bluuebunny/crossref_metadata_2025 huggingface dataset:
Kinase inhibitors and the case for CH…O hydrogen bonds in protein–ligand binding
Authors: Pierce Albert C. , Sandretto Kathryn L. , Bemis Guy W.
Published: October 2002

Although the hydrogen bond is known to be an important mediator of intermolecular interactions, there has yet to be an analysis of the role of CH…O hydrogen bonds in protein–ligand complexes. In this work, we present evidence for such nonstandard hydrogen bonds from a survey of aromatic ligands in 184 kinase crystal structures and 358 high‐resolution structures from the Protein Data Bank. CH groups adjacent to the positively charged nitrogen of nicotinamide exhibit geometric preferences strongly suggestive of hydrogen bonding interactions, as do heterocyclic CH groups in kinase ligands, while other aromatic CH groups do not exhibit these characteristics. Ab initio calculations reveal a considerable range of CH…O hydrogen bonding potentials among different aromatic ring systems, with nicotinamide and heterocycles preferred in kinase inhibitors showing particularly favorable interactions. These results provide compelling evidence for the existence of CH…O hydrogen bonds in protein–ligand interactions, as well as information on the relative strength of various aromatic CH donors. Such knowledge will be of considerable value in protein modeling, ligand design, and structure–activity analysis. Proteins 2002;49:567–576. © 2002 Wiley‐Liss, Inc.
Implementation of a multiagent system for competitive environments on the WWW
Authors: Onjo Hiroyuki , Far Behrouz H.
Published: October 2002

Agents have been receiving a lot of attention as software which behaves autonomously and efficiently on a network and supports human social interactions. Various agent systems have already been proposed. A conventional agent‐based system is based on the assumption that all interacting agents are trustworthy. In practice, however, there are many instances in which agents must compete in an environment in which the other agents cannot be trusted. Thus, in this paper the authors discuss the development of an electronic commerce system which uses agents that behave competitively. The agents in this system can determine autonomously the level of uncertainty in a transaction, then make decisions flexibly. In addition, the authors argue for the validity of their system using operational examples in which their system is used in various market scenarios. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(14): 34–49, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.10032
2D spreading associative neural network simultaneously recognizes object position and shape in 2D space
Authors: Nakamura Kiyomi , Kinoshita Noriki , Kanayama Hirokazu
Published: October 2002

The original “spreading associative neural network,” which imitates the spatial recognition system in the brain, not only recognizes the shape of an object irrespective of its position, but also recognizes its position irrespective of its shape in the input pattern when the object positional movement is limited to only one dimension. In the present study, in order to allow an object presentation in any 2D position on the plane, we propose a “2D spreading associative neural network” which spreads the input pattern in two dimensions. The proposed neural network not only recognizes the shape of the object in the 2D space irrespective of its position, but also recognizes its position irrespective of its shape in the input pattern. The position‐invariant shape recognition and the shape‐invariant positional recognition ability in 2D space are obtained across various kinds of objects—characters and human faces—at the same time. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(13): 11–23, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.10171
Active perception and recognition learning system based on Actor‐Q architecture
Authors: Shibata Katsunari , Nishino Tetsuo , Okabe Yoichi
Published: October 2002

This paper proposes the Actor‐Q architecture, which is a combination of Q‐Learning and Actor‐Critic architecture, as well as the active perception and recognition learning system based on that architecture. In Actor‐Q architecture, the system output is divided into the “action,” which is a discrete value as intention, and the “motion,” which is a continuous‐valued vector. As the first step, the “action” is determined from Q‐values. If the “action” is accompanied with a “motion,” the “motion” is executed according to the corresponding Actor output. Q‐value is learned by Q‐learning, and Actor is trained with the Q‐value corresponding to that “action” on behalf of the Critic output. In this study, the action is defined as the decision of the sensor motion or the recognition of the respective pattern. Q‐value is assigned to each of those. When the sensor motion is selected, the sensor is moved according to the Actor output. When recognition is selected, the recognition result that the presented pattern is the one corresponding to the selected Q‐value is output. The Q‐value is learned, using the reinforcement signal representing the true/false of the result. Both Q‐value computing module and Actor are composed of neural networks, with the visual sensor signals as input. By this architecture, the following three problems of the conventional active perception and recognition learning system are dissolved. (1) The sensor can be trapped in a local maximum of the recognition evaluation. (2) It is necessary that the recognition output should be evaluated for each time‐step, and the reinforcement signal with a continuous value should be provided. (3) The system cannot decide by itself the timing to output the recognition result. The above effect was verified by some simulations, using the visual sensor with nonuniform sensor cells. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(14): 12–22, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.10207
Built‐in Self‐Test for crosstalk faults in a digital VLSI
Authors: Shimizu Kazuya , Itazaki Noriyoshi , Kinoshita Kozo
Published: October 2002

