scholarly journals Overlapping Genes and Size Constraints in Viruses - An Evolutionary Perspective

2015 ◽  
Author(s):  
Nadav Brandes ◽  
Michal Linial
Keyword(s):  
Viral Evolution ◽  
High Rate ◽  
Evolutionary Constraints ◽  
Absolute Amount ◽  
Evolutionary Perspective ◽  
Overlapping Genes ◽  
Viral Capsids ◽  
Size Constraints ◽  
Gene Overlapping ◽  
The Common

Viruses are the simplest replicating units, characterized by a limited number of coding genes and an exceptionally high rate of overlapping genes. We sought a unified explanation for the evolutionary constraints that govern genome sizes, gene overlapping and capsid properties. We performed an unbiased statistical analysis over the ~100 known viral families, and came to refute widespread assumptions regarding viral evolution. We found that the volume utilization of viral capsids is often low, and greatly varies among families. Most notably, we show that the total amount of gene overlapping is tightly bounded. Although viruses expand three orders of magnitude in genome length, their absolute amount of gene overlapping almost never exceeds 1500 nucleotides, and mostly confined to <4 significant overlapping instances. Our results argue against the common theory by which gene overlapping is driven by a necessity of viruses to compress their genome. Instead, we support the notion that overlapping has a role in gene novelty and evolution exploration.

scholarly journals The Missing Tailed Phages: Prediction of Small Capsid Candidates

2020 ◽  
Vol 8 (12) ◽  
pp. 1944
Author(s):  
Antoni Luque ◽  
Sean Benler ◽  
Diana Y. Lee ◽  
Colin Brown ◽  
Simon White
Keyword(s):  
Phage Therapy ◽  
Viral Evolution ◽  
Diverse Group ◽  
Genome Length ◽  
Geometrical Features ◽  
Phage Capsid ◽  
The Common ◽  
Icosahedral Capsid ◽  
Gut Metagenome ◽  
Physical Principles

Tailed phages are the most abundant and diverse group of viruses on the planet. Yet, the smallest tailed phages display relatively complex capsids and large genomes compared to other viruses. The lack of tailed phages forming the common icosahedral capsid architectures T = 1 and T = 3 is puzzling. Here, we extracted geometrical features from high-resolution tailed phage capsid reconstructions and built a statistical model based on physical principles to predict the capsid diameter and genome length of the missing small-tailed phage capsids. We applied the model to 3348 isolated tailed phage genomes and 1496 gut metagenome-assembled tailed phage genomes. Four isolated tailed phages were predicted to form T = 3 icosahedral capsids, and twenty-one metagenome-assembled tailed phages were predicted to form T < 3 capsids. The smallest capsid predicted was a T = 4/3 ≈ 1.33 architecture. No tailed phages were predicted to form the smallest icosahedral architecture, T = 1. We discuss the feasibility of the missing T = 1 tailed phage capsids and the implications of isolating and characterizing small-tailed phages for viral evolution and phage therapy.

scholarly journals Immunological and mutational analysis of SARS-CoV-2 structural proteins from Asian countries

2021 ◽  
Vol 8 (5) ◽  
pp. 4367-4390
Author(s):  
Deepak Kumar Jha ◽  
Niti Yashvardhini ◽  
Amit Kumar
Keyword(s):  
Envelope Protein ◽  
Mutational Analysis ◽  
Viral Evolution ◽  
Point Mutations ◽  
High Rate ◽  
World Health ◽  
Structural Proteins ◽  
Structural Protein ◽  
Health Crisis ◽  
Novel Coronavirus

