PHANOTATE: a novel approach to gene identification in phage genomes.

MOTIVATION: Currently there are no tools specifically designed for annotating genes in phages. Several tools are available that have been adapted to run on phage genomes, but due to their underlying design, they are unable to capture the full complexity of phage genomes. Phages have adapted their genomes to be extremely compact, having adjacent genes that overlap and genes completely inside of other longer genes. This non-delineated genome structure makes it difficult for gene prediction using the currently available gene annotators. Here we present PHANOTATE, a novel method for gene calling specifically designed for phage genomes. Although the compact nature of genes in phages is a problem for current gene annotators, we exploit this property by treating a phage genome as a network of paths: where open reading frames are favorable, and overlaps and gaps are less favorable, but still possible. We represent this network of connections as a weighted graph, and use dynamic programing to find the optimal path. RESULTS: We compare PHANOTATE to other gene callers by annotating a set of 2133 complete phage genomes from GenBank, using PHANOTATE and the three most popular gene callers. We found that the four programs agree on 82% of the total predicted genes, with PHANOTATE predicting more genes than the other three. We searched for these extra genes in both GenBank's non-redundant protein database and all of the metagenomes in the sequence read archive, and found that they are present at levels that suggest that these are functional protein-coding genes. AVAILABILITY AND IMPLEMENTATION: https://github.com/deprekate/PHANOTATE. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

multiPhATE: bioinformatics pipeline for functional annotation of phage isolates.

SUMMARY: To address the need for improved phage annotation tools that scale, we created an automated throughput annotation pipeline: multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de novo phage gene calling algorithm and assigns putative functions to gene calls using protein-, virus- and phage-centric databases. multiPhATE's modular construction allows the user to implement all or any portion of the analyses by acquiring local instances of the desired databases and specifying the desired analyses in a configuration file. We demonstrate multiPhATE by annotating two newly sequenced Yersinia pestis phage genomes. Within multiPhATE, the PhATE processing pipeline can be readily implemented across multiple processors, making it adaptable for throughput sequencing projects. Software documentation assists the user in configuring the system. AVAILABILITY AND IMPLEMENTATION: multiPhATE was implemented in Python 3.7, and runs as a command-line code under Linux or Unix. multiPhATE is freely available under an open-source BSD3 license from https://github.com/carolzhou/multiPhATE. Instructions for acquiring the databases and third-party codes used by multiPhATE are included in the distribution README file. Users may report bugs by submitting to the github issues page associated with the multiPhATE distribution. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Benefits and limitations of isokinetic force assessments in swimmer's shoulders: A systematic review.

OBJECTIVE: To indicate the benefits and limitations of the isokinetic test results for the performance of the main shoulder joint movements in swimmers, considering the different competitive levels, swimming techniques, race distances, and sex. METHODS: Search on the PubMed, CENTRAL, Medline, LILACS, and SCOPUS databases for the oldest records up to October 2022. Risk of bias, methodological quality, and level of evidence were evaluated based on the NHLBI checklist. RESULTS: 29 articles met the criteria and were included in this study. The quality analysis classified three as "good" and 26 as "regular", with a KAPPA index of 0.87. The main benefits found involved assessments of the clinical condition of the shoulder joint complex, relationships with performance, and reliability studies. The limitations found point to the participant's positioning in the instrument, use of angular velocity above 180°/s, and sample size. CONCLUSION: The use of the isokinetic dynamometer allows verifying the levels of strength, endurance, balance, and asymmetries among swimmers of different techniques, distances, competitive levels, and sex. Thus, it helps in the analysis and monitoring of the clinical conditions of swimmers' shoulder joints, contributing to the decision-making process of physiotherapists and coaches.

Fabrication and Tribological Performance of Self-Lubricating Porous Materials and Composites: A Review.

Porous materials have recently attracted significant attention in the aerospace and biomedical fields for addressing issues related to friction and wear. Porous materials are beneficial in applications where continuous lubrication is not feasible or for components that operate under extreme conditions, such as high speeds, elevated temperatures, and heavy loads. The pores can serve as reservoirs for liquid lubricants, which are gradually released during the operation of the components. The tribological properties of these materials depend on their porosity, the lubricants used, and any additional additives incorporated into the porous materials. This review article provides insight into common fabrication techniques for porous materials and examines their tribological performance for all three classes of materials-polymers, metals, and ceramics. Additionally, it discusses design criteria for porous self-lubricating materials by highlighting the critical properties of both the substrate and lubricants.

Analyzing bronchoalveolar fluid derived small extracellular vesicles using single-vesicle SERS for non-small cell lung cancer detection.

