625 results match your criteria Biology Direct [Journal]


Integrative analysis based on survival associated co-expression gene modules for predicting Neuroblastoma patients' survival time.

Biol Direct 2019 Feb 13;14(1). Epub 2019 Feb 13.

Department of Medicine, Indiana University School of Medicine, Indianapolis, USA.

Background: More than 90% of neuroblastoma patients are cured in the low-risk group while only less than 50% for those with high-risk disease can be cured. Since the high-risk patients still have poor outcomes, we need more accurate stratification to establish an individualized precise treatment plan for the patients to improve the long-term survival rate.

Results: We focus on extracting features and providing a workflow to improve survival prediction for neuroblastoma patients. Read More

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http://dx.doi.org/10.1186/s13062-018-0229-2DOI Listing
February 2019
2 Reads

From tumors to species: a SCANDAL hypothesis.

Biol Direct 2019 Jan 23;14(1). Epub 2019 Jan 23.

Institute for Information Transmission Problems, Bolshoy Karetniy Pereulok 19/1, Moscow, Russian Federation, 127051.

ᅟ: Some tumor cells can evolve into transmissible parasites. Notable examples include the Tasmanian devil facial tumor disease, the canine transmissible venereal tumor and transmissible cancers of mollusks. We present a hypothesis that such transmissible tumors existed in the past and that some modern animal taxa are descendants of these tumors. Read More

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http://dx.doi.org/10.1186/s13062-019-0233-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6343361PMC
January 2019

Exon skipping-rich transcriptomes of animals reflect the significance of exon-shuffling in metazoan proteome evolution.

Authors:
Laszlo Patthy

Biol Direct 2019 Jan 16;14(1). Epub 2019 Jan 16.

Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, H-1117, Hungary.

ᅟ: Animals are known to have higher rates of exon skipping than other eukaryotes. In a recent study, Grau-Bové et al. (Genome Biology 19:135, 2018) have used RNA-seq data across 65 eukaryotic species to investigate when and how this high prevalence of exon skipping evolved. Read More

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http://dx.doi.org/10.1186/s13062-019-0231-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335736PMC
January 2019
1 Read

Interface residues of transient protein-protein complexes have extensive intra-protein interactions apart from inter-protein interactions.

Biol Direct 2019 Jan 15;14(1). Epub 2019 Jan 15.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.

Background: Protein-protein interactions are crucial for normal biological processes and to regulate cellular reactions that affect gene expression and function. Several previous studies have emphasized the roles of residues at the interface of protein-protein complexes in conferring stability and specificity to the complex. Interface residues in a protein are well known for their interactions with sidechain and main chain atoms with the interacting protein. Read More

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http://dx.doi.org/10.1186/s13062-019-0232-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6334431PMC
January 2019
2 Reads

Response to Martin and colleagues: mitochondria do not boost the bioenergetic capacity of eukaryotic cells.

Biol Direct 2018 11 29;13(1):26. Epub 2018 Nov 29.

Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA.

A recent paper by (Gerlitz et al., Biol Direct 13:21, 2018) questions the validity of the data underlying prior analyses on the bioenergetics capacities of cells, and continues to promote the idea that the mitochondrion endowed eukaryotic cells with energetic superiority over prokaryotes. The former point has been addressed previously, with no resultant changes in the conclusions, and the latter point remains inconsistent with multiple lines of empirical data. Read More

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http://dx.doi.org/10.1186/s13062-018-0228-3DOI Listing
November 2018
1 Read

Sense-antisense gene overlap is probably a cause for retaining the few introns in Giardia genome and the implications.

Biol Direct 2018 10 17;13(1):23. Epub 2018 Oct 17.

State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.

Background: It is widely accepted that the last eukaryotic common ancestor and early eukaryotes were intron-rich and intron loss dominated subsequent evolution, thus the presence of only very few introns in some modern eukaryotes must be the consequence of massive loss. But it is striking that few eukaryotes were found to have completely lost introns. Despite extensive research, the causes of massive intron losses remain elusive. Read More

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http://dx.doi.org/10.1186/s13062-018-0226-5DOI Listing
October 2018
1 Read
4.658 Impact Factor

Assessment of urban microbiome assemblies with the help of targeted in silico gold standards.

Biol Direct 2018 10 12;13(1):22. Epub 2018 Oct 12.

Department Bioengineering, University of Applied Sciences FH Campus Wien, Vienna, Austria.

