International Journal of Molecular Sciences

239 KiB

Open AccessReview

Third Generation Biofuels via Direct Cellulose Fermentation

by Carlo R. Carere, Richard Sparling, Nazim Cicek and David B. Levin

Int. J. Mol. Sci. 2008, 9(7), 1342-1360; https://doi.org/10.3390/ijms9071342 - 22 Jul 2008

Cited by 236 | Viewed by 23611

Consolidated bioprocessing (CBP) is a system in which cellulase production, substrate hydrolysis, and fermentation are accomplished in a single process step by cellulolytic microorganisms. CBP offers the potential for lower biofuel production costs due to simpler feedstock processing, lower energy inputs, and higher [...] Read more.

Consolidated bioprocessing (CBP) is a system in which cellulase production, substrate hydrolysis, and fermentation are accomplished in a single process step by cellulolytic microorganisms. CBP offers the potential for lower biofuel production costs due to simpler feedstock processing, lower energy inputs, and higher conversion efficiencies than separate hydrolysis and fermentation processes, and is an economically attractive near-term goal for “third generation” biofuel production. In this review article, production of third generation biofuels from cellulosic feedstocks will be addressed in respect to the metabolism of cellulolytic bacteria and the development of strategies to increase biofuel yields through metabolic engineering. Full article

(This article belongs to the Special Issue Biofuels R&D: Securing the Planet's Future Energy Needs)

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254 KiB

Open AccessArticle

Effects of Various Temperatures and pH Values on the Extraction Yield of Phenolics from Litchi Fruit Pericarp Tissue and the Antioxidant Activity of the Extracted Anthocyanins

by Neungnapa Ruenroengklin, Jia Zhong, Xuewu Duan, Bao Yang, Jianrong Li and Yueming Jiang

Int. J. Mol. Sci. 2008, 9(7), 1333-1341; https://doi.org/10.3390/ijms9071333 - 22 Jul 2008

Cited by 109 | Viewed by 12295

Abstract

Litchi fruit pericarp tissue is considered an important source of dietary phenolics. This study consisted of two experiments. The first was conducted to examine the effects of various extraction temperatures (30, 40, 50, 60, 70 and 80 °C) and pH values (2, 3, [...] Read more.

Litchi fruit pericarp tissue is considered an important source of dietary phenolics. This study consisted of two experiments. The first was conducted to examine the effects of various extraction temperatures (30, 40, 50, 60, 70 and 80 °C) and pH values (2, 3, 4, 5 and 6) on the extraction yield of phenolics from litchi fruit pericarp. Extraction was most efficient at pH 4.0, while an extraction temperature of 60 °C was the best in terms of the combined extraction yield of phenolics and the stability of the extracted litchi anthocyanins. The second experiment was carried out to further evaluate the effects of various temperatures (25, 35, 45, 55 and 65 °C) and pH values (1, 3, 5 and 7) on the total antioxidant ability and scavenging activities of DPPH radicals, hydroxyl radical and superoxide anion of the extracted anthocyanins. The results indicated that use of 45−60 °C or pH 3−4 exhibited a relatively high antioxidant activity. The study will help improve extraction yield of phenolics from litchi fruit pericarp and promote better utilization of the extracted litchi anthocyanins as antioxidants. Full article

(This article belongs to the Section Biochemistry)

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361 KiB

Open AccessArticle

Application of Electron Paramagnetic Resonance Spectroscopy for Validation of the Novel (AN+DN) Solvent Polarity Scale

by Luciana Malavolta, Erick F. Poletti, Elias H. Silva, Shirley Schreier and Clovis R. Nakaie

Int. J. Mol. Sci. 2008, 9(7), 1321-1332; https://doi.org/10.3390/ijms9071321 - 17 Jul 2008

Cited by 20 | Viewed by 10212

Abstract

Based on solvation studies of polymers, the sum (1:1) of the electron acceptor (AN) and electron donor (DN) values of solvents has been proposed as an alternative polarity scale. To test this, the electron paramagnetic resonance isotropic hyperfine splitting constant, a parameter known [...] Read more.

