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This research aimed to identify the misconceptions experienced by the eighth-grade students of junior high school in Bandar Lampung on photosynthesis material. Also, this research aimed to investigate the causes of the misconceptions. The research method was qualitative, with three schools randomly selected based on their accreditation, namely accreditation A, B, and C. The data collecting techniques used in this research were multiple choice objective tests accompanied by the reasons and column Certainty of Response Index (CRI). Furthermore, the researchers also interviewed the teachers. The analysis showed that the highest percentage of misconceptions appeared in six question indicators, with a percentage above 50%. This result showed that the percentage of students who experienced misconceptions about photosynthesis material was greater than students who understand the concept and do not know the concept. ABSTRAK: Penelitian ini bertujuan untuk mengidentifikasi miskonsepsi peserta didik kelas VIII SMP Negeri sekota Bandar Lampung pada materi fotosintesis, serta penyebab dari adanya miskonsepsi pada peserta didik tersebut. Metode pada penelitian ini adalah metode kualitatif. Pengambilan sampel menggunakan teknik random sampling dengan tiga tempat sekolah yang akan dijadikan bahan penelitian berdasarkan dari akreditasi sekolah SMP Negeri tersebut yaitu akreditasi (A, B, dan C). Teknik pengumpulan data yang digunakan dalam penelitian ini adalah tes objektif multiple choice yang disertai alasan dan kolom Certainty Of Response Index (CRI), dan wawancara kepada pendidik. Data hasil analisis menunjukkan miskonsepsi dengan persentase terbesar muncul pada 6 indikator soal dengan persentase di atas 50%. Hal ini menunjukkan bahwa persentase persentase peserta didik yang mengalami miskonsepsi pada materi fotosintesis lebih besar dibandingkan peserta didik yang paham konsep dan tidak tahu konsep.

Masalah utama yang terjadi yaitu kemampuan berpikir kreatif peserta didik setiap indikatornya masih rendah, hal ini dapat dilihat dari data hasil pra-penelitian berupa tes soal essay. Hasil wawancara pada salah satu guru yang ada di sekolah menyatakan bahwa proses pembelajaran yang diterapkan oleh guru di sekolah sudah baik, namun perlu menerapkan model pembelajaran yang dapat dijadikan perantara dalam berkolaborasi, berkomunikasi, dan membagikan tugas secara daring. Penelitian ini bertujuan untuk mengetahui pengaruh model pembelajaran Project Based Learning berbasis Trello terhadap kemampuan berpikir kreatif peserta didik. Jenis penelitian yaitu kuantitatif dengan metode Quasy Eksperimental Research yaitu pretest-postest control group design. Populasi dalam penelitian ini yaitu seluruh peserta didik kelas VIII A-E yang berjumlah 104 dengan sampel 3 kelas yang berjumlah 64 peserta didik di SMP Negeri 1 Atap Pagelaran Utara. Instrumen penelitian yang digunakan berupa tes kemampuan berpikir kreatif. Teknik analisis data yaitu uji normalitas, uji homogenitas, dan uji hipotesis menggunakan One Way Anova. Berdasarkan hasil penelitian diperoleh bahwa ada pengaruh model Project Based Learning berbasis Trello terhadap kemampuan berpikir kreatif siswa.

In the present study, we assessed whether nootkatone (NKT), a sesquiterpene in edible plants, can provide protection against dyslipidemia, intramyocardial lipid accumulation, and altered lipid metabolism in a rat model of myocardial infarction (MI) induced by subcutaneous injections of isoproterenol (ISO, 85 mg/kg) on days 9 and 10. The rats were pre- and co-treated with NKT (10 mg/kg, p.o.) administered daily for 11 days. A significant reduction in the activities of myocardial creatine kinase and lactate dehydrogenase, as well as non-enzymatic antioxidants, and alterations in lipids and lipoproteins, along with a rise in plasma lipid peroxidation and intramyocardial lipid accumulation, were observed in ISO-treated rats. ISO administration induced alterations in the activities of enzymes/expressions that played a significant role in altering lipid metabolism. However, NKT treatment favorably modulated all biochemical and molecular parameters altered by ISO and showed protective effects against oxidative stress, dyslipidemia, and altered lipid metabolism, attributed to its free-radical-scavenging and antihyperlipidemic activities in rats with ISO-induced MI. Additionally, NKT decreased the accumulation of lipids in the myocardium as evidenced from Oil red O staining. Furthermore, the in vitro observations demonstrate the potent antioxidant property of NKT. The present study findings are suggestive of the protective effects of NKT on dyslipidemia and the underlying mechanisms. Based on our findings, it can be suggested that NKT or plants rich in NKT can be promising for use as a phytopharmaceutical or nutraceutical in protecting the heart and correcting lipid abnormalities and dyslipidemia, which are risk factors for ischemic heart diseases.