An emerging body of research by biologists and clinicians has demonstrated the clinical application of small extracellular vesicles (sEVs, also commonly referred to as exosomes) as biomarkers for cancer detections. sEVs isolated from various body fluids such as blood, saliva, urine, and cerebrospinal fluid have been used for biomarker discoveries with highly encouraging outcomes. Among the biomarkers discovered are those responsible for multiple cancer types and immune responses. These biomarkers are recapitulated from the tumor microenvironments. Yet, despite numerous discussions of sEVs in scientific literature, sEV-based biomarkers have so far played only a minor role for cancer diagnostics in the clinical setting, notably less so than other techniques such as imaging and biopsy. In this paper, we report the results of a pilot study (n = 10 from each of the patient and the control group) using bronchoalveolar lavage fluid to determine the presence of sEVs related to non-small cell lung cancer in twenty clinical samples examined using surface enhanced Raman spectroscopy (SERS).

Characterization of a novel lytic protein encoded by the Bacillus cereus E33L gene ampD as a Bacillus anthracis antimicrobial protein.

Lytic proteins encoded by bacterial genomes have been implicated in cell wall biosynthesis and recycling. The Bacillus cereus E33L ampD gene encodes a putative N-acetylmuramoyl-l-alanine amidase. This gene, expressed in vitro, produced a very stable, highly active lytic protein. Very low concentrations rapidly and efficiently lyse vegetative Bacillus anthracis cells.

A Brief Review on Factors Affecting the Tribological Interaction between Human Skin and Different Textile Materials.

The application of tribology is not just limited to mechanical components of engineering systems. As a matter of fact, the understanding of friction and wear can be applied to everyday life. One of the important fields is skin tribology, as human skin interacts with various surfaces of different materials. This paper focuses on the friction behavior of the skin when in contact with the fabric and other materials in relative motion. The excessive friction at the fabric-skin interface may lead to discomfort, blistering, chafing, and pressure ulcers especially in athletes who experience higher friction due to rapid movement for an extended period. Other than understanding the fabric properties, it is equally important to understand the structure and properties of the skin to evaluate its function and interaction with the different fabric materials. The identification of the contributing factors of skin friction can help to design suitable fabric materials. An overview of skin functions and the factors that affect the friction on the skin-textile material interface are presented in this review article.

MultiPhATE2: code for functional annotation and comparison of phage genomes.

To address a need for improved tools for annotation and comparative genomics of bacteriophage genomes, we developed multiPhATE2. As an extension of multiPhATE, a functional annotation code released previously, multiPhATE2 performs gene finding using multiple algorithms, compares the results of the algorithms, performs functional annotation of coding sequences, and incorporates additional search algorithms and databases to extend the search space of the original code. MultiPhATE2 performs gene matching among sets of closely related bacteriophage genomes, and uses multiprocessing to speed computations. MultiPhATE2 can be re-started at multiple points within the workflow to allow the user to examine intermediate results and adjust the subsequent computations accordingly. In addition, multiPhATE2 accommodates custom gene calls and sequence databases, again adding flexibility. MultiPhATE2 was implemented in Python 3.7 and runs as a command-line code under Linux or MAC operating systems. Full documentation is provided as a README file and a Wiki website.

Utilizing Amino Acid Composition and Entropy of Potential Open Reading Frames to Identify Protein-Coding Genes.

One of the main steps in gene-finding in prokaryotes is determining which open reading frames encode for a protein, and which occur by chance alone. There are many different methods to differentiate the two; the most prevalent approach is using shared homology with a database of known genes. This method presents many pitfalls, most notably the catch that you only find genes that you have seen before. The four most popular prokaryotic gene-prediction programs (GeneMark, Glimmer, Prodigal, Phanotate) all use a protein-coding training model to predict protein-coding genes, with the latter three allowing for the training model to be created ab initio from the input genome. Different methods are available for creating the training model, and to increase the accuracy of such tools, we present here GOODORFS, a method for identifying protein-coding genes within a set of all possible open reading frames (ORFS). Our workflow begins with taking the amino acid frequencies of each ORF, calculating an entropy density profile (EDP), using KMeans to cluster the EDPs, and then selecting the cluster with the lowest variation as the coding ORFs. To test the efficacy of our method, we ran GOODORFS on 14,179 annotated phage genomes, and compared our results to the initial training-set creation step of four other similar methods (Glimmer, MED2, PHANOTATE, Prodigal). We found that GOODORFS was the most accurate (0.94) and had the best F1-score (0.85), while Glimmer had the highest precision (0.92) and PHANOTATE had the highest recall (0.96).

Concurrent gastro-intestinal nematode infection does not alter the development of experimental cerebral malaria.