Accompanying high‐integration and high‐speed implementation of VLSI in recent years, new faults which cannot be classified in the category of conventional fault models have become a problem. Among these new faults, we will deal with crosstalk faults in this paper. Because of excitation and propagation of the crosstalk faults in the detection of these faults, two successive test vectors are required and thus their generation is difficult. Moreover, it is necessary in the sequential circuit to consider the problem of timing such as gate delay time and FF setup time in the circuit. For that reason, it has been difficult to realize a high fault coverage in the test vector generation methods proposed so far. To solve these problems, we will newly propose in this paper a Built‐In Self‐Test (BIST) method which can detect the crosstalk faults. This method can be realized by a relatively small area overhead; moreover, by adopting a circuit configuration during simulation which is different from the one during test, the simulation time is shortened. In this way, testing of large‐scale circuits has been made possible. We have performed an evaluation on the fault coverage for several benchmark circuits and shown that this method is effective for crosstalk faults. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(13): 35–47, 2002; Published online in Wiley InterScience (www. interscience.wiley.com). DOI 10.1002/scj.1171
High‐accuracy shape decomposition based on mathematical morphology in discrete circle space
Authors: Tong Weiqing , Tatsumi Shoji
Published: October 2002

In this paper, by improving the existing morphological shape decomposition method, we will propose a morphological shape decomposition which uses high‐accuracy circle‐structuring elements and is capable of completely describing the original shape. Moreover, the amount of calculation time for shape decomposition is determined, and it is found that both methods require the same calculation timeO(M4/3) (M2is the area of the object figure). Furthermore, from the viewpoints of shape description error rate and description data quantity, the proposed method is confirmed to be superior to the existing method in the experiments on shape decomposition and restoration. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(13): 85–95, 2002; Published online in Wiley Interscience (www.interscience.wiley.com). DOI 10.1002/scj.1175
On a learning theory in which pattern structure is taken into account
Authors: Uesaka Yoshinori
Published: October 2002

In this paper, pattern recognition is reconsidered in geometrical terms, and issues in learning theory that require further research are discussed. First, it is shown that there is learning that is easy for humans and learning that is difficult for humans, which has not been duly taken into account in existing learning theories. Then the importance of pattern structure in learning is demonstrated. For the purpose of development of a new learning theory, the structure of pattern recognition is revised, and all problems of recognition are shown to have a geometrical structure, thus being treatable by means of transformation groups. In closing, issues are put forward that should be studied in the framework of new learning theory with regard to pattern structure, and coordination between theory and experiments in pattern recognition is discussed. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(13): 103–110, 2002; Published online in Wiley InterScience (www.interscience. wiley.com). DOI 10.1002/scj.1177
Cooperative distributed registration for robust face recognition
Authors: Kato Takekazu , Mukaigawa Yasuhiro , Shakunaga Takeshi
Published: October 2002

This paper describes a cooperative distributed registration system for efficient acquisition of a set of facial images required in realization of robust face recognition. In this system, a lot of agents consisting of a camera and a processor are arranged, and the person detection and tracking as well as registration of facial images are integratively realized. By configuring the cooperative mechanism of this system into a three‐layer structure, the required communication capacity is reduced and efficient cooperative operation is realized. In the first layer, each agent independently performs the detection and two‐dimensional tracking of the target person. In the second layer, the robust three‐dimensional tracking is realized by cooperating agents themselves who are tracking a particular target person within an agency. In the third layer, by the cooperation among agencies, the agency configuration is dynamically changed in accordance with the position and registration conditions of the target person, and the effective registration is realized by changing over the target person of each camera. We will present the experimental results based on a system constructed with eight cameras and confirm the effectiveness of the proposed technique. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(14): 91–100, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.1179
An e‐mail environment with handwriting using the HandsDraw digital ink format
Authors: Kato Naoki , Tanaka Hiroshi , Nakagawa Masaki
Published: October 2002

This paper proposes a handwriting‐based e‐mail environment system, including the HandsDraw format, whose facilities include the reading and writing of handwritten massages, their transmission and reception, annotations or comments by recipients, confirmation of the author and time of writing, and reproduction of handwriting. The system has a user interface which is friendly even to a beginner, and can handle more expressive massages on the Internet. The system is regarded as an advanced mobile communication terminal of the kind which has been fashionable recently. Considering the advantages and disadvantages of pen input, encircling (lasso) selection and a button interface are used for dialogue. Users' opinions (collected by questionnaires, on the Internet, and from laboratory use of the system for 2 1/2 years) confirm all of the functions of the system. Some respondents have suggested the conversion of handwritten characters to a type font (rather than sending them directly) by using the character‐recognition facility in this system. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(14): 101–109, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.1180
A 5‐kHz‐bandwidth low‐bit‐rate speech coder: Bandwidth, noisiness, and opinion scores
Authors: Harada Noboru , Ohmuro Hitoshi , Mano Kazunori
Published: October 2002

With the development of PCs, Internet technology, and mobile communications, the demand for low‐bit‐rate speech coding schemes as well as for high‐information‐level natural speech have increased in recent years. While naturalness increases with the use of speech signals of broad frequency bands, more information is needed for coding. In this paper, we propose a 5‐kHz‐band speech coding scheme that clarifies the relationships between the frequency band feeling, noisiness, and subjective opinions on quality by means of evaluation experiments using multiple frequency bands, while allowing selection between low bit rate and naturalness. The proposed scheme operates in three bit‐rate modes, 7.8, 5.75, and 3.95 kbit/s. Subjective quality evaluation tests confirm that the coding scheme achieves quality almost equal to G.729 (3.4‐kHz bandwidth, 8 kbit/s) and G.722 (7‐kHz bandwidth, 48 kbit/s) at 5.75 kbit/s and quality higher than these at 7.8 kbit/s. © 2002 Wiley Periodicals, Inc. Syst Comp Jpn, 33(14): 110–119, 2002; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/scj.1181
Promoting preservice chemistry teachers' understanding about the nature of science through history
Authors: Lin Huann‐shyang , Chen Chung‐Chih
Published: October 2002

