VIPurPCA: Visualizing and Propagating Uncertainty in Principal Component Analysis

Variables obtained by experimental measurements or statistical inference typically carry uncertainties. When an algorithm uses such quantities as input variables, this uncertainty should propagate to the algorithm's output. Concretely, we consider the classic notion of principal component analysis (PCA): If it is applied to a finite data matrix containing imperfect (i.e., uncertain) multidimensional measurements, its output-a lower-dimensional representation-is itself subject to uncertainty. We demonstrate that this uncertainty can be approximated by appropriate linearization of the algorithm's nonlinear functionality, using automatic differentiation. By itself, however, this structured, uncertain output is difficult to interpret for users. We provide an animation method that effectively visualizes the uncertainty of the lower dimensional map. Implemented as an open-source software package, it allows researchers to assess the reliability of PCA embeddings.

BLASTphylo: An Interactive Web Tool for Taxonomic and Phylogenetic Analysis of Prokaryotic Genes

Identifying a protein's function is crucial to reveal its role in the cellular complex. Computationally, the most common approach is to search for homologous proteins in a large database of proteins of known function using BLAST. One goal of such an analysis is the identification and visualization of the protein in the taxonomy of interest. Another goal is the reconstruction of the phylogenetic history of the protein. However, the BLAST result provides information about the occurrence of the protein in the taxonomy and its putative function mainly in a tabular format. This requires manual interventions and makes the taxonomic identification laborious. Although various tools exist to visualize and annotate large-scale trees, none of them intuitively and interactively visualizes the protein's occurrence in the taxonomy for different taxonomic ranks. To target this gap, we developed BLASTphylo, a web tool that combines BLAST with automatic taxonomic mapping and phylogenetic analysis and provides the results in interactive visualizations. We demonstrate the functionalities of BLASTphylo in two case studies.

Improving taxonomic classification with feature space balancing

Summary

Modern high-throughput sequencing technologies, such as metagenomic sequencing, generate millions of sequences that need to be assigned to their taxonomic rank. Modern approaches either apply local alignment to existing databases, such as MMseqs2, or use deep neural networks, as in DeepMicrobes and BERTax. Due to the increasing size of datasets and databases, alignment-based approaches are expensive in terms of runtime. Deep learning-based approaches can require specialized hardware and consume large amounts of energy. In this article, we propose to use k-mer profiles of DNA sequences as features for taxonomic classification. Although k-mer profiles have been used before, we were able to significantly increase their predictive power significantly by applying a feature space balancing approach to the training data. This greatly improved the generalization quality of the classifiers. We have implemented different pipelines using our proposed feature extraction and dataset balancing in combination with different simple classifiers, such as bagged decision trees or feature subspace KNNs. By comparing the performance of our pipelines with state-of-the-art algorithms, such as BERTax and MMseqs2 on two different datasets, we show that our pipelines outperform these in almost all classification tasks. In particular, sequences from organisms that were not part of the training were classified with high precision.

Availability and implementation

The open-source code and the code to reproduce the results is available in Seafile, at https://tinyurl.com/ysk47fmr.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

The Neuromodulator-Encoding sadA Gene Is Widely Distributed in the Human Skin Microbiome

Trace amines (TA) are endogenously produced in mammals, have a low concentration in the central nervous system (CNS), but trigger a variety of neurological effects and intervene in host cell communication. It emerged that neurotransmitters and TA are produced also by the microbiota. As it has been shown that TA contribute to wound healing, we examined the skin microbiome of probands using shotgun metagenomics. The phyla Actinobacteria, Proteobacteria, Firmicutes, and Bacteroidetes were predominant. Since SadA is a highly promiscuous TA-producing decarboxylase in Firmicutes, the skin microbiome was specifically examined for the presence of sadA-homologous genes. By mapping the reads of certain genes, we found that, although there were less reads mapping to sadA than to ubiquitous housekeeping genes (arcC and mutS), normalized reads counts were still >1000 times higher than those of rare control genes (icaA, icaB, and epiA). At protein sequence level SadA homologs were found in at least 7 phyla: Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Acidobacteria, Chloroflexi, and Cyanobacteria, and in 23 genera of the phylum Firmicutes. A high proportion of the genera that have a SadA homolog belong to the classical skin and intestinal microbiota. The distribution of sadA in so many different phyla illustrates the importance of horizontal gene transfer (HGT). We show that the sadA gene is widely distributed in the human skin microbiome. When comparing the sadA read counts in the probands, there was no correlation between age and gender, but an enormous difference in the sadA read counts in the microbiome of the individuals. Since sadA is involved in TA synthesis, it is likely that the TA content of the skin is correlated with the amount of TA producing bacteria in the microbiome. In this way, the microbiome-generated TA could influence signal transmission in the epithelial and nervous system.

