bluuebunny/crossref_metadata_2025 huggingface dataset:
Low-Temperature Irradiation of Beef and Methods for Evaluation of a Radappertization Process
Authors: Anellis Abe , Shattuck E. , Rowley D. B. , Ross E. W. , Whaley D. N. , Dowell V. R.
Published: December 2020

An inoculated, irradiated beef pack (1,240 cans) study was conducted for the determination of microbiological safety for unrestricted human consumption. Each can contained a mixture of 10
6
spores of each of 10 strains of
Clostridium botulinum
(5 type A and 5 type B), or a total of 10
7
spores/can. The cans were irradiated to various doses (100 cans/dose) with
60
Co gamma rays at -30 � 10 C, incubated at 30 � 2 C for 6 months, and examined for swelling, toxicity, and recoverable botulinal cells. The minimal experimental sterilizing dose based on nonswollen, nontoxic sterile cans was 2.2 < experimental sterilizing dose ≤ 2.6 Mrad. Using recoverable cells as the most stringent criterion of spoilage, and assuming the conventional simple exponential (without an initial shoulder) rate of spore kill, the “12D” dose was 3.7 Mrad when estimated on the basis of a mixture of 10 strains totaling 10
7
spores/can, and 4.3 Mrad if it is assumed that each can of beef contained 10
6
spores of a single most resistant strain and all of these spores were of identical resistances. However, an analysis of the data by extreme value statistics indicated with 90% confidence that the spore death rate was not a simple exponential but might be a shifted exponential (with an initial shoulder), Weibull, lognormal, or normal, with a “12D” equivalent of about 3.0 Mrad regardless of the initial spore density per can. There was an apparent antagonism between the irradiated type A and B strains in the cans. Some of the cans contained type B toxin but did not include type B viable cells. Other cans had a mixture of type A and B toxins, but a large number of these cans did not yield recoverable type B cells. However, type A viable cells could always be demonstrated in those cans containing type A toxin.
Development of a Micromethod for Identification of Anaerobic Bacteria
Authors: Wilkins Tracy D. , Walker Clay B.
Published: December 2020

A microprocedure was described for determining the carbohydrate fermentation patterns of 48 anaerobic bacteria at one time in microtiter plates. The cultures were transferred into agar-filled wells of microtiter plates with a replicator inside an anaerobic glove box. Fermentation was measured both with a colorimetric indicator and with a small pH electrode. The method was approximately 97% accurate. It would be most useful for laboratories that need to identify large numbers of anaerobes at one time.
Micromethod for Identification of Anaerobic Bacteria: Design and Operation of Apparatus
Authors: Wilkins Tracy D. , Walker Clay B. , Moore W. E. C.
Published: December 2020

A replicator is described for transferring 48 bacterial cultures into separate wells of microtiter plates. The device was designed for determination of carbohydrate fermentation patterns of anaerobic bacteria but should be useful for other applications. A simple device for filling microtiter wells with media is also described.
Utilization of Brewery Spent Grain Liquor by
Aspergillus niger
Authors: Hang Y. D. , Splittstoesser D. F. , Woodams E. E.
Published: December 2020

Aspergillus niger
was found capable of rapidly converting about 97% of the sugar from brewery spent grain liquor to fungal mass. The yield of dry mycelium, based on the sugar consumed, was approximately 57%. This fungus produced 1.10% titratable acid calculated as citric acid and reduced the biochemical oxygen demand by 96%.
Ultrastructure of Rhizobium-induced infection threads in clover root hairs
Authors: Napoli C A , Hubbell D H
Published: December 2020

Ultrastructural studies of Rhizobium-induced infection threads in clover root hairs show that the infection thread is initiated by an invagination process. Root hair wall growth is redirected at a localized point, resulting in the formation of an open pore. There is no direct penetration through the wall, and the bacteria remain extracellular within the root hair.
New medium for isolating iron-oxidizing and heterotrophic acidophilic bacteria from acid mine drainage
Authors: Manning H L
Published: December 2020

A new solid medium is described for growing iron and heterotrophic bacteria from acid mine drainage (AMD). Examination of AMD from five states revealed several kinds of colonies of iron-oxidizing bacteria: (i) smooth, (ii) smooth with secondary growth sectors or branching, (iii) star-shaped, (iv) radiating lobe, and (v) flat-rough. All AMD samples yielded whitish colonies that could not use ferrous iron, sulfur, or hydrogen, nor could they grow on nutrient agar, brain heart infusion agar, or Trypticase soy agar. Glucose and sucrose supported growth if the sugar-salts medium was at pH 3.0. The new iron medium has several advantages over others: (i) easy preparation, (ii) rapid growth, (iii) larger colonies, (iv) differentiation of colony morphology, and (v) detection of a new group of heterotrophic acidophilic bacteria.
Detection of Aflatoxin B
1
in Silkworm Larvae Attacked by an
Aspergillus flavus
Isolate from a Sericultural Farm
Authors: Ohtomo Toshichika , Murakoshi Shigeo , Sugiyama Junta , Kurata Hiroshi
Published: December 2020

