Interactive gene networks with KNIT.

SUMMARY: KNIT is a web application that provides a hierarchical, directed graph on how a set of genes is connected to a particular gene of interest. Its primary aim is to aid researchers in discerning direct from indirect effects that a gene might have on the expression of other genes and molecular pathways, a very common problem in omics analysis. As such, KNIT provides deep contextual information for experiments where gene or protein expression might be changed, such as gene knock-out and overexpression experiments. AVAILABILITY AND IMPLEMENTATION: KNIT is publicly available at http://knit.ims.bio. It is implemented with Django and Nuxtjs, with all major browsers supported. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

COPI-mediated transport.

COPI-coated vesicles are protein and liquid carriers that mediate transport within the early secretory pathway. In this Topical Review, we present their main protein components and discuss current models for cargo sorting. Finally, we describe the striking similarities that exist between the COPI system and the two other characterized types of vesicular carriers: COPII- and clathrin-coated vesicles.

Interpretation of thyroid function tests.

The development of radioimmunoassays over the past 20 years has expanded our knowledge of thyroid physiology and improved our management of thyroid disease. The use of these tools in neonatal screening for congenital hypothyroidism alone has reduced the incidence of mental retardation in the industrialized world. Based on an accurate physical examination, the judicious use of immunoassays for thyroxine, triiodothyronine, and thyrotropin and the use of thyroglobulin and thyroid microsomal antibodies will allow the general physician to confidently delineate common thyroid disorders in the great majority of patients. The additional use of an ultrasensitive thyrotropin assay, thyroid scans, and fine-needle aspiration biopsy will complete the accurate diagnosis of the great majority of thyroid diseases. The ultrasensitive thyrotropin assay may become the universal thyroid function test. The major pitfalls in the use of these tests lies in the variable effect chronic illness has on the most frequently used tests: thyroxine and triiodothyronine. Tests for these thyroid hormones, which in the relatively well outpatient are highly accurate, may in the ill, hospitalized patient become very misleading.

Induction of angiogenesis by mixtures of two angiogenic proteins, angiogenin and acidic fibroblast growth factor, in the chick chorioallantoic membrane.

The chick chorioallantoic membrane assay was employed to assess the angiogenic response induced by mixtures of human angiogenin with bovine heparin-binding acidic fibroblast growth factor. Statistical evaluation of data accumulated at several molar ratios of the two proteins indicate that the angiogenic activity observed is neither an additive nor a synergistic resultant of the activities of the proteins separately. The possibility exists, however, that at an approximately 1:1 mole ratio an apparent inhibitory effect can be observed. Mechanisms which could underlie such observed effects are discussed.

Angiogenic activity of human tumor plasma membrane components.

Plasma membranes from the human colon adenocarcinoma cell line HT-29 have been isolated and examined for the presence of angiogenic activity. Membrane-associated macromolecules extracted with Triton X-100 were fractionated on immobilized wheat germ agglutinin. The fraction which bound specifically (about 200 ng of protein/mL packed cells) was highly angiogenic when assayed on the chick embryo chorioallantoic membrane. As little as 0.2 ng of this human tumor derived material consistently induced neovascularization. Similarly, 1-2 ng of this material implanted into the rabbit cornea induced new vessel growth (5-8 mm) within 10 days. The plasma membranes of eight other human tumor lines were examined for angiogenic activity. For each, the wheat germ agglutinin bound material induced neovascularization at the low nanogram level. In contrast, the wheat germ agglutinin bound material derived from purified plasma membranes of two normal human diploid fibroblast cell lines failed to induce an angiogenic response on the chick chorioallantoic membrane, even at microgram levels.

Amino acid sequence of human tumor derived angiogenin.

The amino acid sequence and disulfide bond pairing of human tumor derived angiogenin, the first tumor angiogenesis factor to be isolated in pure form from human sources, have been determined by conventional sequencing techniques adapted and applied to nanomole and subnanomole levels of material. Angiogenin, obtained from conditioned media of a human colonic adenocarcinoma cell line, is a single-chain protein consisting of 123 amino acids with the following sequences: less than Glu1-Asp-Asn-Ser-Arg-Tyr-Thr-His- Phe-Leu-Thr-Gln-His-Tyr-Asp15-Ala-Lys-Pro-Gln-Gly-Arg-Asp-Asp- Arg-Tyr-Cys-Glu-Ser-Ile-Met30- Arg-Arg-Arg-Gly-Leu-Thr-Ser-Pro-Cys-Lys-Asp-Ile-Asn-Thr- Phe45-Ile-His-Gly-Asn-Lys-Arg-Ser -Ile-Lys-Ala-Ile-Cys-Glu-Asn-Lys60-Asn-Gly-Asn-Pro-His-Arg-Glu-Asn -Leu-Arg-Ile -Ser-Lys-Ser-Ser75 -Phe-Gln-Val-Thr-Thr-Cys-Lys-Leu-His-Gly-Gly-Ser-Pro-Trp-Pro90-Pro -Cys-Gln-Tyr -Arg-Ala-Thr-Ala -Gly-Phe-Arg-Asn-Val-Val-Val105-Ala-Cys-Glu-Asn-Gly-Leu-Pro-Val- His-Leu-Asp-Gln-Ser-Ile-Phe120-Arg-Arg-Pro123-OH. Three disulfide bonds link the half-cystinyl residues 26-81, 39-92, and 57-107. The sequence is homologous to that of the pancreatic ribonucleases with 35% identity and many of the remaining residues conservatively replaced. Similarities are especially apparent around the major active-site residues His-12, Lys-41, and His-119 of ribonuclease which are conserved as are three of the four disulfide bonds.(ABSTRACT TRUNCATED AT 250 WORDS)

