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https://www.readbyqxmd.com/read/29047334/a-support-vector-machine-based-method-to-distinguish-long-non-coding-rnas-from-protein-coding-transcripts
#1
Hugo W Schneider, Taina Raiol, Marcelo M Brigido, Maria Emilia M T Walter, Peter F Stadler
BACKGROUND: In recent years, a rapidly increasing number of RNA transcripts has been generated by thousands of sequencing projects around the world, creating enormous volumes of transcript data to be analyzed. An important problem to be addressed when analyzing this data is distinguishing between long non-coding RNAs (lncRNAs) and protein coding transcripts (PCTs). Thus, we present a Support Vector Machine (SVM) based method to distinguish lncRNAs from PCTs, using features based on frequencies of nucleotide patterns and ORF lengths, in transcripts...
October 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29045705/outbreak-and-eradication-of-tropical-rat-mite-acari-macronyssidae-in-a-european-animal-facility
#2
Yeray Brito-Casillas, Mercedes Díaz-Sarmiento, Moisés García-Arencibia, Cristina Carranza, Antonio Castrillo, Leandro Fernández-Pérez, Manuel Zumbado-Peña, Jorge F González, Ana M Wägner, David Florin
A zoonotic, opportunistic out-break of tropical rat mite Ornithonyssus bacoti [Acari: Macronyssidae; Ornithonyssus bacoti (Hirst)] in an animal facility, is described. Immunocompetent mice [Mus musculus (Linnaeus)] and rat [Rattus norvegicus (Berkenhout)] strains in a conventional health status facility suffered from scratching and allopecia and staff members suffered from pruritic, erythemato-papular lesions, presumed to be allergic in origin. O. bacoti was identified and treatment with a 0.1% ivermectin solution led to its complete erradication...
October 17, 2017: Journal of Medical Entomology
https://www.readbyqxmd.com/read/29044990/transcriptome-analysis-for-uvb-induced-phototoxicity-in-mouse-retina
#3
Mi-Jin An, Chul-Hong Kim, Gyu-You Nam, Dae-Hyun Kim, Sangmyung Rhee, Sung-Jin Cho, Jung-Woong Kim
Throughout life, the human eye is continuously exposed to sunlight and artificial lighting. Ambient light exposure can lead to visual impairment and transient or permanent blindness. To mimic benign light stress conditions, Mus musculus eyes were exposed to low-energy UVB radiation, ensuring no severe morphological changes in the retinal structure post-exposure. We performed RNA-seq analysis to reveal the early transcriptional changes and key molecular pathways involved before the activation of the canonical cell death pathway...
October 17, 2017: Environmental Toxicology
https://www.readbyqxmd.com/read/29038520/decrypting-strong-and-weak-single-walled-carbon-nanotubes-interactions-with-mitochondrial-voltage-dependent-anion-channels-using-molecular-docking-and-perturbation-theory
#4
Michael González-Durruthy, Adriano V Werhli, Vinicius Seus, Karina S Machado, Alejandro Pazos, Cristian R Munteanu, Humberto González-Díaz, José M Monserrat
The current molecular docking study provided the Free Energy of Binding (FEB) for the interaction (nanotoxicity) between VDAC mitochondrial channels of three species (VDAC1-Mus musculus, VDAC1-Homo sapiens, VDAC2-Danio rerio) with SWCNT-H, SWCNT-OH, SWCNT-COOH carbon nanotubes. The general results showed that the FEB values were statistically more negative (p < 0.05) in the following order: (SWCNT-VDAC2-Danio rerio) > (SWCNT-VDAC1-Mus musculus) > (SWCNT-VDAC1-Homo sapiens) > (ATP-VDAC)...
October 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29037133/crystal-structure-of-wild-type-centrin-1-from-mus-musculus-occupied-by-ca2
#5
So Young Kim, Da Som Kim, Joo Eun Hong, Jung Hee Park
Mus musculus centrin 1 (MmCen1) is located at the cilium of photoreceptor cells connecting the outer segment through signal transduction components to the metabolically active inner segment. In the cilium, MmCen1 is involved in the translocation of transducin between compartments as a result of photoreceptor activation. In this study, we report the crystal structure of wild-type MmCen1 and its Ca2+-binding properties using structure-based mutagenesis. The crystal structure exhibits three structural features, i...
