Threading Mechanism Research Articles

Efficient preparation of glycoprotein hormones lacking an α-subunit oligosaccharide

The oligosaccharide on α-subunit loop 2 (α2) is needed for full glycoprotein hormone efficacy. Efforts to prepare glycoprotein hormone antagonists usually involve removing the α2 oligosaccharide and are hampered by its requirement for efficient heterodimer secretion from mammalian cells. Here we show that hormones lacking this oligosaccharide can be produced by treating them at low pH to dissociate the heterodimer and permitting the subunits to re-associate in the presence of peptide N-glycosidase F (PNGase F). Re-assembly of human choriogonadotropin, human follitropin, and bovine lutropin occurred rapidly and efficiently following removal of the α2 oligosaccharide by PNGase F. Consequently, virtually all heterodimers formed in the presence of this enzyme lacked this oligosaccharide. These findings support the notion that heterodimer assembly in vitro occurs by a threading mechanism that is impeded by the presence of the α2 oligosaccharide. This procedure should facilitate the study of glycoprotein hormone structure and function.

Java as a Basis for Direct Mechanical System Control

Java has become a very popular alternative to C++ in a number of application areas. The same properties of Java that make it attractive for use in WWW applets or enterprise computing - portability, more rational syntax than C++, modern features included in the specification, automatic memory management, no pointers - naturally suggest its use for direct control of mechanical systems. Java is already used for many embedded applications and is clearly of value for high and mid-level control system software. Its applicability for lower level control functionality as well is tested here in a mechanical system control context.Two popular environments are tested: Windows-2000 and QNX. The problem of software generation of a pulse-width modulated (PWM) signal is used for the testing. Software-based PWM is very sensitive to timing errors so is a simple, but effective test. An environment that implements a task/state model for control of complex mechanical systems is used as the base for development of the test program. The resulting programs provide control multitasking but are single-threaded internally so do not depend on the threading model or mechanisms used by the Java virtual machine (JVM). They achieve real-time performance through the stylistic restriction to all non-blocking code.The result shows that while Java can be very effectively used for prototyping or instruction, it does not yet provide the predicability needed for reliable direct control of mechanical systems. Direct control is defined such that Java is used for all aspects of control, except for those functions that need native methods. Behavior in QNX is more predictable than in Windows-2000, but even Windows-2000, not designed or marketed as a real time operating system, can be used effectively for initial prototyping and debugging. There are current efforts underway to define real time extensions to Java, but their effectiveness is yet to be tested. Thus, Java is certainly useful for higher level functions of mechanical control systems, but further development is needed to make it fully usable for low-level (sub-millisecond) control of mechanical systems.

Dendronized Molecular Knots: Selective Synthesis of Various Generations, Enantiomer Separation, Circular Dichroism

For the first time, knot molecules (of the amide type) are synthesized, which bear one to three dendritic units of various generations at their periphery. They were obtained through two different routes: i) attachment of dendritic wedges to new mono-, di- and trihydroxy functionalized dodecaamide knots that have been obtained by selective debenzylation of oligobenzyloxy substituted knots, or ii) cyclization of already dendron substituted pyridine-2,6-dicarbonyl dichlorides with an "extended diamine" to directly yield the "tri-dendroknots". The derivatization of knot molecules by functional substituents and even large dendritic units is an important advance in the synthesis and property variation of molecular knots. This holds true in particular for substitution of the pyridine units of the knots, whereas the isophthalic acid units seem not to tolerate larger substitutents, as reflected in lower knot yields. These syntheses also demonstrate knots to be accessible indirectly by substitution of the corresponding mono-, di- and tri-functionalized knot skeleton. An advantage of dendritic "decoration" is the control of solubility and chromatographic behaviour of the molecular knots (knotanes). Suggestions are made about the threading mechanism by supramolecular template effects leading to the formation of amide-based molecular knots. The topological chirality of the new "dendroknots" is shown by efficient enantioseparations (separation factor alpha between 1.22 and 1.48). For this purpose (commercially unavailable) chiral column material of the Chiralpak type was used, in which the chiral component is covalently bonded to the silica gel support. The racemate splittings provide additional evidence for the knotted structure, as all other conceivable isomers such as macromonocyclic or catenated dodecaamides would not be chiral. The pure enantiomers obtained exhibit pronounced Cotton effects in their circular dichroism spectra. By comparison with the unsubstituted knot, the absolute configuration (Lambda, Delta) of all new knots is derived.

