Theories focused on kinship and the genetic conflict it induces are widely considered to be the primary explanations for the evolution of genomic imprinting. However, there have appeared many competing ideas that do not involve kinship/conflict. These ideas are often overlooked because kinship/conflict is entrenched in the literature, especially outside evolutionary biology. Here we provide a critical overview of these non-conflict theories, providing an accessible perspective into this literature. We suggest that some of these alternative hypotheses may, in fact, provide tenable explanations of the evolution of imprinting for at least some loci.
evolutionary hypotheses; genetic imprinting; kinship; genetic conflict
Genomic imprinting is manifested as differential allelic expression (DAE) depending on the parent-of-origin. The most direct way to identify imprinted genes is to directly score the DAE in a context where one can identify which parent transmitted each allele. Because many genes display DAE, simply scoring DAE in an individual is not sufficient to identify imprinted genes. In this paper, we outline many technical aspects of a scheme for identification of imprinted genes that makes use of RNA sequencing (RNA-seq) from tissues isolated from F1 offspring derived from the pair of reciprocal crosses. Ideally, the parental lines are from two inbred strains that are not closely related to each other. Aspects of tissue purity, RNA extraction, library preparation and bioinformatic inference of imprinting are all covered. These methods have already been applied in a number of organisms, and one of the most striking results is the evolutionary fluidity with which novel imprinted genes are gained and lost within genomes. The general methodology is also applicable to a wide range of other biological problems that require quantification of allele-specific expression using RNA-seq, such as cis-regulation of gene expression, X chromosome inactivation and random monoallelic expression.
Clostridium difficile remains the leading cause of nosocomial diarrhea worldwide, which is largely considered to be due to the production of two potent toxins: TcdA and TcdB. However, PCR ribotype (RT) 017, one of five clonal lineages of human virulent C. difficile, lacks TcdA expression but causes widespread disease. Whole-genome sequencing was applied to 35 isolates from hospitalized patients with C. difficile infection (CDI) and two environmental ward isolates in London, England. The phylogenetic analysis of single nucleotide polymorphisms (SNPs) revealed a clonal cluster of temporally variable isolates from a single hospital ward at University Hospital Lewisham (UHL) that were distinct from other London hospital isolates. De novo assembled genomes revealed a 49-kbp putative conjugative transposon exclusive to this hospital clonal cluster which would not be revealed by current typing methodologies. This study identified three sublineages of C. difficile RT017 that are circulating in London. Similar to the notorious RT027 lineage, which has caused global outbreaks of CDI since 2001, the lineage of toxin-defective RT017 strains appears to be continually evolving. By utilization of WGS technologies to identify SNPs and the evolution of clonal strains, the transmission of outbreaks caused by near-identical isolates can be retraced and identified.
The encapsulation and packaging reliability in fully integrated, fully wireless 100 channel Utah Slant Electrode Array (USEA)/integrated neural interface-recording version 5 (INI-R5) has been evaluated by monitoring the extended long term in-vitro functional stability and recording longevity. The INI encapsulated with 6-μm Parylene-C was immersed in phosphate buffer saline (PBS) at room temperature for a period of over 12 months. The USEA/INI-R5, while being soaked was powered and configured wirelessly through 2.765 MHz inductive link and the transmitted frequency shift keying (FSK) modulated radio-frequency (RF) (900 MHz Industrial, scientific, medical-ISM band) signal was also recorded wirelessly as a function of soak time. In order to test the long term recording ability, in-vitro wireless recording was performed in agarose for few channels. The full functionality and the ability of the electrodes to record artificial neural signals even after 12 months of PBS soak provides a measure of encapsulation reliability, the functional and recording stability in fully integrated wireless neural interface and potential usefulness for future chronic implants.
