Impedance-based detection of DNA sequences using a silicon transducer with PNA as the probe layer

RAmbler resolves complex repeats in human Chromosomes 8, 19, and X

Repetitive regions in eukaryotic genomes often contain important functional or regulatory elements. Despite significant algorithmic and technological advancements in genome sequencing and assembly over the past three decades, modern de novo assemblers still struggle to accurately reconstruct highly repetitive regions. In this work, we introduce RAmbler (Repeat Assembler), a reference-guided assembler specialized for the assembly of complex repetitive regions exclusively from Pacific Biosciences (PacBio) HiFi reads. RAmbler (1) identifies repetitive regions by detecting unusually high coverage regions after mapping HiFi reads to the draft genome assembly, (2) finds single-copy k-mers from the HiFi reads, (i.e., k-mers that are expected to occur only once in the genome), (3) uses the relative location of single-copy k-mers to barcode each HiFi read, (4) clusters HiFi reads based on their shared barcodes, (5) generates contigs by assembling the reads in each cluster, and (6) generates a consensus assembly from the overlap graph of the assembled contigs. Here, we show that RAmbler can reconstruct human centromeres and other complex repeats to a quality comparable to the manually curated Telomere-to-Telomere human genome assembly. Across more than 250 synthetic data sets, RAmbler outperforms hifiasm, LJA, HiCANU, and Verkko across various parameters such as repeat lengths, number of repeats, heterozygosity rates, and depth of sequencing.

Population dynamics of HIV drug resistance during treatment scale-up in Uganda: a population-based longitudinal study

Background

Clinical studies have reported rising pre-treatment HIV drug resistance during antiretroviral treatment (ART) scale-up in Africa, but representative data are limited. We estimated population-level drug resistance trends during ART expansion in Uganda.

Methods

We analyzed data from the population-based open Rakai Community Cohort Study conducted at agrarian, trading, and fishing communities in southern Uganda between 2012 and 2019. Consenting participants aged 15-49 were HIV tested and completed questionnaires. Persons living with HIV (PLHIV) provided samples for viral load quantification and virus deep-sequencing. Sequence data were used to predict resistance. Population prevalence of class-specific resistance and resistance-conferring substitutions were estimated using robust log-Poisson regression.

Findings

Data from 93,622 participant-visits, including 4,702 deep-sequencing measurements, showed that the prevalence of NNRTI resistance among pre-treatment viremic PLHIV doubled between 2012 and 2017 (PR:1.98, 95%CI:1.34-2.91), rising to 9.61% (7.27-12.7%). The overall population prevalence of pre-treatment viremic NNRTI and NRTI resistance among all participants decreased during the same period, reaching 0.25% (0.18% - 0.33%) and 0.05% (0.02% - 0.10%), respectively (p-values for trend = 0.00015, 0.002), coincident with increasing treatment coverage and viral suppression. By the final survey, population prevalence of resistance contributed by treatment-experienced PLHIV exceeded that from pre-treatment PLHIV, with NNRTI resistance at 0.54% (0.44%-0.66%) and NRTI resistance at 0.42% (0.33%-0.53%). Overall, NNRTI and NRTI resistance was predominantly attributable to rtK103N and rtM184V. While 10.52% (7.97%-13.87%) and 9.95% (6.41%-15.43%) of viremic pre-treatment and treatment-experienced PLHIV harbored the inT97A mutation, no major dolutegravir resistance mutations were observed.

Interpretation

Despite rising NNRTI resistance among pre-treatment PLHIV, overall population prevalence of pre-treatment resistance decreased due to treatment uptake. Most NNRTI and NRTI resistance is now contributed by treatment-experienced PLHIV. The high prevalence of mutations conferring resistance to components of current first-line ART regimens among PLHIV with viremia is potentially concerning.

Identifying genes within pathways in unannotated genomes with PaGeSearch

In biological research, the identification and comparison of genes within specific pathways across the genomes of various species are invaluable. However, annotating the entire genome is resource intensive, and sequence similarity searches often yield results that are not actually genes. To address these limitations, we introduce Pathway Gene Search (PaGeSearch), a tool designed to identify genes from predefined lists, especially those in specific pathways, within genomes. The tool uses an initial sequence similarity search to identify relevant genomic regions, followed by targeted gene prediction and neural network-based result filtering. PaGeSearch suggests the regions that are most likely the orthologs of the genes in the query and is designed to be applicable for species within five classes: mammals, fish, birds, eudicotyledons, and Liliopsida. Compared with GeMoMa and miniprot, PaGeSearch generally outperforms in terms of sensitivity and positive predictive value, as well as negative predictive value. Also, the exon coverage of gene models from PaGeSearch is higher compared with those in GeMoMa and miniprot. Although its performance shows increased variability when applied to actual biological pathways, it nonetheless maintains an acceptable level of accuracy. Evaluating PaGeSearch across different assembly levels, chromosome, scaffold, and contig shows minimal variation in outcomes, indicating that PaGeSearch is resilient to variations in assembly quality.

