Linking stream ecology with morphological variability in a native freshwater fish from semi‐arid Australia

Environmental variation is a potent force affecting phenotypic expression. While freshwater fishes have provided a compelling example of the link between the environment and phenotypic diversity, few studies have been conducted with arid‐zone fishes, particularly those that occur in geographically isolated regions where species typically inhabit intermittent and ephemeral creeks. We investigated morphological variation of a freshwater fish (the western rainbowfish, Melanotaenia australis) inhabiting creeks in the Pilbara region of northwest Australia to determine whether body shape variation correlated with local environmental characteristics, including water velocity, habitat complexity, predator presence, and food availability. We expected that the geographic isolation of creeks within this arid region would result in habitat‐specific morphological specializations. We used landmark‐based geometric morphometrics to quantify the level of morphological variability in fish captured from 14 locations within three distinct subcatchments of a major river system. Western rainbowfish exhibited a range of morphologies, with variation in body depth accounting for a significant proportion (>42%) of the total variance in shape. Sexual dimorphism was also apparent, with males displaying deeper bodies than females. While the measured local habitat characteristics explained little of the observed morphological variation, fish displayed significant morphological differentiation at the level of the subcatchment. Local adaptation may partly explain the geographic patterns of body shape variation, but fine‐scale genetic studies are required to disentangle the effects of genetic differentiation from environmentally determined phenotypic plasticity in body shape. Developing a better understanding of environment–phenotype relationships in species from arid regions will provide important insights into ecological and evolutionary processes in these unique and understudied habitats.     

Sulcus-Based MR Analysis of Focal Cortical Dysplasia Located in the Central Region

Objective

Focal cortical dysplasias (FCDs) are mainly located in the frontal region, with a particular tropism for the central sulcus. Up to 30% of lesions are undetected (magnetic resonance [MR]-negative FCD patients) or belatedly diagnosed by visual analysis of MR images. We propose an automated sulcus-based method to analyze abnormal sulcal patterns associated with central FCD, taking into account the normal interindividual sulcal variability.

Methods

We retrospectively studied 29 right-handed patients with FCD in the central region (including 12 MR negative histologically-confirmed cases) and 29 right-handed controls. The analysis of sulcal abnormalities from T1-weighted MR imaging (MRI) was performed using a graph-based representation of the cortical folds and an automated sulci recognition system, providing a new quantitative criterion to describe sulcal patterns, termed sulcus energy.

Results

Group analysis showed that the central sulcus in the hemisphere ipsilateral to the FCD exhibited an abnormal sulcal pattern compared with controls (p = 0.032). FCDs were associated with abnormal patterns of the central sulci compared with controls (p = 0.006), a result that remained significant when MR-negative and MR-positive patients were considered separately, while the effects of sex, age and MR-field were not significant. At the individual level, sulcus energy alone failed to detect the FCD lesion. We found, however, a significant association between maximum z-scores and the site of FCD (p = 0.0046) which remained significant in MR-negative (p = 0.024) but not in MR-positive patients (p = 0.058). The maximum z-score pointed to an FCD sulcus in four MR-negative and five MR-positive patients.

Conclusions

We identified abnormal sulcal patterns in patients with FCD of the central region compared with healthy controls. The abnormal sulcal patterns ipsilateral to the FCD and the link between sulcus energy and the FCD location strengthen the interest of sulcal abnormalities in FCD patients.     

Development of a Material Sparing Bulk Density Test Comparable to a Standard USP Method for Use in Early Development of API’s

Bulk density can be a key indicator of performance, and may influence choice of formulation route of materials in pharmaceutical development. During early development, the cost of API’s can be expensive and the availability of material for powder property analysis is limited. The aim of this work was to investigate a suitable small-scale, low material requirement, bulk density test which would provide comparable data to the recommended large volume USP test. Materials with a range of morphological characteristics typically seen in the pharmaceutical industry were assessed to ensure that methods were suitably robust. It was found that the USP II “low volume” test does not give equivalent results to other tests in the USP, across the range of materials. An alternative test based on the FT4 powder rheometer at a scale of 25 mL gave results equivalent to the large volume USP I standard test. The use of smaller 10-mL methods was also found to give acceptable results for materials that were considered well-behaved but were more variable with difficult to handle materials with low bulk density.KEY WORDS: active pharmaceutical ingredient (API), bulk density, compressibility index, excipients, pharmaceuticals     

