Diviner uncovers hundreds of novel human (and other) exons though comparative analysis of proteins

Background

Eukaryotic genes are often composed of multiple exons that are stitched together by splicing out the intervening introns. These exons may be conditionally joined in different combinations to produce a collection of related, but distinct, mRNA transcripts. For protein-coding genes, these products of alternative splicing lead to production of related protein variants ( isoforms ) of a gene. Complete labeling of the protein-coding content of a eukaryotic genome requires discovery of mRNA encoding all isoforms, but it is impractical to enumerate all possible combinations of tissue, developmental stage, and environmental context; as a result, many true exons go unlabeled in genome annotations.

Results

One way to address the combinatoric challenge of finding all isoforms in a single organism A is to leverage sequencing efforts for other organisms - each time a new organism is sequenced, it may be under a new combination of conditions, so that a previously unobserved isoform may be sequenced. We present Diviner , a software tool that identifies previously undocumented exons in organisms by comparing isoforms across species. We demonstrate Diviner 's utility by locating hundreds of novel exons in the genomes of human, mouse, and rat, as well as in the ferret genome. Further, we provide analyses supporting the notion that most of the new exons reported by Diviner are likely to be part of a true (but unobserved) isoform of the containing species.

Predicting metabolic modules in incomplete bacterial genomes with MetaPathPredict

The reconstruction of complete microbial metabolic pathways using 'omics data from environmental samples remains challenging. Computational pipelines for pathway reconstruction that utilize machine learning methods to predict the presence or absence of KEGG modules in incomplete genomes are lacking. Here, we present MetaPathPredict, a software tool that incorporates machine learning models to predict the presence of complete KEGG modules within bacterial genomic datasets. Using gene annotation data and information from the KEGG module database, MetaPathPredict employs deep learning models to predict the presence of KEGG modules in a genome. MetaPathPredict can be used as a command line tool or as a Python module, and both options are designed to be run locally or on a compute cluster. Benchmarks show that MetaPathPredict makes robust predictions of KEGG module presence within highly incomplete genomes.

nail: software for high-speed, high-sensitivity protein sequence annotation

" Fast is fine, but accuracy is final. " -- Wyatt Earp.

Background

The extreme diversity of newly sequenced organisms and considerable scale of modern sequence databases lead to a tension between competing needs for sensitivity and speed in sequence annotation, with multiple tools displacing the venerable BLAST software suite on one axis or another. Alignment based on profile hidden Markov models (pHMMs) has demonstrated state of art sensitivity, while recent algorithmic advances have resulted in hyper-fast annotation tools with sensitivity close to that of BLAST.

Results

Here, we introduce a new tool that bridges the gap between advances in these two directions, reaching speeds comparable to fast annotation methods such as MMseqs2 while retaining most of the sensitivity offered by pHMMs. The tool, called nail, implements a heuristic approximation of the pHMM Forward/Backward (FB) algorithm by identifying a sparse subset of the cells in the FB dynamic programming matrix that contains most of the probability mass. The method produces an accurate approximation of pHMM scores and E-values with high speed and small memory requirements. On a protein benchmark, nail recovers the majority of recall difference between MMseqs2 and HMMER, with run time ~26x faster than HMMER3 (only ~2.4x slower than MMseqs2's sensitive variant). nail is released under the open BSD-3-clause license and is available for download at https://github.com/TravisWheelerLab/nail.

A community effort in SARS-CoV-2 drug discovery

The COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small-molecule drugs that are widely available, including in low- and middle-income countries, is an ongoing challenge. In this work, we report the results of an open science community effort, the "Billion molecules against COVID-19 challenge", to identify small-molecule inhibitors against SARS-CoV-2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 molecules, which were subsequently ranked to find 'consensus compounds'. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for biological activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (only the Nsp12 domain), and (alpha) spike protein S. Overall, 27 compounds with weak inhibition/binding were experimentally identified by binding-, cleavage-, and/or viral suppression assays and are presented here. Open science approaches such as the one presented here contribute to the knowledge base of future drug discovery efforts in finding better SARS-CoV-2 treatments.

Sensitive and error-tolerant annotation of protein-coding DNA with BATH

We present BATH, a tool for highly sensitive annotation of protein-coding DNA based on direct alignment of that DNA to a database of protein sequences or profile hidden Markov models (pHMMs). BATH is built on top of the HMMER3 code base, and simplifies the annotation workflow for pHMM-based annotation by providing a straightforward input interface and easy-to-interpret output. BATH also introduces novel frameshift-aware algorithms to detect frameshift-inducing nucleotide insertions and deletions (indels). BATH matches the accuracy of HMMER3 for annotation of sequences containing no errors, and produces superior accuracy to all tested tools for annotation of sequences containing nucleotide indels. These results suggest that BATH should be used when high annotation sensitivity is required, particularly when frameshift errors are expected to interrupt protein-coding regions, as is true with long read sequencing data and in the context of pseudogenes.

VIBES: A Workflow for Annotating and Visualizing Viral Sequences Integrated into Bacterial Genomes

Bacteriophages are viruses that infect bacteria. Many bacteriophages integrate their genomes into the bacterial chromosome and become prophages. Prophages may substantially burden or benefit host bacteria fitness, acting in some cases as parasites and in others as mutualists, and have been demonstrated to increase host virulence. The increasing ease of bacterial genome sequencing provides an opportunity to deeply explore prophage prevalence and insertion sites. Here we present VIBES, a workflow intended to automate prophage annotation in complete bacterial genome sequences. VIBES provides additional context to prophage annotations by annotating bacterial genes and viral proteins in user-provided bacterial and viral genomes. The VIBES pipeline is implemented as a Nextflow-driven workflow, providing a simple, unified interface for execution on local, cluster, and cloud computing environments. For each step of the pipeline, a container including all necessary software dependencies is provided. VIBES produces results in simple tab separated format and generates intuitive and interactive visualizations for data exploration. Despite VIBES' primary emphasis on prophage annotation, its generic alignment-based design allows it to be deployed as a general-purpose sequence similarity search manager. We demonstrate the utility of the VIBES prophage annotation workflow by searching for 178 Pf phage genomes across 1,072 Pseudomonas spp. genomes. VIBES software is available at https://github.com/TravisWheelerLab/VIBES.

