Nothing in evolution makes sense except in the light of code biology

This article highlights the potential contribution of biological codes to the course and dynamics of evolution. The concept of organic codes, developed by Marcello Barbieri, has fundamentally changed our view of how living systems function. The notion that molecular interactions built on adaptors that arbitrarily link molecules from different "worlds" in a conventional, i.e., rule-based way, departs significantly from the law-based constraints imposed on livening things by physical and chemical mechanisms. In other words, living and non-living things behave like rules and laws, respectively, but this important distinction is rarely considered in current evolutionary theory. The many known codes allow quantification of codes that relate to a cell, or comparisons between different biological systems and may pave the way to a quantitative and empirical research agenda in code biology. A starting point for such an endeavour is the introduction of a simple dichotomous classification of structural and regulatory codes. This classification can be used as a tool to analyse and quantify key organising principles of the living world, such as modularity, hierarchy, and robustness, based on organic codes. The implications for evolutionary research are related to the unique dynamics of codes, or ´Eigendynamics´ (self-momentum) and how they determine the behaviour of biological systems from within, whereas physical constraints are imposed mainly from without. A speculation on the drivers of macroevolution in light of codes is followed by the conclusion that a meaningful and comprehensive understanding of evolution depends including codes into the equation of life.

Ensuring wholeness: Using Code Biology to overcome the autonomy-heteronomy divide

This paper presents an alternative to Autopoietic Enactivism in the form of a Code Biology-informed account on human sense-making. It demonstrates the possibility of avoiding a dualism between, on the one hand, the autonomy of individual sense-makers and, on the other, the heteronomy of social facts. This is possible because code biological principles are pertinent to different levels of biological and non-biological organization and cut across the organismic self-non-self border. Analytically, one can maintain the overall integrity of an agent as a separable unit of (inter)action while also avoiding an autonomy-heteronomy divide. We therefore emphasise the constitutive role of codified relations that, while irreducible to operational closure, connect the sense-making agent's social interactions to those of other agents. The move grants a central, constitutive role to external norms (or, heteronomy) as altering the internal, embodied integrity of an autonomous agent. Drawing on the case of prosthetics use in amputees, we show that successful integration of a prothesis cannot be reduced to the substitution of a missing limb. Rather, it demands experienced bodily wholeness on the part of the agent which can only be achieved by attuning and adapting to use of a prosthesis while also internalizing social norms and values. It is concluded that many aspects of the living actualize codified relations which incorporate both heteronomous and autonomous traits.

The modularity codes

The hypothesis presented here is that codes as described by Marcello Barbieri are the fundamental principle behind biological modularity. Modularity has been studied in different life science disciplines, especially in the fields of evolution and development, as well as in network biology, yet there is still no consensus on how modularity evolved itself. Modularity is basically the functional integrity of multiple molecular players involved in a common process. Codes as defined by Barbieri describe a tripartite relation involving an adapter molecule connecting two other independent types of molecules to each other in an arbitrary, but semantic manner. This form of interaction goes beyond predictable mere physical or chemical one-to-one interactions and always relates three molecules to each other. A code of three topologically related molecules interacting in a defined order may be considered a minimal module on its own, but when one regards a set of multiple, overlapping tripartite, coded interactions, this paves the way towards logically and functionally consistent coherence of multiple participants of a certain, modular process. A theoretical outline of how to identify and describe such modular structures is given.

Der Mechanismus einer neuen Synthese von Aromaten- und Triolefin-metall-tricarbonylen aus Diolefin-metall-tetracarbonylen

Kinetische Untersuchungen über den Mechanismus der Bildung von Verbindungen L′M (CO)3 (M=Cr, Mo; L′=Aromat, Triolefin) aus LM(CO)4 (L = Norbornadien) belegen, daß die Reaktionsgeschwindigkeit sowohl von der Konzentration als auch von der Art von L′ abhängt. Die Interpretation der Ergebnisse unter Zugrundelegung des Bodenstein- Theorems läßt erkennen, daß als einleitender Schritt der Umsetzung die partielle Lösung der Diolefin-Metall-Bindung in LM (CO)4 anzunehmen ist. Im Fall L′=Triolefin ergibt sich ein additives Geschwindigkeitsgesetz mit einem Term zweiter Ordnung, d. h. hierbei erfolgt primär neben der Dissoziation auch ein direkter Angriff von L′ auf das Zentralatom des Ausgangskomplexes.