Background and aims: Power plants are the most important infrastructure for economic development with technological advances and sophisticated technology , are subject to risks and accidents. Despite of uncertainty and ambiguity , offer the Solution that can by combine information to identify hazards , assess and risk rank ing may effective to control and reduction of occupational accidents . This survey targeted to identify and assess hazards, determine and rank the effective safety risks in a combined cycle power plant. Methods: To identify hazard , was used documentation review , interviews with experts , brainstorming sessions , knowledge and experience group of experts in occupational health and safety engineering . For risk analysis , used fuzzy classification for severity and frequency by previous studies and expert opinion . Finally the risks were ranked based on using degree of Belief approach in fuzzy logic. Results: in the present study , among the 11 cases of identified hazards , explosion and fire gas turbines and bust steam pipes under pressure, with the degree of belief 0/56 , ranked in the first place and fell in tanks reservoirs and canals with degree of belief 0/21 had second place. Conclusion: So far , few risk assessment tools and techniques have been proposed in power plan t. In this study, despite of use subjective and qualitative variables , but for measuring these variables were used the absolute numbers and mathematical methods . Therefore this study is important and can be suitable and accurate approach to address the technical deficiencies in this section.

Background: Diagnostic models are frequently used to assess the role of risk factors on disease complications, and therefore to avoid them. Missing data is an issue that challenges the model making. The aim of this study was to develop a diagnostic model to predict death in HIV/ AIDS patients when missing data exist.Methods: HIV patients (n=1460) referred to Voluntary Consoling and Testing Center (VCT) of Shiraz southern Iran during 2004-2009 were recruited. Univariate association between variables and death was assessed. Only variables which had univariate P< 0.25 were selected to be offered to the Multifactorial models. First, patients with missing data on candidate variables were deleted (C-C model). Then, applying Multivariable Imputation via Chained Equations (MICE), missing data were imputed. Logistic regression was fitted to C-C and imputed data sets (MICE model). Models were compared in terms of number of variables retained in the final model, width of confidence intervals, and discrimination ability.Result: About 22% of data were lost in C-C model. Number of variables retained in the C-C and MICE models was 2 and 6 respectively. Confidence Intervals (C.I.) corresponding to C-C model was wider than that of MICE. The MICE model showed greater discrimination ability than C-C model (70% versus 64%).Conclusion: The -C analysis resulted to loss of power and wide CI's. Once missing data were imputed, more variables reached significance level and C.I.'s were narrower. Therefore, we do recommend the application of the imputation method for handling missing data.

In the previous paper, the basic concepts of sample size calculation were presented. This paper explores main post-calculation adjustments of the sample size calculation in special circumstances such as multiple group comparisons, unbalanced studies (with unequal number of subjects in different groups); sample size correction for missing data, and adjustment for finite population size. In addition, the concept of design effect in multi-stage sampling

"nCoronary artery bypass grafting (CABG) surgery is being performed increasingly in Iran. So far, no large-scale report has described characteristics and risk factor profile and in-hospital mortality of patients undergoing this procedure in Iran. We conducted this study to address these topics in order to help clarify Iran's current state of CABG and to provide assistance in planning combat against coronary artery disease based on frequency of major risk factors. Patients who underwent isolated, first-time, elective, on-pump (conventional) CABG in a cardiac surgery center in Tehran were prospectively studied from September 2004 and March 2005. Demographic data, risk factor profile and discharge status for each patient were recorded. There were 1258 patients, 937 men (74.5%) and 321 women (25.5%). The mean age was 58.7 years (range 28 to 81); 133 patients (10.6%) were 70 years old or older. Mean body mass index (BMI) was 27.01 and 42.2% of the patients were smokers, 39.4% were hypertensive, and 27.6% had diabetes. Family history was positive in 40.3%. Congestive heart failure was found in 26.6%. New York Heart Association functional class III or IV was observed in 52.8% of patients. Single-vessel, two-vessel, and multi-vessel disease was found in 4.2%, 21.1%, and 74.7% of patients, respectively. Left main was involved in 9.8% and 14.4% had ejection fraction < 35%. The in-hospital mortality was 1.5%, mainly due to cardiac causes. This study indicates significant prevalence of major cardiovascular risk factors in Iranian CABG patients. In-hospital mortality of primary isolated CABG in Iran is similar to reported rates.

Background: The use of cardiac surgical database is necessary for evaluating and improving the quality of care. The aim of this report was to provide useful information for surgeons in Iran and other countries for their daily practice. Methods: We analyzed data from 14288 consecutive patients in four different types of procedures, namely isolated coronary artery bypass grafting (CABG), combined CABG and valve (CABG-V), only valve (V), and other adult cardiac surgical operations from 2002 to 2006. Results: The activity load increased from 1765 in 2002 to 3309 surgical operations in 2006 with almost 87.2% of activity being isolated CABG. The mortality rate for CABG was 1%, which decreased from 1.7% to 0.9% over the five years. The mortality rates for CABG-V and V were 5.8% and 4.8% in the last year of the study, respectively. Over the 5 yr period, the proportion of urgent operations increased substantially from 4% to 24.5% (P< 0.0001), causing a reduction in elective operations. The mean length of hospital stay for the entire population was 8.38±5.74 d, which remained almost steady during the study period. Conclusion: This database can serve as a valuable resource of preoperative measurers and surgical outcomes for surgeons and researchers with a view to improving overall surgical performance.