Introduction: The emergence of a novel coronavirus, SARS-CoV-2, an etiolating agent of coronavirus disease (COVID-19), has become a pandemic of global concern. Considering the huge number of morbidity and mortality worldwide, the World Health Organization, on 11th March 2020, has announced an unprecedented public health crisis. This virus is a member of plus sense RNA viruses that can show a high rate of mutations. The ongoing multiple mutations in the structural proteins of coronavirus drive viral evolution, enabling them to evade the host immunity and rapidly acquire drug resistance against COVID-19. In the present study, we focused mainly on the prevalence of mutations in the four types of structural proteins like S (spike), E (envelope), M (membrane), and N (nucleocapsid) that are required for the assembly of a complete virion particle. Further, we estimated the antigenicity and allergenicity of these structural proteins to design and develop a potentially good candidate vaccine against SARS-CoV-2. Methods: In the present in silico study, envelope protein was found highly antigenic followed by nucleocapsid, membrane, and spike protein of SARS-CoV-2. Results: Consequently, in this study, we detected 987 mutations from 729 sequences of Asia in October 2020 and compared them with China's 1st Wuhan isolate sequence as a reference. Spike showed the highest mutations with 807 point mutations among the four structural proteins, followed by nucleocapsid with 151 mutations, while envelope showed 19 and membrane only 10 point mutations. Conclusion: Taken together, our study revealed, variation occurring in the structural protein of SARS-CoV-2 might be altering their structure and functions, and envelope protein appears to be a promising vaccine candidate to curb coronavirus infections.

scholarly journals A Retrospective and Epidemiological Survey of Patients with Esophagus Cancer in Ilam City During a 10 Years Period

2017 ◽  
Vol 2 (1) ◽  
pp. 11
Author(s):  
Hamed Zarei ◽  
Hamed Tavan
Keyword(s):  
Retrospective Study ◽  
Lipid Profile ◽  
Urban Areas ◽  
Epidemiological Survey ◽  
High Rate ◽  
Anatomical Site ◽  
Tumor Type ◽  
Age Group ◽  
Esophagus Cancer ◽  
The Common

Background: esophagus cancer is the sixth deadly cancer among other types with high rate of death which has made it one of the common cancers. Based on what mentioned, this retrospective study was designed to assess the tumor incidence rate in a 10 years period in Ilam city.Materials and methods: this is a retrospective study during 1385 till 1394 in Ilam city. Our source of patients was the afflicted patients. The sample size and the statistical society of research were determined based on census. The research materials included of two types first included the demographic information of patients (age, gender, tumor type, level of education, residency, smoking and lipid profile) and the second part was some information about the esophagus cancer (anatomical site, pathologic findings and lipid profile).using SPSS version 19, the data was analyzed. Results: the statistical society included 150 individuals afflicted with esophagus cancer in which the most prevalent age group was men older than 70 years (31.3%). In terms of anatomical site, the middle third of esophagus had 75 cases (50%), the last third had 45 cases (30%) and the first third had 30 (20%) individuals. Furthermore, as time went on, the number of new cases increased. Conclusion: the risk factors for occurring the cancer were the age group greater than 70 years, being male, lower educational situation, unemployment, living in an urban areas, smoking, hereditary, hyperlipidemia (LDL, TG, CHOL) and finding tumor in middle third of esophagus (because of existing helicobacter pylori virus and impropriate diet). Being able to identify endangered people, one could begin treating patients and thereby, saving time, cost and increasing the rate of survivors.

Market Receptiveness and Product Positioning Model of Chinese Firms in Emerging Markets

2016 ◽  
pp. 99-119
Author(s):  
Olukayode Ojo Iwaloye ◽  
Guicheng James Shi
Keyword(s):  
Emerging Markets ◽  
Developing Economies ◽  
High Rate ◽  
Market Place ◽  
Product Positioning ◽  
Chinese Firms ◽  
Common Structure ◽  
Research Interview ◽  
The Common ◽  
And Performance

This study looks into the common strategic moves of Chinese firms to create appeal for their products in emerging markets. The focus is on the common competitive factors that make them to have high rate of success and prosperity compared to first movers firms from advanced markets in developing countries marketplace. Past studies showed that a firm without established brands, technology knowhow and management capabilities are likely to face with survival and performance problems, and may also reduce the firm's strategic options and growth opportunities in developing economies. Chinese firms are known to lack established brands and important core capabilities but have been able to demonstrate a unique trend in emerging countries market place. They have a common structure and trend in the ways Chinese firms create appeal to users and potential buyers in emerging market environment. This present research explored the situation with case research interview of seven Chinese firms in Nigeria.

