Frontiers in Biology

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Plant calcium oxalate crystal formation, function, and its impact on human health
Paul A. NAKATA
Front Biol    2012, 7 (3): 254-266.   https://doi.org/10.1007/s11515-012-1224-0
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Crystals of calcium oxalate have been observed among members from most taxonomic groups of photosynthetic organisms ranging from the smallest algae to the largest trees. The biological roles for calcium oxalate crystal formation in plant growth and development include high-capacity calcium regulation, protection against herbivory, and tolerance to heavy metals. Using a variety of experimental approaches researchers have begun to unravel the complex mechanisms controlling formation of this biomineral. Given the important roles for calcium oxalate formation in plant survival and the antinutrient and pathological impact on human health through its presence in plant foods, researchers are avidly seeking a more comprehensive understanding of how these crystals form. Such an understanding will be useful in efforts to design strategies aimed at improving the nutritional quality and production of plant foods.

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Enterococcus faecalis can be distinguished from Enterococcus faecium via differential susceptibility to antibiotics and growth and fermentation characteristics on mannitol salt agar
Maria L. G. Quiloan, John Vu, John Carvalho
Front Biol    2012, 7 (2): 167-177.   https://doi.org/10.1007/s11515-012-1183-5
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Enterococcus faecalis and Enterococcus faecium are both human intestinal colonizers frequently used in medical bacteriology teaching laboratories in order to train students in bacterial identification. In addition, hospitals within the United States and around the world commonly isolate these bacteria because they are a cause of bacteremia, urinary tract infections, endocarditis, wound infections, and nosocomial infections. Given that enterococci are becoming more of a world health hazard, it is important for laboratories to be able to distinguish these bacteria within hospitalized patients from other bacterial genera. In addition, laboratories must differentiate different species within the Enterococcus genus as well as different strains within each species. Though enterococci are differentiated from other bacterial genera via classical culture and biochemical methods, nucleic acid sequencing is required to differentiate species within the genus—a costly, time consuming, and technically challenging procedure for laboratory technicians that, in itself, does not necessarily lead to speedy identification of bactericidal antibiotics. In this study, we perform antibiogram analysis to show (1) that penicillin can be rapidly employed to distinguish strains and clinical isolates of E. faecalis from E. faecium, (2) E. faecalis is susceptible to ampicillin, and (3) that vancomycin resistance in enterococci shows no sign of abating. Additionally, we show that E. faecalis can grow on mannitol salt agar and ferment mannitol, while E. faecium lacks these phenotypes. These data reveal that we now have rapid, cost effective ways to identify enterococci to the species, and not just genus, level and have significance for patient treatment in hospitals.

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Bioreactor technology for clonal propagation of plants and metabolite production
Nazmul H. A. Mamun,Ulrika Egertsdotter,Cyrus K. Aidun
Front. Biol.    2015, 10 (2): 177-193.   https://doi.org/10.1007/s11515-015-1355-1
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Plant cell culture in bioreactors is an enabling tool for large scale production of clonal elite plants in agriculture, horticulture, forestry, pharmaceutical sectors, and for biofuel production. Advantages of bioreactors for plant cell culture have resulted in various types of bioreactors differing in design, operating technologies, instrumentations, and construction of culture vessels. In this review, different types of bioreactors for clonal propagation of plants and secondary metabolites production are discussed. Mechanical and biochemical parameters associated with bioreactor design, such as aeration, flow rate, mixing, dissolved oxygen, composition of built-up gas in the headspace, and pH of the medium, are pivotal for cell morphology, growth, and development of cells within tissues, embryos, and organs. The differences in such parameters for different bioreactor designs are described here, and correlated to the plant materials that have been successfully cultured in different types of bioreactors.

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Production, purification, characterization, immobilization, and application of Serrapeptase: a review
Selvarajan Ethiraj, Shreya Gopinath
Front. Biol.    2017, 12 (5): 333-348.   https://doi.org/10.1007/s11515-017-1461-3
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BACKGROUND: Serrapeptase is a proteolytic enzyme with many favorable biological properties like anti-inflammatory, analgesic, anti-bacterial, fibrinolytic properties and hence, is widely used in clinical practice for the treatment of many diseases. Although Serrapeptase is widely used, there are very few published papers and the information available about the enzyme is very meagre. Hence this review article compiles all the information about this important enzyme Serrapeptase.

METHODS: A literature search against various databases and search engines like PubMed, SpringerLink, Scopus etc. was performed.

RESULTS: We gathered and highlight all the published information regarding the molecular aspects, properties, sources, production, purification, detection, optimizing yield, immobilization, clinical studies, pharmacology, interaction studies, formulation, dosage and safety of the enzyme Serrapeptase.

