Synthetase and Hydrolase Specificity Collectively Excludes 2'-Deoxyguanosine from Bacterial Alarmone

In response to starvation, virtually all bacteria pyrophosphorylate the 3'-hydroxy group of GTP or GDP to produce two messenger nucleotides collectively denoted as (p)ppGpp. Also known as alarmones, (p)ppGpp reprograms bacterial physiology to arrest growth and promote survival. Intriguingly, although cellular concentration of dGTP is two orders of magnitude lower than that of GTP, alarmone synthetases are highly selective against using 2'-deoxyguanosine (2dG) nucleotides as substrates. We thus hypothesize that production of 2dG alarmone, (p)pp(dG)pp, is highly deleterious, which drives a strong negative selection to exclude 2dG nucleotides from alarmone signaling. In this work, we show that the B. subtilis SasB synthetase prefers GDP over dGDP with 65,000-fold higher kcat/Km, a specificity stricter than RNA polymerase selecting against 2'-deoxynucleotides. Using comparative chemical proteomics, we found that although most known alarmone-binding proteins in Escherichia coli cannot distinguish ppGpp from pp(dG)pp, hydrolysis of pp(dG)pp by the essential hydrolase, SpoT, is 1,000-fold slower. This inability to degrade 2'-deoxy-3'-pyrophosphorylated substrate is a common feature of the alarmone hydrolase family. We further show that SpoT is a binuclear metallopyrophoshohydrolase and that hydrolysis of ppGpp and pp(dG)pp shares the same metal dependence. Our results support a model in which 2'-OH directly coordinates the Mn2+ at SpoT active center to stabilize the hydrolysis-productive conformation of ppGpp. Taken together, our study reveals a vital role of 2'-OH in alarmone degradation, provides new insight on the catalytic mechanism of alarmone hydrolases, and leads to the conclusion that 2dG nucleotides must be strictly excluded from alarmone synthesis because bacteria lack the key machinery to down-regulate such products.

Identification of a broadly conserved family of enzymes that hydrolyze (p)ppApp

Bacteria produce a variety of nucleotide second messengers to adapt to their surroundings. Although chemically similar, the nucleotides guanosine penta- and tetraphosphate [(p)ppGpp] and adenosine penta- and tetraphosphate [(p)ppApp] have distinct functions in bacteria. (p)ppGpp mediates survival under nutrient-limiting conditions and its intracellular levels are regulated by synthetases and hydrolases belonging to the RelA-SpoT homolog (RSH) family of enzymes. By contrast, (p)ppApp is not known to be involved in nutrient stress responses and is synthesized by RSH-resembling toxins that inhibit the growth of bacterial cells. However, it remains unclear whether there exists a family of hydrolases that specifically act on (p)ppApp to reverse its toxic effects. Here, we present the structure and biochemical characterization of adenosine 3'-pyrophosphohydrolase 1 (Aph1), the founding member of a monofunctional (p)ppApp hydrolase family of enzymes. Our work reveals that Aph1 adopts a histidine-aspartate (HD)-domain fold characteristic of phosphohydrolase metalloenzymes and its activity mitigates the growth inhibitory effects of (p)ppApp-synthesizing toxins. Using an informatic approach, we identify over 2,000 putative (p)ppApp hydrolases that are widely distributed across bacterial phyla and found in diverse genomic contexts, and we demonstrate that 12 representative members hydrolyze ppApp. In addition, our in silico analyses reveal a unique molecular signature that is specific to (p)ppApp hydrolases, and we show that mutation of two residues within this signature broadens the specificity of Aph1 to promiscuously hydrolyze (p)ppGpp in vitro. Overall, our findings indicate that like (p)ppGpp hydrolases, (p)ppApp hydrolases are widespread in bacteria and may play important and underappreciated role(s) in bacterial physiology.