Structures of Native Doublet Microtubules from Trichomonas vaginalis Reveal Parasite-Specific Proteins as Potential Drug Targets

Doublet microtubules (DMTs) are flagellar components required for the protist Trichomonas vaginalis ( Tv ) to swim through the human genitourinary tract to cause trichomoniasis, the most common non-viral sexually transmitted disease. Lack of DMT structures has prevented structure-guided drug design to manage Tv infection. Here, we determined the cryo-EM structure of native Tv- DMTs, identifying 29 unique proteins, including 18 microtubule inner proteins and 9 microtubule outer proteins. While the A-tubule is simplistic compared to DMTs of other organisms, the B-tubule features specialized, parasite-specific proteins, like Tv FAP40 and Tv FAP35 that form filaments near the inner and outer junctions, respectively, to stabilize DMTs and enable Tv locomotion. Notably, a small molecule, assigned as IP6, is coordinated within a pocket of Tv FAP40 and has characteristics of a drug molecule. This first atomic model of the Tv -DMT highlights the diversity of eukaryotic motility machinery and provides a structural framework to inform the rational design of therapeutics.

ProEnd: A Comprehensive Database for Identifying HbYX Motif-Containing Proteins Across the Tree of Life

The proteasome plays a crucial role in cellular homeostasis by degrading misfolded, damaged, or unnecessary proteins. Understanding the regulatory mechanisms of proteasome activity is vital, particularly the interaction with activators containing the hydrophobic-tyrosine-any amino acid (HbYX) motif. Here, we present ProEnd, a comprehensive database designed to identify and catalog HbYX motif-containing proteins across the tree of life. Using a simple bioinformatics pipeline, we analyzed approximately 73 million proteins from 22,000 reference proteomes in the UniProt/SwissProt database. Our findings reveal the widespread presence of HbYX motifs in diverse organisms, highlighting their evolutionary conservation and functional significance. Notably, we observed an interesting prevalence of these motifs in viral proteomes, suggesting strategic interactions with the host proteasome. As validation two novel HbYX proteins found in this database were tested and found to directly interact with the proteasome. ProEnd's extensive dataset and user-friendly interface enable researchers to explore the potential proteasomal regulator landscape, generating new hypotheses to advance proteasome biology. This resource is set to facilitate the discovery of novel therapeutic targets, enhancing our approach to treating diseases such as neurodegenerative disorders and cancer. Link: http://proend.org/.

Reduced PaxillinB localization to cell-substrate adhesions promotes cell migration in Dictyostelium

Many cells adhere to extracellular matrix for efficient cell migration. This adhesion is mediated by focal adhesions, a protein complex linking the extracellular matrix to the intracellular cytoskeleton. Focal adhesions have been studied extensively in mesenchymal cells, but recent research in physiological contexts and amoeboid cells suggest focal adhesion regulation differs from the mesenchymal focal adhesion paradigm. We used Dictyostelium discoideum to uncover new mechanisms of focal adhesion regulation, as Dictyostelium are amoeboid cells that form focal adhesion-like structures for migration. We show that PaxillinB, the Dictyostelium homologue of Paxillin, localizes to dynamic focal adhesion-like structures during Dictyostelium migration. Unexpectedly, reduced PaxillinB recruitment to these structures increases Dictyostelium cell migration. Quantitative analysis of focal adhesion size and dynamics show that lack of PaxillinB recruitment to focal adhesions does not alter focal adhesion size, but rather increases focal adhesion turnover. These findings are in direct contrast to Paxillin function at focal adhesions during mesenchymal migration, challenging the established focal adhesion model.

GO2Sum: Generating Human Readable Functional Summary of Proteins from GO Terms

Understanding the biological functions of proteins is of fundamental importance in modern biology. To represent function of proteins, Gene Ontology (GO), a controlled vocabulary, is frequently used, because it is easy to handle by computer programs avoiding open-ended text interpretation. Particularly, the majority of current protein function prediction methods rely on GO terms. However, the extensive list of GO terms that describe a protein function can pose challenges for biologists when it comes to interpretation. In response to this issue, we developed GO2Sum (Gene Ontology terms Summarizer), a model that takes a set of GO terms as input and generates a human-readable summary using the T5 large language model. GO2Sum was developed by fine-tuning T5 on GO term assignments and free-text function descriptions for UniProt entries, enabling it to recreate function descriptions by concatenating GO term descriptions. Our results demonstrated that GO2Sum significantly outperforms the original T5 model that was trained on the entire web corpus in generating Function, Subunit Structure, and Pathway paragraphs for UniProt entries.

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic

Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Wholesale Seafood Market, the site with the most reported wildlife vendors in the city of Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected in the Huanan market in early 2020. We demonstrate that the SARS-CoV-2 genetic diversity linked to this market is consistent with market emergence, and find increased SARS-CoV-2 positivity near and within a particular wildlife stall. We identify wildlife DNA in all SARS-CoV-2 positive samples from this stall. This includes species such as civets, bamboo rats, porcupines, hedgehogs, and one species, raccoon dogs, known to be capable of SARS-CoV-2 transmission. We also detect other animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them to those from other markets. This analysis provides the genetic basis for a short list of potential intermediate hosts of SARS-CoV-2 to prioritize for retrospective serological testing and viral sampling.

Digital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs

Fast and accurate detection of nucleic acids is key for pathogen identification. Methods for DNA detection generally rely on fluorescent or colorimetric readout. The development of label-free assays decreases costs and test complexity. We present a novel method combining a one-pot isothermal generation of DNA nanoballs with their detection by electrical impedance. We modified loop-mediated isothermal amplification by using compaction oligonucleotides that self-assemble the amplified target into nanoballs. Next, we use capillary-driven flow to passively pass these nanoballs through a microfluidic impedance cytometer, thus enabling a fully compact system with no moving parts. The movement of individual nanoballs is detected by a change in impedance providing a quantized readout. This approach is flexible for the detection of DNA/RNA of numerous targets (severe acute respiratory syndrome coronavirus 2, HIV, β-lactamase gene, etc.), and we anticipate that its integration into a standalone device would provide an inexpensive (<$5), sensitive (10 target copies), and rapid test (<1 hour).

