Sequence analysis of a 101-kilobase plasmid required for agar degradation by a Microscilla isolate.

An agar-degrading marine bacterium identified as a Microscilla species was isolated from coastal California marine sediment. This organism harbored a single 101-kb circular DNA plasmid designated pSD15. The complete nucleotide sequence of pSD15 was obtained, and sequence analysis indicated a number of genes putatively encoding a variety of enzymes involved in polysaccharide utilization. The most striking feature was the occurrence of five putative agarase genes. Loss of the plasmid, which occurred at a surprisingly high frequency, was associated with loss of agarase activity, supporting the sequence analysis results.     

Social status and reproductive success of male Macaca fascicularis

Dominant males of nonseasonally breeding species should have more opportunity than seasonal breeders to monopolize access to estrous females and thus enhance their reproductive success. They may also use other strategies for maximizing reproductive success such as producing offspring by relatively high ranking females. To test these hypotheses, the paternity of 35 (80%) of 44 Macaca fascicularis offspring, born over a 28-month period, was established using electrophoretically and serologically defined genetic markers. The social ranks of each of the seven potential fathers and 26 potential mothers were determined by recording outcomes of dyadio agonistic interactions. No evidence could be found to support either hypothesis. Further, in view of previously reported significant, positive correlations between male social rank and sexual activity rates in this study group, sexual activity rates do not appear to predict the number of offspring a male sires in this species.     

Chromosomal location and cloning of the gene (trmD) responsible for the synthesis of tRNA (m1G) methyltransferase in Escherichia coli K-12

Summary The trmD gene, which governs the formation of 1-methyl-guanosine (m¹G) in transfer ribonucleic acid (tRNA), has been located by phage P1 transduction at 56 min on the chromosomal map of Escherichia coli. Cotransduction to tyrA at 56 min is 80%. From the Clarke and Carbon collection a ColE1-tyrA ⁺ hybrid plasmid was isolated, which carried the trmD ⁺ gene and was shown to over-produce the tRNA (m¹G)methyltransferase. By subcloning restriction enzyme fragments in vitro, the trmD ⁺ gene was located to a 3.4 kb DNA fragment 6.5 kb clockwise from the tyrA ⁺ gene. The mutation trmD1, which renders the tRNA (m¹G) methyltransferase temperaturesensitive both in vivo and in vitro could be complemented by trmD ⁺ plasmids. These results suggest that the gene trmD ⁺ is the structural gene for the tRNA (m¹G)methyltransferase (EC 2.1.1.3.1).     

Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele

Methods for detecting the genomic signatures of natural selection have been heavily studied, and they have been successful in identifying many selective sweeps. For most of these sweeps, the favored allele remains unknown, making it difficult to distinguish carriers of the sweep from non-carriers. In an ongoing selective sweep, carriers of the favored allele are likely to contain a future most recent common ancestor. Therefore, identifying them may prove useful in predicting the evolutionary trajectory—for example, in contexts involving drug-resistant pathogen strains or cancer subclones. The main contribution of this paper is the development and analysis of a new statistic, the Haplotype Allele Frequency (HAF) score. The HAF score, assigned to individual haplotypes in a sample, naturally captures many of the properties shared by haplotypes carrying a favored allele. We provide a theoretical framework for computing expected HAF scores under different evolutionary scenarios, and we validate the theoretical predictions with simulations. As an application of HAF score computations, we develop an algorithm (PreCIOSS: Predicting Carriers of Ongoing Selective Sweeps) to identify carriers of the favored allele in selective sweeps, and we demonstrate its power on simulations of both hard and soft sweeps, as well as on data from well-known sweeps in human populations.     

Interactions between DNA helicases and frozen topoisomerase IV-quinolone-DNA ternary complexes.

Collisions between replication forks and topoisomerase-drug-DNA ternary complexes result in the inhibition of DNA replication and the conversion of the normally reversible ternary complex to a nonreversible form. Ultimately, this can lead to the double strand break formation and subsequent cell death. To understand the molecular mechanisms of replication fork arrest by the ternary complexes, we have investigated molecular events during collisions between DNA helicases and topoisomerase-DNA complexes. A strand displacement assay was employed to assess the effect of topoisomerase IV (Topo IV)-norfloxacin-DNA ternary complexes on the DnaB, T7 gene 4 protein, SV40 T-antigen, and UvrD DNA helicases. The ternary complexes inhibited the strand displacement activities of these DNA helicases. Unlike replication fork arrest, however, this general inhibition of DNA helicases by Topo IV-norfloxacin-DNA ternary complexes did not require the cleavage and reunion activity of Topo IV. We also examined the reversibility of the ternary complexes after collisions with these DNA helicases. UvrD converted the ternary complex to a nonreversible form, whereas DnaB, T7 gene 4 protein, and SV40 T-antigen did not. These results suggest that the inhibition of DnaB translocation may be sufficient to arrest the replication fork progression but it is not sufficient to generate cytotoxic DNA lesion.     