Aflatoxin B
1
(0.05 μM per larvae) was detected in silkworm larvae artificially attacked by an
Aspergillus flavus
isolate from a sericultural farm in Japan.
Microbiology of Ripening Honey
Authors: Ruiz-Argueso T. , Rodriguez-Navarro A.
Published: December 2020

Two main groups of bacteria, classified as
Gluconobacter
and
Lactobacillus,
are present in ripening honey. A third bacterial group, classified as
Zymomonas,
and several types of yeast are occasionally isolated. Both in natural honey and in synthetic syrup the bacterial population decreases in the course of the ripening process.
Lactobacillus
and
Gluconobacter
disappear after minimum moisture (about 18%) is reached, but the former does so sooner than the latter. The presence of these bacteria in different parts of the bee has been also investigated.
Studies on the biosynthesis of aspergillin by Aspergillus niger
Authors: Ray A C , Eakin R E
Published: December 2020

Two inhibitors of the biosynthesis of aspergillin, the black spore pigment of Aspergillus niger, have been investigated. 2,4-Dithiopyrimidine exerted its inhibitory effect by intracellularly chelating cupric ion required for normal pigmentation. Dimethylsulfoxide prevented the synthesis of certain phenolic precursors of the native pigment. Partial purification and characterization of pigments from mature cultures revealed the presence of at least three components: (i) a high-molecular-weight (approximately 20,000) native pigment fraction in untreated mold cultures, (ii) a lower-molecular-weight (approximately 5,000) melanin pigment found in both types of inhibited cultures, and (iii) a low-molecular-weight (368) green pigment found only in the 2,4-dithiopyrimidine-inhibited cultures and proposed to be a pentacyclic quinonoid derivative. A pathway for aspergillin biosynthesis is suggested based on these results.
Semisolid Fermentation of Ryegrass Straw
Authors: Han Y. W. , Anderson A. W.
Published: December 2020

Candida utilis, Aureobasidium pullulans,
and
Trichoderma viride
were grown on pretreated ryegrass straw. The pretreatment consisted of hydrolysis of straw with 0.5 N H
2
SO
4
(water-substrate, 3:1) at 121 C, 100 C, and room temperature and adjustment of the hydrolysate to pH 4.5 to 5.0 with 5 N NH
4
OH. The 121 C pretreatment yielded a material containing 30% sugar and 2.3% N. The fermentation was carried on semisolid substrate (moisture level, 75%) in rotating jars for 2 to 3 days at room temperature. The organisms grew rapidly during the period from 18 to 42 h of incubation. During this period the number of microbial cells increased by 20- to 200-fold, and the level of NH
3
-N decreased from 1.3 to 0.9%. The fermentation resulted in a fourfold increase in protein, fivefold increase in crude fat, and 40% increase in the digestibility of straw. The best result in terms of increasing protein and digestibility of straw was obtained when
C. utilis
was grown on straw preheated at 121 C.
Growth potential of Clostridium botulinum in fresh mushrooms packaged in semipermeable plastic film
Authors: Sugiyama H , Yang K H
Published: December 2020

Fresh mushrooms (Agaricus bisporus) were inoculated in the stem, gill, or cap with Clostridium botulinum spores. They were placed with uninoculated mushrooms in paper board trays, which were then covered and sealed in a polyvinyl chloride stretch film to simulate prepackaged mushrooms available at retail stores. When incubated at 20 C, botulinum toxin could be detected as early as day 3, or 4, when the mushrooms still appear edible. Mushrooms inoculated in the stem with 1,000 type A spores frequently became botulinogenic; higher spore levels were needed if gills or caps were inoculation sites. Type B spores were less apt to produce toxic mushrooms. Respiration of the fresh mushrooms used up O2 more rapidly than could enter through the semipermeable wrapping film, so that the equilibrium O2 concentration became low enough for growth of C. botulinum. Inoculated mushrooms did not become botulinogenic when held at 4 C.
Microbial Indicators of Oil-Rich Salt Marsh Sediments
Authors: Hood M. A. , Bishop W. S. , Bishop F. W. , Meyers S. P. , Whelan T.
Published: December 2020

Selected microbial parameters were monitored in sediments from a pristine and an oil-field salt marsh. Although numbers of hydrocarbonoclastic bacteria and fungi were significantly greater in the oil field, the values did not show a strong correlation with levels of hydrocarbons (r = 0.43 and r = 0.49, respectively). However, a high correlation was noted between ratios of hydrocarbonoclastic and total aerobic heterotrophic bacteria and levels of hydrocarbons as well as the relative concentration of hydrocarbons (ratio of hydrocarbons to chloroform extractables) (r = 0.87 and r = 0.77, respectively). Data suggest that this first ratio is a more valid microbial indicator of hydrocarbon abundance than other factors examined. Significant differences in the ratio of pigmented to total colony-forming units, the ratio of different to total colony-forming units, and the diversity index were noted between the natural and oil-field marsh. It is suggested that the presence of hydrocarbons alters the relative abundance of the most predominant aerobic heterotrophic bacteria.
Continuous Microbiological Transformation of Steroids
Authors: Reusser F. , Koepsell H. J. , Savage G. M.
Published: December 2020

