Functional Characterization of Bacteria Isolated from Ancient Arctic Soil Exposes Diverse Resistance Mechanisms to Modern Antibiotics

Using functional metagenomics to study the resistomes of bacterial communities isolated from different layers of the Canadian high Arctic permafrost, we show that microbial communities harbored diverse resistance mechanisms at least 5,000 years ago. Among bacteria sampled from the ancient layers of a permafrost core, we isolated eight genes conferring clinical levels of resistance against aminoglycoside, β-lactam and tetracycline antibiotics that are naturally produced by microorganisms. Among these resistance genes, four also conferred resistance against amikacin, a modern semi-synthetic antibiotic that does not naturally occur in microorganisms. In bacteria sampled from the overlaying active layer, we isolated ten different genes conferring resistance to all six antibiotics tested in this study, including aminoglycoside, β-lactam and tetracycline variants that are naturally produced by microorganisms as well as semi-synthetic variants produced in the laboratory. On average, we found that resistance genes found in permafrost bacteria conferred lower levels of resistance against clinically relevant antibiotics than resistance genes sampled from the active layer. Our results demonstrate that antibiotic resistance genes were functionally diverse prior to the anthropogenic use of antibiotics, contributing to the evolution of natural reservoirs of resistance genes.     

Optofluidic rotation of living cells for single‐cell tomography

Flow cytometry provides a high throughput, multi‐dimensional analysis of cells flowing in suspension. In order to combine this feature with the ability to resolve detailed structures in 3D, we developed an optofluidic device that combines a microfluidic system with a dual beam trap. This allows for the rotation of single cells in a continuous flow, around an axis perpendicular to the imaging plane. The combination of both techniques enables the tomographic reconstruction of the 3D structure of the cell. In addition this method is capable to provide detailed 3D structural data for flow cytometry, as it improves the reconstructed z‐resolution of a standard microscopy system to produce images with isotropic resolution in all three axes.

     

Trackway Ratio: A New Look at Trackway Gauge in the Analysis of Quadrupedal Dinosaur Trackways and its Implications for Ichnotaxonomy

A new parameter, the Trackway Ratio (TR), is proposed to supplement the previously used trackway gauge to describe and quantify the relative width of trackways in dinosaur quadrupedal gaits. It is expressed as the ratio of the width of the tracks relative to the total width of the trackway (both measured perpendicular to the long axis of the trackway). The ratio may be used with either pes (PTR) or manus (MTR) tracks. The PTR range of values for wide-, medium- and narrow-gauge trackways of previous authors are provisionally suggested to be ≤35%, 36–49% and ≥50%, respectively. The application of such a ratio would permit a more consistent ichnotaxonomy to be adopted where both track morphology and trackway parameters are used to define ichnotaxa.

Determination of the TR, as well as other parameters, will be affected by track preservation quality. Recent experiments on track simulation in the laboratory have shed further light on observations made in the field concerning the value of track measurements (in particular track length and width) recorded from below the surface on which the maker was moving. Experimental track simulations in the laboratory have shown that the dimensions of transmitted tracks preserved below the surface on which the foot was impressed may vary from 65% to 135% of the true dimensions of the indenter. Two case studies are presented that quantify the errors that may be made on calculating TR and the size, gait and speed of the maker, from trackways if the preservation of the tracks are not fully understood.

It is shown that in individual trackways the PTR may vary along the length of the trackway; so that part of the trackway may be classified as wide-gauge and other parts medium-gauge. There is a relationship between variation in PTR and that of pace angulation along the length of a single trackway. An analysis of 42 trackways, principally sauropod, shows a temporal distribution that does not agree closely with previous suggestions relating to narrow- and wide-gauge trackways.     

