bluuebunny/crossref_metadata_2025 huggingface dataset:
In Situ Identification of Intracellular Bacteria Related to
Paenibacillus
spp. in the Mycelium of the Ectomycorrhizal Fungus
Laccaria bicolor
S238N
Authors: Bertaux J. , Schmid M. , Prevost-Boure N. Chemidlin , Churin J. L. , Hartmann A. , Garbaye J. , Frey-Klett P.
Published: July 2003

Bacterial proliferations have recurrently been observed for the past 15 years in fermentor cultures of the ectomycorrhizal fungus
Laccaria bicolor
S238N, suggesting the presence of cryptic bacteria in the collection culture of this fungus. In this study, intracellular bacteria were detected by fluorescence in situ hybridization in combination with confocal laser scanning microscopy in several collection subcultures of
L. bicolor
S238N. They were small (0.5 μm in diameter), rare, and heterogeneously distributed in the mycelium and were identified as
Paenibacillus
spp. by using a 16S rRNA-directed oligonucleotide probe initially designed for bacteria isolated from a fermentor culture of
L. bicolor
S238N.
Development of Antibiotic-Overproducing Strains by Site-Directed Mutagenesis of the
rpsL
Gene in
Streptomyces lividans
Authors: Okamoto-Hosoya Yoshiko , Okamoto Susumu , Ochi Kozo
Published: July 2003

Certain
rpsL
(which encodes the ribosomal protein S12) mutations that confer resistance to streptomycin markedly activate the production of antibiotics in
Streptomyces
spp. These
rpsL
mutations are known to be located in the two conserved regions within the S12 protein. To understand the roles of these two regions in the activation of silent genes, we used site-directed mutagenesis to generate eight novel mutations in addition to an already known (K88E) mutation that is capable of activating antibiotic production in
Streptomyces lividans
. Of these mutants, two (L90K and R94G) activated antibiotic production much more than the K88E mutant. Neither the L90K nor the R94G mutation conferred an increase in the level of resistance to streptomycin and paromomycin. Our results demonstrate the efficacy of the site-directed mutagenesis technique for strain improvement.
Visualization of an Endophytic
Streptomyces
Species in Wheat Seed
Authors: Coombs Justin T. , Franco Christopher M. M.
Published: July 2003

Endophytic filamentous actinobacteria were isolated from surface-sterilized roots of wheat plants. Endophytic colonization of germinating wheat seed was examined using one of these endophytes,
Streptomyces
sp. strain EN27, tagged with the
egfp
gene. Endophytic colonization was observed from a very early stage of plant development with colonization of the embryo, endosperm, and emerging radicle.
Complement Resistance Is Essential for Colonization of the Digestive Tract of
Hirudo medicinalis
by
Aeromonas
Strains
Authors: Braschler Thomas R. , Merino Susana , Tomás Juan M. , Graf Joerg
Published: July 2003

From the crop of the medicinal leech,
Hirudo medicinalis
, only
Aeromonas veronii
bv. sobria can be cultured consistently. Serum-sensitive
A. veronii
mutants were unable to colonize
H. medicinalis
, indicating the importance of the mammalian complement system for this unusual simplicity. Complementation of one selected mutant restored its ability to colonize. Serum-sensitive mutants are the first mutant class with a colonization defect for this symbiosis.
Rapid Staining and Enumeration of Small Numbers of Total Bacteria in Water by Solid-Phase Laser Cytometry
Authors: Broadaway Susan C. , Barton Stephanie A. , Pyle Barry H.
Published: July 2003

The nucleic acid stain SYBR Green I was evaluated for use with solid-phase laser cytometry to obtain total bacterial cell counts from several water sources with small bacterial numbers. Results were obtained within 30 min and exceeded or equaled counts on R2A agar plates incubated for 14 days at room temperature.
Improved Adaptation to Cold-Shock, Stationary-Phase, and Freezing Stresses in
Lactobacillus plantarum
Overproducing Cold-Shock Proteins
Authors: Derzelle Sylviane , Hallet Bernard , Ferain Thierry , Delcour Jean , Hols Pascal
Published: July 2003

We have investigated the effect of overproducing each of the three cold shock proteins (CspL, CspP, and CspC) in the mesophilic lactic acid bacterium
Lactobacillus plantarum
NC8. CspL overproduction transiently alleviated the reduction in growth rate triggered by exposing exponentially growing cells to cold shock (8°C), suggesting that CspL is involved in cold adaptation. The strain overproducing CspC resumed growth more rapidly when stationary-phase cultures were diluted into fresh medium, indicating a role in the adaptation and recovery of nutritionally deprived cells. Overproduction of CspP led to an enhanced capacity to survive freezing.
Identification and Tracing of
Bifidobacterium
Species by Use of Enterobacterial Repetitive Intergenic Consensus Sequences
Authors: Ventura Marco , Meylan Valerie , Zink Ralf
Published: July 2003

Eighty-nine
Bifidobacterium
strains from 26 species were identified and classified to the species level with an enterobacterial repetitive intergenic consensus (ERIC)-PCR approach. We demonstrated that ERIC-PCR is useful for a phylogenetic and taxonomical analysis but as well as for a species composition analysis of mixed bifidobacterial cultures isolated from dairy products and other environments.
Use of Root Organ Cultures To Investigate the Interaction between
Glomus intraradices
and
Pratylenchus coffeae
Authors: Elsen Annemie , Declerck Stephane , De Waele Dirk
Published: July 2003