October 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29036674/detecting-and-characterizing-micrornas-of-diverse-genomic-origins-via-mirvial
#6
Jing Xia, Lun Li, Tiantian Li, Zhiwei Fang, Kevin Zhang, Junfei Zhou, Hai Peng, Weixiong Zhang
MicroRNAs form an essential class of post-transcriptional gene regulator of eukaryotic species, and play critical parts in development and disease and stress responses. MicroRNAs may originate from various genomic loci, have structural characteristics, and appear in canonical or modified forms, making them subtle to detect and analyze. We present miRvial, a robust computational method and companion software package that supports parameter adjustment and visual inspection of candidate microRNAs. Extensive results comparing miRvial and six existing microRNA finding methods on six model organisms, Mus musculus, Drosophila melanogaste, Arabidopsis thaliana, Oryza sativa, Physcomitrella patens and Chlamydomonas reinhardtii, demonstrated the utility and rigor of miRvial in detecting novel microRNAs and characterizing features of microRNAs...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29030315/natural-history-of-ixodes-affinis-in-virginia
#7
Robyn M Nadolny, Holly D Gaff
The ixodid tick species Ixodes affinis is expanding its range northward, changing the tick community population dynamics in the Mid-Atlantic United States. We present five years of surveillance on newly established populations of I. affinis throughout southeastern Virginia and discuss the habitat and host associations of I. affinis in this northernmost extent of its range. We found that I. affinis populations tend to persist once they are established, and populations tend to increase as ecological succession progresses, provided a vegetated understory persists...
September 29, 2017: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/29026851/wild-rodent-ectoparasites-collected-from-northwestern-iran
#8
Zabihollah Zarei, Mehdi Mohebali, Zahra Heidari, Eshrat Beigom Kia, Amrollah Azarm, Hasan Bakhshi, Jaber Davoodi, Hamid Hassanpour, Manizhe Roohnavaz, Mahya Khodabakhsh, Zakkyeh Telmadarraiy
BACKGROUND: Rodents play an important role as reservoir of some pathogens, and the host of some ectoparasites as well. These ectoparasites can transmit rodents' pathogens to human or animals. The aim of this study was to assess the distribution and infestation load of ectoparasites on rodents in Meshkin-Shahr District, northwestern Iran. METHODS: Rodents were captured using baited live traps in spring 2014 from Meshkin-Shahr District and were transferred to the laboratory for identification to the species level...
March 2017: Journal of Arthropod-borne Diseases
https://www.readbyqxmd.com/read/28986939/leishmania-infection-in-rodents-in-greece
#9
Ιoannis Tsakmakidis, Katerina Angelopoulou, Chrysostomos I Dovas, Εmmanouil Dokianakis, Αndroniki Tamvakis, Isaia Symeonidou, Μaria Antoniou, Αnastasia Diakou
OBJECTIVE: To investigate the prevalence of Leishmania infection in rodents from various areas of Northern Greece. METHODS: 97 rodents (66 Mus musculus, 18 Rattus norvegicus and 12 R. rattus) were collected during pest control programs and examined by cytology (spleen and liver smears), serology (ELISA) and PCR (real-time and gel-based) for Leishmania. Date, environment, sex, existence of dogs in the close environment were recorded for each rodent. All cytological preparations were negative, whereas specific IgG were detected in 54...
October 6, 2017: Tropical Medicine & International Health: TM & IH
https://www.readbyqxmd.com/read/28979348/natural-intestinal-protozoa-in-rodents-rodentia-gerbillinae-murinae-cricetinae-in-northwestern-iran
#10
Mehdi Mohebali, Zabiholah Zarei, Khadijeh Khanaliha, Eshrat Beigom Kia, Afsaneh Motavalli-Haghi, Jaber Davoodi, Tahereh Rezaeian, Fathemeh Tarighi, Mostafa Rezaeian
BACKGROUND: Majority of parasitic infections in rodents have zoonotic importance. This study aimed to determine the frequency and intensity of intestinal protozoa infections of rodents including Meriones persicus, Mus musculus and, Cricetulus migratorius. METHODS: This survey was conducted in Meshkin Shahr district in northwestern Iran from Mar. to Dec. of 2014. Intestinal samples of 204 rodents including M. persicus (n=117), M. musculus (n=63) and C. migratorius (n=24) were parasitologically examined...
