Parameter estimation and uncertainty quantification using information geometry

In this work, we: (i) review likelihood-based inference for parameter estimation and the construction of confidence regions; and (ii) explore the use of techniques from information geometry, including geodesic curves and Riemann scalar curvature, to supplement typical techniques for uncertainty quantification, such as Bayesian methods, profile likelihood, asymptotic analysis and bootstrapping. These techniques from information geometry provide data-independent insights into uncertainty and identifiability, and can be used to inform data collection decisions. All code used in this work to implement the inference and information geometry techniques is available on GitHub.

Quantitative analysis of tumour spheroid structure

Tumour spheroids are common in vitro experimental models of avascular tumour growth. Compared with traditional two-dimensional culture, tumour spheroids more closely mimic the avascular tumour microenvironment where spatial differences in nutrient availability strongly influence growth. We show that spheroids initiated using significantly different numbers of cells grow to similar limiting sizes, suggesting that avascular tumours have a limiting structure; in agreement with untested predictions of classical mathematical models of tumour spheroids. We develop a novel mathematical and statistical framework to study the structure of tumour spheroids seeded from cells transduced with fluorescent cell cycle indicators, enabling us to discriminate between arrested and cycling cells and identify an arrested region. Our analysis shows that transient spheroid structure is independent of initial spheroid size, and the limiting structure can be independent of seeding density. Standard experimental protocols compare spheroid size as a function of time; however, our analysis suggests that comparing spheroid structure as a function of overall size produces results that are relatively insensitive to variability in spheroid size. Our experimental observations are made using two melanoma cell lines, but our modelling framework applies across a wide range of spheroid culture conditions and cell lines.

Implementation and acceleration of optimal control for systems biology

Optimal control theory provides insight into complex resource allocation decisions. The forward–backward sweep method (FBSM) is an iterative technique commonly implemented to solve two-point boundary value problems arising from the application of Pontryagin’s maximum principle (PMP) in optimal control. The FBSM is popular in systems biology as it scales well with system size and is straightforward to implement. In this review, we discuss the PMP approach to optimal control and the implementation of the FBSM. By conceptualizing the FBSM as a fixed point iteration process, we leverage and adapt existing acceleration techniques to improve its rate of convergence. We show that convergence improvement is attainable without prohibitively costly tuning of the acceleration techniques. Furthermore, we demonstrate that these methods can induce convergence where the underlying FBSM fails to converge. All code used in this work to implement the FBSM and acceleration techniques is available on GitHub at https://github.com/Jesse-Sharp/Sharp2021.

Persistence as an Optimal Hedging Strategy

Bacteria invest in a slow-growing subpopulation, called persisters, to ensure survival in the face of uncertainty. This hedging strategy is remarkably similar to financial hedging, where diversifying an investment portfolio protects against economic uncertainty. We provide a new, to our knowledge, theoretical foundation for understanding cellular hedging by unifying the study of biological population dynamics and the mathematics of financial risk management through optimal control theory. Motivated by the widely accepted role of volatility in the emergence of persistence, we consider several models of environmental volatility described by continuous-time stochastic processes. This allows us to study an emergent cellular hedging strategy that maximizes the expected per capita growth rate of the population. Analytical and simulation results probe the optimal persister strategy, revealing results that are consistent with experimental observations and suggest new opportunities for experimental investigation and design. Overall, we provide a new, to our knowledge, way of conceptualizing and modeling cellular decision making in volatile environments by explicitly unifying theory from mathematical biology and finance.

Designing combination therapies using multiple optimal controls

Strategic management of populations of interacting biological species routinely requires interventions combining multiple treatments or therapies. This is important in key research areas such as ecology, epidemiology, wound healing and oncology. Despite the well developed theory and techniques for determining single optimal controls, there is limited practical guidance supporting implementation of combination therapies. In this work we use optimal control theory to calculate optimal strategies for applying combination therapies to a model of acute myeloid leukaemia. We present a versatile framework to systematically explore the trade-offs that arise in designing combination therapy protocols using optimal control. We consider various combinations of continuous and bang-bang (discrete) controls, and we investigate how the control dynamics interact and respond to changes in the weighting and form of the pay-off characterising optimality. We demonstrate that the optimal controls respond non-linearly to treatment strength and control parameters, due to the interactions between species. We discuss challenges in appropriately characterising optimality in a multiple control setting and provide practical guidance for applying multiple optimal controls. Code used in this work to implement multiple optimal controls is available on GitHub.

