bluuebunny/crossref_metadata_2025_split huggingface dataset:
PRD1: Dissecting the Genome, Structure, and Entry
Authors: Grahn A Marika , Butcher Sarah J , Bamford, Jaana K H , Bamford Dennis H 
Published: November 2023

Abstract
There are six extremely similar phage isolates, from different parts of the world, that all infect Gramnegative bacteria harboring a conjugative plasmid. One of these viruses is PRD1. Viruses with this morphology (protein capsid surrounding a membrane vesicle containing the linear double-stranded DNA genome) also infect Grampositive hosts. These viruses have been classified together forming the Tectiviridae family (2). There have been two characteristics that have drawn considerable interest to these viruses. Firstly, the linear, DNA genome has inverted terminal repeats, a covalently bound terminal protein at the50 ends, and replicates by a protein-primed, sliding-back mechanism. Secondly, due to their membranes, these viruses are considered to be relatively simple model systems for the study of membrane biogenesis, structure, and assembly in a well-characterized Escherichia coli background. As knowledge of the PRD1 structure accumulates, a third line of interest is building up. It appears that the replication mechanism, capsid architecture, major coat protein fold, and vertex structure strongly resemble those of human adenovirus (9, 11, 13, 19, 55). This has led to a proposal that these two viruses belong to the same lineage originating from a common ancestor that precedes the division of the bacterial and eukaryotic domains of life (12). This would mean that viruses are old, maybe older than the divergence of cellular life into three domains. It also appears that there are other viruses, infecting gram-positive bacteria, lower eukaryotes, and maybe archaea that are candidates for this adeno-PRD1 virus lineage. Using this structure-based comparison it has been possible to propose additional viral lineages that have members infecting hosts from different domains of life (4, 12). It should be noted that sequence comparison does not allow the identification of these functional and structural similarities due to the long evolutionary time span involved.
Lipid-Containing Bacteriophage PM2, the Type Organism of Corticoviridae
Authors: Bamford Dennis H , Bamford Jaana K H 
Published: November 2023

Abstract
Bacteriophage PM2 is the only described member of the Corticoviridae family (1). It was isolated from seawater collected from a polluted bay off the coast of Chile (13). The original host was a common marine bacterium Pseudoalteromonas espejiana BAL-31 (originally Pseudomonas BAL-31; 14, 18), which is the source of the DNA exonuclease BAL-31. Alternatively, Pseudoalteromonas sp. ER72M2 obtained from the East River, New York, by Leonard Mindich (26) can be used as a host for PM2. PM2 is the first bacteriophage in which the presence of lipids in the virion was firmly demonstrated (7, 15). The mass of the virion ( 4.5 107 Da) is distributed among nucleic acid (14%), lipid (14%), and protein (72%) constituents (8, 9). The sedimentation coefficient (S20,w) of the particle is 293 S and buoyant density in sucrose and cesium chloride is 1.26 g/cm3 and 1.28 g/cm3, respectively (8, 26). The stability of the virion is dependent on sodium and calcium ions and the virion equilibrated in sucrose is inactive (26). The viral membrane is located internally (7, 20) and it forms, together with the phage-encoded membrane-associated proteins and the phage DNA, a lipid core particle (25). An icosahedrally ordered capsid, about 60 nm in diameter, surrounds the lipid core. Thus the overall architecture of PM2 resembles that of bacteriophage PRD1, a tectivirus, which has a membrane vesicle surrounding the linear double-stranded DNA genome and an outer icosahedral capsid of approximately 65 nm in diameter (see chapter 13).
T4 and Related Phages: Structure and Development
Authors: Mosig Gisela , Eiserling Fred 
Published: November 2023

Abstract
History Bacteriophages T2,T4, and T6 were among seven Escherichia coli phages selected by Max Delbrück to study fundamentals of viral replication in a limited number of model viruses. These studies led to the first formulation of many concepts that are now accepted foundations of molecular biology: the fundamental differences between growth of viruses and cells (figure 18-1) (109); the demonstration that nucleic acids of virus particles suffice to establish infection and to direct synthesis of complete virions (163); the concept of the gene, including distinctions between units of recombination, mutation, and function (30); genetic recombination as exchange between DNA molecules involving ‘‘heterozygous’’ overlaps (91, 164, 165); the demonstration of messenger RNA (mRNA) (55, 414) and the non-overlapping triplet code (83, 390) with nonsense triplets as termination signals (31); the repair of DNA damage in the light (103) and in the dark (149); restriction and modification of DNA (247); the presence of spliced and nonspliced introns in prokaryotes (25, 171); the definition of pathways leading to the assembly of complex macromolecular structures (105); and the importance of protein complexes (machines), which change composition during various DNA transactions (9, 275).
Phage ϕ29 and its Relatives
Authors: Salas Margarita 
Published: November 2023

