Miracle-dz/UniFAR-FTUs huggingface dataset:
The U1 RNA-binding site of the U1 small nuclear ribonucleoprotein (snRNP)-associated A protein suggests a similarity with U2 snRNPs

The site of interaction between human U1 RNA and one of its uniquely associated proteins, A, was examined with in vitro binding assays. The A protein bound directly to stem-loop II of U1 RNA in a region which exhibits sequence similarity to U2 RNA. The similarity with U2 RNA was in a region that has been shown to interact with a U2 RNA-associated protein. The A protein-binding site on U1 RNA overlapped a previously described epitope for an RNA-specific human autoantibody (S. L. Deutscher and J. D. Keene, Proc. Natl. Acad. Sci. USA 85:3299-3303, 1988), supporting the hypothesis that the anti-RNA antibody originated as an anti-idiotypic response to A protein-specific autoantibodies.
Morpheme Conversion for Connecting Speech Recognizer and Language Analyzers in Unsegmented Languages

Connecting automatic speech recognizers (ASRs) and language analyzers is difﬁcult since they may be based on differences in part-of-speech (POS) systems; the latter cannot directly analyze the outputs of the former. In addition, in unsegmented languages such as Japanese, the ASR outputs are likely to have different word segmentation from that of the language analyzer inputs because they are individually developed. A conventional approach is to generate raw texts from the ASR outputs and re-analyze them using a morphological analyzer. However, if the ASR outputs contain recognition errors, the morphological analyzer incorrectly analyzes them even though they contain correctly recognized words. To avoid this problem, we propose a morpheme conversion method that directly converts ASR outputs into morpheme sequences suitable for the language analyzers. Our experiments show that morpheme conversion is more robust than the conventional approach against recognition errors.
Trichoderma reesei ACE4, a Novel Transcriptional Activator Involved in the Regulation of Cellulase Genes during Growth on Cellulose

T. reesei is commonly utilized in industry to produce cellulases, enzymes that degrade lignocellulosic biomass for the production of bioethanol and bio-based products. T. reesei is capable of rapidly initiating the biosynthesis of cellulases in the presence of cellulose, which has made it useful as a model fungus for studying gene expression in eukaryotes. Cellulase gene expression is controlled through multiple transcription factors at the transcriptional level. ABSTRACT The filamentous fungus Trichoderma reesei is a model strain for cellulase production. Cellulase gene expression in T. reesei is controlled by multiple transcription factors. Here, we identified by comparative genomic screening a novel transcriptional activator, ACE4 (activator of cellulase expression 4), that positively regulates cellulase gene expression on cellulose in T. reesei. Disruption of the ace4 gene significantly decreased expression of four main cellulase genes and the essential cellulase transcription factor-encoding gene ace3. Overexpression of ace4 increased cellulase production by approximately 22% compared to that in the parental strain. Further investigations using electrophoretic mobility shift assays, DNase I footprinting assays, and chromatin immunoprecipitation assays indicated that ACE4 directly binds to the promoter of cellulase genes by recognizing the two adjacent 5′-GGCC-3′ sequences. Additionally, ACE4 directly binds to the promoter of ace3 and, in turn, regulates the expression of ACE3 to facilitate cellulase production. Collectively, these results demonstrate an important role for ACE4 in regulating cellulase gene expression, which will contribute to understanding the mechanism underlying cellulase expression in T. reesei. IMPORTANCE T. reesei is commonly utilized in industry to produce cellulases, enzymes that degrade lignocellulosic biomass for the production of bioethanol and bio-based products. T. reesei is capable of rapidly initiating the biosynthesis of cellulases in the presence of cellulose, which has made it useful as a model fungus for studying gene expression in eukaryotes. Cellulase gene expression is controlled through multiple transcription factors at the transcriptional level. However, the molecular mechanisms by which transcription is controlled remain unclear. In the present study, we identified a novel transcription factor, ACE4, which regulates cellulase expression on cellulose by binding to the promoters of cellulase genes and the cellulase activator gene ace3. Our study not only expands the general functional understanding of the novel transcription factor ACE4 but also provides evidence for the regulatory mechanism mediating gene expression in T. reesei.
Genetic networks that regulate development in Dictyostelium cells