DISCO: A deep learning ensemble for uncertainty-aware segmentation of acoustic signals

Recordings of animal sounds enable a wide range of observational inquiries into animal communication, behavior, and diversity. Automated labeling of sound events in such recordings can improve both throughput and reproducibility of analysis. Here, we describe our software package for labeling elements in recordings of animal sounds, and demonstrate its utility on recordings of beetle courtships and whale songs. The software, DISCO, computes sensible confidence estimates and produces labels with high precision and accuracy. In addition to the core labeling software, it provides a simple tool for labeling training data, and a visual system for analysis of resulting labels. DISCO is open-source and easy to install, it works with standard file formats, and it presents a low barrier of entry to use.

DISCO: A deep learning ensemble for uncertainty-aware segmentation of acoustic signals

Recordings of animal sounds enable a wide range of observational inquiries into animal communication, behavior, and diversity. Automated labeling of sound events in such recordings can improve both throughput and reproducibility of analysis. Here, we describe our software package for labeling sound elements in recordings of animal sounds and demonstrate its utility on recordings of beetle courtships and whale songs. The software, DISCO, computes sensible confidence estimates and produces labels with high precision and accuracy. In addition to the core labeling software, it provides a simple tool for labeling training data, and a visual system for analysis of resulting labels. DISCO is open-source and easy to install, it works with standard file formats, and it presents a low barrier of entry to use.

Framework of the Alu Subfamily Evolution in the Platyrrhine Three-Family Clade of Cebidae, Callithrichidae, and Aotidae

The history of Alu retroposons has been choreographed by the systematic accumulation of inherited diagnostic nucleotide substitutions to form discrete subfamilies, each having a distinct nucleotide consensus sequence. The oldest subfamily, AluJ, gave rise to AluS after the split between Strepsirrhini and what would become Catarrhini and Platyrrhini. The AluS lineage gave rise to AluY in catarrhines and to AluTa in platyrrhines. Platyrrhine Alu subfamilies Ta7, Ta10, and Ta15 were assigned names based on a standardized nomenclature. However, with the subsequent intensification of whole genome sequencing (WGS), large scale analyses to characterize Alu subfamilies using the program COSEG identified entire lineages of subfamilies simultaneously. The first platyrrhine genome with WGS, the common marmoset (Callithrix jacchus; [caljac3]), resulted in Alu subfamily names sf0 to sf94 in an arbitrary order. Although easily resolved by alignment of the consensus sequences, this naming convention can become increasingly confusing as more genomes are independently analyzed. In this study, we reported Alu subfamily characterization for the platyrrhine three-family clade of Cebidae, Callithrichidae, and Aotidae. We investigated one species/genome from each recognized family of Callithrichidae and Aotidae and of both subfamilies (Cebinae and Saimiriinae) of the family Cebidae. Furthermore, we constructed a comprehensive network of Alu subfamily evolution within the three-family clade of platyrrhines to provide a working framework for future research. Alu expansion in the three-family clade has been dominated by AluTa15 and its derivatives.

Mirage2's high-quality spliced protein-to-genome mappings produce accurate multiple-sequence alignments of isoforms

The organization of homologous protein sequences into multiple sequence alignments (MSAs) is a cornerstone of modern analysis of proteins. Recent focus on the importance of alternatively-spliced isoforms in disease and cell biology has highlighted the need for MSA software that can appropriately account for isoforms and the exon-length insertions or deletions that isoforms may have relative to each other. We previously developed Mirage, a software package for generating MSAs for isoforms spanning multiple species. Here, we present Mirage2, which retains the fundamental algorithms of the original Mirage implementation while providing substantially improved translated mapping and improving several aspects of usability. We demonstrate that Mirage2 is highly effective at mapping proteins to their encoding exons, and that these protein-genome mappings lead to extremely accurate intron-aware alignments. Additionally, Mirage2 implements a number of engineering improvements that simplify installation and use.

SODA: a TypeScript/JavaScript library for visualizing biological sequence annotation

We present SODA, a lightweight and open-source visualization library for biological sequence annotations that enables straightforward development of flexible, dynamic and interactive web graphics. SODA is implemented in TypeScript and can be used as a library within TypeScript and JavaScript.

Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families

The construction of a high-quality multiple sequence alignment (MSA) from copies of a transposable element (TE) is a critical step in the characterization of a new TE family. Most studies of MSA accuracy have been conducted on protein or RNA sequence families, where structural features and strong signals of selection may assist with alignment. Less attention has been given to the quality of sequence alignments involving neutrally evolving DNA sequences such as those resulting from TE replication. Transposable element sequences are challenging to align due to their wide divergence ranges, fragmentation, and predominantly-neutral mutation patterns. To gain insight into the effects of these properties on MSA accuracy, we developed a simulator of TE sequence evolution, and used it to generate a benchmark with which we evaluated the MSA predictions produced by several popular aligners, along with Refiner, a method we developed in the context of our RepeatModeler software. We find that MAFFT and Refiner generally outperform other aligners for low to medium divergence simulated sequences, while Refiner is uniquely effective when tasked with aligning high-divergent and fragmented instances of a family.