Continuous fermentation trials on the bioconversions of pregnadiene to pregnatriene by
Septomyxa affinis
and progesterone to 11α-hydroxyprogesterone by
Rhizopus nigricans
were conducted successfully in an eight-stage pilot plant reactor. The first stage was used as the mycelial growth stage while the steroid solutions were added continuously to stage 2, thus using the remaining stages as conversion vessels. Recoveries of 50 to 60% oxidized steroid (based on total steroid supplied) were obtained in both cases upon a contact time of 5 hr between mycelium and steroid. Longer contact times resulted in a gradual net loss of steroid. It was concluded that two-stage reactors (one growth stage and one conversion stage) were adequate for efficient continuous operation of such processes. The reaction volumes of both stages have to be kept in proper balance to insure optimal holdup times for both the cell growth and conversion steps.
Theoretical Design of Continuous Antibiotic Fermentation Units
Authors: Reusser F.
Published: December 2020

A graphic method of predicting antibiotic yields in continuous flow reactors is presented and discussed using the novobiocin fermentation as a model process. Extension to other antibiotic fermentations and steroid bioconversions is emphasized. In the case of the novobiocin fermentation it was concluded that a combination of one growth stage and one or two antibiotic production stages would be the most economic reactor system to conduct such a fermentation on a continuous basis.
Studies on the Thermophilic Actinomycetes
Authors: Tendler M. D. , Burkholder P. R.
Published: December 2020

A total of 1,000 isolates of thermophilic actinomycetes representing two genera,
Streptomyces
and
Thermoactinomyces
, were studied. Media for cultivation and for physiological studies were designed. Differences between the two genera are noted and taxonomic criteria for the genus
Thermoactinomyces
are suggested. The importance of the nutritional environment to the thermophilic habit is noted.
Production of Fluorescence on Packaged Chicken
Authors: Kraft A. A. , Ayres J. C.
Published: December 2020

Development of fluorescence caused by pseudomonads proliferating on packaged chicken was determined by examination of the poultry under ultraviolet light and by measurements of absorption spectra. Asparagine broth inoculated with organisms from chicken showed absorption maxima at 270 mμ and 410 mμ; these peaks are characteristic of the fluorescent pigment, pyoverdine. Absorbance calculated as the ratio (
A
270mμ
+
A
410mμ
)/
A
350mμ
provided a convenient measure of amount of pigment produced; this ratio was related to numbers of fluorescing organisms recovered from chicken. Absorption peaks generally increased during the first few days the poultry was stored at 5 C and then declined during the latter part of the 7-day holding period.

Production of fluorescence was influenced by packaging materials. Fluorescence was not visible on poultry until counts of fluorescing bacteria were as great as 100,000 to 1,000,000 per cm
2
. Growth of fluorescent pigment-producing pseudomonads on chicken was stimulated during storage after the poultry was dipped in solutions containing iron.
Relative Humidity and the Killing of Bacteria
Authors: Bateman J. B. , McCaffrey Patricia A. , O'Connor R. J. , Monk G. W.
Published: December 2020

The viability of washed moist cells of
Serratia marcescens
after storage has been measured in relation to variations in the prior treatment of the cells and in conditions of storage. The factors considered were: (i) water content during storage; (ii) method of arriving at water content (partial drying in vacuum or freeze-drying and addition of water); (iii) presence or absence of air during storage.

Increasingly rapid decay occurs as the water content at which the cells are stored is diminished from above 90% to 20 or 30% (“critical” water content). It occurs in presence or absence of air and it occurs whether the final water content is approached by removal of water from wet cells or by addition of water to freeze-dried cells.

The rate of decay during storage at 20 to 30% water is somewhat diminished by the presence of air (“protective” effect of air).

As the water content is further reduced to less than 10%, the stability of cells stored in a vacuum approaches that of wet cells. In presence of air the reverse is true: the stability decreases until at less than 1% water, the decay rate is about as great as at the “critical” water content (“toxic” effect of air).

Particularly rapid decay of
S. marcescens
at the “critical” water content has escaped attention in aerosol studies because accurate control of relative humidity (RH) in this region, RH 94 to 99%, is virtually impossible in such studies. On the other hand, values of decay rates referred to measured water contents are quite unreliable in the 20 to 80% RH zone because the corresponding variation of water content is too small to measure reliably. Thus data of the kind reported in this paper cannot be directly compared to the published results of studies of air-borne bacteria, although they are relevant to the practical question of air-borne infection in humid atmospheres.
The ras oncogene--an important regulatory element in lower eucaryotic organisms
Authors: Gibbs J B , Marshall M S
Published: December 2020