Effective caspase inhibition blocks neutrophil apoptosis and reveals Mcl-1 as both a regulator and a target of neutrophil caspase activation

Human tissue inflammation is terminated, at least in part, by the death of inflammatory neutrophils by apoptosis. The regulation of this process is therefore key to understanding and manipulating inflammation resolution. Previous data have suggested that the short-lived pro-survival Bcl-2 family protein, Mcl-1, is instrumental in determining neutrophil lifespan. However, Mcl-1 can be cleaved following caspase activity, and the possibility therefore remains that the observed fall in Mcl-1 levels is due to caspase activity downstream of caspase activation, rather than being a key event initiating apoptosis in human neutrophils.We demonstrate that apoptosis in highly purified neutrophils can be almost completely abrogated by caspase inhibition with the highly effective di-peptide caspase inhibitor, Q-VD.OPh, confirming the caspase dependence of neutrophil apoptosis. Effective caspase inhibition does not prevent the observed fall in Mcl-1 levels early in ultrapure neutrophil culture, suggesting that this fall in Mcl-1 levels is not a consequence of neutrophil apoptosis. However, at later timepoints, declines in Mcl-1 can be reversed with effective caspase inhibition, suggesting that Mcl-1 is both an upstream regulator and a downstream target of caspase activity in human neutrophils.     

Human papillomavirus 18 E1^E4 protein interacts with cyclin A/CDK 2 through an RXL motif

The human papilloma virus E4 protein is highly expressed in late times of infection. Evidence to date suggests that E4 is essential for amplification of the viral genome and that it can influence cell cycle. Examination of the sequences encoding the E4 proteins from several genotypes of human papillomavirus revealed the presence of RXL-containing motifs reminiscent of the cyclin-binding motifs that have been identified in several cyclin-binding proteins. When baculovirus-produced human cyclin E and cyclin A with cdk2 were incubated in vitro with a GST-E4 fusion protein, both cyclin E and A stably interacted with the GST-E4 protein containing the full E4 sequence from HPV18. The interaction was not dependent on the presence of the kinase subunit but was dependent on the integrity of the RXL motif in E4. When incubated with cell extracts from the C33A human cervical carcinoma cell line or when expressed in C33A cells, the GST-E4 protein formed interactions with cyclin A and cdk2 and kinase activity could be demonstrated in the GST-E4 complex. In contrast to the baculovirus-produced cyclin E, cellular cyclin E failed to detectably interact with GST-E4 suggesting that the HPV18 E4 sequences are capable of interacting only with cyclin A in mammalian cells. These observations suggest that human papillomavirus E4 proteins can interact with cyclin A/cdk2, which may contribute to viral manipulation of the host cell cycle.     

Microbial diversity of active layer and permafrost in an acidic wetland from the Canadian High Arctic

The abundance and structure of archaeal and bacterial communities from the active layer and the associated permafrost of a moderately acidic (pH < 5.0) High Arctic wetland (Axel Heiberg Island, Nunavut, Canada) were investigated using culture- and molecular-based methods. Aerobic viable cell counts from the active layer were ～100-fold greater than those from the permafrost (2.5 × 10(5) CFU·(g soil dry mass)(-1)); however, a greater diversity of isolates were cultured from permafrost, as determined by 16S rRNA gene sequencing. Isolates from both layers demonstrated growth characteristics of a psychrotolerant, halotolerant, and acidotolerant community. Archaea constituted 0.1% of the total 16S rRNA gene copy number and, in the 16S rRNA gene clone library, predominantly (71% and 95%) consisted of Crenarchaeota related to Group I. 1b. In contrast, bacterial communities were diverse (Shannon's diversity index, H = ～4), with Acidobacteria constituting the largest division of active layer clones (30%) and Actinobacteria most abundant in permafrost (28%). Direct comparisons of 16S rRNA gene sequence data highlighted significant differences between the bacterial communities of each layer, with the greatest differences occurring within Actinobacteria. Comparisons of 16S rRNA gene sequences with those from other Arctic permafrost and cold-temperature wetlands revealed commonly occurring taxa within the phyla Chloroflexi, Acidobacteria, and Actinobacteria (families Intrasporangiaceae and Rubrobacteraceae).     