The interaction between
Glomus intraradices
and
Pratylenchus coffeae
on transformed carrot roots was studied in root organ culture.
G. intraradices
provided the roots with increased protection against
P. coffeae
by suppressing nematode reproduction in the roots. The internal and external mycorrhizal development was not influenced by the presence of the nematodes.
Nontyphoidal Salmonellae in United Kingdom Badgers: Prevalence and Spatial Distribution
Authors: Wilson J. Sian , Hazel Sarah M. , Williams Nicola J. , Phiri Amos , French Nigel P. , Hart C. Anthony
Published: July 2003

Eighteen (72%) of 25 badger social groups were found to excrete
Salmonella enterica
serovar Ried,
S. enterica
serovar Binza,
S. enterica
serovar Agama, or
S. enterica
serovar Lomita. Each serovar was susceptible to a panel of antimicrobials. Based on results of pulsed-field gel electrophoresis, the
S. enterica
serovar Agama and
S. enterica
serovar Binza isolates were very similar, but two clones each of
S. enterica
serovar Lomita and
S. enterica
serovar Ried were found. Badgers excreting
S. enterica
serovar Agama were spatially clustered.
Oligonucleotide Probes That Detect Quantitatively Significant Groups of Butyrate-Producing Bacteria in Human Feces
Authors: Hold Georgina L. , Schwiertz Andreas , Aminov Rustam I. , Blaut Michael , Flint Harry J.
Published: July 2003

16S rRNA-targeted oligonucleotide probes were designed for butyrate-producing bacteria from human feces. Three new cluster-specific probes detected bacteria related toRoseburia intestinalis,Faecalibacterium prausnitzii, andEubacterium halliiat mean populations of 2.3, 3.8, and 0.6%, respectively, in samples from 10 individuals. Additional species-level probes accounted for no more than 1%, with a mean of 7.7%, of the total human fecal microbiota identified as butyrate producers in this study. Bacteria related toE. halliiand the generaRoseburiaandFaecalibacteriumare therefore among the most abundant known butyrate-producing bacteria in human feces.
Inactivation of Vegetative Cells, but Not Spores, of
Bacillus anthracis
,
B. cereus
, and
B. subtilis
on Stainless Steel Surfaces Coated with an Antimicrobial Silver- and Zinc-Containing Zeolite Formulation
Authors: Galeano Belinda , Korff Emily , Nicholson Wayne L.
Published: July 2003

Stainless steel surfaces coated with paints containing a silver- and zinc-containing zeolite (AgION antimicrobial) were assayed in comparison to uncoated stainless steel for antimicrobial activity against vegetative cells and spores of three
Bacillus
species, namely,
B. anthracis
Sterne,
B. cereus
T, and
B. subtilis
168. Under the test conditions (25°C and 80% relative humidity), the zeolite coating produced approximately 3 log
10
inactivation of vegetative cells within a 5- to 24-h period, but viability of spores of the three species was not significantly affected.
The Diffuse Interstellar Bands
Authors: Herbig G. H.
Published: July 2003

The diffuse interstellar bands are absorption features observed in the spectra of stars seen through significant column densities of interstellar material. Of the 127 confirmed DIBs in the optical region between 0.4 and about 1.3 /Lm, only 2 have (tentatively) been identified with a specific carrier. Because DIB strengths increase roughly in proportion to color excess, they were originally suspected of being produced on or in the interstellar grains, but current evidence favors some species of free polyatomic molecules, either neutral or ionized. DIBs are conspicuously broader than the atomic interstellar lines, having widths at half-depth ranging from 0.8 to about 30 Å. These widths are presumably due to unresolved rotational structure, possibly compounded by lifetime broadening of the upper state. Recent proposals that C60, some members of the PAH family, or polycarbon chains are responsible for the DIB spectrum are either not supported by observation or await better data.
Explosive Nucleosynthesis Revisited: Yields
Authors: Arnett David
Published: July 2003

Three new, independent projects that provide detailed predictions of nucleosynthesis yields (up to Z = 36) from massive stars are examined and compared. The general agreement is surprisingly good. Preliminary comparison with abundance data, especially for elemental abundances in extreme Population II stars, is promising. Implications of these comparisons and critical uncertainties are discussed.
Completing the Copernican Revolution: The Search for Other Planetary Systems
Authors: Black David C.
Published: July 2003

The past few decades have witnessed significant advances in our understanding of how stars form, and there has been an associated increase in our knowledge of conditions and phenomena in the early solar system. These have led to the formulation of a paradigm for the origin of the solar system that is sufficiently complete that its basic elements can be tested directly through observations. A simple, but profound, consequence of the paradigm is that most if not all stars should be accompanied by planetary systems. The accuracy of instruments that can be used in such searches has improved to the point that Jupiter-like companions to a number of nearby stars could be detected. However, the results to date are that no other planetary systems have been detected, and the absence of detection is becoming statistically significant, particularly as it relates to the existence of brown dwarf companions to main-sequence stars.
Mathematical Anthropology
Authors: Burton Michael L.
Published: July 2003