The ras proto-oncogene in mammalian cells encodes a 21-kilodalton guanosine triphosphate (GTP)-binding protein. This gene is frequently activated in human cancer. As one approach toward understanding the mechanisms of cellular transformation by ras, the function of this gene in lower eucaryotic organisms has been studied. In the yeast Saccharomyces cerevisiae, the RAS gene products serve as essential function by regulating cyclic adenosine monophosphate metabolism. Stimulation of adenylyl cyclase is dependent not only on RAS protein complexed to GTP, but also on the CDC25 and IRA gene products, which appear to control the RAS GTP-guanosine diphosphate cycle. Although analysis of RAS biochemistry in S. cerevisiae has identified mechanisms central to RAS action, RAS regulation of adenylyl cyclase appears to be strictly limited to this particular organism. In Schizosaccharomyces pombe, Dictyostelium discoideum, and Drosophila melanogaster, ras-encoded proteins are not involved with regulation of adenylyl cyclase, similar to what is observed in mammalian cells. However, the ras gene product in these other lower eucaryotes is clearly required for appropriate responses to extracellular signals such as mating factors and chemoattractants and for normal growth and development of the organism. The identification of other GTP-binding proteins in S. cerevisiae with distinct yet essential functions underscores the fundamental importance of G-protein regulatory processes in normal cell physiology.
The family of highly interrelated single-stranded deoxyribonucleic acid plasmids
Authors: Gruss A , Ehrlich S D
Published: December 2020

Many plasmids from gram-positive bacteria replicate via a single-stranded deoxyribonucleic acid (ssDNA) intermediate, most probably by a rolling-circle mechanism (these plasmids are referred to in this paper as ssDNA plasmids). Their plus and minus origins are physically separated, and replicative initiations are not simultaneous; it is this feature that allows visualization of ssDNA replication intermediates. The insertion of foreign DNA into an ssDNA plasmid may provoke a high frequency of deletions, changes of replicative products to high-molecular-weight forms, segregational loss, and decreased plasmid copy numbers. When an ssDNA plasmid is inserted into the chromosome, both deletions and amplifications may be induced. Both the mode of replication and the copy control mechanism affect the fate of inserted foreign material, usually selecting for its loss. Thus, after having tasted various morsels of DNA, the resulting plasmid stays trim. The features of the ssDNA plasmids seem to be beneficial for their viability and propagation, but not for their use as cloning vectors. However, plasmids replicating via ssDNA intermediates are being exploited to yield insights into the mechanisms of recombination and amplification.
Insecticidal crystal proteins of Bacillus thuringiensis
Authors: Höfte H , Whiteley H R
Published: December 2020

A classification for crystal protein genes of Bacillus thuringiensis is presented. Criteria used are the insecticidal spectra and the amino acid sequences of the encoded proteins. Fourteen genes are distinguished, encoding proteins active against either Lepidoptera (cryI), Lepidoptera and Diptera (cryII), Coleoptera (cryIII), or Diptera (cryIV). One gene, cytA, encodes a general cytolytic protein and shows no structural similarities with the other genes. Toxicity studies with single purified proteins demonstrated that every described crystal protein is characterized by a highly specific, and sometimes very restricted, insect host spectrum. Comparison of the deduced amino acid sequences reveals sequence elements which are conserved for Cry proteins. The expression of crystal protein genes is affected by a number of factors. Recently, two distinct sigma subunits regulating transcription during different stages of sporulation have been identified, as well as a protein regulating the expression of a crystal protein at a posttranslational level. Studies on the biochemical mechanisms of toxicity suggest that B. thuringiensis crystal proteins induce the formation of pores in membranes of susceptible cells. In vitro binding studies with radiolabeled toxins demonstrated a strong correlation between the specificity of B. thuringiensis toxins and the interaction with specific binding sites on the insect midgut epithelium. The expression of B. thuringiensis crystal proteins in plant-associated microorganisms and in transgenic plants has been reported. These approaches are potentially powerful strategies for the protection of agriculturally important crops against insect damage.
Synthesis of ribosomes in Saccharomyces cerevisiae
Authors: Warner J R
Published: December 2020

The assembly of a eucaryotic ribosome requires the synthesis of four ribosomal ribonucleic acid (RNA) molecules and more than 75 ribosomal proteins. It utilizes all three RNA polymerases; it requires the cooperation of the nucleus and the cytoplasm, the processing of RNA, and the specific interaction of RNA and protein molecules. It is carried out efficiently and is exquisitely sensitive to the needs of the cell. Our current understanding of this process in the genetically tractable yeast Saccharomyces cerevisiae is reviewed. The ribosomal RNA genes are arranged in a tandem array of 100 to 200 copies. This tandem array has led to unique ways of carrying out a number of functions. Replication is asymmetric and does not initiate from every autonomously replicating sequence. Recombination is suppressed. Transcription of the major ribosomal RNA appears to involve coupling between adjacent transcription units, which are separated by the 5S RNA transcription unit. Genes for many ribosomal proteins have been cloned and sequenced. Few are linked; most are duplicated; most have an intron. There is extensive homology between yeast ribosomal proteins and those of other species. Most, but not all, of the ribosomal protein genes have one or two sites that are essential for their transcription and that bind a common transcription factor. This factor binds also to many other places in the genome, including the telomeres. There is coordinated transcription of the ribosomal protein genes under a variety of conditions. However, the cell seems to possess no mechanism for regulating the transcription of individual ribosomal protein genes in response either to a deficiency or an excess of a particular ribosomal protein. A deficiency causes slow growth. Any excess ribosomal protein is degraded very rapidly, with a half-life of 1 to 5 min. Unlike most types of cells, yeast cells appear not to regulate the translation of ribosomal proteins. However, in the case of ribosomal protein L32, the protein itself causes a feedback inhibition of the splicing of the transcript of its own gene. The synthesis of ribosomes involves a massive transfer of material across the nuclear envelope in both directions. Nuclear localization signals have been identified for at least three ribosomal proteins; they are similar but not identical to those identified for the simian virus 40 T antigen. There is no information about how ribosomal subunits are transported from the nucleus to the cytoplasm.(ABSTRACT TRUNCATED AT 400 WORDS)
Replication of plasmids in gram-negative bacteria
Authors: Kües U , Stahl U
Published: December 2020