Drugsniffer: An Open Source Workflow for Virtually Screening Billions of Molecules for Binding Affinity to Protein Targets

The SARS-CoV2 pandemic has highlighted the importance of efficient and effective methods for identification of therapeutic drugs, and in particular has laid bare the need for methods that allow exploration of the full diversity of synthesizable small molecules. While classical high-throughput screening methods may consider up to millions of molecules, virtual screening methods hold the promise of enabling appraisal of billions of candidate molecules, thus expanding the search space while concurrently reducing costs and speeding discovery. Here, we describe a new screening pipeline, called drugsniffer, that is capable of rapidly exploring drug candidates from a library of billions of molecules, and is designed to support distributed computation on cluster and cloud resources. As an example of performance, our pipeline required ∼40,000 total compute hours to screen for potential drugs targeting three SARS-CoV2 proteins among a library of ∼3.7 billion candidate molecules.

Complete genomic and epigenetic maps of human centromeres

Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, and functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere human genome assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric and centromeric repeats, which constitute 6.2% of the genome (189.9 megabases). Detailed maps of these regions revealed multimegabase structural rearrangements, including in active centromeric repeat arrays. Analysis of centromere-associated sequences uncovered a strong relationship between the position of the centromere and the evolution of the surrounding DNA through layered repeat expansions. Furthermore, comparisons of chromosome X centromeres across a diverse panel of individuals illuminated high degrees of structural, epigenetic, and sequence variation in these complex and rapidly evolving regions.

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

Mobile elements and repetitive genomic regions are sources of lineage-specific genomic innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such repeat elements, including those found in more complex regions of the genome, require a complete, linear genome assembly. We present a de novo repeat discovery and annotation of the T2T-CHM13 human reference genome. We identified previously unknown satellite arrays, expanded the catalog of variants and families for repeats and mobile elements, characterized classes of complex composite repeats, and located retroelement transduction events. We detected nascent transcription and delineated CpG methylation profiles to define the structure of transcriptionally active retroelements in humans, including those in centromeres. These data expand our insight into the diversity, distribution, and evolution of repetitive regions that have shaped the human genome.

An optimized FM-index library for nucleotide and amino acid search

BACKGROUND

Pattern matching is a key step in a variety of biological sequence analysis pipelines. The FM-index is a compressed data structure for pattern matching, with search run time that is independent of the length of the database text. Implementation of the FM-index is reasonably complicated, so that increased adoption will be aided by the availability of a fast and flexible FM-index library.

RESULTS

We present AvxWindowedFMindex (AWFM-index), a lightweight, open-source, thread-parallel FM-index library written in C that is optimized for indexing nucleotide and amino acid sequences. AWFM-index introduces a new approach to storing FM-index data in a strided bit-vector format that enables extremely efficient computation of the FM-index occurrence function via AVX2 bitwise instructions, and combines this with optional on-disk storage of the index's suffix array and a cache-efficient lookup table for partial k-mer searches. The AWFM-index performs exact match count and locate queries faster than SeqAn3's FM-index implementation across a range of comparable memory footprints. When optimized for speed, AWFM-index is [Formula: see text]2-4x faster than SeqAn3 for nucleotide search, and [Formula: see text]2-6x faster for amino acid search; it is also [Formula: see text]4x faster with similar memory footprint when storing the suffix array in on-disk SSD storage.

CONCLUSIONS

AWFM-index is easy to incorporate into bioinformatics software, offers run-time performance parameterization, and provides clients with FM-index functionality at both a high-level (count or locate all instances of a query string) and low-level (step-wise control of the FM-index backward-search process). The open-source library is available for download at https://github.com/TravisWheelerLab/AvxWindowFmIndex.

TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation

Transposable elements (TEs) play powerful and varied evolutionary and functional roles, and are widespread in most eukaryotic genomes. Research into their unique biology has driven the creation of a large collection of databases, software, classification systems, and annotation guidelines. The diversity of available TE-related methods and resources raises compatibility concerns and can be overwhelming to researchers and communicators seeking straightforward guidance or materials. To address these challenges, we have initiated a new resource, TE Hub, that provides a space where members of the TE community can collaborate to document and create resources and methods. The space consists of (1) a website organized with an open wiki framework,  https://tehub.org , (2) a conversation framework via a Twitter account and a Slack channel, and (3) bi-monthly Hub Update video chats on the platform's development. In addition to serving as a centralized repository and communication platform, TE Hub lays the foundation for improved integration, standardization, and effectiveness of diverse tools and protocols. We invite the TE community, both novices and experts in TE identification and analysis, to join us in expanding our community-oriented resource.

Transposable element subfamily annotation has a reproducibility problem

Background

Transposable element (TE) sequences are classified into families based on the reconstructed history of replication, and into subfamilies based on more fine-grained features that are often intended to capture family history. We evaluate the reliability of annotation with common subfamilies by assessing the extent to which subfamily annotation is reproducible in replicate copies created by segmental duplications in the human genome, and in homologous copies shared by human and chimpanzee.

Results

We find that standard methods annotate over 10% of replicates as belonging to different subfamilies, despite the fact that they are expected to be annotated as belonging to the same subfamily. Point mutations and homologous recombination appear to be responsible for some of this discordant annotation (particularly in the young Alu family), but are unlikely to fully explain the annotation unreliability.

Conclusions

The surprisingly high level of disagreement in subfamily annotation of homologous sequences highlights a need for further research into definition of TE subfamilies, methods for representing subfamily annotation confidence of TE instances, and approaches to better utilizing such nuanced annotation data in downstream analysis.

The Dfam community resource of transposable element families, sequence models, and genome annotations

Dfam is an open access database of repetitive DNA families, sequence models, and genome annotations. The 3.0-3.3 releases of Dfam ( https://dfam.org ) represent an evolution from a proof-of-principle collection of transposable element families in model organisms into a community resource for a broad range of species, and for both curated and uncurated datasets. In addition, releases since Dfam 3.0 provide auxiliary consensus sequence models, transposable element protein alignments, and a formalized classification system to support the growing diversity of organisms represented in the resource. The latest release includes 266,740 new de novo generated transposable element families from 336 species contributed by the EBI. This expansion demonstrates the utility of many of Dfam's new features and provides insight into the long term challenges ahead for improving de novo generated transposable element datasets.

