scholarly journals Identifying genome level variation in generalist and specialist bacteria and their relationship to abiotic conditions in European freshwater ecosystems

2021 ◽  
Vol 4 ◽  
Author(s):  
Manan Shah ◽  
Till Bornemann ◽  
Julia Nuy ◽  
Alexander Probst ◽  
Daniela Beisser ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Genetic Basis ◽  
Abiotic Factors ◽  
Gc Content ◽  
Nutrient Content ◽  
Freshwater Ecosystems ◽  
Different Types ◽  
Genome Level ◽  
Physical Changes ◽  
Insight Into

Microbial biodiversity is one of the increasingly studied fields, yet we are unable to accurately pinpoint the intricacies of how the biotic landscape changes with its abiotic counterpart. Every organism reacts differently to physical changes in its surrounding(Zeglin (2015)). While there are some generalist microbes that can grow in limited capacity in many different types of environment, there are also some specialists that can flourish in very specific environments(Monard et al. (2016)). We hypothesize that both generalists and specialists have developed advanced strategies that allow them thrive under diverse conditions or in very specific niches, and that these changes should be traceable on the genomic level. We expect to see variations in factors like genome sizes, number of genes, GC content, metabolic pathways that yield growth and replication advantages in nutrient deficient niches and defense mechanisms. We also expect to identify genomic streamlining in organisms that survive in nutrient deficient environments. We are currently studying the genetic basis of why these generalists are so universally present though in smaller numbers, and what allows the specialists to efficiently exploit the abiotic factors of their specific environment in order to flourish. To pursue this, we have sampled and sequenced metagenomes from 47 lakes spread across Europe with strongly diverging environmental conditions such as pH, temperature, organic and nutrient content, elevation, and conductivity. We’ve identified reads from more than 9000 taxonomically unique organisms, of which 700 were identified as generalists and 1200 as specialists, based on niche width permutations. In total we have assembled 313 high quality Metagenome Assembled Genomes (MAGs). Which now allow us to get a more detailed insight into the genetic basis and specific adaptations of these organisms.

“Where is Dementia?” A Systematic Literature Review Exploring Neuroanatomical Aspects of Dementia

2017 ◽  
Vol 2 (15) ◽  
pp. 9-23 ◽  
Author(s):  
Chorong Oh ◽  
Leonard LaPointe
Keyword(s):  
English Language ◽  
Signs And Symptoms ◽  
Behavioral Symptoms ◽  
Journal Articles ◽  
People With Dementia ◽  
Different Types ◽  
Precise Diagnosis ◽  
Physical Changes ◽  
The Brain ◽  
Language Literature

Dementia is a condition caused by and associated with separate physical changes in the brain. The signs and symptoms of dementia are very similar across the diverse types, and it is difficult to diagnose the category by behavioral symptoms alone. Diagnostic criteria have relied on a constellation of signs and symptoms, but it is critical to understand the neuroanatomical differences among the dementias for a more precise diagnosis and subsequent management. With this regard, this review aims to explore the neuroanatomical aspects of dementia to better understand the nature of distinctive subtypes, signs, and symptoms. This is a review of English language literature published from 1996 to the present day of peer-reviewed academic and medical journal articles that report on older people with dementia. This review examines typical neuroanatomical aspects of dementia and reinforces the importance of a thorough understanding of the neuroanatomical characteristics of the different types of dementia and the differential diagnosis of them.

The participation of Palestinian-Israeli politicians in public and commercial television and radio in Israel as capability

2021 ◽  
pp. 174804852199056
Author(s):  
Baruch Shomron ◽  
Amit Schejter
Keyword(s):  
Capabilities Approach ◽  
Media Representations ◽  
Community Members ◽  
Commercial Television ◽  
Radio Stations ◽  
Modes Of Representation ◽  
Current Affairs ◽  
Different Types ◽  
The Media ◽  
Insight Into

This study examines how media representations of Palestinian-Israeli politicians, can help community members realize their capabilities. The study’s database is comprised of 1,207 interviews conducted with Palestinian-Israeli politicians on news and current affairs programs on the three national television channels and the two national radio stations in Israel, for 24 months (2016-2017). We identified and analyzed the differences in the modes of representation between national and local Palestinian-Israeli politicians and between Palestinian-Israeli parliament members in the Joint List and Palestinian-Israeli parliament members in Zionist parties, all through the capabilities prism. In this study, we demonstrated how different types of Palestinian-Israeli politicians may potentially affect the realization of different political functions and capabilities. Analyzing political representations in the media through the theoretical framework of the ‘capabilities approach’ contributes to a more comprehensive insight into the roles the media can play promoting people’s wellbeing and human rights, relative to traditional media theories.

