O-BN05 The management of pancreatitis and complications that require intervention in a Benign Specialist Surgical Unit

Background

Acute pancreatitis or inflammation of the pancreas is a common surgical pathology that presents with a spectrum of severity. The condition itself ranges from a mild/moderate self-limiting pathology to one associated with a systemic inflammatory response that can lead to organ dysfunction and death. We aim to investigate the aetiology/management and outcomes of patients presenting with pancreatitis in a benign specialist surgical unit with dedicated upper GI surgical care.

Methods

A retrospective analysis of all patients presenting and falling under surgical care with biochemical/radiological pancreatitis was conducted, using hospital archiving systems, reviewing operative notes and follow up events was conducted over an 8-year period.

Results

Within our benign specialist centre, 1393 patients were treated over an 8-year period. 73% of patients presenting with acute pancreatitis were male, whereas only 37% were female. The age range of patients presenting was 12 to 100 years, with the median age being 44 years. Within our population, 36.8% of acute pancreatitis was caused by gallstones, and 29.6% caused by alcohol and 33.6% other causes. 81% of patients seen had mild/moderate self-resolving pancreatitis requiring only fluids and analgesia. 19% had complicated pancreatitis requiring complex medical/surgical treatment.4.8% patients developed pancreatic necrosis, and 3.7% developed pancreatic pseudocysts. 8 patients required necrosectomy, 19 patients required cystogastrostomy and 1 patient required distal pancreatectomy with no 90-day mortality.

Conclusions

Our specialist unit with the support of gastroenterology, nutrition team, radiology and ITU have managed a large cohort of pancreatitic patients, the small number patients who require a surgical intervention have had good outcomes.

O-BN03 Laparoscopic Common Bile Duct Exploration – Delivered within UK NHS Healthcare Framework

Background

Cholelithiasis is a common problem in the UK affecting approximately 15% of the population. The incidence of synchronous choledocholithiasis is approximately 10-18%. The approach to bile duct stones is variable. Single stage bile duct exploration and cholecystectomy (LC) vs two stage ERCP followed by LC has been shown to be equally safe and as effective with reduced length of stay and number of procedures. We describe the results of a single, high volume centre performing laparoscopic common bile duct exploration (LCBDE) as an alternative to ERCP.

Methods

All patients undergoing LCBDE at our institution from November 2013 – July 2021 were included in the study. Data were collected from a prospectively maintained institutional database and data points corroborated by electronic patient data on hospital systems.

Results

304 patients underwent LCBDE. Median age was 68 (range 21-94). Most cases were performed as urgent/emergency (n = 204, 67% vs n = 100, 33% elective). Bile duct stones were diagnosed pre-operatively in 32.8% cases (n = 100). Intra-operative diagnosis was made using laparoscopic ultrasound (n = 221, 73%), cholangiogram (n = 44, 15%) or combination of both (n = 31, 10%). Laparoscopic completion rate was 92%. Successful stone clearance rate was 98%. 56% were via choledochotomy and 44% trans-cystic. Incidence of bile leak was 4.9% (n = 15). Median length of stay was 2 days post-operatively (range 0–62). The rate of all complications was 13.2%. The rate of mortality was 0.66%.

Conclusions

This is the largest single case series of LCBDE published. This study has demonstrated that a safe and effective LCBDE service can be delivered within the NHS, with outcome data comparable to defined performance standards. With the evolution of specialist training, intra-operative imaging +/- LCBDE is likely to be the preferred modality of treatment.

