Cellulose-bound Peptide Arrays: Preparation and Applications

Spatial organization of metabolic enzymes may represent a general cellular mechanism to regulate metabolic flux. One recent example of this type of cellular phenomenon is the purinosome, a newly discovered multi-enzyme metabolic assembly that includes all of the enzymes within the de novo purine biosynthetic pathway. Our understanding of the components and regulation of purinosomes has significantly grown in recent years. This paper reviews the purine de novo biosynthesis pathway and its regulation, and presents the evidence supporting the purinosome assembly and disassembly processes under the control of G-protein-coupled receptor (GPCR) signaling. This paper also discusses the implications of purinosome and GPCR regulation in drug discovery.     

Mechanisms of cohesin-mediated gene regulation and lessons learned from cohesinopathies

Cohesins are conserved and essential Structural Maintenance of Chromosomes (SMC) protein-containing complexes that physically interact with chromatin and modulate higher-order chromatin organization. Cohesins mediate sister chromatid cohesion and cellular long-distance chromatin interactions affecting genome maintenance and gene expression. Discoveries of mutations in cohesin's subunits and its regulator proteins in human developmental disorders, so-called “cohesinopathies,” reveal crucial roles for cohesins in development and cellular growth and differentiation. In this review, we discuss the latest findings concerning cohesin's functions in higher-order chromatin architecture organization and gene regulation and new insight gained from studies of cohesinopathies. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.     

A second Warburg-like effect in cancer metabolism: The metabolic shift of glutamine-derived nitrogen

Carbon and nitrogen are essential elements for life. Glucose as a carbon source and glutamine as a nitrogen source are important nutrients for cell proliferation. About 100 years ago, it was discovered that cancer cells that have acquired unlimited proliferative capacity and undergone malignant evolution in their host manifest a cancer-specific remodeling of glucose metabolism (the Warburg effect). Only recently, however, was it shown that the metabolism of glutamine-derived nitrogen is substantially shifted from glutaminolysis to nucleotide biosynthesis during malignant progression of cancer—which might be referred to as a “second” Warburg effect. In this review, address the mechanism and relevance of this metabolic shift of glutamine-derived nitrogen in human cancer. We also examine the clinical potential of anticancer therapies that modulate the metabolic pathways of glutamine-derived nitrogen. This shift may be as important as the shift in carbon metabolism, which has long been known as the Warburg effect.     

First record of non-marine ostracods from the Paleogene “hamadian deposits” of Méridja area,west of Bechar (southwestern Algeria)

A new non-marine ostracod fauna from the Paleogene “hamadian deposits” outcropping west of Bechar (southwestern Algeria) has been recovered from lacustrine to fluvial deposits of the Oued Méridja section and fluvial deposits on the southern edge of the Hamada de Méridja section. Recently, these sections have been dated as late Thanetian – early Ypresian (latest Paleocene to earliest Eocene) and Ypresian – earliest Lutetian (early to earliest middle Eocene), respectively, based on charophytes. The associated ostracod fauna recovered consists of relatively mostly moderately to badly preserved specimens and comprises 14 taxa, none of which could be identified to species level in view of its poor state of preservation; we have nevertheless been able to identify and describe the following taxa: Herpetocypris sp., Cyprinotus? sp., Heterocypris? sp. 1 and sp. 2, Cypris? sp., Ilyocypris sp., Cytheroidea indet. sp. 1 and sp. 2, Limnocytheridae indet. sp. 1, Cypridoidea indet. sp. 1, Cyprididae indet. sp. 1, and Ostracoda indet. sp. 1, 2 and 3. Only Heterocypris sp. 1 occurs in both sections. Although the fauna can as yet not be related to the few other contemporaneous faunas reported from the wider palaeogeographic area, it adds important new information to our poor knowledge on Eocene non-marine ostracods in North Africa and southern Europe. The Méridja sections and area are promising regarding the discovery of more, better preserved material and further studies, and one main limitation to the correlation of the fauna is the hitherto insufficient taxonomic knowledge on many faunal elements of Eocene non-marine ostracods to which our section contributes considerably.     