The purpose of this quasi‐experimental study was to document the benefits of teaching chemistry through history. The experimental group consisted of seniors enrolled in a teacher preparation program in which they learned how to teach chemistry through the history of science. Their understanding of the nature of science was compared with that of a control group, which consisted of juniors in the same department. The results of the analysis of covariance revealed that the experimental group outperformed the control group on an instrument documenting respondents' understanding of the nature of science. Additional frequency analysis and interview data indicated that the experimental group students had a better understanding of the nature of creativity, the theory‐based nature of scientific observations, and the functions of theories. In the pretreatment interviews, students in the experimental group based their explanations concerning the nature of science primarily on their intuition. In the posttreatment interview, however, they were able to explain their beliefs by using scientists' arguments or hypotheses as examples. This result indicates that the experimental group's understanding about the nature of science was enhanced by learning to teach through the history of science. © 2002 Wiley Periodicals, Inc. J Res Sci Teach 39: 773–792, 2002
Student use of narrative and paradigmatic forms of talk in elementary science conversations
Authors: Kurth Lori A. , Kidd Raymond , Gardner Roberta , Smith Edward L.
Published: October 2002

The purpose of this work was to examine and characterize student use of narrative and paradigmatic expression in elementary science discourse. This interpretive study occurred over a 2‐year period in a professional development school with a largely international population. This analysis focused on the narrative and paradigmatic modes of expression used by combined first–second‐ and second‐grade students in a semistructured, fairly autonomous, whole‐class conversational format. Students demonstrated competence with both modes of talk at the beginning of the year. Over time, students moved toward more paradigmatic talk, but narrative examples continued to be key components of the science conversations. Topically, students used narrative more often for life sciences and paradigmatic talk for physical sciences. For gender there were no qualitative differences in narrative or paradigmatic expression. However, boys obtained more opportunities to practice their use of both discourse forms by either receiving more speaking turns or expressing more language features per turn. These conversations show that narrative and paradigmatic modes in science need not be in opposition but can, in fact, be used together in complementary ways that are mutually enhancing. © 2002 Wiley Periodicals, Inc. J Res Sci Teach 39: 793–818, 2002
Comparing three attitude‐behavior theories for predicting science teachers' intentions
Authors: Zint Michaela
Published: October 2002

Social psychologists' attitude‐behavior theories can contribute to understanding science teachers' behaviors. Such understanding can, in turn, be used to improve professional development. This article describes leading attitude‐behavior theories and summarizes results from past tests of these theories. A study predicting science teachers' intention to incorporate environmental risk education based on these theories is also reported. Data for that study were collected through a mail questionnaire (n = 1336, radjusted = 80%) and analyzed using confirmatory factor and multiple regression analysis. All determinants of intention to act in the Theory of Reasoned Action and Theory of Planned Behavior and some determinants in the Theory of Trying predicted science teachers' environmental risk education intentions. Given the consistency of results across studies, the Theory of Planned Behavior augmented with past behavior is concluded to provide the best attitude‐behavior model for predicting science teachers' intention to act. Thus, science teachers' attitude toward the behavior, perceived behavioral control, and subjective norm need to be enhanced to modify their behavior. Based on the Theory of Trying, improving their attitude toward the process and toward success, and expectations of success may also result in changes. Future research should focus on identifying determinants that can further enhance the ability of these theories to predict and explain science teachers' behaviors. © 2002 Wiley Periodicals, Inc. J Res Sci Teach 39: 819–844, 2002
Learning to teach science for all in the elementary grades: What do preservice teachers bring?
Authors: Howes Elaine V.
Published: October 2002

Implicit in the goal of recent reforms is the question: What does it mean to prepare teachers to teach “science for all”? Through a teacher research study, I have encountered characteristics that may assist prospective elementary teachers in developing effective, inclusive science instruction. I describe these strengths, link them to requirements for teaching, and suggest how science teacher educators might draw on the strengths of their own students to support teaching practices aimed at universal scientific literacy. My conceptual framework is constructed from scholarship concerning best practice in elementary science education, as well as that which describes the dispositions of successful teachers of diverse learners. This study is based on a model of teacher research framed by the concept of “research as praxis” and phenomenological research methodology. The findings describe the research participants' strengths thematically as propensity for inquiry, attention to children, and awareness of school/society relationships. I view these as potentially productive aspects of knowledge and dispositions about science and about children that I could draw on to further students' development as elementary science teachers. © 2002 Wiley Periodicals, Inc. J Res Sci Teach 39: 845–869, 2002
PBX, MEIS, and IGF‐I are potential mediators of retinoic acid‐induced proximodistal limb reduction defects
Authors: Qin Pu , Cimildoro Rebecca , Kochhar Devendra M. , Soprano Kenneth J. , Soprano Dianne Robert
Published: October 2002

Background

Phocomelia, which is primarily due to a disruption in the proximodistal axis, is found in virtually all mouse embryos exposed to high doses of retinoic acid (RA) on 11 days post coitum (dpc).

