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https://www.readbyqxmd.com/read/28645204/when-homoplasy-is-not-homoplasy-dissecting-trait-evolution-by-contrasting-composite-and-reductive-coding
#1
Alejandro Torres-Montúfar, Thomas Borsch, Helga Ochoterena
The conceptualization and coding of characters is a difficult issue in phylogenetic systematics, no matter which inference method is used when reconstructing phylogenetic trees or if the characters are just mapped onto a specific tree. Complex characters are groups of features that can be divided into simpler hierarchical characters (reductive coding), although the implied hierarchical relational information may change depending on the type of coding (composite vs reductive). Up to now, there is no common agreement to either code characters as complex or simple...
June 22, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28645197/pht%C3%AE-promoted-mobilization-of-non-conjugative-resistance-plasmids-from-enterococcus-faecium-to-enterococcus-faecalis
#2
Laura Di Sante, Gianluca Morroni, Andrea Brenciani, Carla Vignaroli, Alberto Antonelli, Marco Maria D'Andrea, Andrea Di Cesare, Eleonora Giovanetti, Pietro E Varaldo, Gian Maria Rossolini, Francesca Biavasco
Objectives: : To analyse the recombination events associated with conjugal mobilization of two multiresistance plasmids, pRUM 17i48 and pLAG (formerly named pDO1-like), from Enterococcus faecium 17i48 to Enterococcus faecalis JH2-2. Methods: : The plasmids from two E. faecalis transconjugants (JH-4T, tetracycline resistant, and JH-8E, erythromycin resistant) and from the E. faecium donor (also carrying a pHTβ-like conjugative plasmid, named pHTβ 17i48 ) were investigated by several methods, including PCR mapping and sequencing, S1-PFGE followed by Southern blotting and hybridization, and WGS...
June 22, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28645175/perturbation-to-cholesterol-at-the-neuromuscular-junction-confers-botulinum-neurotoxin-a-sensitivity-to-neonatal-mice
#3
Baskaran Thyagarajan, Joseph G Potian, Joseph J McArdle, Padmamalini Baskaran
Botulinum neurotoxin A (BoNT/A) cleaves SNAP25 at the motor nerve terminals (MNT) and inhibits stimulus evoked acetylcholine release (SEAR). This causes skeletal muscle paralysis. However, younger neonatal mice (<P7; less than 7 days old) are resistant to the neuroparalytic effects of BoNT/A. That is, in vivo injection of BoNT/A at the innervations of Extensor digitorum longus (EDL) muscle in the hindlimbs inhibited the toe spread reflex within 24 hours following BoNT/A injection in adult mouse and in older (> P7) neonatal mice younger than 7 days-age remained unaffected by BoNT/A injection...
June 22, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28645169/heterodimerization-of-arabidopsis-calcium-proton-exchangers-contributes-to-regulation-of-guard-cell-dynamics-and-plant-defense-responses
#4
Bradleigh Hocking, Simon J Conn, Murli Manohar, Bo Xu, Asmini Athman, Matthew A Stancombe, Alex R Webb, Kendal D Hirschi, Matthew Gilliham
Arabidopsis thaliana cation exchangers (CAX1 and CAX3) are closely related tonoplast-localized calcium/proton (Ca2+/H+) antiporters that contribute to cellular Ca2+ homeostasis. CAX1 and CAX3 were previously shown to interact in yeast; however, the function of this complex in plants has remained elusive. Here, we demonstrate that expression of CAX1 and CAX3 occurs in guard cells. Additionally, CAX1 and CAX3 are co-expressed in mesophyll tissue in response to wounding or flg22 treatment, due to the induction of CAX3 expression...
June 22, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28645168/genomic-reconstruction-of-the-history-of-native-sheep-reveals-the-peopling-patterns-of-nomads-and-the-expansion-of-early-pastoralism-in-east-asia
#5
Yong-Xin Zhao, Ji Yang, Feng-Hua Lv, Xiao-Ju Hu, Xing-Long Xie, Min Zhang, Wen-Rong Li, Ming-Jun Liu, Yu-Tao Wang, Jin-Quan Li, Yong-Gang Liu, Yan-Ling Ren, Feng Wang, EEr Hehua, Juha Kantanen, Johannes Arjen Lenstra, Jian-Lin Han, Meng-Hua Li
China has a rich resource of native sheep (Ovis aries) breeds associated with historical movements of several nomadic societies. However, the history of sheep and the associated nomadic societies in ancient China remains poorly understood. Here, we studied the genomic diversity of Chinese sheep using genome-wide SNPs, mitochondrial and Y-chromosomal variations in more than 1,000 modern samples. Population genomic analyses combined with archaeological records and historical ethnic demographics data revealed genetic signatures of their origins, secondary expansions and admixtures, thereby revealing the peopling patterns of nomads and the expansion of early pastoralism in East Asia...