Background: Microbial communities play a crucial role in our environment and may influence human health tremendously. Despite being the place where human interaction is most abundant we still know little about the urban microbiome. This is highlighted by the large amount of unclassified DNA reads found in urban metagenome samples. Read More

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http://dx.doi.org/10.1186/s13062-018-0225-6DOI Listing
October 2018
1 Read

Darwinian selection of host and bacteria supports emergence of Lamarckian-like adaptation of the system as a whole.

Biol Direct 2018 10 26;13(1):24. Epub 2018 Oct 26.

Department of Biological Chemistry, Weizmann Institute of Science, 76100, Rehovot, Israel.

Background: The relatively fast selection of symbiotic bacteria within hosts and the potential transmission of these bacteria across generations of hosts raise the question of whether interactions between host and bacteria support emergent adaptive capabilities beyond those of germ-free hosts.

Results: To investigate possibilities for emergent adaptations that may distinguish composite host-microbiome systems from germ-free hosts, we introduce a population genetics model of a host-microbiome system with vertical transmission of bacteria. The host and its bacteria are jointly exposed to a toxic agent, creating a toxic stress that can be alleviated by selection of resistant individuals and by secretion of a detoxification agent ("detox"). Read More

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http://dx.doi.org/10.1186/s13062-018-0224-7DOI Listing
October 2018
1 Read

Molecular mechanisms of the juvenile form of Batten disease: important role of MAPK signaling pathways (ERK1/ERK2, JNK and p38) in pathogenesis of the malady.

Biol Direct 2018 09 25;13(1):19. Epub 2018 Sep 25.

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, GSP-7, 117997, Moscow, Russia.

Background: Mutations in the CLN3 gene lead to so far an incurable juvenile-onset neuronal ceroid lipofuscinosis (JNCL) or Batten disease that starts at the age of 4-6 years with a progressive retinopathy leading to blindness. Motor disturbances, epilepsy and dementia manifest during several following years. Most JNCL patients carry the same 1. Read More

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http://dx.doi.org/10.1186/s13062-018-0212-yDOI Listing
September 2018
1 Read

Reconstruction of endosomal organization and function by a combination of ODE and agent-based modeling strategies.

Biol Direct 2018 11 23;13(1):25. Epub 2018 Nov 23.

Nutritional Immunology and Molecular Medicine Laboratory, Biocomplexity Institute, Virginia Tech, Blacksburg, VA, USA.

Background: Reproducing cell processes using an in silico system is an essential tool for understanding the underlying mechanisms and emergent properties of this extraordinary complex biological machine. However, computational models are seldom applied in the field of intracellular trafficking. In a cell, numerous molecular interactions occur on the surface or in the interior of membrane-bound compartments that continually change position and undergo dynamic processes of fusion and fission. Read More

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http://dx.doi.org/10.1186/s13062-018-0227-4DOI Listing
November 2018
1 Read

Predicting clinical outcomes in neuroblastoma with genomic data integration.

Biol Direct 2018 09 27;13(1):20. Epub 2018 Sep 27.

Department of Computer Engineering, Antalya Bilim University, Antalya, Turkey.

Background: Neuroblastoma is a heterogeneous disease with diverse clinical outcomes. Current risk group models require improvement as patients within the same risk group can still show variable prognosis. Recently collected genome-wide datasets provide opportunities to infer neuroblastoma subtypes in a more unified way. Read More

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http://dx.doi.org/10.1186/s13062-018-0223-8DOI Listing
September 2018
1 Read

Stable coevolutionary regimes for genetic parasites and their hosts: you must differ to coevolve.

Biol Direct 2018 12 14;13(1):27. Epub 2018 Dec 14.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.

Background: Genetic parasites are ubiquitous satellites of cellular life forms most of which host a variety of mobile genetic elements including transposons, plasmids and viruses. Theoretical considerations and computer simulations suggest that emergence of genetic parasites is intrinsic to evolving replicator systems.

Results: Using methods of bifurcation analysis, we investigated the stability of simple models of replicator-parasite coevolution in a well-mixed environment. Read More

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http://dx.doi.org/10.1186/s13062-018-0230-9DOI Listing
December 2018
1 Read

Is pre-Darwinian evolution plausible?

Authors:
Marc Tessera

Biol Direct 2018 09 21;13(1):18. Epub 2018 Sep 21.

, Meudon, France.

Background: This essay highlights critical aspects of the plausibility of pre-Darwinian evolution. It is based on a critical review of some better-known open, far-from-equilibrium system-based scenarios supposed to explain processes that took place before Darwinian evolution had emerged and that resulted in the origin of the first systems capable of Darwinian evolution. The researchers' responses to eight crucial questions are reviewed. Read More

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http://dx.doi.org/10.1186/s13062-018-0216-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6151046PMC
September 2018
1 Read

Integration of multiple types of genetic markers for neuroblastoma may contribute to improved prediction of the overall survival.

