Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies.

Abstract:

:The study of the human microbiome has become a very popular topic. Our microbial counterpart, in fact, appears to play an important role in human physiology and health maintenance. Accordingly, microbiome alterations have been reported in an increasing number of human diseases. Despite the huge amount of data produced to date, less is known on how a microbial dysbiosis effectively contributes to a specific pathology. To fill in this gap, other approaches for microbiome study, more comprehensive than 16S rRNA gene sequencing, i.e., shotgun metagenomics and metatranscriptomics, are becoming more widely used. Methods standardization and the development of specific pipelines for data analysis are required to contribute to and increase our understanding of the human microbiome relationship with health and disease status.

journal_name

Int J Mol Sci

authors

D'Argenio V

doi

10.3390/ijms19020383

subject

Has Abstract

pub_date

2018-01-27 00:00:00

issue

2

issn

1422-0067

pii

ijms19020383

journal_volume

19

pub_type

杂志文章,评审
  • Concentration of rutin model solutions from their mixtures with glucose using ultrafiltration.

    abstract::Separation of polyphenolic phytochemical compounds from their mixtures with sugars is necessary to produce an added-value sugar-reduced extract with high biological activity from fruit juice processing industry waste streams. The separation characteristics of a binary mixture of rutin and glucose using a Pellicon-2 re...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms11020672

    authors: Wei S,Hossain MM,Saleh ZS

    更新日期:2010-02-09 00:00:00

  • ProNGF, but Not NGF, Switches from Neurotrophic to Apoptotic Activity in Response to Reductions in TrkA Receptor Levels.

    abstract::Nerve growth factor (NGF) promotes the survival and differentiation of neurons. NGF is initially synthesized as a precursor, proNGF, which is the predominant form in the central nervous system. NGF and proNGF bind to TrkA/p75NTR to mediate cell survival and to sortilin/p75NTR to promote apoptosis. The ratio of TrkA to...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms18030599

    authors: Ioannou MS,Fahnestock M

    更新日期:2017-03-09 00:00:00

  • Role of Forkhead Box O Transcription Factors in Oxidative Stress-Induced Chondrocyte Dysfunction: Possible Therapeutic Target for Osteoarthritis?

    abstract::Chondrocyte dysfunction occurs during the development of osteoarthritis (OA), typically resulting from a deleterious increase in oxidative stress. Accordingly, strategies for arresting oxidative stress-induced chondrocyte dysfunction may lead to new potential therapeutic targets for OA treatment. Forkhead box O (FoxO)...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms19123794

    authors: Wang R,Zhang S,Previn R,Chen D,Jin Y,Zhou G

    更新日期:2018-11-28 00:00:00

  • Transcriptomic Analysis Reveals Candidate Genes Responsive to Sclerotinia scleroterum and Cloning of the Ss-Inducible Chitinase Genes in Morus laevigata.

    abstract::Sclerotinia sclerotiorum (Ss) is a devastating fungal pathogen that causes Sclerotinia stem rot in rapeseed (Brassica napus), and is also detrimental to mulberry and many other crops. A wild mulberry germplasm, Morus laevigata, showed high resistance to Ss, but the molecular basis for the resistance is largely unknown...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms21218358

    authors: Jiang H,Jin X,Shi X,Xue Y,Jiang J,Yuan C,Du Y,Liu X,Xie R,Liu X,Li L,Wei L,Zhang C,Tong L,Chai Y

    更新日期:2020-11-07 00:00:00

  • Proteostasis and Proteotoxicity in the Network Medicine Era.

    abstract::Neurodegenerative proteinopathies are complex diseases that share some pathogenetic processes. One of these is the failure of the proteostasis network (PN), which includes all components involved in the synthesis, folding, and degradation of proteins, thus leading to the aberrant accumulation of toxic protein aggregat...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms21176405

    authors: Lualdi M,Alberio T,Fasano M

    更新日期:2020-09-03 00:00:00

  • Energy-Dependent Endocytosis is Involved in the Absorption of Indomethacin Nanoparticles in the Small Intestine.

    abstract::We previously reported that oral formulations containing indomethacin nanoparticles (IND-NPs) showed high bioavailability, and, consequently, improved therapeutic effects and reduced injury to the small intestine. However, the pathway for the transintestinal penetration of nanoparticles remained unclear. Thus, in this...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms20030476

    authors: Ishii M,Fukuoka Y,Deguchi S,Otake H,Tanino T,Nagai N

    更新日期:2019-01-22 00:00:00

  • Some Aspects of the Liquid Water Thermodynamic Behavior: From The Stable to the Deep Supercooled Regime.

