Attainment of peak bone mass and bone turnover rate in relation to estrous cycle, pregnancy and lactation in colony-bred Sprague-Dawley rats: suitability for studies on pathophysiology of bone and therapeutic measures for its management

Alteration in biochemical markers of bone turnover and bone mineral density (BMD) of whole body and isolated femur and tibia in relation to age, estrous cycle, pregnancy and lactation and suitability of use of rat as model for studies on pathophysiology of bone and therapeutic measures for its management were investigated. Immature rats (1, 1.5 and 2 month of age; weighing, respectively, 39.3 ± 1.0, 67.8 ± 2.4 and 87.2 ± 5.2 g) exhibited high rate of bone turnover, as evidenced by high serum osteocalcin and alkaline phosphatase and urine calcium/creatinine ratio. However, their BMD (whole body or of isolated long bones) was below measurable levels. Marked increase in body weight at 3 months (185.5 ± 5.2 g) was associated with low serum osteocalcin and alkaline phosphatase and urine calcium/creatinine ratio. Biochemical markers and BMD attained at puberty at 3 months were maintained until 36 month of age. No significant change in serum calcium was observed with increasing age or on any of the biomarkers during estrous cycle, and BMD of femur and tibia isolated during proestrus and diestrus stages was almost similar. Onset of pregnancy was associated with significant increase in serum total alkaline phosphatase and osteocalcin levels, but serum calcium, urine calcium/creatinine ratio or BMD of whole body or isolated long bones were not significantly different from that at proestrus stage. No marked change, except increase in body weight (P < 0.05), was also evident in these parameters between days 5 and 19 of pregnancy, irrespective of number of implantations in the uterus. A significant decrease in BMD of isolated femur (neck and mid-shaft regions) was observed on days 5 and 21 of lactation as compared to that during pregnancy or diestrus/proestrus stages of estrous cycle; the decrease being almost similar in females lactating two or six young ones. BMD of isolated tibia (global and region proximal to tibio-fibular separation point), though generally lower than that during cycle and pregnancy, was statistically non-significant. However, clear evidence of occurrence of osteoporosis during lactation, with decrease in BMD of >2.5 × S.D. in isolated femur (global, neck and mid-shaft) as well as tibia (global) was observed only when BMD data was analysed on T-/Z-score basis. Serum biochemical markers of bone turnover, too, were significantly increased in comparison to cyclic rats. Findings demonstrate marked increase in body weight and bone turnover during first 3 months of age, direct correlation between peak bone mass and onset of puberty at 3 months of age and increase in bone resorption rate during lactation. Finding of the study while might suggests possible use of rat as useful model for studies on bone turnover rate during lactation and post-weaning periods and extrapolation of the result to the human situation, but not in relation to ageing.     

The Calvin cycle in cyanobacteria is regulated by CP12 via the NAD(H)/NADP(H) ratio under light/dark conditions

In Synechococcus PCC7942 cells grown in the dark, the concentrations of NAD(H) and NADP(H) were 128+/-2.5 and 483+/-4.0 microm, respectively, while those in the cells under light conditions were 100+/-5.0 and 649+/-7.0 microm, respectively. Analysis of gel filtration indicated that the change of the ratio of NADP(H) to NAD(H) in cyanobacterial cells under light/dark conditions controls the reversible dissociation of the PRK/CP12/GAPDH complex (approximately 520 kDa) consisting of phosphoribulokinase (PRK), CP12, and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). S. 7942 CP12 lacked the two Cys residues essential for formation of the N-terminal peptide loop in the CP12 of higher plants, but the N-terminal region of S. 7942 CP12 had the ability to be associated with PRK. The growth of mutant cells in which the CP12 gene was disrupted by a kanamycin resistance cartridge gene was almost the same as that of wild-type cells under continuous light conditions. However, under the light/dark cycle (12 h/12 h), the growth of CP12-disrupted mutant cells was significantly inhibited compared with that of wild-type cells. The mutant cells showed a decreased rate of O2 consumption and an increased level of ribulose 1,5-bisphosphate compared with wild-type cells in the dark. These data suggest that under light and dark conditions, the oligomerization of CP12 with PRK and GAPDH regulates the activities of both enzymes and thus the carbon flow from the Calvin cycle to the oxidative pentose phosphate cycle.     