The production of graceful skeletal movements requires coordinated activation of multiple muscles that produce torques around multiple joints. The work described herein is focused on one such movement, stance, that requires coordinated activation of extensor muscles acting around the hip, knee and ankle joints. The forces evoked in these muscles by external stimulation all have a complex dependence on muscle length and shortening velocities, and some of these muscles are bi-articular. In order to recreate sit-to-stand maneuvers in the anesthetized feline, we excited the hind limb musculature using intrafascicular multielectrode stimulation (IFMS) of the muscular branch of the sciatic nerve, the femoral nerve, and the main branch of the sciatic nerve. Stimulation was achieved with either acutely or chronically implanted Utah Slanted Electrode Arrays (USEAs) via subsets of electrodes 1) that activated motor units in the extensor muscles of the hip, knee, and ankle joints, 2) that were able to evoke large extension forces, and 3) that manifested minimal coactivation of the targeted motor units. Three hind limb force-generation strategies were investigated, including sequential activation of independent motor units to increase force, and interleaved or simultaneous IFMS of three sets of six or more USEA electrodes that excited the hip, knee, and ankle extensors. All force-generation strategies evoked stance, but the interleaved IFMS strategy also reduced muscle fatigue produced by repeated sit-to-stand maneuvers compared with fatigue produced by simultaneous activation of different motor neuron pools. These results demonstrate the use of interleaved IFMS as a means to recreate coordinated, fatigue-resistant multi-joint muscle forces in the unilateral hind limb. This muscle activation paradigm could provide a promising neuroprosthetic approach for the restoration of sit-to-stand transitions in individuals who are paralyzed by spinal cord injury, stroke, or disease.
Neural prosthetics; intrafascicular stimulation; motor system; stance
This paper characterizes the Utah Slant Optrode Array (USOA) as a means to deliver infrared light deep into tissue. An undoped crystalline silicon (100) substrate was used to fabricate 10 × 10 arrays of optrodes with rows of varying lengths from 0.5 mm to 1.5 mm on a 400-μm pitch. Light delivery from optical fibers and loss mechanisms through these Si optrodes were characterized, with the primary loss mechanisms being Fresnel reflection, coupling, radiation losses from the tapered shank and total internal reflection in the tips. Transmission at the optrode tips with different optical fiber core diameters and light in-coupling interfaces was investigated. At λ = 1.55μm, the highest optrode transmittance of 34.7%, relative to the optical fiber output power, was obtained with a 50-μm multi-mode fiber butt-coupled to the optrode through an intervening medium of index n = 1.66. Maximum power is directed into the optrodes when using fibers with core diameters of 200 μm or less. In addition, the output power varied with the optrode length/taper such that longer and less tapered optrodes exhibited higher light transmission efficiency. Output beam profiles and potential impacts on physiological tests were also examined. Future work is expected to improve USOA efficiency to greater than 64%.
(170.3890) Medical optics instrumentation; (220.4610) Optical fabrication; (230.7380) Waveguides, channeled; (260.3060) Infrared
Endosymbiotic bacteria were identified in the parasitic ciliate Ichthyophthirius multifiliis, a common pathogen of freshwater fish. PCR amplification of DNA prepared from two isolates of I. multifiliis, using primers that bind conserved sequences in bacterial 16S rRNA genes, generated an ∼1,460-bp DNA product, which was cloned and sequenced. Sequence analysis demonstrated that 16S rRNA gene sequences from three classes of bacteria were present in the PCR product. These included Alphaproteobacteria (Rickettsiales), Sphingobacteria, and Flavobacterium columnare. DAPI (4′,6-diamidino-2-phenylindole) staining showed endosymbionts dispersed throughout the cytoplasm of trophonts and, in most, but not all theronts. Endosymbionts were observed by transmission electron microscopy in the cytoplasm, surrounded by a prominent, electron-translucent halo characteristic of Rickettsia. Fluorescence in situ hybridization demonstrated that bacteria from the Rickettsiales and Sphingobacteriales classes are endosymbionts of I. multifiliis, found in the cytoplasm, but not in the macronucleus or micronucleus. In contrast, F. columnare was not detected by fluorescence in situ hybridization. It likely adheres to I. multifiliis through association with cilia. The role that endosymbiotic bacteria play in the life history of I. multifiliis is not known.
