Strategies for the identification and purification of ligands for orphan biomolecules

The isolation of related genes with evolutionary conserved motifs by the application ofpolymerase chain reaction-based molecular biology techniques, or from database searchingstrategies, has facilitated the identification of new members of protein families. Many of theseprotein molecules will be involved in protein–protein interactions (e.g. growth factors,receptors, adhesion molecules), since such interactions are intrinsic to virtually every cellularprocess. However, the precise biological function and specific binding partners of these novelproteins are frequently unknown, hence they are known as orphan molecules.Complementary technologies are required for the identification of the specific ligands orreceptors for these and other orphan proteins (e.g., antibodies raised against crude biologicalextracts or whole cells). We describe herein several alternative strategies for the identification,purification and characterisation of orphan peptide and protein molecules, specifically thesynergistic use of micropreparative HPLC and biosensor techniques.     

Computer determination of perfusion patterns in pulmonary capillary networks

Hanger, Christopher C., Robert G. Presson, Jr., Osamu Okada,Steven J. Janke, John J. Watkins, Wiltz W. Wagner, Jr., and Ronald L. Capen. Computer determination of perfusion patterns in pulmonarycapillary networks. J. Appl. Physiol.82(4): 1283-1289, 1997.Individual pulmonary capillaries are notsteadily perfused. By using in vivo microscopy, it can readily bedemonstrated that perfusion continually switches between capillarysegments and between portions of the network within a single alveolarwall. These changes in capillary perfusion occur even when upstream pressure and flow are constant. Flow switching between capillary segments in the absence of hemodynamic changes in large upstream vessels suggests that capillary perfusion patterns could be random. Tocalculate the probability that perfusion patterns could occur bychance, it is necessary to know the total number of possible perfusionpatterns in a given capillary network. We developed a computer programthat can determine every possible perfusion pattern for any givencapillary network, and from that information we can calculate whetherperfusion of individual segments in the network is random. With theresults of the computer program, we have obtained statistical evidencethat some capillary segments in a network are nonrandomly perfused.

     

Effects of vigorous exercise training and beta -agonist administration on bone response to hindlimb suspension

Bloomfield, Susan A., Beverly E. Girten, and Steven E. Weisbrode. Effects of vigorous exercise training and -agonist administration on bone response to hindlimb suspension.J. Appl. Physiol. 83(1):172-178, 1997.The effectiveness of dobutamine (Dob) inpreventing bone loss during 14 days of hindlimb suspension (Sus) wastested in exercise-trained (Ex; n = 25) and sedentary (Sed; n = 22) rats(age 155 days). One-half of each group was given Dob (2 mg · kg¹ · day¹)or saline (Sal). Histomorphometric measurements at midfemur revealed a17% smaller cortical bone area (CBA) and a 32% lower periostealmineral apposition rate (MAR) in suspended vs. nonsuspended Sed/Salrats. Dob abolished this decline in CBA in Sed/Sus rats, probably via an attenuation of the decrease in periosteal MAR; similarbut nonsignificant effects on cross-sectional moment of inertia wereobserved. Nonsuspended Ex rats had no change in bone CBA when CBA isindexed to body weight. Sus appeared to uncouple the relationshipbetween soleus weight and CBA. Dob attenuated the 43% decline insoleus weight after Sus in Ex but not in Sed rats. In summary, vigorousEx before Sus does not affect loss of bone mass due to unloading; Dobeffectively maintains CBA in Sed rats subjected to suspension.

     

Molecular analysis of the two-component genes, ompR and envZ, in the symbiotic bacterium Xenorhabdus nematophilus

In Escherichia coli the histidine kinase sensor protein, EnvZ, undergoes autophosphorylation and subsequently phosphorylates the regulatory protein, OmpR. Modulation of the levels of OmpR-phosphate controls the differential expression of ompF and ompC . While the phosphotransfer reaction between EnvZ and OmpR has been extensively studied, the domains involved in the sensing function of EnvZ are not well understood. We have used a comparative approach to study the sensing function of EnvZ. During our search of numerous bacteria we found that the symbiotic/pathogenic bacterium Xenorhabdus nematophilus contained the operon encoding both ompR and envZ . Nucleotide sequence analysis revealed that EnvZ of X. nematophilus (EnvZ^X.n.) is composed of 342 amino acid residues, which is 108 residues shorter than EnvZ of E. coli (EnvZ^E.c.). Amino acid sequence comparison showed that the cytoplasmic domains of the EnvZ moleculsshared 57% sequence identity. In contrast, the large hydrophilic periplasmic domain of EnvZ^E.c. was absent in EnvZ^X.n., and was replaced by a shorter hydrophobic region. Although the periplasmic domains had diverged extensively, envZ^X.n. was able to complement a Δ envZ strain of E. coli . OmpF and OmpC were differentially produced in response to changes in medium osmolarity in this strain. Further genetic analysis established that heterologous phosphorylation between EnvZ^X.n. and OmpR of E. coli (OmpR^E.c.) accounted for the complementation of the Δ envZ strain. In addition we show that the OmpR molecules of X. nematophilus and E. coli share 78% amino acid sequence identity. These results indicate that the EnvZ protein of X. nematophilus was able to sense changes in the osmolarity of the growth environment and properly regulate the levels of OmpR-phosphate in E. coli .     