Polyethylenimine PEI F25-LMW allows the long-term storage of frozen complexes as fully active reagents in siRNA-mediated gene targeting and DNA delivery

BACKGROUND

Polyethylenimines (PEIs) are synthetic, charged polymers which function as transfection reagents based on their ability to compact DNA into complexes. Recently, PEI-mediated delivery of nucleic acids has been extended towards small interfering RNAs (siRNAs) which are instrumental in the induction of RNA interference (RNAi). Since RNAi represents a powerful method for specific gene silencing, the PEI-based delivery of siRNAs is a promising tool for novel putative therapeutic strategies.

AIM

For therapeutic use, major requirements are the development of formulations which (i) are sufficiently stable in the presence of serum, and which can be (ii) easily and reproducibly manufactured and (iii) stored for a prolonged time with full retention of their integrity and bioactivity. In this paper, we explore the potential of PEI F25-LMW, a low-molecular weight PEI with superior transfection efficacy and low toxicity, towards these goals.

RESULTS

We have systematically analyzed and determined optimal DNA and siRNA complexation conditions with regard to various parameters including buffer concentration, ionic strength, pH and incubation time. As opposed to 22kDa linear PEI (L-PEI), the low-molecular weight (4-10kDa) PEI F25-LMW performs DNA transfection and siRNA gene targeting with identical efficacies in the presence of serum, thus emphasizing its usefulness in vivo. Furthermore, in contrast to other polyethylenimines, PEI F25-LMW-based DNA or siRNA complexes allow freeze/thawing and frozen storage for several months. Their activity is fully retained without requiring specific buffer conditions or the addition of any lyoprotectant. Physicochemical analysis and atomic force microscopy reveal a distinct size pattern with the presence of two complex subgroups and show that frozen PEI F25-LMW complexes remain stable with little increase in complex size, no changes regarding their zeta potential and cytotoxicity, and full retention of nucleic acid protection.

CONCLUSIONS

Frozen PEI F25-LMW-based complexes represent efficient and stable ready-to-use formulations of DNA- or siRNA-based gene therapy products.

Normalization of intraoperative parathyroid hormone does not predict normal postoperative parathyroid function

Background

Intraoperative measurement of intact parathyroid hormone (iPTH) has been used increasingly as a means of confirming complete removal of hyperfunctioning parathyroid tissue. It remains uncertain, however, whether normalization of iPTH levels at operation accurately predicts postoperative values of iPTH.

Methods

Forty-five consecutive patients with primary hyperparathyroidism underwent parathyroidectomy between March and November 1999. Baseline intraoperative iPTH levels were measured before and at manipulation, then subsequently at 5 and 10 min after tissue was removed. Follow-up values were measured at 1- and 3-month intervals.

Results

Before operation the mean(s.d.) iPTH concentration was 211(182) pg ml−1 with a mean serum calcium level of 11·4(1·0) mg dl−1. In all but four patients, the final intraoperative iPTH normalized to absolute values below 60 pg ml−1 (mean 38(36) pg ml−1). One week after operation, serum calcium levels had returned to normal (mean 9·2(0·9) mg dl−1) and this correlated directly with final intraoperative iPTH values when assessed by linear regression analysis (r = 0·373, P < 0·03). By 1 month, all but two patients were normocalcaemic (mean 9·6(0·6) mg dl−1) with a mean iPTH of 81(99) pg ml−1. There was no correlation between the final intraoperative iPTH and postoperative iPTH values as determined by linear regression analysis (r = 0·035, P < 0·881). Both patients with persistent hypercalcaemia at 1 month had appropriate intraoperative decreases in iPTH level.

Conclusion

Although there is significant correlation between intraoperative iPTH levels and postoperative serum calcium levels, this does not hold true for postoperative iPTH levels. There was a 4 per cent failure rate in correcting postoperative calcium levels and a 20 per cent failure rate in normalizing postoperative iPTH levels despite appropriate intraoperative decreases in iPTH.

The role of positron emission tomography in selecting patients with metastatic cancer for adrenalectomy

