Nuclear protein in the liver in protein–calorie deficiency

1. The effect of protein–calorie deficiency on nuclear proteins was studied in growing and adult rats by using chemical and electrophoretic methods of fractionation. 2. After 7 days on protein-deficient diets, the amount of neutral-soluble proteins increased, and their electrophoretic pattern changed, with the appearance of a new component. 3. The histone fraction of the liver nuclei in rapidly growing rats was lower than that in either deficient or adult animals. 4. The possible role of nuclear proteins in relation to synthesis of the proteins and nucleic acids of the other parts of the cells is discussed.     

Shaping the science–industry–policy interface in synthetic biology

Current advances in the emerging field of synthetic biology and the improvements in key technologies promise great impacts, not only on future scientific development, but also on the economy. In this paper we will adopt the triple helix concept for analyzing the early stages of a new field of science and innovation, namely synthetic biology. Synthetic biology is based on the creation and assembly of parts in order to create new and more complex structures and functions. These features of synthetic biology raise questions related to standardization and intellectual property, but also to security and public perception issues that go beyond the classical biotechnology discussions. These issues concern all involved actors in the synthetic biology field and affect the interrelationship between science, industry and policy. Based on the results of the recently finished EU FP-6 funded project TESSY (http://www.tessy-europe.de), the article analyzes these issues. Additionally, it illustrates the setting of clear framework conditions for synthetic biology research and development and the identification and definition of common goals for the future development of the field which will be needed for efficient science–industry–policy interaction. It was shown that it will be crucial to develop approaches that consider the needs of science and industry, on the one hand, and comply with the expectations of society, on the other hand. As synthetic biology is a global activity, the involvement of national decision-makers in international initiatives will further stimulate the development of the field.     

X–linked Recessive Inheritance in the Ehlers–Danlos Syndrome

Two families are described in which the Ehlers–Danlos syndrome is apparently transmitted as an X-linked recessive character. The results of tests for the Xg blood groups and for colour vision show that the locus for the Ehlers–Danlos syndrome is not close to that for the Xg groups nor very close to the locus for deutan colour-blindness.The clinical features of this variety of the Ehlers–Danlos syndrome include considerable hyperextensibility of the skin and a bruising tendency.     

Scientific Authority in the Creation–Evolution Debates

At the heart of debates among creationists and evolutionists are questions about scientific integrity and rigor. Creationists often justify their rejection of biological evolution by claiming that the methodologies and interpretations of evolutionary scientists are flawed. A consideration of creationists’ critiques of the scientific data, however, reveals a deficient understanding and appreciation of the nature of the scientific process. It is essential that our schools educate students about the character of scientific inquiry. Clarifying the nature and limitation of scientific knowledge for our students will equip our students to evaluate evolutionary or creationist arguments critically. Recognizing and teaching both the strengths and limitations of the scientific process will do much to further the ongoing dialogue between science and religion.     

The role of the abnormalities in the distal pathway of cholesterol biosynthesis in the Conradi–Hünermann–Happle syndrome

Conradi–Hünermann–Happle syndrome (CDPX2, OMIM 302960) is an inherited X-linked dominant variant of chondrodysplasia punctata (CP) caused by mutations in one gene of the distal pathway of cholesterol biosynthesis. It exhibits intense phenotypic variation and primarily affects the skin, bones and eyes. The ichthyosis following Blaschko's lines, chondrodysplasia punctata and cataracts are the typical clinical findings. The cardinal biochemical features are an increase in 8(9)-cholestenol and 8-dehydrocholesterol (8DHC), which suggest a deficiency in 3β-hydroxysteroid-Δ8,Δ7-isomerase, also called emopamil binding protein (EBP). The EBP gene is located on the short arm of the X chromosome (Xp11.22–p11.23) and encodes a 230 amino acid protein with dual function. Explaining the clinical phenotype in CDPX2 implies an understanding of both the genetics and biochemical features of this disease. CDPX2 displays an X-linked dominant pattern of inheritance, which is responsible for the distribution of lesions in some tissues. The clinical phenotype in CDPX2 results directly from impairment in cholesterol biosynthesis, and indirectly from abnormalities in the hedgehog signaling protein pathways. This article is part of a Special Issue entitled The Important Role of Lipids in the Epidermis and their Role in the Formation and Maintenance of the Cutaneous Barrier. Guest Editors: Kenneth R. Feingold and Peter Elias.     

