CFP: a web-server for constructing sequence-based protein conformational flexibility profiles

Many proteins contain conformationally flexible segments that undergo significant changes in the backbone conformation or completely lack a well­defined conformation. Previously, we have developed the generalized local propensity (GLP), a quantitative sequence-based measure of the protein backbone flexibility. In this paper, we present the CFP (Conformational Flexibility Profile) web­server that constructs the GLP flexibility profile for a user­submitted sequence and uses this profile to identify segments with high backbone flexibility. The statistical significance of a flexible sequence segment is assessed using the discrete scan statistics based on the density of flexible residues observed in this segment.

Availability

CFP is publicly available at http://cfp.rit.albany.edu     

Reconstitution of Mammary Epithelial Morphogenesis by Murine Embryonic Stem Cells Undergoing Hematopoietic Stem Cell Differentiation

Background

Mammary stem cells are maintained within specific microenvironments and recruited throughout lifetime to reconstitute de novo the mammary gland. Mammary stem cells have been isolated through the identification of specific cell surface markers and in vivo transplantation into cleared mammary fat pads. Accumulating evidence showed that during the reformation of mammary stem cell niches by dispersed epithelial cells in the context of the intact epithelium-free mammary stroma, non-mammary epithelial cells may be sequestered and reprogrammed to perform mammary epithelial cell functions and to adopt mammary epithelial characteristics during reconstruction of mammary epithelium in regenerating mammary tissue in vivo.

Methodology/Principal Findings

To examine whether other types of progenitor cells are able to contribute to mammary branching morphogenesis, we examined the potential of murine embryonic stem (mES) cells, undergoing hematopoietic differentiation, to support mammary reconstitution in vivo. We observed that cells from day 14 embryoid bodies (EBs) under hematopoietic differentiation condition, but not supernatants derived from these cells, when transplanted into denuded mammary fat pads, were able to contribute to both the luminal and myoepithelial lineages in branching ductal structures resembling the ductal-alveolar architecture of the mammary tree. No teratomas were observed when these cells were transplanted in vivo.

Conclusions/Significance

Our data provide evidence for the dominance of the tissue-specific mammary stem cell niche and its role in directing mES cells, undergoing hematopoietic differentiation, to reprogram into mammary epithelial cells and to promote mammary epithelial morphogenesis. These studies should also provide insights into regeneration of damaged mammary gland and the role of the mammary microenvironment in reprogramming cell fate.     

Proton-sensing Ca2+ binding domains regulate the cardiac Na+/Ca2+ exchanger

The cardiac Na(+)/Ca(2+) exchanger (NCX) regulates cellular [Ca(2+)](i) and plays a central role in health and disease, but its molecular regulation is poorly understood. Here we report on how protons affect this electrogenic transporter by modulating two critically important NCX C(2) regulatory domains, Ca(2+) binding domain-1 (CBD1) and CBD2. The NCX transport rate in intact cardiac ventricular myocytes was measured as a membrane current, I(NCX), whereas [H(+)](i) was varied using an ammonium chloride "rebound" method at constant extracellular pH 7.4. At pH(i) = 7.2 and [Ca(2+)](i) < 120 nM, I(NCX) was less than 4% that of its maximally Ca(2+)-activated value. I(NCX) increases steeply at [Ca(2+)](i) between 130-150 nM with a Hill coefficient (n(H)) of 8.0 ± 0.7 and K(0.5) = 310 ± 5 nM. At pH(i) = 6.87, the threshold of Ca(2+)-dependent activation of I(NCX) was shifted to much higher [Ca(2+)](i) (600-700 nM), and the relationship was similarly steep (n(H) = 8.0±0.8) with K(0.5) = 1042 ± 15 nM. The V(max) of Ca(2+)-dependent activation of I(NCX) was not significantly altered by low pH(i). The Ca(2+) affinities for CBD1 (0.39 ± 0.06 μM) and CBD2 (K(d) = 18.4 ± 6 μM) were exquisitely sensitive to [H(+)], decreasing 1.3-2.3-fold as pH(i) decreased from 7.2 to 6.9. This work reveals for the first time that NCX can be switched off by physiologically relevant intracellular acidification and that this depends on the competitive binding of protons to its C(2) regulatory domains CBD1 and CBD2.     

Acoustic and optical transduction of BuChE binding to procainamide modified surfaces

A novel polymer, poly(procainamide), PPA, containing numerous binding sites for cholinesterases was synthesized as a recognition layer for butyryl cholinesterase (BuChE) interaction with the ligand procainamide, utilizing TSM and SPR sensors. The polymer was synthesized by the reaction of methacryloyl chloride and procainamide followed by radical polymerization. Sensor surfaces (Au or SiO(2)) were spin-coated by the polymer solution to form thin layers. Binding of BuChE was found to be sensitive to the drying procedure of the polymer layer. The binding of BuChE to the polymer coated sensors was monitored on-line by following the response of thickness shear mode (TSM) and surface plasmon resonance (SPR) sensors. Binding of BuChE to PPA-coated TSM sensors were shown to follow a Langmuir isotherm giving association constant 3.4x10(6) M(-1).     

