Somatic hypermutation introduces insertions and deletions into immunoglobulin V genes

During a germinal center reaction, random mutations are introduced into immunoglobulin V genes to increase the affinity of antibody molecules and to further diversify the B cell repertoire. Antigen-directed selection of B cell clones that generate high affinity surface Ig results in the affinity maturation of the antibody response. The mutations of Ig genes are typically basepair substitutions, although DNA insertions and deletions have been reported to occur at a low frequency. In this study, we describe five insertion and four deletion events in otherwise somatically mutated VH gene cDNA molecules. Two of these insertions and all four deletions were obtained through the sequencing of 395 cDNA clones (approximately 110,000 nucleotides) from CD38+IgD- germinal center, and CD38-IgD- memory B cell populations from a single human tonsil. No germline genes that could have encoded these six cDNA clones were found after an extensive characterization of the genomic VH4 repertoire of the tonsil donor. These six insertions or deletions and three additional insertion events isolated from other sources occurred as triplets or multiples thereof, leaving the transcripts in frame. Additionally, 8 of 9 of these events occurred in the CDR1 or CDR2, following a pattern consistent with selection, and making it unlikely that these events were artifacts of the experimental system. The lack of similar instances in unmutated IgD+CD38- follicular mantle cDNA clones statistically associates these events to the somatic hypermutation process (P = 0.014). Close scrutiny of the 9 insertion/deletion events reported here, and of 25 additional insertions or deletions collected from the literature, suggest that secondary structural elements in the DNA sequences capable of producing loop intermediates may be a prerequisite in most instances. Furthermore, these events most frequently involve sequence motifs resembling known intrinsic hotspots of somatic hypermutation. These insertion/deletion events are consistent with models of somatic hypermutation involving an unstable polymerase enzyme complex lacking proofreading capabilities, and suggest a downregulation or alteration of DNA repair at the V locus during the hypermutation process.

Imaging of collagen and proteoglycan in cartilage sections using Fourier transform infrared spectral imaging

OBJECTIVE

To test the hypothesis that Fourier transform infrared (FTIR) spectral imaging, coupled with multivariate data processing techniques, can image the spatial distribution of matrix constituents in native and engineered cartilage samples.

METHODS

Tissue sections from native and trypsin-digested bovine nasal cartilage (BNC) and from engineered cartilage, generated by chick sternal chondrocytes grown in a hollow fiber bioreactor, were placed either on calcium fluoride windows for FTIR analysis or gelatinized microscope slides for histologic analysis. Based on the assumption that cartilage is predominantly chondroitin sulfate (CS) and type II collagen, chemical images were extracted from FTIR spectral imaging data sets using 2 multivariate methods: the Euclidean distance algorithm and a least-squares approach.

RESULTS

Least-squares analysis of the FTIR data of native BNC yielded a collagen content of 54 +/- 13% and a CS content of 37 +/- 16% (mean +/- SD). Euclidean distance analysis of measurements made on trypsin-digested BNC demonstrated only trace amounts of CS. For engineered cartilage, the CS content was significantly lower (15 +/- 5%), while the collagen content (73 +/- 6%) was significantly higher than biochemically determined values (CS 34%, collagen 5%, protein 61%). These differences are due to the fact that the dimethylmethylene blue assay overestimated the CS content of the tissue because it is not specific for CS, while the FTIR spectral imaging technique overestimated the collagen content because it lacks specificity for different proteins.

CONCLUSION

FTIR spectral imaging combines histology-like spatial localization with the quantitative capability of bulk chemical analysis. For molecules with a unique spectral signature, such as CS, the FTIR technique coupled with multivariate analysis can define a unique spatial distribution. However, for some applications, the lack of specificity of this technique for different types of proteins may be a limitation.

Divergence of species responses to climate change

Climate change can have profound impacts on biodiversity and the sustainability of many ecosystems. Various studies have investigated the impacts of climate change, but large-scale, trait-specific impacts are less understood. We analyze abundance data over time for 86 tree species/groups across the eastern United States spanning the last three decades. We show that more tree species have experienced a westward shift (73%) than a poleward shift (62%) in their abundance, a trend that is stronger for saplings than adult trees. The observed shifts are primarily due to the changes of subpopulation abundances in the leading edges and are significantly associated with changes in moisture availability and successional processes. These spatial shifts are associated with species that have similar traits (drought tolerance, wood density, and seed weight) and evolutionary histories (most angiosperms shifted westward and most gymnosperms shifted poleward). Our results indicate that changes in moisture availability have stronger near-term impacts on vegetation dynamics than changes in temperature. The divergent responses to climate change by trait- and phylogenetic-specific groups could lead to changes in composition of forest ecosystems, putting the resilience and sustainability of various forest ecosystems in question.

