Reciprocal EGFR signaling in the anchor cell ensures precise inter-organ connection during Caenorhabditis elegans vulval morphogenesis.

During Caenorhabditis elegans vulval development, the uterine anchor cell (AC) first secretes an epidermal growth factor (EGF) to specify the vulval cell fates and then invades the underlying vulval epithelium. By doing so, the AC establishes direct contact with the invaginating primary vulF cells and attaches the developing uterus to the vulva. The signals involved and the exact sequence of events joining these two organs are not fully understood. Using a conditional let-23 EGF receptor (EGFR) allele along with novel microfluidic short- and long-term imaging methods, we discovered a specific function of the EGFR in the AC during vulval lumen morphogenesis. Tissue-specific inactivation of let-23 in the AC resulted in imprecise alignment of the AC with the primary vulval cells, delayed AC invasion and disorganized adherens junctions at the contact site forming between the AC and the dorsal vulF toroid. We propose that EGFR signaling, activated by a reciprocal EGF cue from the primary vulval cells, positions the AC at the vulval midline, guides it during invasion and assembles a cytoskeletal scaffold organizing the adherens junctions that connect the developing uterus to the dorsal vulF toroid. Thus, EGFR signaling in the AC ensures the precise alignment of the two developing organs.

Tissue-specific inhibition of protein sumoylation uncovers diverse SUMO functions during C. elegans vulval development.

The sumoylation (SUMO) pathway is involved in a variety of processes during C. elegans development, such as gonadal and vulval fate specification, cell cycle progression and maintenance of chromosome structure. The ubiquitous expression and pleiotropic effects have made it difficult to dissect the tissue-specific functions of the SUMO pathway and identify its target proteins. To overcome these challenges, we have established tools to block protein sumoylation and degrade sumoylated target proteins in a tissue-specific and temporally controlled manner. We employed the auxin-inducible protein degradation system (AID) to down-regulate the SUMO E3 ligase GEI-17 or the SUMO ortholog SMO-1, either in the vulval precursor cells (VPCs) or in the gonadal anchor cell (AC). Our results indicate that the SUMO pathway acts in multiple tissues to control different aspects of vulval development, such as AC positioning, basement membrane (BM) breaching, VPC fate specification and morphogenesis. Inhibition of protein sumoylation in the VPCs resulted in abnormal toroid formation and ectopic cell fusions during vulval morphogenesis. In particular, sumoylation of the ETS transcription factor LIN-1 at K169 is necessary for the proper contraction of the ventral vulA toroids. Thus, the SUMO pathway plays several distinct roles throughout vulval development.

Microfluidic-based imaging of complete Caenorhabditis elegans larval development.

Several microfluidic-based methods for Caenorhabditis elegans imaging have recently been introduced. Existing methods either permit imaging across multiple larval stages without maintaining a stable worm orientation, or allow for very good immobilization but are only suitable for shorter experiments. Here, we present a novel microfluidic imaging method that allows parallel live-imaging across multiple larval stages, while maintaining worm orientation and identity over time. This is achieved through an array of microfluidic trap channels carefully tuned to maintain worms in a stable orientation, while allowing growth and molting to occur. Immobilization is supported by an active hydraulic valve, which presses worms onto the cover glass during image acquisition only. In this way, excellent quality images can be acquired with minimal impact on worm viability or developmental timing. The capabilities of the devices are demonstrated by observing the hypodermal seam and P-cell divisions and, for the first time, the entire process of vulval development from induction to the end of morphogenesis. Moreover, we demonstrate feasibility of on-chip RNAi by perturbing basement membrane breaching during anchor cell invasion.

Sensitivity of Pharmacokinetics to Differences in the Particle Size Distribution for Formulations of Locally Acting Mometasone Furoate Suspension-Based Nasal Sprays.