Biol Direct 2018 09 20;13(1):17. Epub 2018 Sep 20.

Institute of Informatics, University of Białystok, Konstantego Ciołkowskiego 1M, Białystok, 15-245, Poland.

Background: Modern experimental techniques deliver data sets containing profiles of tens of thousands of potential molecular and genetic markers that can be used to improve medical diagnostics. Previous studies performed with three different experimental methods for the same set of neuroblastoma patients create opportunity to examine whether augmenting gene expression profiles with information on copy number variation can lead to improved predictions of patients survival. We propose methodology based on comprehensive cross-validation protocol, that includes feature selection within cross-validation loop and classification using machine learning. Read More

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http://dx.doi.org/10.1186/s13062-018-0222-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6148774PMC
September 2018
1 Read

MetaBinG2: a fast and accurate metagenomic sequence classification system for samples with many unknown organisms.

Biol Direct 2018 08 22;13(1):15. Epub 2018 Aug 22.

Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.

Background: Many methods have been developed for metagenomic sequence classification, and most of them depend heavily on genome sequences of the known organisms. A large portion of sequencing sequences may be classified as unknown, which greatly impairs our understanding of the whole sample.

Result: Here we present MetaBinG2, a fast method for metagenomic sequence classification, especially for samples with a large number of unknown organisms. Read More

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http://dx.doi.org/10.1186/s13062-018-0220-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6104016PMC
August 2018
2 Reads

Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome.

Biol Direct 2018 08 22;13(1):16. Epub 2018 Aug 22.

Clinical Bioinformatics Area, Fundación Progreso y Salud (FPS), CDCA, Hospital Virgen del Rocio, c/Manuel Siurot s/n, 41013, Sevilla, Spain.

Background: Despite the progress in neuroblastoma therapies the mortality of high-risk patients is still high (40-50%) and the molecular basis of the disease remains poorly known. Recently, a mathematical model was used to demonstrate that the network regulating stress signaling by the c-Jun N-terminal kinase pathway played a crucial role in survival of patients with neuroblastoma irrespective of their MYCN amplification status. This demonstrates the enormous potential of computational models of biological modules for the discovery of underlying molecular mechanisms of diseases. Read More

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http://dx.doi.org/10.1186/s13062-018-0219-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6106876PMC
August 2018
3 Reads

Accumulation of potential driver genes with genomic alterations predicts survival of high-risk neuroblastoma patients.

Biol Direct 2018 07 16;13(1):14. Epub 2018 Jul 16.

Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Box 281, Nobels vag 12A, Karolinska Institutet, 171 77, Stockholm, PO, Sweden.

Background: Neuroblastoma is the most common pediatric malignancy with heterogeneous clinical behaviors, ranging from spontaneous regression to aggressive progression. Many studies have identified aberrations related to the pathogenesis and prognosis, broadly classifying neuroblastoma patients into high- and low-risk groups, but predicting tumor progression and clinical management of high-risk patients remains a big challenge.

Results: We integrate gene-level expression, array-based comparative genomic hybridization and functional gene-interaction network of 145 neuroblastoma patients to detect potential driver genes. Read More

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http://dx.doi.org/10.1186/s13062-018-0218-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048860PMC
July 2018
4 Reads
1 Citation
4.660 Impact Factor

Modeling protein folding in vivo.

Biol Direct 2018 07 6;13(1):13. Epub 2018 Jul 6.

, McLean, USA.

A half century of studying protein folding in vitro and modeling it in silico has not provided us with a reliable computational method to predict the native conformations of proteins de novo, let alone identify the intermediates on their folding pathways. In this Opinion article, we suggest that the reason for this impasse is the over-reliance on current physical models of protein folding that are based on the assumption that proteins are able to fold spontaneously without assistance. These models arose from studies conducted in vitro on a biased sample of smaller, easier-to-isolate proteins, whose native structures appear to be thermodynamically stable. Read More

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http://dx.doi.org/10.1186/s13062-018-0217-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6035440PMC
July 2018
3 Reads

Predicting clinical outcome of neuroblastoma patients using an integrative network-based approach.

Biol Direct 2018 06 7;13(1):12. Epub 2018 Jun 7.

Proteome and Genome Research Unit, Department of Oncology, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, Strassen, L-1445, Luxembourg.

Background: One of the main current challenges in computational biology is to make sense of the huge amounts of multidimensional experimental data that are being produced. For instance, large cohorts of patients are often screened using different high-throughput technologies, effectively producing multiple patient-specific molecular profiles for hundreds or thousands of patients.