    abstract::Liquid water is considered to be a peculiar example of glass forming materials because of the possibility of giving rise to amorphous phases with different densities and of the thermodynamic anomalies that characterize its supercooled liquid phase. In the present work, literature data on the density of bulk liquid wat...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms21197269

    authors: Mallamace F,Mensitieri G,Mallamace D,Salzano de Luna M,Chen SH

    更新日期:2020-10-01 00:00:00

  • Expression of Chemerin and Its Receptors in the Porcine Hypothalamus and Plasma Chemerin Levels during the Oestrous Cycle and Early Pregnancy.

    abstract::Chemerin (CHEM) may act as an important link integrating energy homeostasis and reproductive functions of females, and its actions are mediated by three receptors: chemokine-like receptor 1 (CMKLR1), G protein-coupled receptor 1 (GPR1), and C-C motif chemokine receptor-like 2 (CCRL2). The aim of the current study was ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms20163887

    authors: Smolinska N,Kiezun M,Dobrzyn K,Rytelewska E,Kisielewska K,Gudelska M,Zaobidna E,Bogus-Nowakowska K,Wyrebek J,Bors K,Kopij G,Kaminska B,Kaminski T

    更新日期:2019-08-09 00:00:00

  • miR-1285-3p Controls Colorectal Cancer Proliferation and Escape from Apoptosis through DAPK2.

    abstract::MicroRNAs are tiny but powerful regulators of gene expression at the post-transcriptional level. Aberrant expression of oncogenic and tumor-suppressor microRNAs has been recognized as a common feature of human cancers. Colorectal cancer represents a major clinical challenge in the developed world and the design of inn...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms21072423

    authors: Villanova L,Barbini C,Piccolo C,Boe A,De Maria R,Fiori ME

    更新日期:2020-03-31 00:00:00

  • In Vitro Assays: Friends or Foes of Cell-Penetrating Peptides.

    abstract::The cell membrane is a complex and highly regulated system that is composed of lipid bilayer and proteins. One of the main functions of the cell membrane is the regulation of cell entry. Cell-penetrating peptides (CPPs) are defined as peptides that can cross the plasma membrane and deliver their cargo inside the cell....

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms21134719

    authors: Liu J,Afshar S

    更新日期:2020-07-02 00:00:00

  • Identification of a plastid-localized bifunctional nerolidol/linalool synthase in relation to linalool biosynthesis in young grape berries.

    abstract::Monoterpenoids are a diverse class of natural products and contribute to the important varietal aroma of certain Vitis vinifera grape cultivars. Among the typical monoterpenoids, linalool exists in almost all grape varieties. A gene coding for a nerolidol/linalool (NES/LINS) synthase was evaluated in the role of linal...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms151221992

    authors: Zhu BQ,Cai J,Wang ZQ,Xu XQ,Duan CQ,Pan QH

    更新日期:2014-12-01 00:00:00

  • In Vitro Evaluation of Gentamicin or Vancomycin Containing Bone Graft Substitute in the Prevention of Orthopedic Implant-Related Infections.

    abstract::Antibiotic-loaded bone graft substitutes are attractive clinical options and have been used for years either for prophylaxis or therapy for periprosthetic and fracture-related infections. Calcium sulfate and hydroxyapatite can be combined in an injectable and moldable bone graft substitute that provides dead space man...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms21239250

    authors: Bidossi A,Bottagisio M,Logoluso N,De Vecchi E

    更新日期:2020-12-04 00:00:00

  • Extracellular-Signal Regulated Kinase: A Central Molecule Driving Epithelial-Mesenchymal Transition in Cancer.

    abstract::Epithelial-mesenchymal transition (EMT) is a reversible cellular process, characterized by changes in gene expression and activation of proteins, favoring the trans-differentiation of the epithelial phenotype to a mesenchymal phenotype. This process increases cell migration and invasion of tumor cells, progression of ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms20122885

    authors: Olea-Flores M,Zuñiga-Eulogio MD,Mendoza-Catalán MA,Rodríguez-Ruiz HA,Castañeda-Saucedo E,Ortuño-Pineda C,Padilla-Benavides T,Navarro-Tito N

    更新日期:2019-06-13 00:00:00

  • Fast Vibrational Modes and Slow Heterogeneous Dynamics in Polymers and Viscous Liquids.

    abstract::Many systems, including polymers and molecular liquids, when adequately cooled and/or compressed, solidify into a disordered solid, i.e., a glass. The transition is not abrupt, featuring progressive decrease of the microscopic mobility and huge slowing down of the relaxation. A distinctive aspect of glass-forming mate...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms20225708

    authors: Puosi F,Tripodo A,Leporini D

    更新日期:2019-11-14 00:00:00

  • Deep Insight into the Transcriptome of the Single Silk Gland of Bombyx mori.