Cell–cell Signaling in the Neurovascular Unit

Historically, the neuron has been the conceptual focus for almost all of neuroscience research. In recent years, however, the concept of the neurovascular unit has emerged as a new paradigm for investigating both physiology and pathology in the CNS. This concept proposes that a purely neurocentric focus is not sufficient, and emphasizes that all cell types in the brain including neuronal, glial and vascular components, must be examined in an integrated context. Cell–cell signaling and coupling between these different compartments form the basis for normal function. Disordered signaling and perturbed coupling form the basis for dysfunction and disease. In this mini-review, we will survey four examples of this phenomenon: hemodynamic neurovascular coupling linking blood flow to brain activity; cellular communications that evoke the blood–brain barrier phenotype; parallel systems that underlie both neurogenesis and angiogenesis in the CNS; and finally, the potential exchange of trophic factors that may link neuronal, glial and vascular homeostasis. Special issue in honor of Naren Banik.     

EMG in rotation–flexion of the torso

The objective of this study was to determine the magnitude and phasic relationship of the torso muscles in rotation–flexion of varying degree of asymmetries of the trunk. Nineteen normal young subjects (7 males and 12 females) were stabilized on a posture stabilizing platform and instructed to assume a flexed and right rotated posture. A combination 20°, 40° and 60° of rotation and 20°, 40° and 60° of flexion resulted in nine postures. These postures were assumed in a random order. The subjects were asked to exert their maximal voluntary isometric contraction (MVC) in the plane of rotation of the posture assumed for a period of 5 s. The surface EMG from the external and internal obliques, rectus abdominis, latissimus dorsi and erector spinae at the 10th thoracic and 3rd lumbar vertebral levels was recorded. The abdominal muscles had the least response at 40° of flexion, the dorsal muscles had the highest magnitude.With increasing right rotation, the left external oblique continued to decrease its activity. The ANOVA revealed that rotation and muscles had a significant main effect on normalized peak EMG (p < 0.02) in both genders. There was a significant interaction between rotation and flexion in both genders (p < 0.02) and rotation and muscle in females. The erector spinae activity was highest at 40° flexion, due to greater mechanical disadvantage and having not reached the state of flexion–relaxation. The abdominal muscle activity declined with increasing asymmetry, due to the decreasing initial muscle length. The EMG activity was significantly affected by rotation than flexion (p < 0.02).     

Y-Chromosome Haplotypes in the Greek–Turkish Area

Various populations have contributed to the present-day gene pool in oriental Mediterranean (Aegean Sea) and are well documented for ancient history. The primary objective of the study is to report on the analysis of the paternal component of the variation (Y chromosome haplotypes) in contemporary populations in Greece, Crete, Turkey and Cyprus. A total of 245 males who hailed from five different locations in Turkey, Greece, and the islands of Crete and Cyprus were analyzed for Y-chromosome-specific haplotypes based on p49a,f TaqI polymorphism. The main haplotype observed (21.2%) in the Greek–Turkish area is haplotype VII. The second haplotype in terms of frequency (13.5%) is haplotype VIII, which is characteristic of Semitic populations. The third (11.4%), fourth (6.9%) and fifth (5.7%) haplotypes in frequency are haplotype XI (a typical eastern European haplotype), haplotype V (the North African haplotype) and haplotype XV (the Western European haplotype), respectively. The distribution of haplotype VII is significantly heterogeneous genetically among the five localities studied, with a peak of frequency (43.8%) in Crete. It is proposed that haplotype VII reflects the ancient Minoan civilization. Haplotype VII frequencies actually known are mapped in countries surrounding the Mediterranean Sea.     