Conserved molecular recognition by an intrinsically disordered region in the absence of sequence conservation

Intrinsically disordered regions (IDRs) are critical for cellular function, yet often appear to lack sequence conservation when assessed by multiple sequence alignments. This raises the question of if and how function can be encoded and preserved in these regions despite massive sequence variation. To address this question, we have applied coarse-grained molecular dynamics simulations to investigate non-specific RNA binding of coronavirus nucleocapsid proteins. Coronavirus nucleocapsid proteins consist of multiple interspersed disordered and folded domains that bind RNA. We focussed here on the first two domains of coronavirus nucleocapsid proteins, the disordered N-terminal domain (NTD) followed by the folded RNA binding domain (RBD). While the NTD is highly variable across evolution, the RBD is structurally conserved. This combination makes the NTD-RBD a convenient model system to explore the interplay between an IDR adjacent to a folded domain, and how changes in IDR sequence can influence molecular recognition of a partner. Our results reveal a surprising degree of sequence-specificity encoded by both the composition and the precise order of the amino acids in the NTD. The presence of an NTD can - depending on the sequence - either suppress or enhance RNA binding. Despite this sensitivity, large-scale variation in NTD sequences is possible while certain sequence features are retained. Consequently, a conformationally-conserved fuzzy RNA:protein complex is found across nucleocapsid protein orthologs, despite large-scale changes in both NTD sequence and RBD surface chemistry. Taken together, these insights shed light on the ability of disordered regions to preserve functional characteristics despite their sequence variability.

A Biodegradable Bioactive Glass-Based Hydration Sensor for Biomedical Applications

Monitoring changes in edema-associated intracranial pressure that complicates trauma or surgery would lead to improved outcomes. Implantable pressure sensors have been explored, but these sensors require post-surgical removal, leading to the risk of injury to brain tissue. The use of biodegradable implantable sensors would help to eliminate this risk. Here, we demonstrate a bioactive glass (BaG)-based hydration sensor. Fluorine (CaF₂) containing BaG (BaG-F) was produced by adding 5, 10 or 20 wt.% of CaF₂ to a BaG matrix using a melting manufacturing technique. The structure, morphology and electrical properties of the resulting constructs were evaluated to understand the physical and electrical behaviors of this BaG-based sensor. Synthesis process for the production of the BaG-F-based sensor was validated by assessing the structural and electrical properties. The structure was observed to be amorphous and dense, the porosity decreased and grain size increased with increasing CaF₂ content in the BaG matrix. We demonstrated that this BaG-F chemical composition is highly sensitive to hydration, and that the electrical sensitivity (resistive-capacitive) is induced by hydration and reversed by dehydration. These properties make BaG-F suitable for use as a humidity sensor to monitor brain edema and, consequently, provide an alert for increased intracranial pressure.

A second riboswitch class for the enzyme cofactor NAD. RNA (NEW YORK, N.Y.) 2021;27:99-105. [PMID: 33087526 PMCID: PMC7749635 DOI: 10.1261/rna.077891.120]

A bacterial noncoding RNA motif almost exclusively associated with pnuC genes was uncovered using comparative sequence analysis. Some PnuC proteins are known to transport nicotinamide riboside (NR), which is a component of the ubiquitous and abundant enzyme cofactor nicotinamide adenine dinucleotide (NAD⁺). Thus, we speculated that the newly found "pnuC motif" RNAs might function as aptamers for a novel class of NAD⁺-sensing riboswitches. RNA constructs that encompass the conserved nucleotides and secondary structure features that define the motif indeed selectively bind NAD⁺, nicotinamide mononucleotide (NMN), and NR. Mutations that disrupt strictly conserved nucleotides of the aptamer also disrupt ligand binding. These bioinformatic and biochemical findings indicate that pnuC motif RNAs are likely members of a second riboswitch class that regulates gene expression in response to NAD⁺ binding.

Ultra-sensitive biomolecular detection by external referencing optofluidic microbubble resonators

We propose an effective method for biomolecular detection based on an external referencing optofluidic microbubble resonator system (EROMBRS), which possesses good long-term stability and low noise. In this study, EROMBRSs were used for nonspecific detection of bovine serum albumin (BSA) molecules and specific detection of D-biotin molecules. Ultra-low practical detection limits of 1 fg/mL for nonspecific and specific biomolecular detection were achieved.

Control of Probe Density at DNA Biosensor Surfaces Using Poly(l-lysine) with Appended Reactive Groups

Biosensors and materials for biomedical applications generally require chemical functionalization to bestow their surfaces with desired properties, such as specific molecular recognition and antifouling properties. The use of modified poly(l-lysine) (PLL) polymers with appended oligo(ethylene glycol) (OEG) and thiol-reactive maleimide (Mal) moieties (PLL-OEG-Mal) offers control over the presentation of functional groups. These reactive groups can readily be conjugated to, for example, probes for DNA detection. Here we demonstrate the reliable conjugation of thiol-functionalized peptide nucleic acid (PNA) probes onto predeposited layers of PLL-OEG-Mal and the control over their surface density in the preceding synthetic step of the PLL modification with Mal groups. By monitoring the quartz crystal microbalance (QCM) frequency shifts of the binding of complementary DNA versus the density of Mal moieties grafted to the PLL, a linear relationship between probe density and PLL grafting density was found. Cyclic voltammetry experiments using Methylene Blue-functionalized DNA were performed to establish the absolute probe density values at the biosensor surfaces. These data provided a density of 1.2 × 10¹² probes per cm² per % of grafted Mal, thus confirming the validity of the density control in the synthetic PLL modification step without the need of further surface characterization.