Isolation and characterization of angiogenin, an angiogenic protein from human carcinoma cells.

The first human tumor derived protein with in vivo angiogenic activity to be obtained in pure form has been isolated from serum-free supernatants of an established human adenocarcinoma cell line (HT-29) and named angiogenin. It was purified by cation-exchange and reversed-phase high-performance liquid chromatography; the yield was approximately 0.5 microgram/L of medium. Biological activity of angiogenin was monitored throughout purification by using the chick embryo chorioallantoic membrane assay. Statistical evaluation demonstrates that it displays activity in this system with as little as 35 fmol per egg. Moreover, only 3.5 pmol is required to induce extensive blood vessel growth in the rabbit cornea. The amino acid composition of this basic (isoelectric point greater than 9.5), single-chain protein of molecular weight approximately 14 400 has been determined. The amino terminus is blocked, and the carboxyl-terminal residue is proline.

The role of the student ward in the medical clerkships.

The authors describe the structure and the development of an internal medicine clerkship designed to promote proficiency in the process of clinical reasoning. The clerkship is centered around a "student ward" in which the student assumes the role of primary physician. The environment provides not only close supervision and counsel but also allows a great deal of autonomy as students embark on their first clinical medicine rotation. The student ward offers a structured environment where the emphasis is on in-depth clinical exposure and the acquisition of clinical knowledge in a manner consistent with the principles of problem-based learning. Breadth of clinical exposure is accomplished through a variety of educational approaches.

Tumor-derived angiogenesis factors from rat Walker 256 carcinoma: an experimental investigation and review.

Angiogenesis, the process of developing a hemovascular network, is an essential feature of the growth of solid tumors, and is induced by factors secreted by tumor cells. Assay procedures suitable for the investigation of angiogenesis, and for the screening of angiogenesis factors during purification are reviewed; and a number of reports describing the purification of angiogenesis factors, primarily from the rat Walker 256 carcinoma as starting material, are discussed. Work from the authors' laboratory is also presented. Walker 256 cells grown in large-scale culture were the source of a reproducible and homogeneous source of angiogenic material. Factors secreted by these cells were isolated by a series of chromatographic steps. Ion exchange chromatography on carboxymethyl-Sephadex produced two active fractions, one of which was fractionated into several macromolecular species by lectin affinity and hydrophobic adsorption chromatography. The other gave a high mol.wt, active fraction that was resolved into a low mol.wt, active component and a non-angiogenic but possibly carrier molecule with a mol.wt of 140,000. While none of the angiogenic factors were identified chemically, the results demonstrate the existence of both high and low mol.wt tumor-secreted angiogenic substances, confirming the hypothesis for tumor-induced angiogenesis and predicting potential means to interfere with the process of tumor growth.

Formamide-induced dissociation and inactivation of Escherichia coli alkaline phosphatase. Metal-dependent reassociation and restoration of activity from isolated subunits.

Alkaline phosphatase from Escherichia coli has been reversibly dissociated by treatment with low concentrations of formamide. The monomer retains the capacity to bind metals and to regenerate catalytically active dimer that is identical with the native dimeric enzyme. The rate and extent of dissociation of dimer to monomer depend upon pH, ionic strength, temperature, formamide concentration, and enzyme-bound metal. Under appropriate experimental conditions, reassociation can be greatly slowed, allowing the properties of the monomer to be examined in solution. The formamide-induced apo monomer has a conformation distinct from that of the dimer and zinc- or cobalt-containing monomers. The monomer tightly binds 1 mol of zinc or cobalt in a metal-binding site altered from those of the dimer but is catalytically inactive. pH, ionic strength, and formamide concentration all influence reassociation. Hydrophobic forces are implicated as important in subunit interactions. The effect of metal content on the dissociation--reassociation process underscores the essential role that metals play in maintaining enzyme tertiary structure and reveals a new role in stabilizing the quaternary structure.

Renal tubular maximum for magnesium in normal, hyperparathyroid, and hypoparathyroid man.