Methods

To identify genes that potentially mediate the effects of retinoic acid (RA) on limb development, we have examined the expression of 9,000 clones from the IMAGE consortium by microarray analysis of RNA isolated from 11 dpc mouse forelimbs exposed to RA or vehicle for 6 hr. Eight genes that demonstrated altered expression were chosen for further study of their mRNA levels using RT‐PCR. Protein levels were determined by Western blot analysis.

Results

Of the 9,000 genes examined in the microarray, approximately 111 demonstrated altered expression (33 known genes and 78 ESTs). Of the eight known genes chosen for further study using RT‐PCR, four mRNAs (PBX1a, PBX1b, IGF‐Ia, and IGF‐Ib) demonstrated consistent elevation (≈3‐fold) in their levels after RA treatment in both the forelimbs and hindlimbs as early as 3 hr after RA treatment. In addition to the two PBX1 isoforms, the mRNA level of the other two subtypes (PBX2 and PBX3) and the level of PBX1/2/3 protein were also found to be elevated in limb buds after RA treatment. Finally, we examined the expression of MEIS1, MEIS2, and MEIS3 because these proteins are necessary for PBX nuclear localization. The mRNA level of all three subtypes of MEIS were elevated approximately three‐ to four‐fold in both the forelimbs and hindlimbs after RA treatment.

Conclusions

Because both PBX and MEIS (and their orthologs) are believed to be involved in the control of proximodistal axis formation in mouse and fly limbs and IGFs in the development of limbs, we suggest that increases in PBX, MEIS and IGF‐1 mRNA levels may contribute to proximodistal limb reduction defects caused by teratogenic doses of RA. Teratology 66:224–234, 2002. © 2002 Wiley‐Liss, Inc.
Decline of neural tube defects cases after a folic acid campaign in Nuevo León, México
Authors: Martínez de Villarreal Laura , Pérez Jesús Z. Villarreal , Vázquez Patricia Arredondo , Herrera Ricardo Hernández , Campos Ma. Del Roble Velazco , López Roberto Ambriz , Ramírez José Luis Herrera , Sánchez Jesús Manuel Yañez , Villarreal Juan José Morales , Garza Manuel Treviño , Limón Adriana , López Abel Guzmán , Bárcenas Mario , García Juan Ramón Cepeda , Domínguez Andrés Sánchez , Nuñez Rogelio Hernández , Ayala Jorge Luis García , Martínez Jorge Garza , González Mario Tijerina , Alvarez Carlos García , Castro Roberto Negrete
Published: October 2002

Background

Nuevo León is a state in northeastern Mexico, near the border of Texas. Mean mortality rate from 1996–98 due to anencephaly cases was 0.6/1,000. In 1999 a surveillance program for the registry and prevention of neural tube defects (NTD) cases was initiated.

Methods

Cases were obtained from hospitals and OB‐GYN clinics by immediate notification, death certificates, or fetal death registries. Only isolated cases of NTD were included. In August 1999 a folic acid campaign was initiated with the free distribution of the vitamin to low‐income women with a recommendation to take a 5.0‐mg pill once a week. Number of cases and rates from 1999 to 2001 were compared (χ2 test).

Results

After 2 years there has been a significant reduction in the number of cases and rates. In 1999 there were 95 NTD cases and in the years 2000 and 2001 there were only 59 and 55 respectively (P < 0.001). NTD rate decreased from 1.04/1,000 in 1999 to 0.58/1,000 in 2001. Anencephaly and spina bifida rates decreased from 0.55/1,000 to 0.29/1,000 and from 0.47/1,000 to 0.22/1,000 respectively, from 1999–2001. Decrease of female cases was higher than male cases for both phenotypes.

Conclusion

After 2 years there was a 50% decrease in the incidence of anencephaly and spina bifida cases with a significant reduction of infant mortality and disability. These results encourage us to propose the use of a single tablet of 5.0‐mg of folic acid per week as an alternative to supplementation on a daily basis. Teratology 66:249–256, 2002. © 2002 Wiley‐Liss, Inc.
Apolipoprotein E and apolipoprotein B genotypes and risk for spina bifida
Authors: Volcik Kelly A. , Zhu Huiping , Shaw Gary M. , Lammer Edward J. , Finnell Richard H.
Published: October 2002

Background

Altered cholesterol metabolism and defects in cholesterol biosynthesis may influence abnormal central nervous system (CNS) development. During early stages of embryonic development, high levels of cholesterol are needed by rapidly proliferating cells that utilize cholesterol as a key cell membrane component. Alterations in cholesterol levels are influenced by variations in the apolipoprotein E (apoE) and apolipoprotein B (apoB) genes. The purpose of our study was to explore the possible association between infant genetic variations in the apoE and apoB genes and spina bifida (SB) risk.

Methods

Genomic DNA was extracted from newborn screening blood spots obtained from 26 infants with SB and 73 non‐malformed control infants. ApoE and apoB genotypes were determined by restriction enzyme digestion of PCR amplification products.

Results

Genotype frequencies for the apoE and apoB polymorphisms were not statistically different between case and control infants. For each apoB polymorphism, however, the frequency of the wild‐type allele was higher in SB infants as compared to controls. Additionally, the apoE genotype E2/E3 was observed more frequently in the controls than in SB infants [15% in controls compared to 4% in cases; OR = 0.2 (0–1.6)].