Replication of plasmid deoxyribonucleic acid (DNA) is dependent on three stages: initiation, elongation, and termination. The first stage, initiation, depends on plasmid-encoded properties such as the replication origin and, in most cases, the replication initiation protein (Rep protein). In recent years the understanding of initiation and regulation of plasmid replication in Escherichia coli has increased considerably, but it is only for the ColE1-type plasmids that significant biochemical data about the initial priming reaction of DNA synthesis exist. Detailed models have been developed for the initiation and regulation of ColE1 replication. For other plasmids, such as pSC101, some hypotheses for priming mechanisms and replication initiation are presented. These hypotheses are based on experimental evidence and speculative comparisons with other systems, e.g., the chromosomal origin of E. coli. In most cases, knowledge concerning plasmid replication is limited to regulation mechanisms. These mechanisms coordinate plasmid replication to the host cell cycle, and they also seem to determine the host range of a plasmid. Most plasmids studied exhibit a narrow host range, limited to E. coli and related bacteria. In contrast, some others, such as the IncP plasmid RK2 and the IncQ plasmid RSF1010, are able to replicate in nearly all gram-negative bacteria. This broad host range may depend on the correct expression of the essential rep genes, which may be mediated by a complex regulatory mechanism (RK2) or by the use of different promoters (RSF1010). Alternatively or additionally, owing to the structure of their origin and/or to different forms of their replication initiation proteins, broad-host-range plasmids may adapt better to the host enzymes that participate in initiation. Furthermore, a broad host range can result when replication initiation is independent of host proteins, as is found in the priming reaction of RSF1010.
Anion-exchange mechanisms in bacteria
Authors: Maloney P C , Ambudkar S V , Anatharam V , Sonna L A , Varadhachary A
Published: December 2020

This article discusses the physiological, biochemical, and molecular properties of bacterial anion-exchange reactions, with a particular focus on a family of phosphate (Pi)-linked antiporters that accept as their primary substrates sugar phosphates such as glucose 6-phosphate (G6P), mannose 6-phosphate, or glycerol 3-phosphate. Pi-linked antiporters may be found in both gram-positive and gram-negative cells. As their name suggests, these exchange proteins accept both inorganic and organic phosphates, but the two classes of substrate interact very differently with the protein. Thus, Pi is always accepted with a relatively low affinity, and when it participates in exchange, it is always taken as the monovalent anion. By contrast, when the high-affinity organic phosphates are used, these same systems fail to discriminate between monovalent and divalent forms. Tests of heterologous exchange (e.g., Pi: G6P) indicate that these proteins have a bifunctional active site that accepts a pair of negative charges, whether as two monovalent anions or as a single divalent anion. For this reason, exchange stoichiometry moves between limits of 2:1 and 2:2, according to the ratio of mono- and divalent substrates at either membrane surface. Since G6P has a pK2 within the physiological range (pK of 6.1), this predicts a novel reaction sequence in vivo because internal pH is more alkaline than external pH. Accordingly, one expects an asymmetric exchange as two monovalent G6P anions from the relatively acidic exterior move against a single divalent G6P from the alkaline interior. In this way an otherwise futile self-exchange of G6P can be biased towards a net inward flux driven (indirectly) by the pH gradient. Despite the biochemical complexity exhibited by Pi-linked antiporters, they resemble all other secondary carriers at a molecular level and show a likely topology in which two sets of six transmembrane alpha-helices are connected by a central hydrophilic loop. Speculations on the derivation of this common form suggest a limited number of structural models to accommodate such proteins. Three such models are presented.
The search for scrapie agent nucleic acid
Authors: Aiken J M , Marsh R F
Published: December 2020

Despite decades of research, the identity of the scrapie agent has remained elusive. Recent studies have discovered much about the influence of the host genome upon scrapie infection, yet relatively little is known about the causative agent itself. The predominant hypothesis in the scrapie field (the prion hypothesis) argues that the disease is the result of an infectious protein and that nucleic acid is not required for infection. Biological studies of the scrapie agent, however, suggest that a nucleic acid may be involved in the disease. Sensitive molecular biology techniques have yet to identify this putative nucleic acid.
TraT lipoprotein, a plasmid-specified mediator of interactions between gram-negative bacteria and their environment
Authors: Sukupolvi S , O'Connor C D
Published: December 2020