This review is written at a time of great activity in mathematical anthropology, including the recent publication of edited volumes by Kay on mathematical anthropology (35), by Romney, Shepard & Nerlove on multidimensional scaling (50), and by Buchler & Nutini on game theory (8). In addition there have been recent reviews of the field by White (63) and Holfman (31). Space does not permit a complete discussion of all instances where mathematics may have a place in anthropology, so I have chosen to emphasize some topics which have not been fully discussed in the other two review articles. These are measurement problems, some probabilistic topics in social organization, and spatial analyses.
The Life of an Academic: A Personal Record of a Teacher, Administrator, and Anthropologist
Authors: Friedl Ernestine
Published: July 2003

An account, spanning 50 years, of how I became an anthropologist, my graduate education at Columbia University, and my academic positions at Brooklyn and Queens College and at Duke University. I discuss my fieldwork among the Chippewa of Wisconsin and among modern Greeks in Boetia and Athens. I comment on the new ethnography as it applies to modern Greek studies and discuss how and why I turned to gender studies. I comment on teaching, university administration, and trends in contemporary anthropology and make a recommendation for a future thrust of the field. Reconnecting biology and cultural anthropology is, I believe, a necessary step if anthropology is to continue to be useful for ameliorating the human condition.
The Persistent Power of "Race" in the Cultural and Political Economy of Racism
Authors: Harrison Faye V.
Published: July 2003

Historically, anthropology has occupied a central place in the construction and reconstruction of race as both an intellectual device and a social reality. Critiques of the biological concept of race have led many anthropologists to adopt a “no-race” posture and an approach to intergroup difference highlighting ethnicity-based principles of classification and organization. Often, however, the singular focus on ethnicity has left unaddressed the persistence of racism and its invidious impact on local communities, nation-states, and the global system. Within the past decade, anthropologists have revitalized their interest in the complex and often covert structures and dynamics of racial inequality. Recent studies shed light on race’s heightened volatility on contemporary sociocultural landscapes, the racialization of ethno-nationalist conflicts, anthropology’s multiple traditions of antiracism, and intranational as well as international variations in racial constructions, including the conventionally neglected configurations of whiteness.
The Archaeology of Slavery in North America
Authors: Singleton Theresa A.
Published: July 2003

Archaeologists began to study slavery more than two decades ago, and since that time this interest has rapidly grown to become one of the most popular research specialties in the archaeology of the post-Columbian period. This essay reviews the interpretation of the archaeological record of slavery directed toward the analysis of four themes: living conditions under slavery, status differences within the plantation community, relationships of planter dominance and slave resistance, and formation of African-American cultural identity. It also discusses the sociopolitical context within which this study has operated and strongly recommends that greater efforts be taken to include African-American perspectives to inform this research.
Miocene Hominoids and Hominid Origins
Authors: Benefit Brenda R. , McCrossin Monte L.
Published: July 2003

Recent discoveries have greatly clarified the family tree relationships of Miocene apes to modern apes and humans. Contrary to most previous interpretations, new fossil evidence indicates that well-known middle-late Miocene large-bodied apes such as Kenyapithecus, Sivapithecus, and Dryopithecus branched off before the ancestor that gave rise to all living hominoids; therefore, these extinct genera are not members of the great ape and human grouping. Jaw and tooth features that Miocene large-bodied apes share with great apes and humans can now be regarded as conservative retentions from the ancestral condition for living apes, including gibbons. The first appearance of these great ape-like features in the African middle Miocene is correlated with an adaptive shift to consumption of hard fruit and nuts. Although the transition from life in the trees to life on the ground is deeply embedded in models of human evolution as a primary motive force in human origins, among African large-bodied apes this change occurred approximately 15 million years ago and is not directly linked with the advent of bipedalism or colonization of grassland environments 3-4 million years ago.
Political Economy in Early Mesopotamian States
Authors: Yoffee Norman
Published: July 2003

An enormous amount of work has been done in recent years on what can be called the political economy of the earliest states in ancient Mesopotamia. These investigations appraise the organization of the great manorial estates of temples and palaces and show that local systems of power and authority coexisted with and often resisted centralized governments. It is also apparent that social institutions were permeable and that individuals played multiple and varied roles, reducing risks, cooperating, and competing as political fortunes changed over time. The interaction of autonomous city-states within a Mesopotamian cultural sphere has been foregrounded in certain work. Studies of production, trade, and consumption are reviewed from ca 3200-1600 B.C.
Metrical Phonology
Authors: Hammond Michael
Published: July 2003

Metrical theory is a branch of phonology that posits a hierarchical structure to represent stress patterns in the minds of speakers. This review examines the basic arguments for this theory and surveys the central issues of the field over the past 18 years. These issues include questions about whether the foot typology is symmetric, whether there is a strict binarity requirement, and how to treat ternary iteration. The review concludes with a brief overview of the impact of constraint-based phonology on metrical theory.
Kinship Studies in Late Twentieth-Century Anthropology
Authors: Peletz Michael G.
Published: July 2003

