Spastin is an essential regulator of male meiosis, acrosome formation, manchette structure and nuclear integrity.

The development and function of male gametes is dependent on a dynamic microtubule network, yet how this is regulated remains poorly understood. We have recently shown that microtubule severing, via the action of the meiotic AAA ATPase protein clade, plays a crucial role in this process. Here, we sought to elucidate the roles of spastin, an as-yet-unexplored member of this clade in spermatogenesis. Using a SpastKO/KO mouse model, we reveal that spastin loss resulted in a complete loss of functional germ cells. Spastin plays a crucial role in the assembly and function of the male meiotic spindle. Consistent with meiotic failure, round spermatid nuclei were enlarged, indicating aneuploidy, but were still able to enter spermiogenesis. During spermiogenesis, we observed extreme abnormalities in manchette structure, acrosome biogenesis and, commonly, a catastrophic loss of nuclear integrity. This work defines an essential role for spastin in regulating microtubule dynamics during spermatogenesis, and is of potential relevance to individuals carrying spastin variants and to the medically assisted reproductive technology industry.

SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression.

High-dimensional, localized ribonucleic acid (RNA) sequencing is now possible owing to recent developments in spatial transcriptomics (ST). ST is based on highly multiplexed sequence analysis and uses barcodes to match the sequenced reads to their respective tissue locations. ST expression data suffer from high noise and dropout events; however, smoothing techniques have the promise to improve the data interpretability prior to performing downstream analyses. Single-cell RNA sequencing (scRNA-seq) data similarly suffer from these limitations, and smoothing methods developed for scRNA-seq can only utilize associations in transcriptome space (also known as one-factor smoothing methods). Since they do not account for spatial relationships, these one-factor smoothing methods cannot take full advantage of ST data. In this study, we present a novel two-factor smoothing technique, spatial and pattern combined smoothing (SPCS), that employs the k-nearest neighbor (kNN) technique to utilize information from transcriptome and spatial relationships. By performing SPCS on multiple ST slides from pancreatic ductal adenocarcinoma (PDAC), dorsolateral prefrontal cortex (DLPFC) and simulated high-grade serous ovarian cancer (HGSOC) datasets, smoothed ST slides have better separability, partition accuracy and biological interpretability than the ones smoothed by preexisting one-factor methods. Source code of SPCS is provided in Github (https://github.com/Usos/SPCS).

AIscEA: unsupervised integration of single-cell gene expression and chromatin accessibility via their biological consistency.

MOTIVATION: The integrative analysis of single-cell gene expression and chromatin accessibility measurements is essential for revealing gene regulation, but it is one of the key challenges in computational biology. Gene expression and chromatin accessibility are measurements from different modalities, and no common features can be directly used to guide integration. Current state-of-the-art methods lack practical solutions for finding heterogeneous clusters. However, previous methods might not generate reliable results when cluster heterogeneity exists. More importantly, current methods lack an effective way to select hyper-parameters under an unsupervised setting. Therefore, applying computational methods to integrate single-cell gene expression and chromatin accessibility measurements remains difficult. RESULTS: We introduce AIscEA-Alignment-based Integration of single-cell gene Expression and chromatin Accessibility-a computational method that integrates single-cell gene expression and chromatin accessibility measurements using their biological consistency. AIscEA first defines a ranked similarity score to quantify the biological consistency between cell clusters across measurements. AIscEA then uses the ranked similarity score and a novel permutation test to identify cluster alignment across measurements. AIscEA further utilizes graph alignment for the aligned cell clusters to align the cells across measurements. We compared AIscEA with the competing methods on several benchmark datasets and demonstrated that AIscEA is highly robust to the choice of hyper-parameters and can better handle the cluster heterogeneity problem. Furthermore, AIscEA significantly outperforms the state-of-the-art methods when integrating real-world SNARE-seq and scMultiome-seq datasets in terms of integration accuracy. AVAILABILITY AND IMPLEMENTATION: AIscEA is available at https://figshare.com/articles/software/AIscEA_zip/21291135 on FigShare as well as {https://github.com/elhaam/AIscEA} onGitHub. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

TSAFinder: exhaustive tumor-specific antigen detection with RNAseq.