Conclusions

Results from this study suggest that genetic variations in the apoE and apoB genes, known to regulate cholesterol metabolism, do not substantially contribute to the risk of SB in infants. Teratology 66:257–259, 2002. © 2002 Wiley‐Liss, Inc.
Overexpressed yeast mitochondrial putative RNA helicase Mss116 partially restores proper mtRNA metabolism in strains lacking the Suv3 mtRNA helicase
Authors: Minczuk Michal , Dmochowska Aleksandra , Palczewska Malgorzata , Stepien Piotr P.
Published: October 2002

RNA helicase, encoded by the Saccharomyces cerevisiae nuclear gene SUV3, is a subunit of the mitochondrial (mt) degradosome: an enzyme complex that takes part in turnover of mtRNAs. Deletion of the SUV3 gene leads to a variety of disturbances in mtRNA metabolism and results in respiratory incompetence of yeast cells. Here we show that the nuclear gene MSS116, which codes for a mitochondrial putative RNA helicase necessary for splicing of several mt introns, can suppress the lack of the SUV3 gene. Overexpression of the Mss116 putative helicase from a multicopy plasmid present in the SUV3‐deleted strains partially restores respiratory competence, brings the steady‐state levels of COB and ATP6/8 mRNA back almost to normal and lowers the accumulation of 21S rRNA and ATP6/8 RNA precursors to the wild‐type levels. To the best of our knowledge, this is the first reported case of a substitution of one RNA helicase by another, belonging to a different class of RNA helicases. Copyright © 2002 John Wiley & Sons, Ltd.
Non‐respiratory oxygen consumption pathways in anaerobically‐grown Saccharomyces cerevisiae: evidence and partial characterization
Authors: Rosenfeld Eric , Beauvoit Bertrand , Rigoulet Michel , Salmon Jean‐Michel
Published: October 2002

Despite the absence of an alternative mitochondrial ubiquinol oxidase, Saccharomyces cerevisiae consumes oxygen in an antimycin A‐ and cyanide‐resistant manner. Cyanide‐resistant respiration is typically used when the classical respiratory chain is impaired or absent (i.e in anaerobically‐grown cells shifted to normoxia or in respiratory‐deficient cells). We characterized the non‐respiratory oxygen consumption pathways operating during anoxic–normoxic transitions in glucose‐repressed resting cells. High‐resolution oxygraphy confirmed that the cellular non‐respiratory oxygen consumption pathway is sensitive to high concentrations of cyanide, azide, SHAM and TTFA, and revealed several new characteristics. First, the use of sterol biosynthesis inhibitors showed that this pathway makes a considerable contribution (about 25%) to both endogenous and glucose‐dependent oxygen consumption. Anaerobically‐grown glucose‐repressed cells exhibited high apparent oxygen affinities (Km for oxygen = 0.5–1 µM), even in mutants deficient in respiration or sterol synthesis. Exogeneously added glucose and endogenous stored carbohydrates were the only substrates that were efficient for cellular oxygen consumption (apparent Km for exogenous glucose = 2–3 mM). On the other hand, fluorimetric measurements of the cellular NAD(P)H pool showed that the cellular oxygen consumption (sterol biosynthesis and unknown pathways) was dependent more on the intracellular level of NADPH than of NADH. High oxygen affinity NADPH‐dependent oxygen consumption systems were thought to be mainly localized in microsomal membranes, and several data indicated a significant contribution made by uncoupled P450 systems, together with still uncharacterized systems. Such activities are associated in vitro with a massive production of O2·− and, to a lower extent, H2O2 and a likely concomitant production of H2O. Copyright © 2002 John Wiley & Sons, Ltd.
Metabolic physiology of aroma‐producing Kluyveromyces marxianus
Authors: Wittmann Christoph , Hans Michael , Bluemke Wilfried
Published: October 2002

Kluyveromyces marxianus has a high potential for industrial production of aroma compounds, such as 2‐phenylethanol, which is derived in a bioconversion from L‐phenylalanine. In the present work the product yield of K. marxianus in batch cultivation was estimated as 0.65 mol 2‐phenylethanol/mol L‐phenylalanine and thus significantly below the theoretical optimum of 1 mol/mol. By a comprehensive approach of stoichiometric balancing and GC–MS analysis of various substrates and products of K. marxianus a detailed insight into its metabolism was gained. For this purpose ring‐labelled (13C6) L‐phenylalanine and naturally labelled glucose were applied as substrates in tracer studies in batch culture. The produced aroma compounds 2‐phenylethanol and 2‐phenylethylacetate stem exclusively from the supplied L‐phenylalanine, whereas glucose was not converted into these products because of efficient feed‐back inhibition of prephenate dehydratase in the L‐phenylalanine biosynthetic pathway. It could be further shown that the supplied L‐phenylalanine completely covers the anabolic cellular demand for this amino acid. Quantification of 13CO2 in the exhaust gas provided clear evidence for catabolic breakdown of L‐phenylalanine during cultivation. Metabolic balancing around the pool of free intracellular L‐phenylalanine revealed a significant loss of L‐phenylalanine into catabolic and anabolic pathways. While 73.3% of L‐phenylalanine was converted into 2‐phenylethanol or 2‐phenylethylacetate, 22.4% was catabolized through the cinnamate pathway and 4.3% was directed towards protein biosynthesis. Catabolic breakdown of L‐phenylalanine via hydroxylation to L‐tyrosine could be excluded. In addition to an insight into metabolic functioning and regulation of 2‐phenylethanol‐producing K. marxianus, the approach presented here provides important information on potential targets for genetic optimization of 2‐phenylethanol‐producing yeasts. Copyright © 2002 John Wiley & Sons, Ltd.
Molecular and structural characterization of the spindle pole bodies in the fission yeast Schizosaccharomyces japonicus var. japonicus
Authors: Horio Tetsuya , Kimura Nachi , Basaki Akemi , Tanaka Yasuko , Noguchi Tetsuko , Akashi Tomohiro , Tanaka Kenji
Published: October 2002