July 2017: Iranian Journal of Parasitology
https://www.readbyqxmd.com/read/28973976/why-do-individuals-differ-in-viral-susceptibility-a-story-told-by-model-organisms
#11
REVIEW
Lisa van Sluijs, Gorben P Pijlman, Jan E Kammenga
Viral susceptibility and disease progression is determined by host genetic variation that underlies individual differences. Genetic polymorphisms that affect the phenotype upon infection have been well-studied for only a few viruses, such as HIV-1 and Hepatitis C virus. However, even for well-studied viruses the genetic basis of individual susceptibility differences remains elusive. Investigating the effect of causal polymorphisms in humans is complicated, because genetic methods to detect rare or small-effect polymorphisms are limited and genetic manipulation is not possible in human populations...
September 30, 2017: Viruses
https://www.readbyqxmd.com/read/28971448/a-paris-system-based-implant-approach-to-hyperthermia-cancer-tumor-with-gold-seeds-and-ultrasound
#12
C Austerlitz, J Melo, A L S Barros, I Gkigkitzis, I Haranas, D Campos
A Paris system-based implant approach has been used to improve the bio-heat distribution from implanted gold rods in insonated tissues. Experiments with single-plane implants using parallel equidistant 1.018 ± 0.015 cm height and 0.136 ± 0.001 cm diameter 24-K gold rods) arranged in triangular and square shapes were performed in Mus musculus white mice (medial dorsal region). The mice were anesthetized and gold rods were implanted by means of a trocar needle and the implanted region was insonated with a 4-cm diameter transducer oscillating with a nominal frequency of 1 MHz and power of about 75 W...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28971446/determination-of-soft-tissue-breakpoint-based-on-its-temperature-enhancement-pattern-in-vivo-and-in-vitro-experiments
#13
C Austerlitz, I Gkigkitzis, A L S Barros, J Melo, I Haranas, D Campos
The breakpoint of fresh commercial meats and in vivo mice has been assessed using tissue temperature enhancement pattern. A 1 cm length and 0.1 cm diameter gold rod was implanted in fresh chicken breast, beef, fish, and in vivo Mus musculus white mice and was insonated with ultrasound. The temperature enhancement of gold rods was measured with a needle type thermistor over a temperature range from 35 to 50 °C. From these results the breakpoints were determined by plotting the gold rod temperature versus ultrasound exposure duration using the interception point of two curves fitted by a linear regression equations of thermal response above and below 43 °C...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28969930/do-as-i-say-not-ch-as-i-do-lateral-control-of-cell-fate
#14
REVIEW
Marika Sjöqvist, Emma R Andersson
Breaking symmetry in populations of uniform cells, to induce adoption of an alternative cell fate, is an essential developmental mechanism. Similarly, domain and boundary establishment are crucial steps to forming organs during development. Notch signaling is a pathway ideally suited to mediating precise patterning cues, as both receptors and ligands are membrane-bound and can thus act as a precise switch to toggle cell fates on or off. Fine-tuning of signaling by positive or negative feedback mechanisms dictate whether signaling results in lateral induction or lateral inhibition, respectively, allowing Notch to either induce entire regions of cell specification, or dictate binary fate choices...
September 29, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28969710/molecular-detection-of-leishmania-infantum-and-leishmania-tropica-in-rodent-species-from-endemic-cutaneous-leishmaniasis-areas-in-morocco
#15
Mohamed Echchakery, Carmen Chicharro, Samia Boussaa, Javier Nieto, Eugenia Carrillo, Ortega Sheila, Javier Moreno, Ali Boumezzough
BACKGROUND: Leishmaniasis remains a major public health problem in African nations, including Morocco, where little is known about the vertebrate reservoirs involved in the causal parasites' transmission cycles. The present study investigates the role of rodent species as potential reservoirs of Leishmania spp. in central Morocco, where both L. tropica and L. infantum have been reported. METHODS: Rodents were caught from 22 sites in central Morocco, by using Sherman metal traps, and identified morphologically...