Graphite surfaces interact weakly with molecules compared to other conducting surfaces, bringing the molecule–molecule interaction to the foreground. C60 on highly oriented pyrolytic graphite is a model system for studying the molecular self-assembly on surfaces. Our scanning tunneling microscopy measurements at liquid nitrogen temperatures confirm the previously observed island growth mode. Our results indicate that there is an epitaxial relationship of the molecular islands and the substrate with three possible orientations of the islands. For one of these orientations, we determine this epitaxial relationship by analyzing in detail an image taken across a C60 island step edge. In this image we have obtained high-resolution on both the molecular island and the substrate. The result of this analysis is confirmed by two-dimensional Fourier analysis. [ABSTRACT FROM AUTHOR]

Objective: Animal experiments have demonstrated that selenium can partly reduce nephrotoxicity and neurotoxicity of lead. There is no study about possible interactions between lead and selenium in functioning of salivary glands. This study was designed to explore the possible protective effects of selenium on lead-induced alterations on rat submandibular gland function. Methods: Pure submandibular saliva was collected intraorally by micro polyethylene cannula from anaesthetized rats using pilocarpine as secretagogue. Findings: A twenty-four day treatment with lead 0.04% and 0.05% as acetate in drinking water altered salivary function. Flow rate was significantly increased by lead (0.04% and 0.05%, P

Background: Diagnostic models are frequently used to assess the role of risk factors on disease complications, and therefore to avoid them. Missing data is an issue that challenges the model making. The aim of this study was to develop a diagnostic model to predict death in HIV/ AIDS patients when missing data exist. Methods: HIV patients (n=1460) referred to Voluntary Consoling and Testing Center (VCT) of Shiraz southern Iran during 2004-2009 were recruited. Univariate association between variables and death was assessed. Only variables which had univariate P< 0.25 were selected to be offered to the Multifactorial models. First, patients with missing data on candidate variables were deleted (C-C model). Then, applying Multivariable Imputation via Chained Equations (MICE), missing data were imputed. Logistic regression was fitted to C-C and imputed data sets (MICE model). Models were compared in terms of number of variables retained in the final model, width of confidence intervals, and discrimination ability. Result: About 22% of data were lost in C-C model. Number of variables retained in the C-C and MICE models was 2 and 6 respectively. Confidence Intervals (C.I.) corresponding to C-C model was wider than that of MICE. The MICE model showed greater discrimination ability than C-C model (70% versus 64%). Conclusion: The C-C analysis resulted to loss of power and wide CI's. Once missing data were imputed, more variables reached significance level and C.I.'s were narrower. Therefore, we do recommend the application of the imputation method for handling missing data.

Background: The use of cardiac surgical database is necessary for evaluating and improving the quality of care. The aim of this report was to provide useful information for surgeons in Iran and other countries for their daily practice. Methods: We analyzed data from 14288 consecutive patients in four different types of procedures, namely isolated coro­nary artery bypass grafting (CABG), combined CABG and valve (CABG-V), only valve (V), and other adult cardiac surgical op­erations from 2002 to 2006. Results: The activity load increased from 1765 in 2002 to 3309 surgical operations in 2006 with almost 87.2% of activity be­ing isolated CABG. The mortality rate for CABG was 1%, which decreased from 1.7% to 0.9% over the five years. The mor­tality rates for CABG-V and V were 5.8% and 4.8% in the last year of the study, respectively. Over the 5 yr period, the pro­portion of urgent operations increased substantially from 4% to 24.5% (P< 0.0001), causing a reduction in elective op­erations. The mean length of hospital stay for the entire population was 8.38±5.74 d, which remained almost steady dur­ing the study period. Conclusion: This database can serve as a valuable resource of preoperative measurers and surgical outcomes for surgeons and researchers with a view to improving overall surgical performance.

We study the structure and the electronic properties of Au nanocontacts created by controlled electromigration of thin film devices, a method frequently used to contact molecules. In contrast to electromigration testing, a current is applied in a cyclic fashion and during each cycle the resistance increase of the metal upon heating is used to avoid thermal runaway. In this way, nanometer sized-gaps are obtained. The thin film devices with an optimized structure at the origin of the electromigration process are made by shadow evaporation without contamination by organic materials. Defining rounded edges and a thinner area in the center of the device allow to pre-determine the location where the electromigration takes place. Scanning force microscopy images of the pristine Au film and electromigrated contact show its grainy structure. Through electromigration, a 1.5 μm-wide slit is formed, with extensions only on the anode side that had previously not been observed in narrower structures. It is discussed whether this could be explained by asymmetric heating of both electrodes. New grains are formed in the slit and on the extensions on both, the anode and the cathode side. The smaller structures inside the slit lead to an electrode distance below 150 nm. Kelvin probe force microscopy images show a local work function difference with fluctuations of 70 mV on the metal before electromigration. Between the electrodes, disconnected through electromigration, a work function difference of 3.2 V is observed due to charging. Some of the grains newly formed by electromigration are electrically disconnected from the electrodes. [ABSTRACT FROM AUTHOR]