Response of engineered cartilage tissue to biochemical agents as studied by proton magnetic resonance microscopy

OBJECTIVE

To test the hypothesis that magnetic resonance imaging (MRI) results correlate with the biochemical composition of cartilage matrix and can therefore be used to evaluate natural tissue development and the effects of biologic interventions.

METHODS

Chondrocytes harvested from day-16 chick embryo sterna were inoculated into an MRI-compatible hollow-fiber bioreactor. The tissue that formed over a period of 2-4 weeks was studied biochemically, histologically, and with MRI. Besides natural development, the response of the tissue to administration of retinoic acid, interleukin-1beta (IL-1beta), and daily dosing with ascorbic acid was studied.

RESULTS

Tissue wet and dry weight, glycosaminoglycan (GAG) content, and collagen content all increased with development time, while tissue hydration decreased. The administration of retinoic acid resulted in a significant reduction in tissue wet weight, proteoglycan content, and cell number and an increase in hydration as compared with controls. Daily dosing with ascorbic acid increased tissue collagen content significantly compared with controls, while the administration of IL-1beta resulted in increased proteoglycan content. The water proton longitudinal and transverse relaxation rates correlated well with GAG and collagen concentrations of the matrix as well as with tissue hydration. In contrast, the magnetization transfer value for the tissue correlated only with total collagen. Finally, the self-diffusion coefficient of water correlated with tissue hydration.

CONCLUSION

Parameters derived from MR images obtained noninvasively can be used to quantitatively assess the composition of cartilage tissue generated in a bioreactor. We conclude that MRI is a promising modality for the assessment of certain biochemical properties of cartilage in a wide variety of settings.

Global genetic diversity status and trends: towards a suite of Essential Biodiversity Variables (EBVs) for genetic composition

Biodiversity underlies ecosystem resilience, ecosystem function, sustainable economies, and human well‐being. Understanding how biodiversity sustains ecosystems under anthropogenic stressors and global environmental change will require new ways of deriving and applying biodiversity data. A major challenge is that biodiversity data and knowledge are scattered, biased, collected with numerous methods, and stored in inconsistent ways. The Group on Earth Observations Biodiversity Observation Network (GEO BON) has developed the Essential Biodiversity Variables (EBVs) as fundamental metrics to help aggregate, harmonize, and interpret biodiversity observation data from diverse sources. Mapping and analyzing EBVs can help to evaluate how aspects of biodiversity are distributed geographically and how they change over time. EBVs are also intended to serve as inputs and validation to forecast the status and trends of biodiversity, and to support policy and decision making. Here, we assess the feasibility of implementing Genetic Composition EBVs (Genetic EBVs), which are metrics of within‐species genetic variation. We review and bring together numerous areas of the field of genetics and evaluate how each contributes to global and regional genetic biodiversity monitoring with respect to theory, sampling logistics, metadata, archiving, data aggregation, modeling, and technological advances. We propose four Genetic EBVs: (i) Genetic Diversity; (ii) Genetic Differentiation; (iii) Inbreeding; and (iv) Effective Population Size (N_e). We rank Genetic EBVs according to their relevance, sensitivity to change, generalizability, scalability, feasibility and data availability. We outline the workflow for generating genetic data underlying the Genetic EBVs, and review advances and needs in archiving genetic composition data and metadata. We discuss how Genetic EBVs can be operationalized by visualizing EBVs in space and time across species and by forecasting Genetic EBVs beyond current observations using various modeling approaches. Our review then explores challenges of aggregation, standardization, and costs of operationalizing the Genetic EBVs, as well as future directions and opportunities to maximize their uptake globally in research and policy. The collection, annotation, and availability of genetic data has made major advances in the past decade, each of which contributes to the practical and standardized framework for large‐scale genetic observation reporting. Rapid advances in DNA sequencing technology present new opportunities, but also challenges for operationalizing Genetic EBVs for biodiversity monitoring regionally and globally. With these advances, genetic composition monitoring is starting to be integrated into global conservation policy, which can help support the foundation of all biodiversity and species' long‐term persistence in the face of environmental change. We conclude with a summary of concrete steps for researchers and policy makers for advancing operationalization of Genetic EBVs. The technical and analytical foundations of Genetic EBVs are well developed, and conservation practitioners should anticipate their increasing application as efforts emerge to scale up genetic biodiversity monitoring regionally and globally.