This review examines the state of play of kinship studies in late twentieth-century anthropology, paying close attention to theoretical advances and shifts in methodology and intent that have occurred since the 1970s. It highlights developments in Marxist, feminist, and historical approaches, the repatriation of kinship studies, various aspects of lesbian/gay kinship, and issues bearing on the new reproductive technologies. Contemporary kinship studies tend to be historically grounded; tend to focus on everyday experiences, understandings, and representations of gender, power, and difference; and tend to devote considerable analytic attention to themes of contradiction, paradox, and ambivalence.
Frontiers and Boundaries in Archaeological Perspective
Authors: Lightfoot Kent G. , Martinez Antoinette
Published: July 2003

Most archaeological studies of frontiers and boundaries are informed by a colonialist perspective of core-periphery relationships. In this review, we identify three problems with colonialist models of territorial expansion, boundary maintenance, and homogeneousc olonial populations. These problems are (a) insular models of culture change that treat frontiers as passive recipients of core innovations, (b) the reliance on macro scales of analysis employed frontier research, and (c) the expectation of sharp frontier boundaries visible material culture. In the final section, we reconceptualize frontiers as zones of cross-cutting social networks based largely on our research on fur-trade outposts in western North America. Our approach considers the study of diverse and overlapping segmentary or factional groups that cross-cut traditionally perceived colonial-indigenous boundaries on the frontier at different spatial and temporal scales of analysis.
All Made Up: Performance Theory and the New Anthropology of Sex and Gender
Authors: Morris Rosalind C.
Published: July 2003

This review considers the impact of recent performance theory, especially the theory of gender performativity, on anthropological efforts to theorize sex and gender. In brief, the theory of performativity defines gender as the effect of discourse, and sex as the effect of gender. The theory is characterized by a concern with the productive force rather than the meaning of discourse and by its privileging of ambiguity and indeterminacy. This review treats recent performance theory as the logical heir, but also the apotheosis, of two anthropological traditions. The first tradition is feminist anti-essentialism, which first distinguished between sex and gender in an effort to denaturalize asymmetry. The second tradition is practice theory, which emphasized habitual forms of embodiment in its effort to overcome the oppositions between individual and society. In concluding, questions are raised about the degree to which current versions of performance theory enact rather than critically engage the political economies of value and desire from which they arise.
Photosynthesis of Overwintering Evergreen Plants
Authors: Öquist Gunnar , Huner Norman P.A.
Published: July 2003

In this review we focus on photosynthetic behavior of overwintering evergreens with an emphasis on both the acclimative responses of photosynthesis to cold and the winter behavior of photosynthesis in conifers. Photosynthetic acclimation is discussed in terms of the requirement for a balance between the energy absorbed through largely temperature-insensitive photochemical processes and the energy used for temperature-sensitive biochemical processes and growth. Cold acclimation transforms the xanthophyll-mediated nonphotochemical antenna quenching of absorbed light from a short-term dynamic response to a long-term sustained quenching for the whole winter period. This acclimative response helps protect the evergreen foliage from photooxidative damage during the winter when photosynthesis is restricted or prevented by low temperatures. Although the molecular mechanisms behind the sustained winter excitation quenching are largely unknown, it does involve major alterations in the organization and composition of the photosystem II antenna. In addition, photosystem I may play an important role in overwintering evergreens not only by quenching absorbed light photochemically via its support of cyclic electron transport at low temperatures, but also by nonphotochemical quenching of absorbed light irrespective of temperature. The possible role of photosystem II reaction centers in nonphotochemical quenching of absorbed energy in overwintering evergreens is also discussed. Processes like chlororespiration and cyclic electron transport may also be important for maintaining the functional integrity of the photosynthetic apparatus of overwintering evergreens both during periods of thawing in winter and during recovery from winter stress in spring. We suggest that the photosynthetic acclimation responses of overwintering evergreens represent specific evolutionary adaptations for plant species that invest in the long-term maintenance of leaf structure in cold climatic zones as exemplified by the boreal forests of the Northern Hemisphere.
Circular Oligonucleotides: New Concepts in Oligonucleotide Design
Authors: Kool Eric T.
Published: July 2003

Recent progress in the synthesis and properties of circular oligonucleotides as ligands for DNA and RNA and as templates for polymerase enzymes is described. Small synthetic circular DNAs, RNAs, and chimeric analogues ranging from 28 to 74 nucleotides in size have been synthesized with the use of a nonenzymatic ligation strategy. Some of these were designed to undergo triplex formation with single-stranded DNA and RNA targets, and many bind with affinities and sequence selectivities considerably greater than those seen for linear oligonucleotides. Design strategies and modes of binding are discussed in the light of possible use of such molecules as hybridization probes, molecular diagnostics, and sequence-specific inhibitors of gene expression. Small circular oligonucleotides have also been shown to act as unusually efficient templates for DNA and RNA polymerases, which produce long, repeating copies of the circular sequence by a rolling circle process.
Growth-Regulating Substances in Plants
Authors: van Overbeek J.
Published: July 2003

Auxins have been made the main topic of this discussion in which the reviewer has attempted to be informative rather than comprehensive. Papers have been selected from those which have appeared since the last review on auxins in this publication in 1939 (1). The subject has been divided into four parts: (a) terminology; (b) the different forms of auxin and their analysis; (c) the action of auxin; and (d) practical aspects.
Sir Edward Mellanby, G.B.E., K.C.B., M.D., F.R.C.P., F.R.S. (1884-1955): The Man, Research Worker, and Statesman
Authors: Platt B. S.
Published: July 2003

Sir Edward MelIanby had accepted a cordial invitation from the Editorial Committee of the Annual Review of Biochemistry to contribute this Prefatory Chapter. Unhappily, before he had completed his seventy-first year, he died suddenly on Sunday, January 30, 1955, about mid-day, after he had spent the morning at his research. His draft of the introduction to his contribution to this volume is printed below in the section“ to British Biochemistry.”