Critical Properties of the Assembly Call of the Common American Crow

Behaviour ◽  
1978 ◽  
Vol 64 (3-4) ◽  
pp. 184-203 ◽  
Author(s):  
Nicholas S. Thompson ◽  
David B. Richards
Keyword(s):  
Sound Source ◽  
Traditional View ◽  
High Rate ◽  
American Crow ◽  
Corvus Brachyrhynchos ◽  
Temporal Properties ◽  
Series Of Experiments ◽  
The Common ◽  
Functional Context ◽  
Better Than

AbstractAccording to tradition, the communication system of the American crow, Corvus brachyrhynchos, consists of an assortment of distinct sounds each of which is used in a particular context and has a unique meaning. Despite this traditional view, we have made field observations which suggested that the sounds employed in various different functional contexts overlap considerably. These observations further suggested that each sound does not have a single unique meaning, but that its meaning varies depending upon how it and similar sounds are temporally organized into calling sequences. In order to investigate this idea, a series of experiments were performed in which the temporal properties of natural sounds recorded from crows in the field were changed. These experiments were concerned primarily with the vocalization known as the assembly call. The assembly call consists of series of sounds which are low, harsh, and variable in pitch and timing. Broadcast to crows in the field, recorded assembly calls provoke an aggregation of crows to the sound source about twenty-five percent of the time. The recordings broadcasted were of two sorts: sequences made up by modifying the temporal properties of a natural assembly call and sequences of sounds derived from calls given in other functional contexts which were then rearranged to approximate the temporal properties of an assembly call. These calls were tested on wild crows in the field. A presentation of a call was counted successful if at least one crow approached the sound source on a direct line. Different calls were compared with respect to the proportion of successful presentations. The results show that not all types of crow sounds can be manufactured into effective assembly calls. A high pitched call, even when arranged to approximate the temporal properties of the assembly call does not assemble crows at rates approaching the rate of assembly to natural assembly calls. On the other hand, the results also show that a sound need not be derived from an assembly call in order to be arranged into an effective assembly call. A call recorded in another functional context, but which has a harsh, grainy quality will assemble crows as well as or better than an assembly call if it is presented in the proper temporal arrangement. In fact, the highest rates of success were provoked by a sequence of such sounds having a high rate of emission and organized into short cycles of increasing rate. Such a call is two to four times more effective than a natural assembly call. These results are inconsistent with the traditional view that each particular caw in the repertoire of a crow has a discrete stable meaning. An alternate hypothesis is suggested in which the meaning of a sequence of crow sounds is thought to depend not only on the properties of the caws but upon the temporal properties of the sequence as well.

scholarly journals Ethnic Differences in the Incidence of Leukemia

Blood ◽  
1957 ◽  
Vol 12 (1) ◽  
pp. 1-10 ◽  
Author(s):  
BRIAN MACMAHON ◽  
ERNEST K. KOLLER
Keyword(s):  
Age Differences ◽  
Census Data ◽  
Vital Statistics ◽  
High Rate ◽  
Foreign Born ◽  
Social Differences ◽  
High Incidence ◽  
The Common ◽  
Males And Females ◽  
Two Populations

Abstract A series of 1636 patients with leukemia, representing the white residents of Brooklyn diagnosed in the period 1943-52, is compared with selected census data for the population. After standardization for age differences in the two populations, the incidences of leukemia in the native-born and foreign-born populations of the borough are 45.3 and 61.0 per million per annum, respectively. The data suggest that a high incidence of leukemia in the Russian-born population accounts for the higher rate in the foreign-born group. Using affiliation of cemetery of burial as an index of religion, a series of 1368 deaths from leukemia is compared with a systematic one in 200 samples of all deaths in the same area. Leukemia is recorded as cause of death twice as frequently among Jews, as among others. This relationship is seen in both native-born and foreign-born groups, in males and females, at all ages and in all the common pathologic varieties of leukemia. No difference in leukemia incidence is seen between predominantly Catholic and predominantly Protestant groups. Evidence from United States vital statistics is used to show that the commonly observed difference between whites and Negroes imi leukemia death rates is closely associated with social differences between the two groups. Little or no difference in leukemia death rate exists between these two groups in Brooklyn, when allowance is made for the apparently high rate in the white Jewish population.