Results: We propose and implement a network-based method that integrates such patient omics data into Patient Similarity Networks. Read More

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http://dx.doi.org/10.1186/s13062-018-0214-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5992838PMC
June 2018
4 Reads

Predicting survival times for neuroblastoma patients using RNA-seq expression profiles.

Biol Direct 2018 05 30;13(1):11. Epub 2018 May 30.

Department of BiostatisticsUniversity of Florida, 2004 Mowry Rd, Gainesville, 32611, USA.

Background: Neuroblastoma is the most common tumor of early childhood and is notorious for its high variability in clinical presentation. Accurate prognosis has remained a challenge for many patients. In this study, expression profiles from RNA-sequencing are used to predict survival times directly. Read More

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http://dx.doi.org/10.1186/s13062-018-0213-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5977759PMC
May 2018
4 Reads

Unraveling bacterial fingerprints of city subways from microbiome 16S gene profiles.

Biol Direct 2018 05 22;13(1):10. Epub 2018 May 22.

Department of Biostatistics, University of Florida, 2004 Mowry Rd, Gainesville, FL, 32610, USA.

Background: Microbial communities can be location specific, and the abundance of species within locations can influence our ability to determine whether a sample belongs to one city or another. As part of the 2017 CAMDA MetaSUB Inter-City Challenge, next generation sequencing (NGS) data was generated from swipe samples collected from subway stations in Boston, New York City hereafter New York, and Sacramento. DNA was extracted and Illumina sequenced. Read More

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http://dx.doi.org/10.1186/s13062-018-0215-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5964687PMC
May 2018
6 Reads

Use of designed sequences in protein structure recognition.

Biol Direct 2018 05 9;13(1). Epub 2018 May 9.

Lab 103, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India.

Background: Knowledge of the protein structure is a pre-requisite for improved understanding of molecular function. The gap in the sequence-structure space has increased in the post-genomic era. Grouping related protein sequences into families can aid in narrowing the gap. Read More

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http://dx.doi.org/10.1186/s13062-018-0209-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5960202PMC
May 2018
5 Reads

Profiling microbial strains in urban environments using metagenomic sequencing data.

Biol Direct 2018 05 9;13(1). Epub 2018 May 9.

Centre for Integrative Biology, University of Trento, Via Sommarive 9, 38123, Trento, TN, Italy.

Background: The microbial communities populating human and natural environments have been extensively characterized with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a sample. Microbes thriving in urban environments may be crucially important for human health, but have received less attention than those of other environments. Ongoing efforts started to target urban microbiomes at a large scale, but the most recent computational methods to profile these metagenomes have never been applied in this context. Read More

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https://biologydirect.biomedcentral.com/articles/10.1186/s13
Publisher Site
http://dx.doi.org/10.1186/s13062-018-0211-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5944035PMC
May 2018
7 Reads

Conservation of the separase regulatory domain.

Biol Direct 2018 04 27;13(1). Epub 2018 Apr 27.

Department of Microbiology, University of Tennessee, 1414 Cumberland Ave, Knoxville, TN, 37996, USA.

ᅟ: We report a protein sequence analysis of the cell cycle regulatory protease, separase. The sequence and structural conservation of the C-terminal protease domain has long been recognized, whereas the N-terminal regulatory domain of separase was reported to lack detectable sequence similarity. Here we reveal significant sequence conservation of the separase regulatory domain and report a discovery of a cysteine motif (CxCxxC) conserved in major lineages of Metazoa including nematodes and vertebrates. Read More

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http://dx.doi.org/10.1186/s13062-018-0210-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5921967PMC
April 2018
3 Reads

MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs.

Biol Direct 2018 04 20;13(1). Epub 2018 Apr 20.

Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.

Background: There are numerous computational tools for taxonomic or functional analysis of microbiome samples, optimized to run on hundreds of millions of short, high quality sequencing reads. Programs such as MEGAN allow the user to interactively navigate these large datasets. Long read sequencing technologies continue to improve and produce increasing numbers of longer reads (of varying lengths in the range of 10k-1M bps, say), but of low quality. Read More

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http://dx.doi.org/10.1186/s13062-018-0208-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5910613PMC
April 2018
18 Reads

Multi-omics integration for neuroblastoma clinical endpoint prediction.

Biol Direct 2018 04 3;13(1). Epub 2018 Apr 3.

Fondazione Bruno Kessler, Via Sommarive 18, Trento, 38123, Italy.

Background: High-throughput methodologies such as microarrays and next-generation sequencing are routinely used in cancer research, generating complex data at different omics layers. The effective integration of omics data could provide a broader insight into the mechanisms of cancer biology, helping researchers and clinicians to develop personalized therapies.