The Genome of Staphylococcus epidermidis O47

The skin colonizing coagulase-negative Staphylococcus epidermidis causes nosocomial infections and is an important opportunistic and highly adaptable pathogen. To gain more insight into this species, we sequenced the genome of the biofilm positive, methicillin susceptible S. epidermidis O47 strain (hereafter O47). This strain belongs to the most frequently isolated sequence type 2. In comparison to the RP62A strain, O47 can be transformed, which makes it a preferred strain for molecular studies. S. epidermidis O47’s genome has a single chromosome of about 2.5 million base pairs and no plasmid. Its oriC sequence has the same directionality as S. epidermidis RP62A, S. carnosus, S. haemolyticus, S. saprophyticus and is inverted in comparison to Staphylococcus aureus and S. epidermidis ATCC 12228. A phylogenetic analysis based on all S. epidermidis genomes currently available at GenBank revealed that O47 is closest related to DAR1907. The genome of O47 contains genes for the typical global regulatory systems known in staphylococci. In addition, it contains most of the genes encoding for the typical virulence factors for S. epidermidis but not for S. aureus with the exception of a putative hemolysin III. O47 has the typical S. epidermidis genetic islands and several mobile genetic elements, which include staphylococcal cassette chromosome (SCC) of about 54 kb length and two prophages φO47A and φO47B. However, its genome has no transposons and the smallest number of insertion sequence (IS) elements compared to the other known S. epidermidis genomes. By sequencing and analyzing the genome of O47, we provide the basis for its utilization in genetic and molecular studies of biofilm formation.

The GET pathway can increase the risk of mitochondrial outer membrane proteins to be mistargeted to the ER

Tail-anchored (TA) proteins are anchored to their corresponding membrane via a single transmembrane segment (TMS) at their C-terminus. In yeast, the targeting of TA proteins to the endoplasmic reticulum (ER) can be mediated by the guided entry of TA proteins (GET) pathway, whereas it is not yet clear how mitochondrial TA proteins are targeted to their destination. It is widely observed that some mitochondrial outer membrane (OM) proteins are mistargeted to the ER when overexpressed or when their targeting signal is masked. However, the mechanism of this erroneous sorting is currently unknown. In this study, we demonstrate the involvement of the GET machinery in mistargeting of non-optimal mitochondrial OM proteins to the ER. These findings suggest that the GET machinery can, in principle, recognize and guide mitochondrial and non-canonical TA proteins. Hence, under normal conditions, an active mitochondrial targeting pathway must exist that dominates the kinetic competition against other pathways.

Clinical and Microscopic Characteristics of Canine Toxic Epidermal Necrolysis

Canine toxic epidermal necrosis (TEN), a rare and life-threatening cutaneous drug reaction, traditionally has been described as full-thickness devitalization of the epidermis with minimal dermal inflammation; however, few reports detail the histologic findings. We characterize the clinical features and histologic variations of 3 canine TEN patients. Clinically, irregular erythematous and purpuric macules evolved into widespread and severely painful erosions. The number of eroded mucosae varied; however, periocular and perilabial mucocutaneous junctions frequently were affected. Thirteen of 17 biopsies were evaluated. Apoptosis at multiple epidermal levels was the most common pattern of epidermal necrosis (12/13 biopsies, 92%). In contrast, full-thickness coagulation necrosis was present less often (7/13 biopsies, 52%). Lymphocytic interface dermatitis was the predominant inflammatory pattern, and intraepidermal lymphocytes, along with fewer histiocytes, were present to some degree in all samples along with lymphocytic satellitosis of apoptotic keratinocytes. The sequence of changes points to lymphocyte-mediated keratinocyte apoptosis as an early step in lesion development with subsequent variation in progression to coagulation necrosis among patients. Histopathologic changes overlapped with those reported for erythema multiforme, in contrast to traditional histologic descriptions of canine TEN. A specific algorithm for assessment of drug causality in epidermal necrolysis (ALDEN) was applied for each patient; carprofen was associated with a probable score for causality in 1 dog. Clinicians should be encouraged to take multiple biopsies in TEN suspect cases as nearly 25% of all biopsies lacked epithelium and were not diagnostic.