To assess bioequivalence of locally acting suspension-based nasal sprays, the U.S. FDA currently recommends a weight-of-evidence approach. In addition to in vitro and human pharmacokinetic (PK) studies, this includes a comparative clinical endpoint study to ensure equivalent bioavailability of the active pharmaceutical ingredient (API) at the site of action. The present study aimed to assess, within an in vitro/in vivo correlation paradigm, whether PK studies and dissolution kinetics are sensitive to differences in drug particle size for a locally acting suspension-based nasal spray product. Two investigational suspension-based nasal formulations of mometasone furoate (MF-I and MF-II; delivered dose: 180 µg) differed in API particle size and were compared in a single-center, double-blind, single-dose, randomized, two-way crossover PK study in 44 healthy subjects with oral charcoal block. Morphology-directed Raman spectroscopy yielded volume median diameters of 3.17 µm for MF-I and 5.50 µm for MF-II, and dissolution studies showed that MF-II had a slower dissolution profile than MF-I. The formulation with larger API particles (MF-II) showed a 45% smaller Cmax and 45% smaller AUC0-inf compared to those of MF-I. Systemic bioavailability of MF-I (2.20%) and MF-II (1.18%) correlated well with the dissolution kinetics, with the faster dissolving formulation yielding the higher bioavailability. This agreement between pharmacokinetics and dissolution kinetics cross-validated both methods and supported their use in assessing potential differences in slowly dissolving suspension-based nasal spray products.

Cardiac dysfunction in mixed connective tissue disease: a nationwide observational study.

We aimed to identify cardiac function in patients with established mixed connective tissue disease (MCTD). This was a cross-sectional case-control study of well-characterised MCTD patients who had previously been included in a nationwide cohort. Assessments comprised protocol transthoracic echocardiography, electrocardiogram and blood samples. In patients only, we evaluated the findings of high-resolution pulmonary computed tomography and disease activity. We assessed 77 MCTD patients (mean age 50.5 ± 12.3 years) with a mean disease duration of 16.4 years, and 59 age- and sex-matched healthy controls (49.9 ± 11.7 years). By echocardiography, measures of left ventricular function, i.e. fractional shortening (38.1 ± 6.4% vs. 42.3 ± 6.6%, p < 0.001), mitral annulus plane systolic excursion (MAPSE) (13.7 ± 2.1 mm vs. 15.3 ± 2.3 mm, p < 0.001) and early diastolic velocity of the mitral annulus (e') (0.09 ± 0.02 m/s vs. 0.11 ± 0.03 m/s, p = 0.002) were subclinical and lower in patients than controls. Right ventricular dysfunction was found in patients assessed by tricuspid annular plane systolic excursion (TAPSE) (22.7 ± 4.0 mm vs. 25.5 ± 4.0 mm, p < 0.001). While cardiac dysfunction was not associated with pulmonary disease, e' and TAPSE were found to correlate with disease activity at baseline. In this cohort of MCTD patients, echocardiographic examinations demonstrated a higher frequency of cardiac dysfunction than in matched controls. Cardiac dysfunction was associated with disease activity at baseline, but was independent of cardiovascular risk factors and pulmonary disease. Our study indicates that cardiac dysfunction is part of the multi-organ affliction seen in MCTD.

Inactivation of aerosolized SARS-CoV-2 by 254 nm UV-C irradiation.

Surface residing SARS-CoV-2 is efficiently inactivated by UV-C irradiation. This raises the question whether UV-C-based technologies are also suitable to decontaminate SARS-CoV-2- containing aerosols and which doses are needed to achieve inactivation. Here, we designed a test bench to generate aerosolized SARS-CoV-2 and exposed the aerosols to a defined UV-C dose. Our results demonstrate that the exposure of aerosolized SARS-CoV-2 with a low average dose in the order of 0.42-0.51 mJ/cm2 UV-C at 254 nm resulted in more than 99.9% reduction in viral titers. Altogether, UV-C-based decontamination of aerosols seems highly effective to achieve a significant reduction in SARS-CoV-2 infectivity.

Generation, characterization, and comparison of human exhaled and technical aerosols for the evaluation of different air-purifying technologies against infectious aerosols.