Results: In the context of CAMDA 2017 Neuroblastoma Data Integration challenge, we explore the use of Integrative Network Fusion (INF), a bioinformatics framework combining a similarity network fusion with machine learning for the integration of multiple omics data. Read More

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http://dx.doi.org/10.1186/s13062-018-0207-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5907722PMC
April 2018
4 Reads

Prevalence of loss-of-function alleles does not correlate with lifetime fecundity and other life-history traits in metazoans.

Biol Direct 2018 03 2;13(1). Epub 2018 Mar 2.

Laboratory of Evolutionary Genomics, A.N. Belozersky Institute of Physico-Chemical Biology of Lomonosov Moscow State Universit, Moscow, 119992, Russia.

Background: Natural selection is possible only because all species produce more offsprings than what is needed to maintain the population. Still, the lifetime number of offspring varies widely across species. One may expect natural selection to be stronger in high-fecundity species. Read More

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http://dx.doi.org/10.1186/s13062-018-0206-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5834895PMC
March 2018
8 Reads

Genes sharing the protein family domain decrease the performance of classification with RNA-seq genomic signatures.

Biol Direct 2018 02 21;13(1). Epub 2018 Feb 21.

Scientific IT Services, ETH Zurich, Weinbergstrasse 11, Zürich, 8092, Switzerland.

Background: The experience with running various types of classification on the CAMDA neuroblastoma dataset have led us to the conclusion that the results are not always obvious and may differ depending on type of analysis and selection of genes used for classification. This paper aims in pointing out several factors that may influence the downstream machine learning analysis. In particular those factors are: type of the primary analysis, type of the classifier and increased correlation between the genes sharing a protein domain. Read More

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http://dx.doi.org/10.1186/s13062-018-0205-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5822623PMC
February 2018
5 Reads

Finite-size effects in transcript sequencing count distribution: its power-law correction necessarily precedes downstream normalization and comparative analysis.

Biol Direct 2018 02 12;13(1). Epub 2018 Feb 12.

Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Matrix, Singapore, 138671, Singapore.

Background: Though earlier works on modelling transcript abundance from vertebrates to lower eukaroytes have specifically singled out the Zip's law, the observed distributions often deviate from a single power-law slope. In hindsight, while power-laws of critical phenomena are derived asymptotically under the conditions of infinite observations, real world observations are finite where the finite-size effects will set in to force a power-law distribution into an exponential decay and consequently, manifests as a curvature (i.e. Read More

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https://biologydirect.biomedcentral.com/articles/10.1186/s13
Publisher Site
http://dx.doi.org/10.1186/s13062-018-0204-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5809866PMC
February 2018
5 Reads

Efficient differentially private learning improves drug sensitivity prediction.

Biol Direct 2018 02 6;13(1). Epub 2018 Feb 6.

Helsinki Institute for Information Technology HIIT, Department of Computer Science, Aalto University, Helsinki, Finland.

Background: Users of a personalised recommendation system face a dilemma: recommendations can be improved by learning from data, but only if other users are willing to share their private information. Good personalised predictions are vitally important in precision medicine, but genomic information on which the predictions are based is also particularly sensitive, as it directly identifies the patients and hence cannot easily be anonymised. Differential privacy has emerged as a potentially promising solution: privacy is considered sufficient if presence of individual patients cannot be distinguished. Read More

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http://dx.doi.org/10.1186/s13062-017-0203-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5801888PMC
February 2018
4 Reads

Inevitability of the emergence and persistence of genetic parasites caused by evolutionary instability of parasite-free states.

Biol Direct 2017 Dec 4;12(1):31. Epub 2017 Dec 4.

Institute for Molecules and Materials, Radboud University, 6525AJ, Nijmegen, Netherlands.

Genetic parasites, including viruses and mobile genetic elements, are ubiquitous among cellular life forms, and moreover, are the most abundant biological entities on earth that harbor the bulk of the genetic diversity. Here we examine simple thought experiments to demonstrate that both the emergence of parasites in simple replicator systems and their persistence in evolving life forms are inevitable because the putative parasite-free states are evolutionarily unstable.

Reviewers: This article has been reviewed by Yitzhak Pilpel, Bojan Zagrovic, and Eric van Nimwegen. Read More

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http://dx.doi.org/10.1186/s13062-017-0202-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5715634PMC
December 2017
14 Reads

Domestication of self-splicing introns during eukaryogenesis: the rise of the complex spliceosomal machinery.

Biol Direct 2017 Dec 1;12(1):30. Epub 2017 Dec 1.

Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.