The structure and localization of the microtubule organization centres (MTOCs) of the fission yeast Schizosaccharomyces japonicus var. japonicus were examined by fluorescence microscopy and electron microscopy. Spindle pole bodies (SPBs), which are the fungal equivalent of centrosomes, of Sz. japonicus were visualized by immunofluorescent staining using a monoclonal anti‐γ‐tubulin antibody. The behaviour of the SPBs during the cell cycle mostly coincided with previous reports on the most widely used fission yeast Schizosaccharomyces pombe. We cloned the γ‐tubulin gene from Sz. japonicus by PCR using redundant sets of primers corresponding to conserved regions of known γ‐tubulins. The predicted amino acid sequence of Sz. japonicus γ‐tubulin was most similar to the Sz. pombe γ‐tubulin. Under the electron microscope, the SPBs of Sz. japonicus were detected as electron‐dense multilayered structures located just outside the nuclear envelope. The SPBs of Sz. japonicus were composed of three electron‐dense layers and were surrounded by fuzzy material. Each layer showed structural changes according to the progression of the cell cycle. In mitotic cells, the SPBs were located on the fenestrae of the nuclear envelopes through which the mitotic spindle microtubules ran into the nucleoplasm. Our results show that Sz. japonicus is a very potent and attractive organism for the investigation of the microtubule nucleation system and morphogenesis in yeasts. The Accession No. for the nucleotide sequence of the Sz. japonicus gtb1+ gene is AF159163. Copyright © 2002 John Wiley & Sons, Ltd.
Cation/H+ antiporters mediate potassium and sodium fluxes in Pichia sorbitophila. Cloning of the PsNHA1 and PsNHA2 genes and expression in Saccharomyces cerevisiae
Authors: Bañuelos María A. , Ramos José , Calero Fernando , Braun Valerie , Potier Serge
Published: October 2002

Pichia sorbitophila grows rapidly in the presence of very high NaCl concentrations. Under these conditions, even when the K+ concentration is low, P. sorbitophila cells can maintain low Na+ and high K+ contents. This remarkable capacity of P. sorbitophila fails when the external pH is not acidic. This indicates that Na+ efflux is mediated by an electroneutral Na+/H+ antiporter. We have cloned and sequenced two genes designated as PsNHA1 and PsNHA2, which probably encode two antiporters of this type. The genes present high similarity with the corresponding genes from other yeasts. The heterologous expression of PsNHA1 or PsNHA2 in a Saccharomyces cerevisiae mutant lacking the Na+ efflux systems and sensitive to high concentrations of Na+ and K+ rescued the tolerance and the ability to extrude both cations. The Accession Nos of the sequenced DNA fragments are: PsNHA1, AJ496431; PsNHA2, AJ496432. (TC 2.A.36) Copyright © 2002 John Wiley & Sons, Ltd.
Vitamin E sensitive genes in the developing rat fetal brain: a high‐density oligonucleotide microarray analysis
Authors: Roy Sashwati , Lado Beatrice H , Khanna Savita , Sen Chandan K
Published: October 2002

Vitamin E (tocopherols and tocotrienols) is essential for normal neurological function. Recently we have reported that the neuroprotective properties of tocotrienols are much more potent than that of the widely studied tocopherols (Sen, C.K., Khanna, S., Roy, S. and Parker, L. (2000) J. Biol. Chem. 275, 13049–13055). The objective of this study was to evaluate whether (i) oral supplementation of tocotrienols during pregnancy is bioavailable to fetal and mother brains; (ii) short‐term change in dietary vitamin E levels of pregnant rats influences gene expression profile of developing fetal brains. We report that dietary tocotrienol is bioavailable to both mother and fetal brains. The enrichment is more in fetal brain tissue. Using a GeneChip microarray expression profiling approach we have identified a specific set of vitamin E sensitive genes in the developing rat fetal brain.
The new MATH: homology suggests shared binding surfaces in meprin tetramers and TRAF trimers
Authors: Sunnerhagen Maria , Pursglove Sharon , Fladvad Malin
Published: October 2002

Although apparently functionally unrelated, intracellular TRAFs and extracellular meprins share a region with conserved meprin and traf homology, MATH1. Both TRAFs and meprins require subunit assembly for function. By structural analysis of the sequences, we provide an explanation of how meprins, which form tetramers, and TRAF molecules, which form trimers, can share homology. Our analysis suggests it is highly likely that the same oligomerization surface is used. The analysis has implications for the widely distributed group of proteins containing MATH domains.
β1/β2/β3‐adrenoceptor knockout mice are obese and cold‐sensitive but have normal lipolytic responses to fasting
Authors: Jimenez Maria , Léger Bertrand , Canola Kriss , Lehr Lorenz , Arboit Patrizia , Seydoux Josiane , Russell Aaron P , Giacobino Jean-Paul , Muzzin Patrick , Preitner Frédéric
Published: October 2002