Bio-optical evidence for increasing Phaeocystis dominance in the Barents Sea

Increasing contributions of prymnesiophytes such as Phaeocystis pouchetii and Emiliania huxleyi to Barents Sea (BS) phytoplankton production have been suggested based on in situ observations of phytoplankton community composition, but the scattered and discontinuous nature of these records confounds simple inference of community change or its relationship to salient environmental variables. However, provided that meaningful assessments of phytoplankton community composition can be inferred based on their optical characteristics, ocean-colour records offer a potential means to develop a synthesis between sporadic in situ observations. Existing remote-sensing algorithms to retrieve phytoplankton functional types based on chlorophyll-a (chl-a) concentration or indices of pigment packaging may, however, fail to distinguish Phaeocystis from other blooms of phytoplankton with high pigment packaging, such as diatoms. We develop a novel algorithm to distinguish major phytoplankton functional types in the BS and apply it to the MODIS-Aqua ocean-colour record, to study changes in the composition of BS phytoplankton blooms in July, between 2002 and 2018, creating time series of the spatial distribution and intensity of coccolithophore, diatom and Phaeocystis blooms. We confirm a north-eastward expansion in coccolithophore bloom distribution, identified in previous studies, and suggest an inferred increase in chl-a concentrations, reported by previous researchers, may be partly explained by increasing frequencies of Phaeocystis blooms. This article is part of the theme issue 'The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning'.

Phenological Responses to ENSO in the Global Oceans

Phenology relates to the study of timing of periodic events in the life cycle of plants or animals as influenced by environmental conditions and climatic forcing. Phenological metrics provide information essential to quantify variations in the life cycle of these organisms. The metrics also allow us to estimate the speed at which living organisms respond to environmental changes. At the surface of the oceans, microscopic plant cells, so-called phytoplankton, grow and sometimes form blooms, with concentrations reaching up to 100 million cells per litre and extending over many square kilometres. These blooms can have a huge collective impact on ocean colour, because they contain chlorophyll and other auxiliary pigments, making them visible from space. Phytoplankton populations have a high turnover rate and can respond within hours to days to environmental perturbations. This makes them ideal indicators to study the first-level biological response to environmental changes. In the Earth's climate system, the El Niño-Southern Oscillation (ENSO) dominates large-scale inter-annual variations in environmental conditions. It serves as a natural experiment to study and understand how phytoplankton in the ocean (and hence the organisms at higher trophic levels) respond to climate variability. Here, the ENSO influence on phytoplankton is estimated through variations in chlorophyll concentration, primary production and timings of initiation, peak, termination and duration of the growing period. The phenological variabilities are used to characterise phytoplankton responses to changes in some physical variables: sea surface temperature, sea surface height and wind. It is reported that in oceanic regions experiencing high annual variations in the solar cycle, such as in high latitudes, the influence of ENSO may be readily measured using annual mean anomalies of physical variables. In contrast, in oceanic regions where ENSO modulates a climate system characterised by a seasonal reversal of the wind forcing, such as the monsoon system in the Indian Ocean, phenology-based mean anomalies of physical variables help refine evaluation of the mechanisms driving the biological responses and provide a more comprehensive understanding of the integrated processes.

'Born in Michigan? You're in the biobank': engaging population biobank participants through Facebook advertisements

BACKGROUND/AIMS

Despite a broad call for biobanks to use social media, data is lacking regarding the capacity of social media tools, especially advertising, to engage large populations on this topic.

METHODS

We used Facebook advertising to engage Michigan residents about the BioTrust for Health. We conducted a low-budget (<USD 5,000), 26-day social media campaign targeting Michigan residents aged 18-28. We placed 25 Facebook advertisements and analyzed their performance in terms of reach and cost across 3 engagement types: passive, active and interactive. We compared engagement before, during and after the campaign.

RESULTS

The Facebook page was viewed 1,249 times during the month of the advertising campaign, versus once in the month prior. 779,004 Michigan residents saw ads an average of 25.8 times; 4,275 clicked ads; the average click-through-ratio was 0.021%. Interactions included 516 'likes' and 30 photo contest entries. Cost per outcome ranged from <USD 0.005 per exposure to USD 182 per photo entry. The average cost per click was USD 1.04.

CONCLUSION

A social media strategy to build public awareness about biobanking is not likely to be effective without a promotional 'push' to distribute content. Social media advertisements have the capacity to scale-up engagement on biobanking while keeping costs manageable. Facebook advertisements provide necessary access points for unaware participants, with implications for public trust.