Dendronized molecular knots: selective synthesis of various generations, enantiomer separation, circular dichroism.

For the first time, knot molecules (of the amide type) are synthesized, which bear one to three dendritic units of various generations at their periphery. They were obtained through two different routes: i) attachment of dendritic wedges to new mono-, di- and trihydroxy functionalized dodecaamide knots that have been obtained by selective debenzylation of oligobenzyloxy substituted knots, or ii) cyclization of already dendron substituted pyridine-2,6-dicarbonyl dichlorides with an "extended diamine" to directly yield the "tri-dendroknots". The derivatization of knot molecules by functional substituents and even large dendritic units is an important advance in the synthesis and property variation of molecular knots. This holds true in particular for substitution of the pyridine units of the knots, whereas the isophthalic acid units seem not to tolerate larger substitutents, as reflected in lower knot yields. These syntheses also demonstrate knots to be accessible indirectly by substitution of the corresponding mono-, di- and tri-functionalized knot skeleton. An advantage of dendritic "decoration" is the control of solubility and chromatographic behaviour of the molecular knots (knotanes). Suggestions are made about the threading mechanism by supramolecular template effects leading to the formation of amide-based molecular knots. The topological chirality of the new "dendroknots" is shown by efficient enantioseparations (separation factor alpha between 1.22 and 1.48). For this purpose (commercially unavailable) chiral column material of the Chiralpak type was used, in which the chiral component is covalently bonded to the silica gel support. The racemate splittings provide additional evidence for the knotted structure, as all other conceivable isomers such as macromonocyclic or catenated dodecaamides would not be chiral. The pure enantiomers obtained exhibit pronounced Cotton effects in their circular dichroism spectra. By comparison with the unsubstituted knot, the absolute configuration (Lambda, Delta) of all new knots is derived.

Comparative performance evaluation of Java threads for embedded applications: Linux Thread vs. Green Thread

Despite the portability and platform independence of Java programs, their performance depends on the threading mechanisms of the host operating system. In this paper, we measure the performance of Java threads for two different multi-threading implementations, Linux Thread and Green Thread, using PersonalJava (TM) on a Linux-based platform. The experimental results show the relative strengths and weaknesses of the two threading mechanisms with respect to synchronization overhead, I/O efficiency, and thread control.

Cranial distraction osteogenesis in sheep using a totally implantable hydraulic mechanism: early results

Conventional distraction osteogenesis has been performed by using either percutaneous pins attached to a thread and screw mechanism, or a thread and screw mechanism that is implanted but still requires turning by a percutaneous instrument or device. In these situations there is always the risk of infection passing to the bone via the percutaneous connection. We have developed a totally implantable hydraulic mechanism, which is activated in much the same way as injection into the port of a tissue expander. Preliminary in vitro testing has suggested that our mechanism can produce sufficient force at appropriate rates of distraction to have a promising role in distraction osteogenesis. We examined the effect of osseous distraction on the cranial vault. Expansion of the cranial vault by distraction osteogenesis is not widespread in clinical practice, in part because of the risk of infective complications of the extra-dural space. We were, therefore, presented with an ideal opportunity both to test the new distraction device and to examine the effect of distraction osteogenesis on the cranial vault. A sheep animal model was used in a pilot study to test the plausibility and examine the physiology of cranial-vault distraction osteogenesis using a totally implantable hydraulic device. Two sheep had a device implanted in the temporal fossa so as to push the craniotomised cranial cap upwards. Distraction was performed for 13 days beginning 1 week after craniotomy. After 9 weeks of consolidation, 5.5 mm and 7.4 mm of new woven bone of normal cranial thickness were demonstrated.