The Rfam database, a widely used repository of non-coding RNA families, has undergone significant updates in release 15.0. This paper introduces major improvements, including the expansion of Rfamseq to 26 106 genomes, a 76% increase, incorporating the latest UniProt reference proteomes and additional viral genomes. Sixty-five RNA families were enhanced using experimentally determined 3D structures, improving the accuracy of consensus secondary structures and annotations. R-scape covariation analysis was used to refine structural predictions in 26 families. Gene Ontology (GO) and Sequence Ontology annotations were comprehensively updated, increasing GO term coverage to 75% of families. The release adds 14 new Hepatitis C Virus RNA families and completes microRNA family synchronization with miRBase, resulting in 1603 microRNA families. New data types, including FULL alignments, have been implemented. Integration with APICURON for improved curator attribution and multiple website enhancements further improve user experience. These updates significantly expand Rfam's coverage and improve annotation quality, reinforcing its critical role in RNA research, genome annotation and the development of machine learning models. Rfam is freely available at https://rfam.org., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

The Rfam database, a widely-used repository of non-coding RNA (ncRNA) families, has undergone significant updates in release 15.0. This paper introduces major improvements, including the expansion of Rfamseq to 26,106 genomes, a 76% increase, incorporating the latest UniProt reference proteomes and additional viral genomes. Sixty-five RNA families were enhanced using experimentally determined 3D structures, improving the accuracy of consensus secondary structures and annotations. R-scape covariation analysis was used to refine structural predictions in 26 families. Gene Ontology and Sequence Ontology annotations were comprehensively updated, increasing GO term coverage to 75% of families. The release adds 14 new Hepatitis C Virus RNA families and completes microRNA family synchronisation with miRBase, resulting in 1,603 microRNA families. New data types, including FULL alignments, have been implemented. Integration with APICURON for improved curator attribution and multiple website enhancements further improve user experience. These updates significantly expand Rfam's coverage and improve annotation quality, reinforcing its critical role in RNA research, genome annotation, and the development of machine learning models. Rfam is freely available at https://rfam.org., Competing Interests: Conflict of interest AB is a member of the Nucleic Acids Research Editorial Board.

Competing Interests: Author DM was employed by Oncgnostics GmbH. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Bats are ecologically diverse vertebrates characterized by their ability to host a wide range of viruses without apparent illness and the presence of numerous endogenous viral elements (EVEs). EVEs are well preserved, expressed, and may affect host biology and immunity, but their role in bat immune system evolution remains unclear. Among EVEs, endogenous bornavirus-like elements (EBLs) are bornavirus sequences integrated into animal genomes. Here, we identified a novel EBL in the microbat Myotis daubentonii , EBLL-Cultervirus.10-MyoDau (short name is CV.10-MyoDau) that shows protein-level conservation with the L-protein of a Cultervirus (Wuhan sharpbelly bornavirus). Surprisingly, we discovered a transcript on the antisense strand comprising three exons, which we named AMCR-MyoDau. The active transcription in Myotis daubentonii tissues of AMCR-MyoDau, confirmed by RNA-Seq analysis and RT-PCR, highlights its potential role during viral infections. Using comparative genomics comprising 63 bat genomes, we demonstrate nucleotide-level conservation of CV.10-MyoDau and AMCR-MyoDau across various bat species and its detection in 22 Yangochiropera and 12 Yinpterochiroptera species. To the best of our knowledge, this marks the first occurrence of a conserved EVE shared among diverse bat species, which is accompanied by a conserved antisense transcript. This highlights the need for future research to explore the role of EVEs in shaping the evolution of bat immunity.

Hepatitis C virus (HCV) is a plus-stranded RNA virus that often chronically infects liver hepatocytes and causes liver cirrhosis and cancer. These viruses replicate their genomes employing error-prone replicases. Thereby, they routinely generate a large 'cloud' of RNA genomes (quasispecies) which-by trial and error-comprehensively explore the sequence space available for functional RNA genomes that maintain the ability for efficient replication and immune escape. In this context, it is important to identify which RNA secondary structures in the sequence space of the HCV genome are conserved, likely due to functional requirements. Here, we provide the first genome-wide multiple sequence alignment (MSA) with the prediction of RNA secondary structures throughout all representative full-length HCV genomes. We selected 57 representative genomes by clustering all complete HCV genomes from the BV-BRC database based on k-mer distributions and dimension reduction and adding RefSeq sequences. We include annotations of previously recognized features for easy comparison to other studies. Our results indicate that mainly the core coding region, the C-terminal NS5A region, and the NS5B region contain secondary structure elements that are conserved beyond coding sequence requirements, indicating functionality on the RNA level. In contrast, the genome regions in between contain less highly conserved structures. The results provide a complete description of all conserved RNA secondary structures and make clear that functionally important RNA secondary structures are present in certain HCV genome regions but are largely absent from other regions. Full-genome alignments of all branches of Hepacivirus C are provided in the supplement., (© 2024. The Author(s).)