Identification of O-glycan Structures from Chicken Intestinal Mucins Provides Insight into Campylobactor jejuni Pathogenicity

The Gram-negative bacteria Campylobactor jejuni is the primary bacteria responsible for food poisoning in industrialized countries, and acute diarrheal illness is a leading cause of mortality among children in developing countries. C. jejuni are commensal in chickens. They are particularly abundant in the caecal crypts, and poultry products are commonly infected as a result of cross-contamination during processing. The interactions between C. jejuni and chicken intestinal tissues as well as the pathogenic molecular mechanisms of colonization in humans are unknown, but identifying these factors could provide potential targets to reduce the incidence of campylobacteriosis. Recently, purified chicken intestinal mucin was shown to attenuate adherence and invasion of C. jejuni in the human colorectal adenocarcinoma cell line HCT-8 in vitro, and this effect was attributed to mucin O-glycosylation. Mucins from different regions of the chicken intestine inhibited C. jejuni binding and internalization differentially, with large intestine>small intestine>caecum. Here, we use LC-MS to perform a detailed structural analysis of O-glycans released from mucins purified from chicken large intestine, small intestine, and caecum. The O-glycans identified were abundantly sulfated compared with the human intestines, and sulfate moieties were present throughout the chicken intestinal tract. Interestingly, alpha 1–2 linked fucose residues, which have a high binding affinity to C. jejuni, were identified in the small and large intestines. Additionally, N-glycolylneuraminic/N-acetylneuraminic acid containing structures present as Sd^a-like epitopes were identified in large intestine samples but not small intestine or caecum. O-glycan structural characterization of chicken intestinal mucins provides insights into adherence and invasion properties of C. jejuni, and may offer prospective candidate molecules aimed at reducing the incidence of infection.Campylobactor jejuni infection is widespread in industrialized countries and is the greatest source of food poisoning worldwide. Infection and the resulting diarrhea are the most common cause of death among young children in developing countries, with an estimated 2.1–2.5 million cases per year in the USA. C. jejuni leads to severe gastroenteritis and is also linked to Guillain-Barré and irritable bowel disease (1, 2). Contaminated poultry meat is the most common source of infection, with up to 88% of poultry products being infected (3). The bacteria are commensal in chickens and exist throughout their intestinal tract. However, they do not invade the epithelium of the gut. Purified mucin glycoproteins from the caecum and small and large intestine have been shown to exhibit inhibitory properties against the bacteria in vitro (4). The commensal relationship between C. jejuni occurrence in chickens and the inability to invade the intestinal tissues is poorly understood. Enhanced understanding of how the properties of the chicken mucosal barrier differ from humans; as well as changes in mucin composition along the chicken intestinal tract, have the potential to explain the commensal behavior of C. jejuni in this species. Such information could also provide leads for the development of agents to limit infection.Intestinal mucus in vertebrates is a hydrated gel comprised mainly of very high molecular weight and polymeric secreted mucin glycoproteins that are heavily O-glycosylated. O-linked glycans constitute up to 80% of the mucin by weight and represent an abundant potential carbon source for the resident microflora. They also present targets for bacterial adhesion and chemotaxis that may be exploited by both commensal and pathogenic organisms. Intestinal mucus is a dynamic barrier layer that is mainly secreted by goblet cells. It forms a supramucosal layer to protect the gastrointestinal epithelial cells against infection. A density gradient of viscoelastic and highly hydrated mucins polymers exists from the inner to the outer mucus layer. This stratification is most clearly demonstrable in the colon, where a relatively tightly attached mucus layer proximal to the epithelium is normally devoid of bacteria, but a less cross-linked more superficial layer is heavily colonized (5). In humans, it has been shown that the abundance of bacteria is highest in the large intestine, where colonization of the mucosal epithelium is contested by a thick mucus layer (∼700 μm) and more rapid mucus turnover (6). In the small intestine, however, where bacteria are much less abundant, the mucus layer is between 100–400 μm thick. O-glycosylation confers the mucus component of the mucosal barrier with much of the protective properties required to separate the abundant gut microflora from the immune system of its host. Defects in mucin glycosylation lead to severe inflammation and susceptibility to infection, and the glycans themselves have been shown to be ligands that can block the binding of microorganisms (7–14). Thus, secreted gel-forming mucins are key components of intestinal defense, beyond which bacterial pathogens must normally penetrate to cause pathology through interaction with epithelial cells.Several C. jejuni adhesion proteins required for colonization of chickens have been identified (15), but the mechanisms by which the bacteria initiate interactions with carbohydrates on mucosal surfaces remain unclear. However, many hypotheses can be made from previous studies where bacterial-carbohydrate interactions have been investigated (7). Additionally, bovine mucins and l-fucose are known chemoattractants for C. jejuni (8), and l-fucose is a substrate for C. jejuni growth (13). Glycans from human breast milk bearing the H(O) blood group antigen (which presents α1–2-linked fucose) also inhibits infection (12). d-glucose, d-mannose, and d-fucose, but not the l-sugar equivalents, inhibited the binding of C. jejuni to human colonic Caco-2 cells (16). Muc1, a membrane-bound mucin, is up-regulated during infection in mice, and knockouts are highly prone to C. jejuni infection with transepithelial translocation (11). These studies have provided considerable insight into C. jejuni behavior, but the specific relationship between the bacteria and mucin glycans in vivo remains unidentified.