The TraT protein is a cell-surface-exposed, outer membrane lipoprotein specified by large, usually conjugative, F-like plasmids. Two biological activities have been associated with the protein: (i) prevention of self-mating of cells carrying identical or closely related conjugative plasmids, by blocking the formation of stable mating aggregates; and (ii) resistance to the bactericidal activities of serum, possibly by inhibiting the correct assembly or efficient functioning of the terminal membrane attack complex of complement. The protein therefore interacts not only with components of the outer membrane but also with specific external agents. In conjugative plasmids the traT gene lies within the region necessary for the conjugal transfer of DNA (tra), although its expression is not necessarily dependent on the expression of other tra genes. Recently, however, the gene has been discovered in isolation from other tra genes in nonconjugative virulence-associated plasmids, providing further evidence that the TraT protein may have a role in pathogenesis. The nucleotide sequences of several traT genes have been determined, and comparison of the corresponding amino acid sequences suggests that a central region of five amino acid residues flanked by hydrophobic domains determines the specificity of the protein in surface exclusion. Additionally, studies of mutants with different amino acid alterations within the hydrophobic domains have shown that insertion of charged residues disrupts normal outer membrane integrity. This review considers our current knowledge of the distribution, structure, and biological role(s) of the protein. Recent applications of the protein in studies of the unusual permeability properties of the outer membrane and for the transport of foreign antigenic determinants to the bacterial cell surface are also discussed.
To shape a cell: an inquiry into the causes of morphogenesis of microorganisms
Authors: Harold F M
Published: December 2020

We recognize organisms first and foremost by their forms, but how they grow and shape themselves still largely passes understanding. The objective of this article is to survey what has been learned of morphogenesis of walled eucaryotic microorganisms as a set of problems in cellular heredity, biochemistry, physiology, and organization. Despite the diversity of microbial forms and habits, some common principles can be discerned. (i) That the form of each organism represents the expression of a genetic program is almost universally taken for granted. However, reflection on the findings with morphologically aberrant mutants suggests that the metaphor of a genetic program is misleading. Cellular form is generated by a web of interacting chemical and physical processes, whose every strand is woven of multiple gene products. The relationship between genes and form is indirect and cumulative; therefore, morphogenesis must be addressed as a problem not of molecular genetics but of cellular physiology. (ii) The shape of walled cells is determined by the manner in which the wall is laid down during growth and development. Turgor pressure commonly, perhaps always, supplies the driving force for surface enlargement. Cells yield to this scalar force by localized, controlled wall synthesis; their forms represent variations on the theme of local compliance with global force. (iii) Growth and division in bacteria display most immediately the interplay of hydrostatic pressure, localized wall synthesis, and structural constraints. Koch's surface stress theory provides a comprehensive and quantitative framework for understanding bacterial shapes. (iv) In the larger and more versatile eucaryotic cells, expansion is mediated by the secretion of vesicles. Secretion and ancillary processes, such as cytoplasmic transport, are spatially organized on the micrometer scale. The diversity of vectorial physiology and of the forms it generates is illustrated by examples: apical growth of fungal hyphae, bud formation in yeasts, germination of fucoid zygotes, and development of cells of Nitella, Closterium, and other unicellular algae. (v) Unicellular organisms, no less than embryos, have a remarkable capacity to impose spatial order upon themselves with or without the help of directional cues. Self-organization is reviewed here from two perspectives: the theoretical exploration of morphogens, gradients, and fields, and experimental study of polarization in Fucus cells, extension of hyphal tips, and pattern formation in ciliates. Here is the heart of the matter, yet self-organization remains nearly as mysterious as it was a century ago, a subject in search of a paradigm.
Role of water in some biological processes
Authors: Wiggins P M
Published: December 2020

The state of intracellular water has been a matter of controversy for a long time for two reasons. First, experiments have often given conflicting results. Second, hitherto, there have been no plausible grounds for assuming that intracellular water should be significantly different from bulk water. A collective behavior of water molecules is suggested here as a thermodynamically inevitable mechanism for generation of appreciable zones of abnormal water. At a highly charged surface, water molecules move together, generating a zone of water perhaps 6 nm thick, which is weakly hydrogen bonded, fluid, and reactive and selectively accumulates small cations, multivalent anions, and hydrophobic solutes. At a hydrophobic surface, molecules move apart and local water becomes strongly bonded, inert, and viscous and accumulates large cations, univalent anions, and compatible solutes. Proteins and many other biopolymers have patchy surfaces which therefore induce, by the two mechanisms described, patchy interfacial water structures, which extended appreciable distances from the surface. The reason for many conflicting experimental results now becomes apparent. Average values of properties of water measured in gels, cells, or solutions of proteins are often not very different from the same properties of normal water, giving no indication that they are averages of extreme values. To detect the operation of this phenomenon, it is necessary to probe selectively a single abnormal population. Examples of such experiments are given. It is shown that this collective behavior of water molecules amounts to a considerable biological force, which can be equivalent to a pressure of 1,000 atm (1.013 x 10(5) kPa). It is suggested that cells selectively accumulate K+ ions and compatible solutes to avoid extremes of water structure in their aqueous compartments, but that cation pumps and other enzymes exploit the different solvent properties and reactivities of water to perform work of transport or synthesis.
Interaction of chlamydiae and host cells in vitro
Authors: Moulder J W
Published: December 2020