Resource partitioning by ungulates on the Isle of Rhum

This paper describes the seasonal changes in vegetation community use by red deer, cattle, goats and ponies on the Isle of Rhum, Scotland. During the winter, when food resources were of low abundance and digestibility, the ungulates showed extensive resource partitioning. During the summer, when resource availability and digestibility was high, the grazing species, red deer, cattle and ponies congregated on the vegetation communities which contained high biomasses of a high quality resource, mesotrophic graminoids and forbs. Goats, with a digestive system adapted to dealing with browse, foraged primarily on the communities dominated by dwarf shrubs. The patterns of resource use in this group of ungulates are discussed in relation to competition; species had relatively exclusive esource use during periods of low food availability during tye winter and had a high degree of resource use overlap when food was abundant during the summer. This suggests that there was little competition for food during the summer and that exploitative competition for the high quality foods led to resource partitioning during the winter. Senarios are described which predict the pattern of resource use between two species (one competitively superior to the other on the preferred resource) utilizing mutually or exclusively preferred resources. A model developed by Illius and Gordon (1987), based on the allometry of metabolic requirements and bite size, is used to provide a mechanistic explanation for the observation that the red deer were able to exploit the high quality plant communities during the winter, whereas the cattle moved off to feed on poorer quality communities at this time.

Long-term density-dependent changes in habitat selection in red deer (Cervus elaphus)

Understanding how habitat selection changes with population density is a key concept in population regulation, community composition and managing impacts on biodiversity and ecosystem services. At low density, it is expected that individuals select habitats in terms of their preference, but as population density increases, the availability of resources per individual declines on preferred habitats, leading to competition which forces some individuals to exploit less preferred habitats. Using spatial information of Scottish red deer (Cervus elaphus) winter counts, carried out in 110 areas across Scotland between 1961 and 2004 (a total of 1,206,495 deer observations), we showed how winter habitat niche breadth in red deer has widened with increasing population density. Heather moorland and montane habitats were most and least preferred for deer, respectively. Increasing density favoured the selection of grassland, to the detriment of the selection of heather moorland. The selection of heather and grassland decreased when temperature increased, while the selection of montane and peatland habitats increased. These findings are important for understanding how habitat use, density and population are likely to be affected by weather, and allow us to predict habitat impacts by large mammal herbivory and climate.

Genetic diversity and population structure of Scottish Highland red deer (Cervus elaphus) populations: a mitochondrial survey

The largest population of red deer (Cervus elaphus) in Europe is found in Scotland. However, human impacts through hunting and introduction of foreign deer stock have disturbed the population's genetics to an unknown extent. In this study, we analysed mitochondrial control region sequences of 625 individuals to assess signatures of human and natural historical influence on the genetic diversity and population structure of red deer in the Scottish Highlands. Genetic diversity was high with 74 haplotypes found in our study area (115 x 87 km). Phylogenetic analyses revealed that none of the individuals had introgressed mtDNA from foreign species or subspecies of deer and only suggested a very few localized red deer translocations among British localities. A haplotype network and population analyses indicated significant genetic structure (Phi(ST)=0.3452, F(ST)=0.2478), largely concordant with the geographical location of the populations. Mismatch distribution analysis and neutrality tests indicated a significant population expansion for one of the main haplogroups found in the study area, approximately dated c. 8200 or 16 400 years ago when applying a fast or slow mutation rate, respectively. Contrary to general belief, our results strongly suggest that native Scottish red deer mtDNA haplotypes have persisted in the Scottish Highlands and that the population retains a largely natural haplotype diversity and structure in our study area.

Landscape features affect gene flow of Scottish Highland red deer (Cervus elaphus)

Landscape features have been shown to strongly influence dispersal and, consequently, the genetic population structure of organisms. Studies quantifying the effect of landscape features on gene flow of large mammals with high dispersal capabilities are rare and have mainly been focused at large geographical scales. In this study, we assessed the influence of several natural and human-made landscape features on red deer gene flow in the Scottish Highlands by analysing 695 individuals for 21 microsatellite markers. Despite the relatively small scale of the study area (115 x 87 km), significant population structure was found using F-statistics (F(ST) = 0.019) and the program structure, with major differentiation found between populations sampled on either side of the main geographical barrier (the Great Glen). To assess the effect of landscape features on red deer population structure, the ArcMap GIS was used to create cost-distance matrices for moving between populations, using a range of cost values for each of the landscape features under consideration. Landscape features were shown to significantly affect red deer gene flow as they explained a greater proportion of the genetic variation than the geographical distance between populations. Sea lochs were found to be the most important red deer gene flow barriers in our study area, followed by mountain slopes, roads and forests. Inland lochs and rivers were identified as landscape features that might facilitate gene flow of red deer. Additionally, we explored the effect of choosing arbitrary cell cost values to construct least cost-distance matrices and described a method for improving the selection of cell cost values for a particular landscape feature.