The value of decreasing the duration of the infectious period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection

Finding medications or vaccines that may decrease the infectious period of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could potentially reduce transmission in the broader population. We developed a computational model of the U.S. simulating the spread of SARS-CoV-2 and the potential clinical and economic impact of reducing the infectious period duration. Simulation experiments found that reducing the average infectious period duration could avert a median of 442,852 [treating 25% of symptomatic cases, reducing by 0.5 days, reproductive number (R₀) 3.5, and starting treatment when 15% of the population has been exposed] to 44.4 million SARS-CoV-2 cases (treating 75% of all infected cases, reducing by 3.5 days, R₀ 2.0). With R₀ 2.5, reducing the average infectious period duration by 0.5 days for 25% of symptomatic cases averted 1.4 million cases and 99,398 hospitalizations; increasing to 75% of symptomatic cases averted 2.8 million cases. At $500/person, treating 25% of symptomatic cases saved $209.5 billion (societal perspective). Further reducing the average infectious period duration by 3.5 days averted 7.4 million cases (treating 25% of symptomatic cases). Expanding treatment to 75% of all infected cases, including asymptomatic infections (R₀ 2.5), averted 35.9 million cases and 4 million hospitalizations, saving $48.8 billion (societal perspective and starting treatment after 5% of the population has been exposed). Our study quantifies the potential effects of reducing the SARS-CoV-2 infectious period duration.     

Two Penicillium camembertii mutants affected in the production of cyclopiazonic acid.

Penicillium camembertii was mutated and screened for cyclopiazonic acid-negative mutants. With a simple and rapid mini-extraction method for detection of cyclopiazonic acid production, we were able to isolate two strains which were affected in the production of this metabolite. One strain had completely lost the ability to synthesize detectable amounts of this secondary metabolite, whereas the other mutant produced 50 to 100 times less cyclopiazonic acid than the wild type. Also, the former strain had a changed morphology compared with the wild type. This morphological alteration appears to be coupled to the inability to produce cyclopiazonic acid because morphological revertants were able to synthesize cyclopiazonic acid to a level comparable to the wild type. The second mutant accumulated a new metabolite which was detectable by two-dimensional thin-layer chromatography. This new metabolite, however, appears not to be a direct precursor of cyclopiazonic acid.     

Parasites, diseases and health status of sympatric populations of sambar deer and white-tailed deer in Florida

From December 1983 to December 1984 a study on parasites, diseases and health status was conducted on sympatric populations of sambar deer (Cervus unicolor) and white-tailed deer (Odocoileus virginianus) from St. Vincent Island, Franklin County, Florida. Ten sambar and six white-tailed deer were examined. White-tailed deer had antibodies to epizootic hemorrhagic disease virus and bluetongue virus. Serologic tests for antibodies to the etiologic agents of bovine virus diarrhea, infectious bovine rhinotracheitis, vesicular stomatitis, parainfluenza 3, brucellosis, and leptospirosis were negative in both species of deer. White-tailed deer harbored 19 species of parasites; all were typical of the parasite fauna of this species in coastal regions of the southeastern United States. Sambar deer harbored 13 species of parasites, which apparently were derived largely from white-tailed deer. The only exception was Dermacentor variabilis which occurs frequently on wild swine on the island. The general health status of sambar deer appeared to be better than that of white-tailed deer. This was hypothesized to result from the sambar deer's utilization of food resources unavailable or unacceptable to white-tailed deer and to the absence and/or lower frequency of certain pathogens in sambar deer.     

Problems of body-weight estimation in fossil primates

Body-weight estimates of fossil primates are commonly used to infer many important aspects of primate paleobiology, including diet, ecology, and relative encephalization. It is important to examine carefully the methodologies and problems associated with such estimates and the degree to which one can have confidence in them. New regression equations for predicting body weight in fossil primates are given which provide body-weight estimates for most nonhominid primate species in the fossil record. The consequences of using different subgroups (evolutionary “grades”) of primate species to estimate fossil-primate body weights are explored and the implications of these results for interpreting the primate fossil record are discussed. All species (fossil and extant) were separated into the following “grades”: prosimian grade, monkey grade, ape grade, anthropoid grade, and all-primates grade. Regression equations relating lower molar size to body weight for each of these grades were then calculated. In addition, a female-anthropoid grade regression was also calculated for predicting body weight infernales of extinct, sexually dimorphic anthropoid species. These equations were then used to generate the fossil-primate body weights. In many instances, the predicted fossil-primate body weights differ substantially from previous estimates.