scholarly journals ‘Ow Cockney is Beckham Twenty Years On? An Investigation into H-dropping and T-glottaling

2006 ◽  
Vol 2 (2) ◽  
pp. 20-27
Author(s):  
Sofia Dahou ◽  
Jasmine Hamlin
Keyword(s):  
Language Change ◽  
Football Player ◽  
High Rate ◽  
Socioeconomic Background ◽  
Linguistic Change ◽  
Language Choices ◽  
Lower Socioeconomic ◽  
Celebrity Status ◽  
The Common ◽  
Social Causes

This research paper examines how language change can occur across the lifespan through the linguistic analysis of East Londoner, and world renowned football player, David Beckham. Specifically, we look at his use of the consonantal variables of t-glottaling and h-dropping and how the frequency of these forms change over a 20-year period. We discuss the background of the linguistic phenomena under investigation and the common environments in which these non-standard variants are likely to occur. We also take a closer look at how the forms are being used in certain phonotactic environments, for example, word-medial and word-final positions, and the potential reasons behind them being less common when preceding or following certain sounds. We discuss some common theories associated with language change across the lifespan, using quantitative data to find trends and qualitative interpretation to suggest social causes for our findings. The paper allows us to critically evaluate language change theories, such as Labov’ s (1978) apparent time theory.In designing our study, we hypothesised that Beckham would be seen to undergo linguistic change from his classic East London Cockney features to more prestigious forms. As t-glottaling and h-dropping are stigmatised forms which are commonly associated with a working-class background, we believed that Beckham would go from using a high rate of these variants in his teenage years, due to his lower socioeconomic background, to producing standard /t/ and /h/ more frequently, reflecting his dramatic upward social climb. Due to his rise to fame, we expected that his celebrity status would bring an added pressure to speak in a “correct”  manner, therefore influencing Beckham to opt for the standard variants more frequently. The variants we looked at are also commonly associated with younger speakers, so we expected Beckham’ s aging to further affect his language.Our results support our hypothesis, showing the extent to which David Beckham’s language choices have changed over time. We found that he showed a significant decrease in both h-dropping and t-glottaling in all phonotactic environments. However, we also found a surprisingly high rate of t-glottalisation before consonants and after vowels in Beckham’ s 2014 recordings. Our data support theories concerning age, social class, sex and dialect convergence. Overall, our paper offers insight into the methodology and theory surrounding language change across the lifespan through the analysis of particular linguistics variables of an English speaker.

scholarly journals The Missing Tailed Phages: Prediction of Small Capsid Candidates

2020 ◽  
Author(s):  
Antoni Luque ◽  
Sean Benler ◽  
Diana Lee ◽  
Colin Brown ◽  
Simon White
Keyword(s):  
Phage Therapy ◽  
Viral Evolution ◽  
Diverse Group ◽  
Genome Length ◽  
Geometrical Features ◽  
Phage Capsid ◽  
The Common ◽  
Icosahedral Capsid ◽  
Gut Metagenome ◽  
Physical Principles

Tailed phages are the most abundant and diverse group of viruses on the planet. Yet, the smallest tailed phages display relatively complex capsids and large genomes compared to other viruses. The lack of tailed phages forming the common icosahedral capsid architectures T = 1 and T = 3 is puzzling. Here, we extracted geometrical features from high-resolution tailed phage capsid reconstructions and built a statistical model based on physical principles to predict the capsid diameter and genome length of the missing small tailed phage capsids. We applied the model to 3,348 isolated tailed phage genomes and 1,496 gut metagenome-assembled tailed phage genomes. Four isolated tailed phages were predicted to form T = 3 icosahedral capsids, and twenty-one metagenome-assembled tailed phages were predicted to form T &lt; 3 capsids. The smallest capsid predicted was a T = 4/3 ≈ 1.33 architecture. No tailed phages were predicted to form the smallest icosahedral architecture, T = 1. We discuss the feasibility of the missing T = 1 tailed phage capsids and the implications of isolating and characterizing small tailed phages for viral evolution and phage therapy.