A comprehensive understanding of molecular changes during brain aging is essential to mitigate cognitive decline and delay neurodegenerative diseases. The interpretation of mRNA alterations during brain aging is influenced by the health and age of the animal cohorts studied. Here, we carefully consider these factors and provide an in-depth investigation of mRNA splicing and dynamics in the aging mouse brain, combining short- and long-read sequencing technologies with extensive bioinformatic analyses. Our findings encompass a spectrum of age-related changes, including differences in isoform usage, decreased mRNA dynamics and a module showing increased expression of neuronal genes. Notably, our results indicate a reduced abundance of mRNA isoforms leading to nonsense-mediated RNA decay and suggest a regulatory role for RNA-binding proteins, indicating that their regulation may be altered leading to the reshaping of the aged brain transcriptome. Collectively, our study highlights the importance of studying mRNA splicing events during brain aging., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Extensive remodeling of the female mammary epithelium during development and pregnancy has been linked to cancer susceptibility. The faithful response of mammary epithelial cells (MECs) to hormone signaling is key to avoiding breast cancer development. Here, we show that lactogenic differentiation of murine MECs requires silencing of genes encoding ribosomal RNA (rRNA) by the antisense transcript PAPAS. Accordingly, knockdown of PAPAS derepresses rRNA genes, attenuates the response to lactogenic hormones, and induces malignant transformation. Restoring PAPAS levels in breast cancer cells reduces tumorigenicity and lung invasion and activates many interferon-regulated genes previously linked to metastasis suppression. Mechanistically, PAPAS transcription depends on R-loop formation at the 3' end of rRNA genes, which is repressed by RNase H1 and replication protein A (RPA) overexpression in breast cancer cells. Depletion of PAPAS and upregulation of RNase H1 and RPA in human breast cancer underpin the clinical relevance of our findings., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

Importance: A common hypothesis holds that bats (order Chiroptera ) are outstanding reservoirs for zoonotic viruses because of a special antiviral interferon (IFN) system. However, functional studies about key components of the bat IFN system are rare. RIG-I is a cellular sensor for viral RNA signatures that activates the antiviral signaling chain to induce IFN. We cloned and functionally characterized RIG-I genes from two species of the suborders Yangochiroptera and Yinpterochiroptera . The bat RIG-Is were conserved in their sequence and domain organization, and similar to human RIG-I in (i) mediating virus- and IFN-activated gene expression, (ii) antiviral signaling, (iii) temperature dependence, and (iv) recognition of RNA ligands. Moreover, RIG-I of Rousettus aegyptiacus (suborder Yinpterochiroptera ) and of humans were found to recognize SARS-CoV-2 infection. Thus, members of both bat suborders encode RIG-Is that are comparable to their human counterpart. The ability of bats to harbor zoonotic viruses therefore seems due to other features., Competing Interests: The authors declare no conflict of interest.

Neutrophils are critical phagocytic cells in innate immunity, playing a significant role in defending against invasive fungal pathogens. This study aimed to explore the transcriptional activation of human neutrophils in response to different fungal pathogens, including Candida albicans and Aspergillus fumigatus , compared to the bacterial pathogen Escherichia coli . We identified distinct transcriptional profiles and stress-related pathways in neutrophils during fungal infections, highlighting their functional diversity and adaptability. The transcriptional response was largely redundant across all pathogens in immune-relevant categories and cytokine pathway activation. However, differences in the magnitude of differentially expressed genes (DEGs) were observed, with A. fumigatus inducing a lower transcriptional effect compared to C. albicans and E. coli . Notably, specific gene signatures associated with cell death were differentially regulated by fungal pathogens, potentially increasing neutrophil susceptibility to autophagy, pyroptosis, and neutrophil extracellular trap (NET) formation. These findings provide valuable insights into the complex immunological responses of neutrophils during fungal infections, offering new avenues for diagnostic and therapeutic strategies, particularly in the management of invasive fungal diseases.