    abstract::The silk gland synthesizes and secretes a large amount of protein and stores liquid silk protein at an extremely high concentration. Interestingly, silk proteins and serine protease inhibitors are orderly arranged in the silk gland lumen and cocoon shells. Silk fiber formation and the spinning mechanism have not been ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms20102491

    authors: Shi R,Ma S,He T,Peng J,Zhang T,Chen X,Wang X,Chang J,Xia Q,Zhao P

    更新日期:2019-05-20 00:00:00

  • Participation of Amyloid and Tau Protein in Neuronal Death and Neurodegeneration after Brain Ischemia.

    abstract::Current evidence indicates that postischemic brain injury is associated with the accumulation of folding proteins, such as amyloid and tau protein, in the intra- and extracellular spaces of neuronal cells. In this review, we summarize protein changes associated with Alzheimer's disease and their gene expression (amylo...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms21134599

    authors: Pluta R,Ułamek-Kozioł M,Januszewski S,Czuczwar SJ

    更新日期:2020-06-28 00:00:00

  • The influence of polyunsaturated fatty acids on the phospholipase D isoforms trafficking and activity in mast cells.

    abstract::The impact of polyunsaturated fatty acid (PUFA) supplementation on phospholipase D (PLD) trafficking and activity in mast cells was investigated. The enrichment of mast cells with different PUFA including α-linolenic acid (LNA), eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), linoleic acid (LA) or arachidonic...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms14059005

    authors: Basiouni S,Fuhrmann H,Schumann J

    更新日期:2013-04-25 00:00:00

  • Non-Ligand-Induced Dimerization is Sufficient to Initiate the Signalling and Endocytosis of EGF Receptor.

    abstract::The binding of epidermal growth factor (EGF) to EGF receptor (EGFR) stimulates cell mitogenesis and survival through various signalling cascades. EGF also stimulates rapid EGFR endocytosis and its eventual degradation in lysosomes. The immediate events induced by ligand binding include receptor dimerization, activatio...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms17081200

    authors: Kourouniotis G,Wang Y,Pennock S,Chen X,Wang Z

    更新日期:2016-07-25 00:00:00

  • Kaempferol promotes apoptosis in human bladder cancer cells by inducing the tumor suppressor, PTEN.

    abstract::Kaempferol (Kae), a natural flavonoid, is widely distributed in fruits and vegetables. Previous studies have identified Kae as a possible cancer preventive and therapeutic agent. We found Kae to exhibit potent antiproliferation and anti-migration effects in human bladder cancer EJ cells. Kaempferol robustly induced ap...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms141121215

    authors: Xie F,Su M,Qiu W,Zhang M,Guo Z,Su B,Liu J,Li X,Zhou L

    更新日期:2013-10-24 00:00:00

  • Pine bark and green tea concentrated extracts: antioxidant activity and comprehensive characterization of bioactive compounds by HPLC-ESI-QTOF-MS.

    abstract::The consumption of polyphenols has frequently been associated with low incidence of degenerative diseases. Most of these natural antioxidants come from fruits, vegetables, spices, grains and herbs. For this reason, there has been increasing interest in identifying plant extract compounds. Polymeric tannins and monomer...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms151120382

    authors: de la Luz Cádiz-Gurrea M,Fernández-Arroyo S,Segura-Carretero A

    更新日期:2014-11-06 00:00:00

  • Roles of Erythroid Differentiation Regulator 1 (Erdr1) on Inflammatory Skin Diseases.

    abstract::Erythroid Differentiation Regulator 1 (Erdr1) is known as a hemoglobin synthesis factor which also regulates cell survival under conditions of stress. In addition, previous studies have revealed the effects of Erdr1 on cancer progression and its negative correlation with interleukin (IL)-18, a pro-inflammatory cytokin...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms17122059

    authors: Houh YK,Kim KE,Park HJ,Cho D

    更新日期:2016-12-08 00:00:00

  • Prevalence of Quinolone Resistance of Extended-Spectrum β-Lactamase-Producing Escherichia coli with ST131-fimH30 in a City Hospital in Hyogo, Japan.

    abstract::Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolates are known to tolerate superior quinolone antimicrobials compared with other antibacterial agents. Among the clones belonging to sequence type (ST) 131 by multilocus sequence typing, the involvement of the H30-Rx subclone has been reported worldwi...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms20205162

    authors: Teramae M,Osawa K,Shigemura K,Kitagawa K,Shirakawa T,Fujisawa M,Miyara T

    更新日期:2019-10-18 00:00:00

  • Plant defense against insect herbivores.

    abstract::Plants have been interacting with insects for several hundred million years, leading to complex defense approaches against various insect feeding strategies. Some defenses are constitutive while others are induced, although the insecticidal defense compound or protein classes are often similar. Insect herbivory induce...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms140510242

    authors: Fürstenberg-Hägg J,Zagrobelny M,Bak S

    更新日期:2013-05-16 00:00:00

  • Stress Marks on the Genome: Use or Lose?

