before, during or after a lethal ischemic insult. This approach has been found to confer profound tissue protection against IRI. We discuss the translation of ischemic conditioning strategies from bench to bedside, and highlight where transition into human clinical studies has been less successful than in animal models, reviewing potential reasons for this. We explore the challenges that preclude more extensive clinical translation of these strategies and emphasize the role that underlying comorbidities have in altering the efficacy of these strategies in improving patient outcomes.KEY WORDS: Comorbidities, Ischemic postconditioning, Ischemic preconditioning, Remote ischemic preconditioning     

Top-Down Proteomic Identification of Shiga Toxin 2 Subtypes from Shiga Toxin-Producing Escherichia coli by Matrix-Assisted Laser Desorption Ionization–Tandem Time of Flight Mass Spectrometry

We have analyzed 26 Shiga toxin-producing Escherichia coli (STEC) strains for Shiga toxin 2 (Stx2) production using matrix-assisted laser desorption ionization (MALDI)–tandem time of flight (TOF-TOF) tandem mass spectrometry (MS/MS) and top-down proteomic analysis. STEC strains were induced to overexpress Stx2 by overnight culturing on solid agar supplemented with either ciprofloxacin or mitomycin C. Harvested cells were lysed by bead beating, and unfractionated bacterial cell lysates were ionized by MALDI. The A2 fragment of the A subunit and the mature B subunit of Stx2 were analyzed by MS/MS. Sequence-specific fragment ions were used to identify amino acid subtypes of Stx2 using top-down proteomic analysis using software developed in-house at the U.S. Department of Agriculture (USDA). Stx2 subtypes (a, c, d, f, and g) were identified on the basis of the mass of the A2 fragment and the B subunit as well as from their sequence-specific fragment ions by MS/MS (postsource decay). Top-down proteomic identification was in agreement with DNA sequencing of the full Stx2 operon (stx₂) for all strains. Top-down results were also compared to a bioassay using a Vero-d2EGFP cell line. Our results suggest that top-down proteomic identification is a rapid, highly specific technique for distinguishing Stx2 subtypes.     

Autoinsertion of soluble oligomers of Alzheimer's Aβ(1–42) peptide into cholesterol-containing membranes is accompanied by relocation of the sterol towards the bilayer surface

Background  

Soluble Alzheimer's Aβ oligomers autoinsert into neuronal cell membranes, contributing to the pathology of Alzheimer's Disease (AD), and elevated serum cholesterol is a risk factor for AD, but the reason is unknown. We investigated potential connections between these two observations at the membrane level by testing the hypothesis that Aβ(1–42) relocates membrane cholesterol.     

Targeted disruption of cubilin reveals essential developmental roles in the structure and function of endoderm and in somite formation

Background  

Cubilin is a peripheral membrane protein that interacts with the integral membrane proteins megalin and amnionless to mediate ligand endocytosis by absorptive epithelia such as the extraembryonic visceral endoderm (VE).     

A comparative in vitro investigation into the effects of cooked meats on the human faecal microbiota

Protein fermentation is one of the important microbial activities in the human colon. Meat foods rich in protein provide substantial resource for this metabolic activity. However, little information exists on the relative impact of different meats on the composition and activities of the human gut microbiota. Similarly, little information is available on the confounding effects of cooking on these activities. In this study, beef, chicken and fish (salmon) were examined in vitro for their impact on the human faecal microbiota. The influence of cooking method was also investigated by using either frying or boiling. Upon fermentation over 48 h the Clostridium perfringens/histolyticum group increased significantly in number in the beef fermentations, either fried (p = 0.023) or boiled (p = 0.017). Cooking method appeared to influence Clostridium spp. growth, with higher numbers in fried meat compared to boiled meats after 5 h (p = 0.024) and 48 h (p = 0.003) fermentation. Significant differences between meat types were also seen for numbers of Bifidobacterium spp. at 48 h (p = 0.028), Bacteroides group at 24 h (p = 0.016) as well as Coriobacterium/Atopobium group at 10 h (p = 0.038). Most types of short chain fatty acids increased significantly in concentration over the experiment (p < 0.05). Significant differences between meat types were found in n-butyric acid production at 24, 30 and 48 h (p = 0.015, p = 0.024 and p = 0.035 respectively) and in i-valeric acid production at 10, 24, 30 and 48 h (p = 0.026, p = 0.002, p = 0.019 and p = 0.022 respectively). The concentration of i-valeric acid differed significantly between cooking methods at 24 h (p = 0.042). These findings suggest that both the type of meat and cooking process can influence fermentation profiles within the human gut microbiota. Interactions between ingested cooked meats and the gut microbiota may represent a novel corollary to mechanisms underlying the observed increased risk of intestinal and systemic diseases associated with high intake of certain meats/processed meats.     