Abstract
Phage f29 and the related phages PZA, PZE, f15, BS32, B103, Nf, M2Y, and GA-1 are lytic phages that belong to the Podoviridae family. Most of them infect Bacillus subtilis and other related species such as Bacillus amyloliquefaciens, Bacillus pumilus, and Bacillus licheniformis. The host range of phage GA-1 differs from those of the other phages. Thus, GA-1 infects the Bacillus strain G1R. The f29-related phages have been classified in three groups based on serological properties, peptide maps, DNA physical maps, and DNA sequences (11, 90, 153). The first group includes phages f29, PZA, PZE, f15, and BS32; the second includes phages B103, Nf, and M2Y; and the third group contains phage GA-1as the only member. The genome of the f29-related phages, which are the smallest of the Bacillus phages isolated so far, consists in a linear double-stranded DNA of 19^21 kb with a phage-encoded protein, named terminal protein (TP), covalently linked to each 5 end. The complete DNA sequence of phages f29 (19,285 bp), PZA (19,366 bp), B103 (18,630 bp), and GA-1 (21,129 bp) are known (90, 109, 112, 149). Phage f29 and its relatives have a short, inverted terminal repeat, six nucleotides long (50-AAAGTA) for f29, PZA, f15, and B103 DNAs, eight nucleotides long (50-AAAGTAAG) for Nf and M2Y DNAs, and seven nucleotides long (50-AAATAGA) for GA-1 DNA. The remainder of the DNA sequence of phages f29 and PZA is very similar, and different from that of phage B103. The sequence of GA-1 DNA is less related to that of the other phages.
Bacteriophage P22
Authors: Prevelige Peter E 
Published: November 2023

Abstract
Bacteriophage P22, a relative of bacteriophage l, is a temperate phage of Salmonella typhimurium and has played key roles in the development of molecular biology. Originally isolated as a lysogen of Salmonella, it was with P22 that Zinder and Lederberg discovered the phenomenon of generalized transduction (113). In subsequent years, P22 has proven to be an important tool in Salmonella genetics, and equally importantly has served to illustrate key components of genetic and morphogenetic regulation (45). P22 shares many similarities in genetic structure and regulation with phage λ and there are excellent reviews of P22 biology (63, 88). The genome of P22 has been sequenced (11, 24, 61, 72, 100) and 65 genes have been annotated. The sequencing results support the hypothesis that phage P22 is a mosaic that has evolved through extensive recombination with other viruses. Significant progress has been made over the past 15 years in understanding the structural biology of P22 infection and replication which, after a brief overview, will be the focus of this chapter.
Phage-Based Expression Systems
Authors: Murray Noreen E 
Published: November 2023

Abstract
Phage, and plasmid, derivatives that had ‘‘picked up’’ genes from the Escherichia coli chromosome led Campbell (12) to propose his influential model based on recombination between circular genomes (see chapter 7). According to this model, segments of bacterial DNA were added to a phage genome if excision of the prophage was by an ‘‘aberrant’’ recombination event. These unexpected, or illegitimate (2, 27, 96) events fortuitously created the early recombinant clones that became tools at the cutting edge of research in the pioneering days of molecular biology. They, for example, facilitated the analyses of bacterial operons (30, 61) and enabled the amplification of the Lac repressor (60). Monitoring the bacterial enzymes specified by ltrp phages enhanced our understanding of the regulatory mechanisms of bacteriophage λ (18, 28, 29), telling us much about the control of transcription from the early λ promoters and suggesting how a phage promoter might be harnessed to amplify gene products. While these first ‘‘recombinant clones’’ of phages and plasmids were of unpredictable content, by 1974 it was possible to design and make new combinations of genes from any source in either plasmid (15) or phage λ vectors (62, 76, 92). This article will introduce the use of λ promoters within the context of the phage genome and follow the use of these and other phage promoters as components of genetically engineered plasmids, where they are relieved of their essential roles in the normal life cycle of the phage and instead used to amplify gene products.
Bacteriophage as Pollution Indicators
Authors: Gerba Charles P 
Published: November 2023

