Adaptive sequence divergence forged new neurodevelopmental enhancers in humans

Searches for the genetic underpinnings of uniquely human traits have focused on human-specific divergence in conserved genomic regions, which reflects adaptive modifications of existing functional elements. However, the study of conserved regions excludes functional elements that descended from previously neutral regions. Here, we demonstrate that the fastest-evolved regions of the human genome, which we term "human ancestor quickly evolved regions" (HAQERs), rapidly diverged in an episodic burst of directional positive selection prior to the human-Neanderthal split, before transitioning to constraint within hominins. HAQERs are enriched for bivalent chromatin states, particularly in gastrointestinal and neurodevelopmental tissues, and genetic variants linked to neurodevelopmental disease. We developed a multiplex, single-cell in vivo enhancer assay to discover that rapid sequence divergence in HAQERs generated hominin-unique enhancers in the developing cerebral cortex. We propose that a lack of pleiotropic constraints and elevated mutation rates poised HAQERs for rapid adaptation and subsequent susceptibility to disease.

Correcting signal biases and detecting regulatory elements in STARR-seq data

High-throughput reporter assays such as self-transcribing active regulatory region sequencing (STARR-seq) have made it possible to measure regulatory element activity across the entire human genome at once. The resulting data, however, present substantial analytical challenges. Here, we identify technical biases that explain most of the variance in STARR-seq data. We then develop a statistical model to correct those biases and to improve detection of regulatory elements. This approach substantially improves precision and recall over current methods, improves detection of both activating and repressive regulatory elements, and controls for false discoveries despite strong local correlations in signal.

Handheld electronic device use in patient care: the emergency department patient perspective-a cross-sectional survey

BACKGROUND

Staff use of smartphones and tablets in the healthcare setting is increasingly prevalent, but little is known about whether this use is acceptable to patients. Staff are concerned that the use of handheld electronic devices (HEDs) may be negatively misconstrued by patients. The HED can be a valuable tool, offering the emergency clinician access to a wealth of resources; it is therefore vital that patient views are addressed during their widespread adoption into clinical practice.

METHODS

Patients, or those accompanying them, within the ED of the Royal Derby Hospital between April and June 2017 were asked to complete a survey consisting of 22 questions. Data collection took place to include all times of day and every day of the week. Every eligible individual within the department during a data collection period was approached.

RESULTS

A total of 438 respondents successfully completed the survey with a response rate of 92%. Only 2% of those who observed staff using HEDs during their ED visit thought that they were being used for non-clinical purposes. 339 (78%) agreed that staff should be allowed to use HEDs in the workplace. Concerns expressed by respondents included devices being used for non-clinical purposes and data security. The main suggestion by respondents was that the purpose of the HEDs should be explained to patients to avoid misinterpretation.

CONCLUSION

Our survey shows that the majority of survey respondents felt that clinical staff should be allowed to use HEDs in the workplace and that many of the concerns raised could be addressed with adequate patient information and clear governance.

Bayesian estimation of genetic regulatory effects in high-throughput reporter assays

MOTIVATION

High-throughput reporter assays dramatically improve our ability to assign function to noncoding genetic variants, by measuring allelic effects on gene expression in the controlled setting of a reporter gene. Unlike genetic association tests, such assays are not confounded by linkage disequilibrium when loci are independently assayed. These methods can thus improve the identification of causal disease mutations. While work continues on improving experimental aspects of these assays, less effort has gone into developing methods for assessing the statistical significance of assay results, particularly in the case of rare variants captured from patient DNA.

RESULTS

We describe a Bayesian hierarchical model, called Bayesian Inference of Regulatory Differences, which integrates prior information and explicitly accounts for variability between experimental replicates. The model produces substantially more accurate predictions than existing methods when allele frequencies are low, which is of clear advantage in the search for disease-causing variants in DNA captured from patient cohorts. Using the model, we demonstrate a clear tradeoff between variant sequencing coverage and numbers of biological replicates, and we show that the use of additional biological replicates decreases variance in estimates of effect size, due to the properties of the Poisson-binomial distribution. We also provide a power and sample size calculator, which facilitates decision making in experimental design parameters.

AVAILABILITY AND IMPLEMENTATION

The software is freely available from www.geneprediction.org/bird. The experimental design web tool can be accessed at http://67.159.92.22:8080.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia

Schizophrenia genome-wide association studies have identified >150 regions of the genome associated with disease risk, yet there is little evidence that coding mutations contribute to this disorder. To explore the mechanism of non-coding regulatory elements in schizophrenia, we performed ATAC-seq on adult prefrontal cortex brain samples from 135 individuals with schizophrenia and 137 controls, and identified 118,152 ATAC-seq peaks. These accessible chromatin regions in the brain are highly enriched for schizophrenia SNP heritability. Accessible chromatin regions that overlap evolutionarily conserved regions exhibit an even higher heritability enrichment, indicating that sequence conservation can further refine functional risk variants. We identify few differences in chromatin accessibility between cases and controls, in contrast to thousands of age-related differential accessible chromatin regions. Altogether, we characterize chromatin accessibility in the human prefrontal cortex, the effect of schizophrenia and age on chromatin accessibility, and provide evidence that our dataset will allow for fine mapping of risk variants.

Nuclease Footprints in Sperm Project Past and Future Chromatin Regulatory Events

Nuclear remodeling to a condensed state is a hallmark of spermatogenesis. This is achieved by replacement of histones with protamines. Regions retaining nucleosomes may be of functional significance. To determine their potential roles, sperm from wild type and transgenic mice harboring a single copy insert of the human protamine cluster were subjected to Micrococcal Nuclease-seq. CENTIPEDE, a hierarchical Bayesian model, was used to identify multiple spatial patterns, "footprints", of MNase-seq reads along the sperm genome. Regions predicted by CENTIPEDE analysis to be bound by a regulatory factor in sperm were correlated with genomic landmarks and higher order chromatin structure datasets to identify potential roles for these factors in regulating either prior or post spermatogenic, i.e., early embryonic events. This approach linked robust endogenous protamine transcription and transgene suppression to its chromatin environment within topologically associated domains. Of the candidate enhancer-bound regulatory proteins, Ctcf, was associated with chromatin domain boundaries in testes and embryonic stem cells. The continuity of Ctcf binding through the murine germline may permit rapid reconstitution of chromatin organization following fertilization. This likely reflects its preparation for early zygotic genome activation and comparatively accelerated preimplantation embryonic development program observed in mouse as compared to human and bull.