Exact Solutions of Coupled Multispecies Linear Reaction-Diffusion Equations on a Uniformly Growing Domain

Embryonic development involves diffusion and proliferation of cells, as well as diffusion and reaction of molecules, within growing tissues. Mathematical models of these processes often involve reaction–diffusion equations on growing domains that have been primarily studied using approximate numerical solutions. Recently, we have shown how to obtain an exact solution to a single, uncoupled, linear reaction–diffusion equation on a growing domain, 0 < x < L(t), where L(t) is the domain length. The present work is an extension of our previous study, and we illustrate how to solve a system of coupled reaction–diffusion equations on a growing domain. This system of equations can be used to study the spatial and temporal distributions of different generations of cells within a population that diffuses and proliferates within a growing tissue. The exact solution is obtained by applying an uncoupling transformation, and the uncoupled equations are solved separately before applying the inverse uncoupling transformation to give the coupled solution. We present several example calculations to illustrate different types of behaviour. The first example calculation corresponds to a situation where the initially–confined population diffuses sufficiently slowly that it is unable to reach the moving boundary at x = L(t). In contrast, the second example calculation corresponds to a situation where the initially–confined population is able to overcome the domain growth and reach the moving boundary at x = L(t). In its basic format, the uncoupling transformation at first appears to be restricted to deal only with the case where each generation of cells has a distinct proliferation rate. However, we also demonstrate how the uncoupling transformation can be used when each generation has the same proliferation rate by evaluating the exact solutions as an appropriate limit.

Survival probability for a diffusive process on a growing domain

We consider the motion of a diffusive population on a growing domain, 0<x<L(t), which is motivated by various applications in developmental biology. Individuals in the diffusing population, which could represent molecules or cells in a developmental scenario, undergo two different kinds of motion: (i) undirected movement, characterized by a diffusion coefficient, D, and (ii) directed movement, associated with the underlying domain growth. For a general class of problems with a reflecting boundary at x=0, and an absorbing boundary at x=L(t), we provide an exact solution to the partial differential equation describing the evolution of the population density function, C(x,t). Using this solution, we derive an exact expression for the survival probability, S(t), and an accurate approximation for the long-time limit, S=lim(t→∞)S(t). Unlike traditional analyses on a nongrowing domain, where S≡0, we show that domain growth leads to a very different situation where S can be positive. The theoretical tools developed and validated in this study allow us to distinguish between situations where the diffusive population reaches the moving boundary at x=L(t) from other situations where the diffusive population never reaches the moving boundary at x=L(t). Making this distinction is relevant to certain applications in developmental biology, such as the development of the enteric nervous system (ENS). All theoretical predictions are verified by implementing a discrete stochastic model.

Delay and number of food reinforcers: Effects on choice and latencies

Pigeons were given a choice between two identical-duration situations (terminal links of chain schedules). One terminal link of the choice pair provided two food deliveries, and the other provided five. The exact times of these food deliveries differed between the terminal links and were varied over conditions. A single response during the initial link gave immediate access to the corresponding terminal link. Forced trials, during which only one of the initial-link keys was lighted, were interspersed with choice trials during which both initial-link keys were lighted. Choice tended to favor whichever terminal link was correlated with the higher sum of the immediacies (i.e., the sum of the reciprocals of the delays to each of the reinforcers following the choice, with all delays measured from the choice). Latencies on forced trials and on choice trials also were related (negatively) to the sum of the immediacies. This correlation among response measures (choice and latencies) suggests that both measures are manifestations of the effect of conditioned reinforcement on response tendencies.