For nearly six years after retiring from the post of Secretary of the Medical Research Council, he continued to engage in research work and in many scientific affairs. He was, for example, active in the Royal Society, of which he had been a Fellow for 30 years, and he was one of its Vice-Presidents. Sir Henry Dale has recently completed an Obituary Notice of Mellanby for the Royal Society (1955); this tribute is of such grandeur as perhaps only a man of Sir Henry's eminence could contribute, and I shall quote from this to give the weight of wisdom, experience, and knowledge to this chapter.
Biochemistry as Part of My Life
Authors: Nachmansohn David
Published: July 2003

Character, emotions, literary and artistic experience, philosophy, and political involvements form an integral part of a personality. Since scientists are human, all these factors determine their reactions, their way of thinking, and must be essential elements in the formation of scicntific ideas and views, motives, and attitudes. Knowledge alone of a special scientific field, however solid and profound, provides only the tools. What is achieved with these tools depends to a very large extent on the complex factors of a personality. When I was asked to write the prefatory chapter, I was thrilled. It seemed to me not only a great honor but a great challenge, an opportunity to describe my general views, my philosophy, the people who inspired me, the factors which influenced my scientific thinking, the background of my scientific theory. I wanted to omit as much as possible autobiographical data. But soon it became apparent to me, just as to some of my illustrious predecessors of these prefatory chapters, that a purely philosophical-historical essay would lose its special character and flavor and resemble some scientific abstracts without any experimental data. It would lose its attraction and vitality. It would fit into philosophical and historical books rather than into these chapters, where readers may like to know how a scientist who proposed a new concept found his particular way and what specific factors influenced his development and his theories. If one accepts the premise that science forms only a part of a personality, personal experience and background should be included.
DNA POLYMERASE III HOLOENZYME: Structure and Function of a Chromosomal Replicating Machine
Authors: Kelman Zvi , O'Donnell Mike
Published: July 2003

DNA polymerase III holoenzyme contains two DNA polymerases embedded in a particle with 9 other subunits. This multi subunit DNA polymerase is the Escherichia coli chromosomal replicase, and it has several special features that distinguish it as a replicating machine. For example, one of its subunits is a circular protein that slides along DNA while clamping the rest of the machinery to the template. Other subunits act together as a matchmaker to assemble the ring onto DNA. Overall, E. coli DNA polymerase III holoenzyme is very similar in both structure and function to the chromosomal replicases of eukaryotes, from yeast all the way up to humans. This review summarizes our present knowledge about the function of the 10 subunits of this replicating machine and how they coordinate their actions for smooth duplication of chromosomes.
HOW TO GET PAID FOR HAVING FUN
Authors: Koshland Daniel E.
Published: July 2003

When writing a prefatory chapter for Annual Reviews a scientist is confronted with the question of what in his or her life might be interesting to others. In my case I was appalled at the absence of material that generates good novels: no broken homes, no misunderstood childhood, no criminal youth gangs, no disastrous liaisons. A landscape of boredom from sea to shining sea. If there is one overlying theme it is that I got paid for doing what I enjoyed all my life. I wish I could say I had cleverly plotted to achieve this nirvana by a series of Machiavellian measures. The truth, however, is closer to the course of the Lord High Executioner in the Mikado: I was “...wafted by a favoring gale as one sometimes is in trances.”

As I look back, each new chapter in my life seems to have been a mutation of Pasteur’s phrase “chance to the prepared mind.” Once I had decided to be a scientist, the events seemed to flow as if by accident. However, in retrospect I see that the experience of each phase of my life presaged the next “accidental happening.” But I was surprised at the “random walk” nature of my life.
SELENOCYSTEINE
Authors: Stadtman Thressa C.
Published: July 2003

Selenocysteine is recognized as the 21st amino acid in ribosome-mediated protein synthesis and its specific incorporation is directed by the UGA codon. Unique tRNAs that have complementary UCA anticodons are aminoacylated with serine, the seryl-tRNA is converted to selenocysteyl-tRNA and the latter binds specifically to a special elongation factor and is delivered to the ribosome. Recognition elements within the mRNAs are essential for translation of UGA as selenocysteine. A reactive oxygen-labile compound, selenophosphate, is the selenium donor required for synthesis of selenocysteyl-tRNA. Selenophosphate synthetase, which forms selenophosphate from selenide and ATP, is found in various prokaryotes, eukaryotes, and archaebacteria. The distribution and properties of selenocysteine-containing enzymes and proteins that have been discovered to date are discussed. Artificial selenoenzymes such as selenosubtilisin have been produced by chemical modification. Genetic engineering techniques also have been used to replace cysteine residues in proteins with selenocysteine. The mechanistic roles of selenocysteine residues in the glutathione peroxidase family of enzymes, the 5′ deiodinases, formate dehydrogenases, glycine reductase, and a few hydrogenases are discussed. In some cases a marked decrease in catalytic activity of an enzyme is observed when a selenocysteine residue is replaced with cysteine. This substitution caused complete loss of glycine reductase selenoprotein A activity.
MISMATCH REPAIR IN REPLICATION FIDELITY, GENETIC RECOMBINATION, AND CANCER BIOLOGY
Authors: Modrich Paul , Lahue Robert
Published: July 2003