Separation of chitosomes and secretory vesicles from the “slime” variant of Neurospora crassa

Cells from the slime variant of Neurospora crassa were broken in isotonic conditions by use of triethanolamine buffer plus EDTA. After removal of large membranous structures by low-speed centrifugation, chitosomes and secretory vesicles were separated by means of gel filtration, precipitation of membranous contaminants with Concanavalin A, and centrifugation in sucrose or glycerol gradients. Polypeptidic composition of fractions enriched in secretory vesicles or chitosomes was found to be distinct. By these criteria we concluded that chitosomes and secretory vesicles represent different populations of microvesicles. Both microvesicular populations appeared free of endoplasmic reticulum and vacuolar contaminants as demonstrated by determination of appropriate enzymatic markers.Abbreviations ER Endoplasmic reticulum - UDP-GlcNAc uridine-5-diphosphate N-acetyl glucosamine - GlcNAc N-acetyl glucosamine - SDS sodium dodecyl sulfate - PMSF phenyl methyl sulfonyl fluoride - EDTA ethylene diamino tetraacetic acid Investigador Nacional de Mexico. On leave from the Centro de Investigacion y Estudios Avanzados (IPN), and the Universidad de Guanajuato, Gto., Mexico     

Inner structural organization of the mandibular corpus in the late Early Pleistocene human specimens Tighenif 1 and Tighenif 2

The present study investigates the inner structural organization of the two mandible specimens Tighenif 1 and Tighenif 2 from the late early Pleistocene site of Tighenif, Algeria. Using (micro)tomographic scans, we built a new protocol to investigate the cortical bone topography at the post-canine level. We selected two cross-sectional slices placed between the P3/P4 and M1/M2 on the right and left sides and assessed the cortical bone thickness topography (CBT) on each slice. Our analyses demonstrate that the mandibles from Tighenif exhibit higher CBT and a different topographic distribution pattern at the molar level than in modern humans, resulting in a proportionally more robust inner structure, while a similar signal is observed between the fossil and extant specimens at the premolar level. Further studies need to be done in order to determine if this feature is related to functional constraints during mastication or paramasticatory activities; or if it is related to any independent evolutionary process.     

Agrobacterium bohemicum sp. nov. isolated from poppy seed wastes in central Bohemia

Two non-pathogenic strains R89-1 and R90^T isolated from poppy seed (Papaver somniferum L.) wastes were phenotypically and genotypically characterized. Multilocus sequence analysis (MLSA) was conducted with six genes (atpD, glnA, gyrB, recA, rpoB, 16S rRNA). The strains represented a new species which clustered with Agrobacterium rubi NBRC 13261^T and Agrobacterium skierniewicense Ch11^T type strains. MLSA was further accompanied by whole-genome phylogeny, in silico DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses for both strains. ANI and dDDH values were deep below the species delineation threshold. Phenotypic features of the novel strains unequivocally allowed their differentiation from all other Agrobacterium species. Unlike other agrobacteria, the strains were salt sensitive and were able to biotransform morphine alkaloids. The dominant cellular fatty acids are 18:1 w7c, 16:0 and 12:0 aldehyde/16:1 iso I/14:0 3OH summed in feature 2 and the major respiratory quinine is Q-10 (87%). The DNA G + C content is 56 mol%. Microbial community analysis indicated probable association with P. somniferum plant material. Altogether, these characteristics showed that strains R90^T and R89-1 represent a new species of the genus Agrobacterium which we propose to name Agrobacterium bohemicum. The type strain of A. bohemicum is R90^T (=CCM 8736^T = DSM 104667^T).     

VPMCD: variable interaction modeling approach for class discrimination in biological systems

Data classification algorithms applied for class prediction in computational biology literature are data specific and have shown varying degrees of performance. Different classes cannot be distinguished solely based on interclass distances or decision boundaries. We propose that inter-relations among the features be exploited for separating observations into specific classes. A new variable predictive model based class discrimination (VPMCD) method is described here. Three well established and proven data sets of varying statistical and biological significance are utilized as benchmark. The performance of the new method is compared with advanced classification algorithms. The new method performs better during different tests and shows higher stability and robustness. The VPMCD is observed to be a potentially strong classification approach and can be effectively extended to other data mining applications involving biological systems.     

Amblyospora trinus N. Sp. (Microsporida: Amblyosporidae) in the Australian Mosquito Culex halifaxi (Diptera: Culicidae)

ABSTRACT. A new species of Amblyospora , a parasite found in wild populations of the predacious Australian mosquito Culex halifaxi , was investigated with light and electron microscopy. This species was found to be heterosporous with two concurrent sporulation sequences in the host larvae, both arising from diplokaryotic meronts and ending with haploid spores. One sequence was dominant and involved meiosis to produce eight thick-walled, broadly oval meiospores in a sporophorous vesicle (SV). The other sequence involved nuclear dissociation to produce lanceolate, thin-walled spores in a subpersistent SV. Horizontal transmission to the mosquito host, by one or both of two distinctly different pathways (one via an intermediate host, the other by cannibalism of infected individuals) and by vertical transmission, are postulated but have not been demonstrated. A new species, Amblyospora trinus , is proposed and its affinities to other heterosporous microsporidia in mosquitoes are discussed.