Based on solvation studies of polymers, the sum (1:1) of the electron acceptor (AN) and electron donor (DN) values of solvents has been proposed as an alternative polarity scale. To test this, the electron paramagnetic resonance isotropic hyperfine splitting constant, a parameter known to be dependent on the polarity/proticity of the medium, was correlated with the (AN+DN) term using three paramagnetic probes. The linear regression coefficient calculated for 15 different solvents was approximately 0.9, quite similar to those of other well-known polarity parameters, attesting to the validity of the (AN+DN) term as a novel “two-parameter” solvent polarity scale. Full article

(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)

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1328 KiB

Open AccessReview

Recent Developments in Peptide-Based Nucleic Acid Delivery

by Sandra Veldhoen, Sandra D. Laufer and Tobias Restle

Int. J. Mol. Sci. 2008, 9(7), 1276-1320; https://doi.org/10.3390/ijms9071276 - 16 Jul 2008

Cited by 82 | Viewed by 17631

Abstract

Despite the fact that non-viral nucleic acid delivery systems are generally considered to be less efficient than viral vectors, they have gained much interest in recent years due to their superior safety profile compared to their viral counterpart. Among these synthetic vectors are [...] Read more.

Despite the fact that non-viral nucleic acid delivery systems are generally considered to be less efficient than viral vectors, they have gained much interest in recent years due to their superior safety profile compared to their viral counterpart. Among these synthetic vectors are cationic polymers, branched dendrimers, cationic liposomes and cellpenetrating peptides (CPPs). The latter represent an assortment of fairly unrelated sequences essentially characterised by a high content of basic amino acids and a length of 10-30 residues. CPPs are capable of mediating the cellular uptake of hydrophilic macromolecules like peptides and nucleic acids (e.g. siRNAs, aptamers and antisenseoligonucleotides), which are internalised by cells at a very low rate when applied alone. Up to now, numerous sequences have been reported to show cell-penetrating properties and many of them have been used to successfully transport a variety of different cargos into mammalian cells. In recent years, it has become apparent that endocytosis is a major route of internalisation even though the mechanisms underlying the cellular translocation of CPPs are poorly understood and still subject to controversial discussions. In this review, we will summarise the latest developments in peptide-based cellular delivery of nucleic acid cargos. We will discuss different mechanisms of entry, the intracellular fate of the cargo, correlation studies of uptake versus biological activity of the cargo as well as technical problems and pitfalls. Full article

(This article belongs to the Special Issue Nucleic Acid Derivatives in Emerging Technologies)

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2994 KiB

Open AccessReview

Thick and Thin Filament Gene Mutations in Striated Muscle Diseases

by Homa Tajsharghi

Int. J. Mol. Sci. 2008, 9(7), 1259-1275; https://doi.org/10.3390/ijms9071259 - 16 Jul 2008

Cited by 8 | Viewed by 19700

Abstract

The sarcomere is the fundamental unit of cardiac and skeletal muscle contraction. During the last ten years, there has been growing awareness of the etiology of skeletal and cardiac muscle diseases originating in the sarcomere, an important evolving field. Many sarcomeric diseases affect [...] Read more.

The sarcomere is the fundamental unit of cardiac and skeletal muscle contraction. During the last ten years, there has been growing awareness of the etiology of skeletal and cardiac muscle diseases originating in the sarcomere, an important evolving field. Many sarcomeric diseases affect newborn children, i. e. are congenital myopathies. The discovery and characterization of several myopathies caused by mutations in myosin heavy chain genes, coding for the major component of skeletal muscle thick filaments, has led to the introduction of a new entity in the field of neuromuscular disorders: myosin myopathies. Recently, mutations in genes coding for skeletal muscle thin filaments, associated with various clinical features, have been identified. These mutations evoke distinct structural changes within the sarcomeric thin filament. Current knowledge regarding contractile protein dysfunction as it relates to disease pathogenesis has failed to decipher the mechanistic links between mutations identified in sarcomeric proteins and skeletal myopathies, which will no doubt require an integrated physiological approach. The discovery of additional genes associated with myopathies and the elucidation of the molecular mechanisms of pathogenesis will lead to improved and more accurate diagnosis, including prenatally, and to enhanced potential for prognosis, genetic counseling and developing possible treatments for these diseases. The goal of this review is to present recent progress in the identification of gene mutations from each of the major structural components of the sarcomere, the thick and thin filaments, related to skeletal muscle disease. The genetics and clinical manifestations of these disorders will be discussed. Full article