Electrochemical impedance-based DNA sensor using pyrrolidinyl peptide nucleic acids for tuberculosis detection

A label-free electrochemical DNA sensor based on pyrrolidinyl peptide nucleic acid (acpcPNA)-immobilized on a paper-based analytical device (PAD) was developed. Unlike previous PNA-based electrochemical PAD (ePAD) sensors where the capture element was placed directly on the electrode, acpcPNA was covalently immobilized onto partially oxidized cellulose paper allowing regeneration by simple PAD replacement. As an example application, a sensor probe was designed for Mycobacterium tuberculosis (MTB) detection. The ePAD DNA sensor was used to determine a synthetic 15-base oligonucleotide of MTB by measuring the fractional change in the charge transfer resistance (R_ct) obtained from electrochemical impedance spectroscopy (EIS). The R_ct of [Fe(CN)₆]^3-/4- before and after hybridization with the target DNA could be clearly distinguished. Cyclic voltammetry (CV) was used to verify the EIS results, and showed an increase in peak potential splitting in a similar stepwise manner for each immobilization step. Under optimal conditions, a linear calibration curve in the range of 2-200 nM and the limit of detection 1.24 nM were measured. The acpcPNA probe exhibited very high selectivity for complementary oligonucleotides over single-base-mismatch, two-base-mismatch and non-complementary DNA targets due to the conformationally constrained structure of the acpcPNA. Moreover, the ePAD DNA sensor platform was successfully applied to detect PCR-amplified MTB DNA extracted from clinical samples. The proposed paper-based electrochemical DNA sensor has potential to be an alternative device for low-cost, simple, label-free, sensitive and selective DNA sensor.

DRNApred, fast sequence-based method that accurately predicts and discriminates DNA- and RNA-binding residues

Protein-DNA and protein-RNA interactions are part of many diverse and essential cellular functions and yet most of them remain to be discovered and characterized. Recent research shows that sequence-based predictors of DNA-binding residues accurately find these residues but also cross-predict many RNA-binding residues as DNA-binding, and vice versa. Most of these methods are also relatively slow, prohibiting applications on the whole-genome scale. We describe a novel sequence-based method, DRNApred, which accurately and in high-throughput predicts and discriminates between DNA- and RNA-binding residues. DRNApred was designed using a new dataset with both DNA- and RNA-binding proteins, regression that penalizes cross-predictions, and a novel two-layered architecture. DRNApred outperforms state-of-the-art predictors of DNA- or RNA-binding residues on a benchmark test dataset by substantially reducing the cross predictions and predicting arguably higher quality false positives that are located nearby the native binding residues. Moreover, it also more accurately predicts the DNA- and RNA-binding proteins. Application on the human proteome confirms that DRNApred reduces the cross predictions among the native nucleic acid binders. Also, novel putative DNA/RNA-binding proteins that it predicts share similar subcellular locations and residue charge profiles with the known native binding proteins. Webserver of DRNApred is freely available at http://biomine.cs.vcu.edu/servers/DRNApred/.

High-Performance Three-Dimensional Tubular Nanomembrane Sensor for DNA Detection

We report an ultrasensitive label-free DNA biosensor with fully on-chip integrated rolled-up nanomembrane electrodes. The hybridization of complementary DNA strands (avian influenza virus subtype H1N1) is selectively detected down to attomolar concentrations, an unprecedented level for miniaturized sensors without amplification. Impedimetric DNA detection with such a rolled-up biosensor shows 4 orders of magnitude sensitivity improvement over its planar counterpart. Furthermore, it is observed that the impedance response of the proposed device is contrary to the expected behavior due to its particular geometry. To further investigate this difference, a thorough model analysis of the measured signal and the electric field calculation is performed, revealing enhanced electron hopping/tunneling along the DNA chains due to an enriched electric field inside the tube. Likewise, conformational changes of DNA might also contribute to this effect. Accordingly, these highly integrated three-dimensional sensors provide a tool to study electrical properties of DNA under versatile experimental conditions and open a new avenue for novel biosensing applications (i.e., for protein, enzyme detection, or monitoring of cell behavior under in vivo like conditions).

CCProf: exploring conformational change profile of proteins

In many biological processes, proteins have important interactions with various molecules such as proteins, ions or ligands. Many proteins undergo conformational changes upon these interactions, where regions with large conformational changes are critical to the interactions. This work presents the CCProf platform, which provides conformational changes of entire proteins, named conformational change profile (CCP) in the context. CCProf aims to be a platform where users can study potential causes of novel conformational changes. It provides 10 biological features, including conformational change, potential binding target site, secondary structure, conservation, disorder propensity, hydropathy propensity, sequence domain, structural domain, phosphorylation site and catalytic site. All these information are integrated into a well-aligned view, so that researchers can capture important relevance between different biological features visually. The CCProf contains 986 187 protein structure pairs for 3123 proteins. In addition, CCProf provides a 3D view in which users can see the protein structures before and after conformational changes as well as binding targets that induce conformational changes. All information (e.g. CCP, binding targets and protein structures) shown in CCProf, including intermediate data are available for download to expedite further analyses.