MOTIVATION: Tumor-specific antigen (TSA) identification in human cancer predicts response to immunotherapy and provides targets for cancer vaccine and adoptive T-cell therapies with curative potential, and TSAs that are highly expressed at the RNA level are more likely to be presented on major histocompatibility complex (MHC)-I. Direct measurements of the RNA expression of peptides would allow for generalized prediction of TSAs. Human leukocyte antigen (HLA)-I genotypes were predicted with seq2HLA. RNA sequencing (RNAseq) fastq files were translated into all possible peptides of length 8-11, and peptides with high and low expressions in the tumor and control samples, respectively, were tested for their MHC-I binding potential with netMHCpan-4.0. RESULTS: A novel pipeline for TSA prediction from RNAseq was used to predict all possible unique peptides size 8-11 on previously published murine and human lung and lymphoma tumors and validated on matched tumor and control lung adenocarcinoma (LUAD) samples. We show that neoantigens predicted by exomeSeq are typically poorly expressed at the RNA level, and a fraction is expressed in matched normal samples. TSAs presented in the proteomics data have higher RNA abundance and lower MHC-I binding percentile, and these attributes are used to discover high confidence TSAs within the validation cohort. Finally, a subset of these high confidence TSAs is expressed in a majority of LUAD tumors and represents attractive vaccine targets. AVAILABILITY AND IMPLEMENTATION: The datasets were derived from sources in the public domain as follows: TSAFinder is open-source software written in python and R. It is licensed under CC-BY-NC-SA and can be downloaded at https://github.com/RNAseqTSA. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Effect of the First Tarsometatarsal (Modified Lapidus) Arthrodesis on Hindfoot Alignment.

The purpose of this study is to demonstrate the effect of first tarsometatarsal (modified Lapidus) arthrodesis on hindfoot alignment. We reviewed the radiographs of 39 patients, 40 feet (16 right feet and 24 left feet in 6 males and 34 females; mean age 43 years) who underwent hallux valgus reconstruction and isolated first tarsometatarsal arthrodesis. Patients who had ancillary osseous procedures were excluded from the study, with the exception of proximal phalangeal osteotomy to address hallux interphalangeus. The mean time to follow up was 33.78 weeks (8.45 months), median 21.5 weeks. Statistically significant differences were found between preoperative and postoperative measurements for talar declination (-3.3 ± 3.5), lateral talocalcaneal angle (-3.1 ± 3.9), lateral Meary's angle (-4.2 ± 4.9), medial cuneiform height (3.5 ± 4.6), medial cuneiform to fifth metatarsal distance (4.7 ± 4.5), AP talocalcaneal angle (-2.8 ± 5.3), and percentage of talar head uncovering (-6.6 ± 7.6). Our results suggest that first tarsometatarsal arthrodesis can affect hindfoot alignment on AP and lateral radiographs.

Comparing Leg Quasi-Stiffness Methods Across Running Velocities.

This study investigated the differences between 5 commonly used methods to calculate leg stiffness over a range of running velocities. Thirteen male, habitually rearfoot, recreational runners ran on a force instrumented treadmill for a 5-minute running session. Each session consisted of 30-second intervals at 6 progressively faster speeds from 2.5 m·s-1 through 5.0 m·s-1 with each interval speed increasing by 0.5 m·s-1. Two-way within-factors repeated-measures analyses of variance were used to evaluate leg stiffness and length. A one-way repeated-measures analysis of variance was used to evaluate the slope of each trend line of each model across speeds. Pearson correlations were used to compare the relationship between the different computational methods. The results indicated that the direct stiffness methods increased with speed whereas the indirect stiffness methods did not. The direct methods were strongly correlated with each other as were the indirect methods. However, there were no strong correlations between the direct and indirect methods. These differences can be mostly attributed to how each individual stiffness method calculated leg length. It is important for researchers to understand these differences when conducting future studies and comparing past studies.