Concurrent Programming:The Java Programming Language

Stephen J. Hartley Oxford University Press, New York, 1998, 260 pp. ISBN 0-19-511315-2, $45.00 Concurrent Programming is a thorough treatment of Java multi-threaded programming for both a stand-alone and distributed environment. Designed mostly for students in concurrent or parallel programming classes, the text is also an excellent reference for the practicing professional developing multi-threaded programs or applets. Hartley first provides a complete explanation of the features of Java necessary to write concurrent programs, including topics such as exception handling, interfaces, and packages. He then gives the reader a solid background to write multi-threaded programs and also presents the problems introduced when writing concurrent programs—namely race conditions, mutual exclusion, and deadlock. Hartley also provides several software solutions that do not require the use of common process and thread mechanisms. Once the groundwork is laid for writing concurrent programs, Hartley then takes a different approach than most Java references. Rather than presenting how Java handles mutual exclusion with the synchronized keyword (although it is covered later), he first looks at semaphore-based solutions to classic concurrent problems such as bounded-buffer, readers-writers, and the dining philosophers. Hartley also uses the same approach to develop Java classes for monitors and message passing. This unique approach to introducing concurrency allows the readers to both understand how Java threads are synchronized and how the basic synchronization mechanism can be used to construct more abstract tools such as semaphores. If there is a shortcoming with the text it is with the lack of sufficient coverage of remote method invocation (RMI), although there is a section covering RMI. This is quite understandable as RMI is a fairly recent phenomenon with the Java community. Also, the classes that Hartley provides could easily implement RMI rather than sockets to handle communication. The strengths of the book include its ease in reading, several examples at the end of chapters, a package similar to Xtango that provides algorithm animation, and a supportive web site by the author (see www.mcs.drexel.edu/~shartley/ConcProgJava/index.html ) including compressed source code. As Java becomes more dominant on the server side of multi-tier applications, writing thread-safe concurrent applications becomes even more important. Concurrent Programming is a strong step towards teaching students and professionals such skills. Greg Gagne, Westminster College of Salt Lake City Salt Lake City, Utah

Distributed Computing: Fundamentals, Simulations and Advanced Topics

Stephen J. Hartley Oxford University Press, New York, 1998, 260 pp. ISBN 0-19-511315-2, $45.00 Concurrent Programming is a thorough treatment of Java multi-threaded programming for both a stand-alone and distributed environment. Designed mostly for students in concurrent or parallel programming classes, the text is also an excellent reference for the practicing professional developing multi-threaded programs or applets. Hartley first provides a complete explanation of the features of Java necessary to write concurrent programs, including topics such as exception handling, interfaces, and packages. He then gives the reader a solid background to write multi-threaded programs and also presents the problems introduced when writing concurrent programs—namely race conditions, mutual exclusion, and deadlock. Hartley also provides several software solutions that do not require the use of common process and thread mechanisms. Once the groundwork is laid for writing concurrent programs, Hartley then takes a different approach than most Java references. Rather than presenting how Java handles mutual exclusion with the synchronized keyword (although it is covered later), he first looks at semaphore-based solutions to classic concurrent problems such as bounded-buffer, readers-writers, and the dining philosophers. Hartley also uses the same approach to develop Java classes for monitors and message passing. This unique approach to introducing concurrency allows the readers to both understand how Java threads are synchronized and how the basic synchronization mechanism can be used to construct more abstract tools such as semaphores. If there is a shortcoming with the text it is with the lack of sufficient coverage of remote method invocation (RMI), although there is a section covering RMI. This is quite understandable as RMI is a fairly recent phenomenon with the Java community. Also, the classes that Hartley provides could easily implement RMI rather than sockets to handle communication. The strengths of the book include its ease in reading, several examples at the end of chapters, a package similar to Xtango that provides algorithm animation, and a supportive web site by the author (see www.mcs.drexel.edu/~shartley/ConcProgJava/index.html ) including compressed source code. As Java becomes more dominant on the server side of multi-tier applications, writing thread-safe concurrent applications becomes even more important. Concurrent Programming is a strong step towards teaching students and professionals such skills. Greg Gagne, Westminster College of Salt Lake City Salt Lake City, Utah

Java threads and SugarCubes

SugarCubes is a set of Java classes which provides a simple and structured approach to concurrency. It offers a powerful and modular communication mechanism based on instantaneously broadcast events. The semantics of SugarCubes code is deterministic and does not depend on arbitrary choices made by the execution platform. SugarCubes gives programmers a sound and fine control over execution; for example, reactive instructions can be preempted in a completely clean way. The paper compares thread-based programming with SugarCubes programming. It shows that SugarCubes is simpler and more structured than the standard Java threading mechanism. Copyright © 2000 John Wiley & Sons, Ltd.