INTRODUCTION . 135 AGGREGATION.135 Aggregation Gene Network . 137 POSTAGGREGATION.138 Cell-Type-Specific Genes.138 Postaggregative Gene Network.139 CELL TYPE SPECIALIZATION.140 Network That Regulates Cell Type Specialization . 141 CULMINATION.142 Network That Regulates Culmination . 145 NETWORKS OF NETWORKS.146 ACKNOWLEDGMENTS . 147 REFERENCES . 147
Q fever and Coxiella burnetii: a model for host-parasite interactions

HISTORY . 127 EPIDEMIOLOGY . 129 CULTIVATION AND GROWTH OF C. BURNETII. 130 Entry into and Proliferation Within Cultured Cells; Comparison with Other Rickettsiae 130 Enumeration . 131 BIOLOGY OF C. BURNETII. 131 Ultrastructure/Morphology . 131 Genome . 132 Ribosomes . 133 Replication. 133 Phase Variation. 134 LPS. 135 BIOCHEMISTRY OF C. BURNETII . 135 Glycolytic and Related Enzymes . 135 Anabolic Enzymes of Amino Acids, Proteins, and Nucleic Acids . 136 Acidophilic Biochemistry and Intravacuolar Existence. 137 PATHOBIOLOGY. 138 Humans . 138 Embryonated Eggs . 139 Guinea Pigs and Other Animals. 139 Cell Cultures . 141 IMMUNOLOGY. 141 Vaccines . 143 SUMMARY AND PROSPECTS . 143 ACKNOWLEDGMENTS . 144 LITERATURE CITED . 144
Bacterial modulins: a novel class of virulence factors which cause host tissue pathology by inducing cytokine synthesis

Cytokines are a diverse group of proteins and glycoproteins which have potent and wide-ranging effects on eukaryotic cell function and are now recognized as important mediators of tissue pathology in infectious diseases. It is increasingly recognized that for many bacterial species, cytokine induction is a major virulence mechanism. Until recent years, the only bacterial component known to stimulate cytokine synthesis was lipopolysaccharide (LPS). It is only within the past decade that it has been clearly shown that many components associated with the bacterial cell wall, including proteins, glycoproteins, lipoproteins, carbohydrates, and lipids, have the capacity to stimulate mammalian cells to produce a diverse array of cytokines. It has been established that many of these cytokine-inducing molecules act by mechanisms distinct from that of LPS, and thus their activities are not due to LPS contamination. Bacteria produce a wide range of virulence factors which cause host tissue pathology, and these diverse factors have been grouped into four families: adhesins, aggressins, impedins, and invasins. We suggest that the array of bacterial cytokine-inducing molecules represents a new class of bacterial virulence factor, and, by analogy with the known virulence families, we suggest the term "modulin" to describe these molecules, because the action of cytokines is to modulate eukaryotic cell behavior. This review summarizes our current understanding of cytokine biology in relation to tissue homeostasis and disease and concisely reviews the current literature on the cytokine-inducing molecules produced by gram-negative and gram-positive bacteria, with an emphasis on the cellular mechanisms responsible for cytokine induction. We propose that modulins, by controlling the host immune and inflammatory responses, maintain the large commensal flora that all multicellular organisms support.
Mechanisms of gene regulation in the general control of amino acid biosynthesis in Saccharomyces cerevisiae

INTRODUCTION . 248 GENERAL AMINO ACID CONTROL IN S. CEREVISIAE . 249 Derepression Signal . 249 Amino Acid Biosynthetic Enzymes Subject to General Amino Acid Control . 250 Interplay between Pathway-Specific Regulation and General Amino Acid Control.251 Arginine biosynthetic enzymes . 251 Lysine biosynthetic enzymes . 251 Leucine biosynthetic enzymes. 251 Isoleucine-valine biosynthetic enzymes . 252 Glutamine biosynthetic enzymes . 252 Histidine biosynthetic enzymes . 252 Consequences of General Control-Mediated Derepression of Enzyme Activity on Amino Acid Pools.252 cis-ACTING REGULATORY ELEMENTS AT STRUCTURAL GENES SUBJECT TO THE GENERAL CONTROL . 253 HIS4 Regulatory Region . 253 HIS3 Regulatory Region . 256 TRP5 Regulatory Region. 257 HISS Regulatory Region . 258 ARG3 Regulatory Region . 258 Other Structural Genes . 258 trans-ACTING REGULATORY FACTORS IN GENERAL AMINO ACID CONTROL.258 GCN4 Encodes the Most Direct Positive Regulator in the General Control System . 258 GCN4 Protein Binds to the TGACTC Regulatory Sequences.260 GCN and GCD Factors That Function as Translational Regulators of GCN4 Expression.262 Translational Control of GCN4 Expression Requires the Upstream AUG Codons . 264 Translational Control of GCN4 and the Scanning Hypothesis for Translation Initiation . 266 Comparison of Translational Control Mechanisms for GCN4 and CPAI . 267 Pleiotropy of gcd Mutations . 267 Transcriptional Control of GCN4. 269 GENERAL AMINO ACID CONTROL IN OTHER FUNGI AND IN BACTERIA . 269 ACKNOWLEDGMENTS . 270 LITERATURE CITED. 270
Mapping of the p53 and mdm-2 interaction domains