CONCLUSION:Serrapeptase is used in many clinical studies against various diseases for its anti-inflammatory, fibrinolytic and analgesic effects. There is insufficient data regarding the safety of the enzyme as a health supplement. Data about the anti-atherosclerotic activity, safety, tolerability, efficacy and mechanism of action of the Serrapeptase are still required.

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PTEN/PI3K and MAPK signaling in protection and pathology following CNS injuries
Chandler L. WALKER, Nai-Kui LIU, Xiao-Ming XU
Front Biol    2013, 8 (4): 421-433.   https://doi.org/10.1007/s11515-013-1255-1
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Brain and spinal cord injuries initiate widespread temporal and spatial neurodegeneration, through both necrotic and programmed cell death mechanisms. Inflammation, reactive oxidation, excitotoxicity and cell-specific dysregulation of metabolic processes are instigated by traumatic insult and are main contributors to this cumulative damage. Successful treatments rely on prevention or reduction of the magnitude of disruption, and interfering with injurious cellular responses through modulation of signaling cascades is an effective approach. Two intracellular signaling pathways, the phosphatase and tensin homolog (PTEN)/phosphatidylinositol 3-kinase (PI3K) and mitogen-activated protein kinase (MAPK) signaling cascades play various cellular roles under normal and pathological conditions. Activation of both pathways can influence anatomical and functional outcomes in multiple CNS disorders. However, some mechanisms involve inhibiting or enhancing one pathway or the other, or both, in propagating specific downstream effects. Though many intracellular mechanisms contribute to cell responses to insult, this review examines the evidence exploring PTEN/PI3K and MAPK signaling influence on pathology, neuroprotection, and repair and how these pathways may be targeted for advancing knowledge and improving neurological outcome after injury to the brain and spinal cord.

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Actin organization and regulation during pollen tube growth
Xiuhua XUE, Fei DU, Jinsheng ZHU, Haiyun REN
Front Biol    2011, 06 (01): 40-51.   https://doi.org/10.1007/s11515-011-1110-1
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Pollen is the male gametophyte of seed plants and its tube growth is essential for successful fertilization. Mounting evidence has demonstrated that actin organization and regulation plays a central role in the process of its germination and polarized growth. The native structures and dynamics of actin are subtly modulated by many factors among which numerous actin binding proteins (ABPs) are the most direct and significant regulators. Upstream signals such as Ca2+, PIP2 (phosphatidylinositol-4,5-bis-phosphate) and GTPases can also indirectly act on actin organization through several ABPs. Under such elaborate regulation, actin structures show dynamically continuous modulation to adapt to the BoldItalic biologic functions to mediate secretory vesicle transportation and fusion, which lead to normal growth of the pollen tube. Many encouraging progress has been made in the connection between actin regulation and pollen tube growth in recent years. In this review, we summarize different factors that affect actin organization in pollen tube growth and highlight relative research progress.

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Microbial enzyme systems for lignin degradation and their transcriptional regulation
Takanori FURUKAWA,Fatai Olumide BELLO,Louise HORSFALL
Front. Biol.    2014, 9 (6): 448-471.   https://doi.org/10.1007/s11515-014-1336-9
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Lignocellulosic biomass is the most abundant renewable resource in nature and has received considerable attention as one of the most promising alternatives to oil resources for the provision of energy and certain raw materials. The phenolic polymer lignin is the second most abundant constituent of this biomass resource and has been shown to have the potential to be converted into industrially important aromatic chemicals after degradation. However, due to its chemical and structural nature, it exhibits high resistance toward mechanical, chemical, and biological degradation, and this causes a major obstacle for achieving efficient conversion of lignocellulosic biomass. In nature, lignin-degrading microorganisms have evolved unique extracellular enzyme systems to decompose lignin using radical mediated oxidative reactions. These microorganisms produce a set of different combinations of enzymes with multiple isozymes and isoforms by responding to various environmental stimuli such as nutrient availability, oxygen concentration and temperature, which are thought to enable effective decomposition of the lignin in lignocellulosic biomass. In this review, we present an overview of the microbial ligninolytic enzyme systems including general molecular aspects, structural features, and systematic differences in each microorganism. We also describe the gene expression pattern and the transcriptional regulation mechanisms of each ligninolytic enzyme with current data.

