The β-oxidation pathway is downregulated during diapause termination in Calanus copepods

Abstract Calanus copepods are keystone species in marine ecosystems, mainly due to their high lipid content, which is a nutritious food source for e.g. juvenile fish. Accumulated lipids are catabolized to meet energy requirements during dormancy (diapause), which occurs during the last copepodite stage (C5). The current knowledge of lipid degradation pathways during diapause termination is limited. We characterized changes in lipid fullness and generated transcriptional profiles in C5s during termination of diapause and progression towards adulthood. Lipid fullness of C5s declined linearly during developmental progression, but more β-oxidation genes were upregulated in early C5s compared to late C5s and adults. We identified four possible master regulators of energy metabolism, which all were generally upregulated in early C5s, compared to late C5s and adults. We discovered that one of two enzymes in the carnitine shuttle is absent from the calanoid copepod lineage. Based on the geographical location of the sampling site, the field-samples were initially presumed to consist of C. finmarchicus. However, the identification of C. glacialis in some samples underlines the need for performing molecular analyses to reliably identify Calanus species. Our findings contributes to a better understanding of molecular events occurring during diapause and diapause termination in calanoid copepods.

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A Comprehensive Review on Solitary Fibrous Tumor: New Insights for New Horizons

Cancers ◽

10.3390/cancers13122913 ◽

2021 ◽

Vol 13 (12) ◽

pp. 2913

Author(s):

Javier Martin-Broto ◽

Jose L. Mondaza-Hernandez ◽

David S. Moura ◽

Nadia Hindi

Keyword(s):

Solitary Fibrous Tumor ◽

Fusion Gene ◽

Current Knowledge ◽

Fusion Transcript ◽

Chemotherapeutic Agents ◽

Comprehensive Review ◽

Molecular Events ◽

In Series ◽

Prospective Phase ◽

Fibrous Tumor

Solitary fibrous tumor (SFT) is a rare mesenchymal, ubiquitous tumor, with an incidence of 1 new case/million people/year. In the 2020 WHO classification, risk stratification models were recommended as a better tool to determine prognosis in SFT, to the detriment of “typical” or “malignant” classic terms. The risk for metastasis is up to 35–45%, or even greater, in series with a longer follow-up. Over the last few decades, advances in immunohistochemistry and molecular diagnostics identified STAT6 nuclear protein expression and the NAB2–STAT6 fusion gene as more precise tools for SFT diagnosis. Recent evidence taken from retrospective series and from two prospective phase II clinical trials showed that antiangiogenics are active and their sequential use from first line should be considered, except for dedifferentiated SFT for which chemotherapy is the best option. Since the fusion transcript driver’s first description in 2013, new insights have been brought on key molecular events in SFT. This comprehensive review mainly focuses on the superior efficacy of antiangiogenics over chemotherapeutic agents in SFT, provides the current knowledge of key molecules that could co-drive the SFT behavior, and suggests new target candidates that deserve to be explored in preclinical and clinical research in SFT.

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Cancer-associated fibroblasts (CAFs) in thyroid papillary carcinoma: molecular networks and interactions

Journal of Clinical Pathology ◽

10.1136/jclinpath-2020-207357 ◽

2021 ◽

pp. jclinpath-2020-207357

Author(s):

Jeehoon Ham ◽

Bin Wang ◽

Joseph William Po ◽

Amandeep Singh ◽

Navin Niles ◽

...

Keyword(s):

Cell Growth ◽

Cancer Cells ◽

Cancer Cell ◽

Stromal Cells ◽

Cancer Metastasis ◽

Current Knowledge ◽

Molecular Networks ◽

Cancer Cell Growth ◽

Molecular Events

In 1989, Stephen Paget proposed the ‘seed and soil’ theory of cancer metastasis. This theory has led to previous researchers focusing on the role of a tumour as a cancer seed and antiangiogenesis agents as cancer soil fumigant; for the latter to be effective, it is important for them to be able to distinguish cancer cells from stromal cells. However, antiangiogenesis agents have not produced dramatic survival benefits in vivo. This may be related to their inability to destroy the supporting stroma that promote cancer cell growth. Therefore, in order to effectively arrest cancer cell growth for therapeutic purposes, a paradigm shift is required in our fundamental approach to decipher the molecular events and networks in the stromal environment that cancer cells can thrive and proliferate. The pathogenesis of cancer is a multidimensional process of pathological molecular and cellular pathways, influencing different stromal properties and achieving a mutually negotiated crosstalk between cancer cells and stromal cells. This review summarises the clinical presentation of current knowledge of classical papillary thyroid carcinoma (PTC), emerging molecular diagnostics and future directions of classical PTC research.