The 90-kDa cellular protein encoded by the mouse mdm-2 oncogene binds to the p53 protein in vivo and inhibits its transactivation function (J. Momand, G. P. Zambetti, D. C. Olson, D. George, and A. J. Levine, Cell 69:1237-1245, 1992). cDNA clones encoding the human homolog of the mdm-2 protein (also called hdm-2) were isolated from a HeLa cell cDNA library. A series of monoclonal antibodies have been generated against human mdm-2 protein, and the epitopes recognized by these antibodies have been mapped. By construction of a series of deletion mutants, the region of the mdm-2 protein that is critical for complex formation with the p53 protein has been mapped to the N-terminal portion of the human mdm-2 protein. Interestingly, a monoclonal antibody with an epitope located in this same region failed to immunoprecipitate the mdm-2-p53 complex and appeared to recognize only free mdm-2 protein. The domain of the p53 protein that is sufficient for interaction with human mdm-2 protein has been mapped to the N-terminal 52 amino acid residues of the p53 protein. This region contains the transactivation domain of p53, suggesting that mdm-2 may inhibit p53 function by disrupting its interaction with the general transcription machinery.
Neutrophil chemotaxis in liver failure

Background Infection is a serious complication in patients with acute and chronic liver failure. Neutrophil chemotaxis is an important body defense mechanism against infection, which has been reported to be defective in such patients. However, the newly described family of potent chemoattractant cytokines (chemokines) and their relationship to neutrophil chemotaxis has not been previously studied in patients with acute and chronic liver failure. Aim of the thesis To identify the presence of and characterise the neutrophil chemotactic defect to chemokines in patients with acute and chronic liver failure. Patients and methods Neutrophils were isolated from patients with acute and chronic liver failure, and controls. Chemotaxis was determined using the CXC chemokines Interleukin-8 (TL-8) and Growth related oncogen-a (Gro-a) in a 48 well-modified Boyden chamber assay. Serum chemokine concentrations were measured using ELISA and neutrophil CXC chemokine receptors expression by flow cytometry. Results Neutrophil chemotaxis to EL-8 and Gro-a was reduced in patients with acute and chronic liver failure either due to alcoholic liver disease or hepatitis C compared with controls. This impairment was correlated with the severity of the disease. A partial correction in chemotaxis of patients' neutrophils was observed after cross incubation with the control sera and vice versa using control neutrophils and patients' sera. Neutrophil chemotaxis in patients with chronic liver failure is further reduced 2 hours after oral administration of an amino acid solution, which simulates human blood. Neutrophils isolated from the portal venous blood had similar chemotactic defects to neutrophils isolated from peripheral venous blood. However, chemotaxis was significantly reduced in neutrophils isolated from hepatic venous blood compared to neutrophils isolated from portal or peripheral blood. In cross over studies, portal neutrophil chemotaxis was significantly reduced after incubation with hepatic venous serum and vice versa. The CXC chemokines IL-8, IFN-Y-inducible protein (IP-10), and Monokine Induced by Interferony (Mig) were significantly elevated in patients with both acute and chronic liver failure compared with controls. There was no significant
Genome Sequence of the Spinosyns-Producing Bacterium Saccharopolyspora spinosa NRRL 18395