October 2, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28956157/survey-of-intestinal-helminths-collected-from-pet-rodents-in-m%C3%A3-xico
#16
Jesús Alonso Panti-May, Luis Caraveo-Centeno, Silvia F Hernández-Betancourt, María Del Rosario Robles, Carlos Machain-Williams
In this survey, intestinal helminths from pet rodents in Mérida, México, were analyzed. A total of 46 mice Mus musculus, 28 hamsters Mesocricetus auratus, 23 rats Rattus norvegicus, and 1 gerbil Meriones unguiculatus were purchased from six pet shops and one black market for wildlife in the city of Mérida. The overall prevalence of helminths in rodents was 61.2% (60/98). Six species of helminths were identified: the zoonotic cestode Rodentolepis nana, and the nematodes Aspiculuris tetraptera, Dentostomella translucida, Syphacia obvelata, Syphacia mesocriceti, and Syphacia muris...
September 27, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28951219/identification-and-characterization-of-pro-interleukin-16-from-mud-crab-scylla-paramamosain-the-first-evidence-of-proinflammatory-cytokine-in-crab-species
#17
Wen-Bin Gu, Yi-Lian Zhou, Dan-Dan Tu, Zhong-Kai Zhou, Qi-Hui Zhu, Yu-Yin Chen, Miao-An Shu
IL-16 is a pro-inflammatory cytokine originally designated as a lymphocyte chemoattractant factor. In mammal and avian, it has been characterized as an essential regulator of various cellular processes including cell recruitment and activation against pathogen invasion. So far, neither of the full-length of IL-16 homologue nor the response mechanism against pathogen was reported in crab species. In the present study, the pro-IL-16 homologue was firstly cloned and characterized from mud crab Scylla paramamosain...
September 23, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28948547/peptides-epigenetic-regulators-in-the-structure-of-rodents-with-a-long-and-short-lifespan
#18
V Kh Khavinson, D Yu Kormilets, A T Mar'yanovich
We have discovered motives of short-chain epigenetically active peptides in some proteins of long-lived African mole rat Heterocephalus glaber. These epigenetic regulators are located in the protein structure between lysine and arginine residues, thus facilitating their release in limited proteolysis. Some of these epigenetic regulators are not found in the proteins of short-lived species - Norway rat Rattus norvegicus and house mouse Mus musculus.
September 25, 2017: Bulletin of Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28939964/dose-and-dose-rate-extrapolation-factors-for-malignant-and-non-malignant-health-endpoints-after-exposure-to-gamma-and-neutron-radiation
#19
Van Tran, Mark P Little
Murine experiments were conducted at the JANUS reactor in Argonne National Laboratory from 1970 to 1992 to study the effect of acute and protracted radiation dose from gamma rays and fission neutron whole body exposure. The present study reports the reanalysis of the JANUS data on 36,718 mice, of which 16,973 mice were irradiated with neutrons, 13,638 were irradiated with gamma rays, and 6107 were controls. Mice were mostly Mus musculus, but one experiment used Peromyscus leucopus. For both types of radiation exposure, a Cox proportional hazards model was used, using age as timescale, and stratifying on sex and experiment...
September 22, 2017: Radiation and Environmental Biophysics
https://www.readbyqxmd.com/read/28938916/use-of-the-kladh3-promoter-for-the-quantitative-production-of-the-murine-pde5a-isoforms-in-the-yeast-kluyveromyces-lactis
#20
Silvia Cardarelli, Mauro Giorgi, Fabio Naro, Francesco Malatesta, Stefano Biagioni, Michele Saliola
BACKGROUND: Phosphodiesterases (PDE) are a superfamily of enzymes that hydrolyse cyclic nucleotides (cAMP/cGMP), signal molecules in transduction pathways regulating crucial aspects of cell life. PDEs regulate the intensity and duration of the cyclic nucleotides signal modulating the downstream biological effect. Due to this critical role associated with the extensive distribution and multiplicity of isozymes, the 11 mammalian families (PDE1 to PDE11) constitute key therapeutic targets...
September 22, 2017: Microbial Cell Factories
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