ᅟ: The spliceosome is a eukaryote-specific complex that is essential for the removal of introns from pre-mRNA. It consists of five small nuclear RNAs (snRNAs) and over a hundred proteins, making it one of the most complex molecular machineries. Most of this complexity has emerged during eukaryogenesis, a period that is characterised by a drastic increase in cellular and genomic complexity. Read More

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http://dx.doi.org/10.1186/s13062-017-0201-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5709842PMC
December 2017
11 Reads

COGcollator: a web server for analysis of distant relationships between homologous protein families.

Biol Direct 2017 Nov 29;12(1):29. Epub 2017 Nov 29.

Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.

Background: The Clusters of Orthologous Groups (COGs) of proteins systematize evolutionary related proteins into specific groups with similar functions. However, the available databases do not provide means to assess the extent of similarity between the COGs.

Aim: We intended to provide a method for identification and visualization of evolutionary relationships between the COGs, as well as a respective web server. Read More

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http://dx.doi.org/10.1186/s13062-017-0198-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5706428PMC
November 2017
6 Reads

Over-expression of miR-146b and its regulatory role in intestinal epithelial cell viability, proliferation, and apoptosis in piglets.

Biol Direct 2017 Nov 25;12(1):27. Epub 2017 Nov 25.

Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310021, People's Republic of China.

Background: Weaning stress affects the small intestine of piglets. MiR-146b is differentially expressed in suckling and weaned piglets. In this study, we evaluated the effects of miR-146b on cell viability, proliferation, and apoptosis in IPEC-J2 cells. Read More

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http://dx.doi.org/10.1186/s13062-017-0199-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5702241PMC
November 2017
13 Reads

Sugar Lego: gene composition of bacterial carbohydrate metabolism genomic loci.

Biol Direct 2017 Nov 25;12(1):28. Epub 2017 Nov 25.

A.A.Kharkevich Institute for Information Transmission Problems, RAS, Bolshoy Karetny per. 19, Moscow, 127051, Russia.

Background: Bacterial carbohydrate metabolism is extremely diverse, since carbohydrates serve as a major energy source and are involved in a variety of cellular processes. Bacterial genes belonging to same metabolic pathway are often co-localized in the chromosome, but it is not a strict rule. Gene co-localization in linked to co-evolution and co-regulation. Read More

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http://dx.doi.org/10.1186/s13062-017-0200-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5702140PMC
November 2017
7 Reads

COGNAT: a web server for comparative analysis of genomic neighborhoods.

Biol Direct 2017 Nov 22;12(1):26. Epub 2017 Nov 22.

School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, Moscow, Russia.

Background: In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-transcribed genes. Those genes that evolved from a common ancestral gene by speciation (i. Read More

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http://dx.doi.org/10.1186/s13062-017-0196-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5700660PMC
November 2017
6 Reads

Cellular origin of the viral capsid-like bacterial microcompartments.

Biol Direct 2017 Nov 13;12(1):25. Epub 2017 Nov 13.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.

ᅟ: Bacterial microcompartments (BMC) are proteinaceous organelles that structurally resemble viral capsids, but encapsulate enzymes that perform various specialized biochemical reactions in the cell cytoplasm. The BMC are constructed from two major shell proteins, BMC-H and BMC-P, which form the facets and vertices of the icosahedral assembly, and are functionally equivalent to the major and minor capsid proteins of viruses, respectively. This equivalence notwithstanding, neither of the BMC proteins displays structural similarity to known capsid proteins, rendering the origins of the BMC enigmatic. Read More

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http://dx.doi.org/10.1186/s13062-017-0197-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5683377PMC
November 2017
10 Reads

ASXL gain-of-function truncation mutants: defective and dysregulated forms of a natural ribosomal frameshifting product?

Biol Direct 2017 10 16;12(1):24. Epub 2017 Oct 16.

Department of Pathology, Division of Virology, University of Cambridge, Cambridge, CB2 1QP, UK.

Background: Programmed ribosomal frameshifting (PRF) is a gene expression mechanism which enables the translation of two N-terminally coincident, C-terminally distinct protein products from a single mRNA. Many viruses utilize PRF to control or regulate gene expression, but very few phylogenetically conserved examples are known in vertebrate genes. Additional sex combs-like (ASXL) genes 1 and 2 encode important epigenetic and transcriptional regulatory proteins that control the expression of homeotic genes during key developmental stages. Read More

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http://dx.doi.org/10.1186/s13062-017-0195-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5644247PMC
October 2017
5 Reads

Why we don't want another "Synthesis".

Authors:
Arlin Stoltzfus

Biol Direct 2017 10 2;12(1):23. Epub 2017 Oct 2.

