CryoEM grid preparation: a closer look at advancements and impact of preparation mode and new approaches.

Sample preparation can present a significant hurdle within single particle cryo-electron microscopy (cryoEM), resulting in issues with reproducibility, data quality or an inability to visualise the sample. There are several factors which can influence this, including sample or buffer composition, grid type, route of sample preparation and interactions with the air-water interface (AWI). Here, we review some of the current routes for sample preparation and the associated challenges. We discuss a range of approaches for overcoming these challenges, such as minimising the grid preparation time, surfactants, grid type and biochemical approaches such as nanomagnetic beads. Finally, we discuss how a set of commercially available protein samples may serve as a benchmark suite for future technologies. This provides a route to compare techniques' abilities not just to generate high-resolution structures but also to overcome the challenges traditionally associated with cryoEM. As the field continues to produce new approaches to sample preparation and we start to better understand the underlying principles behind the behaviour of proteins within a thin film and in response to different environments, especially grid composition, it is hoped that more universal solutions can be provided that make the intractable systems tractable, improve resolution and, importantly, speed up data collection and reduce the currently required dataset sizes.

Abscisic acid induced a negative geotropic response in dark-incubated Chlamydomonas reinhardtii.

The phytohormone abscisic acid (ABA) plays a role in stresses that alter plant water status and may also regulate root gravitropism and hydrotropism. ABA also exists in the aquatic algal progenitors of land plants, but other than its involvement in stress responses, its physiological role in these microorganisms remains elusive. We show that exogenous ABA significantly altered the HCO3- uptake of Chamydomonas reinhardtii in a light-intensity-dependent manner. In high light ABA enhanced HCO3- uptake, while under low light uptake was diminished. In the dark, ABA induced a negative geotropic movement of the algae to an extent dependent on the time of sampling during the light/dark cycle. The algae also showed a differential, light-dependent directional taxis response to a fixed ABA source, moving horizontally towards the source in the light and away in the dark. We conclude that light and ABA signal competitively in order for algae to position themselves in the water column to minimise photo-oxidative stress and optimise photosynthetic efficiency. We suggest that the development of this response mechanism in motile algae may have been an important step in the evolution of terrestrial plants and that its retention therein strongly implicates ABA in the regulation of their relevant tropisms.

CyberKnife Radiosurgery of Skull-base Tumors: A UK Center Experience.

The study aim was to evaluate patient individualized Cyberknife® treatment for heterogeneous skull-base tumors. Patients treated between 2009 and 2013 at The Harley Street Clinic were studied. In total, 66 patients received 15-30 Gy in 1-5 fractions to a median planning target volume (PTV) of 6.4 cc, including patients with secondary, multiple, residual and recurrent tumors, and those with tumors of uncertain pathological type. Outcome analysis was pragmatically restricted to 35 patients who had single, primary tumors treated with curative intent, and sufficient diagnostic and outcome information. Sixteen vestibular schwannoma patients with median PTV 3.8 cc (range 0.81-19.6) received 18-25 Gy in 3-5 fractions: 81% showed no acute toxicity, 50% reported no late toxicity, 71% of symptoms were stable/improved and local control was 100% at 11.4 months median follow-up. Twelve meningioma patients with median PTV of 5.5 cc (range 0.68-22.3) received 17-30 Gy in 1-5 fractions: 83% experienced no acute toxicity, 33% reported no late toxicity, 88% of symptoms were stable/improved and local control was 100% at 22.1 months median follow-up. Seven patients with other tumor types with median PTV of 24.3 cc (range 7.6-100.5) received 15-28.5 Gy in 1-5 fractions: 57% experienced no acute toxicity, 57% reported no late toxicities, 66% of symptoms were stable and local control was 43% at 14.9 months median follow-up. When tumor types were considered together, smaller tumors (PTV < 6.4 cc) showed reduced acute toxicity (p = 0.01). Overall, smaller benign tumors showed low acute toxicity, excellent local control, and good symptom management: a focus on enhanced neurological preservation may refine outcomes. For other tumor types outcome was encouraging: a focus on optimal dose and fractionation scheduling may reduce toxicity and improve local control. Individual patient experiences are detailed where valuable lessons were gained for optimizing local control and minimizing toxicity.

Influence of somatic state on cardiovascular measurements in pregnancy.