Rapid analysis of amino acids using pre-column derivatization

A new approach to the pre-column derivatization and analysis of amino acids is described. The method is based upon formation of a phenylthiocarbamyl derivative of the amino acids. The derivatization method is rapid, efficient, sensitive, and specific for the analysis of primary and secondary amino acids in protein hydorlyzates. The liquid chromatographic system allows for the rapid, bonded-phase separation with ultraviolet detection of the common amino acids with 12-min analysis time and a 1-pmol sensitivity.     

The polyadenylated RNA of zoospores and growth phase cells of the aquatic fungus,Blastocladiella

The stored poly(A) + RNA from zoospores of the aquatic fungus Blastocladiella emersonii represents 2.5% of the total RNA and has a model MW of 425,000 daltons and an average poly(A) isostich of 32 bases. The poly(A) + RNA also represents 2.5% of the total RNA from early growth phase cells and has a modal MW of 360,000 daltons and an average poly(A) isostich of 38 bases. The poly(A) + RNA from spores and 2-hr plants contains a structure resistant to RNases T₁, T₂, and A, which can be labeled with ³²PO₄ and which will bind to DBAE-cellulose. These characteristics strongly suggest that both the zoospore poly(A) + RNA and the 2-hr cell poly(A) + RNA are capped at the 5′ end; and, hence, it is unlikely that capping is involved in the control of protein synthesis during germination.Approximately 80% of the poly(A) + RNA of the spore is located in the membrane-enclosed ribosomal nuclear cap, and more than 90% of the poly(A) + RNA within the cap is found in the 80S monoribosome and heavier fractions.Synthesis of new poly(A) + RNA occurs very early during zoospore germination, and the labeled poly(A) + RNA rapidly enters the newly organized polysomes. The labeling data for early germination also suggest that cytoplasmic polyadenylation occurs.     

The effect of renal vasodilation and hypotonic volume expansion on water excretion in dogs after anesthesia and surgery

The possible effects of renal vasoconstriction from anesthesia and surgery on water excretion after hypotonic volume expansion (HVE) were studied in 18 well conditioned anesthetized dogs, with and without the infusion of phenoxybenzamine and acetylcholine into the renal artery of the cannulated kidney. In 6 dogs (Group 1 - Control) whose renal artery was infused with isosmotic saline, HVE resulted in a bilateral increase in GFR and UV (p < .05). ERPF, Cosm, C_H2O, U_NaV, U_KV, RBF, RVR and MAP did not change significantly. In 6 other dogs (Group 2), whose cannulated kidney was infused with phenoxybenzamine 50 μg/min before and during HVE, GFR increased on the infused side while CH₂O and UV increased bilaterally (p < .05). ERPF, Cosm, U_NaV, U_KV, RBF, RVR and MAP were not affected significantly. The addition of ADH, 2 mu/min into the phenoxybenzamine infusate, decreased ERPF, RBF and RVR bilaterally and CH₂O on the infused side (p < .05). It had no effect upon GFR, Cosm, U_NaV, U_KV and MAP. In another 6 dogs, (Group 3), whose cannulated renal artery was infused with acetylcholine (20 μg/min) before and during HVE, C_H2O, UV and RVR increased bilaterally (p < .05). ERPF and RBF decreased bilaterally (p < .05), whereas GFR, Cosm, U_NaV and MAP were unaffected. U_KV decreased on the infused side (p < .05). The addition of ADH (2 mu/min)_into the acetylcholine infusate, decreased C_H2O bilaterally and increased Cosm and U_KV on the control side (p < .05). It had no effect on ERPF, GFR, UV, U_NaV, RBF, RVR and MAP. These observations suggest that anesthesia and surgery produce renal vasoconstriction and this together with increased ADH release, interfere with water excretion by the kidney. Previous renal vasodilation prevents these influences of anesthesia and surgery.     

Muramic Acid Assay in Sediments

An improved chromatographic assay for muramic acid which is sufficiently sensitive for marine sandy sediments is described; it involves acid hydrolysis, thin-layer chromatography, and gas-liquid chromatography.     

Chromium oxalate: A new spin label broadening agent for use with thylakoids

Potassium tris(oxalato)chromate(III) trihydrate (chromium oxalate) has been shown to be a more useful broadening agent than potassium ferricyanide for the spin label 2,2,6,6-tetramethylpiperidine-N-oxy-4-amine (Tempamine) in thylakoid suspensions. Our data show that chromium oxalate is less permeable than ferricyanide, does not inhibit thylakoid electron transport or photophosphorylation, and is not photoreduced by thylakoids.