Normal inflammatory markers in appendicitis: evidence from two independent cohort studies

OBJECTIVES

Acute appendicitis is a common surgical condition which can lead to severe complications. Recent work suggested that patients experiencing right lower abdominal pain, with normal white cell count (WCC) and C-reactive protein (CRP) are unlikely to have acute appendicitis and can be discharged. We present two independent data-sets that suggest that this strategy may not be risk-free.

DESIGN

Retrospective cohort study of consecutive patients from two district general hospitals. Sensitivity and specificity of CRP, WCC and neutrophil count (NC) in predicting appendicitis were calculated. Markers were analysed using Fisher's exact test and Kruskul-Wallace test.

SETTING

Two district general hospitals in the UK.

PARTICIPANTS

Patients undergoing appendicectomy for suspected appendicitis.

MAIN OUTCOME MEASURES

Inflammatory markers and appendix histology.

RESULTS

A total of 297 patients were included. Appendicitis occurred in four patients with normal CRP, WCC and NC in centre A and 13 patients in centre B. The sensitivity of all three markers combined was 94% (centre A) and 92% (centre B). The specificity was 60% (centre A) and 64% (centre B). No single marker could differentiate uncomplicated and complicated appendicitis, but a raised NC or a CRP >35.5 mg/l predicted complicated appendicitis. CRP, WCC and NC combined differentiated between patients with a normal appendix, uncomplicated appendicitis and complicated appendicitis.

CONCLUSIONS

Appendicitis in the presence of normal inflammatory markers is not uncommon. We disagree with the view of Sengupta et al. who suggest that patients with normal WCC and CRP are unlikely to have appendicitis, and recommend that clinicians be wary of normal inflammatory markers in patients with a high clinical suspicion of appendicitis.

Autotrophic picoplankton in the tropical ocean

In phytoplankton of the eastern tropical Pacific Ocean from 25 to 90 percent of the biomass (measured as chlorophyll a) and 20 to 80 percent of the inorganic carbon fixation were attributable to particles that could pass a screen with a 1-micrometer pore diameter. Evidence is presented that these are indeed autotrophic cells and not cell fragments.

Oceanic primary production: estimation by remote sensing at local and regional scales

Satellites provide the only avenue by which marine primary production can be studied at ocean-basin scales. With maps of chlorophyll distribution derived from remotely sensed data on ocean color as input, deduction of a suitable algorithm for primary production is a problem in applied plant physiology. An algorithm is proposed that combines a spectral and angular model of submarine light with a model of the spectral response of algal photosynthesis. To apply the algorithm at large horizontal scale, a dynamic biogeography is needed for the physiological rate parameters and the biological structure of the water column. Fieldwork to obtain this type of data should be undertaken so that the use of satellite data in modern biological oceanography may be optimized.

Basin-scale coherence in phenology of shrimps and phytoplankton in the North Atlantic Ocean

Climate change could lead to mismatches between the reproductive cycles of marine organisms and their planktonic food. We tested this hypothesis by comparing shrimp (Pandalus borealis) egg hatching times and satellite-derived phytoplankton bloom dynamics throughout the North Atlantic. At large spatial and long temporal (10 years or longer) scales, hatching was correlated with the timing of the spring phytoplankton bloom. Annual egg development and hatching times were determined locally by bottom water temperature. We conclude that different populations of P. borealis have adapted to local temperatures and bloom timing, matching egg hatching to food availability under average conditions. This strategy is vulnerable to interannual oceanographic variability and long-term climatic changes.

Escherichia coli rho factor induces release of yeast RNA polymerase II but not polymerase I or III

Purified RNA polymerase II (pol II) from the yeast Saccharomyces cerevisiae pauses without releasing at many locations during in vitro transcription. Pausing can be induced by intrinsic DNA sequence as well as by specific DNA bound proteins such as the RNA pol I termination factor, Reb1p, or lac repressor. Addition of rho termination factor from E. coli induces RNA pol II to release at all of these pause sites. Rho-induced release of pol II requires both a rho binding site in the transcript upstream of the pause sites as well as hydrolysis of ATP. In contrast, rho factor has no effect on either pausing or release by RNA pol I or III. When combined with previous observations, these results suggest that RNA pol II may terminate by a mechanism closely related to the rho-dependent mechanism of prokaryotes. In contrast, pol I and III appear to utilize a mechanism more related to the rho-independent terminators of prokaryotes.