Novel product chemistry from mechanistic analysis of ent-copalyl diphosphate synthases from plant hormone biosynthesis

An active-site water molecule coordinated by conserved histidine and asparagine residues seems to serve as the catalytic base in all ent-copalyl diphosphate synthases (CPSs). When these residues are substituted by alanine, the mutant CPSs produce stereochemically novel ent-8-hydroxy-CPP. Given the requisite presence of CPSs in all land plants for gibberellin phytohormone biosynthesis, such plasticity presumably underlies the observed extensive diversification of the resulting labdane-related diterpenoids.

Pictorial review: MRI of chronic spinal cord injury

Patients who have suffered a spinal cord injury and who demonstrate new or changing clinical features such as increasing myelopathy, ascending neurological level, pain or increasing muscle spasms may have developed a late complication such as post-traumatic syrinx. MRI is the investigation of choice for assessment of chronic spinal cord injury. The aim of this pictorial review is to illustrate the various late appearances of the injured spinal cord.

The mental and physical health of female sex workers: a comparative study

OBJECTIVES

The objective of this study was to compare the mental and physical health, adult abuse experiences and social networks of female sex workers with data previously collected from two large community samples of age-matched women.

METHOD

A convenience sample of sex workers were interviewed and completed two well-established questionnaires, the General Health Questionnaire (GHQ-28) and the Intimate Bond Measure (IBM). Sex workers were invited to reflect on their experiences of their work.

RESULTS

There were no differences in mental health on the GHQ-28 or in self-esteem (measured by an item on the Present State Examination) between the two groups. Neither were there any differences in their assessment of their physical health or the quality of their social networks. Sex workers were less likely to be married and had been exposed to more adult physical and sexual abuse than the comparison group. They were more likely to smoke and to drink heavily when they drank. One-third said that their general practitioner was not aware of their work. A subgroup not working with regular clients or in a massage parlour had higher GHQ-28 scores and may be an at-risk group. Narrative information about the work, particularly its intermittent nature, is presented.

CONCLUSIONS

No evidence was found that sex work and increased adult psychiatric morbidity are inevitably associated, although there may be subgroups of workers with particular problems. The illegal and stigmatized nature of sex work are likely to make usual public health strategies more difficult to apply, considerations which should give concern from a preventive health standpoint.

1.55Å-resolution structure of ent-copalyl diphosphate synthase and exploration of general acid function by site-directed mutagenesis

BACKGROUND

The diterpene cyclase ent-copalyl diphosphate synthase (CPS) catalyzes the first committed step in the biosynthesis of gibberellins. The previously reported 2.25Å resolution crystal structure of CPS complexed with (S)-15-aza-14,15-dihydrogeranylgeranyl thiolodiphosphate (1) established the αβγ domain architecture, but ambiguities regarding substrate analog binding remained.

METHOD

Use of crystallization additives yielded CPS crystals diffracting to 1.55Å resolution. Additionally, active site residues that hydrogen bond with D379, either directly or through hydrogen bonded water molecules, were probed by mutagenesis.

RESULTS

This work clarifies structure-function relationships that were ambiguous in the lower resolution structure. Well-defined positions for the diphosphate group and tertiary ammonium cation of 1, as well as extensive solvent structure, are observed.

CONCLUSIONS

Two channels involving hydrogen bonded solvent and protein residues lead to the active site, forming hydrogen bonded "proton wires" that link general acid D379 with bulk solvent. These proton wires may facilitate proton transfer with the general acid during catalysis. Activity measurements made with mutant enzymes indicate that N425, which donates a hydrogen bond directly to D379, and T421, which hydrogen bonds with D379 through an intervening solvent molecule, help orient D379 for catalysis. Residues involved in hydrogen bonds with the proton wire, R340 and D503, are also important. Finally, conserved residue E211, which is located near the diphosphate group of 1, is proposed to be a ligand to Mg(2+) required for optimal catalytic activity.

GENERAL SIGNIFICANCE

This work establishes structure-function relationships for class II terpenoid cyclases.

A single residue change leads to a hydroxylated product from the class II diterpene cyclization catalyzed by abietadiene synthase

Class II diterpene cyclases catalyze bicyclization of geranylgeranyl diphosphate. While this reaction typically is terminated via methyl deprotonation to yield copalyl diphosphate, in rare cases hydroxylated bicycles are produced instead. Abietadiene synthase is a bifunctional diterpene cyclase that usually produces a copalyl diphosphate intermediate. Here it is shown that substitution of aspartate for a conserved histidine in the class II active site of abietadiene synthase leads to selective production of 8α-hydroxy-CPP instead, demonstrating striking plasticity.