Abstract
Because of the difficulty and cost of detecting waterborne enteric pathogens, indicator organisms have been used since the beginning of the twentieth century. Much of the work in this area has focused on bacterial indicators, such as coliform and fecal coliform bacteria. However, it has been recognized in the last 30 years that these traditional indicators do not always reflect the waterborne occurrence of human pathogenic viruses and protozoa. Thus, bacteriophages have been investigated as a better indicator of these groups of pathogens in water, as models of enteric virus removal by treatment processes, and to examine the fate and transport of enteric viruses in the environment (12). The term ‘‘indicator organism’’ is often not clearly defined. By contrast, an ‘‘index organism’’ is usually defined as one related to the occurrence of a selected surrogate microorganism or microorganisms (table 45-1). The relationship may be direct, such as an index of human viruses, or indirect, such as an index of fecal pollution or types of fecal pollution (i.e., human or animal) (27). The criteria for an index organism are very similar to those commonly used for bacterial fecal indicators. An indicator organism, on the other hand, is measured to check the performance of a treatment process against previously set standards. For example, an indicator is used to evaluate the performance of drinking-water disinfection for the inactivation of enteric viruses. To serve as an effective indicator, the resistance of the indicator organism and the pathogen to the disinfectant should be similar.
Bacteriophages in Bacterial Pathogenesis
Authors: Wagner Patrick L , Waldor Matthew K 
Published: November 2023

Abstract
Bacteriophages contribute to the virulence of many bacterial pathogens, largely by encoding the structural genes for virulence factors. The most widely recognized phage-encoded virulence factors are bacterial exotoxins, which account for the characteristic clinical manifestations of a number of human diseases caused by bacterial infections. The previous edition of this chapter focused primarily on phage-encoded toxins, but in the intervening years two themes have emerged (169). First, phages are increasingly recognized for encoding genes that contribute to other aspects of bacterial pathogenesis in addition to toxin production. In fact, phage-encoded gene products contribute to virtually every facet of bacterial pathogenicity, from attachment and invasion to immune evasion and transmission among humans. Second, while phages are like other mobile genetic elements in that they disseminate virulence genes among bacterial populations, phages have unique properties that enable them to contribute to bacterial pathogenesis by mechanisms other than transduction as well. For example, virion particles may themselves contain pathogenic components (12, 13); and prophage induction, through gene amplification, transcriptional upregulation, and phage-mediated lysis, can contribute to production and release of virulence factors from bacterial cells (167, 168). Owing to these developments, the contribution of bacteriophages to bacterial pathogenesis can no longer be conceived of simply as transduction of toxin genes that are regulated by the host bacterium. This chapter presents a summary of bacteriophage involvement in bacterial pathogenesis, in which we consider (i) the nature of the bacterial virulence properties altered by phages, (ii) the basic mechanisms by which phages alter these properties, and (iii) the regulation of the phage-related virulence property by the phage and/or its host bacterium.
October 26 The Full Monty
Authors: Suskin Steven 
Published: November 2023

Abstract
Since the mid-199os, we have been reading continually about Broadway’s four promising young composers: Adam Guettel, Jason Robert Brown, Michael John LaChiusa, and Ricky Ian Gordon. Audra McDonald-the top new Broadway singer of her generation-made it official, in a way, by devoting her smashing 1998 debut album, Way Back to Paradise, solely to their work. The unquestioned promise of these fellows-all four of them-became so generally accepted that they were constantly hailed, in one breath, as the great hope of the American musical. Brown was the first to reach Broadway. Parade (1998), from Lincoln Center Theater, was a serious, tragic musical that failed to enthuse critics or theatregoers; it quickly closed. LaChiusa soon followed, with two Broadway musicals within twenty weeks. Marie Christine (1999), from Lincoln Center Theater, was a serious, tragic musical that failed to enthuse critics or theatregoers; it quickly closed. The Wild Party, from the New York Shakespeare Festival, was a serious, tragic musical that-well, you get the idea.
November 2 The Tale of the Allergist’s Wife
Authors: Suskin Steven 
Published: November 2023