The Tammar Wallaby and Fur Seal: Models to Examine Local Control of Lactation

Mammary development and function are regulated by systemic endocrine factors and by autocrine mechanisms intrinsic to the mammary gland, both of which act concurrently. The composition of milk includes nutritional and developmental factors that are crucial to the development of the suckled young, but it is becoming increasingly apparent that milk also has a role in regulating mammary function. This review examines the option of exploiting the comparative biology of species with extreme adaptation to lactation to examine regulatory mechanisms that are present but not readily apparent in other laboratory and livestock species. The tammar wallaby has adopted a reproductive strategy that includes a short gestation (26 d), birth of an immature young, and a relatively long lactation (300 d). The composition of milk changes progressively during the lactation cycle, and this is controlled by the mother and not the sucking pattern of the young. Furthermore, the tammar can practice concurrent asynchronous lactation; the mother provides a concentrated milk high in protein and fat for an older animal that is out of the pouch and a dilute milk low in fat and protein but high in carbohydrates from an adjacent mammary gland for a newborn pouch young. This phenomenon suggests that the mammary gland is controlled locally. The second study species, the Cape fur seal, has a lactation characterized by a repeated cycle of long at-sea foraging trips (up to 28 d) alternating with short suckling periods of 2 to 3 d ashore. Lactation almost ceases while the seal is off shore, but the mammary gland does not progress to apoptosis and involution, most likely because of local control of the mammary gland. Our studies have exploited the comparative biology of these models to investigate how mammary function is regulated by endocrine factors, and particularly by milk. This review reports 3 major findings using these model animals. First, the mammary epithelial cell has an extraordinary intrinsic capacity for survival in our culture model, and the path to either function or death by apoptosis is actively driven. The second outcome is that the route to apoptosis is most likely regulated by specific milk factors. Finally, whey acidic protein, a major milk protein in some species, may play a role in normal mammary development, but that role in vivo may be limited to marsupials. Evolutionary pressure has led to changes in the structure of the protein with an accompanying change in function. Therefore, we propose that a loss of function of this protein in eutherians may relate to a reproductive strategy that is less dependent on lactation.

Chromatin proteins are determinants of centromere function

Recent advances in the identification of molecular components of centromeres have demonstrated a crucial role for chromatin proteins in determining both centromere identity and the stability of kinetochore-microtubule attachments. Although we are far from a complete understanding of the establishment and propagation of centromeres, this review seeks to highlight the contribution of histones, histone deposition factors, histone modifying enzymes, and heterochromatin proteins to the assembly of this sophisticated, highly specialized chromatin structure. First, an overview of DNA sequence elements at centromeric regions will be presented. We will then discuss the contribution of chromatin to kinetochore function in budding yeast, and pericentric heterochromatin domains in other eukaryotic systems. We will conclude with discussion of specialized nucleosomes that direct kinetochore assembly and propagation of centromere-defining chromatin domains.

Yeast histone deposition protein Asf1p requires Hir proteins and PCNA for heterochromatic silencing

BACKGROUND

Position-dependent gene silencing in yeast involves many factors, including the four HIR genes and nucleosome assembly proteins Asf1p and chromatin assembly factor I (CAF-I, encoded by the CAC1-3 genes). Both cac Delta asfl Delta and cac Delta hir Delta double mutants display synergistic reductions in heterochromatic gene silencing. However, the relationship between the contributions of HIR genes and ASF1 to silencing has not previously been explored.

RESULTS

Our biochemical and genetic studies of yeast Asf1p revealed links to Hir protein function. In vitro, an active histone deposition complex was formed from recombinant yeast Asf1p and histones H3 and H4 that lack a newly synthesized acetylation pattern. This Asf1p/H3/H4 complex generated micrococcal nuclease--resistant DNA in the absence of DNA replication and stimulated nucleosome assembly activity by recombinant yeast CAF-I during DNA synthesis. Also, Asf1p bound to the Hir1p and Hir2p proteins in vitro and in cell extracts. In vivo, the HIR1 and ASF1 genes contributed to silencing the heterochromatic HML locus via the same genetic pathway. Deletion of either HIR1 or ASF1 eliminated telomeric gene silencing in combination with pol30--8, encoding an altered form of the DNA polymerase processivity factor PCNA that prevents CAF-I from contributing to silencing. Conversely, other pol30 alleles prevented Asf1/Hir proteins from contributing to silencing.

CONCLUSIONS

Yeast CAF-I and Asf1p cooperate to form nucleosomes in vitro. In vivo, Asf1p and Hir proteins physically interact and together promote heterochromatic gene silencing in a manner requiring PCNA. This Asf1/Hir silencing pathway functionally overlaps with CAF-I activity.

Medicine information help lines: a survey of hospital pharmacy-based services in the UK and their conformity with guidelines

OBJECTIVE

To describe the prevalence and nature of hospital pharmacy-based medicine help lines for consumers in the UK and to compare service provision with published guidelines.

BACKGROUND

Since 1992, telephone help lines for patients have proliferated in hospital pharmacies in the UK. There is no common template for such services with variations in target group, number and type of calls, and arrangements for training and audit. Data on these factors will help guide further development of such services.