How does pattern of feeding and rate of nutrient delivery influence conditioned food preferences?

Ruminant herbivores have been shown to learn about food properties by associating food flavours with the food's post-ingestive consequences. Previous experimentation supporting the conditioned food aversion/preference hypothesis has generally employed very simple diet learning tasks which do not effectively represent the wide range of foods selected within single bouts typical of wild, free-ranging ruminant herbivores. We tested the ability of a ruminant herbivore to associate a food with artificially administered nutrient rewards in a designed experiment where we altered the temporal pattern of encounter with the food as well as the nature (fast or slow reward) of the post-ingestive outcome. Twenty-four goats were offered branches of Sitka spruce (SS) and Norway spruce (NS) for 4 h per day on two days per week for five weeks. The pattern of feeding varied with treatment such that the species on offer changed every hour (short) or every 2 h (long). The energy treatment altered the reward delivered during Sitka consumption so that animals were dosed either with predominantly sugar (rapidly fermented), predominantly starch (slower fermentation rate), or with water (placebo). Preference was measured on the day following each learning day. We expected that goats would find it easier to associate SS with post-ingestive rewards when the duration of encounter was longest, and that associations would be stronger with the most rapidly digested post-ingestive reward. In the event, goats did not alter their consumption of SS in response to the treatments. Our results suggest that at the scale of temporal resolution of encounters with different plant species (1-2 h), and at the different rates of experiencing post-ingestive consequences tested in this experiment, ruminants do not appear to discriminate the nutritive properties of foods predominantly through a post-ingestive feedback mechanism. They must, instead, use a range of cues-including post-ingestive consequences-to assess food properties.

The evolution of phylogenetic differences in the efficiency of digestion in ruminants

This study investigates, for the first time (to our knowledge) for any animal group, the evolution of phylogenetic differences in fibre digestibility across a wide range of feeds that differ in potential fibre digestibility (fibre to lignin ratio) in ruminants. Data, collated from the literature, were analysed using a linear mixed model that allows for different sources of random variability, covariates and fixed effects, as well as controlling for phylogenetic relatedness. This approach overcomes the problem of defining boundaries to separate different ruminant feeding styles (browsers, mixed feeders and grazers) by using two covariates that describe the browser-grazer continuum (proportion of grass and proportion of browse in the natural diet of a species). The results indicate that closely related species are more likely to have similar values of fibre digestibility than species that are more distant in the phylogenetic tree. Body mass did not have any significant effect on fibre digestibility. Fibre digestibility is estimated to increase with the proportion of grass and to decrease with the proportion of browse in the natural diet that characterizes the species. We applied an evolutionary model to infer rates of evolution and ancestral states of fibre digestibility; the model indicates that the rate of evolution of fibre digestibility accelerated across time. We suggest that this could be caused by a combination of increasing competition among ruminant species and adaptation to diets rich in fibre, both related to climatically driven environmental changes in the past few million years.

Incomplete sexual isolation in sympatry between subspecies of the butterfly Danaus chrysippus (L.) and the creation of a hybrid zone

Subspecies chrysippus, dorippus and alcippus of the butterfly Danaus chrysippus differ at three biallelic colour gene loci. They have partially vicariant distributions, but their ranges overlap over a substantial part of central and East Africa, where hybridism is commonplace. We now report that the West African subspecies alcippus differs from other subspecies, not only in nuclear genotype but also in mitochondrial haplotype in both allopatry and sympatry. The maintenance of concordant nuclear and cytoplasmic genetic differences in sympatry, and in the face of hybridisation, is prima facie evidence for sexual isolation. Other evidence that suggests alcippus may be isolated from chrysippus and dorippus include differences in sex ratio (SR), heterozygote deficiency at one site and deduced differences in patterns of migration. We suggest that, within the hybrid zone, differential infection of subspecies by a male-killing Spiroplasma bacterium causes SR differences that restrict female choice, triggering rounds of heterotypic mating and consequent heterozygote excess that is largely confined to females. The absence of these phenomena from hybrid populations that test negative for Spiroplasma supports the hypothesis. The incomplete sexual isolation and partial vicariance of alcippus suggests that it is a nascent species.