Signal molecules in the peanut–bradyrhizobia interaction

Main nodulation signal molecules in the peanut–bradyrhizobia interaction were examined. Flavonoids exuded by Arachis hypogaea L. cultivar Tegua were genistein, daidzein and chrysin, the latest being released in lower quantities. Thin layer chromatography analysis from genistein-induced bacterial cultures of three peanut bradyrhizobia resulted in an identical Nod factor pattern, suggesting low variability in genes involved in the synthesis of these molecules. Structural study of Nod factor by mass spectrometry and NMR analysis revealed that it shares a variety of substituents with the broad-host-range Rhizobium sp. NGR234 and Bradyrhizobium spp. Nodulation assays in legumes nodulated by these rhizobia demonstrated differences between them and the three peanut bradyrhizobia. The three isolates were classified as Bradyrhizobium sp. Their fixation gene nifD and the common nodulation genes nodD and nodA were also analyzed. Accession numbers: AY427207, EF202193, EF158295 (16S rRNA gene of strains NLH25, NOD31 and NDEHE, respectively); DQ295199, DQ295200, DQ295201 (Partial nifD gene sequences of strains NLH25, NOD31 and NDEHE, respectively).     

A Mutation in the LDL Receptor–Related Protein 5 Gene Results in the Autosomal Dominant High–Bone-Mass Trait

Osteoporosis is a complex disease that affects >10 million people in the United States and results in 1.5 million fractures annually. In addition, the high prevalence of osteopenia (low bone mass) in the general population places a large number of people at risk for developing the disease. In an effort to identify genetic factors influencing bone density, we characterized a family that includes individuals who possess exceptionally dense bones but are otherwise phenotypically normal. This high–bone-mass trait (HBM) was originally localized by linkage analysis to chromosome 11q12-13. We refined the interval by extending the pedigree and genotyping additional markers. A systematic search for mutations that segregated with the HBM phenotype uncovered an amino acid change, in a predicted β-propeller module of the low-density lipoprotein receptor–related protein 5 (LRP5), that results in the HBM phenotype. During analysis of >1,000 individuals, this mutation was observed only in affected individuals from the HBM kindred. By use of in situ hybridization to rat tibia, expression of LRP5 was detected in areas of bone involved in remodeling. Our findings suggest that the HBM mutation confers a unique osteogenic activity in bone remodeling, and this understanding may facilitate the development of novel therapies for the treatment of osteoporosis.     

Diversity of fish species in the trawl catches in the southeastern Barents Sea in 1980–2008

Analysis of trawl catches in the southeastern Barents Sea was performed for the period of 1980–2008. One lamprey and 48 fish species were defined, including 38 marine fish species, 8 anadromous and amphidromous species, and 1 freshwater species. The ichthyofauna of several areas of the southeastern Barents Sea was described (Cheshskaya Inlet, Pomorskiy Strait, southeastern Pechora Sea, Pechora Sea, Khaipudyrskaya Inlet and adjacent areas). Biodiversity indexes and Shannon Index were applied to describe the species diversity. Cluster analysis was applied to compare the species lists from different areas. Multiyear dynamics of ichthyofauna was studied. The tendency of geographical range expansion eastward was observed for boreal species.     

Perturbation Theory in the Catalytic Rate Constant of the Henri–Michaelis–Menten Enzymatic Reaction

The Henry–Michaelis–Menten (HMM) mechanism of enzymatic reaction is studied by means of perturbation theory in the reaction rate constant k ₂ of product formation. We present analytical solutions that provide the concentrations of the enzyme (E), the substrate (S), as well as those of the enzyme-substrate complex (C), and the product (P) as functions of time. For k ₂ small compared to k _?1, we properly describe the entire enzymatic activity from the beginning of the reaction up to longer times without imposing extra conditions on the initial concentrations E _o and?S _o , which can be comparable or much different.     