METHODS

All medicine help lines operating from hospital pharmacies in the UK were identified through the national Drug Information Pharmacists network. They were sent a piloted questionnaire covering many aspects of help line operation, including funding, method of advertisement, procedures, target group, number and nature of calls, and audit procedures.

RESULTS

Eighty-two help lines were identified in England, Scotland, Wales, and Northern Ireland. Completed responses were received from 69 help lines (84% response rate). The pharmacy drug information center was the help line site in 57% of hospitals; all other help lines were located in the dispensary. In 55% of cases, help lines were open only to patients of the hospital. In the remainder of help lines, calls from the public were answered (although the majority of help lines only advertised to hospital patients). Calls were answered by pharmacists only in 45% of services, and additional staff training had been provided in 43%. Only 48% of services had written procedures or guidelines for operation of the help line. Forty-six percent of the services received fewer than five calls per week, 31% received between five and 10 calls per week, and 22% received 11 or more calls per week. In 59% of the sites, calls took an average of 10 minutes or less to answer; it took 11-15 minutes in 32% of the sites and >15 minutes in 9% of the sites. The most common queries related to adverse effects, dosage and administration, and interactions (including alcohol). Only 33% of help lines had any auditing or monitoring of the service in place.

CONCLUSIONS

The increasing use of the telephone to provide services directly to consumers is reflected in the growth of hospital-based medicine help lines in the UK. The telephone route is likely to become more important as patients' needs for information about their medicines increase. However, the rate of calls is low when compared with the number of patients issued prescriptions; further research is needed to investigate the reasons for this low response. There is currently reason for concern because most help lines lack not only professional training in telephone counseling, but also proper documentation, monitoring, and audit procedures.

Tumor cells are the source of osteopontin and bone sialoprotein expression in human breast cancer

Bone sialoprotein (BSP) and osteopontin (OPN) are secreted glycoproteins with a conserved Arg-Gly-Asp (RGD) integrin-binding motif and are expressed predominantly in bone. The RGD tripeptide is commonly present in extracellular attachment proteins and has been shown to mediate the attachment of osteosarcoma cells and osteoclasts. To determine the origin and incidence of BSP and OPN mRNA expression in primary tumor, a cohort of archival, primary invasive breast carcinoma specimens was analyzed. BSP transcripts were detected in 65% and OPN transcripts in 77% of breast cancers examined. In general, BSP and OPN transcripts were detected in both invasive and in situ carcinoma components. The transcripts were not detected in surrounding stromal cells or in peritumoral macrophages. Despite its abundance in carcinomas, BSP expression was not detected in a panel of 11 human breast cancer cell lines (MCF-7, T47D, SK-Br-3, MDA-MB-453, MDA-MB-231, MDA-MB-436, BT549, MCF-7ADR, Hs578T, MDA-MB-435, and LCC15-MB) and OPN expression was detected only in two of these (MDA-MB-435 and LCC15-MB). To examine the possibility that expression of these genes was down-regulated in cell culture, several cell lines were grown as nude mouse xenografts in vivo; however, these tumors also failed to express BSP. OPN expression was identified in all cell lines grown as nude mouse xenografts. Our data suggest that in human primary breast tumors, the origin of BSP and OPN mRNA is predominantly the breast cancer cells and that expression of these transcripts is influenced by the tumor environment.

Purification and characterization of the Sgs1 DNA helicase activity of Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae Sgs1 protein is a member of a family of DNA helicases that include the Escherichia coli RecQ protein and the products of human Bloom's syndrome and Werner's syndrome genes. To study the enzymatic characteristics of the protein, a recombinant Sgs1 fragment (amino acids 400-1268 of the 1447-amino acid full-length protein) was overexpressed in yeast and purified to near homogeneity. The purified protein exhibits an ATPase activity in the presence of single- or double-stranded DNA. In the presence of ATP or dATP, unwinding of duplex DNA or a DNA-RNA heteroduplex by the recombinant Sgs1 fragment was readily observed. Similar to the E. coli RecQ helicase, displacement of the DNA strand occurs in the 3' to 5' direction with respect to the single-stranded DNA flanking the duplex. The efficiency of unwinding was found to correlate inversely with the length of the duplex region and was enhanced by the presence of E. coli single-stranded DNA-binding protein. In addition, the recombinant Sgs1 fragment was found to bind more tightly to a forked DNA substrate than to either single- or double-stranded DNA.