Database URL: http://zoro.ee.ncku.edu.tw/ccprof/

Diazotroph community structure in the deep oxygen minimum zone of the Costa Rica Dome

Oxygen minimum zones (OMZs), characterized by depleted dissolved oxygen concentration in the intermediate depth of the water column, are predicted to expand under the influence of global warming. Recent studies in the Eastern Tropical South Pacific Ocean and Arabian Sea have reported that heterotrophic nitrogen fixation is active in the OMZs. In this study, we investigated the community structure of diazotrophs in the OMZ of the Costa Rica Dome (CRD) upwelling region in the Eastern Tropical North Pacific Ocean, using 454-pyrosequencing of nifH gene amplicons. Comparing diazotroph assemblages in different depth strata of the OMZ (200-1000 m in depth), we found a unique diazotroph community in the OMZ core, which was mainly dominated by methanotroph-like diazotrophs, suggesting a potential coupling of nitrogen cycle and methane assimilation. In addition, some OTUs revealed in this study, especially those belonging to the large sub-cluster Vibrio diazotrophicus, were reported to be abundant and expressing the nifH gene in other OMZs. Our results suggest that the unique hydrographic conditions in OMZs may support similar assemblages of diazotrophs, and heterotrophic nitrogen fixation could also be occurring in our studied region. Our study provides the first insight into the composition and distribution of putative diazotrophs in the CRD OMZ.

sORFs.org: a repository of small ORFs identified by ribosome profiling

With the advent of ribosome profiling, a next generation sequencing technique providing a "snap-shot'' of translated mRNA in a cell, many short open reading frames (sORFs) with ribosomal activity were identified. Follow-up studies revealed the existence of functional peptides, so-called micropeptides, translated from these 'sORFs', indicating a new class of bio-active peptides. Over the last few years, several micropeptides exhibiting important cellular functions were discovered. However, ribosome occupancy does not necessarily imply an actual function of the translated peptide, leading to the development of various tools assessing the coding potential of sORFs. Here, we introduce sORFs.org (http://www.sorfs.org), a novel database for sORFs identified using ribosome profiling. Starting from ribosome profiling, sORFs.org identifies sORFs, incorporates state-of-the-art tools and metrics and stores results in a public database. Two query interfaces are provided, a default one enabling quick lookup of sORFs and a BioMart interface providing advanced query and export possibilities. At present, sORFs.org harbors 263 354 sORFs that demonstrate ribosome occupancy, originating from three different cell lines: HCT116 (human), E14_mESC (mouse) and S2 (fruit fly). sORFs.org aims to provide an extensive sORFs database accessible to researchers with limited bioinformatics knowledge, thus enabling easy integration into personal projects.

SANSparallel: interactive homology search against Uniprot

Proteins evolve by mutations and natural selection. The network of sequence similarities is a rich source for mining homologous relationships that inform on protein structure and function. There are many servers available to browse the network of homology relationships but one has to wait up to a minute for results. The SANSparallel webserver provides protein sequence database searches with immediate response and professional alignment visualization by third-party software. The output is a list, pairwise alignment or stacked alignment of sequence-similar proteins from Uniprot, UniRef90/50, Swissprot or Protein Data Bank. The stacked alignments are viewed in Jalview or as sequence logos. The database search uses the suffix array neighborhood search (SANS) method, which has been re-implemented as a client-server, improved and parallelized. The method is extremely fast and as sensitive as BLAST above 50% sequence identity. Benchmarks show that the method is highly competitive compared to previously published fast database search programs: UBLAST, DIAMOND, LAST, LAMBDA, RAPSEARCH2 and BLAT. The web server can be accessed interactively or programmatically at http://ekhidna2.biocenter.helsinki.fi/cgi-bin/sans/sans.cgi. It can be used to make protein functional annotation pipelines more efficient, and it is useful in interactive exploration of the detailed evidence supporting the annotation of particular proteins of interest.

Label free detection of nucleic acids by modulating nanochannel surfaces

We develop surface-modified 100 nm silica nanofluidic channels that change in measured conductivity upon exposure to single- or double-stranded DNA. Through careful monitoring of both electromigrative and advective current in the channel, we can detect nanomolar concentrations of DNA. These results can be exploited for inexpensive, all-electronic DNA sensors.

FusoBase: an online Fusobacterium comparative genomic analysis platform

Fusobacterium are anaerobic gram-negative bacteria that have been associated with a wide spectrum of human infections and diseases. As the biology of Fusobacterium is still not well understood, comparative genomic analysis on members of this species will provide further insights on their taxonomy, phylogeny, pathogenicity and other information that may contribute to better management of infections and diseases. To facilitate the ongoing genomic research on Fusobacterium, a specialized database with easy-to-use analysis tools is necessary. Here we present FusoBase, an online database providing access to genome-wide annotated sequences of Fusobacterium strains as well as bioinformatics tools, to support the expanding scientific community. Using our custom-developed Pairwise Genome Comparison tool, we demonstrate how differences between two user-defined genomes and how insertion of putative prophages can be identified. In addition, Pathogenomics Profiling Tool is capable of clustering predicted genes across Fusobacterium strains and visualizing the results in the form of a heat map with dendrogram.