Ostracod recovery in the aftermath of the Permian–Triassic crisis: Palaeozoic–Mesozoic turnover

Results of a detailed bathymetric survey of Crater Lake conducted in 2000, combined with previous results of submersible and dredge sampling, form the basis for a geologic map of the lake floor and a model for the filling of Crater Lake with water. The most prominent landforms beneath the surface of Crater Lake are andesite volcanoes that were active as the lake was filling with water, following caldera collapse during the climactic eruption of Mount Mazama 7700 cal. yr B.P. The Wizard Island volcano is the largest and probably was active longest, ceasing eruptions when the lake was 80 m lower than present. East of Wizard Island is the central platform volcano and related lava flow fields on the caldera floor. Merriam Cone is a symmetrical andesitic volcano that apparently was constructed subaqueously during the same period as the Wizard Island and central platform volcanoes. The youngest postcaldera volcanic feature is a small rhyodacite dome on the east flank of the Wizard Island edifice that dates from 4800 cal. yr B.P. The bathymetry also yields information on bedrock outcrops and talus/debris slopes of the caldera walls. Gravity flows transport sediment from wall sources to the deep basins of the lake. Several debris-avalanche deposits, containing blocks up to 280 m long, are present on the caldera floor and occur below major embayments in the caldera walls. Geothermal phenomena on the lake floor are bacterial mats, pools of solute-rich warm water, and fossil subaqueous hot spring deposits. Lake level is maintained by a balance between precipitation and inflow versus evaporation and leakage. High-resolution bathymetry reveals a series of up to nine drowned beaches in the upper 30 m of the lake that we propose reflect stillstands subsequent to filling of Crater Lake. A prominent wave-cut platform between 4 m depth and present lake level that commonly is up to 40 m wide suggests that the surface of Crater Lake has been at this elevation for a very long time. Lake level apparently is limited by leakage through a permeable layer in the northeast caldera wall. The deepest drowned beach approximately corresponds to the base of the permeable layer. Among a group of lake filling models, our preferred one is constrained by the drowned beaches, the permeable layer in the caldera wall, and paleoclimatic data. We used a precipitation rate 70% of modern as a limiting case. Satisfactory models require leakage to be proportional to elevation and the best fit model has a linear combination of 45% leakage proportional to elevation and 55% of leakage proportional to elevation above the base of the permeable layer. At modern precipitation rates, the lake would have taken 420 yr to fill, or a maximum of 740 yr if precipitation was 70% of the modern value. The filling model provides a chronology for prehistoric passage zones on postcaldera volcanoes that ceased erupting before the lake was filled.     

Protein–Protein and Protein–Membrane Associations in the Lignin Pathway

Supramolecular organization of enzymes is proposed to orchestrate metabolic complexity and help channel intermediates in different pathways. Phenylpropanoid metabolism has to direct up to 30% of the carbon fixed by plants to the biosynthesis of lignin precursors. Effective coupling of the enzymes in the pathway thus seems to be required. Subcellular localization, mobility, protein–protein, and protein–membrane interactions of four consecutive enzymes around the main branch point leading to lignin precursors was investigated in leaf tissues of Nicotiana benthamiana and cells of Arabidopsis thaliana. CYP73A5 and CYP98A3, the two Arabidopsis cytochrome P450s (P450s) catalyzing para- and meta-hydroxylations of the phenolic ring of monolignols were found to colocalize in the endoplasmic reticulum (ER) and to form homo- and heteromers. They moved along with the fast remodeling plant ER, but their lateral diffusion on the ER surface was restricted, likely due to association with other ER proteins. The connecting soluble enzyme hydroxycinnamoyltransferase (HCT), was found partially associated with the ER. Both HCT and the 4-coumaroyl-CoA ligase relocalized closer to the membrane upon P450 expression. Fluorescence lifetime imaging microscopy supports P450 colocalization and interaction with the soluble proteins, enhanced by the expression of the partner proteins. Protein relocalization was further enhanced in tissues undergoing wound repair. CYP98A3 was the most effective in driving protein association.     