(This article belongs to the Special Issue Muscle Contraction Mechanism, Motor Proteins Function and Molecular Aspects of Water)

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546 KiB

Open AccessArticle

Cultivation and Characterization of Cynara Cardunculus for Solid Biofuels Production in the Mediterranean Region

by Panagiotis Grammelis, Anastasia Malliopoulou, Panagiotis Basinas and Nicholas G. Danalatos

Int. J. Mol. Sci. 2008, 9(7), 1241-1258; https://doi.org/10.3390/ijms9071241 - 15 Jul 2008

Cited by 90 | Viewed by 14015

Abstract

Technical specifications of solid biofuels are continuously improved towards the development and promotion of their market. Efforts in the Greek market are limited, mainly due to the climate particularity of the region, which hinders the growth of suitable biofuels. Taking also into account [...] Read more.

Technical specifications of solid biofuels are continuously improved towards the development and promotion of their market. Efforts in the Greek market are limited, mainly due to the climate particularity of the region, which hinders the growth of suitable biofuels. Taking also into account the increased oil prices and the high inputs required to grow most annual crops in Greece, cardoon (Cynara cardunculus L.) is now considered the most important and promising sources for solid biofuel production in Greece in the immediate future. The reason is that cardoon is a perennial crop of Mediterranean origin, well adapted to the xerothermic conditions of southern Europe, which can be utilized particularly for solid biofuel production. This is due to its minimum production cost, as this perennial weed may perform high biomass productivity on most soils with modest or without any inputs of irrigation and agrochemicals. Within this framework, the present research work is focused on the planning and analysis of different land use scenarios involving this specific energy crop and the combustion behaviour characterization for the solid products. Such land use scenarios are based on quantitative estimates of the crop’s production potential under specific soil-climatic conditions as well as the inputs required for its realization in comparison to existing conventional crops. Concerning its decomposition behaviour, devolatilisation and char combustion tests were performed in a non-isothermal thermogravimetric analyser (TA Q600). A kinetic analysis was applied and accrued results were compared with data already available for other lignocellulosic materials. The thermogravimetric analysis showed that the decomposition process of cardoon follows the degradation of other lignocellulosic fuels, meeting high burnout rates. This research work concludes that Cynara cardunculus, under certain circumstances, can be used as a solid biofuel of acceptable quality. Full article

(This article belongs to the Special Issue Biofuels R&D: Securing the Planet's Future Energy Needs)

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623 KiB

Open AccessReview

Key Labeling Technologies to Tackle Sizeable Problems in RNA Structural Biology

by Kwaku T. Dayie

Int. J. Mol. Sci. 2008, 9(7), 1214-1240; https://doi.org/10.3390/ijms9071214 - 14 Jul 2008

Cited by 44 | Viewed by 14610

Abstract

The ability to adopt complex three-dimensional (3D) structures that can rapidly interconvert between multiple functional states (folding and dynamics) is vital for the proper functioning of RNAs. Consequently, RNA structure and dynamics necessarily determine their biological function. In the post-genomic era, it is [...] Read more.

