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Topic Review
Styela clava
Tunicates occupy the evolutionary position at the boundary of invertebrates and vertebrates. It exhibits adaptation to broad environmental conditions and is distributed globally. Despite hundreds of years of embryogenesis studies, the genetic basis of the invasive habits of ascidians remains largely unknown. The leathery sea squirt, Styela clava, is an important invasive species. We used the chromosomal‐level genome and transcriptome of S. clava to explore its genomic‐ and molecular‐network‐based mechanisms of adaptation to environments. Compared with Ciona intestinalis type A (C. robusta), the size of the S. clava genome was expanded by 2‐fold, although the gene number was comparable. An increase in transposon number and variation in dominant types were identified as potential expansion mechanisms. In the S. clava genome, the number of genes encoding the heat‐shock protein 70 family and members of the complement system was expanded significantly, and cold‐shock protein genes were transferred horizontally into the S. clava genome from bacteria. The expanded gene families potentially play roles in the adaptation of S. clava to its environments. The loss of key genes in the galactan synthesis pathway might explain the distinct tunic structure and hardness compared with the ascidian Ciona species. And to explore the role of transcription factors (TFs)  in embryonic development and environmental adaptation, we systematically identified and analyzed TFs in S. clava genome. We reported 553 TFs categorized into 60 families from S. clava, based on the whole genome data. Comparison of TFs analysis among the tunicate species revealed that the gene number in the zinc finger superfamily displayed the most significant discrepancy, indicating this family was under the highly evolutionary selection and might be related to species differentiation and environmental adaptation. The greatest number of TFs was discovered in the Cys2His2-type zinc finger protein (zf-C2H2) family in S. clava. From the point of temporal view, more than half the TFs were expressed at the early embryonic stage. The expression correlation analysis revealed the existence of a transition for TFs expression from early embryogenesis to the later larval development in S. clava. Eight Hox genes were identified to be located on one chromosome, exhibiting different arrangement and expression patterns, compared to Ciona robusta. 
  • 1.2K
  • 13 May 2021
Topic Review
Multi-Omics Model for Cancer Genetics
In the coming age of omics technologies, next gen sequencing, proteomics, metabolomics, and other high throughput techniques will become the usual tools in biomedical cancer research. However, their integrative approach is not trivial due to the broad diversity of data types, dynamic ranges and sources of experimental and analytical errors characteristic of each omics.
  • 1.2K
  • 02 Jun 2021
Topic Review
Andean Blueberry
Andean blueberry (Vaccinium floribundum Kunth), also known as mortiño, is a promising wild berry of the family Ericaceae that grows spontaneously in the Andean regions of Ecuador. The demand for these small (~8 mm diameter), black, and round fruits has been increasing due to their antioxidant characteristic, similar to other Vaccinium species, such as cranberry, blueberry, or bilberry, mostly related to the high content of (poly) phenolic compounds.
  • 1.2K
  • 14 May 2021
Topic Review
Phenolic Compounds in Functional Pasta
Phenolic compounds are lost during the refining of flour and semolina, hence commonly consumed pasta is not a carrier of these components. Consumption of food products rich in phenolic compounds has been associated to reduced risk of chronic disease onset. Hence, several strategies have been developed to formulate functional pasta rich in phenolic compounds.  Whole grain, legume and composite flours are the main substituents of durum wheat semolina used for this purpose. Plant by-products from industrial food wastes have been also used as functional ingredients. In addition, pre-processing technologies on raw materials such as sprouting, or the modulation of extrusion/extrusion-cooking conditions, are valuable approaches to increase phenolic content in pasta.
  • 1.2K
  • 22 Jun 2021
Topic Review
Ethylene
Salinity stress is one of the major threats to agricultural productivity across the globe. Research in the past three decades, therefore, has focused on analyzing the effects of salinity stress on the plants. Evidence gathered over the years supports the role of ethylene as a key regulator of salinity stress tolerance in plants. This gaseous plant hormone regulates many vital cellular processes starting from seed germination to photosynthesis for maintaining the plants’ growth and yield under salinity stress. Ethylene modulates salinity stress responses largely via maintaining the homeostasis of Na+/K+, nutrients, and reactive oxygen species (ROS) by inducing antioxidant defense in addition to elevating the assimilation of nitrates and sulfates. Moreover, a cross-talk of ethylene signaling with other phytohormones has also been observed, which collectively regulate the salinity stress responses in plants.
  • 1.2K
  • 09 Jul 2021
Topic Review
Bioinformatics in Plant Breeding and Disease Resistance
In the context of plant breeding, bioinformatics can empower genetic and genomic selection to determine the optimal combination of genotypes that will produce a desired phenotype and help expedite the isolation of these new varieties. Bioinformatics is also instrumental in collecting and processing plant phenotypes, which facilitates plant breeding. Robots that use automated and digital technologies to collect and analyze different types of information to monitor the environment in which plants grow, analyze the environmental stresses they face, and promptly optimize suboptimal and adverse growth conditions accordingly, have helped plant research and saved human resources.