Abstract
Two weeks after the opening of the new Neil Simon play came a new Neil Simon play. Well, really, more like a new, o/,d Neil Simon play. The Tale of the Allergist’s Wife, it was called, and it was written not by old Doc Simon but by a fellow named Charles Busch. One might well refer to The Allergist’s Wife as an old Neil Simon play, as it was as funny as Simon’s plays of the 1960s. Rip-roaring laughter, cascading from the stage for two hours: big laughs, little laughs, belly laughs, time-delayed laughs. I suppose that a theatregoer seeing the two shows in two days without a Playbill in hand might well have wondered just which one was written by the real Simon. The Allergist devolved into a problematic and un-Simon-like sex play, yes; but The Dinner Party-with sexual degradation at its center-was even stranger.
November 16 The Search for Signs of Intelligent Life in the Universe
Authors: Suskin Steven 
Published: November 2023

Abstract
The phone rang on January 1, 1999. Lily had been approached to do a nationwide tour of auditoriums and large arenas. Would I help figure it out? Thus began an adventure that wound up, twenty-one months later, at the Booth Theatre on Shubert Alley, by which time I was no longer involved with the project. Given the situation, it seems unsuitable to discuss The Search in the same precise manner as I do the other shows in this book. But I can think of a thing or two to say. Back in the late twentieth century, I spent about fifteen years as a company manager and six years as a general manager-producer. One of the shows I coproduced turned out to be a big enough hit-and, due to some of the people involved, an unpleasant enough experience-that I was able to, and impelled to, leave theatrical management altogether.
November 30 Seussical
Authors: Suskin Steven 
Published: November 2023

Abstract
Seussical, the big new musical “based on the works of Dr. Seuss,” received raves from hard-boiled.Broadway insiders invited to attend run-throughs of the developmental reading held in Toronto in August 1999. The tuneful, imaginative new musical was clearly destined to be a major hit. The only question was: Would it merely be a lucrative hit (like Beauty and the Beast) or a groundbreaking Broadway legend (like The Lion King)? Things went downhill from there. The idea of creating a musical peopled with characters created by the good Dr. originated with Garth Drabinsky, at that time still the chairman of what used to be Livent. The Seussical, as it was then called, was announced in April 1997 as a collaboration between songwriters Stephen Flaherty and Lynn Ahrens (ofLivent’s Ragtime) and playwright Ken Ludwig (of Crazy for You). By June 1998, Ludwig had been replaced by Eric Idle (of Monty Python).
December 10 Jane Eyre
Authors: Suskin Steven 
Published: November 2023

Abstract
If the Broadway-bound Seussical led a charmed existenceuntil it hit a paying audience, anyway-poor Jane Eyre was forced to endure a tempest-tossed route to opening night. The musicalization of Charlotte Bronte’s 184 7 novel had one “star” name attached, the man who codirected the fabled Adventures of Nicholas Nickelby and the record-breaking box office hit Les Miserables. No, not Trevor Nunn; the other one. John Caird is his name, and his involvement with t,hose two shows is indicative of his talent. But Nunn has the name and acclaim. Caird’s pedigree no doubt helped get]ane Eyre her two full-scale pre-New York tryouts, but his name apparently meant nothing in the Broadway booking wars.
April 5 Follies
Authors: Suskin Steven 
Published: November 2023

Abstract
All right. Thirty years ago, Ben was dating Phyllis. Ben was sleeping with Phyllis’s roommate, Sally. Ben loved Sally. (This last is hazy, as love to Ben is a four-letter word). Ben married Phyllis. Sally, on the rebound, married Ben’s buddy, Buddy. Thirty years later, they are all unhappily married. Meeting once more, Sally still wants Ben. Ben still wants Sally. (This is hazy, too.) Buddy is fed up with Sally; he knows she has always been in love with Ben. Phyllis is just plain fed up. Ben and Sally plan to run off together, but before they can get out the door, Ben has the mental breakdown he’s been heading toward all evening.
April 8 One Flew over the Cuckoo’s Nest
Authors: Suskin Steven 
Published: November 2023

Abstract
Steppenwolf and Gary Sinise and Terry Kinney and One Flew over the Cuckoo’s Nest. What a perfect combination! After a three-month engagement in April 2000 atSteppenwolf’s Chicago home, they paid a two-week London visit in July 2000. Advance reports confirmed that this Cuckoo’s Nest was an electric evening of theatre. So why did it fizzle on Broadway? “Fizzle” is not the word, perhaps. The reaction was wildly mixed and highly unusual. The Critical Scorecard on page 178 shows that four of the tabulated critics loved it (praising the theatricality and the performances) and five of them hated it (ruing the dramaturgy and the misogyny). Little middle ground, here. Business was reasonably good, but not quite good enough to recover the production costs (although income from postBroadway engagements should allow the producers to tum a profit).
April 12 Bells Are Ringing
Authors: Suskin Steven 
Published: November 2023

