The Bioperl toolkit: Perl modules for the life sciences

The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.     

Experimental double infection of Biomphalaria glabrata snails with Angiostrongylus cantonensis and Schistosoma mansoni

Summary Two groups of Biomphalaria glabrata snails primarily infected with Angiostrongylus cantonensis were secondarily exposed to infection with Schistosoma mansoni. To investigate any antagonistic effect of a first infection on a superimposed one and to compare to singly and non-infected snails, a series of experiments was undertaken in which snails were individually exposed, variously, to 1,000 and 2,000 first-stage larvae of A. cantonensis and then to 5 and 10 miracidia of S. mansoni 1 day and 3 weeks later.Snails became infected with S. mansoni in both groups of snails with double infections and shed cercariae after the same incubation period as in the singly infected groups. The number of snails shedding cercariae simultaneously was similar in single and double infection groups during the first two weeks of shedding, after which this number decreased somewhat in doubly infected groups. Snails with double infection showed higher cumulative mortality rates than in snail groups with single infection with either A. cantonensis or S. mansoni. Therefore, initial infection of B. glabrata with A. cantonensis produced no inhibitory or retarding effect on subsequent infection of snails with S. mansoni.

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Zusammenfassung Zwei Gruppen der Süßwasserschnecke Biomphalaria glabrata, die zuvor mit 1000 bzw. 2000 ersten Larven von Angiostrongylus cantonensis pro Schnecke infiziert worden waren, wurden zur Feststellung eines eventuellen antagonistischen Effekts zwischen beiden Parasiten, einen Tag und drei Wochen später mit 5 bzw. 10 Miracidien von Schistosoma mansoni infiziert. Nicht infizierte und mit jeweils nur einer der beiden Parasitenarten infizierte Schnecken dienten als Kontrolle.In beiden doppelt infizierten Gruppen ging die S. mansoni-Infektion sehr gut an, und die Ausscheidung von Cercarien begann nach der gleichen Entwicklungszeit wie bei den nur mit S. mansoni infizierten Kontrollgruppen. Die Anzahl Cercarien ausscheidender Schnecken war in den beiden ersten Wochen bei den jeweils einzeln und doppelt infizierten Gruppen sehr ähnlich, während sie sich in der Folgezeit in den doppelt infizierten Gruppen rasch verminderte. In Gruppen mit Doppelinfektion zeigte sich eine höhere Mortalität als bei den jeweils nur mit A. cantonensis oder S. mansoni infizierten Schnecken. Eine Beeinflussung der Entwicklung von S. mansoni durch die vorausgegangene Nematodeninfektion konnte nicht nachgewiesen werden.

     

Polymere imidazolcarbonsäuren, 2. Über das schwermetallionenbindungsvermögen von chelatharzen mit 4,5-sicarboxyimidazolyl-gruppen

The swelling behaviour, the time-dependence of the uptake of Cu²⁺-ions, and the pH-dependence of the uptake of Cu²⁺-, Ni²⁺-, Cd²⁺-, Zn²⁺- and Mg²⁺-ions of crosslinked poly[1-(4,5-dicarboxy-1-imidiazolyl)ethylene] ( 1 ) and poly{1-[p-(4,5-dicarboxy-2-imidazolyl)phenyl]ethylene} ( 2 ) were investigated. Both resins have a high selectivity for heavy metal ions. For resins 1 the uptake of heavy metal ions in the presence of an excess of EDTA was studied. Furthermore the possibility to remove Hg²⁺-ions from aqueous alkalichloride solutions by resin 1 was investigated.     