Molecular and Functional Evolution at the Odorant Receptor Or22 Locus in Drosophila melanogaster.

Insect odorant receptor (Or) genes determine the responses of sensory neurons that mediate critical behaviors. The Drosophila melanogaster Or22 locus represents an interesting example of molecular evolution, with high levels of sequence divergence and copy number variation between D. melanogaster and other Drosophila species, and a corresponding high level of variability in the responses of the neuron it controls, ab3A. However, the link between Or22 molecular and functional diversity has not been established. Here, we show that several naturally occurring Or22 variants generate major shifts in neuronal response properties. We determine the molecular changes that underpin these response shifts, one of which represents a chimeric gene variant previously suggested to be under natural selection. In addition, we show that several alternative molecular genetic mechanisms have evolved for ensuring that where there is more than one gene copy at this locus, only one functional receptor is generated. Our data thus provide a causal link between the striking levels of phenotypic neuronal response variation found in natural populations of D. melanogaster and genetic variation at the Or22 locus. Since neuronal responses govern animal behavior, we predict that Or22 may be a key player in underlying one or more olfactory-driven behaviors of significant adaptive importance.

A Syndromic Neurodevelopmental Disorder Caused by De Novo Variants in EBF3.

Early B cell factor 3 (EBF3) is a member of the highly evolutionarily conserved Collier/Olf/EBF (COE) family of transcription factors. Prior studies on invertebrate and vertebrate animals have shown that EBF3 homologs are essential for survival and that loss-of-function mutations are associated with a range of nervous system developmental defects, including perturbation of neuronal development and migration. Interestingly, aristaless-related homeobox (ARX), a homeobox-containing transcription factor critical for the regulation of nervous system development, transcriptionally represses EBF3 expression. However, human neurodevelopmental disorders related to EBF3 have not been reported. Here, we describe three individuals who are affected by global developmental delay, intellectual disability, and expressive speech disorder and carry de novo variants in EBF3. Associated features seen in these individuals include congenital hypotonia, structural CNS malformations, ataxia, and genitourinary abnormalities. The de novo variants affect a single conserved residue in a zinc finger motif crucial for DNA binding and are deleterious in a fly model. Our findings indicate that mutations in EBF3 cause a genetic neurodevelopmental syndrome and suggest that loss of EBF3 function might mediate a subset of neurologic phenotypes shared by ARX-related disorders, including intellectual disability, abnormal genitalia, and structural CNS malformations.

LAmbDA: label ambiguous domain adaptation dataset integration reduces batch effects and improves subtype detection.

MOTIVATION: Rapid advances in single cell RNA sequencing (scRNA-seq) have produced higher-resolution cellular subtypes in multiple tissues and species. Methods are increasingly needed across datasets and species to (i) remove systematic biases, (ii) model multiple datasets with ambiguous labels and (iii) classify cells and map cell type labels. However, most methods only address one of these problems on broad cell types or simulated data using a single model type. It is also important to address higher-resolution cellular subtypes, subtype labels from multiple datasets, models trained on multiple datasets simultaneously and generalizability beyond a single model type. RESULTS: We developed a species- and dataset-independent transfer learning framework (LAmbDA) to train models on multiple datasets (even from different species) and applied our framework on simulated, pancreas and brain scRNA-seq experiments. These models mapped corresponding cell types between datasets with inconsistent cell subtype labels while simultaneously reducing batch effects. We achieved high accuracy in labeling cellular subtypes (weighted accuracy simulated 1 datasets: 90%; simulated 2 datasets: 94%; pancreas datasets: 88% and brain datasets: 66%) using LAmbDA Feedforward 1 Layer Neural Network with bagging. This method achieved higher weighted accuracy in labeling cellular subtypes than two other state-of-the-art methods, scmap and CaSTLe in brain (66% versus 60% and 32%). Furthermore, it achieved better performance in correctly predicting ambiguous cellular subtype labels across datasets in 88% of test cases compared with CaSTLe (63%), scmap (50%) and MetaNeighbor (50%). LAmbDA is model- and dataset-independent and generalizable to diverse data types representing an advance in biocomputing. AVAILABILITY AND IMPLEMENTATION: github.com/tsteelejohnson91/LAmbDA. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A protocol to evaluate RNA sequencing normalization methods.