Oxidative DNA damage in mouse sperm chromosomes: Size matters

Normal embryo and foetal development as well as the health of the progeny are mostly dependent on gamete nuclear integrity. In the present study, in order to characterize more precisely oxidative DNA damage in mouse sperm we used two mouse models that display high levels of sperm oxidative DNA damage, a common alteration encountered both in in vivo and in vitro reproduction. Immunoprecipitation of oxidized sperm DNA coupled to deep sequencing showed that mouse chromosomes may be largely affected by oxidative alterations. We show that the vulnerability of chromosomes to oxidative attack inversely correlated with their size and was not linked to their GC richness. It was neither correlated with the chromosome content in persisting nucleosomes nor associated with methylated sequences. A strong correlation was found between oxidized sequences and sequences rich in short interspersed repeat elements (SINEs). Chromosome position in the sperm nucleus as revealed by fluorescent in situ hybridization appears to be a confounder. These data map for the first time fragile mouse sperm chromosomal regions when facing oxidative damage that may challenge the repair mechanisms of the oocyte post-fertilization.

Chromatin and extracellular vesicle associated sperm RNAs

A diverse pool of RNAs remain encapsulated within the transcriptionally silent spermatozoon despite the dramatic reduction in cellular and nuclear volume following cytoplasm/nucleoplasm expulsion. The impact of this pronounced restructuring on the distribution of transcripts inside the sperm essentially remains unknown. To define their compartmentalization, total RNA >100 nt was extracted from sonicated (SS) mouse spermatozoa and detergent demembranated sucrose gradient fractionated (Cs/Tx) sperm heads. Sperm RNAs predominately localized toward the periphery. The corresponding distribution of transcripts and thus localization and complexity were then inferred by RNA-seq. Interestingly, the number of annotated RNAs in the CsTx sperm heads exhibiting reduced peripheral enrichment was restricted. However this included Cabyr, the calcium-binding tyrosine phosphorylation-regulated protein encoded transcript. It is present in murine zygotes prior to the maternal to the zygotic transition yet absent in oocytes, consistent with the delivery of internally positioned sperm-borne RNAs to the embryo. In comparison, transcripts enriched in sonicated sperm contributed to the mitochondria and exosomes along with several nuclear transcripts including the metastasis associated lung adenocarcinoma transcript 1 (Malat1) and several small nucleolar RNAs. Their preferential peripheral localization suggests that chromatin remodeling during spermiogenesis is not limited to nucleoproteins as part of the nucleoprotein exchange.

Mosquito and West Nile virus surveillance in northeast Montana, U.S.A., 2005 and 2006

Mosquito and West Nile virus (WNV) surveillance was conducted on a national wildlife refuge in northeast Montana in 2005 and 2006, during which outbreaks of WNV in a colony of American white pelicans (Pelecanus erythrorhynchos Gmelin) (Pelecaniformes: Pelecanidae) resulted in juvenile mortality rates of ∼ 31%. Both years, floodwater species Ochlerotatus dorsalis (Meigen) (Diptera: Culicidae), Aedes vexans (Meigen) (Diptera: Culicidae) and Ochlerotatus flavescens (Muller) (Diptera: Culicidae) comprised 78% of the total collection and heightened host-seeking activity was observed from mid-June to mid-July. Culex tarsalis Coquillett (Diptera: Culicidae) was most active from mid-July to mid-August and comprised 18% of the collection in 2005 and 20% in 2006. However, fewer than 10% of the Cx. tarsalis females collected in 2006 were obtained adjacent to the pelicans' nesting grounds. Minimum infection rates per 1000 Cx. tarsalis tested for WNV were 1.36 in 2005 and 1.41 in 2006. All pools in which WNV was detected in 2006 were composed of females collected 10 km from the nesting grounds. Substantial juvenile pelican mortality in 2006 despite reductions in the population of the primary vector and in mosquito infection rates near the colony suggests that the methods used to detect the introduction of WNV were too coarse and that amplification of the virus within the colony may reflect causes other than mosquito infection.

Evaluation of mosquito responses to pyrethroid insecticides topically applied to sheep

A rise in the incidence of mosquito-transmitted Cache Valley virus (CVV) in lambs in 2011 prompted a study to evaluate on-animal pyrethroid insecticides to reduce mosquito attacks on sheep. Using enclosure traps for 1 night per wk for 6 wk, we compared engorgement rates of mosquitoes given the opportunity to feed on untreated sheep and sheep treated with 1 Python insecticide ear tag (containing 10% zeta-cypermethrin and 20% piperonyl butoxide) per animal or 2 synergized permethrin body spray treatments (containing 2.5% permethrin and 2.5% piperonyl butoxide). During the 6-wk study, 18,920 mosquitoes were collected in the animal-baited enclosure traps. Thirteen species were identified from these collections with the floodwater species Aedes increpitus and Ae. idahoensis making up 68% of the total. Potential CVV vector species, making up 25% of the samples, included Ae. vexans, Ae. dorsalis, Culex tarsalis, and Culiseta inornata. Traps baited with untreated sheep collected 9,701 mosquitoes with 65% of these engorged. Traps baited with sheep treated with Python ear tags or permethrin spray collected 4,034 and 4,555, respectively, with engorgement rates of 23% and 35%. Blood feeding on ear-tagged sheep was significantly reduced by as much as 90% compared to the untreated sheep, and protection lasted 4 wk or longer. Permethrin spray treatments were most effective within 24 h after application and provided better protection against Ae. dorsalis than the Python tag. Effectiveness of the permethrin spray diminished 1 wk after the 2nd application was made. The effect of these treatments appeared to be repellency because negligible mosquito mortality was observed at the time of collection. Further evaluation of these insecticides under conditions of natural exposure to a mosquito-borne pathogen is warranted.

Stability, delivery and functions of human sperm RNAs at fertilization

Increasing attention has focused on the significance of RNA in sperm, in light of its contribution to the birth and long-term health of a child, role in sperm function and diagnostic potential. As the composition of sperm RNA is in flux, assigning specific roles to individual RNAs presents a significant challenge. For the first time RNA-seq was used to characterize the population of coding and non-coding transcripts in human sperm. Examining RNA representation as a function of multiple methods of library preparation revealed unique features indicative of very specific and stage-dependent maturation and regulation of sperm RNA, illuminating their various transitional roles. Correlation of sperm transcript abundance with epigenetic marks suggested roles for these elements in the pre- and post-fertilization genome. Several classes of non-coding RNAs including lncRNAs, CARs, pri-miRNAs, novel elements and mRNAs have been identified which, based on factors including relative abundance, integrity in sperm, available knockout data of embryonic effect and presence or absence in the unfertilized human oocyte, are likely to be essential male factors critical to early post-fertilization development. The diverse and unique attributes of sperm transcripts that were revealed provides the first detailed analysis of the biology and anticipated clinical significance of spermatozoal RNAs.