Normal pregnancy causes marked changes in cardiac and haemodynamic function but there is continuing debate about the patterns of 'normal' change. We believe that this lack of consensus is in large part caused by inappropriate assessment conditions. This study aimed to assess physiological data obtained from pregnant women during multiple steady-states and during between-state changes. The study was a longitudinal characterization of apparently healthy pregnant women aged >18 years with assessments at three antenatal stages (12-16, 26-28 and 34-36 weeks) and at 12 weeks following birth. Cardiovascular and heart rate variability (HRV) measures were quantified non-invasively during a range of states including postural manoeuvre, exercise and respiratory regulation. Cardiovascular and HRV variables were influenced by pregnancy in specific ways: (1) steady-state values were influenced differently to state-change responses; (2) cardiac output (CO) increased progressively throughout pregnancy in all states except supine rest; (3) the ΔCO response to the supine-standing manoeuvre was particularly sensitive to pregnancy stage; (4) blood pressure was unaffected by pregnancy; (6) ΔCO and ΔSBP (systolic blood pressure) were enhanced from mid-pregnancy onwards; (7) ΔHRV responses to state changes were markedly and progressively influenced by pregnancy. This study indicates that cardiovascular function in pregnant women is best quantified during at least one physical state change (in particular during the supine-to-standing manoeuvre) and that assessment during supine rest is inadequate for quantifying antenatal physiological function.

Spontaneous cardiomyopathy in young Sprague-Dawley rats: evaluation of biological and environmental variability.

Cardiovascular safety signals in nonclinical studies remain among the main reasons for drug attrition during pharmaceutical research and development. Drug-induced changes can be functional and/or associated with morphological alterations in the normal heart histology. It is therefore crucial to understand the normal variations in histology to discriminate test article-related changes from background lesions. Rodent progressive cardiomyopathy is probably the most commonly encountered change in control animals of nonclinical toxicity studies. A multisite study mimicking standard short-term toxicity studies using young male Sprague-Dawley rats was performed to better characterize this finding. Using an enhanced sectioning method for this research study, it was observed that the incidence of background cardiomyopathy was 100%. The vast majority of the microscopic findings were inflammatory in nature, with associated necrotic changes (defined as necrosis/inflammatory cell infiltrate) and these changes were mainly located in the myocardium of the mid region of the ventricles (the left side being predominantly affected). The monitored environmental factors in this study (multiple facilities, study duration, handling) did not have an effect on the incidence or severity of the spontaneous cardiomyopathy. In addition, cardiac-specific serum troponin levels were measured and were within the published control range.

Intra- and inter-specific variation in metabolic gene expression in relationship to environmental hypoxia.

In this study, we explored how environmental oxygen levels affect the metabolic phenotype of sympatric sunfish known to differ in their hypoxia tolerance. We examined bluegill (Lepomis macrochirus) and pumpkinseed (Lepomis gibbosus), two species commonly found in the same water bodies, though pumpkinseed are considered more hypoxia tolerant, and survive in hypoxic lakes that exclude bluegill. Freshly caught Lake Opinicon pumpkinseed possessed significantly higher glycolytic enzyme activities (PGI, ALD, GAPDH, ENO, and LDH) than bluegill, but after holding the fish in an oxygenated environment for 7days, pumpkinseed glycolytic enzymes (PGI, ALD, and LDH) and mRNA (LDHA and HIF1α) declined to bluegill's levels. When glycolytic enzymes and mRNA were compared in pumpkinseed populations from seven lakes, only Penyck Lake pumpkinseed had significantly elevated glycolytic enzyme activity that did not diminish with normoxic holding. The levels of mRNA for LDHA and HIF1α did not differ between lakes and did not change in response to normoxic holding in the Penyck Lake fish. Collectively, these studies on sunfish show that hypoxia tolerance contributes to ecological niche specialization between species, and provides an example of a population that has adapted chronically elevated glycolytic enzyme activity independent of current dissolved oxygen in the water.

The effect of hypoxia on gill morphology and ionoregulatory status in the Lake Qinghai scaleless carp, Gymnocypris przewalskii.

