Molecular and evolutionary analyses of Dictyostelium discoideum mitochondrial DNA

Thesis (Ph.D. in Science)--University of Tsukuba, (A), no. 1329, 1995.3.2

Downstream processing of high chain length polysialic acid using membrane adsorbers and clay minerals for application in tissue engineering

Polysialic acid (polySia) is a carbohydrate polymer of varying chain length. It is a promising scaffold material for tissue engineering. In this work, high chain length polySia was produced by an Escherichia coli K1 strain in a 10-L bioreactor in batch and fed-batch mode, respectively. A new downstream process for polySia is presented, based on membrane adsorber technology and use of inorganic anion exchanger. These methods enable the replacement of precipitation steps, such as acetone, cetavlon, and ethanol precipitation of the already established purification process. The purification process was simplified, while process efficiency and product qualities were improved. The overall yield of polySia from a 10-L batch cultivation process was 61% and for 10-L fed-batch cultivation process the yield was 40% with an overall purity of 98%. The endotoxin content was determined to be negligible (14 EU mg-1). The main advantage of this new downstream process is that polySia with high chain length of more than 130 degree of polymerization can be obtained. In fed-batch cultivation, chain lengths up to 160 degree of polymerization were obtained.DFG/FOR/54

Influence of SIGLEC9 polymorphisms on COPD phenotypes including exacerbation frequency.

BACKGROUND AND OBJECTIVE: The exacerbation-prone phenotype of COPD is particularly important, as exacerbations lead to poor quality of life and disease progression. We previously found that COPD patients who lack Siglec-14, a myeloid cell protein that recognizes bacteria and triggers inflammatory responses, are less prone to exacerbation. We hypothesized that the variations in other SIGLEC genes could also influence COPD exacerbation frequency, and investigated the association between SIGLEC9 polymorphisms and the exacerbation-prone phenotype of COPD. METHODS: We examined whether SIGLEC9 polymorphisms affect the frequency of COPD exacerbation in 135 subjects within our study population, and also analysed the correlation between the genotypes and the severity of airflow obstruction and emphysema in 362 Japanese smokers including 244 COPD patients. The association between these single nucleotide polymorphisms (SNPs) and COPD phenotypes were also assessed in a Caucasian population of ECLIPSE study. The effects of these coding SNPs (cSNPs) on Siglec-9 protein functions were analysed using in vitro assays. RESULTS: The G allele of rs2075803 and rs2075803 G/rs2258983 A(GA) haplotype in SIGLEC9 was associated with higher frequency of exacerbations and the extent of emphysema in COPD. These results did not replicate in the ECLIPSE study. A myeloid cell line expressing the Siglec-9 variant corresponding to GA haplotype produced more TNF-α than the one expressing the variant corresponding to the other major haplotype. CONCLUSION: The SIGLEC9 rs2075803 G/rs2258983 A haplotype, which corresponds to a Siglec-9 variant that is less effective at suppressing inflammatory response, may be a risk factor for the development of emphysema

Membrane-enclosed multienzyme (MEME) synthesis of 2,7-anhydro-sialic acid derivatives

Naturally occurring 2,7-anhydro-alpha-N-acetylneuraminic acid (2,7-anhydro-Neu5Ac) is a transglycosylation product of bacterial intramolecular trans-sialidases (IT-sialidases). A facile one-pot two-enzyme approach has been established for the synthesis of 2,7-anhydro-sialic acid derivatives including those containing different sialic acid forms such as Neu5Ac and N-glycolylneuraminic acid (Neu5Gc). The approach is based on the use of Ruminoccocus gnavus IT-sialidase for the release of 2,7-anhydro-sialic acid from glycoproteins, and the conversion of free sialic acid by a sialic acid aldolase. This synthetic method, which is based on a membrane-enclosed enzymatic synthesis, can be performed on a preparative scale. Using fetuin as a substrate, high-yield and cost-effective production of 2,7-anhydro-Neu5Ac was obtained to high-purity. This method was also applied to the synthesis of 2,7-anhydro-Neu5Gc. The membrane-enclosed multienzyme (MEME) strategy reported here provides an efficient approach to produce a variety of sialic acid derivatives

Possible Influences of Endogenous and Exogenous Ligands on the Evolution of Human Siglecs

Sialic acids, a group of acidic sugars abundantly expressed in the tissues of deuterostome animals but rarely found in microbes, serve as a “signature of self” for these animals. Cognate sensors for sialic acids include Siglecs, a family of transmembrane lectins of vertebrate immune systems that recognize glycans containing sialic acids. A type of sialic acid called N-glycolylneuraminic acid (Neu5Gc) is abundant in many mammalian lineages including great apes, the closest extant relatives of modern human, but was lost in the lineage leading to modern human via the pseudogenization of the CMAH gene encoding the enzyme that converts N-acetylneuraminic acid (Neu5Ac) to Neu5Gc. Loss of Neu5Gc appears to have influenced the evolution of human Siglecs, such as the adjustment of sialic acid binding preferences and the inactivation of at least one Siglec. In addition, various mechanistic studies using model systems and genetic association studies have revealed that some human Siglecs interact with pathogens and influence the outcome of infections, and these pathogens in turn likely influence the evolution of these Siglecs. By understanding the evolutionary forces affecting Siglecs, we shall achieve a better appreciation of Siglec functions, and by understanding Siglec functions, we can obtain deeper insight into the evolutionary processes driving Siglec evolution