Characterization of the Aspergillus nidulans nmrA gene involved in nitrogen metabolite repression

The gene nmrA of Aspergillus nidulans has been isolated and found to be a homolog of the Neurospora crassa gene nmr-1, involved in nitrogen metabolite repression. Deletion of nmrA results in partial derepression of activities subject to nitrogen repression similar to phenotypes observed for certain mutations in the positively acting areA gene.

The acetate regulatory gene facB of Aspergillus nidulans encodes a Zn(II)2Cys6 transcriptional activator

Genetic studies have indicated that the facB gene of Aspergillus nidulans is a major regulatory gene involved in acetamide and acetate utilisation. Sequencing of the facB gene revealed that it encodes a protein that contains an N-terminal GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster for DNA binding, leucine zipper-like heptad repeat motifs and central and C-terminal acidic alpha-helical regions, consistent with a function as a DNA-binding transcriptional activator. The Zn(II)2Cys6 cluster shows strong similarity with those of the Saccharomyces cerevisiae carbon metabolism regulatory proteins CAT8 and SIP4. A significant level of similarity with CAT8 is found throughout the length of the protein, suggesting at least partial functional homology. The facB genes of Aspergillus oryzae and Aspergillus niger were also sequenced and found to be highly conserved. Deletion of the facB gene confirmed that it is required for growth on acetate as a sole carbon source. Functional dissection using deletion and fusion constructs and in vitro mutagenesis indicated that the Zn(II)2Cys6 cluster and the C-terminal end of the protein are required for function.

The hapC gene of Aspergillus nidulans is involved in the expression of CCAAT-containing promoters

The 5' regulatory region of the amdS gene of Aspergillus nidulans, which encodes an acetamidase required for growth on acetamide as a carbon and nitrogen source, contains a CCAAT sequence which is required for setting the basal level of amdS expression. Mobility shift studies have identified a factor in A. nidulans nuclear extracts which binds to this CCAAT sequence. In Saccharomyces cerevisiae the HAP3 gene encodes one component of a multisubunit complex that binds CCAAT sequences. A search of the EMBL and SwissProt databases has revealed an A. nidulans sequence with significant homology to the HAP3 gene adjacent to the previously cloned regulatory gene amdR. Sequencing of the remainder of this region has confirmed the presence of a gene, designated hapC, with extensive homology to HAP3. The predicted amino acid sequence of HapC shows extensive identity to HAP3 in the central conserved domain, but shows little conservation in the flanking sequences. A haploid carrying a hapC deletion has been created and is viable, but grows poorly on all media tested. This null mutant grows especially slowly on acetamide as a sole carbon and nitrogen source, indicating that hapC plays a role in amdS expression. In agreement with this notion, it has been shown that the hapC deletion results in reduced levels of expression of an amdS::lacZ reporter gene and this effect is particularly evident under conditions of carbon limitation. Nuclear extracts prepared from the hapC deletion mutant show no CCAAT binding activity to the amdS or gatA promoters, indicating that hapC may encode a component of the complex binding at this sequence.

The rho-115 mutation in transcription termination factor rho affects its primary polynucleotide binding site

We have investigated the effect of the rho-115 mutation on the catalytic properties of the Escherichia coli termination protein, rho. Comparison of the primary and secondary polynucleotide binding sites activities reveals dramatic differences between the mutant and wild-type molecules. Wild-type rho must bind single-stranded polynucleotides to activate its nucleotide triphosphatase (NTPase) activity, and either poly(C), or poly(dC) plus oligo(C), will suffice. In contrast, attempted activation of the rho-115 NTPase with poly(C) in the presence of poly(dC) showed the latter to be a potent inhibitor. Inclusion of small oligonucleotides such as oligo(C) in the activation assay does not inhibit the poly(C)-induced NTPase reaction of either wild-type rho or rho-115. This would indicate, in the two polynucleotide binding site model for rho proposed by Richardson (Richardson, J.P. (1982) J. Biol. Chem. 251, 5760-5766), that the mutation in rho-115 affects the primary polynucleotide binding site. Transcription termination in vitro at the rho-dependent site trp t' showed dramatically reduced termination with rho-115 protein compared to wild-type rho. In the presence of rho-115, the transcript is longer and termination occurs over a narrower range of nucleotides than with wild-type rho. This suggests that the primary polynucleotide binding site is important not only for efficient termination of transcription but may also be involved in determining the terminal end point of the transcript itself.