The ability to adopt complex three-dimensional (3D) structures that can rapidly interconvert between multiple functional states (folding and dynamics) is vital for the proper functioning of RNAs. Consequently, RNA structure and dynamics necessarily determine their biological function. In the post-genomic era, it is clear that RNAs comprise a larger proportion (>50%) of the transcribed genome compared to proteins (≤ 2%). Yet the determination of the 3D structures of RNAs lags considerably behind those of proteins and to date there are even fewer investigations of dynamics in RNAs compared to proteins. Site specific incorporation of various structural and dynamic probes into nucleic acids would likely transform RNA structural biology. Therefore, various methods for introducing probes for structural, functional, and biotechnological applications are critically assessed here. These probes include stable isotopes such as²H, ¹³C, ¹⁵N, and ¹⁹F. Incorporation of these probes using improved RNA ligation strategies promises to change the landscape of structural biology of supramacromolecules probed by biophysical tools such as nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography and Raman spectroscopy. Finally, some of the structural and dynamic problems that can be addressed using these technological advances are outlined. Full article

(This article belongs to the Special Issue Nucleic Acid Derivatives in Emerging Technologies)

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249 KiB

Open AccessArticle

Synthesis and Characterization of Novel Dimeric Ionic Liquids by Conventional Approaches

by Kilivelu Ganesan and Yatimah Alias

Int. J. Mol. Sci. 2008, 9(7), 1207-1213; https://doi.org/10.3390/ijms9071207 - 14 Jul 2008

Cited by 28 | Viewed by 8670

Abstract

The ¹H-NMR shifts of the imidazolium protons of some novel dimeric ionic liquids were examined in various deuterated solvents. Interactions between the solvent and the imidazolium salt of butyl substituted ionic liquids were observed to give higher chemical shifts than methyl substitution. Full article

(This article belongs to the Special Issue Ionic Liquids)

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171 KiB

Open AccessReview

Tea Polyphenols and Their Roles in Cancer Prevention and Chemotherapy

by Di Chen and Q. Ping Dou

Int. J. Mol. Sci. 2008, 9(7), 1196-1206; https://doi.org/10.3390/ijms9071196 - 12 Jul 2008

Cited by 84 | Viewed by 15954

Abstract

Many plant-derived, dietary polyphenols have been studied for their chemopreventive and chemotherapeutic properties against human cancers, including green tea polyphenols, genistein (found in soy), apigenin (celery, parsley), luteolin (broccoli), quercetin (onions), kaempferol (broccoli, grapefruits), curcumin (turmeric), etc. The more we understand their involved [...] Read more.

Many plant-derived, dietary polyphenols have been studied for their chemopreventive and chemotherapeutic properties against human cancers, including green tea polyphenols, genistein (found in soy), apigenin (celery, parsley), luteolin (broccoli), quercetin (onions), kaempferol (broccoli, grapefruits), curcumin (turmeric), etc. The more we understand their involved molecular mechanisms and cellular targets, the better we could utilize these “natural gifts” for the prevention and treatment of human cancer. Furthermore, better understanding of their structure-activity relationships will guide synthesis of analog compounds with improved bio-availability, stability, potency and specificity. This review focuses on green tea polyphenols and seeks to summarize several reported biological effects of tea polyphenols in human cancer systems, highlight the molecular targets and pathways identified, and discuss the role of tea polyphenols in the prevention and treatment of human cancer. The review also briefly describes several other dietary polyphenols and their biological effects on cancer prevention and chemotherapy. Full article

(This article belongs to the Special Issue Natural Compounds for Cancer Treatment and Prevention)

184 KiB

Open AccessReview

Towards Sustainable Production of Biofuels from Microalgae

by Vishwanath Patil, Khanh-Quang Tran and Hans Ragnar Giselrød

Int. J. Mol. Sci. 2008, 9(7), 1188-1195; https://doi.org/10.3390/ijms9071188 - 9 Jul 2008

Cited by 384 | Viewed by 30346

Abstract

Renewable and carbon neutral biofuels are necessary for environmental and economic sustainability. The viability of the first generation biofuels production is however questionable because of the conflict with food supply. Microalgal biofuels are a viable alternative. The oil productivity of many microalgae exceeds [...] Read more.