Catecholamines are viewed as major stimulants of diet‐ and cold‐induced thermogenesis and of fasting‐induced lipolysis, through the β‐adrenoceptors (β1/β2/β3). To test this hypothesis, we generated β1/β2/β3‐adrenoceptor triple knockout (TKO) mice and compared them to wild type animals. TKO mice exhibited normophagic obesity and cold‐intolerance. Their brown fat had impaired morphology and lacked responses to cold of uncoupling protein‐1 expression. In contrast, TKO mice had higher circulating levels of free fatty acids and glycerol at basal and fasted states, suggesting enhanced lipolysis. Hence, β‐adrenergic signalling is essential for the resistance to obesity and cold, but not for the lipolytic response to fasting.
Expression profiling of pectinolytic genes from Aspergillus niger
Authors: de Vries Ronald P. , Jansen Jenny , Aguilar Guillermo , Pařenicová Lucie , Joosten Vivi , Wülfert Florian , Benen Jacques A.E. , Visser Jaap
Published: October 2002

The expression of 26 pectinolytic genes from Aspergillus niger was studied in a wild type strain and a CreA derepressed strain, under 16 different growth conditions, to obtain an expression profile for each gene. These expression profiles were then submitted to cluster analysis to identify subsets of genes with similar expression profiles. With the exception of the feruloyl esterase encoding genes, all genes were expressed in the presence of D‐galacturonic acid, polygalacturonate, and/or sugar beet pectin. Despite this general observation five distinct groups of genes were identified. The major group consisted of 12 genes of which the corresponding enzymes act on the pectin backbone and for which the expression, in general, is higher after 8 and 24 h of incubation, than after 2 or 4 h. Two other groups of genes encoding pectin main chain acting enzymes were detected. Two additional groups contained genes encoding L‐arabinose and D‐galactose releasing enzymes, and ferulic acid releasing enzymes, respectively. The genes encoding β‐galactosidase and the L‐arabinose releasing enzymes were not only expressed in the presence of D‐galacturonic acid, but also in the presence of L‐arabinose, suggesting that they are under the control of two regulatory systems. Similarly, the rhamnogalacturonan acetylesterase encoding gene was not only expressed in the presence of D‐galacturonic acid, polygalacturonate and sugar beet pectin, but also in the presence of L‐rhamnose. The data presented provides indications for a general pectinolytic regulatory system responding to D‐galacturonic acid or a metabolite derived from it. In addition, subsets of pectinolytic genes are expressed in response to the presence of L‐arabinose, L‐rhamnose or ferulic acid.
Ile‐Lys‐Val‐Ala‐Val (IKVAV)‐containing laminin α1 chain peptides form amyloid‐like fibrils
Authors: Yamada Masanori , Kadoya Yuichi , Kasai Shingo , Kato Kozue , Mochizuki Mayumi , Nishi Norio , Watanabe Nobuhisa , Kleinman Hynda K. , Yamada Yoshihiko , Nomizu Motoyoshi
Published: October 2002

The Ile‐Lys‐Val‐Ala‐Val (IKVAV) sequence derived from laminin‐1 promotes cell adhesion, neurite outgrowth, and tumor growth and metastasis. Here, we examined amyloid formation of an IKVAV‐containing peptide (LAM‐L: AASIKVAVSADR, mouse laminin α1 chain 2097–2108). The LAM‐L peptide was stained with Congo red and exhibited fibrils in electron microscopy with a characteristic cross‐β X‐ray diffraction pattern. Further, infrared spectra of LAM‐L suggested a β‐sheet structure. These results indicate that LAM‐L forms amyloid‐like fibrils. We also examined amyloid‐like fibril formation of LAM‐L analogs. The neurite outgrowth activity of the LAM‐L analogs was closely related to their amyloid‐like fibril formation.
Crystal structure of phosphodiesterase 4D and inhibitor complex1
Authors: Lee Mi Eun , Markowitz Joseph , Lee Jie-Oh , Lee Hayyoung
Published: October 2002

Cyclic nucleotide phosphodiesterases (PDEs) regulate physiological processes by degrading intracellular second messengers, adenosine‐3′,5′‐cyclic phosphate or guanosine‐3′,5′‐cyclic phosphate. The first crystal structure of PDE4D catalytic domain and a bound inhibitor, zardaverine, was determined. Zardaverine binds to a highly conserved pocket that includes the catalytic metal binding site. Zardaverine fills only a portion of the active site pocket. More selective PDE4 inhibitors including rolipram, cilomilast and roflumilast have additional functional groups that can utilize the remaining empty space for increased binding energy and selectivity. In the crystal structure, the catalytic domain of PDE4D possesses an extensive dimerization interface containing residues that are highly conserved in PDE1, 3, 4, 8 and 9. Mutations of R358D or D322R among these interface residues prohibit dimerization of the PDE4D catalytic domain in solution.
Y‐chromosomal red‐green opsin genes of nocturnal New World monkey1
Authors: Kawamura Shoji , Takenaka Naomi , Hiramatsu Chihiro , Hirai Momoki , Takenaka Osamu
Published: October 2002