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Functional protein microarray: an ideal platform for investigating protein binding property
Shu-Min ZHOU, Li CHENG, Shu-Juan GUO, Heng ZHU, Sheng-Ce TAO
Front Biol    2012, 7 (4): 336-349.   https://doi.org/10.1007/s11515-012-1236-9
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Functional protein microarray is an important tool for high-throughput and large-scale systems biology studies. Besides the progresses that have been made for protein microarray fabrication, significant advancements have also been achieved for applying protein microarrays on determining a variety of protein biochemical activities. Among these applications, detection of protein binding properties, such as protein-protein interactions (PPIs), protein-DNA interactions (PDIs), protein-RNA interactions, and antigen-antibody interactions, are straightforward and have substantial impacts on many research fields. In this review, we will focus on the recent progresses in protein-protein, protein-DNA, protein-RNA, protein-small molecule, protein-lipid, protein-glycan, and antigen-antibody interactions. We will also discuss the challenges and future directions of protein microarray technologies. We strongly believe that protein microarrays will soon become an indispensible tool for both basic research and clinical applications.

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Avian metabolism: its control and evolution
Colin G. SCANES, Eldon BRAUN
Front Biol    2013, 8 (2): 134-159.   https://doi.org/10.1007/s11515-012-1206-2
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This review discussed metabolism in poultry and wild birds with an emphasis on what remains to be elucidated. Circulating concentrations of glucose are much greater in both poultry and wild birds than in mammals which in turn are higher than in reptiles. The basis for this difference is unknown but does not appear to be related to the requirements of flight. Furthermore, birds exhibit a refractoriness to potential adverse effects of very high circulating concentrations of glucose. Again the basis of this is unclear. There is substantial information on the control of metabolism in poultry, although which hormones are exerting physiologic roles remains to be clarified. There is a tacit but unverified assumption that the control mechanisms are the same in wild birds and in poultry. Despite, significant research focus on metabolism in poultry and to a less extent wild birds, there is a dearth of studies determining metabolism in a quantitative manner.

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A review of target gene specificity of flavonoid R2R3-MYB transcription factors and a discussion of factors contributing to the target gene selectivity
Yunsong LAI, Huanxiu LI, Masumi YAMAGISHI
Front Biol    2013, 8 (6): 577-598.   https://doi.org/10.1007/s11515-013-1281-z
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Flavonoid biosynthetic genes are often coordinately regulated in a temporal manner during flower or fruit development, resulting in specific accumulation profiles of flavonoid compounds. R2R3-MYB-type transcription factors (TFs) “recruit” a set of biosynthetic genes to produce flavonoids, and, therefore, R2R3-MYBs are responsible for the coordinated expression of structural genes. Although a wealth of information regarding the identified and functionally characterized R2R3-MYBs that are involved in flavonoid accumulation is available to date, this is the first review on the global regulation of MYB factors in the flavonoid pathway. The data presented in this review demonstrate that anthocyanin, flavone/flavonol/3-deoxyflavonoid (FFD), proanthocyanidin (PA), and isoflavonoid are independently regulated by different subgroups of R2R3-MYBs. Furthermore, FFD-specific R2R3-MYBs have a preference for early biosynthetic genes (EBGs) as their target genes; anthocyanin-specific R2R3-MYBs from dicot species essentially regulate late biosynthetic genes (LBGs); the remaining R2R3-MYBs have a wider range of target gene specificity. To elucidate the nature of the differential target gene specificity between R2R3-MYBs, we analyzed the DNA binding domain (also termed the MYB-domain) of R2R3-MYBs and the distribution of the recognition cis-elements. We identified four conserved amino acid residues located in or just before helix-3 of dicot anthocyanin R2R3-MYBs that might account for the different recognition DNA sequence and subsequently the different target gene specificity to the remaining R2R3-MYB TFs.

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An overview of inflammation: mechanism and consequences
Afsar U. AHMED
Front Biol    2011, 6 (4): 274-281.   https://doi.org/10.1007/s11515-011-1123-9
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Inflammation is an essential response provided by the immune systems that ensures the survival during infection and tissue injury. Inflammatory responses are essential for the maintenance of normal tissue homeostasis. The molecular mechanism of inflammation is quite a complicated process which is initiated by the recognition of specific molecular patterns associated with either infection or tissue injury. The entire process of the inflammatory response is mediated by several key regulators involved in the selective expression of proinflammatory molecules. Prolonged inflammations are often associated with severe detrimental side effects on health. Alterations in inflammatory responses due to persistent inducers or genetic variations are on the rise over the last couple of decades, causing a variety of inflammatory diseases and pathophysiological conditions.

