scholarly journals A Transcriptomic Approach to the Metabolism of Tetrapyrrolic Photosensitizers in a Marine Annelid

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3924
Author(s):  
Maria Leonor Santos ◽  
Mariaelena D’Ambrosio ◽  
Ana P. Rodrigo ◽  
A. Jorge Parola ◽  
Pedro M. Costa
Keyword(s):  
Metabolic Pathways ◽  
Molecular Networks ◽  
Bile Pigments ◽  
Rna Seq ◽  
The Past ◽  
Wide Range ◽  
Genes Encoding ◽  
Organ Specific ◽  
Bright Green ◽  
Green Coloration

The past decade has seen growing interest in marine natural pigments for biotechnological applications. One of the most abundant classes of biological pigments is the tetrapyrroles, which are prized targets due their photodynamic properties; porphyrins are the best known examples of this group. Many animal porphyrinoids and other tetrapyrroles are produced through heme metabolic pathways, the best known of which are the bile pigments biliverdin and bilirubin. Eulalia is a marine Polychaeta characterized by its bright green coloration resulting from a remarkably wide range of greenish and yellowish tetrapyrroles, some of which have promising photodynamic properties. The present study combined metabolomics based on HPLC-DAD with RNA-seq transcriptomics to investigate the molecular pathways of porphyrinoid metabolism by comparing the worm’s proboscis and epidermis, which display distinct pigmentation patterns. The results showed that pigments are endogenous and seemingly heme-derived. The worm possesses homologs in both organs for genes encoding enzymes involved in heme metabolism such as ALAD, FECH, UROS, and PPOX. However, the findings also indicate that variants of the canonical enzymes of the heme biosynthesis pathway can be species- and organ-specific. These differences between molecular networks contribute to explain not only the differential pigmentation patterns between organs, but also the worm’s variety of novel endogenous tetrapyrrolic compounds.

scholarly journals Improved gene co-expression network quality through expression dataset down-sampling and network aggregation

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Franziska Liesecke ◽  
Johan-Owen De Craene ◽  
Sébastien Besseau ◽  
Vincent Courdavault ◽  
Marc Clastre ◽  
...  
Keyword(s):  
Large Scale ◽  
Expression Profiles ◽  
Expression Data ◽  
Rna Seq ◽  
Network Construction ◽  
The Past ◽  
Wide Range ◽  
Gene Associations ◽  
New Gene ◽  
Network Quality

Abstract Large-scale gene co-expression networks are an effective methodology to analyze sets of co-expressed genes and discover new gene functions or associations. Distances between genes are estimated according to their expression profiles and are visualized in networks that may be further partitioned to reveal communities of co-expressed genes. Creating expression profiles is now eased by the large amounts of publicly available expression data (microarrays and RNA-seq). Although many distance calculation methods have been intensively compared and reviewed in the past, it is unclear how to proceed when many samples reflecting a wide range of different conditions are available. Should as many samples as possible be integrated into network construction or be partitioned into smaller sets of more related samples? Previous studies have indicated a saturation in network performances to capture known associations once a certain number of samples is included in distance calculations. Here, we examined the influence of sample size on co-expression network construction using microarray and RNA-seq expression data from three plant species. We tested different down-sampling methods and compared network performances in recovering known gene associations to networks obtained from full datasets. We further examined how aggregating networks may help increase this performance by testing six aggregation methods.

scholarly journals The Fast and the Furious: Golgi Contact Sites

Contact ◽  
2021 ◽  
Vol 4 ◽  
pp. 251525642110344
Author(s):  
Yotam David ◽  
Inês G. Castro ◽  
Maya Schuldiner
Keyword(s):  
Stress Responses ◽  
Metabolic Pathways ◽  
Secretory Pathway ◽  
Current Knowledge ◽  
Close Apposition ◽  
Cellular Functions ◽  
Future Directions ◽  
Contact Sites ◽  
The Past ◽  
Wide Range

Contact sites are areas of close apposition between two membranes that coordinate nonvesicular communication between organelles. Such interactions serve a wide range of cellular functions from regulating metabolic pathways to executing stress responses and coordinating organelle inheritance. The past decade has seen a dramatic increase in information on certain contact sites, mostly those involving the endoplasmic reticulum. However, despite its central role in the secretory pathway, the Golgi apparatus and its contact sites remain largely unexplored. In this review, we discuss the current knowledge of Golgi contact sites and share our thoughts as to why Golgi contact sites are understudied. We also highlight what exciting future directions may exist in this emerging field.