  • 1.2K
  • 02 Dec 2022
Topic Review
Bifunctional Non-Canonical Amino Acids
Genetic code expansion is a powerful tool for the study of protein interactions, as it allows for the site-specific incorporation of a photoreactive group via non-canonical amino acids. Recently, several groups have published bifunctional amino acids that carry a handle for click chemistry in addition to the photo-crosslinker. This allows for the specific labeling of crosslinked proteins and therefore the pulldown of peptides for further analysis. This review describes the properties and advantages of different bifunctional amino acids, and gives an overview about current and future applications.
  • 1.2K
  • 17 Jun 2021
Topic Review
Early Follicles
Early follicles' development, especially the activation of primordial follicles, is strictly modulated by a network of signaling pathways. Recent advance in ovarian physiology has been allowed the development of several therapies to improve reproductive outcomes by manipulating early folliculogenesis. Among these, in vitro activation (IVA) has been recently developed to extend the possibility of achieving genetically related offspring for patients with premature ovarian insufficiency and ovarian dysfunction. This method was established based on basic science studies of the intraovarian signaling pathways: the phosphoinositide 3-kinase (PI3K)/Akt and the Hippo signaling pathways. These two pathways were found to play crucial roles in folliculogenesis from the primordial follicle to the early antral follicle. Following the results of rodent experiments, IVA was implemented in clinical practice. There have been multiple recorded live births and ongoing pregnancies. Further investigations are essential to confirm the efficacy and safety of IVA before used widely in clinics.
  • 1.1K
  • 27 Apr 2021
Topic Review
S-Nitrosylation
Nitric oxide (NO) is a highly reactive molecule, generated through metabolism of L-arginine by NO synthase (NOS). Abnormal NO levels in mammalian cells are associated with multiple human diseases, including cancer. Recent studies have uncovered that the NO signaling is compartmentalized, owing to the localization of NOS and the nature of biochemical reactions of NO, including S-nitrosylation. S-nitrosylation is a selective covalent post-translational modification adding a nitrosyl group to the reactive thiol group of a cysteine to form S-nitrosothiol (SNO), which is a key mechanism in transferring NO-mediated signals. While S-nitrosylation occurs only at select cysteine thiols, such a spatial constraint is partially resolved by transnitrosylation, where the nitrosyl moiety is transferred between two interacting proteins to successively transfer the NO signal to a distant location. As NOS is present in various subcellular locales, a stress could trigger concerted S-nitrosylation and transnitrosylation of a large number of proteins involved in divergent signaling cascades. S-nitrosylation is an emerging paradigm of redox signaling by which cells confer protection against oxidative stress.
  • 1.1K
  • 09 Aug 2021
Topic Review
Quantum Biology and Non-Targeted Effects
Non-targeted effects (NTE) are an intriguing phenomenon where the biological responses observed in cells or tissues are not directly exposed to a stressor (e.g., ionizing radiation or chemical agents). onventional radiation biology approaches have predominantly focused on the macroscopic effects of ionizing radiation, overlooking the quantum-scale interactions that may play a crucial role in NTE. Quantum biology (QB) offers a unique perspective to explore and understand the intricate and subtle processes underlying NTE.
  • 1.1K
  • 04 Dec 2023
Topic Review
Type
In biology, a type is a particular specimen (or in some cases a group of specimens) of an organism to which the scientific name of that organism is formally attached. In other words, a type is an example that serves to anchor or centralize the defining features of that particular taxon. In older usage (pre-1900 in botany), a type was a taxon rather than a specimen. A taxon is a scientifically named grouping of organisms with other like organisms, a set that includes some organisms and excludes others, based on a detailed published description (for example a species description) and on the provision of type material, which is usually available to scientists for examination in a major museum research collection, or similar institution.
  • 1.1K
  • 02 Dec 2022
Topic Review
Satellite DNA
Repetitive DNA is a major organizational component of eukaryotic genomes, being intrinsically related with their architecture and evolution. Tandemly repeated satellite DNAs (satDNAs) can be found clustered in specific heterochromatin-rich chromosomal regions, building vital structures like functional centromeres and also dispersed within euchromatin. Interestingly, despite their association to critical chromosomal structures, satDNAs are widely variable among species due to their high turnover rates. This dynamic behavior has been associated with genome plasticity and chromosome rearrangements, leading to the reshaping of genomes.
  • 1.1K
  • 19 Jul 2021
Topic Review
Poly ADP-ribosylation in DNA Damage Response and Repair
Poly ADP-ribosylation (PARylation) is a post-translational modification process. Following the discovery of PARP-1, numerous studies have demonstrated the role of PARylation in the DNA damage and repair responses for cellular stress and DNA damage.