A forensic investigation into the etiology of bat mortality at a wind farm: barotrauma or traumatic injury?

Migrating bats have increased mortality near moving turbine blades at wind farms. The authors evaluated competing hypotheses of barotrauma and traumatic injury to determine the cause. They first examined the utility of lungs from salvaged bat carcasses for histopathologic diagnosis of barotrauma and studied laboratory mice as a model system. Postmortem time, environmental temperature, and freezing of carcasses all affected the development of vascular congestion, hemorrhage, and edema. These common tissue artifacts mimicked the diagnostic criteria of pulmonary barotrauma; therefore, lung tissues from salvaged bats should not be used for barotrauma diagnosis. The authors next compared wind farm (WF) bats to building collision (BC) bats collected near downtown Chicago buildings. WF bats had an increased incidence in fracture cases and specific bone fractures and had more external lacerations than BC bats. WF bats had additional features of traumatic injury, including diaphragmatic hernia, subcutaneous hemorrhage, and bone marrow emboli. In summary, 73% (190 of 262) of WF bats had lesions consistent with traumatic injury. The authors then examined for ruptured tympana, a sensitive marker of barotrauma in humans. BC bats had only 1 case (2%, 1 of 42), but this was attributed to concurrent cranial fractures, whereas WF bats had a 20% (16 of 81) incidence. When cases with concurrent traumatic injury were excluded, this yielded a small fraction (6%, 5 of 81) of WF bats with lesions possibly consistent with barotrauma etiology. Forensic pathology examination of the data strongly suggests that traumatic injury is the major cause of bat mortality at wind farms and, at best, barotrauma is a minor etiology.

Trends in presentation of bone and soft tissue sarcomas over 25 years: little evidence of earlier diagnosis

Earlier diagnosis is a key aim in achieving improved outcomes for patients with cancer. Bone and soft tissue sarcomas represent approximately 1% of all malignant tumours. Delays in diagnosis are frequent both because of their rarity and because the clinical features are easily confused with other conditions. In 2000 advice on earlier diagnosis was widely publicised. This study investigates how two factors that may act as a proxy for delay in diagnosis have varied over a 25-year period and whether there is evidence of improvement. Data on symptom duration and tumour size were collected prospectively on all new sarcoma patients referred to an orthopaedic oncology unit over 25 years. Data were available for 2,568 patients with primary bone sarcomas and 2,366 with soft tissue sarcomas. The mean sarcoma size at diagnosis was 10.7 cm and 9.9 cm respectively. The size of bone sarcomas had not changed over time but there had been a slight decrease in the size of soft tissue sarcomas (10.3 cm before 2000 vs 9.6 cm after 2000, p=0.03). The duration of symptoms reported by patients varied widely with a median of 16 weeks for bone sarcomas and 26 weeks for soft tissue sarcomas. The median duration of symptoms for bone sarcomas had actually increased since 2000 (16 weeks before vs 20 weeks after 2000, p<0.01). It remained unchanged for soft tissue sarcomas. These data show there is huge room for improvement in diagnosing bone and soft tissue sarcomas. New strategies are needed urgently.

Local and global factors affecting RNA sequencing analysis

High-throughput RNA sequencing (RNA-seq) continues to provide unparalleled insight into transcriptome complexity. Now the "gold standard" for assessing global transcript levels, RNA-seq is poised to revolutionize our understanding of transcription and posttranscriptional regulation of RNA. Despite significant advantages over prior experimental strategies, RNA-seq is not without pitfalls. We have identified a number of confounding factors that significantly affect sequencing coverage. These include regional GC content, preferential sites of fragmentation, and read "pile-up" due to primer affinity and transcript end effects. Independent of cell type and laboratory, when ignored, these factors can bias analyses. Understanding the underlying principles responsible for producing these artifacts is key to recognizing both their presence and how their effects may be controlled. Here we outline the causes of and strategies to avoid several previously unreported complicating factors common to RNA-seq experiments.

Cleavage of rRNA ensures translational cessation in sperm at fertilization

Intact ribosomal RNAs (rRNAs) comprise the majority of somatic transcripts, yet appear conspicuously absent in spermatozoa, perhaps reflecting cytoplasmic expulsion during spermatogenesis. To discern their fate, total RNA retained in mature spermatozoa from three fertile donors was characterized by Next Generation Sequencing. In all samples, >75% of total sequence reads aligned to rRNAs. The distribution of reads along the length of these transcripts exhibited a high degree of non-uniformity that was reiterated between donors. The coverage of sequencing reads was inversely correlated with guanine-cytosine (GC)-richness such that sequences greater than ∼70% GC were virtually absent in all sperm RNA samples. To confirm the loss of sequence, the relative abundance of specific regions of the 28S transcripts in sperm was established by 7-Deaza-2'-deoxy-guanosine-5'-triphosphate RT-PCR. The inability to amplify specific regions of the 28S sequence from sperm despite the abundant representation of this transcript in the sequencing libraries demonstrates that approximately three-quarters of RNA retained in the mature male gamete are products of rRNA fragmentation. Hence, cleavage (not expulsion of the RNA component of the translational machinery) is responsible for preventing spurious translation following spermiogenesis. These results highlight the potential importance of those transcripts, including many mRNAs, which evade fragmentation and remain intact when sperm are delivered at fertilization. Sequencing data are deposited in GEO as: GSE29160.

Interrogating the transgenic genome: development of an interspecies tiling array

A single expressing copy of the human protamine domain was randomly inserted into an intron of Cyp2c38. The transgenic locus was shown to recapitulate the level of expression observed in normal human testis while not perturbing endogenous protamine expression. The development of an interspecies tiling array was pursued to enable direct comparison of the orthologous protamine domains in a single experiment. Probe design was adapted to generate species-specific high resolution probe sets that would tolerate repetitive elements. Results from competitive hybridizations demonstrate that interspecies tiling arrays are a valuable tool for parallel analysis of highly similar DNA sequences. This approach provides a rapid and reliable means of interrogating samples prior to deep sequencing analysis. These arrays should readily compliment most DNA isolation and analysis techniques such as ChIP, nuclease sensitivity and nuclear matrix association assays.