Database URL:http://fusobacterium.um.edu.my.

An extremely simple method for fabricating 3D protein microarrays with an anti-fouling background and high protein capacity

Protein microarrays have become vital tools for various applications in biomedicine and bio-analysis during the past decade. The intense requirements for a lower detection limit and industrialization in this area have resulted in a persistent pursuit to fabricate protein microarrays with a low background and high signal intensity via simple methods. Here, we report on an extremely simple strategy to create three-dimensional (3D) protein microarrays with an anti-fouling background and a high protein capacity by photo-induced surface sequential controlled/living graft polymerization developed in our lab. According to this strategy, "dormant" groups of isopropyl thioxanthone semipinacol (ITXSP) were first introduced to a polymeric substrate through ultraviolet (UV)-induced surface abstraction of hydrogen, followed by a coupling reaction. Under visible light irradiation, the ITXSP groups were photolyzed to initiate surface living graft polymerization of poly(ethylene glycol) methyl methacrylate (PEGMMA), thus introducing PEG brushes to the substrate to generate a full anti-fouling background. Due to the living nature of this graft polymerization, there were still ITXSP groups on the chain ends of the PEG brushes. Therefore, by in situ secondary living graft cross-linking copolymerization of glycidyl methacrylate (GMA) and polyethylene glycol diacrylate (PEGDA), we could finally plant height-controllable cylinder microarrays of a 3D PEG network containing reactive epoxy groups onto the PEG brushes. Through a commonly used reaction of amine and epoxy groups, the proteins could readily be covalently immobilized onto the microarrays. This delicate design aims to overcome two universal limitations in protein microarrays: a full anti-fouling background can effectively eliminate noise caused by non-specific absorption and a 3D reactive network provides a larger protein-loading capacity to improve signal intensity. The results of non-specific protein absorption tests demonstrated that the introduction of PEG brushes greatly improved the anti-fouling properties of the pristine low-density polyethylene (LDPE), for which the absorption to bovine serum albumin was reduced by 83.3%. Moreover, the 3D protein microarrays exhibited a higher protein capacity than the controls to which were attached the same protein on PGMA brushes and monolayer epoxy functional groups. The 3D protein microarrays were used to test the immunoglobulin G (IgG) concentration in human serum, suggesting that they could be used for biomedical diagnosis, which indicates that more potential bio-applications could be developed for these protein microarrays in the future.

StaphyloBase: a specialized genomic resource for the staphylococcal research community

With the advent of high-throughput sequencing technologies, many staphylococcal genomes have been sequenced. Comparative analysis of these strains will provide better understanding of their biology, phylogeny, virulence and taxonomy, which may contribute to better management of diseases caused by staphylococcal pathogens. We developed StaphyloBase with the goal of having a one-stop genomic resource platform for the scientific community to access, retrieve, download, browse, search, visualize and analyse the staphylococcal genomic data and annotations. We anticipate this resource platform will facilitate the analysis of staphylococcal genomic data, particularly in comparative analyses. StaphyloBase currently has a collection of 754 032 protein-coding sequences (CDSs), 19 258 rRNAs and 15 965 tRNAs from 292 genomes of different staphylococcal species. Information about these features is also included, such as putative functions, subcellular localizations and gene/protein sequences. Our web implementation supports diverse query types and the exploration of CDS- and RNA-type information in detail using an AJAX-based real-time search system. JBrowse has also been incorporated to allow rapid and seamless browsing of staphylococcal genomes. The Pairwise Genome Comparison tool is designed for comparative genomic analysis, for example, to reveal the relationships between two user-defined staphylococcal genomes. A newly designed Pathogenomics Profiling Tool (PathoProT) is also included in this platform to facilitate comparative pathogenomics analysis of staphylococcal strains. In conclusion, StaphyloBase offers access to a range of staphylococcal genomic resources as well as analysis tools for comparative analyses.

Database URL: http://staphylococcus.um.edu.my/

Construction of DNA microarrays on cyclic olefin copolymer surfaces using confined photocatalytic oxidation

A novel strategy for DNA immobilization on cyclic olefin copolymer surfaces.

Theory, fabrication and applications of microfluidic and nanofluidic biosensors

Biosensors are a broad array of devices that detect the type and amount of a biological species or biomolecule. Several different types of biosensors have been developed that rely on changes to mechanical, chemical or electrical properties of the transduction or sensing element to induce a measurable signal. Often, a biosensor will integrate several functions or unit operations such as sample extraction, manipulation and detection on a single platform. This review begins with an overview of the current state-of-the-art biosensor field. Next, the review delves into a special class of biosensors that rely on microfluidics and nanofluidics by presenting the underlying theory, fabrication and several examples and applications of microfluidic and nanofluidic sensors.