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Gamma-glutamyl transferases: A structural, mechanistic and physiological perspective
Sharath BALAKRISHNA,Asmita A. PRABHUNE
Front. Biol.    2014, 9 (1): 51-65.   https://doi.org/10.1007/s11515-014-1288-0
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Gamma glutamyl transferases (GGT) are highly conserved enzymes that occur from bacteria to humans. They remove terminal γ-glutamyl residue from peptides and amides. GGTs play an important role in the homeostasis of glutathione (a major cellular antioxidant) and in the detoxification of xenobiotics in mammals. They are implicated in diseases like diabetes, inflammation, neurodegenerative diseases and cardiovascular diseases. The physiological role of GGTs in bacteria is still unclear. Nothing is known about the basis for the strong conservation of the enzyme across the living system. The review focuses on the enzyme’s physiology, chemistry and structural properties of the enzyme with emphasis on the evolutionary relationships. The available data indicate that the members of the GGT family share common structural features but are functionally heterogenous.

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The balancing act of AKT in T cells
Mary Catherine RENEER, Francesc MARTI
Front Biol    2013, 8 (2): 160-174.   https://doi.org/10.1007/s11515-012-1202-6
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The serine/threonine-specific protein kinase AKT is gaining recognition as a major crossroad in numerous cellular signaling pathways through its ability to regulate cell differentiation, proliferation, survival and metabolism. This review focuses on the recent advances in AKT signaling and downstream events in T cells, emphasizing its contrasting role in conventional and regulatory (Treg) T cell populations. Activation of AKT has been known for many years to be critical in the development and function of conventional T cells. However, it has just recently been uncovered that AKT exerts an inhibitory effect on Treg generation and suppressor function. These studies have placed AKT at the nexus of Treg development and function, thus opening novel avenues for therapeutic manipulation.

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Mass spectrometry-based phosphoproteomics in cancer research
Xiao-Shan YUE, Amanda B. HUMMON
Front Biol    2012, 7 (6): 566-586.   https://doi.org/10.1007/s11515-012-2022-4
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Phosphorylation is one of the most common post translational modifications (PTM), participating in a large number of processes to regulate cellular functions. Phosphorylation is also one of the key factors in the origin and development of cancer. The rapid development of mass spectrometric-based phosphoproteomic technologies has made it possible for high-throughput identification and quantification of phosphorylation events. In this review, we provide a general introduction and summary of the achievements made in mass spectrometry based phosphoproteomic research, including the approaches for phosphopeptide identification and quantification, as well as instrumentation and data interpretation methods. We also review some discoveries in cancer research made possible by phosphoproteomic analysis technologies.

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Functional states of resident vascular stem cells and vascular remodeling
Desiree F. Leach,Mitzi Nagarkatti,Prakash Nagarkatti,Taixing Cui
Front. Biol.    2015, 10 (5): 387-397.   https://doi.org/10.1007/s11515-015-1375-x
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Recent evidence indicates that different types of vascular stem cells (VSCs) reside within the mural layers of arteries and veins. The precise identities of these resident VSCs are still unclear; generally, postnatal vasculature contains multilineage stem cells and vascular cell lineage-specific progenitor/stem cells which may participate in both vascular repair and lesion formation. However, the underlying mechanism remains poorly understood. In this review, we summarize the potential molecular mechanisms, which may control the quiescence and activation of resident VSCs and highlight a notion that the differential states of resident VSCs are directly linked to vascular repair or lesion formation.

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Neural stem cell heterogeneity through time and space in the ventricular-subventricular zone
Gabrielle Rushing,Rebecca A. Ihrie
Front. Biol.    2016, 11 (4): 261-284.   https://doi.org/10.1007/s11515-016-1407-1
Abstract   HTML   PDF (1445KB)

BACKGROUND: The origin and classification of neural stem cells (NSCs) has been a subject of intense investigation for the past two decades. Efforts to categorize NSCs based on their location, function and expression have established that these cells are a heterogeneous pool in both the embryonic and adult brain. The discovery and additional characterization of adult NSCs has introduced the possibility of using these cells as a source for neuronal and glial replacement following injury or disease. To understand how one could manipulate NSC developmental programs for therapeutic use, additional work is needed to elucidate how NSCs are programmed and how signals during development are interpreted to determine cell fate.

OBJECTIVE: This review describes the identification, classification and characterization of NSCs within the large neurogenic niche of the ventricular-subventricular zone (V-SVZ).

METHODS: A literature search was conducted using Pubmed including the keywords “ventricular-subventricular zone,” “neural stem cell,” “heterogeneity,” “identity” and/or “single cell” to find relevant manuscripts to include within the review. A special focus was placed on more recent findings using single-cell level analyses on neural stem cells within their niche(s).

