Joint determination by Brownian dynamics and fluorescence quenching of the in-depth location profile of biomolecules in membranes

The in-depth molar distribution function of fluorophores is revealed by a new methodology for fluorescence quenching data analysis in membranes. Brownian dynamics simulation was used to study the in-depth location profile of quenchers. A Lorentzian profile was reached. Since the Stern-Volmer equation is valid at every depth in the membrane for low quencher concentrations, the molar distribution of the fluorophore (also regarded as a Lorentzian) can be achieved. The average location and the broadness of the fluorophore distribution can be calculated. The importance of the knowledge of the location width is demonstrated and discussed, since this parameter reveals important conclusions on structural features of the interaction of membranes with probes and biomolecules (e.g., conformational freedom in proteins), as well as photophysical properties (e.g., differential fluorophore quantum yields). Subsequent use of this methodology by the reader does not, necessarily, involve the performance of simulations and is not limited to the use of Lorentzian function distributions.     

Amplification of multiple copies of mitochondrial Cytochrome b gene fragments in the Australian freshwater crayfish,Cherax destructor Clark (Parastacidae: Decapoda)

Non-coding copies of fragments of the mitochondrial genome translocated to the nucleus or pseudogenes are being found with increasing frequency in a diversity of organisms. As part of a study to evaluate the utility of a range of mitochondrial gene regions for population genetic and systematic studies of the Australian freshwater crayfish, Cherax destructor (the yabby), we report the first detection of Cytochrome b (Cyt b) pseudogenes in crustaceans. We amplified and sequenced fragments of the mitochondrial Cyt b gene from 14 individuals of C. destructor using polymerase chain reaction (PCR) with primers designed from conserved regions of Penaeus monodon and Drosophila melanogaster mitochondrial genomes. The phylogenetic tree produced from the amplified fragments using these primers showed a very different topology to the trees obtained from sequences from three other mitochondrial genes, suggesting one or more nuclear pseudogenes have been amplified. Supporting this conclusion, two highly divergent sequences were isolated from each of two single individuals, and a 2 base pair (bp) deletion in one sequence was observed. There was no evidence to support inadvertent amplification of parasite DNA or contamination of samples from other sources. These results add to other recent observations of pseudogenes suggesting the frequent transfer of mitochondrial DNA (mtDNA) genes to the nucleus and reinforces the necessity of great care in interpreting PCR-generated Cyt b sequences used in population or evolutionary studies in freshwater crayfish and crustaceans more generally.     

Genetic diversity of rhizobia isolated from Caragana intermedia in Maowusu sandland,north of China

AIMS: Thirty-three rhizobial strains isolated from nodules of Caragana intermedia in Maowusu sandland were examined for their genetic diversity and putative phylogenetic position. METHODS AND RESULTS: Isolates from Caragana intermedia were classified into 12 genotypes by 16S rDNA polymerase chain reaction-restriction fragment length polymorphism (RFLP), which showed no distinct relationships with those of the reference strains. The genotypes of rhizobia were not related to geographical location. Thr 16S rDNA sequence of representative strain GH2001 from dominant genotype 2 shared high homologuey with some Rhizobium species: Rh. giardinii (96.4%), Rh. huautlense (95.3%), Rh. galegae (95.7%), Rh. yanglingense (95.2%), Rh. mongolense (95.6%), Rh. radiobacter (99%) and Rh. rubi (98.3%). CONCLUSIONS: A high degree of genetic diversity existed among rhizobia nodulating Caragana intermedia in Maowusu sandland. Most of the new isolates might belong to Rhizobium. SIGNIFICANCE AND IMPACT OF THE STUDY: The results suggest that the rich diversity of rhizobia might have contributed to the adaptation of the arid region. These strains could be valuable at the economic and ecosystem level.     