The sperm nucleus: chromatin, RNA, and the nuclear matrix

Within the sperm nucleus, the paternal genome remains functionally inert and protected following protamination. This is marked by a structural morphogenesis that is heralded by a striking reduction in nuclear volume. Despite these changes, both human and mouse spermatozoa maintain low levels of nucleosomes that appear non-randomly distributed throughout the genome. These regions may be necessary for organizing higher order genomic structure through interactions with the nuclear matrix. The promoters of this transcriptionally quiescent genome are differentially marked by modified histones that may poise downstream epigenetic effects. This notion is supported by increasing evidence that the embryo inherits these differing levels of chromatin organization. In concert with the suite of RNAs retained in the mature sperm, they may synergistically interact to direct early embryonic gene expression. Irrespective, these features reflect the transcriptional history of spermatogenic differentiation. As such, they may soon be utilized as clinical markers of male fertility. In this review, we explore and discuss how this may be orchestrated.

Real-time PCR quantification using a variable reaction efficiency model

The quantitative real-time polymerase chain reaction (PCR) remains a cornerstone technique in gene expression analysis and sequence characterization. Despite the importance of the approach to experimental biology, the confident assignment of reaction efficiency to the early cycles of real-time PCR reactions remains problematic. Considerable noise may be generated when few cycles in the amplification are available to estimate peak efficiency. An alternate approach that uses data from beyond the log-linear amplification phase is explored in this article with the aim of reducing noise and adding confidence to efficiency estimates. PCR reaction efficiency is regressed to estimate the per-cycle profile of an asymptotically departed peak efficiency even when this is not closely approximated in the measurable cycles. The process can be repeated over replicates to develop a robust estimate of peak reaction efficiency. This leads to an estimate of the maximum reaction efficiency that may be considered primer design specific. Using a series of biological scenarios, we demonstrate that this approach can provide an accurate estimate of initial template concentration.

Orthophenylphenol and phenylhydroquinone residues in citrus fruit and processed citrus products after postharvest fungicidal treatments with sodium orthophenylphenate in California and Florida

Sodium orthophenylphenate (SOPP) has been used extensively for >40 years to control postharvest diseases of citrus fruits. Studies of the metabolism of [(14)C]SOPP have identified orthophenylphenol (OPP) as the major metabolite with phenylhydroquinone (PHQ) as a minor metabolite. The whole-fruit tolerance in the United States for OPP is 10 ppm. This study was conducted to quantify terminal OPP and PHQ residues in whole Navel oranges, grapefruit, and lemons following SOPP applications at maximum application rates and following commercial application and fruit storage practices. OPP and PHQ residues also were determined in products processed from treated Navel oranges. OPP residues in lemons, Navel oranges, and grapefruit treated with SOPP using foamer wash and shipping wax applications remained below the 10 ppm tolerance, and PHQ residues were all < or =0.439 ppm. PHQ residues in whole fruit increased with time in commercial storage. OPP residues in all Navel orange matrices except oil remained relatively stable with time in commercial storage; residues in oil declined substantially while in storage.

Inhibitor potencies and substrate preference for endothelin-converting enzyme-1 are dramatically affected by pH

Phosphoramidon has been shown to inhibit endothelin-converting enzyme-1 (ECE-1) in a remarkably pH-dependent manner (Ahn et al. Arch Biochem Biophys 1998;359:258-68). In order to determine whether this dramatic pH-dependence is a general phenomenon of ECE-1, two structurally unrelated ECE-1 inhibitors, PD 069185 and CGS 31447, were tested for ECE-1 inhibition at various pH values. Our data indicate that the potencies of these ECE-1 inhibitors are also highly affected by pH. ECE-1 is known to have a very sharp activity optimum at neutral pH which is in marked contrast to the acidic pH optimum for ECE-2. However, our results show that the pH optimum for ECE-1 activity is highly substrate-dependent. ECE-1 hydrolyzes the small peptide hormones bradykinin and substance P with acidic pH optima of 5.6-5.8, which sharply contrasts the neutral pH optimum with big ET-1 as substrate. These data suggest that the substrate preference for ECE-1 is highly affected by pH and that this pH-dependence for substrate preference might be one way of controlling the specificity of the enzyme in vivo.

Development of an internally quenched fluorescent substrate selective for endothelin-converting enzyme-1

Endothelin-converting enzyme-1 (ECE-1) is a membrane-bound zinc-metallopeptidase that is related to neprilysin in amino acid sequence. A major in vivo function of ECE-1 is the proteolytic conversion of big endothelin-1 to endothelin-1, one of the most potent vasconstricting peptides known. Although ECE-1 was once thought to be specific for the processing of endothelin precursors, it is now known that the enzyme hydrolyzes a number of peptide hormones. We have incorporated knowledge gained from recent studies of ECE-1 substrate specificity to aid the design of internally-quenched fluorescent substrates derived from bradykinin. The best of these substrates, (7-methoxycoumarin-4-yl)acetyl-Arg-Pro-Pro-Gly-Phe-Ser-Ala-Phe-Lys(2, 4-dinitrophenyl), is hydrolyzed by ECE-1 with a k(cat)/K(m) value of 1.9 x 10(7) M(-1) s(-1), making it the most sensitive substrate yet described for ECE-1. The substrate is suitable for the rapid, continuous assay of the enzyme using a microplate format in a fluorescence plate reader, thereby simplifying both the purification of ECE-1 and the characterization of its inhibitors. It is demonstrated that (7-methoxycoumarin-4-yl)acetyl-Arg-Pro-Pro-Gly-Phe-Ser-Ala-Phe-Lys(2, 4-dinitrophenyl) is also a substrate for neprilysin, but is hydrolyzed 10-fold more efficiently by ECE-1, making this substrate selective for ECE-1. Furthermore, this synthetic peptide is a poor substrate for the matrix metalloproteinases.