Mismatch repair stabilizes the cellular genome by correcting DNA replication errors and by blocking recombination events between divergent DNA sequences. The reaction responsible for strand-specific correction of mispaired bases has been highly conserved during evolution, and homologs of bacterial MutS and MutL, which play key roles in mismatch recognition and initiation of repair, have been identified in yeast and mammalian cells. Inactivation of genes encoding these activities results in a large increase in spontaneous mutability, and in the case of mice and men, predisposition to tumor development.
MOLECULAR MECHANISMS OF DRUG RESISTANCE IN MYCOBACTERIUM TUBERCULOSIS
Authors: Blanchard John S.
Published: July 2003

In spite of forty years of effective chemotherapy for tuberculosis, the molecular mechanisms of antibacterial compounds in Mycobacterium tuberculosis have only recently been revealed. Broad spectrum antibacterials, including streptomycin, rifampicin, and fluoroquinolones have been demonstrated to act on the same targets in M. tuberculosis as they do in E. coli. Resistance to these agents results from single mutagenic events that lead to amino acid substitutions in their target proteins. The mechanisms of action of the unique antitubercular drugs, including isoniazid, ethambutol, and pyrazinamide have also recently been defined. Resistance to isoniazid can be caused either by mutations in the katG-encoded catalase-peroxidase, the enzyme responsible for drug activation, or by the molecular target, the inhA-encoded long chain enoyl-ACP reductase. Ethambutol appears to block specifically the biosynthesis of the arabinogalactan component of the mycobacterial cell envelope, and pyrazinamide has no known target. With the resurgence of tuberculosis and the appearance of strains which are multiply resistant to the above compounds, present tuberculosis chemotherapies are threatened. New approaches to the treatment of multi drug-resistant tuberculosis are needed.
PROTEIN PRENYLATION: Molecular Mechanisms and Functional Consequences
Authors: Zhang Fang L. , Casey Patrick J.
Published: July 2003

Prenylation is a class of lipid modification involving covalent addition of either farnesyl (15-carbon) or geranylgeranyl (20-carbon) isoprenoids to conserved cysteine residues at or near the C-terminus of proteins. Known prenylated proteins include fungal mating factors, nuclear lamins, Ras and Ras-related GTP-binding proteins (G proteins), the subunits of trimeric G proteins, protein kinases, and at least one viral protein. Prenylation promotes membrane interactions of most of these proteins, which is not surprising given the hydrophobicity of the lipids involved. In addition, however, prenylation appears to play a major role in several protein-protein interactions involving these species. The emphasis in this review is on the enzymology of prenyl protein processing and the functional significance of prenylation in cellular events. Several other recent reviews provide more detailed coverage of aspects of prenylation that receive limited attention here owing to length restrictions (1-4).
PROTEIN TRANSPORT ACROSS THE EUKARYOTIC ENDOPLASMIC RETICULUM AND BACTERIAL INNER MEMBRANES
Authors: Rapoport Tom A. , Jungnickel Berit , Kutay Ulrike
Published: July 2003

Protein transport across the endoplasmic reticulum membrane can occur by two pathways, a co- and a post-translational one. In both cases, polypeptides are first targeted to translocation sites in the membrane by virtue of their signal sequences and then transported across or inserted into the phospholipid bilayer, most likely through a protein-conducting channel. Key components of the translocation apparatus have now been identified and the translocation pathways Seem likely to be related to each other but mechanistically distinct. Protein transport across the bacterial inner membrane is both similar to and different from the process in eukaryotes. Other pathways of protein translocation exist that bypass the ones involving classical signal sequences.
ELECTRON TRANSFER IN PROTEINS
Authors: Gray Harry B. , Winkler Jay R.
Published: July 2003

Electron-transfer (ET) reactions are key steps in a diverse array of biological transformations ranging from photosynthesis to aerobic respiration. A powerful theoretical formalism has been developed that describes ET rates in terms of two parameters: the nuclear reorganization energy (γ) and the electroniccoupling strength (HAB). Studies of ET reactions in ruthenium-modified proteins have probed γ and HAB in several metalloproteins (cytochrome c, myoglobin, azurin). This work has shown that protein reorganization energies are sensitive to the medium surrounding the redox sites and that an aqueous environment, in particular, leads to large reorganization energies. Analyses of electronic-coupling strengths suggest that the efficiency of long-range ET depends on the protein secondary structure: β sheets appear to mediate coupling more efficiently than α-helical structures, and hydrogen bonds play a critical role in both.
DNA TOPOISOMERASES
Authors: Wang James C.
Published: July 2003