Double, triple or quadruple hits? Exploring the impact of cybercrime on victims in the Netherlands

2021 ◽  
pp. 026975802110106
Author(s):  
Raoul Notté ◽  
E.R. Leukfeldt ◽  
Marijke Malsch
Keyword(s):  
Public Opinion ◽  
Literature Review ◽  
The Netherlands ◽  
Public Discourse ◽  
Moral Judgments ◽  
Victim Blaming ◽  
High Prevalence ◽  
Different Types ◽  
The Impact ◽  
Insight Into

This article explores the impact of online crime victimisation. A literature review and 41 interviews – 19 with victims and 22 with experts – were carried out to gain insight into this. The interviews show that most impacts of online offences correspond to the impacts of traditional offline offences. There are also differences with offline crime victimisation. Several forms of impact seem to be specific to victims of online crime: the substantial scale and visibility of victimhood, victimisation that does not stop in time, the interwovenness of online and offline, and victim blaming. Victims suffer from double, triple or even quadruple hits; it is the accumulation of different types of impact, enforced by the limitlessness in time and space, which makes online crime victimisation so extremely invasive. Furthermore, the characteristics of online crime victimisation greatly complicate the fight against and prevention of online crime. Finally, the high prevalence of cybercrime victimisation combined with the severe impact of these crimes seems contradictory with public opinion – and associated moral judgments – on victims. Further research into the dominant public discourse on victimisation and how this affects the functioning of the police and victim support would be valuable.

scholarly journals Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
So-Ra Han ◽  
Byeollee Kim ◽  
Jong Hwa Jang ◽  
Hyun Park ◽  
Tae-Jin Oh
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Cold Adaptation ◽  
Gc Content ◽  
Glycogen Metabolism ◽  
Extreme Environment ◽  
Circular Chromosome ◽  
Cold Regions ◽  
Insight Into

Abstract Background The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of 16 strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that help it to survive in the cold environment. Results Using 16 S rRNA sequence analysis, we found and identified a species of Arthrobacter isolated from cryoconite. We designated it as strain PAMC25564 and elucidated its complete genome sequence. The genome of PAMC25564 is composed of a circular chromosome of 4,170,970 bp with a GC content of 66.74 % and is predicted to include 3,829 genes of which 3,613 are protein coding, 147 are pseudogenes, 15 are rRNA coding, and 51 are tRNA coding. In addition, we provide insight into the redundancy of the genes using comparative genomics and suggest that PAMC25564 has glycogen and trehalose metabolism pathways (biosynthesis and degradation) associated with carbohydrate active enzyme (CAZymes). We also explain how the PAMC26654 produces energy in an extreme environment, wherein it utilizes polysaccharide or carbohydrate degradation as a source of energy. The genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how they adapt and survive in such environments. Conclusions We have characterized the complete Arthrobacter sp. PAMC25564 genome and used comparative analysis to provide insight into the redundancy of its CAZymes for potential cold adaptation. This provides a foundation to understanding how the Arthrobacter strain produces energy in an extreme environment, which is by way of CAZymes, consistent with reports on the use of these specialized enzymes in cold environments. Knowledge of glycogen metabolism and cold adaptation mechanisms in Arthrobacter species may promote in-depth research and subsequent application in low-temperature biotechnology.