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

The regulatory elements that direct tissue-specific gene expression in the developing mammalian embryo remain largely unknown. Although chromatin profiling has proven to be a powerful method for mapping regulatory sequences in cultured cells, chromatin states characteristic of active developmental enhancers have not been directly identified in embryonic tissues. Here we use whole-transcriptome analysis coupled with genome-wide profiling of H3K27ac and H3K27me3 to map chromatin states and enhancers in mouse embryonic forelimb and hindlimb. We show that gene-expression differences between forelimb and hindlimb, and between limb and other embryonic cell types, are correlated with tissue-specific H3K27ac signatures at promoters and distal sites. Using H3K27ac profiles, we identified 28,377 putative enhancers, many of which are likely to be limb specific based on strong enrichment near genes highly expressed in the limb and comparisons with tissue-specific EP300 sites and known enhancers. We describe a chromatin state signature associated with active developmental enhancers, defined by high levels of H3K27ac marking, nucleosome displacement, hypersensitivity to sonication, and strong depletion of H3K27me3. We also find that some developmental enhancers exhibit components of this signature, including hypersensitivity, H3K27ac enrichment, and H3K27me3 depletion, at lower levels in tissues in which they are not active. Our results establish histone modification profiling as a tool for developmental enhancer discovery, and suggest that enhancers maintain an open chromatin state in multiple embryonic tissues independent of their activity level.

Evolution of the land plant exocyst complexes

Exocyst is an evolutionarily conserved vesicle tethering complex functioning especially in the last stage of exocytosis. Homologs of its eight canonical subunits - Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70, and Exo84 - were found also in higher plants and confirmed to form complexes in vivo, and to participate in cell growth including polarized expansion of pollen tubes and root hairs. Here we present results of a phylogenetic study of land plant exocyst subunits encoded by a selection of completely sequenced genomes representing a variety of plant, mostly angiosperm, lineages. According to their evolution histories, plant exocyst subunits can be divided into several groups. The core subunits Sec6, Sec8, and Sec10, together with Sec3 and Sec5, underwent few, if any fixed duplications in the tracheophytes (though they did amplify in the moss Physcomitrella patens), while others form larger families, with the number of paralogs ranging typically from two to eight per genome (Sec15, Exo84) to several dozens per genome (Exo70). Most of the diversity, which can be in some cases traced down to the origins of land plants, can be attributed to the peripheral subunits Exo84 and, in particular, Exo70. As predicted previously, early land plants (including possibly also the Rhyniophytes) encoded three ancestral Exo70 paralogs which further diversified in the course of land plant evolution. Our results imply that plants do not have a single "Exocyst complex" - instead, they appear to possess a diversity of exocyst variants unparalleled among other organisms studied so far. This feature might perhaps be directly related to the demands of building and maintenance of the complicated and spatially diverse structures of the endomembranes and cell surfaces in multicellular land plants.

BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences

We introduce BAR-PLUS (BAR(+)), a web server for functional and structural annotation of protein sequences. BAR(+) is based on a large-scale genome cross comparison and a non-hierarchical clustering procedure characterized by a metric that ensures a reliable transfer of features within clusters. In this version, the method takes advantage of a large-scale pairwise sequence comparison of 13,495,736 protein chains also including 988 complete proteomes. Available sequence annotation is derived from UniProtKB, GO, Pfam and PDB. When PDB templates are present within a cluster (with or without their SCOP classification), profile Hidden Markov Models (HMMs) are computed on the basis of sequence to structure alignment and are cluster-associated (Cluster-HMM). Therefrom, a library of 10,858 HMMs is made available for aligning even distantly related sequences for structural modelling. The server also provides pairwise query sequence-structural target alignments computed from the correspondent Cluster-HMM. BAR(+) in its present version allows three main categories of annotation: PDB [with or without SCOP (*)] and GO and/or Pfam; PDB (*) without GO and/or Pfam; GO and/or Pfam without PDB (*) and no annotation. Each category can further comprise clusters where GO and Pfam functional annotations are or are not statistically significant. BAR(+) is available at http://bar.biocomp.unibo.it/bar2.0.

Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88

The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook whole-genome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi.

Electrochemical Studies of Morpholino-DNA Surface Hybridization

Surface hybridization, in which nucleic acids from solution bind to complementary "probe" strands immobilized on a solid support, is widely used to analyze composition of nucleic acid mixtures. Most often, detection is accomplished with fluorescent techniques whose sensitivity can be extended down to individual molecules. Applications, however, benefit as much if not more from convenience, accuracy, and affordability of the diagnostic test. By eliminating the need for fluorescent labeling and more complex sample workup, label-free electrochemical assays have significant advantages provided transduction remains sufficiently sensitive for applications. To this end, we have been exploring morpholinos, which are uncharged DNA analogues, as the immobilized probe species in surface hybridization assays based on measurement of interfacial capacitance. Through comparison of experimental trends with those predicted from basic physical models, the origins of diagnostic contrast in capacitive sensing are reviewed for assays based on morpholino as well as on DNA probes.

Food analysis and food authentication by peptide nucleic acid (PNA)-based technologies

This tutorial review will address the issue of DNA determination in food by using Peptide Nucleic Acid (PNA) probes with different technological platforms, with a particular emphasis on the applications devoted to food authentication. After an introduction aimed at describing PNAs structure, binding properties and their use as genetic probes, the review will then focus specifically on the use of PNAs in the field of food analysis. In particular, the following issues will be considered: detection of genetically modified organisms (GMOs), of hidden allergens, of microbial pathogens and determination of ingredient authenticity. Finally, the future perspectives for the use of PNAs in food analysis will be briefly discussed according to the most recent developments.