The X‐chromosomal locality of the red‐green‐sensitive opsin genes has been the norm for all mammals and is essential for color vision of higher primates. Owl monkeys (Aotus), a genus of New World monkeys, are the only nocturnal higher primates and are severely color‐blind. We demonstrate that the owl monkeys possess extra red‐green opsin genes on the Y‐chromosome. The Y‐linked opsin genes were found to be extremely varied, in one male appearing to be a functional gene and in other males to be multicopy pseudogenes. These Y‐linked opsin genes should offer a rare opportunity to study the evolutionary fate of genes translocated to the Y chromosome.
Functional screening of five PYPAF family members identifies PYPAF5 as a novel regulator of NF‐κB and caspase‐1
Authors: Grenier Jill M. , Wang Lin , Manji Gulam A. , Huang Waan-Jeng , Al-Garawi Amal , Kelly Roxanne , Carlson Adam , Merriam Sarah , Lora Jose M. , Briskin Michael , DiStefano Peter S. , Bertin John
Published: October 2002

PYRIN‐containing Apaf‐1‐like proteins (PYPAFs) are a recently identified family of proteins thought to function in apoptotic and inflammatory signaling pathways. PYPAF1 and PYPAF7 proteins have been found to assemble with the PYRIN–CARD protein ASC and coordinate the activation of NF‐κB and pro‐caspase‐1. To determine if other PYPAF family members function in pro‐inflammatory signaling pathways, we screened five other PYPAF proteins (PYPAF2, PYPAF3, PYPAF4, PYPAF5 and PYPAF6) for their ability to activate NF‐κB and pro‐caspase‐1. Co‐expression of PYPAF5 with ASC results in a synergistic activation of NF‐κB and the recruitment of PYPAF5 to punctate structures in the cytoplasm. The expression of PYPAF5 is highly restricted to granulocytes and T‐cells, indicating a role for this protein in inflammatory signaling. In contrast, PYPAF2, PYPAF3, PYPAF4 and PYPAF6 failed to colocalize with ASC and activate NF‐κB. PYPAF5 also synergistically activated caspase‐1‐dependent cytokine processing when co‐expressed with ASC. These findings suggest that PYPAF5 functions in immune cells to coordinate the transduction of pro‐inflammatory signals to the activation of NF‐κB and pro‐caspase‐1.
Human spermatid‐specific thioredoxin‐1 (Sptrx‐1) is a two‐domain protein with oxidizing activity
Authors: Jiménez Alberto , Johansson Catrine , Ljung Johanna , Sagemark Johan , Berndt Kurt D , Ren Bin , Tibbelin Gudrun , Ladenstein Rudolf , Kieselbach Thomas , Holmgren Arne , Gustafsson Jan-Åke , Miranda-Vizuete Antonio
Published: October 2002

Spermatid‐specific thioredoxin‐1 (Sptrx‐1) is the first member of the thioredoxin family of proteins with a tissue‐specific expression pattern, found exclusively in the tail of elongating spermatids and spermatozoa. We describe here further biochemical characterization of human Sptrx‐1 protein structure and enzymatic activity. In gel filtration chromatography human Sptrx‐1 eluates as a 400 kDa protein consistent with either an oligomeric form, not maintained by intermolecular disulfide bonding, and/or a highly asymmetrical structure. Analysis of circular dichroism spectra of fragments 1–360 and 361–469 and comparison to spectra of full‐length Sptrx‐1 supports a two‐domain organization with a largely unstructured N‐terminal domain and a folded thioredoxin‐like C‐terminal domain. Functionally, Sptrx‐1 behaves as an oxidant in vitro when using selenite, but not oxidized glutathione, as electron acceptor. This oxidizing enzymatic activity suggests that Sptrx‐1 might govern the stabilization (by disulfide cross‐linking) of the different structures in the developing tail of spermatids and spermatozoa.
A comparison of the molecular specificities of whole cell and endonuclear phosphatidylcholine synthesis
Authors: Hunt Alan N , Clark Graeme T , Neale James R , Postle Anthony D
Published: October 2002

Deuterated choline‐d9
labelling of IMR‐32 cells enabled comparison of the molecular specificities of whole cell and endonuclear phosphatidylcholine synthesis after 96 h polyunsaturated fatty acid supplementation. Surprisingly, while cell phosphatidylcholine synthesis and remodelling reflected a pattern of polyunsaturated fatty acid accretion, the saturated endonuclear phosphatidylcholine pool was only transiently labelled with polyunsaturates. Periodic endonuclear accumulations of the lipid second messenger diacylglycerol, mobilised from unsaturated phosphatidylinositol or saturated phosphatidylcholine, accompany cell proliferation. Non‐specific incorporation into endonuclear phosphatidylcholine and selective removal or remodelling of unsaturated molecular species may form part of a single ‘off switch’ recycling all endonuclear diacylglycerol accumulations.
Omnipotent RNA
Authors: Spirin Alexander S
Published: October 2002

The capability of polyribonucleotide chains to form unique, compactly folded structures is considered the basis for diverse non‐genetic functions of RNA, including the function of recognition of various ligands and the catalytic function. Together with well‐known genetic functions of RNA – coding and complementary replication – this has led to the concept of the functional omnipotence of RNA and the hypothesis that an ancient RNA world supposedly preceded the contemporary DNA–RNA–protein life. It is proposed that the Woese universal precursor in the ancient RNA world could be a cell‐free community of mixed RNA colonies growing and multiplying on solid surfaces.