Abstract
The idea of producing Broadway revivals of Broadway musicals didn’t come up much in the fifties or sixties. The potential Broadway audience was smaller in those days, when a two-year run was exceptional. How many people were likely to pay good money to see a show they had already seen? It was also problematic financially. The original producers and investors shared in a full slate of subsidiary rights, including motion picture rights and stock and amateur licensing; few of these income sources were available to backers of a revival. And then there was the theatre situation. With as many as fifteen new musicals on the boards in any given season, not to mention holdovers, theatre owners had their pick of n,ew potential hits.
April 17 Blast
Authors: Suskin Steven 
Published: November 2023

Abstract
You could say that Blast, the self-described “explosive musical celebration;’ hit Broadway with a blast when it came to town for a ten-week engagement in mid-April. You could also say, though, that it was blasted by half the critics. Two of the four major New York dailies loved it, while the others positively excoriated it. Consider this: “Exhilarating! Extraordinary!”-Howard Kissel in the Daily News. “Beguiling!” “Blissed-out”-Clive Barnes in the Post. “An unrelenting, amazingly whitebread amateur show”-Linda Winer in Newsday. And from Bruce Weber, the second-string critic of the allimportant Times: “Blast bored me cross-eyed.” Not what we call a money review.
April 19 The Producers
Authors: Suskin Steven 
Published: November 2023

Abstract
In retrospect, The Producers sounded like a surefire can’tmiss crowd-pleaser. Start with that brilliant, comic gem of a film; put the whole thing in the hands of comic genius Mel Brooks; and cast expert farceurs Nathan Lane and Matthew Broderick in the leading roles. What could possibly have gone wrong? Plenty. The first rule of adaptations is-or should be-if you can’t enhance the experience of the original, don’t do it. As, for instance, the 1966 musical Breakfast at Tiffany’s. This highly anticipated blockbuster garnered a massive million-dollar advance (at an $11.90 top), thanks to the popularity of the 1961 film and the musical’s stars Mary Tyler Moore and Richard Chamberlain.
May 3 Hair
Authors: Suskin Steven 
Published: November 2023

Abstract
The trouble with the Encores! concert version of Hair can I be boiled down to one word: “choreography:’ Not the choreography per se, by former Encores! artistic director Kathleen Marshall; but the concept of choreography itself. The world of Hair, the self-described American Tribal Love-Rock Musical, existed on the streets of the East (and West) Village back in the Vietnam War years. The authors called their cast of characters not a chorus nor an ensemble but a tribe. A tribe of hippies, of dropouts, of highly individual individuals united by certain passions (peace, flowers, freedom, happiness) and certain hates (war and any sort of authority figures). While this tribe does many things together in the course of the evening, the one thing that the tribe members do not do-and cannot do-are synchronized dance steps.
Tony Wrap-Up (and Other Awards)
Authors: Suskin Steven 
Published: November 2023

Abstract
The 2000-2001 season’s Tony Award nominations are listed below, with asterisks denoting the winners. Overlooked people who— for various reasons—might have been expected to receive nominations are also mentioned. Proof seemed the obvious winner- especially with its Pulitzer Prize in hand- until The Invention of Love took the Drama Critics Circle Award for Best Play. (As a consolation, the Drama Critics gave Proof the award for Best American Play.) The Tony voters favored Proof over Invention of Love (as did I), with neither Hedle y nor Allergist having a chance.
Holdovers
Authors: Suskin Steven 
Published: November 2023

Abstract
Musical. Opened March 23, 2000, at the Palace. Music by Elton John; lyrics by Tim Rice; book by Linda Woolverton and Robert Falls & David Henry Hwang; directed by Robert Falls; choreographed by Wayne Cilento. 2000 Tony Awards: Score; Leading Actress (Heather Headley); Scenic Design (Bob Crowley); Lighting Design (Natasha Katz). Still playing May 28, 2oor. To date: 492 performances (and 27 previews). Profit/loss: to be determined.