Pf Bacteriophage and Their Impact on Pseudomonas Virulence, Mammalian Immunity, and Chronic Infections

Pf bacteriophage are temperate phages that infect the bacterium Pseudomonas aeruginosa, a major cause of chronic lung infections in cystic fibrosis (CF) and other settings. Pf and other temperate phages have evolved complex, mutualistic relationships with their bacterial hosts that impact both bacterial phenotypes and chronic infection. We and others have reported that Pf phages are a virulence factor that promote the pathogenesis of P. aeruginosa infections in animal models and are associated with worse skin and lung infections in humans. Here we review the biology of Pf phage and what is known about its contributions to pathogenesis and clinical disease. First, we review the structure, genetics, and epidemiology of Pf phage. Next, we address the diverse and surprising ways that Pf phages contribute to P. aeruginosa phenotypes including effects on biofilm formation, antibiotic resistance, and motility. Then, we cover data indicating that Pf phages suppress mammalian immunity at sites of bacterial infection. Finally, we discuss recent literature implicating Pf in chronic P. aeruginosa infections in CF and other settings. Together, these reports suggest that Pf bacteriophage have direct effects on P. aeruginosa infections and that temperate phages are an exciting frontier in microbiology, immunology, and human health.

The Dfam database of repetitive DNA families

Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). The initial release of Dfam, featured in the 2013 NAR Database Issue, contained 1143 families of repetitive elements found in humans, and was used to produce more than 100 Mb of additional annotation of TE-derived regions in the human genome, with improved speed. Here, we describe recent advances, most notably expansion to 4150 total families including a comprehensive set of known repeat families from four new organisms (mouse, zebrafish, fly and nematode). We describe improvements to coverage, and to our methods for identifying and reducing false annotation. We also describe updates to the website interface. The Dfam website has moved to http://dfam.org. Seed alignments, profile HMMs, hit lists and other underlying data are available for download.

A call for benchmarking transposable element annotation methods

DNA derived from transposable elements (TEs) constitutes large parts of the genomes of complex eukaryotes, with major impacts not only on genomic research but also on how organisms evolve and function. Although a variety of methods and tools have been developed to detect and annotate TEs, there are as yet no standard benchmarks-that is, no standard way to measure or compare their accuracy. This lack of accuracy assessment calls into question conclusions from a wide range of research that depends explicitly or implicitly on TE annotation. In the absence of standard benchmarks, toolmakers are impeded in improving their tools, annotators cannot properly assess which tools might best suit their needs, and downstream researchers cannot judge how accuracy limitations might impact their studies. We therefore propose that the TE research community create and adopt standard TE annotation benchmarks, and we call for other researchers to join the authors in making this long-overdue effort a success.

HMMER web server: 2015 update

The HMMER website, available at http://www.ebi.ac.uk/Tools/hmmer/, provides access to the protein homology search algorithms found in the HMMER software suite. Since the first release of the website in 2011, the search repertoire has been expanded to include the iterative search algorithm, jackhmmer. The continued growth of the target sequence databases means that traditional tabular representations of significant sequence hits can be overwhelming to the user. Consequently, additional ways of presenting homology search results have been developed, allowing them to be summarised according to taxonomic distribution or domain architecture. The taxonomy and domain architecture representations can be used in combination to filter the results according to the needs of a user. Searches can also be restricted prior to submission using a new taxonomic filter, which not only ensures that the results are specific to the requested taxonomic group, but also improves search performance. The repertoire of profile hidden Markov model libraries, which are used for annotation of query sequences with protein families and domains, has been expanded to include the libraries from CATH-Gene3D, PIRSF, Superfamily and TIGRFAMs. Finally, we discuss the relocation of the HMMER webserver to the European Bioinformatics Institute and the potential impact that this will have.

nhmmer: DNA homology search with profile HMMs

SUMMARY

Sequence database searches are an essential part of molecular biology, providing information about the function and evolutionary history of proteins, RNA molecules and DNA sequence elements. We present a tool for DNA/DNA sequence comparison that is built on the HMMER framework, which applies probabilistic inference methods based on hidden Markov models to the problem of homology search. This tool, called nhmmer, enables improved detection of remote DNA homologs, and has been used in combination with Dfam and RepeatMasker to improve annotation of transposable elements in the human genome.

AVAILABILITY

nhmmer is a part of the new HMMER3.1 release. Source code and documentation can be downloaded from http://hmmer.org. HMMER3.1 is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X.

nhmmer: DNA homology search with profile HMMs

Summary: Sequence database searches are an essential part of molecular biology, providing information about the function and evolutionary history of proteins, RNA molecules and DNA sequence elements. We present a tool for DNA/DNA sequence comparison that is built on the HMMER framework, which applies probabilistic inference methods based on hidden Markov models to the problem of homology search. This tool, called nhmmer, enables improved detection of remote DNA homologs, and has been used in combination with Dfam and RepeatMasker to improve annotation of transposable elements in the human genome.

Availability: nhmmer is a part of the new HMMER3.1 release. Source code and documentation can be downloaded from http://hmmer.org. HMMER3.1 is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X.