BACKGROUND: RNA sequencing technologies have allowed researchers to gain a better understanding of how the transcriptome affects disease. However, sequencing technologies often unintentionally introduce experimental error into RNA sequencing data. To counteract this, normalization methods are standardly applied with the intent of reducing the non-biologically derived variability inherent in transcriptomic measurements. However, the comparative efficacy of the various normalization techniques has not been tested in a standardized manner. Here we propose tests that evaluate numerous normalization techniques and applied them to a large-scale standard data set. These tests comprise a protocol that allows researchers to measure the amount of non-biological variability which is present in any data set after normalization has been performed, a crucial step to assessing the biological validity of data following normalization. RESULTS: In this study we present two tests to assess the validity of normalization methods applied to a large-scale data set collected for systematic evaluation purposes. We tested various RNASeq normalization procedures and concluded that transcripts per million (TPM) was the best performing normalization method based on its preservation of biological signal as compared to the other methods tested. CONCLUSION: Normalization is of vital importance to accurately interpret the results of genomic and transcriptomic experiments. More work, however, needs to be performed to optimize normalization methods for RNASeq data. The present effort helps pave the way for more systematic evaluations of normalization methods across different platforms. With our proposed schema researchers can evaluate their own or future normalization methods to further improve the field of RNASeq normalization.

MACPF/CDC proteins in development: Insights from Drosophila torso-like.

The Membrane Attack Complex Perforin-like/Cholesterol-Dependent Cytolysin (MACPF) superfamily is an ancient and biologically diverse group of proteins that are best known for pore-forming roles in mammalian immunity and bacterial pathogenesis. Intriguingly, however, some eukaryotic proteins which contain the MACPF domain that defines this family do not act in attack or defence, and instead have distinct developmental functions. It remains unclear whether these proteins function via pore formation or have a different mechanism of action. Of these, by far the best characterised is Torso-like (Tsl), the only MACPF member that has been identified in the fruit fly, Drosophila melanogaster. While it has long been known to have a role in embryonic patterning, recent studies have shown that Tsl in fact has multiple roles in development. As such, it presents an excellent opportunity to investigate how the MACPF domain functions in a developmental context. Here, we review what is known about Tsl in Drosophila and other insects, and discuss the potential molecular mechanism by which Tsl and thus other developmental MACPF proteins may function.

Control of growth factor signalling by MACPF proteins.

Members of the membrane attack complex/perforin-like (MACPF) protein superfamily have long captured interest because of their unique ability to assemble into large oligomeric pores on the surfaces of cells. The best characterised of these act in vertebrate immunity where they function to deliver pro-apoptotic factors or induce the cytolysis and death of targeted cells. Less appreciated, however, is that rather than causing cell death, MACPF proteins have also evolved to control cellular signalling pathways and influence developmental programmes such as pattern formation and neurogenesis. Torso-like (Tsl) from the fruit fly Drosophila, for example, functions to localise the activity of a growth factor for patterning its embryonic termini. It remains unclear whether these developmental proteins employ an attenuated form of the classical MACPF lytic pore, or if they have evolved to function via alternative mechanisms of action. In this minireview, we examine the evidence that links pore-forming MACPF proteins to the control of growth factor and cytokine signalling. We will then attempt to reconcile how the MACPF domain may have been repurposed during evolution for developmental events rather than cell killing.