Goldfish and crucian carp at low temperature exhibit plasticity in gill morphology during exposure to hypoxia to enhance gas exchange. Hypoxia-induced changes in gill morphology and cellular ultrastructure of the high altitude scaleless carp from Lake Qinghai, China, were investigated to determine whether this is a general characteristic of cold water carp species. Fish were exposed to acute hypoxia (0.3 mg O2 l(-1)) for 24 h followed by 12 h recovery in normoxic water (6 mg O2 l(-1) at 3200 m altitude), with no mortality. Dramatic alterations in gill structure were initiated within 8 h of hypoxia and almost complete by 24 h, and included a gradual reduction of filament epithelial thickness (>50%), elongation of respiratory lamellae, expansion of lamellar respiratory surface area (>60%) and reduction in epithelial water-blood diffusion distance (<50%). An increase in caspase 3 activity in gills occurred following 24 h exposure to hypoxia, indicating possible involvement of apoptosis in gill remodeling. Extensive gill mucous production during hypoxia may have been part of a general stress response or may have played a role in ion exchange and water balance. The large increase in lamellar surface area and reduction in diffusion distance presumably enhances gas transfer during hypoxia (especially in the presence of increased mucous production) but comes with an ionoregulatory cost, as indicated by a 10 and 15% reduction in plasma [Na+] and [Cl-], respectively, within 12-24 h of hypoxia. Within 12 h of hypoxia exposure, ;wavy-convex'-mitochondria rich cells (MRCs) with large apical crypts and numerous branched microvilli were transformed into small ;shallow-basin' cells with a flattened surface. As the apical membrane of MRCs is the site for active ion uptake from the water, a reduction in apical crypt surface area may have contributed to the progressive reduction in plasma [Na+] and [Cl-] observed during hypoxia. The changes in the macro- and ultra-structure of fish gills, and plasma [Na+] and [Cl-] during hypoxia were reversible, showing partial recovery by 12 h following return to normoxia. Although the large morphological changes in the gill observed in the scaleless carp support the hypothesis that gill remodeling during hypoxia is a general characteristic of cold water carp species, the reduced magnitude of the response in scaleless carp relative to goldfish and crucian carp may be a reflection of their more active lifestyle or because they reside in a moderately hypoxic environment at altitude.

Allometric scaling in centrarchid fish: origins of intra- and inter-specific variation in oxidative and glycolytic enzyme levels in muscle.

The influence of body size on metabolic rate, muscle enzyme activities and the underlying patterns of mRNA for these enzymes were explored in an effort to explain the genetic basis of allometric variation in metabolic enzymes. We studied two pairs of sister species of centrarchid fish: black bass (largemouth bass Micropterus salmoides and smallmouth bass Micropterus dolomieui) and sunfish (pumpkinseed Lepomis gibbosus and bluegill Lepomis macrochirus). Our goal was to assess the regulatory basis of both intraspecific and interspecific variation relative to body size, as well as to gain insights into the evolutionary constraints within lineages. Whole animal routine metabolic rate showed scaling coefficients not significantly different from 1, ranging from (+0.87 to +0.96). However, there were significant effects of body size on the specific activities of oxidative and glycolytic enzymes. Mass-specific activity of the oxidative enzyme citrate synthase (CS) scaled negatively with body size in each species, with scaling coefficients ranging from -0.15 to -0.19, whereas the glycolytic enzyme pyruvate kinase (PK) showed positive scaling, with scaling coefficients ranging from +0.08 to +0.23. The ratio of mass-specific enzyme activity in PK to CS increased with body size, whereas the ratio of mRNA transcripts of PK to CS was unaffected, suggesting the enzyme relationships were not due simply to transcriptional regulation of both genes. The mass-dependent differences in PK activities were best explained by transcriptional regulation of the muscle PK gene; PK mRNA was a good predictor of PK specific enzyme activity within species and between species. Conversely, CS mRNA did not correlate with CS specific enzyme activities, suggesting post-transcriptional mechanisms may explain the observed inter-specific and intraspecific differences in oxidative enzymes.

Identification and typing of Cameroonian isolates of P. malariae using monoclonal antibodies against P. brasilianum.

In the present study, monoclonal antibodies raised against Plasmodium brasilianum were used to demonstrate, for the first time, antigenic diversity in natural populations of Plasmodium malariae isolates and as diagnostic tool to detect low parasitaemia P. malariae infection. Seventeen McAbs reacting by indirect immunoflorescence antibody (IFA) assay with no other Plasmodium species than P. brasilianum, were shown to react with P. malariae and were used for typing 29 P. malariae isolates from hyperendemic areas in Yaounde and in three villages of South Cameroon with parasitaemia ranging from 0.01% to 1.8%. All 29 isolates were distinguished by their ability to react with certain antibodies and considered as representing different isolates of P. malariae. One of these McAbs (No. 14) recognized P. malariae isolates to both in Yaounde and from Mengang but not in Edou or in Nkol Mvae, which may recognize a specific epitope that is less common in strains found in these villages and provide evidence of regional variation within the P. malariae parasites. The McAbs Nos. 16 and 17 were used to determine their usefulness as diagnostic tools for 30 suspected blood samples that were collected from patients with fever and it became clear that they could detect sub-microscopical infections of P. malariae. This study supports the concept of using of P. brasilianum as a substitute for P. malariae during immuno-diagnosis of malaria in endemic areas where PCR assay cannot be used for identification of the P. malariae parasites. In addition our results for the first time provide evidence of considerable antigenic diversity of clinical P. malariae isolates in Cameroon.