Small rodent communities (Muridae) in Gabonese savannas: species diversity and biogeographical affinities

Mammalia ◽  
2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Jean-François Mboumba ◽  
Maxime R. Hervé ◽  
Véronique Guyot ◽  
Frederic Ysnel
Keyword(s):  
Ecological Factors ◽  
Abundant Species ◽  
Small Rodent ◽  
Small Rodents ◽  
South West ◽  
New Information ◽  
Different Types ◽  
Mus Minutoides ◽  
Insight Into ◽  
Coastal Basin

Abstract The study contributes to the knowledge of species composition and biogeographical affinities of savannas rodent in Gabon. Unlike small rodents in Gabonese forests, there is little data on the diversity of small rodents in Gabonese savannas. The diversity and distribution of rodent murid communities was studied in four different types of savanna in Gabon: Coastal Basin (South-West), Lopé/Okanda (in the Center), Batéké Plateaux (Southeastern) and Ngougnié/ N’yanga (in the South). A total of 428 individuals representing six species were captured over 11,920 trap nights. Trap success was highly variable (2.2–6.9 %). The most abundant species were Mus minutoides (69%) followed by Lemniscomys striatus (21.5%). Indices of species richness varied from 2 to 5 and diversity (Shannon and Weaver) was low in the four savannas with the highest value at Ngougnié/N’yanga (H′ = 1.2). Species distributions show that Gabonese savanna small rodents conform to four distribution types, with one species known from Zambesian savannas exhibiting austral affinities (Pelomys campanae: occurs in three southern savannas). This new information provides important insight into the biogeography of small rodents at a local and regional level. Moreover, the correspondence analysis highlighted an influence of local ecological factors on population abundance.

scholarly journals Evaluating the Efficiency of gRNAs in CRISPR/Cas9 Mediated Genome Editing in Poplars

2019 ◽  
Vol 20 (15) ◽  
pp. 3623 ◽  
Author(s):  
Tobias Bruegmann ◽  
Khira Deecke ◽  
Matthias Fladung
Keyword(s):  
Genome Editing ◽  
Gene Editing ◽  
Constitutive Expression ◽  
Gc Content ◽  
Seed Region ◽  
Research Topics ◽  
Target Region ◽  
Cas9 Nuclease ◽  
Different Types ◽  
Poplar Hybrid

CRISPR/Cas9 has become one of the most promising techniques for genome editing in plants and works very well in poplars with an Agrobacterium-mediated transformation system. We selected twelve genes, including SOC1, FUL, and their paralogous genes, four NFP-like genes and TOZ19 for three different research topics. The gRNAs were designed for editing, and, together with a constitutively expressed Cas9 nuclease, transferred either into the poplar hybrid Populus × canescens or into P. tremula. The regenerated lines showed different types of editing and revealed several homozygous editing events which are of special interest in perennial species because of limited back-cross ability. Through a time series, we could show that despite the constitutive expression of the Cas9 nuclease, no secondary editing of the target region occurred. Thus, constitutive Cas9 expression does not seem to pose any risk to additional editing events. Based on various criteria, we obtained evidence for a relationship between the structure of gRNA and the efficiency of gene editing. In particular, the GC content, purine residues in the gRNA end, and the free accessibility of the seed region seemed to be highly important for genome editing in poplars. Based on our findings on nine different poplar genes, efficient gRNAs can be designed for future efficient editing applications in poplars.

EFFECT OF PERACETIC ACID OXIDATION ON N-CONTAINING COMPONENTS OF HUMIC MATERIALS

1980 ◽  
Vol 60 (3) ◽  
pp. 541-548 ◽  
Author(s):  
M. SCHNITZER ◽  
D. A. HINDLE
Keyword(s):  
Amino Acid ◽  
Peracetic Acid ◽  
Amino Sugar ◽  
Chemical Oxidation ◽  
Acid Oxidation ◽  
Mild Oxidation ◽  
Total N ◽  
Different Types ◽  
Humic Materials ◽  
Insight Into

Three humic and one fulvic acid were degraded by mild chemical oxidation with peracetic acid, with special emphasis on the effects of this type of oxidation on N-containing components. The different types of N that were considered were NH4+-N, amino acid-N, amino sugar-N, NO2−-N + NO3−-N, and by difference from total N, "unknown" N. The behaviour toward mild chemical oxidation of all four preparations was essentially similar: there were decreases in mino acid-N, amino sugar-N and "unknown" N, increases in NH4+-N, NO2−-N + NO3−-N with one material, and in N-gases. The "unknown" N was not inert. Between 16.6 and 59.1% of the latter appeared to be converted, as a result of mild chemical oxidation, to NH3 and N-gases which were expelled from the systems. The results presented provide an insight into what happens to N-containing humic components as a result of mild oxidation.

scholarly journals The genomics of adaptation

2012 ◽  
Vol 279 (1749) ◽  
pp. 5024-5028 ◽  
Author(s):  
Jacek Radwan ◽  
Wiesław Babik
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Royal Society ◽  
Genetic Basis ◽  
Genomic Data ◽  
Evolutionary Change ◽  
Introductory Article ◽  
Technological Advances ◽  
A Genome ◽  
Genome Level

The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation.