Neurotrophic factor gene delivery supports axonal regeneration after injury

A successful treatment for spinal cord injury (SCI) must include means to induce axonal regeneration and synaptogenesis. Though much research has demonstrated the effectiveness of neurotrophic factors (NFs) in supporting axonal regeneration, systemic delivery of doses sufficient to reach therapeutic concentrations and overcome their short half‐lives has caused adverse effects. Local expression of NFs would overcome these limitations. We tested whether local expression of NFs would induce axonal regeneration without adverse effects in two models of neural injury. In a chemical injury model the rat serotonergic system was lesioned with p‐chloroamphetamine. When an adenoviral vector carrying the gene for brain‐derived neurotrophic factor (BDNF) was injected into the denervated cortex BDNF expressed by the transfected cells induced serotonergic axon reinnervation only in area around the injection site. In a mechanical injury model the cortical spinal tract (CST) in rats was lesioned unilaterally at the level of the hindbrain. Neurotorphin‐3 (NT‐3) was expressed locally in the spinal cord either by direct injection of an adenoviral vector carrying the gene for NT‐3 or by retrograde delivery of the vector from the sciatic nerve. Axons were observed growing from the unlesioned CST across the midline to the denervated side. These data demonstrate that local expression of NFs will induce and support axonal regeneration in a circumscribed area after injury without adverse effects and suggest that a therapy for SCI based upon this strategy may include NF gene delivery. Acknowledgements: Supported by NIH grant NS35280 and Mission Connect of the TIRR Foundation.     

An ATP-driven proton pump in clathrin-coated vesicles

Clathrin containing coated vesicles prepared from bovine brain catalyzed ATP-driven proton translocation and a 32Pi-ATP exchange reaction. Both activities were measured in the presence of 5 micrograms of oligomycin/mg of protein which completely inhibited these reactions catalyzed by submitochondrial particles. Analyses performed during the purification procedure demonstrated that the oligomycin-resistant pump was concentrated and highly purified in the fractions containing coated vesicles. Moreover, vesicles precipitated by either monoclonal or polyclonal antibodies against clathrin contained the H+ pump activity. Dicyclohexylcarbodiimide (0.5 mM) and N-ethylmaleimide (1 mM) added to the assay mixture inhibited the pump completely, whereas neither vanadate, sodium azide, efrapeptin, or mitochondrial ATPase inhibitor had an effect.     

Photosynthetic temperature responses of four neem (Azadirachta indica A. Juss) provenances in the dry-hot valley area of China

The temperature dependences of net photosynthetic rate (P _N), stomatal conductance (g _s), transpiration rate (E) and dark respiration (R _D) of four neem (Azadirachta indica A. Juss) provenances of 11 years old were measured in three seasons of 2006 in the dry-hot valley area of southwest China under field conditions. The results indicated that P _N of four neem provenances showed clear parabolic responses with the increase of temperature. The optimum temperature of P _N was around 25°C in initiation stage and 30°C in prosperous stage except for neem originating from Jodhpur (MA) provenance which was very close to the mean daily temperature of the preceding week while it was around 27°C (MA provenance excepted) in last stage which was rather close to the mean daily maximum temperature of the preceding week. The optimum temperature for P _N of MA provenance was about 2–4°C higher than that of the other three neem provenances in prosperous stage and last stage. According to the fitted parameters of photosynthetic temperature response curves, the photosynthetic performance in prosperous stage was more sensitive to temperature changes than that in initiation stage and last stage while the photosynthetic performance of neem originating from MA provenance was less sensitive to temperatures than that of neem originating from Kalyani, New Delhi and Kulapachta provenances in each growing stage. Furthermore, the temperature ranges for P _N of MA provenance were much wider than those of the remaining provenances in each growing stage. These differences in photosynthetic temperature acclimation between neem provenances not only reflected temperature regime of native habitats of these provenances but suggested that MA provenance could be more tolerant to extreme temperatures compared with the remaining provenances. The temperature response curves of g _s and E were generally similar in form in the same growing stage for all neem provenances; however, shape of the response curves in initiation stage and last stage was similar to parabolic curve while that in prosperous stage was similar to linear relation. The temperature for maximum g _s and E in initiation stage was close to the optimum temperature of P _N, but the maximum g _s reached at much lower temperature than P _N and E in last stage. The response of R _D to temperature increased exponentially with temperature; however, there were obvious differences in different growing stages. R _D in initiation stage was markedly higher than that in prosperous stage and last stage at a given temperature for four neem provenances. These results suggested that four neem provenances can acclimate to their growing environment through changed photosynthetic ecophysiological responses in course of subjecting to seasonal variation of temperature.     