Plasmodium knowlesi is an intracellular malaria parasite whose natural vertebrate host is Macaca fascicularis (the ‘kra’ monkey); however, it is now increasingly recognized as a significant cause of human malaria, particularly in southeast Asia1,2. Plasmodium knowlesi was the first malaria parasite species in which antigenic variation was demonstrated3, and it has a close phylogenetic relationship to Plasmodium vivax4, the second most important species of human malaria parasite (reviewed in ref. 4). Despite their relatedness, there are important phenotypic differences between them, such as host blood cell preference, absence of a dormant liver stage or ‘hypnozoite’ in P. knowlesi, and length of the asexual cycle (reviewed in ref. 4). Here we present an analysis of the P. knowlesi (H strain, Pk1(A+) clone5) nuclear genome sequence. This is the first monkey malaria parasite genome to be described, and it provides an opportunity for comparison with the recently completed P. vivax genome4 and other sequenced Plasmodium genomes6-8. In contrast to other Plasmodium genomes, putative variant antigen families are dispersed throughout the genome and are associated with intrachromosomal telomere repeats. One of these families, the KIRs9, contains sequences that collectively match over one-half of the host CD99 extracellular domain, which may represent an unusual form of molecular mimicry.
Although guidance exists for the use of many laboratory tests in a wide range of clinical situations, this guidance is spread among a range of literature sources, and is often directed at laboratory specialists rather than test users. Individual general practices display large variations in standardised test requesting, yet much of their testing activity involves a relatively small range of tests. This paper describes a methodological approach to review the available evidence and guidance and to extract relevant primary research work to examine a range of testing scenarios in general practice, with the aim of formulating guidance based on the best available evidence or consensus opinions.
appropriateness; best practice; evidence based pathology; multidisciplinary
Apolipoproteins (apo) A-I and C-III are components of high-density lipoprotein-cholesterol (HDL-C), a quantitative trait negatively correlated with risk of cardiovascular disease (CVD). We analyzed the contribution of individual and pairwise combinations of single nucleotide polymorphisms (SNPs) in the APOA1/APOC3 genes to HDL-C variability to evaluate (1) consistency of published single-SNP studies with our single-SNP analyses; (2) consistency of single-SNP and two-SNP phenotype–genotype relationships across race-, gender-, and geographical location-dependent contexts; and (3) the contribution of single SNPs and pairs of SNPs to variability beyond that explained by plasma apo A-I concentration. We analyzed 45 SNPs in 3,831 young African–American (N=1,858) and European–American (N=1,973) females and males ascertained by the Coronary Artery Risk Development in Young Adults (CARDIA) study. We found three SNPs that significantly impact HDL-C variability in both the literature and the CARDIA sample. Single-SNP analyses identified only one of five significant HDL-C SNP genotype relationships in the CARDIA study that was consistent across all race-, gender-, and geographical location-dependent contexts. The other four were consistent across geographical locations for a particular race–gender context. The portion of total phenotypic variance explained by single-SNP genotypes and genotypes defined by pairs of SNPs was less than 3%, an amount that is miniscule compared to the contribution explained by variability in plasma apo A-I concentration. Our findings illustrate the impact of context-dependence on SNP selection for prediction of CVD risk factor variability.
APOA1 gene; APOC3 gene; High-density lipoprotein-cholesterol; Cardiovascular disease
Aims: To compare differences in microbiology testing activity between general practices within and between five hospitals in two National Health Service (NHS) regions in England.
Methods: Retrospective capture of standardised microbiology testing activity from the laboratory computer databases. Six equivalent tests were identified and compared. Data were obtained for 174 general practices in eight primary care groups, served by two NHS hospital trusts and three public health laboratories. The total catchment population was 1 180 000 people. Comparative test activities were displayed graphically and differences in median test activity and the hospital activity distributions were examined by the Wilcoxon signed rank test.
Results: Median testing activity differed by 200% (urine) to 800% (wound swabs) between the trusts that performed the highest and the lowest number of tests, and from 300% to 1900% between the top and bottom 10% activity bands of general practices. Large and significant differences were found between the hospitals, irrespective of whether they belonged to the same trust, and irrespective of their geographical location.