RESULTS: This review discusses over 20 research articles detailing findings on V-SVZ NSC heterogeneity, over 25 articles describing fate determinants of NSCs, and focuses on 8 recent publications using distinct single-cell analyses of neural stem cells including flow cytometry and RNA-seq. Additionally, over 60 manuscripts highlighting the markers expressed on cells within the NSC lineage are included in a chart divided by cell type.

CONCLUSIONS: Investigation of NSC heterogeneity and fate decisions is ongoing. Thus far, much research has been conducted in mice however, findings in human and other mammalian species are also discussed here. Implications of NSC heterogeneity established in the embryo for the properties of NSCs in the adult brain are explored, including how these cells may be redirected after injury or genetic manipulation.

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Metabolic regulation by salt inducible kinases
Rebecca BERDEAUX
Front Biol    2011, 6 (3): 231-241.   https://doi.org/10.1007/s11515-011-1148-0
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In fasting mammals, the liver is the primary source of glucose production for maintenance of normoglycemia. In this setting, circulating peptide hormones and catecholamines cause hepatic glucose output by stimulating glycogen breakdown as well as de novo glucose production through gluconeogenesis. Fasting gluconeogenesis is regulated by a complex transcriptional cascade culminating in elevated expression of hepatic enzymes that promote gluconeogenesis and glucose export to the blood. The cAMP response element binding protein CREB and its co-activator CRTC2 play crucial roles in signal-dependent transcriptional regulation of gluconeogenesis. Recent work has identified a family of serine/threonine kinases, the salt inducible kinases (SIKs), which are subject to hormonal control and constrain gluconeogenic and lipogenic gene expression in liver. As normal regulation of gluconeogenesis and lipogenesis is disrupted in diabetic states, SIK kinases are poised to serve as therapeutic targets to modulate metabolic disturbances in diabetic patients. The purpose of this review is to 1) describe the identification of CRTCs CREB co-activators and their regulation by SIKs, 2) discuss recent progress toward understanding regulation and function of SIKs in metabolism and 3) examine the potential clinical impact of therapeutics that target SIK kinase function.

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IRF4 and IRF8: governing the virtues of B lymphocytes
Vipul SHUKLA,Runqing LU
Front. Biol.    2014, 9 (4): 269-282.   https://doi.org/10.1007/s11515-014-1318-y
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Interferon regulatory factor 4 (IRF4) and IRF8 are critical regulators of immune system development and function. In B lymphocytes, IRF4 and IRF8 have been shown to control important events during their development and maturation including pre-B cell differentiation, induction of B cell tolerance pathways, marginal zone B cell development, germinal center reaction and plasma cell differentiation. Mechanistically, IRF4 and IRF8 are found to function redundantly to control certain stages of B cell development, but in other stages, they function nonredundantly to play distinct roles in B cell biology. In line with their essential roles in B cell development, deregulated expressions of IRF4 and IRF8 have been associated to the pathogenesis of several B cell malignancies and diseases. Recent studies have elucidated diverse transcriptional networks regulated by IRF4 and IRF8 at distinct B cell developmental stages and related malignancies. In this review we will discuss the recent advances for the roles of IRF4 and IRF8 during B cell development and associated diseases.

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The stomata frontline of plant interaction with the environment-perspectives from hormone regulation
Mengmeng ZHU, Shaojun DAI, Sixue CHEN
Front Biol    2012, 7 (2): 96-112.   https://doi.org/10.1007/s11515-012-1193-3
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Plants have evolved elaborate mechanisms to perceive and integrate signals from various environmental conditions. On leaf surface, stomata formed by pairs of guard cells mediate gas exchange, water transpiration as well as function in response to abiotic and biotic stresses. Stomatal closure could be induced by drought, salt, pathogen and other adverse conditions. This constitutes an instant defense response to prevent further damage to plants. Abscisic acid (ABA) is a major plant hormone involved in stress responses. Stress-activated ABA synthesis causes stomatal closure and prevents opening to reduce water loss and cell dehydration. Key regulatory receptor complex and other important components in the ABA signaling pathway have been identified. However, our knowledge of ABA signal transduction in guard cells is far from complete. Jasmonates are a group of phytohormones generally known to be important for plant defense against insects and necrotrophic pathogens. The increased levels of methyl jasmonate (MeJA) induced by herbivory and pathogen invasion show a similar effect on stomatal movement associated with ROS production as ABA. Investigation of guard cell signaling networks involving the two important phytohormones is significant and exciting. Information about protein and metabolite components and how they interact in guard cells is lacking. Here we review recent advances on hormone signaling networks in guard cells and how the networks integrate environmental signals to plant physiological output.