The origins of sexual dimorphism in body size in ungulates

Jarman (1974) proposed a series of relationships between habitat use, food dispersion, and social behavior and hypothesized a series of evolutionary steps leading to sexual dimorphism in body size through sexual selection in African antelope species. The hypothesis states that sexual size dimorphism evolved in a three-step process. Initially, ancestral monomorphic and monogamous ungulate species occupying closed habitats radiated into open grassland habitats. Polygynous mating systems then rapidly evolved in response to the aggregation of males and females, perhaps in relation to the clumped distribution of food resources in open habitats. Subsequently, size dimorphism evolved in those species occupying open habitats, but not in species that remained in closed habitats or retained monogamy. This hypothesis has played an important role in explaining the origins of sexual dimorphism in mammals. However, the temporal sequence of the events that Jarman proposed has never been demonstrated. Here we use a phylogeny of extant ungulate species, along with maximum-likelihood statistical techniques, to provide a test of Jarman's hypothesis.

Relationships between oral morphology and feeding style in the Ungulata: a phylogenetically controlled evaluation

In ungulates it is argued that specialization in the consumption of a particular type of food (feeding style) is reflected in morphological adaptations of the organs involved in the selection, processing and digestion of food. We analysed the differences in size and morphology of some oral traits that have been functionally related to food-selection ability (muzzle width, incisor-arcade shape, incisor shape), prehension of food (incisor protrusion), food comminution (molar occlusal surface area, hypsodonty (high-crowned molars)) and intake rate (incisor breadth) between ungulate species with different feeding styles (browser, mixed feeder, grazer). Grazers were characterized by large-body-size species. After controlling only for body mass, we found that grazers had wider muzzles and incisors, more-protruding incisors and more-bulky and higher-crowned molars than did mixed feeders and browsers. When the analyses took into account both body mass and phylogeny, only body mass and two out of the three hypsodonty indexes used remained significantly different between feeding styles. Browsers were smaller, on average, than mixed feeders and grazers, whilst grazers and mixed feeders did not differ in size. Also, browsers had shorter and less-bulky molars than did mixed feeders and grazers; the latter two feeding styles did not differ from each other in any of the hypsodonty indexes. We conclude that the adaptation to different dietary types in most of the oral traits studied is subsumed by the effects of body mass and the sharing of common ancestors. We hypothesize that differences in the ability to exploit different food resources primarily result from differences in body mass between species, and also discuss why hypsodonty characterizes feeding styles.

Status epilepticus treated with a muscle relaxant: the first success

In 1958, an 11-year-old girl with status epilepticus was given the current treatments which failed to control the convulsions. In order to stop the fits, protect the airway, prevent hypoxia and hyperpyrexia, intermittent positive pressure ventilation (IPPV) and complete muscle paralysis with d-tubocurarine was used for a total of 6 h. The girl made a complete recovery, the first patient to do so using this plan of action.

Strategies for the avoidance of faeces by grazing sheep

Experiments were conducted to investigate which environmental cues were used by sheep when discriminating against patches of pasture contaminated with faeces. The influence of the spatial distribution of contaminated patches and the parasite infection status of sheep on avoidance of contaminated patches and ingestion of parasite larvae was also investigated. In experiment 1, sheep infected with the parasite Ostertagia circumcincta were given the opportunity to graze in uncontaminated or aggregated contaminated patches. Patch contamination comprised of either faeces from sheep infected with O. circumcincta larvae, faeces from uninfected sheep, or O. circumcincta larvae only. Infected sheep discriminated against faeces from parasite-infected animals and faeces from uninfected animals equally. Sheep did not discriminate against patches contaminated with parasite larvae only. In experiment 2, sheep infected with O. circumcincta and uninfected sheep grazed experimental plots with differing spatial patterns of faecal-contaminated patches, allowing animals the opportunity to forage in contaminated or uncontaminated patches of herbage. Plots were also grazed by infected and uninfected animals that were fistulated at the oesophagus to enable the collection of ingested herbage. Sheep spent a greater proportion of their time foraging in uncontaminated patches than in contaminated patches. Where patches were highly aggregated, infected animals spent a greater proportion of total grazing time in uncontaminated patches than did uninfected animals, and grazed uncontaminated patches for longer on each sampling occasion. On grazing plots where all patches were contaminated, the difference between the numbers of larvae isolated from pasture herbage and ingested herbage was greatest for infected animals. In this situation, infected animals avoided parasites most. On grazing plots consisting of both contaminated and uncontaminated patches, the difference between the numbers of larvae isolated from pasture herbage and ingested herbage was greatest for uninfected animals. In this situation, uninfected animals were most effective at parasite avoidance as they consumed fewer parasite larvae relative to what was available on pasture.