Table I

Oligosaccharide-specific C. jejuni interactions

Should the WHO Growth Charts Be Used in France?

Background

Growth charts are an essential clinical tool for evaluating a child''s health and development. The current French reference curves, published in 1979, have recently been challenged by the 2006 World Health Organization (WHO) growth charts.

Objective

To evaluate and compare the growth of French children who were born between 1981 and 2007, with the WHO growth charts and the French reference curves currently used.

Design

Anthropometric measurements from French children, who participated in 12 studies, were analyzed: 82,151 measurements were available for 27,257 children in different age groups, from birth to 18 years. We calculated and graphically compared mean z-scores based on the WHO and French curves, for height, weight and Body Mass Index (BMI) according to age and sex. The prevalence of overweight using the WHO, the French and International Obesity Task Force definitions were compared.

Results

Our population of children was on average 0.5 standard deviations taller than the French reference population, from the first month of life until puberty age. Mean z-scores for height, weight and BMI were closer to zero based on the WHO growth charts than on the French references from infancy until late adolescence, except during the first six months. These differences not related to breastfeeding rates. As expected, the prevalence of overweight depended on the reference used, and differences varied according to age.

Conclusion

The WHO growth charts may be appropriate for monitoring growth of French children, as the growth patterns in our large population of French children were closer to the WHO growth charts than to the French reference curves, from 6 months onwards. However, there were some limitations in the use of these WHO growth charts, and further investigation is needed.     

cAMP production by adenylyl cyclase G induces prespore differentiation in Dictyostelium slugs

Encystation and sporulation are crucial developmental transitions for solitary and social amoebae, respectively. Whereas little is known of encystation, sporulation requires both extra- and intracellular cAMP. After aggregation of social amoebae, extracellular cAMP binding to surface receptors and intracellular cAMP binding to cAMP-dependent protein kinase (PKA) act together to induce prespore differentiation. Later, a second episode of PKA activation triggers spore maturation. Adenylyl cyclase B (ACB) produces cAMP for maturation, but the cAMP source for prespore induction is unknown. We show that adenylyl cyclase G (ACG) protein is upregulated in prespore tissue after aggregation. acg null mutants show reduced prespore differentiation, which becomes very severe when ACB is also deleted. ACB is normally expressed in prestalk cells, but is upregulated in the prespore region of acg null structures. These data show that ACG induces prespore differentiation in wild-type cells, with ACB capable of partially taking over this function in its absence.     