Renewable and carbon neutral biofuels are necessary for environmental and economic sustainability. The viability of the first generation biofuels production is however questionable because of the conflict with food supply. Microalgal biofuels are a viable alternative. The oil productivity of many microalgae exceeds the best producing oil crops. This paper aims to analyze and promote integration approaches for sustainable microalgal biofuel production to meet the energy and environmental needs of the society. The emphasis is on hydrothermal liquefaction technology for direct conversion of algal biomass to liquid fuel. Full article

(This article belongs to the Special Issue Biofuels R&D: Securing the Planet's Future Energy Needs)

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965 KiB

Open AccessArticle

Electrochemical Investigation of Oligonucleotide-DNA Hybridization on Poly(4-Methoxyphenethylamine)

by Francielle B. Silva, Sabrina N. Vieira, Luiz R. Goulart, Filho, Julien F. C. Boodts, Ana G. Brito-Madurro and João M. Madurro

Int. J. Mol. Sci. 2008, 9(7), 1173-1187; https://doi.org/10.3390/ijms9071173 - 8 Jul 2008

Cited by 24 | Viewed by 10983

Abstract

This work describes the immobilization of purine and pyrimidine bases and immobilization/hybridization of synthetic oligonucleotides on graphite electrodes modified with poly(4-methoxyphenethylamine) produced in acid medium. The immobilization of adenine, guanine, cytosine and thymine on these modified electrodes was efficient, producing characteristic peaks. Another [...] Read more.

This work describes the immobilization of purine and pyrimidine bases and immobilization/hybridization of synthetic oligonucleotides on graphite electrodes modified with poly(4-methoxyphenethylamine) produced in acid medium. The immobilization of adenine, guanine, cytosine and thymine on these modified electrodes was efficient, producing characteristic peaks. Another relevant observation is that, according to the literature, pyrimidine bases, cytosine and thymine are more difficult to detect. However, when immobilized onto the poly(4-methoxyphenethylamine), a significant increase in the magnitude of the current was obtained. The observation of the hybridization between the poly(GA) probe and its complementary, poly(CT) target, was possible by monitoring the guanosine and adenosine peaks or through methylene blue indicator, using differential pulse voltammetry. Hybridization results in a decrease of the peak current of guanosine and adenosine or the signal of methylene blue accumulated on the modified electrode surface. The hybridization with the complementary target was also investigated by electrochemical impedance spectroscopy. The results showed a significant modification in the Nyquist plot, after addition of the complementary target, with increase of the charge transference resistance. Full article

(This article belongs to the Special Issue Nucleic Acid Derivatives in Emerging Technologies)

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246 KiB

Open AccessReview

Photoinduced Biohydrogen Production from Biomass

by Yutaka Amao

Int. J. Mol. Sci. 2008, 9(7), 1156-1172; https://doi.org/10.3390/ijms9071156 - 8 Jul 2008

Cited by 11 | Viewed by 11349

Abstract

Photoinduced biohydrogen production systems, coupling saccharaides biomass such as sucrose, maltose, cellobiose, cellulose, or saccharides mixture hydrolysis by enzymes and glucose dehydrogenase (GDH), and hydrogen production with platinum colloid as a catalyst using the visible light-induced photosensitization of Mg chlorophyll-a (Mg Chl-a) from [...] Read more.

Photoinduced biohydrogen production systems, coupling saccharaides biomass such as sucrose, maltose, cellobiose, cellulose, or saccharides mixture hydrolysis by enzymes and glucose dehydrogenase (GDH), and hydrogen production with platinum colloid as a catalyst using the visible light-induced photosensitization of Mg chlorophyll-a (Mg Chl-a) from higher green plant or artificial chlorophyll analog, zinc porphyrin, are introduced. Full article

(This article belongs to the Special Issue Energy Technology for the 21st Century - Materials and Devices)