Saccharopolyspora spinosa is a Gram-positive bacterium that produces spinosad, a well-known biodegradable insecticide that is used for agricultural pest control and has an excellent environmental and mammalian toxicological proﬁle. Here, we present the ﬁrst draft genome sequence of the type strain Saccharopolyspora spinosa NRRL 18395, which consists of 22 scaffolds. Saccharopolyspora spinosa S.
Regulation of fatty acid biosynthesis in Escherichia coli

Our understanding of fatty acid biosynthesis in Escherichia coli has increased greatly in recent years. Since the discovery that the intermediates of fatty acid biosynthesis are bound to the heat-stable protein cofactor termed acyl carrier protein, the fatty acid synthesis pathway of E. coli has been studied in some detail. Interestingly, many advances in the field have aided in the discovery of analogous systems in other organisms. In fact, E. coli has provided a paradigm of predictive value for the synthesis of fatty acids in bacteria and plants and the synthesis of bacterial polyketide antibiotics. In this review, we concentrate on four major areas of research. First, the reactions in fatty acid biosynthesis and the proteins catalyzing these reactions are discussed in detail. The genes encoding many of these proteins have been cloned, and characterization of these genes has led to a better understanding of the pathway. Second, the function and role of the two essential cofactors in fatty acid synthesis, coenzyme A and acyl carrier protein, are addressed. Finally, the steps governing the spectrum of products produced in synthesis and alternative destinations, other than membrane phospholipids, for fatty acids in E. coli are described. Throughout the review, the contribution of each portion of the pathway to the global regulation of synthesis is examined. In no other organism is the bulk of knowledge regarding fatty acid metabolism so great; however, questions still remain to be answered. Pursuing such questions should reveal additional regulatory mechanisms of fatty acid synthesis and, hopefully, the role of fatty acid synthesis and other cellular processes in the global control of cellular growth.
A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli

We present a collection of 182 isogenic strains containing genetically linked antibiotic resistance elements located at approximately 1-min intervals around the Escherichia coli chromosome. At most positions both Tn10 (Tetr) and TN10kan (Kanr) elements are available, so that the collection contains a linked set of alternating antibiotic resistance markers. The map position of each insertion has been aligned to the E. coli genetic map as well as to the Kohara ordered clone bank. These strains are designed to be used in a rapid two-step mapping system in E. coli. In the first step, the mutation is localized to a 5- to 15-min region of the chromosome by Hfr mapping with a set of Hfr strains containing either Tn10 or Tn10kan elements located 20 min from their respective origins of transfer. In the second step, the mutation is localized to a 1-min region by P1 transduction, with a collection of isogenic insertion strains as donors. We discuss the uses of this collection of strains to map and eventually to clone a variety of mutations in E. coli.
Biochemistry of homologous recombination in Escherichia coli

Homologous recombination is a fundamental biological process. Biochemical understanding of this process is most advanced for Escherichia coli. At least 25 gene products are involved in promoting genetic exchange. At present, this includes the RecA, RecBCD (exonuclease V), RecE (exonuclease VIII), RecF, RecG, RecJ, RecN, RecOR, RecQ, RecT, RuvAB, RuvC, SbcCD, and SSB proteins, as well as DNA polymerase I, DNA gyrase, DNA topoisomerase I, DNA ligase, and DNA helicases. The activities displayed by these enzymes include homologous DNA pairing and strand exchange, helicase, branch migration, Holliday junction binding and cleavage, nuclease, ATPase, topoisomerase, DNA binding, ATP binding, polymerase, and ligase, and, collectively, they define biochemical events that are essential for efficient recombination. In addition to these needed proteins, a cis-acting recombination hot spot known as Chi (chi: 5'-GCTGGTGG-3') plays a crucial regulatory function. The biochemical steps that comprise homologous recombination can be formally divided into four parts: (i) processing of DNA molecules into suitable recombination substrates, (ii) homologous pairing of the DNA partners and the exchange of DNA strands, (iii) extension of the nascent DNA heteroduplex; and (iv) resolution of the resulting crossover structure. This review focuses on the biochemical mechanisms underlying these steps, with particular emphases on the activities of the proteins involved and on the integration of these activities into likely biochemical pathways for recombination.
Evolutionary divergence and salinity-mediated selection in halophilic archaea