Laboratory and field evaluations of imidacloprid against Melanoplus sanguinipes (Orthoptera: Acrididae) on small grains

The toxicity of imidaloprid to the migratory grasshopper, Melanoplus sanguinipes (F.), was measured in bioassays, greenhouse trials, and field trials. An LD50 of 53 and 86 ppm for the oral/topical applications of imidacloprid confirmed a low toxicity for this chemical when compared with carbofuran as a standard. However, 100% debilitation was observed at concentrations of > or = 1 ppm. Grasshoppers exhibited leg flexing, abdominal quivering, and tremors before becoming motionless and appearing dead. Knockdown was temporary with a high percentage of recovery within 1 h. Efficacy and feeding damage were determined from artificial infestations of M. sanguinipes at the 2nd, 4th, and early tillering growth stages of winter and spring wheat treated with foliar and seed treatments of imidacloprid. All rates of imidacloprid tested resulted in < 45% mortality to 4th instar and adult M. sanguinipes in the greenhouse and field. Although efficacy was low, high rates of debilitation in bioassays suggest that improved control may be gained by combining imidacloprid with insect pathogens or additional chemicals.

Efficacy of imidacloprid for control of cereal leaf beetle (Coleoptera: Chrysomelidae) in barley

The toxicity of imidacloprid to the cereal leaf beetle, Oulema melanopus (L.), was measured under laboratory and field conditions. Insect mortality and plant damage were determined from artificial and natural infestations of O. melanopus applied to various growth stages of barley. All rates of imidacloprid formulated and applied as a seed treatment caused >90% mortality to cereal leaf beetle larvae when barley was infested with eggs at the 4-leaf stage, but were ineffective when barley was infested with eggs at the early tillering or flag-leaf stages of barley. This window of susceptibility influenced results obtained in field trials where peak larval emergence did not occur until the early tillering stage of barley. The resulting mortality in plants from treated seeds never exceeded 40% in the field. Foliar imidacloprid, however, caused >90% mortality in the field, and may be another option in the management of the cereal leaf beetle.

Disulfide bonds in big ET-1 are essential for the specific cleavage at the Trp(21)-Val(22) bond by soluble endothelin converting enzyme-1 from baculovirus/insect cells

Endothelin converting enzyme-1 (ECE-1) is a type II integral membrane protein and a zinc metalloendopeptidase. ECE-1 generates endothelin-1 (ET-1), the most potent vasoconstrictor yet discovered, by specific proteolytic processing of a precursor peptide, big ET-1. An insect cell expression system, which generates up to 4.3 mg of a secreted, soluble form of ECE-1 (solECE-1) per liter culture medium, has been established and solECE-1 was purified to homogeneity using five chromatographic steps. SolECE-1 expressed in insect cells could be suitable for X-ray structure determination as it is much less glycosylated than solECE-1 from mammalian cells. SolECE-1 from both sources, nonetheless, has comparable enzymatic properties. Despite apparent structural similarities, ECE-1 cleaves big ET-1 exclusively between Trp(21) and Val(22), in contrast to neprilysin, which cleaves big ET-1 at various sites. However, when linear big ET-1, in which the formation of disulfide bonds has been prevented by alkylation of the four cysteines, was used as substrate, it was cleaved by solECE-1 at multiple sites. This result indicates that secondary/tertiary structure of big ET-1 induced by disulfide bonds is essential for the specific cleavage of the Trp(21)-Val(22) bond by ECE-1. A continuous, fluorescent ECE-1 assay has been developed using a novel substrate, 2-aminobenzoyl-Arg-Pro-Pro-Gly-Phe-Ser-Pro-(p-nitro-Phe(8))-Arg. This simple and rapid assay can greatly facilitate discovery of novel ECE inhibitors useful as pharmaceutical agents.

Coping with technological disaster: an application of the conservation of resources model to the Exxon Valdez oil spill

One hundred twenty-five commercial fishers in Cordova, Alaska, completed a mailed survey regarding current mental health functioning 6 years after the Exxon Valdez oil spill. Economic and social impacts of the oil spill and coping and psychological functioning (modified Coping Strategies Scales, Symptom Checklist 90-R) were measured. Multiple regression was used to test the utility of the Conservation of Resources stress model for explaining observed psychological symptoms. Current symptoms of depression, anxiety, and Posttraumatic Stress Disorder were associated with conditions resource loss and avoidant coping strategies. The Conservation of Resources model provided a framework for explaining psychological impacts of the oil spill. Future research is needed to identify factors related to recovery.

The phylogenetic relationships of the suborder Acanthuroidei (Teleostei: Perciformes) based on molecular and morphological evidence

Fragments of 12S and 16S mitochondrial DNA genes were sequenced for 14 acanthuroid taxa (representing all six families) and seven outgroup taxa. The combined data set contained 1399 bp after removal of all ambiguously aligned positions. Examination of site saturation indicated that loop regions of both genes are saturated for transitions, which led to a weighted parsimony analysis of the data set. The resulting tree topology generally agreed with previous morphological hypotheses, most notably placing the Luvaridae within the Acanthuroidei, but it also differed in several areas. The putative sister group of Acanthuroidei, Drepane, was recovered within the suborder, and the sister group of the family Acanthuridae, Zanclus, was likewise recovered within the family. Morphological characters were included to produce a combined data set of 1585 characters for 14 acanthuroid taxa and a single outgroup taxon. An analysis of the same 15 taxa was performed with only the DNA data for comparison. The total-evidence analysis supports the monophyly of the Acanthuridae. A parametric bootstrap suggests the possibility that the paraphyly of Acanthuridae indicated by the molecular analyses is the result of long-branch attraction. The disagreement between molecular and morphological data on the relationships of the basal acanthuroids and its putative sister taxon is unresolved.

Hydrolysis of peptide hormones by endothelin-converting enzyme-1. A comparison with neprilysin

Endothelins are peptide hormones with a potent vasoconstrictor activity that are also known to function as intercellular signaling molecules. The final step in the biosynthesis of endothelins is the proteolytic processing of precursor peptides by endothelin-converting enzymes (ECEs). ECE-1 is a zinc metalloendopeptidase related in amino acid sequence to neprilysin, a mammalian cell-surface peptidase involved in the metabolism of numerous biologically active peptides. Despite apparent structural similarities, ECE-1 and neprilysin have been considered to differ significantly in substrate specificity. In this study we have examined the activity of recombinant ECE-1 against a collection of biologically active peptides. ECE-1, unlike neprilysin, was found to have minimal activity against substrates smaller than hexapeptides, such as Leu-enkephalin. Larger peptides such as neurotensin, substance P, bradykinin, and the oxidized insulin B chain were hydrolyzed by ECE-1 as efficiently as big endothelin-1, a known in vivo substrate. Identification of the products of hydrolysis of six peptides indicates that ECE-1 has a substrate specificity similar to that of neprilysin, preferring to cleave substrates at the amino side of hydrophobic residues. The data indicate that ECE-1 possesses a surprisingly broad substrate specificity and is potentially involved in the metabolism of biologically active peptides distinct from the endothelins.