Conclusions: Large differences in microbiology testing exist within individual trust catchment areas in primary care, and there are also considerable differences between trusts. These inequalities may also introduce a selection bias into epidemiological and antibiotic resistance surveillance. This indicates a widespread need to examine and deal with the reasons responsible for these differences.
Appropriateness; evidence based medicine; microbiology; primary care
Despite years of research and hundreds of reports on tumour markers in oncology, the number of markers that have emerged as clinically useful is pitifully small. Often initially reported studies of a marker show great promise, but subsequent studies on the same or related markers yield inconsistent conclusions or stand in direct contradiction to the promising results. It is imperative that we attempt to understand the reasons that multiple studies of the same marker lead to differing conclusions. A variety of methodological problems have been cited to explain these discrepancies. Unfortunately, many tumour marker studies have not been reported in a rigorous fashion, and published articles often lack sufficient information to allow adequate assessment of the quality of the study or the generalisability of the study results. The development of guidelines for the reporting of tumour marker studies was a major recommendation of the US National Cancer Institute and the European Organisation for Research and Treatment of Cancer (NCI-EORTC) First International Meeting on Cancer Diagnostics in 2000. Similar to the successful CONSORT initiative for randomised trials and the STARD statement for diagnostic studies, we suggest guidelines to provide relevant information about the study design, preplanned hypotheses, patient and specimen characteristics, assay methods, and statistical analysis methods. In addition, the guidelines suggest helpful presentations of data and important elements to include in discussions. The goal of these guidelines is to encourage transparent and complete reporting so that the relevant information will be available to others to help them to judge the usefulness of the data and understand the context in which the conclusions apply.
tumour marker; guidelines; REMARK; NCI; EORTC; prognostic
Aims: To determine the value of squamous mucosal histology in the assessment of patients with gastro-oesophageal reflux symptoms.
Methods: Sixty six patients with reflux symptoms underwent endoscopy with oesophageal biopsy, manometry, and 24 hour oesophageal pH testing. The following histological features were assessed in squamous mucosa: the degree of basal cell hyperplasia, the degree of papillary zone elongation, and the density of neutrophil and eosinophil infiltration. Comparisons were made between the histological findings and the oesophageal function tests.
Results: The correlation between the traditionally accepted histological markers of gastro-oesophageal reflux disease in squamous mucosa and 24 hour pH testing was predominantly negative, with the exception of neutrophil inflammation in the squamous mucosa of patients with complicated reflux disease.
Conclusions: This study was unable to confirm the value of the Ismail-Beigi criteria as histological markers of acid reflux. By inference, biopsy of the oesophageal squamous mucosa is of limited value in the assessment of patients with reflux symptoms.
ambulatory pH monitoring; gastro-oesphageal reflux disease; histology; oesophagitis
survival analysis; missing data; validation; repeated events
survival analysis; Cox model; AFT model; model checking; choice of coavriates; goodness of fit
survival analysis; Cox model; AFT model; model selection
survival analysis; statistical methods; Kaplan-Meier
BACKGROUND—The cause of inflammation in cardiac mucosa at the gastro-oesophageal junction (GOJ) is unclear, both gastro-oesophageal reflux disease (GORD) and Helicobacter pylori having been implicated.
AIMS—To describe patterns of gastritis in patients with symptomatic GORD.
METHODS—In 150 patients (126 normally located Z-line, 24 Barrett's oesophagus) with symptoms of GORD, biopsies were taken of the GOJ, corpus, and antrum. Inflammation was assessed using the updated Sydney System.
RESULTS—For the 126 patients with a normally located Z-line, biopsies of the GOJ revealed cardiac mucosa in 96, fundic mucosa in 29, and squamous mucosa in one. Inflammation in glandular mucosa at the GOJ was present in 99/125 specimens (79%), including 87/96 (91%) with cardiac mucosa and 12/29 (41%) with fundic mucosa. Inflammation in fundic mucosa was closely related to H pylori and active inflammation was only seen in its presence. Inflammation in cardiac mucosa was less closely linked to H pylori. When H pylori was present in cardiac mucosa (28/96, 29%) active inflammation was usually present (25/28, 89%). However, active inflammation was also found in 34/68 (50%) cardiac mucosa specimens without H pylori. Overall, 28/87 (32%) biopsies with carditis were colonised with H pylori and 59/87 (68%) were not. In H pylori colonised patients, inflammation was seen throughout the stomach, while in non-colonised patients, it was confined to cardiac mucosa.