Concurrent helminth infections have been suggested to be associated with protection against cerebral malaria in humans, a condition characterised by systemic inflammation. Here we show that a concurrent chronic gastro-intestinal nematode infection does not alter the course of murine cerebral malaria. Mice infected with Heligmosomoides polygyrus, and co-infected with Plasmodium berghei ANKA 14 days later, developed malaria parasitemia, weight loss and anemia, at the same rate as mice without nematode infection. Both groups developed cerebral malaria around the same time point. The data suggest that a chronic helminth infection does not affect the development of cerebral malaria in a murine model.

Rhodotorula taiwanensis MD1149 produces hypoacetylated PEFA compounds with increased surface activity compared to Rhodotorula babjevae MD1169.

Biosurfactants have several desirable characteristics in the industrial sector: detergency, antimicrobial effects, skin hydration, and emulsibility. Several yeast glycolipids are currently being utilized in these capacities: sophorolipids, ustilagic acid, and mannosylerythritol lipids (MELs). An emerging class of glycolipids, termed polyol esters of fatty acids (PEFA), have recently been reported for Rhodotorula babjevae, a basidiomycetous yeast species that secretes hyperacetylated congeners of PEFA (typically with 3-6 acetylation modifications). While screening Rhodotorula species for surfactant production, we identified a new environmental isolate identified as Rhodotorula taiwanensis MD1149 that dropped the surface tension of the liquid medium, indicating that it produced a potent biosurfactant. Acid depolymerization of the purified biosurfactants, followed by gas chromatography-mass spectrometry (GC-MS) analysis revealed that the biosurfactants were composed of PEFA compounds composed mainly of mannitol and arabitol esters of 3-hydroxy fatty acid, 3-methoxy fatty acid, and fatty acids with a single double bond; chain lengths were mainly C16 and C18. Liquid chromatography-mass spectrometry (LC-MS) confirmed the predicted accurate mass of these compounds. Interestingly, PEFA compounds produced by Rhodotorula taiwanensis MD1149 were more surface active due to their hypoacetylation profile (0-4 acetylation modifications) compared to Rhodotorula babjevae MD1169. These disparate surface active properties, based on acetylation, change the hydrophilic-lipophilic balance (HLB) of these compounds, and their potential utility within industrial applications.

Detection of Bacillus anthracis from spores and cells by loop-mediated isothermal amplification without sample preparation.

Loop-mediated isothermal amplification (LAMP) is a technique capable of rapidly amplifying specific nucleic acid sequences without specialized thermal cycling equipment. In addition, several detection methods that include dye fluorescence, gel electrophoresis, turbidity and colorimetric change, can be used to measure or otherwise detect target amplification. To date, publications have described the requirement for some form of sample nucleic acid extraction (boiling, lysis, DNA purification, etc.) prior to initiating a LAMP reaction. We demonstrate here, the first LAMP positive results obtained from vegetative cells and spores of Bacillus anthracis without nucleic acid extraction. Our data show that the simple addition of cells or spores to the reaction mixture, followed by heating at 63°C is all that is required to reproducibly amplify and detect target plasmid and chromosomal DNA via colorimetric change. The use of three primer sets targeting both plasmids and the chromosome of B. anthracis allows for the rapid discrimination of non-pathogenic bacteria from pathogenic bacteria within 30 min of sampling. Our results indicate that direct testing of B. anthracis spores and cells via LAMP assay will greatly simplify and shorten the detection process by eliminating nucleic acid purification. These results may allow more rapid detection of DNA from pathogenic organisms present in field and environmental samples.

Characterization of the hamster FancG/Xrcc9 gene and mutations in CHO UV40 and NM3.

The human FANCG/XRCC9 gene, which is defective in Fanconi anemia complementation group G (FA-G) cells, was first cloned by genetic complementation of the mitomycin C (MMC) sensitivity of CHO mutant UV40. The CHO NM3 mutant was subsequently assigned to the same complementation group. The parental AA8 CHO cells are hemizygous at the FancG locus, and we identified frameshift mutations that result in N-terminal truncations of the protein in both UV40 and NM3. Hypersensitivity to DNA cross-linking agents, such as MMC, typically characterizes FA cells. By introducing the native CHO FancG gene into mutant NM3, we demonstrate that hamster FancG fully corrects the 3-fold sensitivity to methyl methanesulfonate (MMS) as well as the 10-fold sensitivity to MMC, whereas resistance to ionizing radiation did not increase appreciably. In contrast, hamster cDNA transformants showed incomplete correction for both MMC and MMS sensitivity. The constitutively expressed FancG protein is present in the cytoplasmic, nuclear and chromatin fractions. FancG protein levels and subcellular localization do not change appreciably as a function of cell cycle position. Our results are consistent with roles of FancG in both the nuclear and cytoplasmic compartments to maintain genomic stability in response to various genotoxic agents.