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Hedgehog signaling: mechanisms and evolution
Xuan YE, Aimin LIU
Front Biol    2011, 6 (6): 504-521.   https://doi.org/10.1007/s11515-011-1146-2
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The Hedgehog (Hh) family of secreted proteins plays essential roles in the development of a wide variety of animal species and underlies multiple human birth defects and cancers. To ensure the proper range of signaling, the Hh proteins are modified with lipids, assembled into water-soluble multimers, and interact with multiple cell surface proteins. In the target cells, a largely conserved intracellular signal transduction pathway, from the cell surface receptor Patched to the Glioma-associated oncogene homolog (Gli) family of transcription factors, mediates the transcriptional responses from fruit flies to mammals. A significant divergence between vertebrates and insects is the vertebrate-specific requirement of cilia for Hh signal transduction and Gli protein activation. Finally, transcription-independent cellular responses to Hh have been described in certain developmental processes. With clinical trial underway to treat Hh-related diseases, more work is urgently needed to reach a more comprehensive understanding of the molecular mechanisms underlying the regulation of Hh signaling in development and diseases.

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Less is more: Nutrient limitation induces cross-talk of nutrient sensing pathways with NAD+ homeostasis and contributes to longevity
Felicia Tsang,Su-Ju Lin
Front. Biol.    2015, 10 (4): 333-357.   https://doi.org/10.1007/s11515-015-1367-x
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Nutrient sensing pathways and their regulation grant cells control over their metabolism and growth in response to changing nutrients. Factors that regulate nutrient sensing can also modulate longevity. Reduced activity of nutrient sensing pathways such as glucose-sensing PKA, nitrogen-sensing TOR and S6 kinase homolog Sch9 have been linked to increased life span in the yeast, Saccharomyces cerevisiae, and higher eukaryotes. Recently, reduced activity of amino acid sensing SPS pathway was also shown to increase yeast life span. Life span extension by reduced SPS activity requires enhanced NAD+ (nicotinamide adenine dinucleotide, oxidized form) and nicotinamide riboside (NR, a NAD+ precursor) homeostasis. Maintaining adequate NAD+ pools has been shown to play key roles in life span extension, but factors regulating NAD+ metabolism and homeostasis are not completely understood. Recently, NAD+ metabolism was also linked to the phosphate (Pi)-sensing PHO pathway in yeast. Canonical PHO activation requires Pi-starvation. Interestingly, NAD+ depletion without Pi-starvation was sufficient to induce PHO activation, increasing NR production and mobilization. Moreover, SPS signaling appears to function in parallel with PHO signaling components to regulate NR/NAD+ homeostasis. These studies suggest that NAD+ metabolism is likely controlled by and/or coordinated with multiple nutrient sensing pathways. Indeed, cross-regulation of PHO, PKA, TOR and Sch9 pathways was reported to potentially affect NAD+ metabolism; though detailed mechanisms remain unclear. This review discusses yeast longevity-related nutrient sensing pathways and possible mechanisms of life span extension, regulation of NAD+ homeostasis, and cross-talk among nutrient sensing pathways and NAD+ homeostasis.

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Adult neurogenesis in the mammalian brain
Simon M.G. BRAUN, Sebastian JESSBERGER
Front Biol    2013, 8 (3): 295-304.   https://doi.org/10.1007/s11515-013-1263-1
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New neurons are generated throughout life in distinct areas of the mammalian brain. This process, called adult neurogenesis, has challenged previously held concepts about adult brain plasticity and opened novel therapeutic avenues to treat certain neuro-psychiatric diseases. Here, we review the current knowledge regarding the fate and potency of neural stem cells (NSCs), as well as the mechanisms underlying neuronal differentiation and subsequent integration. Furthermore, we discuss the functional significance of adult neurogenesis in health and disease, and offer brief insight into the future directions of the adult neurogenesis field.

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Fern spore germination in response to environmental factors
Jinwei Suo,Sixue Chen,Qi Zhao,Lei SHI,Shaojun Dai
Front. Biol.    2015, 10 (4): 358-376.   https://doi.org/10.1007/s11515-015-1342-6
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Fern spore germination gives rise to the rhizoid and protonemal cell through asymmetric cell division, and then develops into a gametophyte. Spore germination is also a representative single-cell model for the investigation of nuclear polar movement, asymmetrical cell division, polarity establishment and rhizoid tip-growth. These processes are affected by various environmental factors, such as light, gravity, phytohormones, metal ions, and temperature. Here, we present a catalog of spore germination in response to different environmental factors. They are as follows: (1) Representative modes of light affecting spore germination from different fern species include red light-stimulated and far red light-inhibited spore germination, far red light-uninhibited spore germination, blue light-inhibited spore germination, and spore germination in the dark. The optimal light intensity and illumination time for spore germination are different among various fern species. Light response upon spore germination is initiated from the cell mitosis that regulated by phytochromes (PHYs) and cryptochromes (CRYs). AcPHY2, AcCRY3 and/or AcCRY4 are hypothesized to be involved in spore germination; (2) Gravity and calcium are crucial to early nuclear movement and polarity establishment of spores; (3) Gibberellin and antheridiogen can initiate and promote spore germination in many species, but abscisic acid, jasmonic acid, and ethylene pose only minor effects; (4) Spores can obtain the maximal germination rate in their favorable growth medium. Moreover, metal ions, pH, and spore density in the culture medium also affect spore germination; (5) Most fern spores germinate at 25°C, and an optimal CO2 concentration is necessary for spore germination of certain fern plants. These provide valuable information for understanding fern spore germination in response to environmental factors.

