journal
MENU ▼
Read by QxMD icon Read
search

Biology Direct

journal
https://www.readbyqxmd.com/read/27906033/the-role-of-the-backbone-torsion-in-protein-folding
#1
EDITORIAL
Irina Sorokina, Arcady Mushegian
BACKGROUND: The set of forces and sequence of events that govern the transition from an unfolded polypeptide chain to a functional protein with correct spatial structure remain incompletely known, despite the importance of the problem and decades of theory development, computer simulations, and laboratory experiments. Information about the correctly folded state of most proteins is likely to be present in their sequences, and yet many proteins fail to attain native structure after overexpression in a non-native environment or upon experimental denaturation and refolding...
December 1, 2016: Biology Direct
https://www.readbyqxmd.com/read/27894340/xhmmer3x2-utilizing-hmmer3-s-speed-and-hmmer2-s-sensitivity-and-specificity-in-the-glocal-alignment-mode-for-improved-large-scale-protein-domain-annotation
#2
Choon-Kong Yap, Birgit Eisenhaber, Frank Eisenhaber, Wing-Cheong Wong
BACKGROUND: While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of domain necessarily implies a unit of function, local-mode HMMER3 alone remains insufficient for precise function annotation tasks. In addition, the incomparable E-values for the same domain model by different HMMER builds create difficulty when checking for domain annotation consistency on a large-scale basis...
November 29, 2016: Biology Direct
https://www.readbyqxmd.com/read/27871336/zfas1-a-long-noncoding-rna-associated-with-ribosomes-in-breast-cancer-cells
#3
Herah Hansji, Euphemia Y Leung, Bruce C Baguley, Graeme J Finlay, David Cameron-Smith, Vandre C Figueiredo, Marjan E Askarian-Amiri
BACKGROUND: Most of the eukaryotic genome is transcribed, yielding a complex network of transcripts including thousands of lncRNAs that generally lack protein coding potential. However, only a small percentage of these molecules has been functionally characterised, and discoveries of specific functions demonstrate layers of complexity. A large percentage of lncRNAs is located in the cytoplasm, associated with ribosomes but the function of the majority of these transcripts is unclear. The current study analyses putative mechanisms of action of the lncRNA species member ZFAS1 that was initially discovered by microarray analysis of murine tissues undergoing mammary gland development...
November 21, 2016: Biology Direct
https://www.readbyqxmd.com/read/27835978/importins-promote-high-frequency-nf-%C3%AE%C2%BAb-oscillations-increasing-information-channel-capacity
#4
Zbigniew Korwek, Karolina Tudelska, Paweł Nałęcz-Jawecki, Maciej Czerkies, Wiktor Prus, Joanna Markiewicz, Marek Kochańczyk, Tomasz Lipniacki
BACKGROUND: Importins and exportins influence gene expression by enabling nucleocytoplasmic shuttling of transcription factors. A key transcription factor of innate immunity, NF-κB, is sequestered in the cytoplasm by its inhibitor, IκBα, which masks nuclear localization sequence of NF-κB. In response to TNFα or LPS, IκBα is degraded, which allows importins to bind NF-κB and shepherd it across nuclear pores. NF-κB nuclear activity is terminated when newly synthesized IκBα enters the nucleus, binds NF-κB and exportin which directs the complex to the cytoplasm...
November 11, 2016: Biology Direct
https://www.readbyqxmd.com/read/27825385/neurogenomics-and-the-role-of-a-large-mutational-target-on-rapid-behavioral-change
#5
Craig E Stanley, Rob J Kulathinal
BACKGROUND: Behavior, while complex and dynamic, is among the most diverse, derived, and rapidly evolving traits in animals. The highly labile nature of heritable behavioral change is observed in such evolutionary phenomena as the emergence of converged behaviors in domesticated animals, the rapid evolution of preferences, and the routine development of ethological isolation between diverging populations and species. In fact, it is believed that nervous system development and its potential to evolve a seemingly infinite array of behavioral innovations played a major role in the successful diversification of metazoans, including our own human lineage...
November 8, 2016: Biology Direct
https://www.readbyqxmd.com/read/27809935/identification-of-micrornas-regulating-escherichia-coli-f18-infection-in-meishan-weaned-piglets
#6
Zhengchang Wu, Weiyun Qin, Seng Wu, Guoqiang Zhu, Wenbin Bao, Shenglong Wu
BACKGROUND: Escherichia coli F18 is mainly responsible for post-weaning diarrhea (PWD) in piglets. The molecular regulation of E. coli F18 resistance in Chinese domestic weaned piglets is still obscure. We used Meishan piglets as model animals to test their susceptibility to E. coli F18. Small RNA duodenal libraries were constructed for E. coli F18-sensitive and -resistant weaned piglets challenged with E. coli F18 and sequenced using Illumina Solexa high-throughput sequencing technology...