    abstract::Oxidative stress and the resulting damage to DNA are inevitable consequence of endogenous physiological processes further amplified by cellular responses to environmental exposures. If left unrepaired, oxidative DNA lesions can block essential processes such as transcription and replication or can induce mutations. Em...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms20020364

    authors: Bokhari B,Sharma S

    更新日期:2019-01-16 00:00:00

  • Pulmonary Hypertension Phenotypes in Systemic Sclerosis: The Right Diagnosis for the Right Treatment.

    abstract::Systemic sclerosis is an auto-immune disease characterized by skin involvement that often affects multiple organ systems. Pulmonary hypertension is a common finding that can significantly impact prognosis. Molecular pathophysiological mechanisms underlying pulmonary hypertension in systemic sclerosis can be extremely ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms21124430

    authors: Attanasio U,Cuomo A,Pirozzi F,Loffredo S,Abete P,Petretta M,Marone G,Bonaduce D,De Paulis A,Rossi FW,Tocchetti CG,Mercurio V

    更新日期:2020-06-22 00:00:00

  • Nanoparticles and Colloidal Hydrogels of Chitosan-Caseinate Polyelectrolyte Complexes for Drug-Controlled Release Applications.

    abstract::Chitosan-caseinate nanoparticles were synthesized by polyelectrolyte complex (PEC) formation. Caseinate is an anionic micellar nanocolloid in aqueous solutions, which association with the polycationic chitosan yielded polyelectrolyte complexes with caseinate cores surrounded by a chitosan corona. The pre-structuration...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms21165602

    authors: Lall A,Kamdem Tamo A,Doench I,David L,Nunes de Oliveira P,Gorzelanny C,Osorio-Madrazo A

    更新日期:2020-08-05 00:00:00

  • Copaifera of the Neotropics: A Review of the Phytochemistry and Pharmacology.

    abstract::The oleoresin of Copaifera trees has been widely used as a traditional medicine in Neotropical regions for thousands of years and remains a popular treatment for a variety of ailments. The copaiba resins are generally composed of a volatile oil made up largely of sesquiterpene hydrocarbons, such as β-caryophyllene, α-...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章,评审

    doi:10.3390/ijms19051511

    authors: da Trindade R,da Silva JK,Setzer WN

    更新日期:2018-05-18 00:00:00

  • Chrysin Attenuates VCAM-1 Expression and Monocyte Adhesion in Lipopolysaccharide-Stimulated Brain Endothelial Cells by Preventing NF-κB Signaling.

    abstract::Adhesion of leukocytes to endothelial cells plays an important role in neuroinflammation. Therefore, suppression of the expression of adhesion molecules in brain endothelial cells may inhibit neuroinflammation. Chrysin (5,7-dihydroxyflavone) is a flavonoid component of propolis, blue passion flowers, and fruits. In th...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms18071424

    authors: Lee BK,Lee WJ,Jung YS

    更新日期:2017-07-03 00:00:00

  • Inhibition of Colony-Stimulating Factor 1 Receptor by PLX3397 Prevents Amyloid Beta Pathology and Rescues Dopaminergic Signaling in Aging 5xFAD Mice.

    abstract::Alzheimer's disease (AD) is a progressive neurodegenerative disease. In this study, to investigate the effect of microglial elimination on AD progression, we administered PLX3397, a selective colony-stimulating factor 1 receptor inhibitor, to the mouse model of AD (5xFAD mice). Amyloid-beta (Aβ) deposition and amyloid...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms21155553

    authors: Son Y,Jeong YJ,Shin NR,Oh SJ,Nam KR,Choi HD,Choi JY,Lee HJ

    更新日期:2020-08-03 00:00:00

  • The First Dose of Fingolimod Affects Circulating Extracellular Vesicles in Multiple Sclerosis Patients.

    abstract::Extracellular vesicles (EVs) are membrane-bound particles involved in intercellular communication. They carry proteins, lipids, and nucleotides such as microRNAs (miRNAs) from the secreting cell that can modulate target cells. We and others have previously described the presence of EVs in peripheral blood of multiple ...

    journal_title:International journal of molecular sciences

    pub_type: 杂志文章

    doi:10.3390/ijms19082448

    authors: Sáenz-Cuesta M,Alberro A,Muñoz-Culla M,Osorio-Querejeta I,Fernandez-Mercado M,Lopetegui I,Tainta M,Prada Á,Castillo-Triviño T,Falcón-Pérez JM,Olascoaga J,Otaegui D

    更新日期:2018-08-19 00:00:00