IBBR, 9600 Gudelsky Drive, Rockville, 20850, MD, USA.

High-level debates in evolutionary biology often treat the Modern Synthesis as a framework of population genetics, or as an intellectual lineage with a changing distribution of beliefs. Unfortunately, these flexible notions, used to negotiate decades of innovations, are now thoroughly detached from their historical roots in the original Modern Synthesis (OMS), a falsifiable scientific theory. The OMS held that evolution can be adequately understood as a process of smooth adaptive change by shifting the frequencies of small-effect alleles at many loci simultaneously, without the direct involvement of new mutations. Read More

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http://dx.doi.org/10.1186/s13062-017-0194-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5625744PMC
October 2017
6 Reads

Differential signal sensitivities can contribute to the stability of multispecies bacterial communities.

Biol Direct 2017 09 15;12(1):22. Epub 2017 Sep 15.

Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter Street 50/A, Budapest, H-1085, Hungary.

Background: Bacterial species present in multispecies microbial communities often react to the same chemical signal but at vastly different concentrations. The existence of different response thresholds with respect to the same signal molecule has been well documented in quorum sensing which is one of the best studied inter-cellular signalling mechanisms in bacteria. The biological significance of this phenomenon is still poorly understood, and cannot be easily studied in nature or in laboratory models. Read More

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http://dx.doi.org/10.1186/s13062-017-0192-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5602943PMC
September 2017
12 Reads

Evidence-based gene models for structural and functional annotations of the oil palm genome.

Biol Direct 2017 09 8;12(1):21. Epub 2017 Sep 8.

Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.

Background: Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes. Read More

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http://dx.doi.org/10.1186/s13062-017-0191-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5591544PMC
September 2017
15 Reads

On the global CRISPR array behavior in class I systems.

Biol Direct 2017 08 29;12(1):20. Epub 2017 Aug 29.

Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, 400 Dan Allen Drive, Schaub Hall, Campus box 7624, Raleigh, NC, 27695-7624, USA.

Background: Much effort is underway to build and upgrade databases and tools related to occurrence, diversity, and characterization of CRISPR-Cas systems. As microbial communities and their genome complements are unearthed, much emphasis has been placed on details of individual strains and model systems within the CRISPR-Cas classification, and that collection of information as a whole affords the opportunity to analyze CRISPR-Cas systems from a quantitative perspective to gain insight into distribution of CRISPR array sizes across the different classes, types and subtypes. CRISPR diversity, nomenclature, occurrence, and biological functions have generated a plethora of data that created a need to understand the size and distribution of these various systems to appreciate their features and complexity. Read More

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http://dx.doi.org/10.1186/s13062-017-0193-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5575924PMC
August 2017
5 Reads

Breath-giving cooperation: critical review of origin of mitochondria hypotheses : Major unanswered questions point to the importance of early ecology.

Biol Direct 2017 08 14;12(1):19. Epub 2017 Aug 14.

Eötvös Loránd University, Department of Plant Systematics, Ecology and Theoretical Biology, Pázmány P. sétány 1/C, Budapest, 1117, Hungary.

The origin of mitochondria is a unique and hard evolutionary problem, embedded within the origin of eukaryotes. The puzzle is challenging due to the egalitarian nature of the transition where lower-level units took over energy metabolism. Contending theories widely disagree on ancestral partners, initial conditions and unfolding of events. Read More

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http://dx.doi.org/10.1186/s13062-017-0190-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5557255PMC
August 2017
5 Reads

Cell adhesion heterogeneity reinforces tumour cell dissemination: novel insights from a mathematical model.

Biol Direct 2017 08 11;12(1):18. Epub 2017 Aug 11.

Center for Information Services and High Performance Computing, Technische Universität Dresden, Nöthnitzer Str. 46, Dresden, 01062, Germany.

Background: Cancer cell invasion, dissemination, and metastasis have been linked to an epithelial-mesenchymal transition (EMT) of individual tumour cells. During EMT, adhesion molecules like E-cadherin are downregulated and the decrease of cell-cell adhesion allows tumour cells to dissociate from the primary tumour mass. This complex process depends on intracellular cues that are subject to genetic and epigenetic variability, as well as extrinsic cues from the local environment resulting in a spatial heterogeneity in the adhesive phenotype of individual tumour cells. Read More

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http://dx.doi.org/10.1186/s13062-017-0188-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5553611PMC
August 2017
7 Reads

EMQIT: a machine learning approach for energy based PWM matrix quality improvement.

Biol Direct 2017 08 1;12(1):17. Epub 2017 Aug 1.

Institute of Automatic Control, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland.