Choline transport across a carbon tetrachloride phase containing a chloroform-methanol extract of brain

The presence of a chloroform-methanol extract of cat brain in a carbon tetrachloride phase separating two aqueous phases resulted in an increased passage of [3H]choline across the organic phase which was inhibited by the choline transport inhibitor hemicholinium-3 and by high concentrations of non-radioactive choline. In the absence of cat brain extract, [3H]choline passage across carbon tetrachloride was neither inhibited by hemicholinium-3, nor by non-radioactive choline.

Erythrocyte adenosine transport: effects of Ca2+ channel antagonists and ions

On the basis of observations of adenosine-Ca2+ competition, we assessed the effects on erythrocyte adenosine transport of Ca2+ channel antagonists, mono- and divalent cations, and Cl- and Cl- transport inhibitors. The Ca2+ channel antagonists, diltiazem and verapamil, competitively inhibited adenosine influx (Ki = 158 +/- 17.4 and 13.5 +/- 1.3 microM at 10 microM adenosine, respectively), despite no apparent effect on transport by Ca2+, Mg2+, Na+, or K+. Verapamil also inhibited uridine efflux (Ki = 1.7 +/- 0.3 microM at 84-100 microM intracellular uridine). The absence of Cl- decreased adenosine influx rates from 0.615 +/- 0.013 to 0.386 +/- 0.008 nmol X s-1 X ml intracellular H2O-1. The Cl- transport inhibitors, diisothiocyanostilbene disulfonate (10 microM), furosemide (1 mM), and NO-3 (145 mM), decreased adenosine influx rates to 0.301 +/- 0.008, 0.325 +/- 0.013, and 0.430 +/- 0.009 nmol X s-1 X ml intracellular H2O-1, respectively. These studies indicate that the Ca2+ channel antagonists inhibit adenosine release and uptake and therefore may modulate adenosine-mediated events. Additionally, they suggest that adenosine and anion transport systems are linked or share common features.

Pausing of RNA polymerase during in vitro transcription through the ilvB and ilvGEDA attenuator regions of Escherichia coli K12

Synchronized single-round transcriptions, in vitro, from templates encoding the leader RNA of the ilvB and ilvGEDA operons result in the accumulation of a transcript consistent with RNA polymerase pausing after the 1:2 stem that could form in each of the leader RNAs. Addition of L-factor or guanosine 5'-diphosphate,3-diphosphate extended the pause half-life obtained with the ilvB template; addition of L-factor and guanosine 5'-diphosphate,3'-diphosphate together had an additive effect on the pause half-life. L-factor also extended the pause half-life of the pause obtained with the ilvGEDA template; however, addition of guanosine 5'-diphosphate,3'-diphosphate did not. The results obtained are consistent with the model for attenuation proposed by Yanofsky et al. (Yanofsky, C., Das, A., Fisher, R., Kolter, R., and Berlin, V. (1984) UCLA Symposium of Gene Expression (Hamer, D., and Rosenberg, M., eds) pp. 295-310, Alan R. Liss, Inc., New York) in which transcriptional pausing after the synthesis of the 1:2 stem-loop closely couples transcription and translation of the leader region.

In vitro and in vivo transcription initiation sites on the TK-encoding BamHI Q fragment of HSV-1 DNA

The sites of in vitro transcription initiation on the BamHI Q fragment of herpes simplex virus DNA have been compared with the sites of 5' ends of RNAs made in vivo after virus infection. S1-nuclease protection analysis of these RNAs shows that there are in vivo counterparts for each of the five previously identified in vitro transcripts. The whole-cell-extract RNA polymerase II transcription system faithfully initiates RNAs predominantly at bona fide in vivo start sites and gives few, if any, false positive start sites. Further, antiparallel, self-complementary transcripts from the BamHI Q fragment were observed in the coding region of the HSV thymidine kinase gene.

Each element of the Drosophila tRNAArg gene split promoter directs transcription in Xenopus oocytes

The intragenic control regions of a eukaryotic tRNA gene have been examined by transcribing mutant forms of a Drosophila tRNAArg gene either by injection into the nucleus of Xenopus oocytes or in extracts prepared from isolated oocyte nuclei. These experiments demonstrate that the selection of the transcription initiation site is a complex mechanism that involves the T-control region, the D-control region, and sequences 5' adjacent to the D-control region. In this study either "half" of the Drosophila tRNAArg gene promoted transcription in Xenopus oocytes. This finding supports a recent model for eukaryotic tRNA gene transcription (Dingermann et al., 1983, J. Biol. Chem. 258, 10395-10402) that proposes transcription initiation is dependent on the ability of specific DNA sequences to sequester two RNA polymerase III transcription factors.