Cutaneous mast cell tumors in cats: 32 cases (1991-1994)

Case records of 32 cats with cutaneous mast cell tumors (CMCTs) were reviewed. Using the Patnaik system for grading canine mast cell tumors, the relationships between histopathological grade and patient survival time and tumor recurrence were examined. Tumor histopathological grade had no prognostic significance. One-, two-, and three-year tumor recurrence rates following surgical excision were 16%, 19%, and 13%, respectively. Incomplete excision was not associated with a higher rate of tumor recurrence.

Cartilage formation in a hollow fiber bioreactor studied by proton magnetic resonance microscopy

The ideal in vitro system for investigating the regulation of cartilage formation and maintenance would allow for three-dimensional tissue growth, a wide range of biochemical interventions, and non-destructive evaluation. We have developed a hollow fiber bioreactor (HFBR) system which meets these criteria. After injection with embryonic chick sternal chondrocytes, neocartilage is elaborated around the hollow fibers, reaching a thickness of up to a millimeter after four weeks of growth. This process was monitored over time with nuclear magnetic resonance (NMR) microimaging and correlative biochemical and histologic analyses. Tissue volume and cellularity increased greatly during development. This was accompanied by changes in magnetic resonance properties consistent with increased macromolecular content. Further, tissue heterogeneity, observed as regional variations in cell size in histologic sections, was also observed in quantitative NMR images.

A subcontinental view of forest plant invasions

Over the last few decades, considerable attention has focused on small-scale studies of invasive plants and invaded systems. Unfortunately, small scale studies rarely provide comprehensive insight into the complexities of biological invasions at macroscales. Systematic and repeated monitoring of biological invasions at broad scales are rare. In this report, we highlight a unique invasive plant database from the national Forest Inventory and Analysis (FIA) program of the United States Forest Service. We demonstrate the importance and capability of this subcontinental-wide database by showcasing several critical macroscale invasion patterns that have emerged from its initial analysis: (1) large portion of the forests systems (39%) in the United States are impacted by invasive plants, (2) forests in the eastern United States harbor more invasive species than the western regions, (3) human land-use legacies at regional to national scales may drive large-scale invasion patterns. This accumulated dataset, which continues to grow in temporal richness with repeated measurements, will allow the understanding of invasion patterns and processes at multi-spatial and temporal scales. Such insights are not possible from smaller-scale studies, illustrating the benefit that can be gained by investing in the development of regional to continental-wide invasion monitoring programs elsewhere.

Medication appropriateness tool for co-morbid health conditions in dementia: consensus recommendations from a multidisciplinary expert panel

Background

Medication management for people living with dementia is a complex task as it is unclear what constitutes optimal medication management in this population due to the shifting focus of health priorities and the balance between the benefits and harms of medications.

Aim

This study sought expert opinion to create a consensus list to define appropriate medication management of co‐morbidities for people with dementia.

Methods

This study used the Delphi technique. We invited multidisciplinary experts in geriatric therapeutics including pharmacists, doctors, nurse practitioners, a patient advocate and a psychologist to participate. Participants were asked to engage into three or more rounds of questioning. Round 1 was a questionnaire comprised of one question defining dementia and seven open‐ended questions about appropriate management of co‐morbidities in people with dementia. Two investigators qualitatively analysed the responses to questions from Round 1 using thematic analysis. The results of this analysis were provided to participants as statements in the Round 2 survey. The participants were asked to rate their agreement with each statement on a 5‐point Likert scale. The median and interquartile range (IQR) were calculated for the responses to each statement. Consensus was pre‐specified as an IQR less than or equal to 1. Statements where consensus was not achieved were presented to participants in Round 3. The Round 2 median and IQR values were provided and participants were again asked to rate their agreement with each statement on a 5‐point Likert scale. The statements where participants agreed or strongly agreed were included in the Medication Appropriateness Tool for Co‐morbid Health conditions in Dementia criteria.

Results

Fifty‐seven experts agreed to participate in the study, of whom 58% were pharmacists and 36% were medical practitioners. Fifty‐five participants completed the Round 1 (95% response rate). A total of 128 statements was included in the Round 2 survey. Consensus was reached on 93 statements in Round 2 (n = 48 responders, 84% response rate) and on 18 statements in Round 3 (n = 43 responders, 75% response rate). The participants reached consensus on 111 of 128 statements. Of these statements, 67 statements were included in the Medication Appropriateness Tool for Co‐morbid Health conditions in Dementia criteria. The statements were in the broad themes of preventative medication, symptom management, disease progression, psychoactive medication, treatment goals, principles of medication use, side‐effects and medication reviews.