Capacitive monitoring of morpholino-DNA surface hybridization: experimental and theoretical analysis

Impedance and cyclic voltammetry methods, complemented by Poisson-Boltzmann (PB) modeling, are used to study hybridization of DNA analyte strands to monolayers of morpholino oligomers (MOs) immobilized by one end to mercaptopropanol-passivated gold electrodes. MOs, like peptide nucleic acids (PNAs), are uncharged molecules that recognize nucleic acids following conventional base-pairing rules. The capacitive response to hybridization, determined from real-time impedance measurements, is analyzed with emphasis on understanding the underlying structural changes and on providing a foundation for label-free diagnostics. The capacitive response is correlated with the instantaneous surface molecular populations by labeling DNA and MO strands with ferrocene tags and using cyclic voltammetry to monitor their respective coverages in real-time. This approach allows analysis of hybridization-induced changes in interfacial capacitance as a function of duplex coverage, the DC bias used for readout, buffer molarity, and probe coverage. The results indicate that unhybridized MO layers exist in a compact state on the solid support. For hybridized layers, the intrinsic signal per hybridization event is strongly enhanced at low ionic strengths but, interestingly, does not depend on the readout bias in the sampled range negative of the capacitive minimum. A PB model incorporating an effective medium description of the hybridizing films is used to establish how hybridization-derived changes in dielectric composition and charge distribution at the surface translate into experimentally observed variations in interfacial capacitance.

Elevated evolutionary rate in genes with homopolymeric amino acid repeats constituting nondisordered structure

Homopolymeric amino acid repeats are tandem repeats of single amino acids. About 650 genes are known to have repeats of this kind comprising seven residues or more in the human genome. According to the evolutionary conservativeness, we classified the repeats into three categories: those whose length is conserved among mammals (CM), those whose length differs among nonprimate mammals but is conserved among primates (CP), and those whose length differs among primates (VP). The frequency of each repeat, especially Ala, Leu, Pro, and Glu repeats, varies greatly in each category. The 3D structure of homopolymeric amino acid repeats is considered to be intrinsically disordered. As expected, a large proportion of the repeats had a disordered structure, and nearly half of the repeats were predicted as completely disordered. However, a number of the repeats predicted to have nondisordered structure: 13% and 25% of the repeats for categories CM and VP, respectively. Comparison of the substitution rates showed a higher Ka/Ks ratio for the genes with not disordered repeats than the genes with disordered repeats. These results indicate that amino acid substitution rates have been elevated in the genes with nondisordered repeats.

Dielectrophoresis of DNA: Quantification by impedance measurements

Dielectrophoretic properties of DNA have been determined by measuring capacitance changes between planar microelectrodes. DNA sizes ranged from 100 bp to 48 kbp, DNA concentrations from below 0.1 to 70 mugml. Dielectrophoretic spectra exhibited maximum response around 3 kHz and 3 MHz. The strongest response was found for very long DNA (above 10 kbp) and for short 100 bp fragments, which corresponds to the persistence length of DNA. The method allows for an uncomplicated, automatic acquisition of the dielectrophoretic properties of submicroscopical objects without the need for labeling protocols or optical accessibility.

Morpholino monolayers: preparation and label-free DNA analysis by surface hybridization

Surface hybridization, a reaction in which nucleic acid molecules in solution react with nucleic acid partners immobilized on a surface, is widely practiced in life science research. In these applications the immobilized partner, or "probe", is typically single-stranded DNA. Because DNA is strongly charged, high salt conditions are required to enable binding between analyte nucleic acids ("targets") in solution and the DNA probes. High salt, however, compromises prospects for label-free monitoring or control of the hybridization reaction through surface electric fields; it also stabilizes secondary structure in target species that can interfere with probe-target recognition. In this work, initial steps toward addressing these challenges are taken by introducing morpholinos, a class of uncharged DNA analogues, for surface-hybridization applications. Monolayers of morpholino probes on gold supports can be fabricated with methods similar to those employed with DNA and are shown to hybridize efficiently and sequence-specifically with target strands. Hybridization-induced changes in the interfacial charge organization are analyzed with electrochemical methods and compared for morpholino and DNA probe monolayers. Molecular mechanisms connecting surface hybridization state to the interfacial capacitance are identified and interpreted through comparison to numerical Poisson-Boltzmann calculations. Interestingly, positive as well as negative capacitive responses (contrast inversion) to hybridization are possible, depending on surface populations of mobile ions as controlled by the applied potential. Quantitative comparison of surface capacitance with target coverage (targets/area) reveals a nearly linear relationship and demonstrates sensitivities (limits of quantification) in the picogram per square millimeter range.

Direct electrocatalytic mRNA detection using PNA-nanowire sensors

We report an electrochemical nucleic acids sensing system that exhibits high sensitivity and specificity when challenged with heterogeneous samples of RNA. The platform directly detects specific RNA sequences in cellular and clinical samples without any sample labeling or PCR amplification. The sensor features an electrode platform consisting of three-dimensional gold nanowires, and DNA or RNA hybridization is detected using an electrocatalytic reporter system. In this study, probes made of peptide nucleic acid (PNA) are used to detect a newly identified cancer biomarkera gene fusion recently associated with prostate cancer. The system is able to detect the fusion sequence with 100 fM sensitivity, and retains high sensitivity even in the presence of a large excess of non-complementary sequences. Moreover, the sensor is able to detect the fusion sequence in as little as 10 ng of mRNA isolated from cell lines or 100 ng total RNA from patient tissue samples. The PNA-nanowire nucleic acids sensor described is one of the first electrochemical sensors to directly detect specific mRNAs in unamplified patient samples.