In light of the COVID-19 pandemic, the importance of protective measures against infectious aerosols has drastically increased, as the transmission of diseases via airborne particles is impacting many aspects of everyday life. The protective measures against such infections are determinant in the operation of schools and kindergartens, hygiene in hospitals and medical facilities, in offices, administrative and production facilities, hotels, and the event industry, among others. To test these protective measures, suitable test aerosols and processes are needed. These aerosols ought to be similar to aerosols exhaled by humans as those carry the pathogens and thus need to be removed from the air or inactivated. The exhaled aerosols of several healthy test subjects were characterized by their particle concentration and size distribution. In previous studies, it was found that exhaled particle concentration varies significantly from subject to subject and most of the particles can be found in the submicron size range. Aerosols technically generated through nebulization were emitted by the generators in particle concentrations several orders of magnitude higher than those exhaled by humans, independent of the aerosol generation method and nebulized fluid. The particle size distribution generated by the two nebulizers used, however, was quite similar to the measured size distributions of the human aerosols, with most of the particles below 1 µm in size. Consequently, the used aerosol generators are not suitable to mimic single individuals as active aerosol sources, but rather to provide a sufficient amount of aerosol similar to human aerosols in size distribution, which can be used in the testing of air purification technologies.

Stochastic and Age-Dependent Proteostasis Decline Underlies Heterogeneity in Heat-Shock Response Dynamics.

Significant non-genetic stochastic factors affect aging, causing lifespan differences among individuals, even those sharing the same genetic and environmental background. In Caenorhabditis elegans, differences in heat-shock response (HSR) are predictive of lifespan. However, factors contributing to the heterogeneity of HSR are still not fully elucidated. Here, the authors characterized HSR dynamics in isogenic C. elegans expressing GFP reporter for hsp-16.2 for identifying the key contributors of HSR heterogeneity. Specifically, microfluidic devices that enable cross-sectional and longitudinal measurements of HSR dynamics in C. elegans at different scales are developed: in populations, within individuals, and in embryos. The authors adapted a mathematical model of HSR to single C. elegans and identified model parameters associated with proteostasis-maintenance of protein homeostasis-more specifically, protein turnover, as the major drivers of heterogeneity in HSR dynamics. It is verified that individuals with enhanced proteostasis fidelity in early adulthood live longer. The model-based comparative analysis of protein turnover in day-1 and day-2 adult C. elegans revealed a stochastic-onset of age-related proteostasis decline that increases the heterogeneity of HSR capacity. Finally, the analysis of C. elegans embryos showed higher HSR and proteostasis capacity than young adults and established transgenerational contribution to HSR heterogeneity that depends on maternal age.

Right ventricular involvement in hypertrophic cardiomyopathy: evidence and implications from current literature.

Objectives. In current guidelines, hypertrophic cardiomyopathy (HCM) is defined by hypertrophy of the left ventricle (LV). Less attention has been given to the right ventricle (RV) in patients with HCM. We wanted to provide an overview of current literature on RV involvement in HCM. Design. We performed a systematic search in PubMed and added additional articles by manual screening of references. The quality of the articles was assessed according to the GRADE system. Results. We identified 35 original articles on RV involvement in HCM. Based on these publications, RV hypertrophy occurs in 28-44% of HCM patients, depending on the cut-off value for hypertrophy and the method for assessment. Histological studies show the same structural changes in RV as are typically described in the LV cardiomyocyte hypertrophy and disarray, as well as fibrosis. These changes are similar, but less pronounced in the RV than in the LV. We discuss how HCM can impact the RV, either through a primary involvement similar to the LV or secondary to hemodynamic effects resulting from LV dysfunction. RV dysfunction in HCM is associated with higher mortality, partly due to an increased risk of ventricular tachycardia and sudden cardiac death. Conclusions. The evidence for RV involvement in HCM is limited. Multimodal imaging assessment of the RV should be included in the work-up of patients with HCM, and the added value of including RV function in the risk stratification algorithm should be further explored.

Metagenomic species profiling using universal phylogenetic marker genes.

To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/.

Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context.

Nucleotide positions in the hypervariable V4 and V9 regions of the small subunit (SSU)-rDNA locus are normally difficult to align and are usually removed before standard phylogenetic analyses. Yet, with next-generation sequencing data, amplicons of these regions are all that are available to answer ecological and evolutionary questions that rely on phylogenetic inferences. With ciliates, we asked how inclusion of the V4 or V9 regions, regardless of alignment quality, affects tree topologies using distinct phylogenetic methods (including PairDist that is introduced here). Results show that the best approach is to place V4 amplicons into an alignment of full-length Sanger SSU-rDNA sequences and to infer the phylogenetic tree with RAxML. A sliding window algorithm as implemented in RAxML shows, though, that not all nucleotide positions in the V4 region are better than V9 at inferring the ciliate tree. With this approach and an ancestral-state reconstruction, we use V4 amplicons from European nearshore sampling sites to infer that rather than being primarily terrestrial and freshwater, colpodean ciliates may have repeatedly transitioned from terrestrial/freshwater to marine environments.