Antibody engineering

1989 ◽  
Vol 324 (1224) ◽  
pp. 537-547 ◽  
Keyword(s):  
Binding Sites ◽  
Antibody Engineering ◽  
Past Century ◽  
Antibody Molecule ◽  
Effector Functions ◽  
The Past ◽  
Wide Range ◽  
Genes Encoding ◽  
Complement Lysis

The antibody molecule is a therapeutic agent, designed by nature to bind to a wide range of antigen molecules and to trigger effector functions, such as complement lysis and cell-mediated killing. The genes encoding antibodies can be manipulated in vitro , allowing the binding sites for antigen and effector molecules to be dissected, and new properties to be engineered. The future for the application of engineered antibodies in medicine is reviewed in the context of the past century.

scholarly journals Study on the mechanism of production of γ-PGA and nattokinase in Bacillus subtilis natto based on RNA-seq analysis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Min Li ◽  
Zilong Zhang ◽  
Shenwei Li ◽  
Zhengan Tian ◽  
Xia Ma
Keyword(s):  
Bacillus Subtilis ◽  
Solid State ◽  
Metabolic Pathways ◽  
Molecular Targets ◽  
Commercial Production ◽  
Rna Seq ◽  
Expression Of Genes ◽  
Bacillus Subtilis Natto ◽  
Genes Encoding ◽  
Application Prospects

AbstractPoly-γ-glutamic acid (γ-PGA) and nattokinase (NK) are the main substances produced by Bacillus subtilis natto in solid-state fermentation and have wide application prospects. We found that our strains had higher activity of nattokinase when soybeans were used as substrate to increase the yield of γ-PGA. Commercial production of γ-PGA and nattokinase requires an understanding of the mechanism of co-production. Here, we obtained the maximum γ-PGA yield (358.5 g/kg, w/w) and highest activity of NK during fermentation and analyzed the transcriptome of Bacillus subtilis natto during co-production of γ-PGA and NK. By comparing changes in expression of genes encoding key enzymes and the metabolic pathways associated with the products in genetic engineering, the mechanism of co-production of γ-PGA and nattokinase can be summarized based on RNA-seq analysis. This study firstly provides new insights into the mechanism of co-production of γ-PGA and nattokinase by Bacillus subtilis natto and reveals potential molecular targets to promote the co-production of γ-PGA and nattokinase.

Optical Properties of HVEM Accelerators

1975 ◽  
Vol 33 ◽  
pp. 180-181
Author(s):  
A. Strojnik ◽  
J.W. Scholl ◽  
V. Bevc
Keyword(s):  
Optical Properties ◽  
Electron Accelerator ◽  
Systematic Investigation ◽  
Electron Source ◽  
High Brightness ◽  
The Past ◽  
Wide Range ◽  
Optical Behavior

The electron accelerator, as inserted between the electron source (injector) and the imaging column of the HVEM, is usually a strong lens and should be optimized in order to ensure high brightness over a wide range of accelerating voltages and illuminating conditions. This is especially true in the case of the STEM where the brightness directly determines the highest resolution attainable. In the past, the optical behavior of accelerators was usually determined for a particular configuration. During the development of the accelerator for the Arizona 1 MEV STEM, systematic investigation was made of the major optical properties for a variety of electrode configurations, number of stages N, accelerating voltages, 1 and 10 MEV, and a range of injection voltages ϕ0 = 1, 3, 10, 30, 100, 300 kV).

Pursuit of the Abscopal Effect

2020 ◽  
Vol 04 (04) ◽  
pp. 369-372
Author(s):  
Paul B. Romesser ◽  
Christopher H. Crane
Keyword(s):  
Tumor Immunology ◽  
Antitumor Immunity ◽  
Clinical Success ◽  
Immune Recognition ◽  
Immune Modulators ◽  
Cancer Subtypes ◽  
The Past ◽  
Tumor Irradiation ◽  
Wide Range ◽  
Tumor Recognition

AbstractEvasion of immune recognition is a hallmark of cancer that facilitates tumorigenesis, maintenance, and progression. Systemic immune activation can incite tumor recognition and stimulate potent antitumor responses. While the concept of antitumor immunity is not new, there is renewed interest in tumor immunology given the clinical success of immune modulators in a wide range of cancer subtypes over the past decade. One particularly interesting, yet exceedingly rare phenomenon, is the abscopal response, characterized by a potent systemic antitumor response following localized tumor irradiation presumably attributed to reactivation of antitumor immunity.