Changes of serum glycans during sepsis and acute pancreatitis

Acute inflammatory response is a complex process associated with the production of both pro- and anti-inflammatory mediators. Although it is generally considered to be a single homeostatic mechanism, there are differences associated with the nature and the site of inflammation. We examined the changes of N-linked glycans released from the serum of a patient with sepsis and a patient with acute pancreatitis during the first eight days of the disease. Sera were taken from patients at the time of reporting to hospital and then three more times. The blood from a healthy individual was drawn on one occasion only. Glycans were released using N-glycosidase F and were subjected to normal phase and weak anion exchange high-performance liquid chromatography, exoglycosidase digestions, and mass spectrometry. The levels of identified structures have been followed through the course of disease and compared to the control levels. Changes in serum glycans were found to occur very early in acute inflammation. The most prominent differences include the increase in ratio of outer arm to core fucose, increase in the amount of tetrasialylated structures, changes in the levels of mannose structures, and in the degree of branching. The relative proportions of different glycans changed daily and some differences were also observed between sepsis and pancreatitis, probably reflecting that in these two conditions, the acute phase response is triggered by a different stimulus that is associated with different patterns of production of cytokines.     

Rapid and noninvasive metabonomic characterization of inflammatory bowel disease

Inflammatory bowel diseases (IBD) including Crohn's disease (CD) and ulcerative colitis (UC) have a major impact on the health of individuals and populations. Accurate diagnosis of inflammatory bowel disease (IBD) at an early stage, and correct differentiation between Crohn's disease (CD) and ulcerative colitis (UC), is important for optimum treatment and prognosis. We present here the first characterization of fecal extracts obtained from patients with CD and UC by employing a noninvasive metabonomics approach, which combines high resolution 1H NMR spectroscopy and multivariate pattern recognition techniques. The fecal extracts of both CD and UC patients were characterized by reduced levels of butyrate, acetate, methylamine, and trimethylamine in comparison with a control population, suggesting changes in the gut microbial community. Also, elevated quantities of amino acids were present in the feces from both disease groups, implying malabsorption caused by the inflammatory disease or an element of protein losing enteropathy. Metabolic differences in fecal profiles were more marked in the CD group in comparison with the control group, indicating that the inflammation caused by CD is more extensive in comparison with UC and involves the whole intestine. Furthermore, glycerol resonances were a dominant feature of fecal spectra from patients with CD but were present in much lower intensity in the control and UC groups. This work illustrates the potential of metabonomics to generate novel noninvasive diagnostics for gastrointestinal diseases and may further our understanding of disease mechanisms.     

The diploid genome sequence of an individual human

Presented here is a genome sequence of an individual human. It was produced from ∼32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb) of contiguous sequence with approximately 7.5-fold coverage for any given region. We developed a modified version of the Celera assembler to facilitate the identification and comparison of alternate alleles within this individual diploid genome. Comparison of this genome and the National Center for Biotechnology Information human reference assembly revealed more than 4.1 million DNA variants, encompassing 12.3 Mb. These variants (of which 1,288,319 were novel) included 3,213,401 single nucleotide polymorphisms (SNPs), 53,823 block substitutions (2–206 bp), 292,102 heterozygous insertion/deletion events (indels)(1–571 bp), 559,473 homozygous indels (1–82,711 bp), 90 inversions, as well as numerous segmental duplications and copy number variation regions. Non-SNP DNA variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases. This suggests an important role for non-SNP genetic alterations in defining the diploid genome structure. Moreover, 44% of genes were heterozygous for one or more variants. Using a novel haplotype assembly strategy, we were able to span 1.5 Gb of genome sequence in segments >200 kb, providing further precision to the diploid nature of the genome. These data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information.