CONCLUSIONS—Patients with symptomatic GORD had a high prevalence of carditis. This was of two types, H pylori associated and unassociated. Except on Giemsa staining, the two were morphologically identical, suggesting mediation by a similar immunological mechanism.
Keywords: cardiac mucosa; carditis; gastro- oesophageal junction; gastro-oesophageal reflux; Helicobacter pylori; inflammation
About 6000 women in the United Kingdom develop ovarian cancer each year and about two-thirds of the women will die from the disease. Establishing the prognosis of a woman with ovarian cancer is an important part of her evaluation and treatment. Prognostic models and indices in ovarian cancer should be developed using large databases and, ideally, with complete information on both prognostic indicators and long-term outcome. We developed a prognostic model using Cox regression and multiple imputation from 1189 primary cases of epithelial ovarian cancer (with median follow-up of 4.6 years). We found that the significant (P≤ 0.05) prognostic factors for overall survival were age at diagnosis, FIGO stage, grade of tumour, histology (mixed mesodermal, clear cell and endometrioid versus serous papillary), the presence or absence of ascites, albumin, alkaline phosphatase, performance status on the ZUBROD-ECOG-WHO scale, and debulking of the tumour. This model is consistent with other models in the ovarian cancer literature; it has better predictive ability and, after simplification and validation, could be used in clinical practice. http://www.bjcancer.com © 2001 Cancer Research Campaignhttp://www.bjcancer.com
ovarian cancer; prognostic model; overall survival
In Drosophila, male accessory gland fluid (seminal fluid) has multiple effects on the female's reproductive efficiency. Here, we show the effect of seminal fluid on rate of egg hatch immediately following mating. Singly mated females were remated to two classes of sterile males, one with seminal fluid and one without seminal fluid. Transfer of seminal fluid results in a strong reduction in egg hatch shortly after the mating. Also, it is shown that remating with normal males causes an immediate reduction of egg hatch followed by recovery to normal egg hatch. In all cases, unhatched eggs contained no sperm. These results are consistent with a role for seminal fluid in sperm competition, mediated by incapacitation or inefficient use of resident sperm.
The survival of young patients (⩽ 50 years of age) with carcinoma of the oesophagus or stomach has been reported to be poorer than that of their older counterparts. The aim of the current study was to review the outcome of such young patients with oesophagogastric cancer and to compare the outcome in patients with carcinoma of the oesophagus/cardia with patients with carcinoma of the more distal stomach. The study population was 50 patients. Tumour location was oesophagus/cardia (n=33) and gastric body/antrum (n=17). The most common presenting symptoms were weight loss (66%), epigastric pain (54%), dysphagia (50%), and heartburn (40%). Seventeen patients had experienced foregut symptoms for a period of ⩾6 months. These patients were more likely to have symptoms of gastro-oesophageal reflux disease and to have received acid suppression therapy than patients with shorter symptom durations. Only 20 patients underwent a potentially curative resection, while 10 underwent open and close laparotomy. The overall median survival was 7 months and the 5-year survival was 8%. Multivariate analysis revealed that surgical resection and UICC stage were the only factors that significantly influenced survival. There was no difference in the survival of patients with proximally situated tumours compared to those with distally located tumours. Wide variations in clinical practice were seen between different surgeons. Consequently, a multidisciplinary team designed to manage all patients with oesophagogastric cancer according to nationally agreed protocols has been established in our hospital. Earlier diagnosis of these tumours is to be encouraged, even if this necessitates the more liberal use of endoscopy in the evaluation of young patients with persistent foregut symptoms.