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Incidence of T315I mutation in BCR/ABL-positive CML and ALL patients
Fatemeh Norozi,Javad Mohammadi-asl,Tina Vosoughi,Mohammad Ali Jalali Far,Amal Saki Malehi,Najmaldin Saki
Front. Biol.    2016, 11 (5): 404-411.   https://doi.org/10.1007/s11515-016-1423-1
Abstract   HTML   PDF (801KB)

OBJECTIVES: Targeted therapy of Philadelphia-positive ALL and CML patients using imatinib (IM) has caused significant changes in treatment course and has increased the survival of patients. A small group of patients show resistance to IM. Acquired mutations in tyrosine kinase domain of BCR-ABL protein are a mechanism for development of resistance. T315I is one of the most common acquired mutations in this domain, which occurs in ATP binding site and inhibits the formation of hydrogen bond with IM. The aim of this study was to evaluate the prevalence of this mutation in BCR/ABL-positive CML and ALL patients.

METHODS: To conduct this study, 60 BCR-ABL-positive patients (including 50 CML and 10 ALL patients) who were subject to treatment with IM were selected. After taking the samples, presence of T315I mutation was assessed using ARMS-PCR on cDNA and its polymorphism was evaluated by sequencing.

RESULTS: The results showed that among 60 patients, only three patients had T315I mutation, which was detected using ARMS technique. The three patients bearing mutation were afflicted with CML and no significant association was found between blood parameters with duration of treatment in presence of mutation.

CONCLUSIONS: The mutation was found in three CML patients, which indicated lower likelihood and diagnostic value of this mutation in ALL patients. Given the negative direct sequencing results in T315I patients, it can be concluded that ARMS-PCR is a more sensitive technique when the number of cancer cells is low in patients during treatment.

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Growth arrest signaling of the Raf/MEK/ERK pathway in cancer
Jong-In PARK
Front. Biol.    2014, 9 (2): 95-103.   https://doi.org/10.1007/s11515-014-1299-x
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The Raf/MEK/extracellular signal-regulated kinase (ERK) pathway has a pivotal role in facilitating cell proliferation, and its deregulated activation is a central signature of many epithelial cancers. However paradoxically, sustained activity of Raf/MEK/ERK can also result in growth arrest in many different cell types. This anti-proliferative Raf/MEK/ERK signaling also has physiological significance, as exemplified by its potential as a tumor suppressive mechanism. Therefore, significant questions include in which cell types and by what mechanisms this pathway can mediate such an opposing context of signaling. Particularly, our understating of the role of ERK1 and ERK2, the focal points of pathway signaling, in growth arrest signaling is still limited. This review discusses these aspects of Raf/MEK/ERK-mediated growth arrest signaling.

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Fermentative production of dextran using Leuconostoc spp. isolated from fermented food products
C. SUBATHRA DEVI,Shantan REDDY,V. MOHANASRINIVASAN
Front. Biol.    2014, 9 (3): 244-253.   https://doi.org/10.1007/s11515-014-1303-5
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Leuconostoc spp. (LS1and LI1) isolated from sauerkraut and idli batter was selected for dextran production. To enhance the yield of dextran, effects of various parameters such as sucrose concentration, pH, temperature, incubation and inoculum percentage were analyzed. The optimum sucrose concentration for the Leuconostoc spp. (LS1 and LI1) was found to be 15% and 25% respectively. Isolates produced maximum dextran after 20 h of incubation at 29°C and the optimum pH was found between 8 and 8.5. The inoculum concentration of 7.5% was more favorable for the production of dextran by Leuconostoc spp. (LS1 and LI1). The growth kinetic parameters were studied and compared for the strains LS1 and LI1. Mass production of dextran was carried out using a stirred tank batch reactor. FTIR analysis was done to determine the functional groups of dextran. sephadex is prepared by cross linking dextran using epichlorohydrin and the functional groups are determined by FTIR analysis.