The phylogenetic relationships of lampridiform fishes (Teleostei: acanthomorpha), based on a total-evidence analysis of morphological and molecular data

We investigated the phylogenetic relationships among five species of lampridiform fishes, three basal outgroup species (two aulopiforms and one myctophiform), and two species of non-lampridiform acanthomorphs (Polymixia and Percopsis) using a combined parsimony analysis of morphological and molecular data. Morphological characters included 28 transformation series obtained from the literature. Molecular characters included 223 informative transformation series from an aligned 854-base pair fragment of 12S mtDNA and 139 informative transformation series from an aligned 561-base pair fragment of 16S mtDNA. A total-evidence analysis using the aulopiforms Synodus and Aulopus and the myctophiform Hygophum as outgroups corroborates the monophyly of Lampridiformes and unites Polymixia with Percopsis. Among the lampridiform fishes we examined, Metavelifer is basal, followed in ascending order by Lampris, Lophotus, Regalecus, and Trachipterus. This hypothesis is congruent with the most recent morphological analysis of the Lampridiformes and rejects a diphyletic origin of elongate body form within the clade. Analysis of a combined matrix of 12S and 16S mtDNA data yielded a phylogenetic hypothesis isomorphic with the total-evidence phylogeny. Analyses of partitioned DNA data sets reveals that single gene regions are poor predictors of the total-evidence phylogeny while combined analyses of both DNA data sets are good predictors of the total-evidence phylogeny.

HINT list equivalency using older listeners

HINT list equivalency was examined using 24 listeners between 60 and 70 years old who had sensorineural hearing impairment. A Greco-Latin square design was used to ensure that each list was presented an equal number of times per condition. Four conditions were tested: (1) speech in quiet, (2) speech in 65 dBA noise with noise at 0 degrees azimuth, (3) speech in 65 dBA noise with noise at 90 degrees azimuth, and (4) speech in 65 dBA noise with noise at 270 degrees azimuth. Speech materials were always presented at 0 degrees azimuth. Overall mean scores ranged from 29.9 dBA for the quiet condition to 63.4 dBA for the noise at 0 degrees azimuth condition. A significant difference was found between Lists 13 and 16 only. This was attributed to audibility differences among the listeners. Therefore, the 25 HINT lists should be considered equivalent for older populations with similar hearing impairment. The HINT lists can be used for relative measures, such as comparison of aided versus unaided sentence SRTs or comparison of 2 different hearing aids.

Origin and properties of soluble CD21 (CR2) in human blood

By analysis with a panel of CD21 MoAbs it is shown that a large part of the soluble CD21 in human blood plasma is of the long isoform (CD21L), as judged by comparison with antigen produced by mouse L cells transfected with CD21L-cDNA and reactivity with the restricted CD21 MoAb R4/23. This is compatible with the hypothesis that soluble CD21 in the blood is mainly derived from follicular dendritic cells (FDC). Cells from a human keratinocyte cell line transfected with cDNA from the Burkitt lymphoma cell line Raji also produced soluble CD21L (sCD21L), whereas the short form of sCD21 (sCD21S) was the major component of sCD21 produced by the B lymphoblastoid cell line LICR-LON-HMy and the T cell line Jurkat. Confocal studies of FDC isolated from human tonsil revealed that CD21 was present in the cytoplasm. On gel filtration sCD21 from untreated serum has an apparent size considerably greater than the 130kD found by SDS-PAGE analysis. This may be partly accounted for by the non-globular shape of the molecule, but may also indicate, as reported by others, that in its native state sCD21 is complexed with other proteins. However, no evidence of complexing with sCD23 or C3d could be found.

Homology between a human apoptosis specific protein and the product of APG5, a gene involved in autophagy in yeast

Apoptosis specific proteins (ASP) are expressed in the cytoplasm of cultured mammalian cells of various lineages following induction of apoptosis. The cDNA encoding ASP has been cloned from a human expression library and has significant homology to the Saccharomyces cerevisiae APG5 gene which is essential for yeast autophagy. The ASP gene, known as hAPG5, can be transcribed to give mRNAs of 3.3 kbp, 2.5 kbp and 1.8 kbp which are present at comparable levels in viable and apoptotic cells, demonstrating that protein expression must be regulated at the translational level. These data indicate a possible relationship between apoptosis and autophagy and suggest evolutionary conservation in mammalian apoptosis of a degradative process present in yeast.

Medical management of migraine-related dizziness and vertigo

Historically, review of migraine-related vestibular symptoms has focused on the various clinical presentations that occur and the results of diagnostic studies of vestibular function. Treatment of vestibular symptoms related to migraine has been proposed similar to that used for headache control, but few examples of the effectiveness of this therapy have been published. The purpose of this study is to present the various approaches that can be used to manage vestibular symptoms related to migraine, and to evaluate the overall effectiveness of these treatment approaches. This was a retrospective review of 89 patients diagnosed with migraine-related dizziness and vertigo. The character of vestibular symptoms, pattern of cochlear symptoms, results of auditory and vestibular tests, and comorbidity factors are presented. Treatment was individualized according to symptoms and comorbidity factors, and analyzed regarding effectiveness in control of the major vestibular symptoms of episodic vertigo, positional vertigo, and nonvertiginous dizziness. Medical management included dietary changes, medication, physical therapy, lifestyle adaptations, and acupuncture. Complete or substantial control of vestibular symptoms was achieved in 68 (92%) of 74 patients complaining of episodic vertigo; in 56 (89%) of 63 patients with positional vertigo; and 56 (86%) of 65 patients with non-vertiginous dizziness. Similarly, aural fullness was completely resolved or substantially improved in 34 (85%) of 40 patients; ear pain in 10 (63%) of 16 patients; and phonophobia in 17 (89%) of 19 patients. No patient reported worsened symptoms following medical management. The conflicting concept of a central disorder (migraine) as the cause of cochlear and vestibular dysfunction that often has peripheral features is discussed.