The Pleistocene archaeology and environments of the Wasiriya Beds, Rusinga Island, Kenya

Western Kenya is well known for abundant early Miocene hominoid fossils. However, the Wasiriya Beds of Rusinga Island, Kenya, preserve a Pleistocene sedimentary archive with radiocarbon age estimates of >33–45 ka that contains Middle Stone Age artifacts and abundant, well-preserved fossil fauna: a co-occurrence rare in eastern Africa, particularly in the region bounding Lake Victoria. Artifacts and fossils are associated with distal volcanic ash deposits that occur at multiple localities in the Wasiriya Beds, correlated on the basis of geochemical composition as determined by electron probe microanalysis. Sediment lithology and the fossil ungulates suggest a local fluvial system and associated riparian wooded habitat within a predominantly arid grassland setting that differs substantially from the modern environment, where local climate is strongly affected by moisture availability from Lake Victoria. In particular, the presence of oryx (Oryx gazella) and Grevy’s zebra (Equus grevyi) suggest a pre-Last Glacial Maximum expansion of arid grasslands, an environmental reconstruction further supported by the presence of several extinct specialized grazers (Pelorovis antiquus, Megalotragus sp., and a small alcelaphine) that are unknown from Holocene deposits in eastern Africa. The combination of artifacts, a rich fossil fauna, and volcaniclastic sediments makes the Wasiriya Beds a key site for examining the Lake Victoria basin, a biogeographically important area for understanding the diversification and dispersal of Homo sapiens from Africa, whose pre-Last Glacial Maximum history remains poorly understood.     

Cyclase-associated Protein (CAP) Acts Directly on F-actin to Accelerate Cofilin-mediated Actin Severing across the Range of Physiological pH

Fast actin depolymerization is necessary for cells to rapidly reorganize actin filament networks. Utilizing a Listeria fluorescent actin comet tail assay to monitor actin disassembly rates, we observed that although a mixture of actin disassembly factors (cofilin, coronin, and actin-interacting protein 1 is sufficient to disassemble actin comet tails in the presence of physiological G-actin concentrations this mixture was insufficient to disassemble actin comet tails in the presence of physiological F-actin concentrations. Using biochemical complementation, we purified cyclase-associated protein (CAP) from thymus extracts as a factor that protects against the inhibition of excess F-actin. CAP has been shown to participate in actin dynamics but has been thought to act by liberating cofilin from ADP·G-actin monomers to restore cofilin activity. However, we found that CAP augments cofilin-mediated disassembly by accelerating the rate of cofilin-mediated severing. We also demonstrated that CAP acts directly on F-actin and severs actin filaments at acidic, but not neutral, pH. At the neutral pH characteristic of cytosol in most mammalian cells, we demonstrated that neither CAP nor cofilin are capable of severing actin filaments. However, the combination of CAP and cofilin rapidly severed actin at all pH values across the physiological range. Therefore, our results reveal a new function for CAP in accelerating cofilin-mediated actin filament severing and provide a mechanism through which cells can maintain high actin turnover rates without having to alkalinize cytosol, which would affect many biochemical reactions beyond actin depolymerization.     

Apes and Tricksters: The Evolution and Diversification of Humans’ Closest Relatives

The evolutionary history of humans comprises an important but small branch on the larger tree of ape evolution. Today’s hominoids—gibbons, orangutans, gorillas, chimpanzees, and humans—are a meager representation of the ape diversity that characterized the Old World from 23–5 million years ago. In this paper, I briefly review this evolutionary history focusing on features important for understanding modern ape and human origins. As the full complexity of ape evolution is beyond this review, I characterize major geographic, temporal, and phylogenetic groups using a few flagship taxa. Improving our knowledge of hominoid evolution both complicates and clarifies studies of human origins. On one hand, features thought to be unique to the human lineage find parallels in some fossil ape species, reducing their usefulness for identifying fossil humans. On the other hand, the Miocene record of fossil apes provides an important source for generating hypotheses about the ancestral human condition; this is particularly true given the dearth of fossils representing our closest living relatives: chimpanzees and gorillas.     

Escaping the fate of Sisyphus: assessing resistome hybridization baits for antimicrobial resistance gene capture

Finding, characterizing and monitoring reservoirs for antimicrobial resistance (AMR) is vital to protecting public health. Hybridization capture baits are an accurate, sensitive and cost-effective technique used to enrich and characterize DNA sequences of interest, including antimicrobial resistance genes (ARGs), in complex environmental samples. We demonstrate the continued utility of a set of 19 933 hybridization capture baits designed from the Comprehensive Antibiotic Resistance Database (CARD)v1.1.2 and Pathogenicity Island Database (PAIDB)v2.0, targeting 3565 unique nucleotide sequences that confer resistance. We demonstrate the efficiency of our bait set on a custom-made resistance mock community and complex environmental samples to increase the proportion of on-target reads as much as >200-fold. However, keeping pace with newly discovered ARGs poses a challenge when studying AMR, because novel ARGs are continually being identified and would not be included in bait sets designed prior to discovery. We provide imperative information on how our bait set performs against CARDv3.3.1, as well as a generalizable approach for deciding when and how to update hybridization capture bait sets. This research encapsulates the full life cycle of baits for hybridization capture of the resistome from design and validation (both in silico and in vitro) to utilization and forecasting updates and retirement.