Contact:wheelert@janelia.hhmi.org

Dfam: a database of repetitive DNA based on profile hidden Markov models

We present a database of repetitive DNA elements, called Dfam (http://dfam.janelia.org). Many genomes contain a large fraction of repetitive DNA, much of which is made up of remnants of transposable elements (TEs). Accurate annotation of TEs enables research into their biology and can shed light on the evolutionary processes that shape genomes. Identification and masking of TEs can also greatly simplify many downstream genome annotation and sequence analysis tasks. The commonly used TE annotation tools RepeatMasker and Censor depend on sequence homology search tools such as cross_match and BLAST variants, as well as Repbase, a collection of known TE families each represented by a single consensus sequence. Dfam contains entries corresponding to all Repbase TE entries for which instances have been found in the human genome. Each Dfam entry is represented by a profile hidden Markov model, built from alignments generated using RepeatMasker and Repbase. When used in conjunction with the hidden Markov model search tool nhmmer, Dfam produces a 2.9% increase in coverage over consensus sequence search methods on a large human benchmark, while maintaining low false discovery rates, and coverage of the full human genome is 54.5%. The website provides a collection of tools and data views to support improved TE curation and annotation efforts. Dfam is also available for download in flat file format or in the form of MySQL table dumps.

Complete nucleomorph genome sequence of the nonphotosynthetic alga Cryptomonas paramecium reveals a core nucleomorph gene set

Nucleomorphs are the remnant nuclei of algal endosymbionts that were engulfed by nonphotosynthetic host eukaryotes. These peculiar organelles are found in cryptomonad and chlorarachniophyte algae, where they evolved from red and green algal endosymbionts, respectively. Despite their independent origins, cryptomonad and chlorarachniophyte nucleomorph genomes are similar in size and structure: they are both <1 million base pairs in size (the smallest nuclear genomes known), comprised three chromosomes, and possess subtelomeric ribosomal DNA operons. Here, we report the complete sequence of one of the smallest cryptomonad nucleomorph genomes known, that of the secondarily nonphotosynthetic cryptomonad Cryptomonas paramecium. The genome is 486 kbp in size and contains 518 predicted genes, 466 of which are protein coding. Although C. paramecium lacks photosynthetic ability, its nucleomorph genome still encodes 18 plastid-associated proteins. More than 90% of the “conserved” protein genes in C. paramecium (i.e., those with clear homologs in other eukaryotes) are also present in the nucleomorph genomes of the cryptomonads Guillardia theta and Hemiselmis andersenii. In contrast, 143 of 466 predicted C. paramecium proteins (30.7%) showed no obvious similarity to proteins encoded in any other genome, including G. theta and H. andersenii. Significantly, however, many of these “nucleomorph ORFans” are conserved in position and size between the three genomes, suggesting that they are in fact homologous to one another. Finally, our analyses reveal an unexpected degree of overlap in the genes present in the independently evolved chlorarachniophyte and cryptomonad nucleomorph genomes: ∼80% of a set of 120 conserved nucleomorph genes in the chlorarachniophyte Bigelowiella natans were also present in all three cryptomonad nucleomorph genomes. This result suggests that similar reductive processes have taken place in unrelated lineages of nucleomorph-containing algae.

Extraneous bodily movements and irrelevant vocalizations by dyslexic and non-dyslexic boys during calculation tasks

Thirty dyslexic boys, aged between 9 and 15 years, and 30 age-matched controls were tested on a series of sums involving division, subtraction and addition. During the testing a record was kept of any bodily movements or verbal utterances (vocalizations) irrelevant to the task in hand. It was found that the dyslexics produced many more extraneous bodily movements and many more irrelevant vocalizations than did the controls. Possible reasons for these findings are tentatively suggested.

Multiple alignment by aligning alignments

MOTIVATION

Multiple sequence alignment is a fundamental task in bioinformatics. Current tools typically form an initial alignment by merging subalignments, and then polish this alignment by repeated splitting and merging of subalignments to obtain an improved final alignment. In general this form-and-polish strategy consists of several stages, and a profusion of methods have been tried at every stage. We carefully investigate: (1) how to utilize a new algorithm for aligning alignments that optimally solves the common subproblem of merging subalignments, and (2) what is the best choice of method for each stage to obtain the highest quality alignment.

RESULTS

We study six stages in the form-and-polish strategy for multiple alignment: parameter choice, distance estimation, merge-tree construction, sequence-pair weighting, alignment merging, and polishing. For each stage, we consider novel approaches as well as standard ones. Interestingly, the greatest gains in alignment quality come from (i) estimating distances by a new approach using normalized alignment costs, and (ii) polishing by a new approach using 3-cuts. Experiments with a parameter-value oracle suggest large gains in quality may be possible through an input-dependent choice of alignment parameters, and we present a promising approach for building such an oracle. Combining the best approaches to each stage yields a new tool we call Opal that on benchmark alignments matches the quality of the top tools, without employing alignment consistency or hydrophobic gap penalties.

AVAILABILITY

Opal, a multiple alignment tool that implements the best methods in our study, is freely available at http://opal.cs.arizona.edu.

Adaptive protein evolution and regulatory divergence in Drosophila

Two recent studies demonstrated a positive correlation between divergence in gene expression and protein sequence in Drosophila. This correlation could be driven by positive selection or variation in functional constraint. To distinguish between these alternatives, we compared patterns of molecular evolution for 1,862 genes with two previously reported estimates of expression divergence in Drosophila. We found a slight negative trend (nonsignificant) between positive selection on protein sequence and divergence in expression levels between Drosophila melanogaster and Drosophila simulans. Conversely, shifts in expression patterns during Drosophila development showed a positive association with adaptive protein evolution, though as before the relationship was weak and not significant. Overall, we found no strong evidence for an increase in the incidence of positive selection on protein-coding regions in genes with divergent expression in Drosophila, suggesting that the previously reported positive association between protein and regulatory divergence primarily reflects variation in functional constraint.