Mycoplasmopsis (M.) bovis, the agent of mastitis, pneumonia, and arthritis in cattle, harbors a small genome of approximately 1 Mbp. Combining data from Illumina and Nanopore technologies, we sequenced and assembled the genomes of 35 European strains and isolate DL422&#95;88 from Cuba. While the high proportion of repetitive structures in M. bovis genomes represent a particular challenge, implementation of our own pipeline Mycovista (available on GitHub www.github.com/sandraTriebel/mycovista ) in a hybrid approach enabled contiguous assembly of the genomes and, consequently, improved annotation rates considerably. To put our European strain panel in a global context, we analyzed the new genome sequences together with 175 genome assemblies from public databases. Construction of a phylogenetic tree based on core genes of these 219 strains revealed a clustering pattern according to geographical origin, with European isolates positioned on clades 4 and 5. Genomic data allowing assignment of strains to tissue specificity or certain disease manifestations could not be identified. Seven strains isolated from cattle with systemic circular condition (SCC), still a largely unknown manifestation of M. bovis disease, were located on both clades 4 and 5. Pairwise association analysis revealed 108 genomic elements associated with a particular clade of the phylogenetic tree. Further analyzing these hits, 25 genes are functionally annotated and could be linked to a M. bovis protein, e.g. various proteases and nucleases, as well as ten variable surface lipoproteins (Vsps) and other surface proteins. These clade-specific genes could serve as useful markers in epidemiological and clinical surveys., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Viruses are abundant and diverse entities that have important roles in public health, ecology, and agriculture. The identification and surveillance of viruses rely on an understanding of their genome organization, sequences, and replication strategy. Despite technological advancements in sequencing methods, our current understanding of virus diversity remains incomplete, highlighting the need to explore undiscovered viruses. Virus databases play a crucial role in providing access to sequences, annotations and other metadata, and analysis tools for studying viruses. However, there has not been a comprehensive review of virus databases in the last five years. This study aimed to fill this gap by identifying 24 active virus databases and included an extensive evaluation of their content, functionality and compliance with the FAIR principles. In this study, we thoroughly assessed the search capabilities of five database catalogs, which serve as comprehensive repositories housing a diverse array of databases and offering essential metadata. Moreover, we conducted a comprehensive review of different types of errors, encompassing taxonomy, names, missing information, sequences, sequence orientation, and chimeric sequences, with the intention of empowering users to effectively tackle these challenges. We expect this review to aid users in selecting suitable virus databases and other resources, and to help databases in error management and improve their adherence to the FAIR principles. The databases listed here represent the current knowledge of viruses and will help aid users find databases of interest based on content, functionality, and scope. The use of virus databases is integral to gaining new insights into the biology, evolution, and transmission of viruses, and developing new strategies to manage virus outbreaks and preserve global health.

The study of viral communities has revealed the enormous diversity and impact these biological entities have on various ecosystems. These observations have sparked widespread interest in developing computational strategies that support the comprehensive characterisation of viral communities based on sequencing data. Here we introduce VIRify, a new computational pipeline designed to provide a user-friendly and accurate functional and taxonomic characterisation of viral communities. VIRify identifies viral contigs and prophages from metagenomic assemblies and annotates them using a collection of viral profile hidden Markov models (HMMs). These include our manually-curated profile HMMs, which serve as specific taxonomic markers for a wide range of prokaryotic and eukaryotic viral taxa and are thus used to reliably classify viral contigs. We tested VIRify on assemblies from two microbial mock communities, a large metagenomics study, and a collection of publicly available viral genomic sequences from the human gut. The results showed that VIRify could identify sequences from both prokaryotic and eukaryotic viruses, and provided taxonomic classifications from the genus to the family rank with an average accuracy of 86.6%. In addition, VIRify allowed the detection and taxonomic classification of a range of prokaryotic and eukaryotic viruses present in 243 marine metagenomic assemblies. Finally, the use of VIRify led to a large expansion in the number of taxonomically classified human gut viral sequences and the improvement of outdated and shallow taxonomic classifications. Overall, we demonstrate that VIRify is a novel and powerful resource that offers an enhanced capability to detect a broad range of viral contigs and taxonomically classify them., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Rangel-Pineros et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

C 60 is a model system to study molecule-surface interactions and phase transitions due to its high symmetry and strong covalent π bonding within the molecule versus weak van-der-Waals coupling between neighboring molecules. In the solid, at room temperature, the molecule rotates and behaves as a sphere. However, the pentagonal and hexagonal atomic arrangement imposes deviations from the spherical symmetry that become important at low temperatures. The orientation of the C 60 can be viewed to represent classic spins. For geometrical reasons the preferred orientation of neighboring C 60 cannot be satisfied for all of the neighboring molecules, making C 60 a model for disordered spin systems with frustration. We study several molecular layers of C 60 islands on highly oriented pyrolytic graphite using scanning tunneling microscopy at liquid nitrogen temperatures. By imaging several layers we obtain a limited access to the three-dimensional rotational structure of the molecules in an island. We find one rotationally disordered layer between two partially rotationally ordered layers with hexagonal patterns. This exotic pattern shows an example of the local distribution of order and disorder in geometrically frustrated systems. Scanning tunneling spectroscopy data confirms the weak interactions of neighboring molecules., (Creative Commons Attribution license.)