An Insight into the Polymeric Nanoparticles Applications in Diabetes Diagnosis and Treatment

2021 ◽  
Vol 21 ◽  
Author(s):  
Parisa Dehghani ◽  
Monireh Esameili Rad ◽  
Atefeh Zarepour ◽  
Ponnurengam Malliappan Sivakumar ◽  
Ali Zarrabi
Keyword(s):  
Polymeric Nanoparticles ◽  
Synthetic Polymers ◽  
Diagnostic Methods ◽  
Diagnosis And Treatment ◽  
Diabetes Diagnosis ◽  
Transport Mechanisms ◽  
Different Types ◽  
Treatment And Diagnosis ◽  
Insight Into

: Diabetes mellitus (DM) is a type of chronic metabolic disease that has affected millions of people worldwide and is known with a defect in the amount of insulin secretion, insulin functions, or both. This deficiency leads to an increase in the amounts of glucose, which could be accompanied by long-term damages to other organs such as eyes, kidneys, heart, and nervous system. Thus, introducing an appropriate approach for diagnosis and treatment of different types of DM is the aim of several researches. By the emergence of nanotechnology and its application in medicine, new approaches were presented for these purposes. The object of this review article is to introduce different types of polymeric nanoparticles (PNPs), as one of the most important classes of nanoparticles, for diabetic management. To achieve this goal, at first, some of the conventional therapeutic and diagnostic methods of DM will be reviewed. Then, different types of PNPs, in two forms of natural and synthetic polymers with different properties, as a new method for DM treatment and diagnosis will be introduced. In the next section, the transport mechanisms of these types of nano-carriers across the epithelium, via paracellular and transcellular pathways will be explained. Finally, the clinical use of PNPs in the treatment and diagnosis of DM will be summarized. Based on the results of this literature review, PNPs could be considered one of the most promising methods for DM management.

scholarly journals QTL analysis of self-selected macronutrient diet intake: fat, carbohydrate, and total kilocalories

2002 ◽  
Vol 11 (3) ◽  
pp. 205-217 ◽  
Author(s):  
Brenda K. Smith Richards ◽  
Brenda N. Belton ◽  
Angela C. Poole ◽  
James J. Mancuso ◽  
Gary A. Churchill ◽  
...  
Keyword(s):  
Body Weight ◽  
Qtl Analysis ◽  
Genetic Basis ◽  
Body Weight Gain ◽  
Macronutrient Intake ◽  
Naturally Occurring ◽  
Trait Locus ◽  
Diet Intake ◽  
Insight Into ◽  
Protein Quantitative Trait Locus

The present study investigated the inheritance of dietary fat, carbohydrate, and kilocalorie intake traits in an F2 population derived from an intercross between C57BL/6J (fat-preferring) and CAST/EiJ (carbohydrate-preferring) mice. Mice were phenotyped for self-selected food intake in a paradigm which provided for 10 days a choice between two macronutrient diets containing 78/22% of energy as a composite of either fat/protein or carbohydrate/protein. Quantitative trait locus (QTL) analysis identified six significant loci for macronutrient intake: three for fat intake on chromosomes (Chrs) 8 ( Mnif1), 18 ( Mnif2), and X ( Mnif3), and three for carbohydrate intake on Chrs 17 ( Mnic1), 6 ( Mnic2), and X ( Mnic3). An absence of interactions among these QTL suggests the existence of separate mechanisms controlling the intake of fat and carbohydrate. Two significant QTL for cumulative kilocalorie intake, adjusted for baseline body weight, were found on Chrs 17 ( Kcal1) and 18 ( Kcal2). Without body weight adjustment, another significant kcal locus appeared on distal Chr 2 ( Kcal3). These macronutrient and kilocalorie QTL, with the exception of loci on Chrs 8 and X, encompassed chromosomal regions influencing body weight gain and adiposity in this F2 population. These results provide new insight into the genetic basis of naturally occurring variation in nutrient intake phenotypes.

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