Trends in stage-specific population-based survival of cancer patients in the Czech Republic in the period 2000–2008

BackgroundThe objective of this study was to assess trends in overall and in stage-specific 5-year relative survival rates of the Czech cancer patients between periods 2000–2004 and 2005–2008.MethodsAll Czech cancer patients diagnosed between 1995 and 2008 were included in the analysis. Period analysis was employed to calculate 5-year relative survival for 21 cancers.ResultsSignificant improvements in crude 5-year relative survival for 14 of 21 assessed types of cancer, including the most frequent diagnoses, such as, colorectal, prostate, breast, lung, kidney, pancreatic, and bladder cancer and melanoma, were identified. Moreover, in case of colorectal, lung, and prostate cancer, improvement in stage-specific 5-year relative survival was confirmed as statistically significant for all clinical stages. No diagnosis showed significant decrease in the 5-year relative survival. However, the 5-year relative survival remained poor in patients with metastatic cancers at diagnosis, particularly in case of liver, pancreatic, lung, and oesophageal cancer.ConclusionsThe cancer-specific outcomes in the Czech Republic are improving. Nevertheless, despite the overall significant improvement in 5-year relative survival of most of the cancer diagnoses, the high proportion of patients primarily diagnosed with metastatic cancer still represents a substantial challenge for prevention and early detection.     

Characterization of the peridinin–chlorophyll a-protein complex in the dinoflagellate Symbiodinium

The water-soluble peridinin–chlorophyll a-proteins (PCPs) are one of the major light harvesting complexes in photosynthetic dinoflagellates. PCP contains the carotenoid peridinin as its primary pigment. In this study, we identified and characterized the PCP protein and the PCP gene organization in Symbiodinium sp. CS-156. The protein molecular mass is 32.7 kDa, revealing that the PCP is of the monomeric form. The intronless PCP genes are organized in tandem arrays. The PCP gene cassette is composed of 1095-bp coding regions and spacers in between. Despite the heterogeneity of PCP gene tandem repeats, we identified a single form of PCP, the sequence of which exactly matches the deduced sequence of PCP gene clone 7 (JQ395030) by LC–MS/MS analysis of tryptic digested PCP, revealing the mature PCP apoprotein is 312 amino acids in length. Pigment analysis showed a peridinin-to-Chl a ratio of 4. The peridinin-to-Chl a Q_y energy transfer efficiency is 95% in this complex.     

Re-evaluating the omnivory–stability relationship in food webs

Under equilibrium conditions, previous theory has shown that the presence of omnivory destabilizes food webs. Correspondingly, omnivory ought to be rare in real food webs. Although, early food web data appeared to verify this, recently many ecologists have found omnivory to be ubiquitous in food web data gathered at a high taxonomic resolution. In this paper, we re-investigate the role of omnivory in food webs using a non-equilibrium perspective. We find that the addition of omnivory to a simple food chain model (thus a simple food web) locally stabilizes the food web in a very complete way. First, non-equilibrium dynamics (e.g. chaos) tend to be eliminated or bounded further away from zero via period-doubling reversals invoked by the omnivorous trophic link. Second, food chains without interior attractors tend to gain a stable interior attractor with moderate amounts of omnivory.     

Vascular epiphytes in the temperate zones–a review

Vascular epiphytes are typically associated with tropical rainforests, whereas their occurrence in temperate forests is little appreciated. This review summarises the available information on epiphytism in the temperate zones (> 23.5 latitude), which has not been reviewed omprehensively for more than a century, and critically analyses the proposed mechanisms behind the observed biogeographical patterns. Although in the temperate zone epiphytic vascular plants are rarely as impressive as in tropical forests, there are noteworthy exceptions. Temperate rain forests of Chile and New Zealand, or montane forests in the Himalayas are comparable to many tropical forests in terms of epiphyte biomass and diversity, but differ in their taxonomic spectrum temperate epiphyte communities are generally dominated by ferns and fern-allies. Other temperate areas are not, however, necessarily barren of epiphytes, as repeatedly implied. Quite in contrast, local populations of epiphytes in a large number of other non-tropical areas in both the southern and the northern hemisphere can be quite conspicuous. The proposed reasons for the latitudinal gradients in epiphyte abundance and diversity (water scarcity or low tempera-tures). are not fully convincing and, moreover, still await experimental verification. Other factors, both historical (e.g., Pleistocene extinctions) and ecological (e.g., prevalence of conifers in the northern hemisphere), should also be taken into consideration to obtain a comprehensive explanation of the extant global distribution of vascular epiphytes.