  • 1.1K
  • 08 Oct 2022
Topic Review
The LPA3 Receptor
Lysophosphatidic acid receptor 3 (LPA3) is implicated in different physiological and pathological functions through activation of different signal pathways, the result of the regulation process of this receptor. The knowledge of regulating LPA3 could be a crucial element for defined their roles in health and disease.
  • 1.1K
  • 09 Jul 2021
Topic Review
Biomass-Based Chemical Looping Gasification
Chemical Looping Gasification is a process allowing for the conversion of solid feedstock (e.g. biomass) into N2-free, high-calorific syngas or producer gas. The process utilizes the ability of so-called oxygen carriers (e.g. ilmenite, iron ore) to take up and release oxygen in oxidizing and reducing atmospheres, respectively. Employing this characteristic, the oxygen carrier is cycled between two or more reactors to transport oxygen into the so-called fuel reactor, where the inlet feedstock is firstly gasified using steam or CO2, before intermediate gaseous products (e.g. H2, CH4) are further oxidized by the oxygen carrier, providing additional process heat to drive the endothermic gasification reactions. The loop is then closed as the reduced oxygen carrier is re-oxidized in a so-called air reactor, using the oxygen contained in ambient air, resulting in a stream of pure nitrogen at the air reactor outlet.
  • 1.1K
  • 03 Nov 2021
Topic Review
Spironolactone and XPB
Spironolactone (SP) is commonly used for the treatment of heart failure, hypertension, and complications of cirrhosis by antagonizing the mineralocorticoid receptor. However, SP also antagonizes the androgen receptor, and thus SP has also been shown to be effective in the treatment of acne, hair loss, and hirsutism in women. Interestingly, recent drug repurposing screens have identified new and diverse functions for SP as a simulator of tumor immunosurveillance and as an inhibitor of DNA repair and viral infection. These novel pharmacological effects of SP have all been linked to the ability of SP to induce the rapid proteolytic degradation of the xeroderma pigmentosum group B (XPB) protein. XPB is a critical enzymatic component of the multi-subunit complex known as transcription factor II-H (TFIIH), which plays essential roles in both DNA repair and the initiation of transcription. Given the critical functions for XPB and TFIIH in these processes, the loss of XPB by SP could lead to mutagenesis. However, the ability of SP to promote cancer stem cell death and facilitate immune recognition may counteract the negative consequences of SP to mitigate carcinogenic risk. Thus, SP appears to have new and interesting pharmacological effects that may extend its potential uses.
  • 1.1K
  • 21 Jun 2021
Topic Review
Shipworms
The shipworms are marine bivalve molluscs in the family Teredinidae: a group of saltwater clams with long, soft, naked bodies. They are notorious for boring into (and commonly eventually destroying) wood that is immersed in sea water, including such structures as wooden piers, docks and ships; they drill passages by means of a pair of very small shells borne at one end, with which they rasp their way through. Sometimes called "termites of the sea", they also are known as "Teredo worms" or simply Teredo, from the Greek τερηδών teredōn, via Latin. Eventually biologists adopted the common name Teredo as the name for the best-known genus.
  • 1.1K
  • 15 Nov 2022
Topic Review
Crustacean Waste-Derived Chitosan
Chitosan is obtained from chitin that in turn is recovered from marine crustacean wastes. The recovery methods and their varying types and the advantages of the recovery methods are briefly discussed. Chitin is the major component of cuticles of insects (cockroach, beetle, true fly, and worm), fungal cell walls (Aspergillus niger, Mucor rouxii, Penicillum notatum, yeast) and green algae. The recovery methods and their varying types and the advantages of the recovery methods are briefly discussed. 
  • 1.1K
  • 09 Jun 2022
Topic Review
Trichoderma
There is no doubt that Trichoderma is an inhabitant of the rhizosphere that plays an important role in how plants interact with the environment. Beyond the production of cell wall degrading enzymes and metabolites, Trichoderma spp. can protect plants by inducing faster and stronger immune responses, a mechanism known as priming, which involves enhanced accumulation of dormant cellular proteins that function in intracellular signal amplification. One example of these proteins is the mitogen-activated protein kinases (MAPK) that are triggered by the rise of cytosolic calcium levels and cellular redox changes following a stressful challenge. Transcription factors such as WRKYs, MYBs, and MYCs, play important roles in priming as they act as regulatory nodes in the transcriptional network of systemic defence after stress recognition.
  • 1.1K
  • 06 May 2021
Topic Review
Oral–Gut Microbiome Axis
The oral cavity and gut are the two largest microbial ecosystems. The oral-to-gut and gut-to-oral microbial transmission can regulate pathogenesis, indicating the presence of the oral–gut microbiome axis. 
  • 1.1K
  • 12 May 2021
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