The Many Pasts of Detective Fiction

2020 ◽  
Vol 1 (2) ◽  
pp. 157-172
Author(s):  
Thomas Leitch
Keyword(s):  
Detective Fiction ◽  
Golden Age ◽  
Public History ◽  
Detective Novel ◽  
Sherlock Holmes ◽  
Detective Story ◽  
The Past ◽  
Wide Range ◽  
Detective Novels ◽  
The Many

Building on Tzvetan Todorov's observation that the detective novel ‘contains not one but two stories: the story of the crime and the story of the investigation’, this essay argues that detective novels display a remarkably wide range of attitudes toward the several pasts they represent: the pasts of the crime, the community, the criminal, the detective, and public history. It traces a series of defining shifts in these attitudes through the evolution of five distinct subgenres of detective fiction: exploits of a Great Detective like Sherlock Holmes, Golden Age whodunits that pose as intellectual puzzles to be solved, hardboiled stories that invoke a distant past that the present both breaks with and echoes, police procedurals that unfold in an indefinitely extended present, and historical mysteries that nostalgically fetishize the past. It concludes with a brief consideration of genre readers’ own ambivalent phenomenological investment in the past, present, and future each detective story projects.

Nine Centuries of Man

2017 ◽  
Keyword(s):  
Twentieth Century ◽  
Diverse Range ◽  
Gender Expectations ◽  
Court Records ◽  
The Past ◽  
Wide Range ◽  
Police Reports ◽  
Late Twentieth ◽  
Scottish History ◽  
Late Twentieth Century

What did it mean to be a man in Scotland over the past nine centuries? Scotland, with its stereotypes of the kilted warrior and the industrial ‘hard man’, has long been characterised in masculine terms, but there has been little historical exploration of masculinity in a wider context. This interdisciplinary collection examines a diverse range of the multiple and changing forms of masculinities from the late eleventh to the late twentieth century, exploring the ways in which Scottish society through the ages defined expectations for men and their behaviour. How men reacted to those expectations is examined through sources such as documentary materials, medieval seals, romances, poetry, begging letters, police reports and court records, charity records, oral histories and personal correspondence. Focusing upon the wide range of activities and roles undertaken by men – work, fatherhood and play, violence and war, sex and commerce – the book also illustrates the range of masculinities that affected or were internalised by men. Together, the chapters illustrate some of the ways Scotland’s gender expectations have changed over the centuries and how, more generally, masculinities have informed the path of Scottish history

Free but fragile: Human relations amidst poverty and HIV in democratic South Africa

2015 ◽  
Vol 2 (2) ◽  
pp. 85-94
Author(s):  
Christina Landman
Keyword(s):  
South Africa ◽  
Predominantly White ◽  
Black People ◽  
Hiv Treatment ◽  
Human Relations ◽  
White People ◽  
Black And White ◽  
The Past ◽  
Wide Range ◽  
Black Township

Dullstroom-Emnotweni is the highest town in South Africa. Cold and misty, it is situated in the eastern Highveld, halfway between the capital Pretoria/Tswane and the Mozambique border. Alongside the main road of the white town, 27 restaurants provide entertainment to tourists on their way to Mozambique or the Kruger National Park. The inhabitants of the black township, Sakhelwe, are remnants of the Southern Ndebele who have lost their land a century ago in wars against the whites. They are mainly dependent on employment as cleaners and waitresses in the still predominantly white town. Three white people from the white town and three black people from the township have been interviewed on their views whether democracy has brought changes to this society during the past 20 years. Answers cover a wide range of views. Gratitude is expressed that women are now safer and HIV treatment available. However, unemployment and poverty persist in a community that nevertheless shows resilience and feeds on hope. While the first part of this article relates the interviews, the final part identifies from them the discourses that keep the black and white communities from forming a group identity that is based on equality and human dignity as the values of democracy.

FROM THE HISTORY OF THE FORMATION AND DEVELOPMENT OF PERIODICALS IN NAMANGAN

2019 ◽  
Vol 20 (2) ◽  
pp. 49-54
Author(s):  
Dildora Alinazarova ◽  
Keyword(s):  
The Past ◽  
Wide Range ◽  
History Of ◽  
Printing House

In this article, based on an analysis of a wide range of sources, discusses the emergence and development of periodicals and printing house in Namangan. The activities of Ibrat- as the founder of the first printing house in Namangan are considered. In addition, it describes the functioning and development of "Matbaai Ishokia" in the past and present

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