Java threads and SugarCubes

SugarCubes is a set of Java classes which provides a simple and structured approach to concurrency. It offers a powerful and modular communication mechanism based on instantaneously broadcast events. The semantics of SugarCubes code is deterministic and does not depend on arbitrary choices made by the execution platform. SugarCubes gives programmers a sound and fine control over execution; for example, reactive instructions can be preempted in a completely clean way. The paper compares thread-based programming with SugarCubes programming. It shows that SugarCubes is simpler and more structured than the standard Java threading mechanism. Copyright © 2000 John Wiley & Sons, Ltd.

Endovascular occlusion with a new mechanical detachable coil.

Metallic coils have been used for vascular embolization for many years but controlled-release coils have only recently become commercially available. Most of these devices are microcoils that were manufactured primarily for the packing of intracerebral aneurysms; therefore, they lack radial force and are not ideal agents for the occlusion of high-flow lesions such as pulmonary arteriovenous malformations (PAVMs). The objective of this study was to review our experience with a new detachable coil based on the conventional Gianturco-Wallace coil. The new detachable coil was initially used for the treatment of varicocele in 20 patients. Subsequently, the coil was used in 48 patients during 90 procedures for the treatment of PAVMs. A total of 548 coils were used. Complete occlusion of the testicular vein was achieved in all patients with varicocele. Successful occlusion of the PAVM being treated was achieved in all patients, and no instances of recanalization were documented in any of the patients who returned for follow-up angiography. Forty-one coils had to be removed completely from the catheter before detachment because of inappropriate size or position. Eight coils failed to detach easily, and six of these had to be removed. Most of these device failures were associated with kinking of the screw thread mechanism between the coil and the delivery wire. The Jackson detachable coil allows safer, more accurate, and more distal embolization of PAVMs than is possible with nondetachable coils. Complications associated with its use have been few.

A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease.

THE 5'-exonucleases are enzymes that are essential for DNA replication and repair. As well as their exonucleolytic action, removing nucleotides from the 5'-end of nucleic acid molecules such as Okazaki fragments, many 5'-3'-exonucleases have been shown to possess endonucleolytic activities. T5 5'-3'-exonuclease shares many similarities with the amino terminal of eubacterial DNA polymerases, although, unlike eubacteria, phages such as T5, T4 and T7 express polymerase and 5'-exonuclease proteins from separate genes. Here we report the 2.5-A crystal structure of the phage T5 5'-exonuclease, which reveals a helical arch for binding DNA. We propose a model consistent with a threading mechanism in which single-stranded DNA could slide through the arch, which is formed by two helices, one containing positively charged, and the other hydrophobic, residues. The active site is at the base of the arch, and contains two metal-binding sites.

Design and Fabrication of a PC-based Automatic Thread Cutting Machine

A PC based thread cutting machine is described where the PC is used to control the speed and number of rotations of a stepper motor attached to the threading mechanism. The software is written in GWBASIC. The design can be adopted for mass production of high precision screws.

Accommodation of lattice mismatch and threading of dislocations in GaSb films grown at different temperatures on GaAs (001)

Transmission electron microscopy has been used to investigate the accommodation of lattice mismatch and the threading mechanism of dislocations in GaSb films deposited at 420, 470 and 520°C by molecular beam epitaxy (MBE) on GaAs (001) substrate. The lattice mismatch was relieved by regular 90° dislocations generated during island growth of GaSb films. At high temperature, however, the lattice mismatch was partly accommodated by 60° dislocation arrays which induce a local tilt of GaSb film with respect to the substrate. Even in the best case of misfit accommodation by very regular 90° dislocations, the density of threading dislocations reaches 1 × 10 10 cm -2. The main source of threading dislocations is attributed to the coalescence of randomly distributed GaSb islands. In particular, at low temperature many 90° dislocations thread directly to the film surface, which is explained by the difference of 90° dislocation spacings in two coalesced islands.

Structure of the altromycin B (N7-guanine)-DNA adduct. A proposed prototypic DNA adduct structure for the pluramycin antitumor antibiotics.