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An overview of pyrethroid insecticides
Anudurga Gajendiran, Jayanthi Abraham
Front. Biol.    2018, 13 (2): 79-90.   https://doi.org/10.1007/s11515-018-1489-z
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BACKGROUND: Pesticides are used to control various pests of agricultural crops worldwide. Despite their agricultural benefits, pesticides are often considered a serious threat to the environment because of their persistence. Pyrethroids are synthetic derivates of pyrethrins, which are natural organic insecticides procured from the flowers of Chrysanthemum cinerariaefolium and C. coccineum. Pyrethroids are classified into two groups—class I and class II—based on their toxicity and physical properties. These pyrethroids are now used in many synthetic insecticides and are highly specific against insects; they are generally used against mosquitoes. The prominent site of insecticidal action of pyrethroids is the voltage-sensitive sodium channels.

METHODS and RESULTS: Pyrethroids are found to be stable, and they persist in the environment for a long period. This article provides an overview of the different classes, structure, and insecticidal properties of pyrethroid. Furthermore, the toxicity of pyrethroids is also discussed with emphasis on bioremediation to alleviate pollution.

CONCLUSIONS: The article focuses on various microorganisms used in the degradation of pyrethroids, the molecular basis of degradation, and the role of carboxylesterase enzymes and genes in the detoxification of pyrethroid.

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Role of calmodulin in neuronal Kv7/KCNQ potassium channels and epilepsy
Hee Jung CHUNG
Front. Biol.    2014, 9 (3): 205-215.   https://doi.org/10.1007/s11515-014-1305-3
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Neuronal Kv7/KCNQ channels are critical regulators of neuronal excitability since they potently suppress repetitive firing of action potentials. These voltage-dependent potassium channels are composed mostly of Kv7.2 / KCNQ2 and Kv7.3 / KCNQ3 subunits that show overlapping distribution throughout the brain and in the peripheral nervous system. They are also called ‘M-channels’ since their inhibition by muscarinic agonists leads to a profound increase in action potential firing. Consistent with their ability to suppress seizures and attenuate chronic inflammatory and neuropathic pain, mutations in the KCNQ2 and KCNQ3 genes are associated with benign familial neonatal convulsions, a dominantly-inherited epilepsy in infancy. Recently, de novo mutations in the KCNQ2 gene have been linked to early onset epileptic encephalopathy. Notably, some of these mutations are clustered in a region of the intracellular cytoplasmic tail of Kv7.2 that interacts with a ubiquitous calcium sensor, calmodulin. In this review, we highlight the recent advances in understanding the role of calmodulin in modulating physiological function of neuronal Kv7 channels including their biophysical properties, assembly, and trafficking. We also summarize recent studies that have investigated functional impact of epilepsy-associated mutations localized to the calmodulin binding domains of Kv7.2.

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Receptor-like kinases and receptor-like proteins: keys to pathogen recognition and defense signaling in plant innate immunity
Xin YANG, Fengyang DENG, Katrina M. RAMONELL
Front Biol    2012, 7 (2): 155-166.   https://doi.org/10.1007/s11515-011-1185-8
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Plants have evolved multiple layers of defense against various pathogens in the environment. Receptor-like kinases/proteins (RLKs/RLPs) are on the front lines of the battle between plants and pathogens since they are present at the plasma membrane and perceive signature molecules from either the invading pathogen or damaged plant tissue. With a few notable exceptions, most RLKs/RLPs are positive regulators of plant innate immunity. In this review, we summarize recently discovered RLKs/RLPs that are involved in plant defense responses against various classes of pathogens. We also describe what is currently known about the mechanisms of RLK-mediated initiation of signaling via protein-protein interactions and phosphorylation.

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Mass spectrometry-based proteomics and peptidomics for systems biology and biomarker discovery
Robert CUNNINGHAM, Di MA, Lingjun LI
Front Biol    2012, 7 (4): 313-335.   https://doi.org/10.1007/s11515-012-1218-y
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The scientific community has shown great interest in the field of mass spectrometry-based proteomics and peptidomics for its applications in biology. Proteomics technologies have evolved to produce large data sets of proteins or peptides involved in various biologic and disease progression processes generating testable hypothesis for complex biologic questions. This review provides an introduction to relevant topics in proteomics and peptidomics including biologic material selection, sample preparation, separation techniques, peptide fragmentation, post-translational modifications, quantification, bioinformatics, and biomarker discovery and validation. In addition, current literature, remaining challenges, and emerging technologies for proteomics and peptidomics are presented.

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