Activation mechanism of meprins, members of the astacin metalloendopeptidase family

Meprins are mammalian zinc metalloendopeptidases with protease domains structurally related to astacin, the prototype of the "astacin family" of metalloproteases. Mature, active astacins are produced by proteolytic removal of an activation peptide to generate a new NH2-terminal residue. Structural studies indicate that the NH2-terminal ammonium group inserts into a water-filled cavity adjacent to the active site to form a salt bridge with a Glu residue that is conserved in all astacins. A similar interaction is known to play a crucial role in the activation of trypsin, resulting in the hypothesis that this salt bridge is required for the activation of astacin-like proteases. In this study, we have used the mouse meprin alpha subunit as a model to test this hypothesis of zymogen activation of the astacins. Mutants were generated to vary the NH2-terminal residue of the mature meprin alpha subunit (Asn78) and its putative salt bridge partner (Glu178). In addition, mutants creating NH2-terminal extensions and truncations were expressed in human embryonic kidney 293 cells. The recombinant proteins were activated by limited protease digestion and assayed for enzymatic activity and thermal stability. Point mutations of Asn78 resulted in enzymes with activity comparable to the wild-type enzyme, indicating that the structure of this side chain is not essential for activity. NH2-terminal extension mutants of meprin alpha retained partial activity, with greater decreases against peptide relative to protein substrates. A mutant with a deletion of Asn78 to disrupt salt bridge formation with Glu178 had full activity, indicating that the putative salt bridge with Glu178 is not essential for enzyme activity. However, all changes in meprin alpha subunit NH2-terminal structure were found to decrease the thermal stability of the enzyme. These observations and additional data indicate that the zymogen activation mechanism of meprin and other astacins differs from that of the trypsin family of enzymes, and has some features in common with matrixins. It is proposed that prosequence removal of astacins allows the formation of hydrogen bonds involving the two NH2-terminal residues that are critical for enzyme structure.

Immunodetection of 11 beta-hydroxysteroid dehydrogenase type 2 in human mineralocorticoid target tissues: evidence for nuclear localization

11 beta-Hydroxysteroid dehydrogenase (11 beta HSI) is an enzyme complex responsible for the conversion of hormonally active cortisol to inactive cortisone; two isoforms of the enzyme have been cloned and characterized. Clinical observations from patients with the hypertensive syndrome apparent mineralocorticoid excess, recently explained on the basis of mutations in the human 11 beta HSD2 gene, suggest that it is the 11 beta HSD2 isoform that serves a vital role in dictating specificity upon the mineralocorticoid receptor (MR). We have raised a novel antibody in sheep against human 11 beta HSD2 using synthetic multiantigenic peptides and have examined the localization and subcellular distribution of 11 beta HSD2 in mineralocorticoid target tissues. The immunopurified antibody recognized a single band of approximately 44 kDa in placenta, trophoblast, and distal colon. In kidney tissue, two bands of approximately 44 and 48 kDa were consistently observed. No signal was seen in decidua, adrenal, or liver. Immunoperoxidase studies on the mineralocorticoid target tissues, kidney, colon, and parotid gland indicated positive staining in epithelial cells known to express the MR: respectively, renal collecting ducts, surface and crypt colonic epithelial cells, and parotid duct epithelial cells. No staining was seen in these tissues in other sites. The intracellular localization of 11 beta HSD2 in kidney and colon epithelial cells was addressed using confocal laser microscopy. Parallel measurements of 11 beta HSD2 and nuclear propidium iodide fluorescence on sections scanned through an optical section of approximately 0.1 micron indicated significant 11 beta HSD2 immunofluorescence in the nucleus. In human kidney, colon, and salivary gland, 11 beta HSD2 protects the MR from glucocorticoid excess in an autocrine fashion. Furthermore, within these tissues, 11 beta HSD2, which had been considered to be a microsomal enzyme, is also found in the nucleus, suggesting that the interaction between the MR and aldosterone or cortisol is in part a nuclear event.

Methotrexate management of immune-mediated cochleovestibular disorders

Immune-mediated cochleovestibular disorders continue to present a management challenge to the otolaryngologist. The traditional treatment of these disorders, corticosteroids and/or cyclophosphamide (Cytoxan), has been associated with serious and occasionally life-threatening complications. In this study we report our experience in treating 25 patients with immune-mediated cochleovestibular disorders with methotrexate, a less toxic immunosuppressive agent that has been used extensively in patients with rheumatoid arthritis. Mean duration of treatment was 12.9 months, and adverse reactions were acceptable and reversible. Hearing improved in 69.6% of patients, and vestibular symptoms subsided or improved in 80% of patients. The results of this study suggest that methotrexate treatment is effective in a substantial number of patients with immune-mediated cochleovestibular disorders and has acceptable adverse reactions. A prospective, randomized study is needed to compare the efficacy of methotrexate with that of other immunosuppressive agents.

Bcl-2 delays macrophage engulfment of human B cells induced to undergo apoptosis

The capacity to be recognized and engulfed by phagocytes is an important characteristic of cells dying by apoptosis. Phagocytosis of apoptotic cells occurs rapidly in vivo, probably prior to plasma membrane breakdown. While the molecular mechanisms mediating phagocytosis of apoptotic cells are beginning to be defined, little is yet known of the relationship between the cell-death program itself and the surface changes on the dying cells that signal for engulfment. Here, we investigate to what extent the apoptosis repressor Bcl-2 can modulate the recognition and phagocytosis of human B cells exposed to triggers of apoptosis. Burkitt lymphoma (BL)-derived, Bcl-2- B cells were induced into apoptosis either by the Ca(2+)-ionophore ionomycin or by the inhibitor of protein synthesis cycloheximide. Apoptotic BL cells, but not viable BL cells, were recognized and phagocytosed by monocyte-derived macrophages. bcl-2-transfected BL populations showed a reduced capacity both to undergo apoptosis in response to these inducing agents and to interact with macrophages. Like their Bcl-2- counterparts, Bcl-2+ BL cells interacted with macrophages only after activation of their apoptotic program as assessed by changes in nuclear morphology. These results demonstrate not only that continued protein synthesis in B cells undergoing apoptosis is not essential for their recognition by macrophages, but also that macrophage recognition of apoptotic B cells cannot be uncoupled from the cell-death program that is controlled by Bcl-2. In this respect, the behavior of B cells contrasts markedly with that of neutrophils in which Bcl-2 has been reported to inhibit apoptosis without affecting phagocytic clearance.