Über poly[1-N-(4-isothiocyanatophenyl)carbamoyloxy-methyläthylen-co-1-hydroxymethyläthylen]e als träger zur immobilisierung von papain

Poly[1-N-(4-isothiocyanatophenyl)carbamoyloxymethylethylene-co-1-hydroxymethylethylene]s ( 5a – c ) were obtained by reaction of poly(allyl alcohol) ( 2 ) with 4-isothiocyanatophenyl isocyanate ( 3 ). In some cases 1,4-phenylenediisocyanate ( 4 ) was used as crosslinking agent. These reactive carriers were found to be suitable to immobilize enzymes by covalent bonds. The binding abilities of these polymers 5a – e for butylamine, 3,4-dichloroaniline, peptone (from lactalbumin), and papain were investigated. The enzymatic activity, the pH-optimum, the apparent Michaelis-constant K_M(app), and the activity dependance on temperature were determined for the immobilized papain.     

New catalysts for the oxidative polymerization of 2,6-dimethylphenol, 2. Copper complexes containing the dicyanoethenedithiolatocuprate structure as the ligand

It was found that the reaction of 1,2-dicyano-1,2-ethenedithiolate, resp. of bis(1,2-dicyano-1,2-ethenedithiolato)cuprate(2-), with Cu²⁺ does not lead to copper bis(1,2-dicyano-1,2-ethenedithiolato)cuprate(2-) dihydrate ( 1a ) as described in the literature but to a reaction product which has a complex structure containing mainly Cu⁺. This compound as well as complexes with the same ligand, but with Cu⁺, Cu²⁺ or Cu³⁺ as the central atom, were synthesized and tested with and without added cuprous chloride as catalysts for the oxidative polymerization of 2,6-dimethylphenol. Included in this investigation were some copper complexes with the isomeric ligand 2,2-dicyano-1,1-ethenedithiolate.     

Amphotere ionenaustauscher, 5

Amphoteric ion exchangers with uniform structure were obtained by copolymerization of aziridinyl monomers followed by alkaline saponification of the ester groups of the polymers. The following compounds were copolymerized: Diethyl 2,4-di(1-aziridinyl)glutarate ( 1 ) with either diethyl (1-aziridinyl)succinate ( 4 ), diethyl (1-aziridinyl)fumarate ( 5 ) or dimethyl (1-aziridinylmethyl)succinate ( 6 ); diethyl ester of 3,3′-(1,4-phenylene) and 3,3′-(1,3-phenylene)di[3-(1-aziridinyl)propionic acid] ( 2a ) and ( 2b ), respectively, with either methyl (1-aziridinyl) acetate ( 7 ) or methyl (1-aziridinyl)propionate ( 8 ); dimethyl 3,6-di(1-aziridinyl)cyclohexane-1,2-dicarboxylate ( 3 ) with dimethyl 6-(1-aziridinyl)cyclo-2-hexene-1,2-dicarboxylate ( 9 ). Further the dioctylester of 3,3′-(1,4-phenylene)di[3-(1-aziridinyl)propionic acid] ( 10 ) was homopolymerized. The properties of the amphoteric resins were investigated. In particular the binding ability for Cu^2⊕, Ni^2⊕, Zn^2⊕, and Mg^2⊕ ions and the swelling ability were studied as function of the pH of the solution. The uptake of CU²⁺ ions was determined as a function of time. An average capacity for Cu²⁺ ions of 2,5 to 3,75 mmol/g of dry resin was found at pH 5,5–6.     

Clonogenicity of normal and malignant hematopoietic progenitor cells after exposure to synthetic alkyl-lymphospholipids

Summary Alkyl-lysophospholipids (ALP) are synthetic analogues of natural lysophosphatidylcholine and represent a new class of anti-tumor agents. They are cytotoxic in vitro with a high selectivity for neoplastic cells which, in contrast to normal cells, lack an alkyl-cleavage enzyme to degrade the adsorbed ALP molecules. As ALP accumulates, it interferes with normal membrane phospholipid turnover and eventually causes disruption of membrane integrity. To evaluate the potential value of ALP in eliminating leukemic cells from remission marrows prior to autologous transplantation, we tested the effect of various ALPs on the clongenicity of normal human marrow cells and on promyelocytic leukemia HL-60. A remarkable difference in the dose response to ALP of normal marrow cells an HL-60 was observed. After an incubation period of 24 h, the same inhibition of clonogenicity in HL-60 occurred at ALP concentrations 4 times lower than in normal marrow cells. Reducing the exposure time to 6 h enhanced the selectivity further: whereas HL-60 colonies were nearly completely inhibited at 16 g ALP/ml, more than 50% of normal CFU-c and BFU-E were recovered after incubation with 48 g/ml. No further increase in selectivity was achieved by changing the incubation temperature. Both thioether- and alkyl-analogues were active and no difference was observed between methoxy- and acylamino-substituted ALPs. We conclude that this selective cytotoxicity makes ALP compounds worth further study as purging agents in autologous bone marrow transplantation programs.Supported by the Deutsche Forschungsgemeinschaft An 111/3     