Multiple ITS haplotypes in the genome of the lichenized basidiomycete Cora inversa (Hygrophoraceae): fact or artifact?

The internal transcribed spacer region (ITS) of the nuclear rDNA cistron represents the barcoding locus for Fungi. Intragenomic variation of this multicopy gene can interfere with accurate phylogenetic reconstruction of biological entities. We investigated the amount and nature of this variation for the lichenized fungus Cora inversa in the Hygrophoraceae (Basidiomycota: Agaricales), analyzing base call and length variation in ITS1 454 pyrosequencing data of three samples of the target mycobiont, for a total of 16,665 reads obtained from three separate repeats of the same samples under different conditions. Using multiple fixed alignment methods (PaPaRa) and maximum likelihood phylogenetic analysis (RAxML), we assessed phylogenetic relationships of the obtained reads, together with Sanger ITS sequences from the same samples. Phylogenetic analysis showed that all ITS1 reads belonged to a single species, C. inversa. Pyrosequencing data showed 266 insertion sites in addition to the 325 sites expected from Sanger sequences, for a total of 15,654 insertions (0.94 insertions per read). An additional 3,279 substitutions relative to the Sanger sequences were detected in the dataset, out of 5,461,125 bases to be called. Up to 99.3% of the observed indels in the dataset could be interpreted as 454 pyrosequencing errors, approximately 65% corresponding to incorrectly recovered homopolymer segments, and 35% to carry-forward-incomplete-extension errors. Comparison of automated clustering and alignment-based phylogenetic analysis demonstrated that clustering of these reads produced a 35-fold overestimation of biological diversity in the dataset at the 95% similarity threshold level, whereas phylogenetic analysis using a maximum likelihood approach accurately recovered a single biological entity. We conclude that variation detected in 454 pyrosequencing data must be interpreted with great care and that a combination of a sufficiently large number of reads per taxon, a set of Sanger references for the same taxon, and at least two runs under different emulsion PCR and sequencing conditions, are necessary to reliably separate biological variation from 454 sequencing errors. Our study shows that clustering methods are highly sensitive to artifactual sequence variation and inadequate to properly recover biological diversity in a dataset, if sequencing errors are substantial and not removed prior to clustering analysis.

Active nuclear positioning and actomyosin contractility maintain leader cell integrity during gonadogenesis.

Proper distribution of organelles can play an important role in a moving cell's performance. During C. elegans gonad morphogenesis, the nucleus of the leading distal tip cell (DTC) is always found at the front, yet the significance of this localization is unknown. Here, we identified the molecular mechanism that keeps the nucleus at the front, despite a frictional force that pushes it backward. The Klarsicht/ANC-1/Syne homology (KASH) domain protein UNC-83 links the nucleus to the motor protein kinesin-1 that moves along a polarized acentrosomal microtubule network. Interestingly, disrupting nuclear positioning on its own did not affect gonad morphogenesis. However, reducing actomyosin contractility on top of nuclear mispositioning led to a dramatic phenotype: DTC splitting and gonad bifurcation. Long-term live imaging of the double knockdown revealed that, while the gonad attempted to perform a planned U-turn, the DTC was stretched due to the lagging nucleus until it fragmented into a nucleated cell and an enucleated cytoplast, each leading an independent gonadal arm. Remarkably, the enucleated cytoplast had polarity and invaded, but it could only temporarily support germ cell proliferation. Based on a qualitative biophysical model, we conclude that the leader cell employs two complementary mechanical approaches to preserve its integrity and ensure proper organ morphogenesis while navigating through a complex 3D environment: active nuclear positioning by microtubule motors and actomyosin-driven cortical contractility.

libgapmis: extending short-read alignments.