Habitat selection according to the ability of animals to eat, digest and detoxify foods

Large herbivores play a major role in shaping vegetation community dynamics through selective consumption of particular plants and plant communities. An understanding of the factors influencing diet selection at the level of individual bites ('bite scale') is important for prediction of the impact of herbivores on vegetation at the habitat scale. Bite-scale diet selection represents an integration of the twin goals of maximizing nutrient intake and minimizing toxin intake. Recent research with ruminants in pen-fed situations has shown that animals are able to make choices between artificial foods that maximize growth and other production variables. The role of post-ingestive feedback as an important mechanism for allowing animals to assess the nutritional quality of particular foods, and so select optimal diets, has been recognized in a number of recent experiments. Our understanding of the role of toxin intake minimization in diet selection decisions is more rudimentary. An important advance in the last decade has been the acknowledgement of the role of post-ingestive feedback and learning as a mechanism for avoidance of dietary toxicity. Further research is required to assess the importance of these processes in relation to free-grazing animals. The extent to which an understanding of bite-scale diet selection can be used to predict habitat utilization is not well understood. At the habitat scale additional factors such as predator avoidance, social constraints, avoidance of parasitism and microclimatic effects have an important influence on foraging decisions. Future research needs to focus on developing a quantitative understanding of such decisions at the habitat scale.

I smell a rat!

This is a case history with a difference. The year was 1938 and the story was told to one of us in 1946 by Henry Cohen (HC), then Professor of Medicine at Liverpool (Figure 1). Bothdiagnosis and successful treatment were made in the patient's home without any of the customary investigations. The case is reported because it still provides lessons: there are no substitutes for wide-ranging knowledge and its thorough clinical application

Effective clinical policies in a district general hospital

Effective clinical practice in a hospital needs current knowledge together with the skills and right attitude; these should be applied continuously. Failure of this system can be due to ignorance or arrogance. We attempted to correct these deficiencies by formulating a set of policies which were enforced from 1962 to 1983. The policies related to the following: intensive care (including asthma, nutrition and organ donation), drug prescribing and resuscitation. We believe that these rules improved patient care and the standards of training; the prescribing policy also saved money.

The evolution and nursing history of a general intensive care unit (1962-1983)

In this paper we have reviewed the origin and evolution of Whiston Hospital's General Intensive Care Unit (ICU) from its humble beginnings as an offshoot of a general ward in the early 1960s. The length of service of the senior nursing staff over a period of 21 years was also calculated. The average duration of service was 16.5 years--a figure which significantly surpassed those quoted in the literature. In addition, we have outlined the development of nurse training in intensive care as well as the role of the nurses in research in the ICU. The question as to whether later college-based training was superior to the previous hospital-based course remained unanswered.

The influence of sexual dimorphism in body size and mouth morphology on diet selection and sexual segregation in cervids

In mammals patterns of food resource distribution influence female distribution, leading to aggregation and favouring the evolution of a polygynous mating system. Under polygyny, sexual selection favours an increase of the male body size, since larger bodied males have competitive advantage in fights for mates. As a result, sexual body size dimorphism is a general rule in polygynous artiodactyls and is correlated with the degree of polygyny. Sex differences in body size lead to differences in energy requirements and food selection between the sexes. This has led to the sexual size dimorphism hypothesis being used to explain sexual segregation in ungulates, although from the available studies, it is not possible to deduce a consistent pattern between sexes in the use of forage of different abundance or quality. Two other groups of hypotheses have been put forward to explain sexual segregation in ungulates. These are based on reproductive strategy and social factors, both of which are independent of body size. The mechanistic explanation for differences in food selection ability and intake rate between animals of different body size and how this can lead to an understanding of the sex differences in diet and sexual segregation, both of which are intimately linked, is discussed.