Breed and site predispositions of dogs with atopic dermatitis: a comparison of five locations in three continents

The objectives of this multicentre study were to analyse and compare breed predispositions and lesion distributions of 552 dogs diagnosed with atopic dermatitis from five different dermatologic referral centres located in Australia, Germany (2) and the United States (2). Breeds were compared with the canine population in the respective locations. Breed predispositions varied from geographical site, although golden retrievers and German shepherd dogs were predisposed in three of five practices. Lesions were present most commonly on the paws (62%), ventrum (51%), ears (48%) and face (39%). Various breeds had specific site predilections. Based on this study, breed predispositions can vary greatly both between continents and also between different locations on the same continent. In addition, some breeds showed predispositions for certain body sites which also varied in some instances with the geographical location.

Moraxella catarrhalis induces ERK- and NF- B-dependent COX-2 and prostaglandin E2 in lung epithelium

Moraxella catarrhalis is a major cause of infectious exacerbations of chronic obstructive lung disease. Cyclooxygenase (COX)-derived prostaglandins, such as prostaglandin E(2) (PGE(2)), are considered to be important regulators of lung function. The present authors tested the hypothesis that M. catarrhalis induces COX-2-dependent PGE(2) production in pulmonary epithelial cells. In the present study, the authors demonstrate that M. catarrhalis specifically induces COX-2 expression and subsequent PGE(2) release in pulmonary epithelial cells. Furthermore, the prostanoid receptor subtypes EP2 and EP4 were also upregulated in these cells. The M. catarrhalis-specific ubiquitous cell surface protein A1 was important for the induction of COX-2 and PGE(2). Moreover, M. catarrhalis-induced COX-2 and PGE(2) expression was dependent on extracellular signal-regulated kinase 1/2-driven activation of nuclear factor-kappaB, but not on the activation of p38 mitogen-activated protein kinase. In conclusion, the present data suggest that ubiquitous cell surface protein A1 of Moraxella catarrhalis, extracellular signal-regulated kinase 1/2 and nuclear factor-kappaB control cyclooxygenase-2 expression and subsequent prostaglandin E(2) release by lung epithelial cells. Moraxella catarrhalis-induced prostaglandin E(2) expression might counteract lung inflammation promoting colonisation of the respiratory tract in chronic obstructive pulmonary disease patients.

Concentrations of progesterone, prolactin and relaxin in the luteal phase and pregnancy in normal and short-cycling German Shepherd dogs

Twenty-two nonpregnant and 19 pregnant German Shepherd dogs were assigned to either a control group or a suspected short-cycling group, based on the interestrous interval (> or = 6 month and < 5 month, respectively) and data from previous pregnancies. Blood serum concentrations of progesterone and prolactin were determined from days 5 to 60 (day 0 = ovulation) for characterization of luteal function. In pregnant bitches, placental integrity was additionally assessed by relaxin concentrations. The nonpregnant, suspected short-cycling bitches had significantly lower progesterone concentrations than the controls, indicating decreased luteal activity both in the autonomous and prolactin-dependent period. In the pregnant suspected short-cycling bitches, unavoidable progesterone supplementation prevented assessment of luteal function; it may have suppressed prolactin secretion (significantly lower prolactin concentrations from days 20 to 60, compared with the pregnant control group), but deficient prolactin secretion affecting luteal function cannot be excluded. The significantly lower relaxin concentrations, together with a high incidence of embryonic death found in the pregnant, suspected short-cycling group, may indicate loss of placental integrity and may have caused decreased prolactin concentrations.