November 3, 2016: Biology Direct
https://www.readbyqxmd.com/read/27809888/the-struggle-by-caenorhabditis-elegans-to-maintain-proteostasis-during-aging-and-disease
#7
REVIEW
Elise A Kikis
: The presence of only small amounts of misfolded protein is an indication of a healthy proteome. Maintaining proteome health, or more specifically, "proteostasis," is the purview of the "proteostasis network." This network must respond to constant fluctuations in the amount of destabilized proteins caused by errors in protein synthesis and exposure to acute proteotoxic conditions. Aging is associated with a gradual increase in damaged and misfolded protein, which places additional stress on the machinery of the proteostasis network...
November 3, 2016: Biology Direct
https://www.readbyqxmd.com/read/27776539/clip-gene-a-web-service-of-the-condition-specific-context-laid-integrative-analysis-for-gene-prioritization-in-mouse-tf-knockout-experiments
#8
Benjamin Hur, Sangsoo Lim, Heejoon Chae, Seokjun Seo, Sunwon Lee, Jaewoo Kang, Sun Kim
MOTIVATION: Transcriptome data from the gene knockout experiment in mouse is widely used to investigate functions of genes and relationship to phenotypes. When a gene is knocked out, it is important to identify which genes are affected by the knockout gene. Existing methods, including differentially expressed gene (DEG) methods, can be used for the analysis. However, existing methods require cutoff values to select candidate genes, which can produce either too many false positives or false negatives...
October 24, 2016: Biology Direct
https://www.readbyqxmd.com/read/27770811/long-range-personalized-cancer-treatment-strategies-incorporating-evolutionary-dynamics
#9
Chen-Hsiang Yeang, Robert A Beckman
BACKGROUND: Current cancer precision medicine strategies match therapies to static consensus molecular properties of an individual's cancer, thus determining the next therapeutic maneuver. These strategies typically maintain a constant treatment while the cancer is not worsening. However, cancers feature complicated sub-clonal structure and dynamic evolution. We have recently shown, in a comprehensive simulation of two non-cross resistant therapies across a broad parameter space representing realistic tumors, that substantial improvement in cure rates and median survival can be obtained utilizing dynamic precision medicine strategies...
October 22, 2016: Biology Direct
https://www.readbyqxmd.com/read/27769290/ipc-isoelectric-point-calculator
#10
Lukasz P Kozlowski
BACKGROUND: Accurate estimation of the isoelectric point (pI) based on the amino acid sequence is useful for many analytical biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary isoelectric focusing used in combination with high-throughput mass spectrometry. Additionally, pI estimation can be helpful during protein crystallization trials. RESULTS: Here, I present the Isoelectric Point Calculator (IPC), a web service and a standalone program for the accurate estimation of protein and peptide pI using different sets of dissociation constant (pKa) values, including two new computationally optimized pKa sets...
October 21, 2016: Biology Direct
https://www.readbyqxmd.com/read/27760563/evolution-of-the-tim17-protein-family
#11
Vojtěch Žárský, Pavel Doležal
BACKGROUND: The Tim17 family of proteins plays a fundamental role in the biogenesis of mitochondria. Three Tim17 family proteins, Tim17, Tim22, and Tim23, are the central components of the widely conserved multi-subunit protein translocases, TIM23 and TIM22, which mediate protein transport across and into the inner mitochondrial membrane, respectively. In addition, several Tim17 family proteins occupy the inner and outer membranes of plastids. RESULTS: We have performed comprehensive sequence analyses on 5631 proteomes from all domains of life deposited in the Uniprot database...
October 19, 2016: Biology Direct
https://www.readbyqxmd.com/read/27737715/cancer-heterogeneity-and-multilayer-spatial-evolutionary-games
#12
Andrzej Świerniak, Michał Krześlak
BACKGROUND: Evolutionary game theory (EGT) has been widely used to simulate tumour processes. In almost all studies on EGT models analysis is limited to two or three phenotypes. Our model contains four main phenotypes. Moreover, in a standard approach only heterogeneity of populations is studied, while cancer cells remain homogeneous. A multilayer approach proposed in this paper enables to study heterogeneity of single cells. METHOD: In the extended model presented in this paper we consider four strategies (phenotypes) that can arise by mutations...
October 13, 2016: Biology Direct
https://www.readbyqxmd.com/read/27737689/unexpected-links-reflect-the-noise-in-networks
#13
Anatoly Yambartsev, Michael A Perlin, Yevgeniy Kovchegov, Natalia Shulzhenko, Karina L Mine, Xiaoxi Dong, Andrey Morgun
BACKGROUND: Gene covariation networks are commonly used to study biological processes. The inference of gene covariation networks from observational data can be challenging, especially considering the large number of players involved and the small number of biological replicates available for analysis. RESULTS: We propose a new statistical method for estimating the number of erroneous edges in reconstructed networks that strongly enhances commonly used inference approaches...
October 13, 2016: Biology Direct
https://www.readbyqxmd.com/read/27733173/emergence-of-heterogeneity-in-acute-leukemias
#14
Thomas Stiehl, Christoph Lutz, Anna Marciniak-Czochra
BACKGROUND: Leukemias are malignant proliferative disorders of the blood forming system. Sequencing studies demonstrate that the leukemic cell population consists of multiple clones. The genetic relationship between the different clones, referred to as the clonal hierarchy, shows high interindividual variability. So far, the source of this heterogeneity and its clinical relevance remain unknown. We propose a mathematical model to study the emergence and evolution of clonal heterogeneity in acute leukemias...