Transposable element orientation bias in the Drosophila melanogaster genome

Nonrandom distributions of transposable elements can be generated by a variety of genomic features. Using the full D. melanogaster genome as a model, we characterize the orientations of different classes of transposable elements in relation to the directionality of genes. DNA-mediated transposable elements are more likely to be in the same orientation as neighboring genes when they occur in the nontranscribed region's that flank genes. However, RNA-mediated transposable elements located in an intron are more often oriented in the direction opposite to that of the host gene. These orientation biases are strongest for genes with highly biased codon usage, probably reflecting the ability of such loci to respond to weak positive or negative selection. The leading hypothesis for selection against transposable elements in the coding orientation proposes that transcription termination poly(A) signal motifs within retroelements interfere with normal gene transcription. However, after accounting for differences in base composition between the strands, we find no evidence for global selection against spurious transcription termination signals in introns. We therefore conclude that premature termination of host gene transcription due to the presence of poly(A) signal motifs in retroelements might only partially explain strand-specific detrimental effects in the D. melanogaster genome.

Evaluating and improving cDNA sequence quality with cQC

SUMMARY

Errors are prevalent in cDNA sequences but the extent to which sequence collections differ in frequencies and types of errors has not been investigated systematically. cDNA quality control, or cQC, was developed to evaluate the quality of cDNA sequence collections and to revise those sequences that differ from a higher quality genomic sequence. After removing rRNA, vector, bacterial insertion sequence and chimeric cDNA contaminants, small-scale nucleotide discrepancies were found in 51% of cDNA sequences from one Arabidopsis cDNA collection, 89% from a second Arabidopsis collection and 75% from a rice collection. These errors created premature termination codons in 4 and 42% of cDNA sequences in the respective Arabidopsis collections and in 7% of the rice cDNA sequences.

Stimulation of cardiac glucose transport by inhibitors of oxidative phosphorylation

Previously we showed that hypoxia in heart stimulates glucose transport via translocation of glucose transporters from intracellular membranes to the plasma membrane. We later showed that rotenone, an inhibitor of oxidative phosphorylation, also decreased intracellular transporters. Here, using another membrane fractionation technique, we show that rotenone increases plasma membrane transporters, and that another respiratory chain inhibitor, azide, acts similarly. Thus, they likely activate the same signaling pathway as hypoxia. Genistein, a tyrosine kinase inhibitor, inhibited insulin- and azide-stimulated 3-O-methylglucose transport similarly in cardiac myocytes. It also increased glucose transporters in the plasma membranes of perfused hearts even though it inhibited glucose uptake, suggesting effects on membrane trafficking. Another tyrosine kinase inhibitor, lavendustin A, and the cyclic nucleotide-dependent protein kinase inhibitors H-8 and H-7 had little effect on basal or azide-stimulated transport. Polymyxin B was a weak inhibitor of basal, insulin-stimulated, and azide-stimulated transport. A nitric oxide donor and a nitric oxide synthase inhibitor had no effect on basal and azide-stimulated transport. The results indicate that tyrosine kinases; protein kinases A, G, and C; and nitric oxide are not involved in the hypoxic activation of cardiac glucose transport.

Characterization of glucose transport activity reconstituted from heart and other tissues

We examined several aspects of glucose transport reconstituted in liposomes, with emphasis on transporters of rat heart (mostly GLUT4) compared to those of human erythrocytes (GLUT1), and on effects of agents that modulate transport in intact cells. Several types of samples gave higher reconstituted activity using liposomes of egg lipids rather than soybean lipids. Diacylglycerol, proposed to activate transporters directly as part of the mechanism of insulin action, increased the intrinsic activity of heart transporters by only 25%, but increased the size of the reconstituted liposomes by 90%. The dipeptide Cbz-Gly-Phe-NH2 inhibited GLUT4 with a Ki of 0.2 mM, compared to 2.5 mM for GLUT1, which explains its preferential inhibition of insulin-stimulated glucose transport in adipocytes. Verapamil, which inhibits insulin- and hypoxia-stimulated glucose transport in muscle, had no effect on reconstituted transporters. Heart transporters had a higher Km for glucose uptake (13.4) than did GLUT1 (1.6 mM), in agreement with a recent study of GLUT1 and GLUT4 expressed in yeast and reconstituted in liposomes. Transporters reconstituted from heart and adipocytes were 40-70% inactivated by external trypsin, suggesting the presence of trypsin-sensitive sites on the cytoplasmic domain of GLUT4. NaCl and KCl both reduced reconstituted transport activity, but KCl had a much smaller effect on the size of the liposomes.

Pentobarbital sedation for patients in the pediatric intensive care unit

We present our experience with pentobarbital for sedation during mechanical ventilation in six infants when fentanyl and midazolam failed. The patients ranged in age from 2 to 17 months and in weight from 3.0 to 11.4 kg. Before the switch to pentobarbital, the maximum doses of fentanyl ranged from 7 to 13 micrograms/kg/hr and the midazolam infusions, from 0.2 to 0.4 mg/kg/hr. Pentobarbital was administered as a bolus dose followed by a continuous infusion. The hourly infusion rates ranged from 1 to 4 mg/kg. Adequate sedation was achieved in all six patients. In the four patients who required neuromuscular blocking agents, their use was discontinued after pentobarbital was given. The antihypertensive agents (diazoxide and nitroprusside) required by the two patients receiving extracorporeal membrane oxygenation were also discontinued after pentobarbital administration. Although we continue to use fentanyl and benzodiazepines as first-line drugs for sedation, pentobarbital may be an effective alternative when these agents fail.