scholarly journals Ibutilide is efficacy but not safe in cardioversion of atrial fibrillation for patients aged over 75 years

2020 ◽  
Author(s):  
Chunxia Huang ◽  
ZhiMin Zhang ◽  
Bin Li ◽  
YunTian Li
Keyword(s):  
Atrial Fibrillation ◽  
Body Weight ◽  
Sinus Rhythm ◽  
Torsades De Pointes ◽  
High Rate ◽  
Control Group ◽  
High Morbidity ◽  
Efficacy And Safety ◽  
Recent Onset ◽  
The Common

Abstract Background: Atrial fibrillation (AF) is the common arrhythmia resulting in high morbidity and mortality. Ibutilide is used to convert AF to sinus rhythm pharmacologically. We aimed to evaluate the clinical efficacy and safety of ibutilide for patients over 75 years old with recent onset AF.Methods: 81 patients over 75 years old with recent onset AF less than 72 hours, range from 75 to 85 years, were analyzed retrospectively from January 2015 to January 2019. 40 patients received ibutilide, and another 41 patients received propafenone as the control group. In ibutilide group, patients weighing over 60 kg were received 1 mg of ibutilide, and ibutilide at 0.01 mg / kg were administrated when the patient’s body weight was less than 60 kg. If cardioversion failed, 1 mg or 0.01 mg/kg of ibutilide would be given after 10 minutes. In control group, patients were received propafenone at 75mg. If there was no effect on cardioversion, 35 mg of propafenone would be given after 10 minutes.Results: In control group 26 patients (63.4%) converted to sinus rhythm, and in ibutilide group, 35(87.5%) converted to sinus rhythm (p<0.05, vs control group). The converting time of ibutilide group was shorter than control group(13.5±9.27s vs 43.72±10.27s,P<0.05 ). The corrected QT (QTc) intervals was significantly prolonged in patients after the administration of ibutilide(P<0.05). In ibutilide group, five patients (12.5%) appeared torsades de pointes (TdP) and converted to sinus rhythm via electrical cardioversion. Six patients (14.6%) developed severe bradycardia in control group, and the bradycardia alleviated after discontinuation of propafenone. Nine patients (21.9%) who failed in cardioversion with 24 hours by propafenone converted to sinus rhythm via electrical cardioversion.Conclusion: Ibutilide could effectively convert recent onset (<72 hours) AF in patients aged over 75 years. However, it was worth noting that the high rate of TdP emerged in these elderly patients after the treatment of ibutilide.

scholarly journals Factorial study of the RNA-seq computational workflow identifies biases as technical gene signatures

2020 ◽  
Author(s):  
Joël Simoneau ◽  
Ryan Gosselin ◽  
Michelle S. Scott
Keyword(s):  
Overlapping Genes ◽  
Rna Seq ◽  
Central Importance ◽  
Similar Sequence ◽  
Gene Group ◽  
Rna Molecules ◽  
Rna Biology ◽  
Computational Workflow ◽  
The Common ◽  
Genome Annotations

ABSTRACTRNA-seq is a modular experimental and computational approach that aims in identifying and quantifying RNA molecules. The modularity of the RNA-seq technology enables adaptation of the protocol to develop new ways to explore RNA biology, but this modularity also brings forth the importance of methodological thoroughness. Liberty of approach comes with the responsibility of choices, and such choices must be informed. Here, we present an approach that identifies gene group specific quantification biases in currently used RNA-seq software and references by processing sequenced datasets using a wide variety of RNA-seq computational pipelined, and by decomposing these expression datasets using an independent component analysis matrix factorisation method. By exploring the RNA-seq pipeline using a systemic approach, we highlight the yet inadequately characterized central importance of genome annotations in quantification results. We also show that the different choices in RNA-seq methodology are not independent, through interactions between genome annotations and quantification software. Genes were mainly found to be affected by differences in their sequence, by overlapping genes and genes with similar sequence. Our approach offers an explanation for the observed biases by identifying the common features used differently by the software and references, therefore providing leads for the betterment of RNA-seq methodology.

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