Background: Transcription factor binding affinities to DNA play a key role for the gene regulation. Learning the specificity of the mechanisms of binding TFs to DNA is important both to experimentalists and theoreticians. With the development of high-throughput methods such as, e. Read More

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http://dx.doi.org/10.1186/s13062-017-0189-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5539975PMC
August 2017
5 Reads

Bacterial tail anchors can target to the mitochondrial outer membrane.

Biol Direct 2017 07 24;12(1):16. Epub 2017 Jul 24.

Department of Molecular Biology and Genetics, Koç University, 34450 Sarıyer, İstanbul, Turkey.

Background: During the generation and evolution of the eukaryotic cell, a proteobacterial endosymbiont was re-fashioned into the mitochondrion, an organelle that appears to have been present in the ancestor of all present-day eukaryotes. Mitochondria harbor proteomes derived from coding information located both inside and outside the organelle, and the rate-limiting step toward the formation of eukaryotic cells may have been development of an import apparatus allowing protein entry to mitochondria. Currently, a widely conserved translocon allows proteins to pass from the cytosol into mitochondria, but how proteins encoded outside of mitochondria were first directed to these organelles at the dawn of eukaryogenesis is not clear. Read More

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http://dx.doi.org/10.1186/s13062-017-0187-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5525287PMC
July 2017
6 Reads

Computational prediction of lncRNA-mRNA interactionsby integrating tissue specificity in human transcriptome.

Biol Direct 2017 06 8;12(1):15. Epub 2017 Jun 8.

Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1 Okubo Shinjuku-ku, Tokyo, 169-8555, Japan.

Long noncoding RNAs (lncRNAs) play a key role in normal tissue differentiation and cancer development through their tissue-specific expression in the human transcriptome. Recent investigations of macromolecular interactions have shown that tissue-specific lncRNAs form base-pairing interactions with various mRNAs associated with tissue-differentiation, suggesting that tissue specificity is an important factor controlling human lncRNA-mRNA interactions.Here, we report investigations of the tissue specificities of lncRNAs and mRNAs by using RNA-seq data across various human tissues as well as computational predictions of tissue-specific lncRNA-mRNA interactions inferred by integrating the tissue specificity of lncRNAs and mRNAs into our comprehensive prediction of human lncRNA-RNA interactions. Read More

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http://dx.doi.org/10.1186/s13062-017-0183-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465533PMC
June 2017
42 Reads

Rotational restriction of nascent peptides as an essential element of co-translational protein folding: possible molecular players and structural consequences.

Biol Direct 2017 05 31;12(1):14. Epub 2017 May 31.

McLean, Virginia, USA.

Background: A basic tenet of protein science is that all information about the spatial structure of proteins is present in their sequences. Nonetheless, many proteins fail to attain native structure upon experimental denaturation and refolding in vitro, raising the question of the specific role of cellular machinery in protein folding in vivo. Recently, we hypothesized that energy-dependent twisting of the protein backbone is an unappreciated essential factor guiding the protein folding process in vivo. Read More

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http://dx.doi.org/10.1186/s13062-017-0186-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5452302PMC
May 2017
20 Reads

The complex domain architecture of SAMD9 family proteins, predicted STAND-like NTPases, suggests new links to inflammation and apoptosis.

Biol Direct 2017 05 25;12(1):13. Epub 2017 May 25.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.

We report a comprehensive computational dissection of the domain architecture of the SAMD9 family proteins that are involved in antivirus and antitumor response in humans. We show that the SAMD9 protein family is represented in most animals and also, unexpectedly, in bacteria, in particular actinomycetes. From the N to C terminus, the core SAMD9 family architecture includes DNA/RNA-binding AlbA domain, a variant Sir2-like domain, a STAND-like P-loop NTPase, an array of TPR repeats and an OB-fold domain with predicted RNA-binding properties. Read More

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http://dx.doi.org/10.1186/s13062-017-0185-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5445408PMC
May 2017
31 Reads

Recognition of a structural domain (RWDBD) in Gcn1 proteins that interacts with the RWD domain containing proteins.

Biol Direct 2017 05 19;12(1):12. Epub 2017 May 19.

Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.

The protein Gcn1 (General control non-derepressible 1) is found in virtually all eukaryotes, and is a key component of the general amino acid control signal transduction pathway. This pathway is best known for its importance for cells to sense and overcome amino acid starvation. Gcn1 directly binds to the RWD (RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases) domain of the protein kinase Gcn2, and this is essential for delivering the starvation signal to Gcn2. Read More

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http://dx.doi.org/10.1186/s13062-017-0184-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5438488PMC
May 2017
26 Reads