Metastases to the adrenal glands usually signal disseminated disease. However, isolated metastases do occur that may be curable with adrenalectomy. Functional imaging with positron emission tomography (PET) can differentiate benign from malignant pathology and isolated from disseminated metastases. The purpose of this study was to determine whether PET scanning can influence the outcome of adrenalectomy for metastatic disease. We conducted a retrospective review of eight patients undergoing adrenalectomy for presumed isolated metastatic disease from 1985 through 1997. The patients included six women and two men with an average age of 58 (range, 36-74). Their primary tumors were six lung carcinomas, one renal cell carcinoma, and one colon carcinoma. The adrenal masses were located on the right in six patients, on the left in one, and bilaterally in one. Before operation, all patients were evaluated by chest and abdominal CT. Four patients were also evaluated by PET scan. Six right, one left, and one bilateral adrenalectomies were performed. Associated organ resections included two right partial nephrectomies and one right total nephrectomy, one left partial nephrectomy, two distal pancreatectomies, one splenectomy, and two partial hepatic resections. All eight patients survived operation. There were no major perioperative complications, but one patient required readmission for congestive heart failure. Three of the four patients who did not have PET scanning died from 4 to 48 months after operation with disseminated disease from lung, colon, and renal carcinoma respectively. The remaining patient who did not have PET scanning is alive and well 11 years later. Two of the four patients who had PET scans showing isolated disease are alive at 28 and 43 months after operation, whereas the other two died of disseminated disease at 29 and 36 months after operation. We conclude that 1) adrenalectomy can provide survival benefit in patients with isolated metastases, and 2) PET scanning is useful in confirming isolated metastatic disease and selecting patients for adrenalectomy.

Pancreatic masses: a multi-institutional study of 364 fine-needle aspiration biopsies with histopathologic correlation

Only 15% of primary malignant tumors are confined to the gland at the time of presentation. Fine-needle aspiration (FNA) is valuable in confirming the malignant nature of these unresectable lesions. Benign pancreatic lesions and metastatic neoplasms can also be evaluated by fine-needle aspiration. We undertook a retrospective study to evaluate the efficacy of FNA in assessing pancreatic masses. Three hundred and sixty-four radiologically guided FNAs of the pancreas performed between 1986-1996 were reviewed. Surgical material was also evaluated when available and compared to the FNA material. There were 223 men and 141 women. Their ages ranged from 23-90, with a mean of 64 yr. Two hundred and twelve patients (58%) had primary malignant tumors, 183 had adenocarcinomas, 15 had mucinous cystadenocarcinomas, 12 had neuroendocrine tumors, and 2 had pleomorphic giant-cell carcinomas. Ninety-one (43%) had available surgical material which showed adenocarcinoma. Ninety-one patients (25%) had benign aspirates, including 53 showing benign ductal epithelium, 23 showing pancreatitis/inflammation. 10 showing pseudocysts, and 7 showing serous cystadenomas. Surgical material was available in 24 (26%) of these patients. Two of these showed adenocarcinoma. Sixteen aspirates (4%) were suspicious for malignancy, 13 (81%) of which showed adenocarcinoma on follow-up biopsies. Twenty-two aspirates (6%) showed metastatic neoplasms. Twenty-three (6%) had unsatisfactory specimens. Ten (43%) of these had follow-up biopsies, 3 of which were malignant. FNA of primary benign and malignant pancreatic masses is highly sensitive (98%) and specific (100%). Eighty-one percent of the suspicious lesions showed adenocarcinoma on follow-up biopsy. FNA of metastatic neoplasms to the pancreas is also very accurate. This technique can be useful in avoiding unnecessary surgery.

[Folic acid supply in pregnancy--results of a prospective longitudinal study]

After discussing the problem of folic acid requirements and supply during pregnancy, the results of a longitudinal study on 162 pregnant women are presented. By measuring biochemical and morphological changes in two subgroups (non-substituted vs unspecifically substituted), the necessity of a substitution with folic acid is discussed, as there might be additional requirements for the pregnant and the foetal organism. Concentrations of folic acid in the maternal plasma and in the erythrocytes as well as the segmentation rate and hypersegmentation of the granulocytes show a clear decrease in pregnancy. At the same time there was a significant difference between the subjects substituted and not substituted; the foetus and newborn levels were much higher than their mothers' concentrations. Moreover, there was a correlation between red cells folic acid levels in the last trimester and duration and outcome of pregnancy. These results indicate a substitution with folic acid for certain populations in pregnancy, which are highlighted.

Estrogen receptor in normal and neoplastic human thyroid tissue

Clinical evidence suggests the possible influence of estrogen on the biologic behavior of thyroid neoplasm. In this study we evaluated the distribution and characteristics of intracellular receptors for estrogen in normal and neoplastic thyroid tissue obtained from 54 patients. Forty-two percent of all specimens assayed by the protamine sulfate precipitation technique had a detectable intracellular binding site for estrogen. Differentiated carcinomas (eight of eight) and adenomas (seven of nine) had high incidences of receptors compared with goiter (five of 23) and normal thyroid (three of eight). However, there were no detectable receptors for estrogen in medullary carcinomas of the thyroid (0 of six). Also, carcinomas and adenomas had higher receptor contents than did goiter and normal differentiated thyroid tissue. There was no significant difference in the affinity of estrogen for receptors among the different histologic groups. There were both 4S and 8S receptor types, which were specific for estrogen. The binding of estrogen to thyroid tissue and differentiated neoplasm originating from thyroid tissue were comparable to the binding of estrogen to other hormone-dependent normal and neoplastic tissues.