Translocation of two glucose transporters in heart: effects of rotenone, uncouplers, workload, palmitate, insulin and anoxia

Our previous studies on the acute regulation of glucose transport in perfused rat hearts were extended to explore further the mechanism of regulation by anoxia; to test the effects of palmitate, a transport inhibitor; and to compare the translocation of two glucose transporter isoforms (GLUT1 and GLUT4). Following heart perfusions under various conditions, glucose transporters in intracellular membranes were quantitated by reconstitution of transport activity and by Western blotting. Rotenone stimulated glucose uptake and decreased the intracellular contents of glucose transporters. This indicates that it activates glucose transport via net outward translocation, similarly to anoxia. However, two uncouplers of oxidative phosphorylation produced little or no effect. Increased workload (which stimulates glucose transport) reduced the intracellular contents of transporters, while palmitate increased the contents, indicating that these factors cause net translocation from or to the intracellular pool, respectively. Relative changes in GLUT1 were similar to those in GLUT4 for most factors tested. A plot of changes in total intracellular transporter content vs. changes in glucose uptake was roughly linear, with a slope of -0.18. This indicates that translocation accounts for most of the changes in glucose transport, and the basal pool of intracellular transporters is five times as large as the plasma membrane pool.

Noninvasive monitoring of end-tidal CO2 via nasal cannulas in spontaneously breathing children during the perioperative period

OBJECTIVE

To determine the correlation between end-tidal CO2 and PaCO2 values measured via nasal cannulas in spontaneously breathing children during the perioperative period.

DESIGN

Prospective evaluation.

SETTING

Pediatric intensive/intermediate care unit in a tertiary care referral center.

PATIENTS

Thirty postoperative surgical and trauma patients aged < or = 18 yrs (average age 7.8 yrs [range 6 months to 16 yrs] and average weight 28.3 kg (range 8.5 to 69).

MEASUREMENTS AND MAIN RESULTS

Spontaneously breathing, nonintubated patients with an arterial cannula in place were selected for study. End-tidal CO2 was sampled from nasal cannulas by a sidestream aspirator and was estimated by infrared spectroscopy. The difference between PaCO2 and end-tidal CO2 was compared using linear regression analysis. A total of 55 blood gas measurements were obtained on the 30 patients. The PaCO2 to end-tidal CO2 gradient was < or = 4 torr in 54 of the 55 samples. The mean PaCO2 was 39.5 +/- 3.3 torr (5.27 +/- 0.44 kPa) with a mean end-tidal CO2 value of 39.7 +/- 3.8 torr (5.29 +/- 0.51 kPa). Linear regression analysis of arterial vs. end-tidal CO2 yielded a slope of 0.992 and p = .0001.

CONCLUSIONS

End-tidal CO2 measurement by infrared spectroscopy provided an accurate estimation of PaCO2 in this patient population. Its use may limit the need for invasive monitoring and/or repeated arterial blood gas analysis.

Complications of autotransfusion with salvaged blood

As a means of limiting homologous transfusions, many centers are using autotransfusion devices during the postoperative period. Although their use may limit the risks associated with homologous blood administration, various adverse effects have been reported including sepsis, disseminated intravascular coagulation, and renal insufficiency. The authors present the case of a 9-year-old girl who developed acute cardiorespiratory dysfunction after reinfusion of salvaged blood. The use of autotransfusion devices and the probable mechanisms responsible for adverse effects are discussed.

Accelerated net efflux of 3-O-methylglucose from rat adipocytes: a reevaluation

In a study of 3-O-methylglucose transport in insulin-stimulated rat adipocytes (catalyzed primarily by the GLUT4 isoform), it was reported that at 37 degrees C the Km and Vmax were 2.8-fold higher for net efflux than for equilibrium exchange (Vinten, J. (1984) Biochim. Biophys. Acta 772, 244-250). Because of its implications for the relative sizes of steps in the transport cycle, we reinvestigated this phenomenon. Accelerated net efflux was apparent when the extracellular methylglucose was diluted 26-fold but not when it was diluted 11-fold. When analyzed according to the one-site alternating conformation model, the data indicate about a 1.7-fold higher Vmax for efflux than for exchange, only about 40% of the difference reported previously. Together with other results in the literature, the accelerated net flux indicates that the conformational change of the loaded transporter from its outward-facing to its inward-facing form is likely the slowest step in the transport cycle, in contrast to the case for GLUT1. Experiments at 25 degrees C indicate a lower degree of accelerated net flux than at 37 degrees C. This is consistent with the above conformational change being the step with the lowest activation energy, as for GLUT1.

ATP does not regulate the reconstituted glucose transporter

ATP has been reported to affect glucose transport in human erythrocytes and resealed erythrocyte ghosts [Jacquez, J. A. (1983) Biochim. Biophys. Acta 727, 367-378; Jensen, M. R., & Brahm, J. (1987) Biochim. Biophys. Acta 900, 282-290]. In more detailed studies, effects of micromolar levels of ATP on transport in ghosts and inside-out vesicles, and on the fluorescence of ghosts and the purified glucose transporter [Carruthers, A. (1986) Biochemistry 25, 3592-3602; Hebert, D. N., & Carruthers, A. (1986) J. Biol. Chem. 261, 10093-10099; Carruthers, A. (1986) J. Biol. Chem. 261, 11028-11037], have been interpreted as supporting a model in which ATP regulates the catalytic properties of the transporter. Both allosteric and covalent effects of ATP were proposed; among the allosteric effects was a 60% reduction in the Km for zero-trans uptake. In order to test whether allosteric ATP regulation of the transporter occurs, we reconstituted glucose transport activity into liposomes using erythrocyte membranes without detergent treatment. The effects of ATP, present either outside, inside, or both inside and outside the liposomes, on the transport activity were examined. Effects of ATP on trypsin-treated liposomes, which have only a single orientation of active transporters, were also tested. While the model predicts activation by ATP, only inhibition was observed. This was significant only at millimolar concentrations of ATP, in contrast to the previously reported effects at micromolar levels, and was primarily on the extracellular surface of the transporter. In addition, the ATP effects on reconstituted transport were nonspecific, with similar effects produced by tripolyphosphate.(ABSTRACT TRUNCATED AT 250 WORDS)

Effects of three proposed inhibitors of adipocyte glucose transport on the reconstituted transporter