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Targeting Genome Integrity in Mycobacterium Tuberculosis: From Nucleotide Synthesis to DNA Replication and Repair

Molecules ◽

10.3390/molecules25051205 ◽

2020 ◽

Vol 25 (5) ◽

pp. 1205 ◽

Cited By ~ 1

Author(s):

Riccardo Miggiano ◽

Castrese Morrone ◽

Franca Rossi ◽

Menico Rizzi

Keyword(s):

Mycobacterium Tuberculosis ◽

Drug Discovery ◽

Genome Stability ◽

Current Knowledge ◽

Genome Integrity ◽

Dna Integrity ◽

Dna Metabolism ◽

Nucleotide Synthesis ◽

Antitubercular Drugs ◽

Molecular Events

Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis (TB), an ancient disease which still today causes 1.4 million deaths worldwide per year. Long-term, multi-agent anti-tubercular regimens can lead to the anticipated non-compliance of the patient and increased drug toxicity, which in turn can contribute to the emergence of drug-resistant MTB strains that are not susceptible to first- and second-line available drugs. Hence, there is an urgent need for innovative antitubercular drugs and vaccines. A number of biochemical processes are required to maintain the correct homeostasis of DNA metabolism in all organisms. Here we focused on reviewing our current knowledge and understanding of biochemical and structural aspects of relevance for drug discovery, for some such processes in MTB, and particularly DNA synthesis, synthesis of its nucleotide precursors, and processes that guarantee DNA integrity and genome stability. Overall, the area of drug discovery in DNA metabolism appears very much alive, rich of investigations and promising with respect to new antitubercular drug candidates. However, the complexity of molecular events that occur in DNA metabolic processes requires an accurate characterization of mechanistic details in order to avoid major flaws, and therefore the failure, of drug discovery approaches targeting genome integrity.

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Regulation of ST6GAL1 sialyltransferase expression in cancer cells

Glycobiology ◽

10.1093/glycob/cwaa110 ◽

2020 ◽

Author(s):

Kaitlyn A Dorsett ◽

Michael P Marciel ◽

Jihye Hwang ◽

Katherine E Ankenbauer ◽

Nikita Bhalerao ◽

...

Keyword(s):

Cancer Cells ◽

Translational Regulation ◽

Molecular Mechanisms ◽

Current Knowledge ◽

Sialic Acids ◽

Invasion Resistance ◽

Cell Behaviors ◽

Molecular Events ◽

Wide Range

Abstract The ST6GAL1 sialyltransferase, which adds α2–6 linked sialic acids to N-glycosylated proteins, is overexpressed in a wide range of human malignancies. Recent studies have established the importance of ST6GAL1 in promoting tumor cell behaviors such as invasion, resistance to cell stress, and chemoresistance. Furthermore, ST6GAL1 activity has been implicated in imparting cancer stem cell characteristics. However, despite the burgeoning interest in the role of ST6GAL1 in the phenotypic features of tumor cells, insufficient attention has been paid to the molecular mechanisms responsible for ST6GAL1 upregulation during neoplastic transformation. Evidence suggests that these mechanisms are multifactorial, encompassing genetic, epigenetic, transcriptional, and post-translational regulation. The purpose of this review is to summarize current knowledge regarding the molecular events that drive enriched ST6GAL1 expression in cancer cells.

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Proteomic and Transcriptomic Analyses Indicate Metabolic Changes and Reduced Defense Responses in Mycorrhizal Roots of Oeceoclades maculata (Orchidaceae) Collected in Nature

Journal of Fungi ◽

10.3390/jof6030148 ◽

2020 ◽

Vol 6 (3) ◽

pp. 148

Author(s):

Rafael B. S. Valadares ◽

Silvia Perotto ◽

Adriano R. Lucheta ◽

Eder C. Santos ◽

Renato M. Oliveira ◽

...