Discussion

This research provides consensus‐based guidance for clinicians who manage co‐morbid health conditions in people with dementia.

Assay for bacteria in porous media by diffusion-weighted NMR

In this work, an NMR technique capable of detecting bacterial cells and measuring the cell density in suspension and in porous media has been developed. It is based on the pulsed-field-gradient technique and relies on the fact that extracellular water diffuses freely while intracellular water is completely restricted by the relatively impermeable cell wall of the bacterium. At high wave vectors, the signal from extracellular water is completely suppressed while the signal from intracellular water is comparatively unaffected. This technique has been applied to the mapping of bacterial distributions in porous media. This method is presented as a non-destructive, real-time technique for biomass characterization within laboratory column and flow cell experiments, and possibly for monitoring in situ bioremediation.

Early developmental experiences of female sex workers: a comparative study

OBJECTIVE

The aim of this paper is to explore the early family environment of a sample of female sex workers and compare the findings with a large community data set of similarly aged women.

METHOD

Sex workers recruited by a snowball method were given a semi-structured interview, which included the Parental Bonding Instrument. These results were compared to those from the Otago Women's Child Sexual Abuse (OWCSA) study.

RESULTS

The sex workers' families were of lower socioeconomic status and had experienced more parental separation than had the OWCSA families. The mothers of sex workers were more frequently the family's main wage earner. Sex workers described both parents as less caring than did the OWCSA women. They were significantly more likely than the OWCSA women to report childhood sexual abuse. The sex workers were more likely to have left home early, to have become pregnant before the age of 19 years and to not have completed tertiary study.

CONCLUSIONS

The sex workers studied came from families with more interpersonal difficulties during childhood and adolescence than did a control community sample of similarly aged women. The relevance and generalisability of this conclusion to the wider sex worker population is difficult to determine, given the non-random selection of this sex worker sample.

Is ‘virtual histology’ the next step after the ‘virtual autopsy’? Magnetic resonance microscopy in forensic medicine

AIM

The study aimed to validate magnetic resonance microscopy (MRM) studies of forensic tissue specimens (skin samples with electric injury patterns) against the results from routine histology.

METHODS AND RESULTS

Computed tomography and magnetic resonance imaging are fast becoming important tools in clinical and forensic pathology. This study is the first forensic application of MRM to the analysis of electric injury patterns in human skin. Three-dimensional high-resolution MRM images of fixed skin specimens provided a complete 3D view of the damaged tissues at the site of an electric injury as well as in neighboring tissues, consistent with histologic findings. The image intensity of the dermal layer in T2-weighted MRM images was reduced in the central zone due to carbonization or coagulation necrosis and increased in the intermediate zone because of dermal edema. A subjacent blood vessel with an intravascular occlusion supports the hypothesis that current traveled through the vascular system before arcing to ground.

CONCLUSION

High-resolution imaging offers a noninvasive alternative to conventional histology in forensic wound analysis and can be used to perform 3D virtual histology.

Environmental harshness drives spatial heterogeneity in biotic resistance

Ecological communities often exhibit greater resistance to biological invasions when these communities consist of species that are not closely related. The effective size of this resistance, however, varies geographically. Here we investigate the drivers of this heterogeneity in the context of known contributions of native trees to the resistance of forests in the eastern United States of America to plant invasions. Using 42,626 spatially referenced forest community observations, we quantified spatial heterogeneity in relationships between evolutionary relatedness amongst native trees and both invasive plant species richness and cover. We then modelled the variability amongst the 91 ecological sections of our study area in the slopes of these relationships in response to three factors known to affect invasion and evolutionary relationships –environmental harshness (as estimated via tree height), relative tree density and environmental variability. Invasive species richness and cover declined in plots having less evolutionarily related native trees. The degree to which they did, however, varied considerably amongst ecological sections. This variability was explained by an ecological section’s mean maximum tree height and, to a lesser degree, SD in maximum tree height (R2GLMM = 0.47 to 0.63). In general, less evolutionarily related native tree communities better resisted overall plant invasions in less harsh forests and in forests where the degree of harshness was more homogenous. These findings can guide future investigations aimed at identifying the mechanisms by which evolutionary relatedness of native species affects exotic species invasions and the environmental conditions under which these effects are most pronounced.