The various problems of disentangling DNA strands or duplexes in a cell are all rooted in the double-helical structure of DNA. Three distinct subfamilies of enzymes, known as the DNA topoisomerases, have evolved to solve these problems. This review focuses on work in the past decade on the mechanisms and cellular functions of these enzymes. Newly discovered members and recent biochemical and structural results are reviewed, and mechanistic implications of these results are summarized. The primary cellular functions of these enzymes, including their roles in replication, transcription, chromosome condensation, and the maintenance of genome stability, are then discussed. The review ends with a summary of the regulation of the cellular levels of these enzymes and a discussion of their association with other cellular proteins.
INTERRELATIONSHIPS OF THE PATHWAYS OF mRNA DECAY AND TRANSLATION IN EUKARYOTIC CELLS
Authors: Jacobson Allan , Peltz Stuart W.
Published: July 2003

While the potential importance of mRNA stability to the regulation of gene expression has been recognized, the structures and mechanisms involved in the determination of individual mRNA decay rates have just begun to be elucidated, particularly in mammalian systems and yeast. It is now well established that mRNA decay is not a default process, in which an array of nonspecific nucleases degrades indiscriminately based on target size or ribosome protection of the substrate. Rather, like transcription, RNA processing, and translation, mRNA decay is a precise process dependent on a variety of specific cis-acting sequences and trans-acting factors. Entry into the pathways of mRNA decay is triggered by at least three types of initiating event: poly(A) shortening, arrest of translation at a premature nonsense codon, and endonucleolytic cleavage. Steps subsequent to pol y(A) shortening or premature translational termination converge in a pathway that progresses from removal of the 5′ cap to exonucleolytic digestion of the body of the mRNA. mRNA fragments generated by endonucleolytic cleavage are most likely removed by exonucleolytic decay as well, but these events have not been characterized in detail. Nucleases and other factors (including mRNA sequence elements and autoregulatory proteins) required for the promotion or inhibition of these pathways have been identified by both biochemical and genetic methods and systematic attempts to understand their respective roles have begun. mRNA sequences whose presence or absence has marked effects on mRNA decay rates include the ubiquitous cap and poly(A) tail, sequences that comprise endonuclease cleavage sites, and sequences that promote poly(A) shortening. The latter are found in the 3′-UTR (untranslated region) and in coding regions. Evidence that poly(A) stimulates translation initiation, that some destabilization sequences must be translated in order to function, and that premature translation termination promotes rapid mRNA decay indicates a close linkage between the elements regulating mRNA decay and components of the protein synthesis apparatus. This linkage, and other data, leads us to propose a model for a functional mRNP. In this model, interactions between factors associated with opposite ends of an mRNA stimulate translation initiation and minimize the rate of entry into the pathways of mRNA decay. Events that initiate mRNA decay are postulated to be those that can disrupt this functional complex and create substrates for exonucleolytic digestion.
RECODING: Dynamic Reprogramming of Translation
Authors: Gesteland Raymond F. , Atkins John F.
Published: July 2003

A minority of genes in probably all organisms rely on “recoding” for translation of their mRNAs. In these cases, the rules for decoding are temporarily altered through the action of specific signals built into the mRNA sequences. Three classes are described. 1. Frameshifting at a particular site allows expression of a protein from an mRNA with overlapping open reading frames, often giving two protein products from one mRNA. 2. The meanings of code words are altered: specific stop codons can be redirected to encode selenocysteine, tryptophan, or glutamine. 3. Ribosomes can translate over coding gaps in mRNA. These novel mechanisms expand the repertoire of the genetic code and are at the heart of several regulatory schemes.
STRUCTURE AND FUNCTIONS OF THE 20S AND 26S PROTEASOMES
Authors: Coux Olivier , Tanaka Keiji , Goldberg Alfred L.
Published: July 2003

The proteasome is an essential component of the ATP-dependent proteolytic pathway in eukaryotic cells and is responsible for the degradation of most cellular proteins. The 20S (700-kDa) proteasome contains multiple peptidase activities that function through a new type of proteolytic mechanism involving a threonine active site. The 26S (2000-kDa) complex, which degrades ubiquitinated proteins, contains in addition to the 20S proteasome a 19S regulatory complex composed of multiple ATPases and components necessary for binding protein substrates. The proteasome has been highly conserved during eukaryotic evolution, and simpler forms are even found in archaebacteria and eubacteria. Major advances have been achieved recently in our knowledge about the molecular organization of the 20S and 19S particles, their subunits, the proteasome’s role in MHC-class 1 antigen presentation, and regulators of its activities. This article focuses on recent progress concerning the biochemical mechanisms and intracellular functions of the 20S and 26S proteasomes.
Protein Disulfide Bond Formation in Prokaryotes
Authors: Kadokura Hiroshi , Katzen Federico , Beckwith Jon
Published: July 2003

▪ Abstract  Disulfide bonds formed between pairs of cysteines are important features of the structure of many proteins. Elaborate electron transfer pathways have evolved Escherichia coli to promote the formation of these covalent bonds and to ensure that the correct pairs of cysteines are joined in the final folded protein. These transfers of electrons consist, in the main, of cascades of disulfide bond formation or reduction steps between a series of proteins (DsbA, DsbB, DsbC, and DsbD). A surprising variety of mechanisms and protein structures are involved in carrying out these steps.
The Enzymes, Regulation, and Genetics of Bile Acid Synthesis
Authors: Russell David W.
Published: July 2003