Keyword(s):

Plant Defense ◽

De Novo ◽

Current Knowledge ◽

Defense Responses ◽

Mycorrhizal Symbiosis ◽

Label Free ◽

Molecular Events ◽

Mycorrhizal Roots ◽

Steady State Levels ◽

Isobaric Tagging

Orchids form endomycorrhizal associations with fungi mainly belonging to basidiomycetes. The molecular events taking place in orchid mycorrhiza are poorly understood, although the cellular changes necessary to accommodate the fungus and to control nutrient exchanges imply a modulation of gene expression. Here, we used proteomics and transcriptomics to identify changes in the steady-state levels of proteins and transcripts in the roots of the green terrestrial orchid Oeceoclades maculata. When mycorrhizal and non-mycorrhizal roots from the same individuals were compared, 94 proteins showed differential accumulation using the label-free protein quantitation approach, 86 using isobaric tagging and 60 using 2D-differential electrophoresis. After de novo assembly of transcriptomic data, 11,179 plant transcripts were found to be differentially expressed, and 2175 were successfully annotated. The annotated plant transcripts allowed the identification of up- and down-regulated metabolic pathways. Overall, proteomics and transcriptomics revealed, in mycorrhizal roots, increased levels of transcription factors and nutrient transporters, as well as ethylene-related proteins. The expression pattern of proteins and transcripts involved in plant defense responses suggested that plant defense was reduced in O. maculata mycorrhizal roots sampled in nature. These results expand our current knowledge towards a better understanding of the orchid mycorrhizal symbiosis in adult plants under natural conditions.

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Keystone species and food webs

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2008.0335 ◽

2009 ◽

Vol 364 (1524) ◽

pp. 1733-1741 ◽

Cited By ~ 118

Author(s):

Ferenc Jordán

Keyword(s):

Current Knowledge ◽

Interspecific Interactions ◽

Keystone Species ◽

Ecosystem Functions ◽

General Interest ◽

Interaction Structure ◽

Structure And Dynamics ◽

Rich Interaction ◽

Natural Communities

Different species are of different importance in maintaining ecosystem functions in natural communities. Quantitative approaches are needed to identify unusually important or influential, ‘keystone’ species particularly for conservation purposes. Since the importance of some species may largely be the consequence of their rich interaction structure, one possible quantitative approach to identify the most influential species is to study their position in the network of interspecific interactions. In this paper, I discuss the role of network analysis (and centrality indices in particular) in this process and present a new and simple approach to characterizing the interaction structures of each species in a complex network. Understanding the linkage between structure and dynamics is a condition to test the results of topological studies, I briefly overview our current knowledge on this issue. The study of key nodes in networks has become an increasingly general interest in several disciplines: I will discuss some parallels. Finally, I will argue that conservation biology needs to devote more attention to identify and conserve keystone species and relatively less attention to rarity.

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Sex andEimeria: a molecular perspective

Parasitology ◽

10.1017/s0031182013000838 ◽

2013 ◽

Vol 140 (14) ◽

pp. 1701-1717 ◽

Cited By ~ 22

Author(s):

ROBERT A. WALKER ◽

DAVID J. P. FERGUSON ◽

CATHERINE M. D. MILLER ◽

NICHOLAS C. SMITH

Keyword(s):

Sexual Reproduction ◽

Current Knowledge ◽

Economic Loss ◽

Complex Life Cycle ◽

Parasite Transmission ◽

Oocyst Wall ◽

Molecular Events ◽

Common Genus ◽

Serious Disease ◽

Resilient Structure

SUMMARYEimeriais a common genus of apicomplexan parasites that infect diverse vertebrates, most notably poultry, causing serious disease and economic loss. Like all apicomplexans, eimerians have a complex life cycle characterized by asexual divisions that amplify the parasite population in preparation for sexual reproduction. This can be divided into three events: gametocytogenesis, producing gametocytes from merozoites; gametogenesis, producing microgametes and macrogametes from gametocytes; and fertilization of macrogametes by microgametes, producing diploid zygotes with ensuing meiosis completing the sexual phase. Sexual development inEimeriadepends on the differential expression of stage-specific genes, rather than presence or absence of sex chromosomes. Thus, it involves the generation of specific structures and, implicitly, storage of proteins and regulation of protein expression in macrogametes, in preparation for fertilization. InEimeria, the formation of a unique, resilient structure, the oocyst wall, is essential for completion of the sexual phase and parasite transmission. In this review, we piece together the molecular events that underpin sexual reproduction inEimeriaand use additional details from analogous events inPlasmodiumto fill current knowledge gaps. The mechanisms governing sexual stage formation and subsequent fertilization may represent targets for counteracting parasite transmission.

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European rabbit restocking: a critical review in accordance with IUCN (1998) guidelines for re–introduction

Animal Biodiversity and Conservation ◽

10.32800/abc.2013.36.0177 ◽

2013 ◽

Vol 36 (2) ◽

pp. 177-185

Author(s):

J. Guerrero–Casado ◽

◽

J. Letty ◽

F. S. Tortosa ◽

◽

...