S-adenosyl-L-methionine prevents disruption of canalicular function and pericanalicular cytoskeleton integrity caused by cyclosporin A in isolated rat hepatocyte couplets

Isolated rat hepatocyte couplets were used to study the effect of S-adenosyl-L methionine (SAMe) treatment on disruption of canalicular function caused by cyclosporin A (CyA). Canalicular function was assessed by counting the percentage of couplets that were able to accumulate the fluorescent cholephile choly-lysyl-fluorescein (CLF) into the canalicular vacuole between the two cells, i.e., canalicular vacuole accumulation (CVA). Cotreatment with 1 mmol/L SAMe prevented the inhibition of canalicular vacuole accumulation caused by CyA (75 nmol/L and 100 nmol/L), whereas treatment with it after CyA was unsuccessful. SAMe prevented the dose dependent reduction caused by CyA (5 nmol/L-1 mumol/L) both on CVA and on retention of CLF preaccumulated within the canaliculus, the effect on retention being complete. No difference in intracellular content of reduced glutathione (GSH) between the control and any dose level of the immunosuppressor, with or without SAMe treatment was observed, suggesting that changes in intracellular reduced GSH levels are not involved in the effects of SAMe. F-actin was stained with fluorescein-isothiocyanate phalloidin and fluorescence measurements were performed by confocal microscopy. The ratio of the percanalicular area fluorescence/total couplet fluorescence, indicative of F-actin distribution, significantly decreased with CyA. However, cotreatment of CyA with SAMe protected the integrity of the pericanalicular cytoskeleton, suggesting that this beneficial effect on canalicular function may maintain canalicular contractions and/or preserve tight junction function. Results are discussed in relation to possible involvement of the transmethylation pathway, modifications in membrane fluidity, effects on bile acid transport, and of inhibition of uptake of CyA. They suggest that SAMe could be a good candidate for protecting against CyA-induced membrane dysfunction.

Protein kinase C-delta associates with vimentin intermediate filaments in differentiated HL60 cells

The subcellular localization of protein kinase C (PKC)-delta was determined in HL60 cells differentiated toward monocytes/macrophages by treatment with TPA. PKC-delta was detected in the nucleus and cytoplasm of differentiated HL60 cells and, more specifically, associated with structures resembling intermediate filaments. Indirect immunostaining revealed that PKC-delta colocalized with vimentin in the cytosol and perinuclear region of these cells. Immunoprecipitation studies showed that PKC-delta was in an active (autophosphorylated) state in differentiated HL60 cells and that vimentin immunoprecipitated from these cells was also phosphorylated. Treatment of HL60 cells with the PKC-specific inhibitor chelerythrine decreased the phosphorylation of vimentin. These data suggest that vimentin is a substrate for PKC-delta and that this PKC isoenzyme may play a specific role in the regulation of shape change and cell adhesion during HL60 differentiation.

Doppa induces cell death but not differentiation of U937 cells: evidence for the involvement of PKC-beta 1 in the regulation of apoptosis

Recent reports have claimed that activation of protein kinase C (PKC)-beta is sufficient for both differentiation and apoptosis in promyeloid HL60 cells. Phorbol esters which differentially activate PKC isoenzymes in vitro were used to induce differentiation and apoptosis in U937 cells; TPA and Dopp activate all U937 PKC isoenzymes, except PKC-zeta and Doppa activate only PKC-beta l. At concentrations of Doppa below 50 nM, only PKC-beta l was activated by 2 min and apoptosis was induced, but there was no differentiation of cells towards monocytes. TPA (1-25 nM) and Dopp (5-100 nM) activated PKC-alpha, -beta l and-gamma within 2 min and induced differentiation, but only increased apoptosis at the highest concentrations used. Thus, initial activation of PKC-beta l is insufficient for differentiation of U937 cells, but may lead to the induction of apoptosis.

Expression of subunits of the metalloendopeptidase meprin in renal cortex in experimental hydronephrosis

Meprin A is a metalloendopeptidase in the proximal tubular epithelium of rodents that is capable of hydrolyzing a great variety of peptides and proteins. The aim of the present investigation was to investigate effects of ureteral ligation on the expression of meprin subunits. Ureteral ligation resulted in marked decreases in the expression of both alpha- and beta-meprin subunits within 12 h of ureteral obstruction. Even greater downregulation of expression of meprin alpha- and beta-mRNA was noted at 24, 48, and 96 h after ureteral ligation. The greatest decrease in meprin mRNA expression in obstructed kidneys over contralateral unobstructed control kidneys (CUK) occurred at 24 h postunilateral ureteral obstruction (post-UUO) for the meprin alpha-subunit (20-fold decrease compared with controls) and at 48 h for the meprin beta-subunit (90-fold decrease). On immunolabeling, the intensity for the two meprin subunits at the corticomedullary junction was dramatically decreased at 24 to 96 h after ureteral ligation in contrast to the CUK specimens. Results of in situ hybridization indicated that the CUK specimens expressed meprin beta-mRNA at the corticomedullary junction, whereas the obstructed kidneys exhibited a decrease in mRNA signal for meprin beta-subunit. There was a steady increase in the interstitial macrophage number in UUO rat kidneys over the 96 h of evaluation post-UUO. ED-1-positive macrophages were observed almost exclusively in the peritubular cortical interstitial space in a ringlike pattern with a preponderance of macrophage clusters around glomeruli. Unexpectedly, after reversal of UUO, the interstitial macrophage number remained higher than controls, despite the demonstrable decompression of the renal pelvis and caliceal system. In summary, this investigation demonstrates downregulation of meprin alpha and beta within hours of UUO and indicates a novel tubular response to ureteral obstruction.

Differences in the germinal centres of palatine tonsils and lymph nodes

The germinal centres of human palatine tonsils typically have four clearly recognizable compartments. The dark zone is identified by the presence of centroblasts and a thin follicular dendritic cell (FDC) network. The dense FDC network is divided into a CD23(low/-) portion adjacent to the dark zone (the basal light zone) and a CD23(high) portion, the apical light zone). The outer zone, which lies between the apical light zone and the follicular mantle, has only fine CD23- FDC processes. While these compartments were seen in 48 follicles from eight tonsils, the compartmental structure of 54 germinal centres in lymph nodes from 11 individuals was markedly different. The CD23+ FDC network in lymph node follicles extended into part of the dark zone and the inner part of the follicular mantle, and consequently no outer zone or basal light zone was identified. In both the lymph nodes and tonsils most T cells were CD4+ and located outside the dark zone; the concentration of these cells at the edge of germinal centres was typical of tonsil centres but was noted only occasionally in lymph nodes. The substantial minority of T cells that were CD4,CD57+ were located mainly in the dense FDC network.