The adaptive significance of reproductive strategies in ungulates

We examine the relation between litter size, gestation length, neonate mass and growth rate among ungulates. By using a recent method for analysing comparative data, we show that ungulates can be divided along a slow-fast continuum, even after accounting for the effects of maternal body mass and common ancestry. Some species produce many small offspring during a short period, whereas others take a long time to raise a single large offspring. These differences in life-history strategy are associated with diet, i.e. browsers have relatively larger litters and smaller neonates than grazers.

Circumflex retroesophageal right aortic arch simulating mediastinal tumor or dissecting aneurysm

The authors present three cases of circumflex right aortic arch, a retroesophageal arch in which the aorta crosses from right to left behind the esophagus to descend on the left side. The findings on the frontal chest films resembled those of a left arch with mediastinal widening, simulating a mass. Aortography revealed four-vessel branching of the arch vessels, typical of right aortic arch with aberrant left subclavian artery. Computed tomography and barium studies of the esophagus demonstrated the retroesophageal course of the aorta. In two patients, obstruction of the thoracic portion of the left subclavian artery resulted in differences in blood pressure and pulse between the arms, supporting the clinical impression of dissecting aortic aneurysm.

An index to predict outcome in adult respiratory distress syndrome

Thirty patients with adult respiratory distress syndrome required intermittent positive pressure ventilation; 15 survived. In 25 the syndrome followed bacterial infection or multiple injuries. From the peak upper airway pressure, the oxygen gradient and the age of the patient, an index was obtained which discriminated between the survivors and those who died from the pulmonary lesion of the syndrome.

Algorithm for modified alkaline diuresis in salicylate poisoning

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A comparison of Iohexol and Conray-60 in peripheral angiography

A double-blind clinical trial was performed in 61 adults in an attempt to compare the safety and efficacy of an ionic with a nonionic contrast agent in peripheral angiography. Objective clinical (vital signs) and laboratory factors (complete blood count, serum electrolytes, serum chemistry, urinalysis, and urine chemistry) were monitored before, during, and after the examination on each patient. There was no statistically significant difference in pre- and posttest laboratory and clinical parameters between those patients who received ionic and those who received nonionic contrast material. Data also were collected to evaluate pain and radiographic quality. The most striking finding was the marked diminution of perceived pain in those patients who received nonionic contrast material compared with those who did not. The data suggest that nonionic contrast agents are at least as safe as the ionic agents currently in use and produce an examination of equal quality with considerably less patient discomfort.

Transcatheter vascular occlusion therapy with isobutyl 2-cyanoacrylate (bucrylate) for control of massive upper-gastrointestinal bleeding

Transcatheter embolization with bucrylate, a tissue adhesive, was performed in 16 patients with massive upper-gastrointestinal bleeding. Control of arterial bleeding from the stomach was achieved in 6 of 8 patients, and from the duodenum in 3 of 4. Embolization of gastric veins resulted in temporary control of esophageal variceal bleeding in 3 of 4 patients. Histological study showed no evidence of bucrylate causing histotoxicity in 2 patients. Because bucrylate polymerizes rapidly, a localized vascular occlusion mimicking a surgical ligation is produced. Because collateral vessels are not occluded. localized tissue ischemia is unlikely. Tissue adhesives are, however, difficult to use.

The transjugular technique of hepatic venography and biopsy, cholangiography, and obliteration of esophageal varices

The transjugular technique facilitates various diagnostic and therapeutic procedures in the liver. Even in patients with defective hemostasis, severe ascites, or marked obesity, liver biopsy or cholangiography can be performed with relative safety. It also provides an alternative route for entry into the portal system.

Intra-arterial lidocaine: an effective analgesic for peripheral angiography

Intra-arterial lidocaine was found to be an effective and safe method for reducing pain associated with peripheral angiography. A convenient method for delivery is to directly mix 2% lidocaine and contrast material in a ratio of 1:10 by volume. In a comparative evaluation, 25 of 29 patients experienced significantly less discomfort when the lidocaine-contrast mixture was used as compared to contrast material alone. There were no apparent complications from the use of intra-arterial lidocaine.

The traumatic pneumomyelogram. A previously undescribed entity

Air within the cervical subarachnoid space secondary to skull trauma (traumatic air myelogram or pneumomyelogram) has not been reported previously. Such a case is presented and the findings are reviewed in the light of existing literature.