June 22, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28645155/features-of-genomic-organization-in-a-nucleotide-resolution-molecular-model-of-the-escherichia-coli-chromosome
#6
William C Hacker, Shuxiang Li, Adrian H Elcock
We describe structural models of the Escherichia coli chromosome in which the positions of all 4.6 million nucleotides of each DNA strand are resolved. Models consistent with two basic chromosomal orientations, differing in their positioning of the origin of replication, have been constructed. In both types of model, the chromosome is partitioned into plectoneme-abundant and plectoneme-free regions, with plectoneme lengths and branching patterns matching experimental distributions, and with spatial distributions of highly-transcribed chromosomal regions matching recent experimental measurements of the distribution of RNA polymerases...
June 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28645146/analysis-of-in-vitro-evolution-reveals-the-underlying-distribution-of-catalytic-activity-among-random-sequences
#7
Abe Pressman, Janina E Moretti, Gregory W Campbell, Ulrich F Müller, Irene A Chen
The emergence of catalytic RNA is believed to have been a key event during the origin of life. Understanding how catalytic activity is distributed across random sequences is fundamental to estimating the probability that catalytic sequences would emerge. Here, we analyze the in vitro evolution of triphosphorylating ribozymes and translate their fitnesses into absolute estimates of catalytic activity for hundreds of ribozyme families. The analysis efficiently identified highly active ribozymes and estimated catalytic activity with good accuracy...
June 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28645115/a-comprehensive-review-of-heregulins-her3-and-her4-as-potential-therapeutic-targets-in-cancer
#8
REVIEW
Jose Mauricio Mota, Katharine Ann Collier, Ricardo Lima Barros Costa, Timothy Taxter, Aparna Kalyan, Caio A Leite, Young Kwang Chae, Francis J Giles, Benedito A Carneiro
Heregulins (HRGs) bind to the receptors HER3 or HER4, induce receptor dimerization, and trigger downstream signaling that leads to tumor progression and resistance to targeted therapies. Increased expression of HRGs has been associated with worse clinical prognosis; therefore, attempts to block HRG-dependent tumor growth have been pursued. This manuscript summarizes the function and signaling of HRGs and review the preclinical evidence of its involvement in carcinogenesis, prognosis, and treatment resistance in several malignancies such as colorectal cancer, non-small cell lung cancer, ovarian cancer, and breast cancer...
June 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28645114/association-of-type-2-diabetes-with-liver-cirrhosis-a-nationwide-cohort-study
#9
Ping-Hsin Hsieh, Jing-Yang Huang, Oswald Ndi Nfor, Chia-Chi Lung, Chien-Chang Ho, Yung-Po Liaw
BACKGROUND: The link between the subcategories of liver cirrhosis and type 2 diabetes is not well known. We investigated the association of type 2 diabetes mellitus with alcoholic cirrhosis and cirrhosis without alcohol. METHODS: This nationwide cohort study used the Taiwan National Health Insurance Research Database. Cirrhotic individuals and their matched controls were identified from 2001-2008. In all, 9 313 cirrhotic patients aged 20 years or older were matched by age, sex, and index date with the non-cirrhotic individuals (n = 37 252)...
June 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28645111/intersecting-transcriptomic-profiling-technologies-and-long-non-coding-rna-function-in-lung-adenocarcinoma-discovery-mechanisms-and-therapeutic-applications
#10
REVIEW
Jonathan Castillo, Theresa R Stueve, Crystal N Marconett
Previously thought of as junk transcripts and pseudogene remnants, long non-coding RNAs (lncRNAs) have come into their own over the last decade as an essential component of cellular activity, regulating a plethora of functions within multicellular organisms. lncRNAs are now known to participate in development, cellular homeostasis, immunological processes, and the development of disease. With the advent of next generation sequencing technology, hundreds of thousands of lncRNAs have been identified. However, movement beyond mere discovery to the understanding of molecular processes has been stymied by the complicated genomic structure, tissue-restricted expression, and diverse regulatory roles lncRNAs play...