BACKGROUND: A wide variety of short-read alignment programmes have been published recently to tackle the problem of mapping millions of short reads to a reference genome, focusing on different aspects of the procedure such as time and memory efficiency, sensitivity, and accuracy. These tools allow for a small number of mismatches in the alignment; however, their ability to allow for gaps varies greatly, with many performing poorly or not allowing them at all. The seed-and-extend strategy is applied in most short-read alignment programmes. After aligning a substring of the reference sequence against the high-quality prefix of a short read--the seed--an important problem is to find the best possible alignment between a substring of the reference sequence succeeding and the remaining suffix of low quality of the read--extend. The fact that the reads are rather short and that the gap occurrence frequency observed in various studies is rather low suggest that aligning (parts of) those reads with a single gap is in fact desirable. RESULTS: In this article, we present libgapmis, a library for extending pairwise short-read alignments. Apart from the standard CPU version, it includes ultrafast SSE- and GPU-based implementations. libgapmis is based on an algorithm computing a modified version of the traditional dynamic-programming matrix for sequence alignment. Extensive experimental results demonstrate that the functions of the CPU version provided in this library accelerate the computations by a factor of 20 compared to other programmes. The analogous SSE- and GPU-based implementations accelerate the computations by a factor of 6 and 11, respectively, compared to the CPU version. The library also provides the user the flexibility to split the read into fragments, based on the observed gap occurrence frequency and the length of the read, thereby allowing for a variable, but bounded, number of gaps in the alignment. CONCLUSIONS: We present libgapmis, a library for extending pairwise short-read alignments. We show that libgapmis is better-suited and more efficient than existing algorithms for this task. The importance of our contribution is underlined by the fact that the provided functions may be seamlessly integrated into any short-read alignment pipeline. The open-source code of libgapmis is available at http://www.exelixis-lab.org/gapmis.

Face mask performance related to potentially infectious aerosol particles, breathing mode and facial leakage.

During the COVID 19 pandemic, wearing certified Respiratory Protective Devices (RPDs) provided important means of protection against direct and indirect infections caused by virus-laden aerosols. Assessing the RPD performance associated with infection prevention in standardised certification tests, however, faces drawbacks, such as the representativeness of the test aerosols used, the protection of third parties during exhalation or the effect of facial leaks. To address these drawbacks, we designed a novel test bench to measure RPD performance, namely the number based total efficiency, size-segregated fractional filtration efficiency and net pressure loss, for 11 types of certified surgical masks and Filtering Face Pieces dependent on breathing mode and facial fit. To be representative for the context of potentially infectious particles, we use a test aerosol based on artificial saliva that is in its size distribution similar to exhaled aerosols. In inhalation mode excluding facial leaks, all investigated samples deposit by count more than 85% of artificial saliva particles, which suggests a high efficiency of certified RPD filter media related to these particles. In exhalation mode most RPDs tend to have similar efficiencies but lower pressure losses. This deviation tends to be significant primarily for the RPDs with thin filter layers like surgical masks or Filtering Face Pieces containing nanofibers and may depend on the RPDs shape. Both the filtration efficiency and pressure loss are strongly inter-dependent and significantly lower when RPDs are naturally fitted including facial leaks, leading to a wide efficiency range of approximately 30-85%. The results indicate a much greater influence of the facial fit than the filter material itself. Furthermore, RPDs tend be more effective in self-protection than in third-party protection, which is inversely correlated to pressure loss. Comparing different types of RPDs, the pressure loss partially differs at similar filtration efficiencies, which points out the influence of the material and the filter area on pressure loss.

Prolonging somatic cell proliferation through constitutive hox gene expression in C. elegans.

hox genes encode a conserved family of homeodomain transcription factors that are essential to determine the identity of body segments during embryogenesis and maintain adult somatic stem cells competent to regenerate organs. In contrast to higher organisms, somatic cells in C. elegans irreversibly exit the cell cycle after completing their cell lineage and the adult soma cannot regenerate. Here, we show that hox gene expression levels in C. elegans determine the temporal competence of somatic cells to proliferate. Down-regulation of the central hox gene lin-39 in dividing vulval cells results in their premature cell cycle exit, whereas constitutive lin-39 expression causes precocious Pn.p cell and sex myoblast divisions and prolongs the proliferative phase of the vulval cells past their normal point of arrest. Furthermore, ectopic expression of hox genes in the quiescent anchor cell re-activates the cell cycle and induces proliferation until young adulthood. Thus, constitutive expression of a single hox transcription factor is sufficient to prolong somatic cell proliferation beyond the restriction imposed by the cell lineage. The down-regulation of hox gene expression in most somatic cells at the end of larval development may be one cause for the absence of cell proliferation in adult C. elegans.

Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel.

BACKGROUND: Aligning short DNA reads to a reference sequence alignment is a prerequisite for detecting their biological origin and analyzing them in a phylogenetic context. With the PaPaRa tool we introduced a dedicated dynamic programming algorithm for simultaneously aligning short reads to reference alignments and corresponding evolutionary reference trees. The algorithm aligns short reads to phylogenetic profiles that correspond to the branches of such a reference tree. The algorithm needs to perform an immense number of pairwise alignments. Therefore, we explore vector intrinsics and GPUs to accelerate the PaPaRa alignment kernel. RESULTS: We optimized and parallelized PaPaRa on CPUs and GPUs. Via SSE 4.1 SIMD (Single Instruction, Multiple Data) intrinsics for x86 SIMD architectures and multi-threading, we obtained a 9-fold acceleration on a single core as well as linear speedups with respect to the number of cores. The peak CPU performance amounts to 18.1 GCUPS (Giga Cell Updates per Second) using all four physical cores on an Intel i7 2600 CPU running at 3.4 GHz. The average CPU performance (averaged over all test runs) is 12.33 GCUPS. We also used OpenCL to execute PaPaRa on a GPU SIMT (Single Instruction, Multiple Threads) architecture. A NVIDIA GeForce 560 GPU delivered peak and average performance of 22.1 and 18.4 GCUPS respectively. Finally, we combined the SIMD and SIMT implementations into a hybrid CPU-GPU system that achieved an accumulated peak performance of 33.8 GCUPS. CONCLUSIONS: This accelerated version of PaPaRa (available at http://www.exelixis-lab.org/software.html) provides a significant performance improvement that allows for analyzing larger datasets in less time. We observe that state-of-the-art SIMD and SIMT architectures deliver comparable performance for this dynamic programming kernel when the "competing programmer approach" is deployed. Finally, we show that overall performance can be substantially increased by designing a hybrid CPU-GPU system with appropriate load distribution mechanisms.

Aligning short reads to reference alignments and trees.

MOTIVATION: Likelihood-based methods for placing short read sequences from metagenomic samples into reference phylogenies have been recently introduced. At present, it is unclear how to align those reads with respect to the reference alignment that was deployed to infer the reference phylogeny. Moreover, the adaptability of such alignment methods with respect to the underlying reference alignment strategies/philosophies has not been explored. It has also not been assessed if the reference phylogeny can be deployed in conjunction with the reference alignment to improve alignment accuracy in this context. RESULTS: We assess different strategies for short read alignment and propose a novel phylogeny-aware alignment procedure. Our alignment method can improve the accuracy of subsequent phylogenetic placement of the reads into a reference phylogeny by up to 5.8 times compared with phylogeny-agnostic methods. It can be deployed to align reads to alignments generated by using fundamentally different alignment strategies (e.g. PRANK(+F) versus MUSCLE). AVAILABILITY: http://www.exelixis-lab.org/software.html

Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood.

We present an evolutionary placement algorithm (EPA) and a Web server for the rapid assignment of sequence fragments (short reads) to edges of a given phylogenetic tree under the maximum-likelihood model. The accuracy of the algorithm is evaluated on several real-world data sets and compared with placement by pair-wise sequence comparison, using edit distances and BLAST. We introduce a slow and accurate as well as a fast and less accurate placement algorithm. For the slow algorithm, we develop additional heuristic techniques that yield almost the same run times as the fast version with only a small loss of accuracy. When those additional heuristics are employed, the run time of the more accurate algorithm is comparable with that of a simple BLAST search for data sets with a high number of short query sequences. Moreover, the accuracy of the EPA is significantly higher, in particular when the sample of taxa in the reference topology is sparse or inadequate. Our algorithm, which has been integrated into RAxML, therefore provides an equally fast but more accurate alternative to BLAST for tree-based inference of the evolutionary origin and composition of short sequence reads. We are also actively developing a Web server that offers a freely available service for computing read placements on trees using the EPA.