Differential metabolism of Mycoplasma species as revealed by their genomes

The annotation and comparative analyses of the genomes of Mycoplasma synoviae and Mycoplasma hyopneumonie, as well as of other Mollicutes (a group of bacteria devoid of a rigid cell wall), has set the grounds for a global understanding of their metabolism and infection mechanisms. According to the annotation data, M. synoviae and M. hyopneumoniae are able to perform glycolytic metabolism, but do not possess the enzymatic machinery for citrate and glyoxylate cycles, gluconeogenesis and the pentose phosphate pathway. Both can synthesize ATP by lactic fermentation, but only M. synoviae can convert acetaldehyde to acetate. Also, our genome analysis revealed that M. synoviae and M. hyopneumoniae are not expected to synthesize polysaccharides, but they can take up a variety of carbohydrates via the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS). Our data showed that these two organisms are unable to synthesize purine and pyrimidine de novo, since they only possess the sequences which encode salvage pathway enzymes. Comparative analyses of M. synoviae and M. hyopneumoniae with other Mollicutes have revealed differential genes in the former two genomes coding for enzymes that participate in carbohydrate, amino acid and nucleotide metabolism and host-pathogen interaction. The identification of these metabolic pathways will provide a better understanding of the biology and pathogenicity of these organisms

Glycobiology of immune responses

Unlike their protein roommates and their nucleic acid cousins, carbohydrates remain an enigmatic arm of biology. The central reason for the difficulty in fully understanding how carbohydrate structure and biological function are tied is the non-template nature of their synthesis and the resulting heterogeneity. While this Annals of the NYAS issue does not claim to hold all of the answers, the goal is to highlight what is known about how carbohydrates and their binding partners, on the microbial (non-self), tumor (altered-self) and host (self) sides, cooperate within the immune system while identifying areas of great opportunity to those willing to take up the challenge. In the end, these reviews will serve as specific examples of how carbohydrates are as integral to biology as proteins, nucleic acids, and lipids. In this introductory article we attempt to summarize general concepts on glycans and glycan-binding proteins (mainly C-type lectins, siglecs and galectins) and their contribution to the biology of the immune responses in physiologic and pathologic settings.Fil: Rabinovich, Gabriel Adrián. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Biológica; ArgentinaFil: Van Kooyk, Yvette. VU University Amsterdam. VU University Medical Center; Países BajosFil: Cobb, Brian A.. Case Western Reserve University; Estados Unido

Analisis Energi dan Emisi CO2 Rencana Bus Listrik di Yogyakarta Studi Kasus Trans Jogja

Sektor transportasi memiliki proporsi konsumsi energi terbesar kedua di Indonesia setelah sektor rumah tangga. Berdasarkan Indonesia Energy Outlook 2017, konsumsi energi sektor transportasi mencapai 31% dari total kebutuhan dan meningkat 5,2% per tahunnya dalam kurun waktu 2010-2015. Yogyakarta sebagai kota pelajar dan tujuan wisata mendorong perbaikan sistem transportasi umum untuk menekan jumlah penggunaan kendaraan pribadi. Kendaraan listrik merupakan salah satu cara mengatasi ketergantungan bahan bakar berbasis minyak bumi sekaligus dapat menjadi solusi transportasi umum ramah lingkungan dan rendah emisi. Analisis konsumsi energi pada bus listrik dilakukan dengan menggunakan bus Trans Jogja jalur 3B untuk mendapatkan parameter berkendara yang sesuai, dari hasil analisis tersebut dapat ditentukan bus yang memerlukan konsumsi energi dan emisi CO2 paling sedikit. Melalui hasil penelitian diperoleh siklus berkendara Trans Jogja jalur 3B memiliki jarak 36.818 m, waktu tempuh 5.391 s, dan rerata kecepatan 24,5 km/jam. Berdasarkan pemodelan perhitungan energi tiap lampu lalu lintas, diperoleh konsumsi energi bus listrik sebesar 1,35 kWh/km sedangkan bus konvensional membutuhkan 2,74 kWh/km. Emisi yang dihasilkan dalam satu siklus berkendara bus listrik berdasarkan pemodelan pasokan energi tahun 2025 dan 2050 adalah sebesar 22,13 kgCO2 dan 19,78 kgCO2 sedangkan pada bus konvensional sebesar 26,94 kgCO2

Siglec-5 and Siglec-14 are polymorphic paired receptors that modulate neutrophil and amnion signaling responses to group B Streptococcus

Group B Streptococcus (GBS) causes invasive infections in human newborns. We recently showed that the GBS beta-protein attenuates innate immune responses by binding to sialic acid-binding immunoglobulin-like lectin 5 (Siglec-5), an inhibitory receptor on phagocytes. Interestingly, neutrophils and monocytes also express Siglec-14, which has a ligand-binding domain almost identical to Siglec-5 but signals via an activating motif, raising the possibility that these are paired Siglec receptors that balance immune responses to pathogens. Here we show that beta-protein-expressing GBS binds to both Siglec-5 and Siglec-14 on neutrophils and that the latter engagement counteracts pathogen-induced host immune suppression by activating p38 mitogen-activated protein kinase (MAPK) and AKT signaling pathways. Siglec-14 is absent from some humans because of a SIGLEC14-null polymorphism, and homozygous SIGLEC14-null neutrophils are more susceptible to GBS immune subversion. Finally, we report an unexpected human-specific expression of Siglec-5 and Siglec-14 on amniotic epithelium, the site of initial contact of invading GBS with the fetus. GBS amnion immune activation was likewise influenced by the SIGLEC14-null polymorphism. We provide initial evidence that the polymorphism could influence the risk of prematurity among human fetuses of mothers colonized with GBS. This first functionally proven example of a paired receptor system in the Siglec family has multiple implications for regulation of host immunity