CBP-18, a Ca2+-Binding Protein in Rat Brain: Tissue Distribution and Localization

Abstract: The distribution of a novel calcium-binding protein with a molecular mass of 18 kDa (CBP-18) in the rat brain was studied by means of biochemical methods and immunohistochemistry on cryostat-sectioned tissue and compared with staining patterns of parvalbumin on adjacent sections. The biochemical analysis revealed high levels of CPB-18 in cortex and cerebellum, low levels in the lungs, and undetectable levels in all other tissues tested. Immunohistochemically, the polyclonal rabbit-derived antibody for CPB-18 showed selective affinity with periglomerular cells and dendrites in the olfactory bulb. Distinct immunostaining of scattered cells and their proximal dendrites was found in the anterior olfactory nuclei and in the perirhinal and entorhinal cortex. Strong staining of neuropil with recognizable but diffusely outlined cells was observed in the retrosplenial cortex, central amygdala, hippocampal rudiment, septum, area preoptica, hypothalamus, colliculus superior, and parabrachial nuclei. The cerebellum showed strong neuropil staining of both the molecular and the granule cell layer. Less intense neuropil staining and a few scattered cells were found in the neocortex, the remaining basal forebrain, and in the entire brainstem. Immunoreactivity was barely detectable or missing in the striatum, the hippocampus, the thalamus, and in the colliculus inferior. Thus, CPB-18 shows a unique staining pattern in the CNS, different from all other Ca²⁺-binding proteins studied so far.     

Influence of habitat modification by livestock on páramo bird abundance in southern Andes of Ecuador

Livestock grazing on natural grasslands is widespread with negative consequences to biodiversity. In the High Andes, páramo grassland is a distinctive ecosystem where the influence of livestock grazing on páramo birds is poorly documented. We assessed the influence of habitat modification of páramo grassland related to livestock grazing on bird habitat guilds in the southern Andes of Ecuador. We recorded birds occurring along transects located in areas which showed a gradient (low to high) of grazing pressure. We found a decrease in abundance of páramo specialists in transects with more grazing pressure. We interpret this habitat modification as loss of key habitat necessary for habitat-specialized birds.     

Factors associated with a low prevalence of exclusive breastfeeding during hospital stay in urban and semi-rural areas of southern Vietnam

Background

There is a paucity of data regarding risk factors associated with suboptimal breastfeeding practices in urbanized areas of low-middle income countries (LMICs).

Methods

Through a large prospective birth cohort, which enrolled 6706 infants in Vietnam between 2009 and 2013, we investigated the practice of exclusive breastfeeding during hospital stay in urban and semi-rural populations and aimed to identify factors associated with suboptimal breastfeeding practices. Univariate and multivariable logistic regression were performed to determine factors associated with not exclusive breastfeeding during hospital stay.

Results

Of 6076 mothers, 33% (2187) breastfed their infant exclusively before hospital discharge; 9% (364/4248) in urban and 74% (1823/2458) in semi-rural areas. Exclusive breastfeeding up to 4 months was recorded in 15% (959/6210) of participants; this declined to <?1% (56/6093) at 6 months. Delivery by Caesarean section (Odds Ratio [OR] 0.07; 95% Confidence Interval [CI] 0.04, 0.11 and OR 0.05; 95% CI 0.03, 0.08) and neonatal complications (OR 0.2; 95% CI 0.07, 0.47 and OR 0.25; 95% CI 0.14, 0.46) were common and highly significant risk factors associated with a lack of exclusive breastfeeding during hospital stay in urban and semi-rural settings, respectively.

Conclusions

To our knowledge, this is the first large-scale investigation aimed at identifying factors associated with exclusive breastfeeding during hospital stay in Vietnam. Breastfeeding promotion strategies should prioritize common risk factors in hospital, such as Caesarean section and neonatal complications, and other location specific factors associated with socioeconomics.