Forest biomass,productivity and carbon cycling along a rainfall gradient in West Africa

Net Primary Productivity (NPP) is one of the most important parameters in describing the functioning of any ecosystem and yet it arguably remains a poorly quantified and understood component of carbon cycling in tropical forests, especially outside of the Americas. We provide the first comprehensive analysis of NPP and its carbon allocation to woody, canopy and root growth components at contrasting lowland West African forests spanning a rainfall gradient. Using a standardized methodology to study evergreen (EF), semi‐deciduous (SDF), dry forests (DF) and woody savanna (WS), we find that (i) climate is more closely related with above and belowground C stocks than with NPP (ii) total NPP is highest in the SDF site, then the EF followed by the DF and WS and that (iii) different forest types have distinct carbon allocation patterns whereby SDF allocate in excess of 50% to canopy production and the DF and WS sites allocate 40%–50% to woody production. Furthermore, we find that (iv) compared with canopy and root growth rates the woody growth rate of these forests is a poor proxy for their overall productivity and that (v) residence time is the primary driver in the productivity‐allocation‐turnover chain for the observed spatial differences in woody, leaf and root biomass across the rainfall gradient. Through a systematic assessment of forest productivity we demonstrate the importance of directly measuring the main components of above and belowground NPP and encourage the establishment of more permanent carbon intensive monitoring plots across the tropics.     

Cephapirin: In Vitro Antibacterial Spectrum

Cephapirin, a new semisynthetic cephalosporin derivative, was found to have an antibacterial spectrum similar to that of cephalothin. Staphylococcus aureus was inhibited by cephapirin concentrations of 0.09 to 12.5 mug/ml. S. epidermidis, S. viridans, S. pyogenes, and Diplococcus pneumonia isolates were inhibited by less than 1 mug/ml. The Enterococcus required a concentration of 25 mug of antibiotic per ml for inhibition. Approximately 65% of Escherichia coli, and all Klebsiella, indole-negative Proteus, and Salmonella strains tested were inhibited by the drug. Serratia, Pseudomonas, indole-positive Proteus, and Erwinia strains were highly resistant. Inoculum size was not an important factor in determining the level of sensitivity of S. aureus to cephapirin. The antibiotic does not appear to be significantly bound to serum protein. In vitro development of resistance to the drug was demonstrated with two isolates of S. aureus.     

Vitellogenesis and oocyte development in azadirachtin-induced fifth-instar overage nymphs of Locusta migratoria (L.)

Injection of azadirachtin into females of Locusta migratoria at the beginning of the last nymphal instar prevented molting to the adult stage, and many of these locusts survived for long periods as overage fifth-instar nymphs. Overage female nymphs synthesized vitellogenin; maximum vitellogenin content in their hemolymph was 6–7 times higher than that found in normal adult females. The overage female nymphs developed vitellogenic oocytes, but development was retarded to some extent: although vitellogenin did accumulate in the proximal oocytes, their maximum average length was only about 2.8 mm (compared to 6.2 mm in normal adult females) and extensive oocyte resorption was observed. Thus, attainment of adult competence of the organs and processes involved in female reproduction is independent to a considerable extent from the process of overt adult morphogenesis.     

Bulgarian Jews in Israel: genetic blood markers. Red-cell antigens, serum proteins and red-cell isozymes

Two hundred and sixteen unrelated Bulgarian Jews were typed for the following genetic systems: ABO, MNS, Rh, Kell and Duffy of the blood groups; ADA, AK1, ACP1, ESD, GLO, PGD, PGM1 and PGM2 of the red-cell enzymes, and for the serum proteins HP, GC and PI. A comparison of observed gene frequencies with those of two other Sephardi Jewish groups, from Libya and Morocco, disclosed significant heterogeneity in several systems. This was mostly due to Moroccan Jews differing from Bulgarian or from both the Libyan and Bulgarian Jews. A comparison of gene frequencies in Bulgarian Jews with those in Oriental Jews from Iraq and in Ashkenazi Jews from Poland disclosed a similarity between the three groups in Rh, ADA, GLO, PGM1 and HP. The frequencies for the above systems in the three groups were closer to those of Middle Easterners than to those of Europeans. A different pattern was observed for GC and PI, in which Bulgarian resembled Polish Jews and differed significantly from Iraqi Jews. This probably reflects an outcome of convergent adaptive processes.