The obligately intracellular bacteria of the genus Chlamydia, which is only remotely related to other eubacterial genera, cause many diseases of humans, nonhuman mammals, and birds. Interaction of chlamydiae with host cells in vitro has been studied as a model of infection in natural hosts and as an example of the adaptation of an organism to an unusual environment, the inside of another living cell. Among the novel adaptations made by chlamydiae have been the substitution of disulfide-bond-cross-linked polypeptides for peptidoglycans and the use of host-generated nucleotide triphosphates as sources of metabolic energy. The effect of contact between chlamydiae and host cells in culture varies from no effect at all to rapid destruction of either chlamydiae or host cells. When successful infection occurs, it is usually followed by production of large numbers of progeny and destruction of host cells. However, host cells containing chlamydiae sometimes continue to divide, with or without overt signs of infection, and chlamydiae may persist indefinitely in cell cultures. Some of the many factors that influence the outcome of chlamydia-host cell interaction are kind of chlamydiae, kind of host cells, mode of chlamydial entry, nutritional adequacy of the culture medium, presence of antimicrobial agents, and presence of immune cells and soluble immune factors. General characteristics of chlamydial multiplication in cells of their natural hosts are reproduced in established cell lines, but reproduction in vitro of the subtle differences in chlamydial behavior responsible for the individuality of the different chlamydial diseases will require better in vitro models.
Biodegradation of halogenated organic compounds
Authors: Chaudhry G R , Chapalamadugu S
Published: December 2020

In this review we discuss the degradation of chlorinated hydrocarbons by microorganisms, emphasizing the physiological, biochemical, and genetic basis of the biodegradation of aliphatic, aromatic, and polycyclic compounds. Many environmentally important xenobiotics are halogenated, especially chlorinated. These compounds are manufactured and used as pesticides, plasticizers, paint and printing-ink components, adhesives, flame retardants, hydraulic and heat transfer fluids, refrigerants, solvents, additives for cutting oils, and textile auxiliaries. The hazardous chemicals enter the environment through production, commercial application, and waste. As a result of bioaccumulation in the food chain and groundwater contamination, they pose public health problems because many of them are toxic, mutagenic, or carcinogenic. Although synthetic chemicals are usually recalcitrant to biodegradation, microorganisms have evolved an extensive range of enzymes, pathways, and control mechanisms that are responsible for catabolism of a wide variety of such compounds. Thus, such biological degradation can be exploited to alleviate environmental pollution problems. The pathways by which a given compound is degraded are determined by the physical, chemical, and microbiological aspects of a particular environment. By understanding the genetic basis of catabolism of xenobiotics, it is possible to improve the efficacy of naturally occurring microorganisms or construct new microorganisms capable of degrading pollutants in soil and aquatic environments more efficiently. Recently a number of genes whose enzyme products have a broader substrate specificity for the degradation of aromatic compounds have been cloned and attempts have been made to construct gene cassettes or synthetic operons comprising these degradative genes. Such gene cassettes or operons can be transferred into suitable microbial hosts for extending and custom designing the pathways for rapid degradation of recalcitrant compounds. Recent developments in designing recombinant microorganisms and hybrid metabolic pathways are discussed.
Genetic basis of virulence in Shigella species
Authors: Hale T L
Published: December 2020

Shigella species and enteroinvasive strains of Escherichia coli cause disease by invasion of the colonic epithelium, and this invasive phenotype is mediated by genes carried on 180- to 240-kb plasmids. In addition, at least eight loci on the Shigella chromosome are necessary for full expression of virulence. The products of these genes can be classified as (i) virulence determinants that directly affect the ability of shigellae to survive in the intestinal tissues, e.g., the aerobactin siderophore (iucABCD and iutA), superoxide dismutase (sodB), and somatic antigen expression (rfa and rfb); (ii) cytotoxins that contribute to the severity of disease, e.g., the Shiga toxin (stx) and a putative analog of this toxin (flu); and (iii) regulatory loci that affect the expression of plasmid genes, e.g., ompR-envZ, which mediates response to changes in osmolarity, virR (osmZ), which mediates response to changes in temperature, and kcpA, which affects the translation of the plasmid virG (icsA) gene which is associated with intracellular bacterial mobility and intracellular bacterial spread. A single plasmid regulatory gene (virF) controls a virulence-associated plasmid regulon including virG (icsA) and two invasion-related loci, i.e., (i) ipaABCD, encoding invasion plasmid antigens that may be structural components of the Shigella invasion determinant; and (ii) invAKJH (mxi), which is necessary for insertion of invasion plasmid antigens into the outer membrane.
Microbiological degradation of pesticides in yard waste composting
Authors: Fogarty A M , Tuovinen O H
Published: December 2020