Rho-dependent termination and concomitant NTPase activity requires a specific, intact RNA region

We have investigated the specific DNA and RNA requirements for rho-dependent transcription termination in vitro. As a model, we have used templates containing the rho-dependent terminator of the Escherichia coli trp operon, trp t'. Templates containing the trp t' region direct specific rho-dependent termination in vitro, with concomitant stimulation of the rho NTPase activity, and deletion of the trp t' region results in templates that do not induce rho-dependent termination or rho NTPase activity. Addition of ribonuclease T1 to transcription reactions specifically eliminated transcription termination and rho NTPase activity. These results demonstrate the requirement for a specific RNA component within the trp t' transcript necessary for NTPase activation and rho-dependent transcription termination. Active transcription is not a prerequisite for rho NTPase activation; trp t' RNA (rho-terminated transcripts) and read-through transcripts, which contain the trp t' region, activated the rho NTPase when rho was added after inhibition of transcription. As is true for synthetic polynucleotides known to activate the rho NTPase, the trp t' region has few G residues. This reduces the potential for the formation of stable secondary structures in the RNA transcript, and may be one determinant of sites specifying rho-dependent termination of transcription. The implications of this are discussed in the light of the lack of significant sequence homologies between rho-dependent transcription termination sites.

Ultrasonic detection of subdural collections

Subdural collections in infants are common complications of meningitis, trauma and post surgical procedures. Careful ultrasonic examination via the anterior fontanelle is a reliable method of demonstrating these collections. It has an accuracy comparable to computed tomography and is our first line of investigation.

The effects of Al3+, Cd2+ and Mn2+ on human erythrocyte choline transport

The effects of Al3+, Cd2+ and Mn2+ on human erythrocyte choline transport, Na-K-ATPase, Ca-Mg-ATPase and intracellular K+ levels were examined. The concentrations used were below the levels which caused significant haemolysis (less than or equal to 300 microM). All three cations inhibited concentrative choline accumulation over 3 hr [IC50 values at 1 microM choline were 35 microM (AlCl3), 250 microM (CdCl2) and 300 microM (MnCl2)] but at the concentrations tested, none decreased initial rates of choline uptake. The effects of Cd2+ and Mn2+ (but not Al3+) on choline accumulation were reversed by removing the cations from the extracellular medium by washing. All three cations also inhibited efflux of choline, at 1 microM choline, 30% inhibition being produced by 33 microM AlCl3, 81 microM CdCl2 and 111 microM MnCl2. At subhaemolytic concentrations, only CdCl2 inhibited Na-K-ATPase, (IC50 = 147 microM) and none of the cations significantly inhibited Ca-Mg-ATPase. Intracellular K+ levels were only reduced by the highest concentration of AlCl3 used (100 microM). These results suggest that inhibition of choline accumulation and efflux in erythrocytes by Al3+, Cd2+ and Mn2+ is not explicable solely in terms of either inhibition of Ca-Mg-ATPase, or inhibition of Na-K-ATPase causing reduced intracellular K+. Our conclusions are similar to those previously obtained using synaptosomes and provide support for the hypothesis that inhibition of choline transport by Al3+ may contribute to a number of disease states.

Pausing and termination of human RNA polymerase II transcription at a procaryotic terminator

Kinetic analyses of runoff transcription in a cell-free eucaryotic transcription system revealed that the bacteriophage lambda 4S RNA terminator caused human RNA polymerase II to pause on the template and partially terminate transcription of transcripts initiated by the adenovirus 2 major late promoter. Analogous to the procaryotic RNA polymerase, the eucaryotic enzyme terminated just beyond the guanine-plus-cytosine-rich region of dyad symmetry in the terminator sequence. These results suggest that the eucaryotic RNA polymerase II may respond to transcription termination sequences similar to those used by the procaryotic enzyme. However, similar templates containing lambda tint or lambda tR1 terminators did not elicit pausing or termination, suggesting that other features, such as sequence specificity, may also be involved.