A fundamental step in the influenza A virus (IAV) replication cycle is the coordinated packaging of eight distinct genomic RNA segments (i.e. vRNAs) into a viral particle. Although this process is thought to be controlled by specific vRNA-vRNA interactions between the genome segments, few functional interactions have been validated. Recently, a large number of potentially functional vRNA-vRNA interactions have been detected in purified virions using the RNA interactome capture method SPLASH. However, their functional significance in coordinated genome packaging remains largely unclear. Here, we show by systematic mutational analysis that mutant A/SC35M (H7N7) viruses lacking several prominent SPLASH-identified vRNA-vRNA interactions involving the HA segment package the eight genome segments as efficiently as the wild-type virus. We therefore propose that the vRNA-vRNA interactions identified by SPLASH in IAV particles are not necessarily critical for the genome packaging process, leaving the underlying molecular mechanism elusive., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

A novel actinomycetal strain, designated M600PL45&#95;2 T , was isolated from marine sediments obtained from Ingleses beach, Porto, on the Northern Coast of Portugal and was subjected to a polyphasic taxonomic characterisation study. The here described Gram-reaction-positive strain is characterised by the production of a brown pigment in both solid and liquid medium and forms typical helical hyphae that differentiate into smooth spores. The results of a phylogenetic analysis based on the 16S rRNA gene sequence indicated that M600PL45&#95;2 T has a high similarity to two members of the genus Streptomyces , Streptomyces bathyalis ASO4wet T (98.51 %) and Streptomyces daqingensis NEAU ZJC8 T (98.44 %). The genome of M600PL45&#95;2 T has a size of 6 695 159 bp, a DNA G+C content of 70.71 mol% and 5538 coding sequences. M600PL45&#95;2 T grows at 15-37 °C and with a maximal growth rate between 25 °C and 30 °C. Growth at pH 6.0 to 9.0 with the optimal range between 6.0 and 7.5 was observed. M600PL45&#95;2 T showed a high salinity tolerance, growing with 0-10 % (w/v) NaCl, with best growth with 1-3% (w/v) NaCl. Major cellular fatty acids are iso-C 15:0 (25.03 %), anteiso-C 15:0 (17.70) and iso-C 16:0 (26.90 %). The novel isolate was able to grow in media containing a variety of nitrogen and carbon sources. An antimicrobial activity screening indicated that an extract of M600PL45&#95;2 T has inhibitory activity against Staphylococcus aureus . On the basis of the polyphasic data, M600PL45&#95;2 T (= CECT 30365 T = DSM 114036 T ) is introduced as the type strain of a novel species, that we named Streptomyces marispadix sp. nov.

Bacteria of the genus Salmonella pose a major risk to livestock, the food economy, and public health. Salmonella infections are one of the leading causes of food poisoning. The identification of serovars of Salmonella achieved by their diverse surface antigens is essential to gain information on their epidemiological context. Traditionally, slide agglutination has been used for serotyping. In recent years, whole-genome sequencing (WGS) followed by in silico serotyping has been established as an alternative method for serotyping and the detection of genetic markers for Salmonella . Until now, WGS data generated with Illumina sequencing are used to validate in silico serotyping methods. Oxford Nanopore Technologies (ONT) opens the possibility to sequence ultra-long reads and has frequently been used for bacterial sequencing. In this study, ONT sequencing data of 28 Salmonella strains of different serovars with epidemiological relevance in humans, food, and animals were taken to investigate the performance of the in silico serotyping tools SISTR and SeqSero2 compared to traditional slide agglutination tests. Moreover, the detection of genetic markers for resistance against antimicrobial agents, virulence, and plasmids was studied by comparing WGS data based on ONT with WGS data based on Illumina. Based on the ONT data from flow cell version R9.4.1, in silico serotyping achieved an accuracy of 96.4 and 92% for the tools SISTR and SeqSero2, respectively. Highly similar sets of genetic markers comparing both sequencing technologies were identified. Taking the ongoing improvement of basecalling and flow cells into account, ONT data can be used for Salmonella in silico serotyping and genetic marker detection., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Thomas, Methner, Marz and Linde.)

Background: Chlamydia (C.) psittaci, the causative agent of avian chlamydiosis and human psittacosis, is a genetically heterogeneous species. Its broad host range includes parrots and many other birds, but occasionally also humans (via zoonotic transmission), ruminants, horses, swine and rodents. To assess whether there are genetic markers associated with host tropism we comparatively analyzed whole-genome sequences of 61 C. psittaci strains, 47 of which carrying a 7.6-kbp plasmid., Results: Following clean-up, reassembly and polishing of poorly assembled genomes from public databases, phylogenetic analyses using C. psittaci whole-genome sequence alignment revealed four major clades within this species. Clade 1 represents the most recent lineage comprising 40/61 strains and contains 9/10 of the psittacine strains, including type strain 6BC, and 10/13 of human isolates. Strains from different non-psittacine hosts clustered in Clades 2- 4. We found that clade membership correlates with typing schemes based on SNP types, ompA genotypes, multilocus sequence types as well as plasticity zone (PZ) structure and host preference. Genome analysis also revealed that i) sequence variation in the major outer membrane porin MOMP can result in 3D structural changes of immunogenic domains, ii) past host change of Clade 3 and 4 strains could be associated with loss of MAC/perforin in the PZ, rather than the large cytotoxin, iii) the distinct phylogeny of atypical strains (Clades 3 and 4) is also reflected in their repertoire of inclusion proteins (Inc family) and polymorphic membrane proteins (Pmps)., Conclusions: Our study identified a number of genomic features that can be correlated with the phylogeny and host preference of C. psittaci strains. Our data show that intra-species genomic divergence is associated with past host change and includes deletions in the plasticity zone, structural variations in immunogenic domains and distinct repertoires of virulence factors., (© 2023. The Author(s).)