High-throughput protein localization in Arabidopsis using Agrobacterium-mediated transient expression of GFP-ORF fusions

We describe a streamlined and systematic method for cloning green fluorescent protein (GFP)-open reading frame (ORF) fusions and assessing their subcellular localization in Arabidopsis thaliana cells. The sequencing of the Arabidopsis genome has made it feasible to undertake genome-based approaches to determine the function of each protein and define its subcellular localization. This is an essential step towards full functional analysis. The approach described here allows the economical handling of hundreds of expressed plant proteins in a timely fashion. We have integrated recombinational cloning of full-length trimmed ORF clones (available from the SSP consortium) with high-efficiency transient transformation of Arabidopsis cell cultures by a hypervirulent strain of Agrobacterium. To demonstrate its utility, we have used a selection of trimmed ORFs, representing a variety of key cellular processes and have defined the localization patterns of 155 fusion proteins. These patterns have been classified into five main categories, including cytoplasmic, nuclear, nucleolar, organellar and endomembrane compartments. Several genes annotated in GenBank as unknown have been ascribed a protein localization pattern. We also demonstrate the application of flow cytometry to estimate the transformation efficiency and cell cycle phase of the GFP-positive cells. This approach can be extended to functional studies, including the precise cellular localization and the prediction of the role of unknown proteins, the confirmation of bioinformatic predictions and proteomic experiments, such as the determination of protein interactions in vivo, and therefore has numerous applications in the post-genomic analysis of protein function.     

Candidate nsSNPs that can affect the functions and interactions of cell cycle proteins

Nonsynonymous single nucleotide polymorphisms (nsSNPs) alter the encoded amino acid sequence, and are thus likely to affect the function of the proteins, and represent potential disease-modifiers. There is an enormous number of nsSNPs in the human population, and the major challenge lies in distinguishing the functionally significant and potentially disease-related ones from the rest. In this study, we analyzed the genetic variations that can alter the functions and the interactions of a group of cell cycle proteins (n = 60) and the proteins interacting with them (n = 26) using computational tools. As a result, we extracted 249 nsSNPs from 77 cell cycle proteins and their interaction partners from public SNP databases. Only 31 (12.4%) of the nsSNPs were validated. The majority (64.5%) of the validated SNPs were rare (minor allele frequencies < 5%). Evolutionary conservation analysis using the SIFT tool suggested that 16.1% of the validated nsSNPs may disrupt the protein function. In addition, 58% of the validated nsSNPs were located in functional protein domains/motifs, which together with the evolutionary conservation analysis enabled us to infer possible biological consequences of the nsSNPs in our set. Our study strongly suggests the presence of naturally occurring genetic variations in the cell cycle proteins that may affect their interactions and functions with possible roles in complex human diseases, such as cancer.     

Global gene expression profiling and cluster analysis in Xenopus laevis

We have undertaken a large-scale microarray gene expression analysis using cDNAs corresponding to 21,000 Xenopus laevis ESTs. mRNAs from 37 samples, including embryos and adult organs, were profiled. Cluster analysis of embryos of different stages was carried out and revealed expected affinities between gastrulae and neurulae, as well as between advanced neurulae and tadpoles, while egg and feeding larvae were clearly separated. Cluster analysis of adult organs showed some unexpected tissue-relatedness, e.g. kidney is more related to endodermal than to mesodermal tissues and the brain is separated from other neuroectodermal derivatives. Cluster analysis of genes revealed major phases of co-ordinate gene expression between egg and adult stages. During the maternal-early embryonic phase, genes maintaining a rapidly dividing cell state are predominantly expressed (cell cycle regulators, chromatin proteins). Genes involved in protein biosynthesis are progressively induced from mid-embryogenesis onwards. The larval-adult phase is characterised by expression of genes involved in metabolism and terminal differentiation. Thirteen potential synexpression groups were identified, which encompass components of diverse molecular processes or supra-molecular structures, including chromatin, RNA processing and nucleolar function, cell cycle, respiratory chain/Krebs cycle, protein biosynthesis, endoplasmic reticulum, vesicle transport, synaptic vesicle, microtubule, intermediate filament, epithelial proteins and collagen. Data filtering identified genes with potential stage-, region- and organ-specific expression. The dataset was assembled in the iChip microarray database, , which allows user-defined queries. The study provides insights into the higher order of vertebrate gene expression, identifies synexpression groups and marker genes, and makes predictions for the biological role of numerous uncharacterized genes.     

Is the bark of shining gum (Eucalyptus nitens) a sun or a shade leaf?