Effects of protease inhibitors on coagulation abnormalities in acute canine pancreatitis

Coagulation abnormalities associated with severe pancreatitis were studied in 24 dogs. Group I consists of six control subjects who had duodenotomy alone. Group II consists of six dogs with pancreatitis induced by bile injection ( lcm3 /kg) into the pancreatic duct. The six dogs in Group III and the six in Group IV were given aprotinin (trasylol) 1.0 mg/kg and S-2441 (10mg/kg), a new synthetic protease inhibitor, respectively. These were given over 10 minutes by intravenous infusion, 20 minutes after bile induced pancreatitis. Blood was drawn for amylase, prothrombin time (PT), partial thromboplastin time (PTT), fibrinogen, and platelets, in addition to markers for hypercoagulation, fibrinopeptide A, antithrombin III, and markers for fibrinolysis, B beta 15-42 immunoreactive peptides and alpha 2 antiplasmin at baseline, 30 minutes, 1 hour, 3 hours, 6 hours, and daily for 3 days after injection of bile or duodenotomy. There was no significant difference in PT, platelets, antithrombin III, and fibrinopeptide A among the four groups. Fibrinogen levels and PTT were minimally elevated in animals with bile induced pancreatitis, but these changes reached significance only at 24 hours and 48 hours, respectively (P less than 0.05). Immunoreactive B beta 15-42 became elevated at 30 minutes indicating fibrinolysis in animals with pancreatitis, and these changes were significant compared with Group I control subjects (P less than 0.05) throughout the study. Levels of alpha 2 antiplasmin were decreased in Group II animals with pancreatitis, which also suggests fibrinolysis. Amylase was elevated in Group II animals with pancreatitis (P less than 0.05).(ABSTRACT TRUNCATED AT 250 WORDS)

Metabolism of sulfated glycosaminoglycans in rat hepatocytes. Synthesis of heparan sulfate and distribution into cellular and extracellular pools

Primary cultures of rat hepatocytes grown in a serum-free medium supplemented with [35S]sulfate synthesize 35S-labelled glycosaminoglycans at an almost constant rate for 58 h. Approx. 57% of the newly synthesized 35S-labelled glycosaminoglycans remain within the hepatocytes, approx. 30% become associated with the cell surface and only 13% are secreted into the medium. The amount of cell-surface-associated 35S-labelled glycosaminoglycans became constant within 36 h, whereas no equilibrium was reached in the intra- and extracellular pool. During a 24 h chase more than 50% of the intracellular and cell-surface-associated 35S-labelled glycosaminoglycans disappears, more than 80% of this material is degraded and radioactivity is recovered as inorganic sulfate. A minor part is released into the medium in a macromolecular form. Heparan sulfate accounts for more than 95% of the 35S-labelled glycosaminoglycans in each of the three pools. It is distinguished from heparan sulfates from other sources by the presence of unsubstituted glucosamine residues. In all three pools, heparan sulfate chains of mean molecular weights between 24 000 and 30 000 are part of an alkali labile proteoglycan. Intra- and extracellularly, however, part of the heparan sulfate appears to have little, if any, protein attached. Hepatocytes contain heparan sulfate-degrading endoglycosidase activity, which may contribute to the variation of molecular weights observed for the heparan sulfate.

Homologous low density lipoprotein does not affect proteoglycan metabolism of cultured skin fibroblasts and arterial smooth muscle cells

The relevance of lipoprotein-glycosaminoglycan interactions on the proteoglycan metabolism was investigated. The following results were obtained: 1) Biosynthesis of [35S]proteoglycans by cultured human skin fibroblasts and their distribution to different compartments are neither affected by preincubation of the cells with homologous LDL nor by their presence. The internalisation of LDL was evidenced by a marked depression of [14C]cholesterol synthesis from [1-(14)C]-acetate. 2) Under the conditions of endocytosis experiments the formation of insoluble proteoglycan-LDL complexes is insignificant. Endocytosis and degradation of exogenous proteoglycans by skin fibroblasts or arterial smooth muscle cells proceed at normal rates in the presence of low or excess LDL concentrations. 3) From the results it may be concluded, that internalized LDL and their degradation products neither influence the synthesis and distribution of sulfated proteoglycans nor control expression and function of proteoglycan specific cell surface receptors.