Ornithine decarboxylase in motoneurons during regeneration

The activity of ornithine decarboxylase, the rate-limiting enzyme in polyamine synthesis, was assayed in the isolated facial nucleus of the rat at various times after axotomy of the facial nerve. In addition, it was measured 24 h after the second of a series of two lesions (conditioning lesion design) with various times between the first and second operations. Ornithine decarboxylase activity was found to increase 8 h after nerve transection and was maximum after 24 h (300% of control). Thereafter the activity declined to subnormal levels where it remained for several weeks. Ornithine decarboxylase activity did not increase again when a second axotomy was made 2 weeks after the first lesion. However, ornithine decarboxylase did respond to the second axotomy if it was carried out 3 weeks after the first lesion. Histochemical localization of ornithine decarboxylase demonstrated that the increase in enzyme activity was mainly confined to the perikarya of the motoneurons. These data suggest that this enzyme is somehow involved in triggering the "regeneration program" and clearly indicate that at least some aspects of the neuronal response to axotomy are not further stimulated by a conditioning lesion.     

Polymyxin B,a selective inhibitor of protein kinase C,diminishes the release of noradrenaline and the enhancement of release caused by phorbol 12,13-dibutyrate

Summary Slices of the rabbit hippocampus were labelled with ³H-noradrenaline, superfused continuously with a modified Krebs-Henseleit medium containing the uptake inhibitor cocaine and stimulated electrically (2 ms, 3 Hz, 24 mA, 5 V/cm). Phorbol 12,13-dibutyrate (PDB), a potent activator of protein kinase C (PKC), strongly enhanced the electrically-evoked overflow of tritium. In contrast, polymyxin B, a relatively selective inhibitor of PKC, diminished the evoked tritium overflow in a time-and concentration-dependent manner. The enhancement of the evoked overflow of tritium caused by PDB was strongly reduced in the presence of polymyxin B (100 mol/l). These results suggest 1. that PKC may be involved in the physiological mechanism of action-potential-induced noradrenaline release from noradrenergic nerve terminals and 2. that the PDB-induced enhancement of noradrenaline release may be due to a direct activation of PKC.Abbreviations PKC protein kinase C - PDB phorbol 12,13-dibutyrate - TPA 12-O-tetradecanoyl 13-acetate     

Traumatic aneurysms of the descending thoracic aorta

From July 1979 to December 1985 we observed 51 patients with traumatic lesions of the descending thoracic aorta. Twenty-nine had acute ruptures, mostly accompanied by multiple injuries, and 27 had to be operated upon immediately. Twenty-two patients (19 males, 3 females) had chronic traumatic aneurysms of the descending thoracic aorta (more than six weeks after trauma). Mean age at the time of trauma was 24 years. Mean age at time of surgery was 36.5 years. Twelve patients were symptomatic. All were treated surgically. At surgery, complete aortic disruption was found in 15 patients and partial rupture in seven. We did not use aortic shunting of any kind, only aortic cross-clamping. Hypertension was controlled by intravenous drug infusion. The ruptured aortic segment was replaced in all cases by prosthetic Dacron graft. There were no operative deaths. One patient (age 77) died 11 weeks after surgery from multiple organ failure. One case of postoperative paraplegia was observed. This patient recovered almost completely from his neurological deficit.