Halophilic (literally salt-loving) archaea are a highly evolved group of organisms that are uniquely able to survive in and exploit hypersaline environments. In this review, we examine the potential interplay between fluctuations in environmental salinity and the primary sequence and tertiary structure of halophilic proteins. The proteins of halophilic archaea are highly adapted and magnificently engineered to function in an intracellular milieu that is in ionic balance with an external environment containing between 2 and 5 M inorganic salt. To understand the nature of halophilic adaptation and to visualize this interplay, the sequences of genes encoding the L11, L1, L10, and L12 proteins of the large ribosome subunit and Mn/Fe superoxide dismutase proteins from three genera of halophilic archaea have been aligned and analyzed for the presence of synonymous and nonsynonymous nucleotide substitutions. Compared to homologous eubacterial genes, these halophilic genes exhibit an inordinately high proportion of nonsynonymous nucleotide substitutions that result in amino acid replacement in the encoded proteins. More than one-third of the replacements involve acidic amino acid residues. We suggest that fluctuations in environmental salinity provide the driving force for fixation of the excessive number of nonsynonymous substitutions. Tinkering with the number, location, and arrangement of acidic and other amino acid residues influences the fitness (i.e., hydrophobicity, surface hydration, and structural stability) of the halophilic protein. Tinkering is also evident at halophilic protein positions monomorphic or polymorphic for serine; more than one-third of these positions use both the TCN and the AGY serine codons, indicating that there have been multiple nonsynonymous substitutions at these positions. Our model suggests that fluctuating environmental salinity prevents optimization of fitness for many halophilic proteins and helps to explain the unusual evolutionary divergence of their encoding genes.
The single-stranded DNA-binding protein of Escherichia coli

The single-stranded DNA-binding protein (SSB) of Escherichia coli is involved in all aspects of DNA metabolism: replication, repair, and recombination. In solution, the protein exists as a homotetramer of 18,843-kilodalton subunits. As it binds tightly and cooperatively to single-stranded DNA, it has become a prototypic model protein for studying protein-nucleic acid interactions. The sequences of the gene and protein are known, and the functional domains of subunit interaction, DNA binding, and protein-protein interactions have been probed by structure-function analyses of various mutations. The ssb gene has three promoters, one of which is inducible because it lies only two nucleotides from the LexA-binding site of the adjacent uvrA gene. Induction of the SOS response, however, does not lead to significant increases in SSB levels. The binding protein has several functions in DNA replication, including enhancement of helix destabilization by DNA helicases, prevention of reannealing of the single strands and protection from nuclease digestion, organization and stabilization of replication origins, primosome assembly, priming specificity, enhancement of replication fidelity, enhancement of polymerase processivity, and promotion of polymerase binding to the template. E. coli SSB is required for methyl-directed mismatch repair, induction of the SOS response, and recombinational repair. During recombination, SSB interacts with the RecBCD enzyme to find Chi sites, promotes binding of RecA protein, and promotes strand uptake.
Two-way chemical signaling in Agrobacterium-plant interactions

The discovery in 1977 that Agrobacterium species can transfer a discrete segment of oncogenic DNA (T-DNA) to the genome of host plant cells has stimulated an intense interest in the molecular biology underlying these plant-microbe associations. This attention in turn has resulted in a series of insights about the biology of these organisms that continue to accumulate at an ever-increasing rate. This excitement was due in part to the notion that this unprecedented interkingdom DNA transfer could be exploited to create transgenic plants containing foreign genes of scientific or commercial importance. In the course of these discoveries, Agrobacterium became one of the best available models for studying the molecular interactions between bacteria and higher organisms. One extensively studied aspect of this association concerns the exchange of chemical signals between Agrobacterium spp. and host plants. Agrobacterium spp. can recognize no fewer than five classes of low-molecular-weight compounds released from plants, and other classes probably await discovery. The most widely studied of these are phenolic compounds, which stimulate the transcription of the genes needed for infection. Other compounds include specific monosaccharides and acidic environments which potentiate vir gene induction, acidic polysaccharides which induce one or more chromosomal genes, and a family of compounds called opines which are released from tumorous plant cells to the bacteria as nutrient sources. Agrobacterium spp. in return release a variety of chemical compounds to plants. The best understood is the transferred DNA itself, which contains genes that in various ways upset the balance of phytohormones, ultimately causing neoplastic cell proliferation. In addition to transferring DNA, some Agrobacterium strains directly secrete phytohormones. Finally, at least some strains release a pectinase, which degrades a component of plant cell walls.