Predictable bacterial composition and hydrocarbon degradation in Arctic soils following diesel and nutrient disturbance

Increased exploration and exploitation of resources in the Arctic is leading to a higher risk of petroleum contamination. A number of Arctic microorganisms can use petroleum for growth-supporting carbon and energy, but traditional approaches for stimulating these microorganisms (for example, nutrient addition) have varied in effectiveness between sites. Consistent environmental controls on microbial community response to disturbance from petroleum contaminants and nutrient amendments across Arctic soils have not been identified, nor is it known whether specific taxa are universally associated with efficient bioremediation. In this study, we contaminated 18 Arctic soils with diesel and treated subsamples of each with monoammonium phosphate (MAP), which has successfully stimulated degradation in some contaminated Arctic soils. Bacterial community composition of uncontaminated, diesel-contaminated and diesel+MAP soils was assessed through multiplexed 16S (ribosomal RNA) rRNA gene sequencing on an Ion Torrent Personal Genome Machine, while hydrocarbon degradation was measured by gas chromatography analysis. Diversity of 16S rRNA gene sequences was reduced by diesel, and more so by the combination of diesel and MAP. Actinobacteria dominated uncontaminated soils with <10% organic matter, while Proteobacteria dominated higher-organic matter soils, and this pattern was exaggerated following disturbance. Degradation with and without MAP was predictable by initial bacterial diversity and the abundance of specific assemblages of Betaproteobacteria, respectively. High Betaproteobacteria abundance was positively correlated with high diesel degradation in MAP-treated soils, suggesting this may be an important group to stimulate. The predictability with which bacterial communities respond to these disturbances suggests that costly and time-consuming contaminated site assessments may not be necessary in the future.     

Relationship between upper and lower limb conduit artery vasodilator function in humans

Brachial artery flow-mediated dilation (FMD) is a strong predictor of future cardiovascular disease and is believed to represent a "barometer" of systemic endothelial health. Although a recent study [Padilla et al. Exp Biol Med (Maywood) 235: 1287-1291, 2010] in pigs confirmed a strong correlation between brachial and femoral artery endothelial function, it is unclear to what extent brachial artery FMD represents a systemic index of endothelial function in humans. We conducted a retrospective analysis of data from our laboratory to evaluate relationships between the upper (i.e., brachial artery) vs. lower limb (superficial femoral n = 75; popliteal artery n = 32) endothelium-dependent FMD and endothelium-independent glyceryl trinitrate (GTN)-mediated dilation in young, healthy individuals. We also examined the relationship between FMD assessed in both brachial arteries (n = 42). There was no correlation between brachial and superficial femoral artery FMD (r(2) = 0.008; P = 0.46) or between brachial and popliteal artery FMD (r(2) = 0.003; P = 0.78). However, a correlation was observed in FMD between both brachial arteries (r(2) = 0.34; P < 0.001). Brachial and superficial femoral artery GTN were modestly correlated (r(2) = 0.13; P = 0.007), but brachial and popliteal artery GTN responses were not (r(2) = 0.08; P = 0.11). Collectively, these data indicate that conduit artery vasodilator function in the upper limbs (of healthy humans) is not predictive of that in the lower limbs, whereas measurement of FMD in one arm appears to be predictive of FMD in the other. These data do not support the hypothesis that brachial artery FMD in healthy humans represents a systemic index of endothelial function.     

Adenovirus E1A proteins direct subcellular redistribution of Nek9, a NimA-related kinase

A monoclonal antibody raised against adenovirus E1A-associated cellular proteins recognized Nek9, a NimA-related protein kinase. Subcellular fractionation and immunofluorescence indicated that Nek9 was primarily cytoplasmic with a small portion located in the nucleus whereas E1A was primarily nuclear. Although co-immunoprecipitation experiments indicated that nuclear Nek9 interacted, directly or indirectly, with E1A, the major effect of E1A was to diminish the amount of Nek9 in the nucleus suggesting that E1A alters the subcellular distribution of Nek9 and that the interaction is transient. A Nek9 deletion mutant lacking a central RCC1-like domain interacted stably with E1A and accumulated in the nucleus in the presence of E1A, possibly representing an intermediate stage of the normally transient Nek9/E1A interaction. The interaction of Nek9 with E1A was dependent on the N-terminal sequences of E1A. Attempts to stably overexpress either Nek9 or the kinase-inactive mutant in various cell lines were unsuccessful; however, the presence of E1A allowed stable overexpression of both proteins. These results suggest that E1A disrupts a nuclear function of Nek9.