Review of 15 cases of pemphigus foliaceus in horses and a survey of the literature

The records of 15 horses with pemphigus foliaceus diagnosed on the basis of their history, clinical signs, histopathology and the exclusion of differential diagnoses were evaluated with respect to the age of onset, the clinical signs and the diagnostic tests used. There was no apparent breed predisposition. The horses' mean age was nine years, with a range from three months to 25.5 years, three were foals up to six months old and eight were nine years old or older. The most frequent lesions were scaling in 11, crusting in 10 and alopecia in 10, and they appeared most commonly on the face, neck and trunk, in 10 horses for each of these sites. The extremities were involved in nine of the horses, pruritus occurred in seven, and four of the horses had pustules. The clinical signs mostly corresponded with those described in previous reports, but signs of pain were not a prominent feature. Acantholytic cells were identified cytologically in four of six of the horses.

Effect of omega-3 fatty acids on canine atopic dermatitis

Twenty-nine dogs were included in a double-blinded, placebo-controlled, randomised trial and were orally supplemented for 10 weeks with either flax oil (200 mg/kg/day), eicosapentaenoic acid (50 mg/kg/day) and docosahexaenoic acid (35 mg/kg/day) in a commercial preparation, or mineral oil as a placebo. For each dog, clinical scores were determined based on a scoring system developed prior to the trial. Total omega-6 and omega-3 intake and the ratio of omega-6:omega-3 (omega-6:3) were calculated before and after the trial. The dogs' clinical scores improved in those supplemented with flax oil and the commercial preparation, but not in the placebo group. No correlation was identified between total fatty acid intake or omega-6:3 ratio and clinical scores. Based on the results of this study, the total intake of fatty acids or the omega-6:3 ratio do not seem to be the main factors in determining the clinical response.

Allele-specific losses of heterozygosity on chromosomes 1 and 17 revealed by whole genome scan of ethylnitrosourea-induced BDIX x BDIV hybrid rat gliomas

The induction of neural tumors by N-ethyl-N-nitrosourea (EtNU) in inbred strains of rats has evolved as a valuable model system of developmental stage- and cell type-dependent oncogenesis. Tumor yield and latency times are strongly influenced by genetic background. Compared with BDIX rats, BDIV rats are relatively resistant to the induction of brain tumors by EtNU, with a lower tumor incidence and latency periods prolonged by a factor of 3. To characterize genetic abnormalities associated with impaired tumor suppressor gene function in neuro-oncogenesis, losses of heterozygosity (LOHs) and microsatellite instability (MI) were investigated in brain tumors induced by EtNU in (BDIV x BDIX) F(1) and F(2) rats. The polymerase chain reaction was used to amplify 55 polymorphic microsatellite markers spanning the entire rat genome. The tumors displayed different histologies and grades of malignancy, corresponding to part of the spectrum of human gliomas. MI was not observed in any of the tumors. LOH of rat chromosome 1q was predominantly detected in oligodendrogliomas and mixed gliomas, with a 30% incidence in informative cases. 11p15.5, the human genome region syntenic to the consensus region of LOHs observed on rat chromosome 1, has been shown to be involved in the formation of gliomas in humans. Furthermore, rat brain tumors of different histologies often showed allelic imbalances on chromosome 17p. In both cases of LOH, there was a clear bias in favor of the parental BDIV allele, suggesting the involvement of tumor suppressor genes functionally polymorphic between the two rat strains.

Transformed cells trigger induction of their own apoptosis in coculture with normal cells

In vitro, transforming growth factor type betal triggers normal cells to induce apoptosis in transformed cells. We show that in the absence of exogenous transforming growth factor type betal, induction of apoptosis of transformed cells in coculture with normal cells is dependent on the number of transformed cells per assay and is abrogated by antibodies against TGF-beta 1. Therefore, transforming growth factor type betal produced by transformed cells seems to be responsible for triggering a mechanism that leads to the induction of their apoptosis. This mechanism may be crucial for the control of carcinogenesis in vivo.