June 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28645105/a-three-gene-immunohistochemical-panel-serves-as-an-adjunct-to-clinical-staging-of-patients-with-head-and-neck-cancer
#11
Chin-Ann J Ong, Nicholas B Shannon, Stefan Mueller, Sze Min Lek, Xuan Qiu, Fui Teen Chong, Ke Li, Kelvin K N Koh, Gerald C A Tay, Thakshayeni Skanthakumar, Jacqueline S G Hwang, Tony Kiat Hon Lim, Mei Kim Ang, Daniel S W Tan, Ngian-Chye Tan, Hiang Khoon Tan, Khee Chee Soo, N Gopalakrishna Iyer
BACKGROUND: Current management of head and neck squamous cell carcinoma (HNSCC) depends on tumor staging. Despite refinements in clinical staging algorithms, outcomes remain unchanged for the last two decades. In this study, we set out to identify a small, clinically applicable molecular panel to aid prognostication of patients with HNSCC. MATERIALS AND METHODS: Data from The Cancer Genome Atlas (TCGA) was used to derive copy number aberrations and expression changes to identify putative prognostic genes...
June 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/28645104/b7-h4-as-an-independent-prognostic-indicator-of-cancer-patients-a-meta-analysis
#12
Zibo Meng, Feiyang Wang, Yushun Zhang, Shoukang Li, Heshui Wu
The expression of B7-H4 was observed in a variety of tumors, however the prognostic value in cancer was still controversial. Therefore, we conducted this meta-analysis to explore the potential role of B7-H4 in cancer prognostic prediction. Twenty-seven studies including 3771 patients were brought into the analysis according to the inclusion and exclusion criteria. The pooled results demonstrated that elevated B7-H4 predicted a poor OS (HR = 1.93, 95% CI 1.71-2.18, P < 0.001) and DFS (HR = 1.84, 95% CI 1...
June 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/28645103/colxv-promotes-adipocyte-differentiation-via-inhibiting-dna-methylation-and-camp-pka-pathway-in-mice
#13
Guannv Liu, Meihang Li, Yatao Xu, Song Wu, Muhammad Saeed, Chao Sun
Extracellular matrix (ECM), as an essential component of adipose tissue, not only provides mechanical support for adipocyte growth, but also participates in ECM-adipocyte communication via various secreted proteins, including highly enriched collagens. Collagen XV (ColXV) is a secreted non-fibrillar collagen within ECM Basement Membrane (BM) zones and well recognized as a tumor suppressor. However, the role of ColXV in adipose tissue is still unknown. In this study, high fat diet (HFD) fed mice were used as obese model, in which we deeply investigated the interaction between ColXV and adipocyte differentiation or adipose metabolism...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28645093/identification-of-key-outcome-measures-when-using-the-instrumented-timed-up-and-go-and-or-posturography-for-fall-screening
#14
Renee Beach Sample, Allison L Kinney, Kurt Jackson, Wiebke Diestelkamp, Kimberly Edginton Bigelow
The Timed Up and Go (TUG) has been commonly used for fall risk assessment. The instrumented Timed Up and Go (iTUG) adds wearable sensors to capture sub-movements and may be more sensitive. Posturography assessments have also been used for determining fall risk. This study used stepwise logistic regression models to identify key outcome measures for the iTUG and posturography protocols. The effectiveness of the models containing these measures in differentiating fallers from non-fallers were then compared for each: iTUG total time duration only, iTUG, posturography, and combined iTUG and posturography assessments...
June 10, 2017: Gait & Posture
https://www.readbyqxmd.com/read/28645073/analysis-of-ldlr-variants-from-homozygous-fh-patients-carrying-multiple-mutations-in-the-ldlr-gene
#15
Long Jiang, Asier Benito-Vicente, Ling Tang, Aitor Etxebarria, Wei Cui, Kepa B Uribe, Xiao-Dong Pan, Helena Ostolaza, Shi-Wei Yang, Yu-Jie Zhou, Cesar Martin, Lu-Ya Wang
BACKGROUND AND AIMS: Familial hypercholesterolemia (FH) is an autosomal dominant disease with widespread global prevalence that partially accounts for the high prevalence of premature coronary heart disease. Although the majority of research on FH has focused on single heterozygous LDLR mutations, there have been limited reports of double LDLR mutations on the same chromosome. The aim of this study was to gain insight into the clinical consequences of the presence of multiple mutations in the LDLR gene...