Background: Most plant-pathogenic Xanthomonas bacteria harbor transcription activator-like effector (TALE) genes, which function as transcriptional activators of host plant genes and support infection. The entire repertoire of up to 29 TALE genes of a Xanthomonas strain is also referred to as TALome. The DNA-binding domain of TALEs is comprised of highly conserved repeats and TALE genes often occur in gene clusters, which precludes the assembly of TALE-carrying Xanthomonas genomes based on standard sequencing approaches., Results: Here, we report the successful assembly of the 5 Mbp genomes of five Xanthomonas strains from Oxford Nanopore Technologies (ONT) sequencing data. For one of these strains, Xanthomonas oryzae pv. oryzae (Xoo) PXO35, we illustrate why Illumina short reads and longer PacBio reads are insufficient to fully resolve the genome. While ONT reads are perfectly suited to yield highly contiguous genomes, they suffer from a specific error profile within homopolymers. To still yield complete and correct TALomes from ONT assemblies, we present a computational correction pipeline specifically tailored to TALE genes, which yields at least comparable accuracy as Illumina-based polishing. We further systematically assess the ONT-based pipeline for its multiplexing capacity and find that, combined with computational correction, the complete TALome of Xoo PXO35 could have been reconstructed from less than 20,000 ONT reads., Conclusions: Our results indicate that multiplexed ONT sequencing combined with a computational correction of TALE genes constitutes a highly capable tool for characterizing the TALomes of huge collections of Xanthomonas strains in the future., (© 2023. The Author(s).)

Placenta accreta spectrum (PAS) is one of the major causes of maternal morbidity and mortality worldwide with increasing incidence. PAS refers to a group of pathological conditions ranging from the abnormal attachment of the placenta to the uterus wall to its perforation and, in extreme cases, invasion into surrounding organs. Among them, placenta accreta is characterized by a direct adhesion of the villi to the myometrium without invasion and remains the most common diagnosis of PAS. Here, we identify the potential regulatory miRNA and target networks contributing to placenta accreta development. Using small RNA-Seq followed by RT-PCR confirmation, altered miRNA expression, including that of members of placenta-specific miRNA clusters (e.g., C19MC and C14MC), was identified in placenta accreta samples compared to normal placental tissues. In situ hybridization (ISH) revealed expression of altered miRNAs mostly in trophoblast but also in endothelial cells and this profile was similar among all evaluated degrees of PAS. Kyoto encyclopedia of genes and genomes (KEGG) analyses showed enriched pathways dysregulated in PAS associated with cell cycle regulation, inflammation, and invasion. mRNAs of genes associated with cell cycle and inflammation were downregulated in PAS. At the protein level, NF-κB was upregulated while PTEN was downregulated in placenta accreta tissue. The identified miRNAs and their targets are associated with signaling pathways relevant to controlling trophoblast function. Therefore, this study provides miRNA:mRNA associations that could be useful for understanding PAS onset and progression., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Murrieta-Coxca, Barth, Fuentes-Zacarias, Gutiérrez-Samudio, Groten, Gellhaus, Köninger, Marz, Markert and Morales-Prieto.)

In the past five years, deep learning methods have become state-of-the-art in solving various inverse problems. Before such approaches can find application in safety-critical fields, a verification of their reliability appears mandatory. Recent works have pointed out instabilities of deep neural networks for several image reconstruction tasks. In analogy to adversarial attacks in classification, it was shown that slight distortions in the input domain may cause severe artifacts. The present article sheds new light on this concern, by conducting an extensive study of the robustness of deep-learning-based algorithms for solving underdetermined inverse problems. This covers compressed sensing with Gaussian measurements as well as image recovery from Fourier and Radon measurements, including a real-world scenario for magnetic resonance imaging (using the NYU-fastMRI dataset). Our main focus is on computing adversarial perturbations of the measurements that maximize the reconstruction error. A distinctive feature of our approach is the quantitative and qualitative comparison with total-variation minimization, which serves as a provably robust reference method. In contrast to previous findings, our results reveal that standard end-to-end network architectures are not only resilient against statistical noise, but also against adversarial perturbations. All considered networks are trained by common deep learning techniques, without sophisticated defense strategies.