Keywords: oesophagus; stomach; carcinoma; surgery; age-factors
Yersinia pestis, the causative agent of plague, and the enteropathogen Yersinia pseudotuberculosis have nearly identical nucleotide similarity yet cause markedly different diseases. To investigate this conundrum and to study Yersinia pathogenicity, we developed a high-density oligonucleotide array-based modification of signature-tagged mutagenesis (STM). Y. pseudotuberculosis YPIII mutants constructed with the tagged transposons were evaluated in the murine yersiniosis infection model. The DNA tags were amplified using biotinylated primers and hybridized to high-density oligonucleotide arrays containing DNA complementary to the tags. Comparison of the hybridization signals from input pools and output pools identified a mutant whose relative abundance was significantly reduced in the output pool. Sequence data from 31 transposon insertion regions was compared to the complete Y. pestis CO92 genome sequence. The 26 genes present in both species were found to be almost identical, but five Y. pseudotuberculosis genes identified through STM did not have counterparts in the Y. pestis genome and may contribute to the different tropisms in these closely related pathogens. Potential virulence genes identified include those involved in lipopolysaccharide biosynthesis, adhesion, phospholipase activity, iron assimilation, and gene regulation. The phospholipase A (PldA) mutant exhibited reduced phospholipase activity compared to the wild-type strain and in vivo attenuation of the mutant was confirmed. The combination of optimized double tag sequences and high-density array hybridization technology offers improved performance, efficiency, and reliability over classical STM and permits quantitative analysis of data.
p53 gene mutation is the most common genetic alteration in neoplastic diseases, including breast cancer, for which p53 alteration may indicate poor prognosis. Recent clinical evidence suggests that prostate-specific antigen (PSA) expression may identify breast cancer patients with favourable outcome. Assessment of p53 and PSA in combination, potentially offering improved prediction, has not yet been performed. Extracts from 952 primary breast carcinomas were assayed for PSA and p53 by quantitative enzyme-linked immunosorbent assays (ELISAs) developed by the authors. Concentrations of each marker were classified as negative or positive on the basis of median and 30th percentile cut-off points for p53 and PSA respectively. Patients followed for a median of 6 years having different combinations of negative or positive status for PSA and p53 were compared with respect to the relative risks (RRs) for relapse and death by Cox proportional hazards regression analysis, in which an interaction term was also evaluated, and with respect to disease-free survival (DFS) and overall survival (OS) probabilities by Kaplan–Meier plots and log-rank tests. Multivariate models were adjusted for oestrogen and progesterone receptor status, nodal status, patient age, tumour size, DNA ploidy, S phase fraction and receipt of chemotherapy. Interactions were not found between the status of PSA and p53 in the Cox models, in which PSA-negativity (RR = 1.47, P = 0.020 for DFS, and RR = 1.49, P = 0.023 for OS) and p53-positivity (RR = 1.46, P = 0.017 for DFS, and RR = 1.41, P = 0.033 for OS) were individually associated with prognosis. Evaluation of a combined three-level variable revealed that PSA(–)/p53(+) patients had significantly higher risks for relapse (RR = 2.13, P < 0.001) and death (RR = 2.08, P = 0.001) than PSA(+)/p53(–) patients, and that patients positive or negative for both markers had intermediate risks for the outcome events in the same multivariate analysis (RR = 1.45 for both DFS and OS). The results of our study demonstrate that the assessment of combined PSA and p53 expression status by ELISAs, easily applicable to breast tumour extracts prepared for steroid hormone receptor analyses, may stratify breast cancer patients into groups differing by relapse and death risks of greater magnitude than offered by the assessment of either p53 or PSA alone. © 1999 Cancer Research Campaign
prostate-specific antigen; protein, p53; ELISA; breast neoplasms
Recent dengue outbreaks in the Caribbean and Central and South America and the presence of competent mosquito vectors increase the likelihood of future autochthonous transmission in Florida. During April 1997 to March 1998, a laboratory-based active surveillance program detected 18 cases of dengue involving all four dengue serotypes. All patients reported recent travel to countries with indigenous dengue transmission. These results demonstrate that dengue infections are imported into Florida at a much higher rate than reflected by previous passive surveillance; therefore, the risk for local dengue transmission may be increasing.