Photoinhibition and pigment composition of green stem tissues of field-grown adult Eucalyptus nitens were measured on clear spring days with low morning temperatures—conditions that cause photoinhibition in leaves of many plant species. The sun-exposed (north-facing) bark contained less chlorophyll a+b (531 vs 748 mol m^–2), neoxanthin (29 vs 41), and -carotene (54 vs 73), more xanthophyll cycle pigments per unit surface area and per unit chlorophyll (71 vs 53 mol m^–2 and 141 vs 66 mmol mol^–1 chlorophyll), and less lutein per unit chlorophyll (239 vs 190) than the shaded (southern) side. Maximum electron flow rates were 60 mol m^–2 s^–1 on the sun-exposed side, and about 10 mol m^–2 s^–1 on the shaded side. F_v/F_m was always lower than 0.8 on the sun-exposed side and the de-epoxidation state (DEPS) of the xanthophyll cycle was dominated by zeaxanthin in midday samples. F_v/F_m increased quickly after darkening, but DEPS recovered more slowly to 40% overnight. This suggested that rapidly reversible pH-dependent quenching was responsible for the bulk of changes in PS II efficiency. F_v/F_m remained below 0.8 overnight, which may well be indicative of photo-damage to PSII. In contrast, DEPS of the shaded side was lower, and F_v/F_m was higher, than for the sun-exposed side. We conclude that E. nitens chlorenchyma on the sun-exposed stem side has a photosynthetic pigment composition similar to sun leaves and it experiences significant photoinhibition in the field.     

Life Cycle Inventory Information of the United States Electricity System (11/17 pp)

Goal and Scope This study estimates the life cycle inventory (LCI) of the electricity system in the United States, including the 10 NERC (North American Electric Reliability Council) regions, Alaska, Hawaii, off-grid non-utility plants and the US average figures. The greenhouse gas emissions associated with the United States electricity system are also estimated. Methods The fuel mix of the electricity system based on year 2000 data is used. The environmental burdens associated with raw material extraction, petroleum oil production and transportation for petroleum oil and natural gas to power plants are adopted from the DEAMTM LCA database. Coal transportation from a mining site to a power plant is specified with the data from the Energy Information Administration (EIA), which includes the mode of transportation as well as the distance traveled. The gate-to-gate environmental burdens associated with generating electricity from a fossil-fired power plant are obtained from the DEAMTM LCA database and the eGRID model developed by the United States Environmental Protection Agency. For nuclear power plants and hydroelectric power plants, the data from the DEAMTM LCA database are used.Results and Discussion Selected environmental profiles of the US electricity system are presented in the paper version, while the on-line version presents the whole LCI data. The overall US electricity system in the year 2000 released about 2,654 Tg CO2 eq. of greenhouse gas emissions based on 100-year global warming potentials with 193 g CO2 eq. MJe–1 as an weighted average emission rate per one MJ electricity generated. Most greenhouse gases are released during combusting fossil fuels, accounting for 78–95% of the total. The greenhouse gas emissions released from coal-fired power plants account for 81% of the total greenhouse gas emissions associated with electricity generation, and natural gas-fired power plants contribute about 16% of the total. The most significant regions for the total greenhouse gas emissions are the SERC (Southeastern Electric Reliability Council) and ECAR (East Central Area Reliability Coordination Agreement) regions, which account for 22% and 21% of the total, respectively. A sensitivity analysis on the generation and consumption based calculations indicates that the environmental profiles of electricity based on consumption are more uncertain than those based on generation unless exchange data from the same year are available because the exchange rates (region to region import and export of electricity) vary significantly from year to year.Conclusions and Outlook Those who are interested in the LCI data of the US electricity system can refer to the on-line version. When the inventory data presented in the on-line version are used in a life cycle assessment study, the distribution and transmission losses should be taken into account, which is about 9.5% of the net generation [1]. The comprehensive technical information presented in this study can be used in estimating the environmental burdens when new information on the regional fuel mix or the upstream processes is available. The exchange rates presented in this study also offer useful information in consequential LCI studies.     

Extending the Life Cycle Methodology to Cover Impacts of Land Use Systems on the Water Balance (7 pp)

Goal, Scope and Background Whilst initially designed for industrial production systems, environmental life cycle assessment (LCA) has recently been increasingly applied to agriculture and forestry projects. Several authors suggested that the standard LCA methodology needs to be refined to cover the particularities of agri- and silvicultural production systems. Until now, water quantity received little attention in these methodological revisions, notwithstanding the well-known impact of agriculture and forestry on issues like water availability, drought and flood risk. This paper proposes an add-on to existing LCA methods in the form of an indicator set that integrates water quantity impacts of agri- and silvicultural production. Method First, system boundaries are discussed in order to identify the water flows between the production system and the environment. These flows are attributed to impact categories, linked to environmental burdens and to the areas of protection. Appropriate indicators are selected for each potential burden. Results and Discussion At the present, two input related impact categories deal with water quantity: Abiotic resource depletion and land use. The list of output related impact categories presented by Udo de Haes et al. (1999) does not include water quantity impacts like flood and drought risk. A new impact category “regional water balance” is introduced to cover these risks. Exceedance probabilities are used as indicators for these temporal variations in streamflow. Conclusion and Outlook The method presented in this paper can bring a life cycle assessment closer to real world concerns. The main drawback, however, is the increasing data requirement that might hinder the feasibility of the method. Future research should focus on this problem, for instance by applying a relatively simple numerical model that can calculate the indicator scores from more easily accessible data.