Three compounds which inhibit glucose transport in rat adipocytes have been proposed to act directly on the glucose transporter protein. We tested these proposals by examining the effects of the compounds on the stereospecific glucose uptake catalyzed by adipocyte membrane proteins after reconstitution into liposomes. Effects on the transport activity reconstituted from human erythrocyte membranes were also examined. Glucose 6-phosphate, which was suggested to inhibit the transporter noncompetitively (Foley, J.E. and Huecksteadt, T.P. (1984) Biochim. Biophys. Acta 805, 313-316), had no effect on either type of reconstituted transporter, even when present at 5 mM on both sides of the liposomal membranes. Thus, it is unlikely to act directly on the transporter. The metalloendoproteinase substrate dipeptide Cbz-Gly-Phe-NH2, which inhibited insulin-stimulated but not basal glucose uptake in adipocytes (Aiello, L.P., Wessling-Resnick, M. and Pilch, P.F. (1986) Biochemistry 25, 3944-3950), inhibited the reconstituted erythrocyte transporter noncompetitively with a Ki of 1.5-2 mM. The inhibition of the erythrocyte transporter was identical in liposomes of soybean and egg lipid. Transport reconstituted using adipocyte membrane fractions was also inhibited by the dipeptide, with the activity from basal microsomes more sensitive than that from insulin-stimulated plasma membranes. These results indicate that the dipeptide interacts directly with the transporter, and may be a potentially useful probe for changes in transporter structure accompanying insulin action. Phenylarsine oxide, which was suggested to act directly on the adipocyte transporter (Douen, A.G., and Jones, M.N. (1988) Biochim. Biophys. Acta 968, 109-118), produced only slight (about 10%) inhibition of the reconstituted adipocyte and erythrocyte transporters, even when present at 100-200 microM and after 30 min of pretreatment. These results suggest that the major actions of phenylarsine oxide observed in adipocytes are not direct effects on the transporter, but rather effects on the pathways by which insulin regulates glucose transport activity (Frost, S.C. and Lane, M.D. (1985) J. Biol. Chem. 260, 2646-2652).

Translocation of glucose transporters in response to anoxia in heart

We tested whether translocation of glucose transporters between subcellular membrane fractions is involved in the stimulation of glucose transport by anoxia by perfusing rat hearts in the presence or absence of oxygen. The hearts were then fractionated by a modification of the procedures of Watanabe, et al. (Watanabe, T., Smith, M. M., Robinson, F. W., and Kono, T. (1984) J. Biol. Chem. 259, 13117-13122), who previously demonstrated translocation in response to insulin in heart, to give plasma membrane and high-speed pellet fractions. The contents of glucose transporters in the two fractions were determined by reconstitution of transport activity, D-glucose-reversible binding of cytochalasin B, and labeling with antibodies against the erythrocyte transporter. The heart transporter was also recognized by antibodies against the COOH-terminal peptide of the glucose transporter. All three types of assays revealed a decrease (20-30%) in the high-speed pellet fraction and an increase (20-70%) in the plasma membranes in response to anoxia. Treatment of hearts with insulin produced a similar extent of translocation and a similar stimulation (about 2-fold) of glucose uptake, indicating that translocation plays a role of similar importance in the stimulation of transport by both of these effectors.

Infinite-cis kinetics support the carrier model for erythrocyte glucose transport

It has been claimed that the Km for infinite-cis uptake of glucose in human erythrocytes is so low that the carrier model for transport must be rejected. We redetermined this parameter for three experimental conditions and found instead that the Km values were in good agreement with the model. For each of a variety of cis glucose concentrations, cells were preequilibrated with various concentrations of glucose, and the apparent Km was determined as the intracellular concentration reducing the initial rate of net uptake by half. The dependence of the apparent Km values on the cis glucose was as predicted by the carrier model; the infinite-cis Km was determined from both this concentration dependence and the extrapolated value at infinite cis glucose. The resulting values were 15 mM for fresh blood at 0 degrees C, 39 mM for outdated blood at 0 degrees C, and 11 mM for outdated blood at 25 degrees C. Previous measurements of the Km at room temperature yielded values of 2-3 mM. These earlier studies used a time course procedure that indicated rapid changes in rates during the initial 10 s of uptake but did not directly measure such changes. We examined the uptake of 60 mM glucose at 20 degrees C into cells containing 0 and 5 mM glucose; rapid changes in rates were not observed in the first few seconds, and the time courses were more consistent with our higher Km values. Our new values, together with other initial rate measurements in the literature, support the adequacy of the carrier model to account for the kinetics of glucose transport in human erythrocytes.

Reconstitution of the glucose transporter from rat skeletal muscle

As a step in the purification and characterization of the glucose transporter from rat skeletal muscle, we have reconstituted glucose transport activity in liposomes. Plasma membranes were prepared from skeletal muscle which display D-glucose reversible binding of cytochalasin B (10 pmol sites/mg protein; KD = 0.3 microM). Older rats gave a slightly lower specific activity and much lower yield of sites per g muscle than young rats. Glucose transport activity was reconstituted into liposomes by the freeze-thaw procedure using either plasma membranes directly or cholate-extracted membrane proteins; the latter gave a 50% higher specific activity. The reconstituted transport activity was stereospecific, saturable, and inhibited by cytochalasin B, phloretin, and mercuric chloride. The optimum cholate concentration for extraction and reconstitution of transport activity was about 1.5%, and the highest specific activity of reconstituted transport was seen only at low ratios of protein to lipid in the reconstitution. Chromatography on agarose lentil lectin and agarose ethanethiol doubled both the specific activity of reconstituted transport and the fraction of glucose uptake which was stereospecific. In all of these respects the results were similar to our results with the bovine heart transporter (T. J. Wheeler and M. A. Hauck, Biochim. Biophys. Acta 818, 171-182 (1985)). Our findings suggest that further purification procedures developed for the heart transporter may be applicable to the skeletal muscle transporter as well.