Magnesium infusions were carried out in normal subjects and patients with hypoparathyroidism and primary hyperparathyroidism in order to determine if a tubular maximum for magnesium (TmMg) existed in man and what influence endogenous parathyroid hormone played in renal magnesium handling. The increase in the serum ultrafiltrable magnesium concentration during the magnesium infusions resulted in an increase in urinary magnesium excretion. A TmMg of 1.4 mg/100 ml GF/1.73 m2 was found in the normal subjects under basal conditions. Similarly, TmMg values of 1.4 and 1.3 mg/100 ml GF/1.73 m2, were found in hypoparathyroid and primary hyperparathyroid subjects, respectively. Both were present under basal conditions and neither differed significantly from normal. It is concluded that a TmMg is present in man and that endogenous parathyroid hormone does not appear to play a significant physiological role in renal magnesium homeostasis.

A proposed cellular mechanism for calcium transport in the intestinal epithelial cell.

Intracellular transport of calcium from the apical to the basal-lateral region of the intestinal epithelial cell was investigated in duodenum from normal fed, fasted, and calcium-loaded rats. The process was followed with time using electron microscopy with potassium pyroantimonate to precipitate calcium. The observations made were subjected to morphometric analysis. The specificity of the method was demonstrated in the villus cell by resistance to microincineration and by absence of deposits following exposure to EGTA. Using this method calcium was seen in cells from calcium-fed rats at the microvillus border, in the Golgi zone, and within the internal compartments of the mitochondria. In cells from fasted rats calcium was not seen. Mitochondria were found largely at the apex of the cell and were free of detectable calcium. By 5 min, in the cells of fasted rats given a calcium load, the calcium had reached the Golgi apparatus and the inner mitochondrial compartment. After 15 min mitochondria were heavily loaded with calcium and had moved to the basal region of the cell. These observations suggest that mitochondria play an important role in absorption of calcium and appear to transport this ion from the apex to the basal region of the cell where entry into the capillaries takes place.

Effect of hypophosphatemia on myocardial performance in man.

Severe hypophosphatemia is associated in man with low intracellular stores of ATP and a set of specific cellular dysfunctions. To investigate whether hypophosphatemia affects myocardial performance, we measured cardiac output by thermodilution and calculated stroke work in seven patients with severe hypophosphatemia before, during and after repletion with an intravenous potassium phosphate solution. Mean left ventricular stroke work for these patients increased from 49.57 to 71.71 g-m per beat (P less than 0.01) at the same or higher afterload whereas pulmonary-artery wedge pressure fell from a mean value of 10.1 to 6.7 torr (P less than 0.02). Return of serum phosphate to normal, therefore, improved myocardial stroke work independently of the Starling effect. The mechanism of this improvement in contractile force is unknown but may be related to intracellular availability of ATP.

Hypercalcemia and hypocalcemia.

This report discusses the various aspects of the hypercalcemic and hypocalcemic disorders. We first describe the physicochemical state of serum calcium and the interpretation of a rise or a fall in total serum calcium. The various diseases associated with alterations in the concentration of serum calcium are presented. The clinical manifestations of the hypercalcemic and hypocalcemic disorders and their management are described.

Kinetic properties of crystalline enzymes. Carboxypeptidase A.

Spectrochemical probes have demonstrated that the conformations of carboxypeptidase A differ in solution and in the crystalline state. Detailed kinetic studies of carboxypeptidase A crystals and solutions now show that the physical state of the enzyme is also a critical parameter that affects this enzyme's function. Thus, for all substrates examined, crystallization of the enzyme markedly reduces catalytic efficiency, kcat, from 20- to 1000-fold. In addition, substrate inhibition, apparent in solution for some di- and depsipeptides, is abolished with crystals, while longer substrates with normal kinetics in solution may exhibit activation with the crystals. The physical state of the enzyme also affects the mode of action of known modifiers of peptidase activity of the enzyme. In solution, addition of benzoylglycine or cinnamic acid markedly increases the rate of hydrolysis of CbzGly-Phe, but, with the crystalline enzyme, their addition hardly alters the activity. This is in accord with the weakening or absence of inhibitory enzyme-substrate binding modes. Kinetic studies on crystals were carried out over a range of enzyme concentrations, substrate concentrations, and crystal sizes, and in all instances the results are in good agreement with the theory developed by Katchalski for enzymes insolubilized by other means. Importantly, these kinetic parameters are determined under conditions which obviate artifacts due to diffusion limitation of substrates or products. The differences in the kinetic behavior of carboxypeptidase crystals, on the one hand, and of their solutions, on the other hand, bear importantly on efforts to interpret the function of the enzyme in structural terms. Hypothetical modes of substrate-enzyme interaction, generated by superimposing substrate models on the crystal structure of carboxypeptidase to stimulate kinetics in solution, have failed to detect all of these changes which affect inhibitory or activating binding modes.