June 8, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28645070/passive-smoking-and-mortality-from-aortic-dissection-or-aneurysm
#16
Tomomi Kihara, Kazumasa Yamagishi, Hiroyasu Iso, Akiko Tamakoshi
BACKGROUND AND AIMS: Evidence on the association between passive smoking and risk of aortic dissection or aneurysm is limited. This study aimed to investigate whether passive smoking increases risk of mortality from aortic dissection or aneurysm. METHODS: The Japan Collaborative Cohort (JACC) Study is a prospective community-based cohort study begun in 1988-90 and followed up to the end of 2009. We examined 48,677 individuals (mean age, 56 years; women, 46%) without history of stroke, coronary heart disease, or cancer, who provided valid responses to a lifestyle questionnaire including questions on active and passive smoking...
June 9, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28645053/assessment-of-imaging-in-flow-system-flowcam-for-systematic-ballast-water-management
#17
Leonardo Romero-Martínez, Cees van Slooten, Enrique Nebot, Asunción Acevedo-Merino, Louis Peperzak
Assessing the disinfection of ballast water and its compliance with international standards requires determining the size, viability, and concentration of planktonic organisms. The FlowCAM (Flow Cytometer and Microscope) is an Imaging Flow Cytometry designed to obtain the particle concentration, images, and quantitative morphologic information. The objective in this paper is to establish the basis for transforming the FlowCAM from being a laboratory analyzer into a tool for systematic monitoring of ballast water...
June 20, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28645051/enantioselective-disturbance-of-chiral-herbicide-dichlorprop-to-nitrogen-metabolism-of-arabidopsis-thaliana-regular-analysis-and-stable-isotope-attempt
#18
Zunwei Chen, Jia Wang, Siyu Chen, Yuezhong Wen
As the most essential element, nitrogen play a pivotal role in plant physiological process, which is susceptible to contaminants. However, the enantioselective effects of chiral herbicides on nitrogen metabolism have not been comprehensively understood. In this study, effects of chiral herbicide dichlorprop (DCPP) on the nitrogen behaviors in Arabidopsis thaliana were investigated. The results revealed that the uptakes of inorganic nitrogen (NO3(-) and NH4(+)) were preferentially impacted by herbicidal active (R)-DCPP, where the transportation of beneficial NO3(-) was inhibited but the toxic NH4(+) was accumulated...
June 20, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28645043/in-vitro-and-in-vivo-behavior-of-dna-tetrahedrons-as-tumor-targeting-nanocarriers-for-doxorubicin-delivery
#19
Ji Hee Kang, Kyoung-Ran Kim, Hyukjin Lee, Dae-Ro Ahn, Young Tag Ko
Deoxyribonucleic acid (DNA) is a versatile material with high applicability and inherent biocompatibility. L-DNA, the perfect mirror form of the naturally occurring D-DNA, has been used in DNA nanotechnology. It has thermodynamically identical properties to D-DNA, is capable of self-assembly and bio-orthogonal base-pairing, and is resistant to nuclease activity. We previously constructed an L-DNA tetrahedron (L-Td) and found that this nanostructure has remarkably higher capacity for cell penetration than its natural counterpart (D-Td)...
June 16, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28645023/maternal-serum-pfoa-concentration-and-dna-methylation-in-cord-blood-a-pilot-study
#20
Samantha L Kingsley, Karl T Kelsey, Rondi Butler, Aimin Chen, Melissa N Eliot, Megan E Romano, Andres Houseman, Devin C Koestler, Bruce P Lanphear, Kimberly Yolton, Joseph M Braun
Perfluorooctanoic acid (PFOA), a perfluoroalkyl substance, is commonly detected in the serum of pregnant women and may impact fetal development via epigenetic re-programming. In a pilot study, we explored associations between serum PFOA concentrations during pregnancy and offspring peripheral leukocyte DNA methylation at delivery in women with high (n = 22, range: 12-26ng/mL) and low (n = 22, range: 1.1-3.1ng/mL) PFOA concentrations. After adjusting for cell type, child sex, and income, we did not find differences in CpG methylation in the two exposure groups that reached epigenome-wide significance...
June 20, 2017: Environmental Research
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