Receptor Tyrosine Kinases in Development: Insights from Drosophila.

Cell-to-cell communication mediates a plethora of cellular decisions and behaviors that are crucial for the correct and robust development of multicellular organisms. Many of these signals are encoded in secreted hormones or growth factors that bind to and activate cell surface receptors, to transmit the cue intracellularly. One of the major superfamilies of cell surface receptors are the receptor tyrosine kinases (RTKs). For nearly half a century RTKs have been the focus of intensive study due to their ability to alter fundamental aspects of cell biology, such as cell proliferation, growth, and shape, and because of their central importance in diseases such as cancer. Studies in model organisms such a Drosophila melanogaster have proved invaluable for identifying new conserved RTK pathway components, delineating their contributions, and for the discovery of conserved mechanisms that control RTK-signaling events. Here we provide a brief overview of the RTK superfamily and the general mechanisms used in their regulation. We further highlight the functions of several RTKs that govern distinct cell-fate decisions in Drosophila and explore how their activities are developmentally controlled.

Lack of human cytomegalovirus expression in single cells from glioblastoma tumors and cell lines.

The relationship between human cytomegalovirus (HCMV) and glioblastoma (GBM) is an ongoing debate with extensive evidence supporting or refuting its existence through molecular assays, pre-clinical studies, and clinical trials. We focus primarily on the crux of the debate, detection of HCMV in GBM samples using molecular assays. We propose that these differences in detection could be affected by cellular heterogeneity. To take this into account, we align the single-cell RNA sequencing (scRNA-seq) reads from five GBM tumors and two cell lines to HCMV and analyze the alignments for evidence of (i) complete viral transcripts and (ii) low-abundance viral reads. We found that neither tumor nor cell line samples showed conclusive evidence of full HCMV viral transcripts. We also identified low-abundance reads aligned across all tumors, with two tumors having higher alignment rates than the rest of the tumor samples. This work is meant to rigorously test for HCMV RNA expression at a single cell level in GBM samples and examine the possible utility of single cell data in tumor virology.

The Drosophila melanogaster phospholipid flippase dATP8B is required for odorant receptor function.

The olfactory systems of insects are fundamental to all aspects of their behaviour, and insect olfactory receptor neurons (ORNs) exhibit exquisite specificity and sensitivity to a wide range of environmental cues. In Drosophila melanogaster, ORN responses are determined by three different receptor families, the odorant (Or), ionotropic-like (IR) and gustatory (Gr) receptors. However, the precise mechanisms of signalling by these different receptor families are not fully understood. Here we report the unexpected finding that the type 4 P-type ATPase phospholipid transporter dATP8B, the homologue of a protein associated with intrahepatic cholestasis and hearing loss in humans, is crucial for Drosophila olfactory responses. Mutations in dATP8B severely attenuate sensitivity of odorant detection specifically in Or-expressing ORNs, but do not affect responses mediated by IR or Gr receptors. Accordingly, we find dATP8B to be expressed in ORNs and localised to the dendritic membrane of the olfactory neurons where signal transduction occurs. Localisation of Or proteins to the dendrites is unaffected in dATP8B mutants, as is dendrite morphology, suggesting instead that dATP8B is critical for Or signalling. As dATP8B is a member of the phospholipid flippase family of ATPases, which function to determine asymmetry in phospholipid composition between the outer and inner leaflets of plasma membranes, our findings suggest a requirement for phospholipid asymmetry in the signalling of a specific family of chemoreceptor proteins.

Impact of Personality on Cognitive Aging: A Prospective Cohort Study.