Changes in public opinion and legislation have led to the general recognition that solid waste treatment practices must be changed. Solid-waste disposal by landfill is becoming increasingly expensive and regulated and no longer represents a long-term option in view of limited land space and environmental problems. Yard waste, a significant component of municipal solid waste, has previously not been separated from the municipal solid-waste stream. The treatment of municipal solid waste including yard waste must urgently be addressed because disposal via landfill will be prohibited by legislation. Separation of yard waste from municipal solid waste will be mandated in many localities, thus stressing the importance of scrutinizing current composting practices in treating grass clippings, leaves, and other yard residues. Yard waste poses a potential environmental health problem as a result of the widespread use of pesticides in lawn and tree care and the persistence of the residues of these chemicals in plant tissue. Yard waste containing pesticides may present a problem due to the recalcitrant and toxic nature of the pesticide molecules. Current composting processes are based on various modifications of either window systems or in-vessel systems. Both types of processes are ultimately dependent on microbial bioconversions of organic material to innocuous end products. The critical stage of the composting process is the thermophilic phase. The fate and mechanism of removal of pesticides in composting processes is largely unknown and in need of comprehensive analysis.
Domains in microbial beta-1, 4-glycanases: sequence conservation, function, and enzyme families
Authors: Gilkes N R , Henrissat B , Kilburn D G , Miller R C , Warren R A
Published: December 2020

Several types of domain occur in beta-1, 4-glycanases. The best characterized of these are the catalytic domains and the cellulose-binding domains. The domains may be joined by linker sequences rich in proline or hydroxyamino acids or both. Some of the enzymes contain repeated sequences up to 150 amino acids in length. The enzymes can be grouped into families on the basis of sequence similarities between the catalytic domains. There are sequence similarities between the cellulose-binding domains, of which two types have been identified, and also between some domains of unknown function. The beta-1, 4-glycanases appear to have arisen by the shuffling of a relatively small number of progenitor sequences.
Aromatic amino acid biosynthesis in the yeast Saccharomyces cerevisiae: a model system for the regulation of a eukaryotic biosynthetic pathway
Authors: Braus G H
Published: December 2020

This review focuses on the gene-enzyme relationships and the regulation of different levels of the aromatic amino acid biosynthetic pathway in a simple eukaryotic system, the unicellular yeast Saccharomyces cerevisiae. Most reactions of this branched pathway are common to all organisms which are able to synthesize tryptophan, phenylalanine, and tyrosine. The current knowledge about the two main control mechanisms of the yeast aromatic amino acid biosynthesis is reviewed. (i) At the transcriptional level, most structural genes are regulated by the transcriptional activator GCN4, the regulator of the general amino acid control network, which couples transcriptional derepression to amino acid starvation of numerous structural genes in multiple amino acid biosynthetic pathways. (ii) At the enzyme level, the carbon flow is controlled mainly by modulating the enzyme activities at the first step of the pathway and at the branch points by feedback action of the three aromatic amino acid end products. Implications of these findings for the relationship of S. cerevisiae to prokaryotic as well as to higher eukaryotic organisms and for general regulatory mechanisms occurring in a living cell such as initiation of transcription, enzyme regulation, and the regulation of a metabolic branch point are discussed.
Genetic competence in Bacillus subtilis
Authors: Dubnau D
Published: December 2020

Genetic competence may be defined as a physiological state enabling a bacterial culture to bind and take up high-molecular-weight exogenous DNA (transformation). In Bacillus subtilis, competence develops postexponentially and only in certain media. In addition, only a minority of the cells in a competent culture become competent, and these are physiologically distinct. Thus, competence is subject to three regulatory modalities: growth stage specific, nutritionally responsive, and cell type specific. This review summarizes the present state of knowledge concerning competence in B. subtilis. The study of genes required for transformability has permitted their classification into two broad categories. Late competence genes are expressed under competence control and specify products required for the binding, uptake, and processing of transforming DNA. Regulatory genes specify products that are needed for the expression of the late genes. Several of the late competence gene products have been shown to be membrane localized, and others are predicted to be membrane associated on the basis of amino acid sequence data. Several of these predicted protein sequences show a striking resemblance to gene products that are involved in the export and/or assembly of extracellular proteins and structures in gram-negative organisms. This observation is consistent with the idea that the late products are directly involved in transport of DNA and is equally consistent with the notion that they play a morphogenetic role in the assembly of a transport apparatus. The competence regulatory apparatus constitutes an elaborate signal transduction system that senses and interprets environmental information and passes this information to the competence-specific transcriptional machinery. Many of the regulatory gene products have been identified and partially characterized, and their interactions have been studied genetically and in some cases biochemically as well. These include several histidine kinase and response regulator members of the bacterial two-component signal transduction machinery, as well as a number of known transcriptionally active proteins. Results of genetic studies are consistent with the notion that the regulatory proteins interact in a hierarchical way to make up a regulatory pathway, and it is possible to propose a provisional scheme for the organization of this pathway. It is remarkable that almost all of the regulatory gene products appear to play roles in the control of various forms of postexponential expression in addition to competence, e.g., sporulation, degradative-enzyme production, motility, and antibiotic production. This has led to the notion of a signal transduction network which transduces environmental information to determine the levels and timing of expression of the ultimate products characteristic of each of these systems.