October 12, 2016: Biology Direct
https://www.readbyqxmd.com/read/27681389/weighted-samgsr-combining-significance-analysis-of-microarray-gene-set-reduction-algorithm-with-pathway-topology-based-weights-to-select-relevant-genes
#15
Suyan Tian, Howard H Chang, Chi Wang
BACKGROUND: It has been demonstrated that a pathway-based feature selection method that incorporates biological information within pathways during the process of feature selection usually outperforms a gene-based feature selection algorithm in terms of predictive accuracy and stability. Significance analysis of microarray-gene set reduction algorithm (SAMGSR), an extension to a gene set analysis method with further reduction of the selected pathways to their respective core subsets, can be regarded as a pathway-based feature selection method...
September 29, 2016: Biology Direct
https://www.readbyqxmd.com/read/27671203/the-essence-of-life
#16
Wentao Ma
: Although biology has achieved great successes in recent years, we have not got a clear idea on "what is life?" Actually, as explained here, the main reason for this situation is that there are two completely distinct aspects for "life", which are usually talked about together. Indeed, in respect to these two aspects: Darwinian evolution and self-sustaining, we must split the concept of life correspondingly, for example, by defining "life form" and "living entity", separately. For life's implementation (related to the two aspects) in nature, three mechanisms are crucial: the replication of DNA/RNA-like polymers by residue-pairing, the sequence-dependent folding of RNA/protein-like polymers engendering special functions, and the assembly of phospholipid-like amphiphiles forming vesicles...
September 26, 2016: Biology Direct
https://www.readbyqxmd.com/read/27639379/computational-inference-of-a-genomic-pluripotency-signature-in-human-and-mouse-stem-cells
#17
Esra Kurum, Bérénice A Benayoun, Ankit Malhotra, Joshy George, Duygu Ucar
UNLABELLED: Recent analyses of next-generation sequencing datasets have shown that cell-specific regulatory elements in stem cells are marked with distinguishable patterns of transcription factor (TF) binding and epigenetic marks. For example, we recently demonstrated that promoters of cell-specific genes are covered with expanded trimethylation of histone H3 at lysine 4 (H3K4me3) marks (i.e., broad H3K4me3 domains). Moreover, binding of specific TFs, such as OCT4, NANOG, and SOX2, have been shown to play a critical role in maintaining the pluripotency of stem cells...
September 17, 2016: Biology Direct
https://www.readbyqxmd.com/read/27179769/biochemical-and-biophysical-characterization-of-cell-free-synthesized-rift-valley-fever-virus-nucleoprotein-capsids-enables-in-vitro-screening-to-identify-novel-antivirals
#18
Sean Broce, Lisa Hensley, Tomoharu Sato, Joshua Lehrer-Graiwer, Christian Essrich, Katie J Edwards, Jacqueline Pajda, Christopher J Davis, Rami Bhadresh, Clarence R Hurt, Beverly Freeman, Vishwanath R Lingappa, Colm A Kelleher, Marcela V Karpuj
BACKGROUND: Viral capsid assembly involves the oligomerization of the capsid nucleoprotein (NP), which is an essential step in viral replication and may represent a potential antiviral target. An in vitro transcription-translation reaction using a wheat germ (WG) extract in combination with a sandwich ELISA assay has recently been used to identify small molecules with antiviral activity against the rabies virus. RESULTS: Here, we examined the application of this system to viruses with capsids with a different structure, such as the Rift Valley fever virus (RVFV), the etiological agent of a severe emerging infectious disease...
May 14, 2016: Biology Direct
https://www.readbyqxmd.com/read/27055810/infinitely-long-branches-and-an-informal-test-of-common-ancestry
#19
Leonardo de Oliveira Martins, David Posada
BACKGROUND: The evidence for universal common ancestry (UCA) is vast and persuasive. A phylogenetic test has been proposed for quantifying its odds against independently originated sequences based on the comparison between one versus several trees. This test was successfully applied to a well-supported homologous sequence alignment, which was however criticized on the basis of simulations showing that alignments without any phylogenetic structure could mislead its conclusions. RESULTS: Here we present a simplified version of this same counterexample, which can be interpreted as a tree with arbitrarily long branches, and where the UCA test fails again...
April 7, 2016: Biology Direct
https://www.readbyqxmd.com/read/27655048/modpdzpep-a-web-resource-for-structure-based-analysis-of-human-pdz-mediated-interaction-networks
#20
Neetu Sain, Debasisa Mohanty
BACKGROUND: PDZ domains recognize short sequence stretches usually present in C-terminal of their interaction partners. Because of the involvement of PDZ domains in many important biological processes, several attempts have been made for developing bioinformatics tools for genome-wide identification of PDZ interaction networks. Currently available tools for prediction of interaction partners of PDZ domains utilize machine learning approach. Since, they have been trained using experimental substrate specificity data for specific PDZ families, their applicability is limited to PDZ families closely related to the training set...
2016: Biology Direct
journal
journal
41186
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"