▪ Abstract  The synthesis and excretion of bile acids comprise the major pathway of cholesterol catabolism in mammals. Synthesis provides a direct means of converting cholesterol, which is both hydrophobic and insoluble, into a water-soluble and readily excreted molecule, the bile acid. The biosynthetic steps that accomplish this transformation also confer detergent properties to the bile acid, which are exploited by the body to facilitate the secretion of cholesterol from the liver. This role in the elimination of cholesterol is counterbalanced by the ability of bile acids to solubilize dietary cholesterol and essential nutrients and to promote their delivery to the liver. The synthesis of a full complement of bile acids requires 17 enzymes. The expression of selected enzymes in the pathway is tightly regulated by nuclear hormone receptors and other transcription factors, which ensure a constant supply of bile acids in an ever changing metabolic environment. Inherited mutations that impair bile acid synthesis cause a spectrum of human disease; this ranges from liver failure in early childhood to progressive neuropathy in adults.
The Rotary Motor of Bacterial Flagella
Authors: Berg Howard C.
Published: July 2003

▪ Abstract  Flagellated bacteria, such as Escherichia coli, swim by rotating thin helical filaments, each driven at its base by a reversible rotary motor, powered by an ion flux. A motor is about 45 nm in diameter and is assembled from about 20 different kinds of parts. It develops maximum torque at stall but can spin several hundred Hz. Its direction of rotation is controlled by a sensory system that enables cells to accumulate in regions deemed more favorable. We know a great deal about motor structure, genetics, assembly, and function, but we do not really understand how it works. We need more crystal structures. All of this is reviewed, but the emphasis is on function.
Aliphatic Epoxide Carboxylation
Authors: Ensign Scott A. , Allen Jeffrey R.
Published: July 2003

▪ Abstract  Aliphatic epoxides (epoxyalkanes) are highly reactive electrophilic molecules that are formed from the monooxygenase-catalyzed epoxidation of aliphatic alkenes. The bacterial metabolism of short-chain epoxyalkanes occurs by a three-step pathway resulting in net carboxylation to β-ketoacids. This pathway uses the atypical cofactor coenzyme M (CoM; 2-mercaptoethanesulfonic acid) as the nucleophile for the epoxide ring opening and as the carrier of 2-hydroxyalkyl- and 2-ketoalkyl-CoM intermediates. Four enzymes are involved in epoxide carboxylation: a zinc-dependent alkyltransferase, two short-chain dehydrogenases with specificities for the chiral products of the R- and S-1,2-epoxyalkane ring opening, and an NADPH:disulfide oxidoreductase/carboxylase that reduces the thioether bond of the 2-ketoalkyl-CoM conjugate and carboxylates the resulting carbanion. In this review, we summarize the biochemical, mechanistic, and structural features of the enzymes of epoxide carboxylation and show how these enzymes, together with CoM, work in concert to achieve this highly unusual carboxylation reaction.
The Role of Dynamics in Enzyme Activity
Authors: Daniel R.M. , Dunn R.V. , Finney J.L. , Smith J.C.
Published: July 2003

▪ Abstract  Although protein function is thought to depend on flexibility, precisely how the dynamics of the molecule and its environment contribute to catalytic mechanisms is unclear. We review experimental and computational work relating to enzyme dynamics and function, including the role of solvent. The evidence suggests that fast motions on the 100 ps timescale, and any motions coupled to these, are not required for enzyme function. Proteins where the function is electron transfer, proton tunneling, or ligand binding may have different dynamical dependencies from those for enzymes, and enzymes with large turnover numbers may have different dynamical dependencies from those that turn over more slowly. The timescale differences between the fastest anharmonic fluctuations and the barrier-crossing rate point to the need to develop methods to resolve the range of motions present in enzymes on different time- and lengthscales.
Asia-Wide Emissions of Greenhouse Gases
Authors: Siddiqi Toufiq A.
Published: July 2003

Emissions of principal greenhouse gases (GHGs) from Asia are increasing faster than those from any other continent. This is a result of rapid economic growth, as well as the fact that almost half of the world's population lives in Asian countries. In this paper, we provide estimates of emissions of the two principal greenhouse gases, carbon dioxide (C02) and methane (CH4), from individual countries and areas. Recent literature has been reviewed for emission estimates for individual sources, such as carbon dioxide from cement manufacture, and methane from rice fields. There are very large uncertainties in many of these estimates, so several estimates are provided, where available.

The largest anthropogenic source of CO2 emissions is the use of fossil fuels. Energy consumption data from 1992 have been used to calculate estimated emissions of CO2 from this source. In view of the ongoing negotiations to limit future greenhouse gas emissions, estimates of projected CO2 emissions from the developing countries of Asia are also provided. These are likely to be 3 times their 1986 levels by 2010, under “business as usual” scenarios. Even with the implementation of energy efficiency measures and fuel switching where feasible, the emissions of CO2 are likely to double within the same time period.