OBJECTIVES: The aim of this study was to assess the association between personality factors and age-related longitudinal cognitive performance, and explore interactions of stress-proneness with apolipoprotein E (APOE) ɛ4, a prevalent risk factor for Alzheimer's disease (AD). METHODS: A total of 510 neuropsychiatrically healthy residents of Maricopa County recruited through media ads (mean age 57.6±10.6 years; 70% women; mean education 15.8±2.4 years; 213 APOE ɛ4 carriers) had neuropsychological testing every 2 years (mean duration follow-up 9.1±4.4 years), and the complete Neuroticism Extraversion Openness Personality Inventory-Revised. Several tests were administered within each of the following cognitive domains: memory, executive skills, language, visuospatial skills, and general cognition. Primary effects on cognitive trajectories and APOE ɛ4 interactions were ascertained with quadratic models. RESULTS: With personality factors treated as continuous variables, Neuroticism was associated with greater decline, and Conscientiousness associated with reduced decline consistently across tests in memory and executive domains. With personality factors trichotomized, the associations of Neuroticism and Conscientiousness were again highly consistent across tests within memory and to a lesser degree executive domains. While age-related memory decline was greater in APOE ɛ4 carriers as a group than ɛ4 noncarriers, verbal memory decline was mitigated in ɛ4 carriers with higher Conscientiousness, and visuospatial perception and memory decline was mitigated in ɛ4 carriers with higher Openness. CONCLUSIONS: Neuroticism and Conscientiousness were associated with changes in longitudinal performances on tests sensitive to memory and executive skills. APOE interactions were less consistent. Our findings are consistent with previous studies that have suggested that personality factors, particularly Neuroticism and Conscientiousness are associated with cognitive aging patterns. (JINS, 2016, 22, 765-776).

Torso-like functions independently of Torso to regulate Drosophila growth and developmental timing.

Activation of the Drosophila receptor tyrosine kinase Torso (Tor) only at the termini of the embryo is achieved by the localized expression of the maternal gene Torso-like (Tsl). Tor has a second function in the prothoracic gland as the receptor for prothoracicotropic hormone (PTTH) that initiates metamorphosis. Consistent with the function of Tor in this tissue, Tsl also localizes to the prothoracic gland and influences developmental timing. Despite these commonalities, in our studies of Tsl we unexpectedly found that tsl and tor have opposing effects on body size; tsl null mutants are smaller than normal, rather than larger as would be expected if the PTTH/Tor pathway was disrupted. We further found that whereas both genes regulate developmental timing, tsl does so independently of tor. Although tsl null mutants exhibit a similar length delay in time to pupariation to tor mutants, in tsl:tor double mutants this delay is strikingly enhanced. Thus, loss of tsl is additive rather than epistatic to loss of tor. We also find that phenotypes generated by ectopic PTTH expression are independent of tsl. Finally, we show that a modified form of tsl that can rescue developmental timing cannot rescue terminal patterning, indicating that Tsl can function via distinct mechanisms in different contexts. We conclude that Tsl is not just a specialized cue for Torso signaling but also acts independently of PTTH/Tor in the control of body size and the timing of developmental progression. These data highlight surprisingly diverse developmental functions for this sole Drosophila member of the perforin-like superfamily.

Neuropathological comparisons of amnestic and nonamnestic mild cognitive impairment.