Initial-velocity kinetics of succinoyl-coenzyme A-3-oxo acid coenzyme A-transferase from sheep kidney

The initial-velocity kinetics of sheep kidney CoA-transferase are consistent with a Ping Pong mechanism. A KAcAc-CoA of 2.7 X 10(-5) M, KSucc-CoA of 1.6 X 10(-4) M, KSucc of 5.6 X 10(-3) M and KAcAc of 6.7 X 10(-5) M were determined by using a direct assay system that monitors the concentration of magnesium acetoacetyl-CoA enolate. However, product-inhibition kinetics of sheep kidney CoA-transferase are inconsistent with a Ping Pong mechanism. The possible involvement of separate binding sites for succinate and acetoacetate are discussed.

A kinetic mechanism for the poly(C)-dependent ATPase of the Escherichia coli transcription termination protein, rho

A study of the initial velocity kinetics of the Escherichia coli transcription termination protein rho, with respect to its poly(C)-dependent ATPase, indicates that this reaction occurs by an ordered sequential mechanism. Product inhibition and substrate analogue studies suggest that ATP binding must precede the binding of poly(C) and that the order of release of the products is ADP followed by Pi, then poly(C). A possible mechanism for relating the ATPase to the termination reaction of rho is discussed in relation to the model for rho proposed by Richardson (5).

Transcription of herpes simplex virus genes in vivo: overlap of a late promoter with the 3' end of the early thymidine kinase gene

We identified in herpes simplex virus type 1-infected cells six cytoplasmic transcripts which were complementary to BamHI restriction endonuclease fragment Q. Two transcripts appeared in major amounts compared with the other four. One major transcript of about 1.4 kilobases was the mRNA for the viral thymidine kinase, was synthesized at intermediate times, and was classified as a beta transcript. The other major transcript was synthesized at late times and was classified as a gamma transcript. This late transcript was about 3 kilonucleotides long and was transcribed in the same direction as the gene for thymidine kinase. The 5' end of this late RNA was located by RNA sequence analysis and was 23 nucleotides downstream from the polyadenylation site for the thymidine kinase mRNA. This finding led to the conclusion that the control region for the 3-kilobase gamma transcript is contained within the 3' untranslated region of the thymidine kinase transcript.

Nucleotide sequence of the thymidine kinase gene of herpes simplex virus type 1

We have determined the complete nucleotide sequence of the thymidine kinase (ATP:thymidine 5' phosphotransferase, EC 2.7.1.21) gene of herpes simplex virus type 1 strain CL101 from a plasmid clone of viral DNA derived by Enquist et al. [Enquist, L. W., Vande Woude, G. F., Wagner, M., Smiley, J. R. & Summers, W. C. (1979) Gene 7, 335-342]. A cDNA copy of the 5' end of thymidine kinase mRNA was also analyzed to locate the transcribed sequences. The transcribed portion of the gene is approximately 1300 nucleotides in length and appears to contain no intervening sequences. There is an untranslated region of 107 nucleotides at the 5' end of the mRNA followed by an open reading frame of 1128 nucleotides. The gene is thus capable of coding for a protein of 376 amino acids. Sequences similar to those thought to be involved in control of transcription and translation of a variety of eukaryotic and viral genes such as a "Hogness box" and A-A-T-A-A-A polyadenylylation signals are also present in the herpesvirus thymidine kinase gene.

Purification and properties of succinyl-coenzyme A-3-oxo acid coenzyme A-transferase from sheep kidney

CoA-transferase (succinyl-CoA-3-oxo acid CoA-transferase, EC 2.8.3.5) isolated from sheep kidney was purified to homogeneity. The purified enzyme has a specific activity of approx. 200 units/mg. A mol.wt. of 110000 was obtained by gel filtration on Sephadex G-200, and a lower mol.wt. of 102000 was determined by analytical ultracentrifugation. A sedimentation coefficient of 5.6S was also determined. A subunit mol.wt. of 56000 was obtained by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis. Isoelectric focusing of sheep kidney extracts indicated the presence of a single band of CoA-transferase activity with pI9.0. However, isoelectric focusing of purified CoA-transferase showed the presence of two peaks of CoA-transferase activity with pI values of 8.7 and 8.4, suggesting the presence of proteolytic activity during purification. Evidence for sheep kidney CoA-transferase being a dimer of two identical subunits has been obtained from sodium dodecyl sulphate/polyacrylamide-gel electrophoresis, the amino acid composition, peptide 'mapping' and N-terminal analysis.

ALEXANDER MONRO SECUNDUS AND THE INTERVENTRICULAR FORAMEN

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