Keyword(s):

Success Rate ◽

Critical Review ◽

Current Knowledge ◽

Keystone Species ◽

European Rabbit ◽

Management Guidelines ◽

Conservation Projects ◽

Review Current ◽

Long Term Studies

European rabbit restocking is one of the most frequent actions in hunting estates and conservation projects in Spain, France and Portugal where rabbit is a keystone species. The aim of this work was to review current knowledge regarding rabbit restocking in accordance with the IUCN (1998) guidelines for re–introduction in order to identify gaps in knowledge and highlight the techniques that improve the overall success rate. Eight of 17 items selected from these guidelines were identified as partly studied or unknown, including important items such as the management and release of captive–reared wild rabbits, the development of transport and monitoring programs, the application of vaccine programs, and post–release long–term studies. Researchers should therefore concentrate their efforts on bridging these knowledge gaps, and wildlife managers should consider all the factors reviewed herein so as to establish accurate management guidelines for subsequent rabbit restocking programs.

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Bioenergetics of Mammalian Sperm Capacitation

BioMed Research International ◽

10.1155/2014/902953 ◽

2014 ◽

Vol 2014 ◽

pp. 1-8 ◽

Cited By ~ 47

Author(s):

Alessandra Ferramosca ◽

Vincenzo Zara

Keyword(s):

Metabolic Pathways ◽

Current Knowledge ◽

Mammalian Species ◽

Primary Source ◽

Male Gamete ◽

Sperm Capacitation ◽

Metabolic Substrates ◽

Mammalian Sperm ◽

Molecular Events ◽

Broad Overview

After ejaculation, the mammalian male gamete must undergo the capacitation process, which is a prerequisite for egg fertilization. The bioenergetics of sperm capacitation is poorly understood despite its fundamental role in sustaining the biochemical and molecular events occurring during gamete activation. Glycolysis and mitochondrial oxidative phosphorylation (OXPHOS) are the two major metabolic pathways producing ATP which is the primary source of energy for spermatozoa. Since recent data suggest that spermatozoa have the ability to use different metabolic substrates, the main aim of this work is to present a broad overview of the current knowledge on the energy-producing metabolic pathways operating inside sperm mitochondria during capacitation in different mammalian species. Metabolism of glucose and of other energetic substrates, such as pyruvate, lactate, and citrate, is critically analyzed. Such knowledge, besides its obvious importance for basic science, could eventually translate into the development of novel strategies for treatment of male infertility, artificial reproduction, and sperm selection methods.

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Identification and differentiation of Pseudomonas species in field samples using an rpoD amplicon sequencing methodology

10.1101/2021.06.08.447643 ◽

2021 ◽

Author(s):

Jonas Greve Lauritsen ◽

Morten Lindqvist Hansen ◽

Pernille Kjersgaard Bech ◽

Lars Jelsbak ◽

Lone Gram ◽

...

Keyword(s):

16S Rrna ◽

Large Scale ◽

Sampling Site ◽

Amplicon Sequencing ◽

Soil Samples ◽

Species Differentiation ◽

Rrna Gene ◽

Rpod Gene ◽

Field Samples ◽

Pseudomonas Species

Species of the genus Pseudomonas are used for several biotechnological purposes, including plant biocontrol and bioremediation. To exploit the Pseudomonas genus in environmental, agricultural or industrial settings, the organisms must be profiled at species level as their bioactivity potential differs markedly between species. Standard 16S rRNA gene amplicon profiling does not allow for accurate species differentiation. Thus, the purpose of this study was to develop an amplicon-based high-resolution method targeting a 760 nt region of the rpoD gene enabling taxonomic differentiation of Pseudomonas species in soil samples. The method was benchmarked on a sixteen membered Pseudomonas species mock community. All 16 species were correctly and semi-quantitatively identified using rpoD gene amplicons, whereas 16S rRNA V3V4 amplicon sequencing only correctly identified one species. We analysed the Pseudomonas profile in thirteen soil samples in northern Zealand, Denmark, where samples were collected from grassland (3 samples) and agriculture soil (10 samples). Pseudomonas species represented up to 0.7% of the microbial community, of which each sampling site contained a unique Pseudomonas composition. Thirty culturable Pseudomonas strains were isolated from each grassland site and ten from each agriculture site and identified by Sanger sequencing of the rpoD gene. In all cases, the rpoD-amplicon approach identified more species than found by cultivation, including hard-to-culture non-fluorescent pseudomonads, as well as more than found by 16S rRNA V3V4 amplicon sequencing. Thus, rpoD profiling can be used for species profiling of Pseudomonas, and large scale prospecting of bioactive Pseudomonas may be guided by initial screening using this method.

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