BACKGROUND: Although there are studies investigating the pathologic origins of mild cognitive impairment (MCI), they have revolved around comparisons to normal elderly individuals or those with Alzheimer's disease (AD) or other dementias. There are few studies directly comparing the comprehensive neuropathology of amnestic (aMCI) and nonamnestic (naMCI) MCI. METHODS: The database of the Brain and Body Donation Program ( www.brainandbodydonationprogram.org ), a longitudinal clinicopathological study of normal aging and neurodegenerative disorders, was queried for subjects who were carrying a diagnosis of aMCI or naMCI at the time of autopsy. Neuropathological lesions, including neuritic plaques, neurofibrillary tangles (NFTs), Lewy bodies (LBs), infarcts, cerebral white matter rarefaction (CWMR), cerebral amyloid angiopathy (CAA), and concurrent major clinicopathological diagnoses, including Parkinson's disease (PD) were analyzed. RESULTS: Thirty four subjects with aMCI and 15 naMCI met study criteria. Subjects with aMCI were older at death (88 vs. 83 years of age, p = 0.03). Individuals with naMCI had higher densities of LBs within the temporal lobe (p = 0.04) while subjects with aMCI had a propensity for increased NFTs in parietal and temporal lobes (p values = 0.07). After adjusting for age at death, the only significant difference was greater densities of temporal lobe NFTs within the aMCI group. Other regional pathology scores for plaques, NFTs, and LBs were similar between groups. Subjects met clinico-pathological criteria for co-existent PD in 24 % aMCI and 47 % naMCI while neuropathological criteria for AD were met in equal percentages of aMCI and of naMCI cases (53 %); these proportional differences were not significant (p values > 0.35). Furthermore, regardless of amnestic status, there was a greater presence of CAA (71 % of MCI with executive dysfunction vs. 39 % without p = 0.03) and a greater presence of CWMR (81 % of MCI with executive dysfunction and 54 % without p = 0.046) in MCI cases with executive dysfunction. CONCLUSIONS: No single pathologic entity strongly dichotomized MCI groups, perhaps due to the pathologic heterogeneity found within both entities. However, these data suggest the possibility for naMCI to have a propensity for increased LBs and aMCI for increased NFTs in select anatomic regions.

High resolution structure of cleaved Serpin 42 Da from Drosophila melanogaster.

BACKGROUND: The Drosophila melanogaster Serpin 42 Da gene (previously Serpin 4) encodes a serine protease inhibitor that is capable of remarkable functional diversity through the alternative splicing of four different reactive centre loop exons. Eight protein isoforms of Serpin 42 Da have been identified to date, targeting the protease inhibitor to both different proteases and cellular locations. Biochemical and genetic studies suggest that Serpin 42 Da inhibits target proteases through the classical serpin 'suicide' inhibition mechanism, however the crystal structure of a representative Serpin 42 Da isoform remains to be determined. RESULTS: We report two high-resolution crystal structures of Serpin 42 Da representing the A/B isoforms in the cleaved conformation, belonging to two different space-groups and diffracting to 1.7 Å and 1.8 Å. Structural analysis reveals the archetypal serpin fold, with the major elements of secondary structure displaying significant homology to the vertebrate serpin, neuroserpin. Key residues known to have central roles in the serpin inhibitory mechanism are conserved in both the hinge and shutter regions of Serpin 42 Da. Furthermore, these structures identify important conserved interactions that appear to be of crucial importance in allowing the Serpin 42 Da fold to act as a versatile template for multiple reactive centre loops that have different sequences and protease specificities. CONCLUSIONS: In combination with previous biochemical and genetic studies, these structures confirm for the first time that the Serpin 42 Da isoforms are typical inhibitory serpin family members with the conserved serpin fold and inhibitory mechanism. Additionally, these data reveal the remarkable structural plasticity of serpins, whereby the basic fold is harnessed as a template for inhibition of a large spectrum of proteases by reactive centre loop exon 'switching'. This is the first structure of a Drosophila serpin reported to date, and will provide a platform for future mutational studies in Drosophila to ascertain the functional role of each of the Serpin 42 Da isoforms.

The toll and Imd pathways are not required for wolbachia-mediated dengue virus interference.

Wolbachia blocks dengue virus replication in Drosophila melanogaster as well as in Aedes aegypti. Using the Drosophila model and mutations in the Toll and Imd pathways, we showed that neither pathway is required for expression of the dengue virus-blocking phenotype in the Drosophila host. This provides additional evidence that the mechanistic basis of Wolbachia-mediated dengue virus blocking in insects is more complex than simple priming of the host insect innate immune system.