Effect of lectins on the metabolism of sulfated glycosaminolycans in cultured fibroblasts

A short exposure of human skin fibroblasts to Concanavalin A and wheat germ agglutinin led to an intra- and extracellular accumulation of sulfated glycosaminoglycans. The intracellular accumulation was caused by an impaired degradation of sulfated glycosaminoglycans. The increase of extracellular and cell surface associated 35S-labeled proteoglycans could be ascribed to a lectin-mediated inhibition of endocytosis of these polysaccharides. Results obtained with mono- and divalent Concanavalin A derivatives were in agreement with the view that lectins inhibit endocytosis of sulfated proteoglycans by binding to the cell surface receptors specific for these polysaccharides. Proteoglycans secreted by fibroblasts formed precipitable complexes with Concanavalin A. Complex formation reduced markedly the uptake of the proteoglycan. All effects on glycosaminoglycan metabolism mediated by Concanavalin A and wheat germ agglutinin could be prevented by methyl alpha-D-mannoside and N-acetylglucoseamine, respectively.

Endocytosis of sulphated proteoglycans by cultured skin fibroblasts

1. Human skin fibroblasts internalize homologous sulphated proteoglycans by adsorptive endocytosis. Endocytosis rate is half maximal when the concentration of the proteoglycans is 0.1 nM. At saturation, a single fibroblast may endocytose up to 8 X 10(6) proteoglycan molecules/h. 2. The kinetics of prote;glycan binding to the cell surface suggest the presence of 6 X 10(5) high-affinity binding sites per cell. The bulk of sulphated proteoglycans associates to low-affinity binding sites on the cell surface. 3. Glycosaminoglycans and other anionic macromolecules inhibit endocytosis of sulphated proteoglycans non-competitively. The lack of interaction of glycosaminoglycans with the cell-surface receptors for sulphated proteoglycans suggests that the protein core of proteoglycans is essential for binding to the cell surface. 4. The effects of trypsin, cell density, serum concentration and medium pH on endocytosis and degradation of endocytosed sulphated proteoglycans is described. 5. A comparison of the number of the high-affinity binding sites and the number of molecules endocytosed with respect to time suggests a recycling of the proteoglycan receptors between the cell surface and the endocytotic vesicles and/or the lysosomes.

Foliar Iron Spray Potentiates Growth of Seedlings on Iron-free Media

Growth of bean (Phaseolus vulgaris cv. ;Brittle Wax') seedlings in iron-free media caused large reductions in root size and dye reduction capacity. Shoot growth was also severely retarded and the classical symptoms of chlorosis were observed. A single prophylactic spray of FeSO(4), applied to the primary leaves of 7-day seedlings, enabled subsequent growth to equal that obtained when iron was continuously supplied to the roots over a 12-day period, although chlorophyll levels were lower. By adding a silicone-based surfactant to FeSO(4) spray solutions, the burn damage normally caused to seedlings by such sprays was largely eliminated and the irreversible adsorption of iron increased. Foliar spray of an iron chelate (ferric ethylenediaminedi (o-hydroxyphenylacetic acid)) were less effective than those of FeSO(4).

A naturally occurring Cu-thionein in Saccharomyces cerevisiae

A naturally occurring monodisperse Cu-thionein was prepared using ammonium sulfate precipitation followed by ion exchange (DEAE 23) and gel chromatography (Sephadex G-75). The chromatographic steps were repeated at least twice, or until the Cu-thionein remained homogeneous when subjected to analytical polyacrylamide disc electrophoresis. The molecular weight of this copper protein was 9500+/-500. Up to 24.3% cysteine residues were determined, indicating the relationship to the metallothioneins. Aromatic amino acids were virtually absent, while there were about three times as many acidic amino acid residues, including aspartate and glutamate, as in metallothioneins. 10 g atoms of Cu were measured per mole of protein. The copper binding strength of thionein was extremely high. Displacement by protons (pH 1.5) and gel chromatography or dialysis employing EDTA were not effective. Dialysis against diethyldithiocarbamate produced a protein essentially free of copper. Both the ultraviolet properties and the circular dichroism measurements proved identical with those properties reported for artificially prepared Cu-thionein (see ref.[1]. The major absorption was in the far ultraviolet region with a weak shoulder at 270 nm attributable to copper charge-transfer transititions. 6 Cotton extrema were seen at 213, 283 and 302 nm (negative) and 245, 328 and 359 nm (positive). The possible role of Cu-thionein as an electron transport system was discussed.