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862 KiB

Open AccessArticle

IL-12 and IL-18 Induction and Subsequent NKT Activation Effects of the Japanese Botanical Medicine Juzentaihoto

by Kazuhiko Fujiki, Masanori Nakamura, Takako Matsuda, Mariko Isogai, Minako Ikeda, Yutaka Yamamoto, Mari Kitamura, Naoko Sazaki, Fumiatsu Yakushiji, Shinji Suzuki, Junji Tomiyama, Takashi Uchida and Ken Taniguchi

Int. J. Mol. Sci. 2008, 9(7), 1142-1155; https://doi.org/10.3390/ijms9071142 - 8 Jul 2008

Cited by 22 | Viewed by 12870

Abstract

In this study, we first measured some cytokine concentrations in the serum of patients treated with Juzentaihoto (JTT). Of the cytokines measured interleukin (IL) -18 was the most prominently up-regulated cytokine in the serum of patients under long term JTT administration. We next [...] Read more.

In this study, we first measured some cytokine concentrations in the serum of patients treated with Juzentaihoto (JTT). Of the cytokines measured interleukin (IL) -18 was the most prominently up-regulated cytokine in the serum of patients under long term JTT administration. We next evaluated the effects of JTT in mice, focusing especially on natural killer T (NKT) cell induction. Mice fed JTT were compared to control group ones. After sacrifice, the liver was fixed, embedded and stained. Transmission electron microscope (TEM) observations were performed. Although the mice receiving the herbal medicine had same appearance, their livers were infiltrated with massive mononuclear cells, some of which were aggregated to form clusters. Immunohistochemical staining revealed that there was abundant cytokine expression of IL-12 and IL-18 in the liver of JTT treated mice. To clarify what the key molecules that induce immunological restoration with JTT might be, we next examined in vitro lymphocyte cultures. Mononuclear cells isolated and prepared from healthy volunteers were cultured with and without JTT. Within 24 hours, JTT induced the IL-12 and IL-18 production and later (72 hours) induction of interferon (IFN)-gamma. Oral administration of JTT may induce the expression of IL-12 in the early stage, and IL-18 in the chronic stage, followed by NKT induction. Their activation, following immunological restoration could contribute to anti-tumor effects. Full article

(This article belongs to the Special Issue Natural Compounds for Cancer Treatment and Prevention)

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Open AccessArticle

Microseeding – A Powerful Tool for Crystallizing Proteins Complexed with Hydrolyzable Substrates

by Christine Oswald, Sander H. J. Smits, Erhard Bremer and Lutz Schmitt

Int. J. Mol. Sci. 2008, 9(7), 1131-1141; https://doi.org/10.3390/ijms9071131 - 8 Jul 2008

Cited by 8 | Viewed by 11880

Abstract

Hydrolysis is an often-encountered obstacle in the crystallization of proteins complexed with their substrates. As the duration of the crystallization process, from nucleation to the growth of the crystal to its final size, commonly requires several weeks, non-enzymatic hydrolysis of an “unstable” ligand [...] Read more.

Hydrolysis is an often-encountered obstacle in the crystallization of proteins complexed with their substrates. As the duration of the crystallization process, from nucleation to the growth of the crystal to its final size, commonly requires several weeks, non-enzymatic hydrolysis of an “unstable” ligand occurs frequently. In cases where the crystallization conditions exhibit non neutral pH values this hydrolysis phenomenon may be even more pronounced. ChoX, the substrate binding protein of a choline ABC-importer, produced crystals with its substrate acetylcholine after one month. However, these crystals exhibited only choline, an acetylcholine hydrolysis product, in the binding site. To overcome this obstacle we devised a microseeding protocol leading to crystals of ChoX with bound acetylcholine within 24 hours. One drawback we encountered was the high twinning fraction of the crystals, possibly was due to the rapid crystal growth. Full article

(This article belongs to the Special Issue Protein Crystallography)

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Int. J. Mol. Sci., Volume 9, Issue 7 (July 2008) – 14 articles , Pages 1131-1360

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