Altromycin B belongs to the pluramycin family of antitumor antibiotics, which also includes kidamycin, hedamycin, pluramycin, neopluramycin, DC92-B, and rubiflavin A. These potent antitumor compounds react with DNA in as yet imprecisely determined ways. In the present investigation, we have used gel electrophoresis methods in combination with nuclear magnetic resonance and mass spectrometry to determine the structure of the altromycin B-DNA adduct. High-resolution gel electrophoresis demonstrated that guanine was the reactive base, and N7 was implicated from experiments in which N7-deazaguanine was used in place of guanine in a strand breakage assay. Experiments using supercoiled DNA demonstrated that altromycin B and related drugs intercalated into DNA, which implicated this as a common mechanism for binding of the pluramycin antibiotics to DNA. The altromycin B-guanine adduct was isolated from calf thymus DNA after thermal depurination of the alkylated DNA. Mass spectrometry confirmed that altromycin alkylated DNA through guanine, and 1H- and 13C-NMR was used to confirm the covalent linkage sites between altromycin B and guanine. On the basis of these results, we propose that altromycin B first intercalates into DNA via a threading mechanism, reminiscent of nogalamycin, to insert the disaccharide into the minor groove and position the epoxide in the major groove in proximity to N7 of guanine. Nucleophilic attack from N7 of guanine leads to an acid-catalyzed opening of the epoxide, resulting in the altromycin B-DNA adduct. On the basis of these results, a general mechanism for the interaction of the pluramycin family of antibiotics with DNA is proposed.

Entry of Rhizobia into Roots of Mimosa scabrella Bentham Occurs between Epidermal Cells

The nitrogen-fixing symbiosis between Mimosa scabrella and Rhizobium Br 3454 was initiated by an infection sequence consisting of (a) surface colonization of roots; (b) penetration of mucigel and primary layers of radial walls of epidermal cells; (c) further penetration through primary wall layers and intercellular air spaces; (d) occasional intracellular penetration of epidermal and cortical cells, always occurring from a boundary between two neighbouring cells. Root hairs, when present, were never seen to be infected by the well-known infection thread mechanism, nor were infections seen to occur through wounds. This newly described method of infection may be common in legumes.

Inability of circular mRNA to attach to eukaryotic ribosomes.

IN contrast to prokaryotic systems, initiation by eukaryotic ribosomes seems to be restricted to a single site near the 5′-terminus of the message. However, nucleotide sequence analyses have not revealed a common ‘recognition sequence’ within the 5′-proximal portion of eukaryotic messages. We have previously suggested that the position of an AUG codon within a eukaryotic message—rather than the surrounding nucleotide sequence—might be the primary feature defining an initiation site. We proposed1,2 that a 40S ribosomal subunit binds initially at or near the 5′-end of a message and migrates along the RNA chain until the first AUG codon is encountered, whereupon it stops, a 60S subunit joins, and polypeptide synthesis begins. Although this mechanism accounts for many of the peculiarities of eukaryotic translational initiation, it leaves unanswered the question of how ribosomes recognise the 5′-terminus of mRNA. The m7G cap which blocks the end of most eukaryotic messages3 is not, responsible for directing ribosomes to the 5′-terminus since ribosomes initiate at the 5′-proximal AUG even in uncapped or unmethylated RNAs4,5. The ability of ribosomes to select the 5′-end of a message irrespective of its chemical structure (that is, whether the terminus is m7GpppN…, GpppN… or pppN…) is difficult to explain. An intriguing possibility is that eukaryotic ribosomes attach to mRNA by a threading mechanism. A simple prediction of the threading mechanism is that circularisation of a message should abolish its ability to interact with ribosomes. The experiments described below fulfill this prediction. The possibility of threading by prokaryotic ribosomes was ruled out, several years ago, by the demonstration that Escherichia coli ribosomes were able to translate the circular DNA of phage fd6,7. Indeed, the simplest version of a threading mechanism (entry at the 5′-terminus of a message with translation beginning at the first AUG codon encountered by the ribosome) is contradicted by the ability of E. coli ribosomes to initiate at multiple internal sites in poly-cistronic messages, such as bacteriophage R17 RNA. Conversely, the threading mechanism is consistent with the mono-cistronic character of eukaryotic messages.