Ocean-color model incorporating transspectral processes

Ocean color is determined by spectral variations in reflectance at the sea surface, which in turn result from both elastic and inelastic processes. We extend an elastic-scattering model of sea surface reflectance to deal with Raman scattering, which is an inelastic process. The analytic solutions are derived for a vertically homogeneous and optically deep water column. The model presented here is based on the quasi-single-scattering approximation of Gordon [Appl. Opt. 12, 2803 (1973)] and is an extension of the model of Sathyendranath and Platt [Appl. Opt. 36, 2620 (1997)]. The Raman-scattering model includes a first-order Raman-scattering term and four second-order terms. Two of the second-order terms result from a combination of an elastic and a Raman-scattering event, whereas the other two second-order terms result from two Raman-scattering events. We show that the contribution to reflectance from these last two terms is typically of the order of 1% of the first-order Raman-scattering term. Therefore these terms and higher-order terms can be neglected for most applications. Issues related to the implementation of the model are discussed, with special reference to remote-sensing applications. Results from the analytic model are compared with Monte Carlo simulations of reflectance at the sea surface.

Are individuals with mental retardation at high risk for chronic disease?

BACKGROUND AND OBJECTIVES

Family physicians are responsible for the health and illness care of individuals with mental retardation (MR) in many community practices. Therefore, it is important to determine the special disease patterns for this group. This study determined if individuals with MR are at increased risk for selected chronic diseases.

METHODS

We analyzed 366 individuals, living in the community, with a primary diagnosis of MR. The two comparison groups without MR were 427 individual Medicaid recipients and 746 privately insured individuals.

RESULTS

Individuals with MR had higher rates of neurophysical conditions (eg, seizures, central nervous system conditions, and sensory loss) compared to the other two groups. However, they had lower rates of some chronic conditions and health behaviors (eg, hypertension, migraines/chronic headaches, diabetes, depression or anxiety, obesity, substance abuse, and smoking) compared to other Medicaid and insured patients.

CONCLUSIONS

Individuals with MR have lower rates of many chronic conditions, compared with other Medicaid recipients. This finding should reduce concerns among family physicians that treatment of this special population involves higher rates of chronic illness.

Analytic model of ocean color

Ocean color is determined by spectral variations in reflectance at the sea surface. In the analytic model presented here, reflectance at the sea surface is estimated with the quasi-single-scattering approximation that ignores transspectral processes. The analytic solutions we obtained are valid for a vertically homogeneous water column. The solution provides a theoretical expression for the dimensionless, quasi-stable parameter (r), with a value of ~0.33, that appears in many models in which reflectance at the sea surface is expressed as a function of absorption coefficient (a) and backscattering coefficient (b(b)). In the solution this parameter is represented as a function of the mean cosines for downwelling and upwelling irradiances and as the ratio of the upward-scattering coefficient to the backscattering coefficient. Implementation of the model is discussed for two cases: (1) that in which molecular scattering is the main source of upwelling light, and (2) that in which particle scattering is responsible for all the upwelled light. Computations for the two cases are compared with Monte Carlo simulations, which accounts for processes not considered in the analytic model (multiple scattering, and consequent depth-dependent changes in apparent optical properties). The Monte Carlo models show variations in reflectance with the zenith angle of the incident light. The analytic model can be used to reproduce these variations fairly well for the case of molecular scattering. For the particle-scattering case also, the analytic and Monte Carlo models show similar variations in r with zenith angle. However, the analytic model (as implemented here) appears to underestimate r when the value of the backscattering coefficient b(b) increases relative to the absorption coefficient a. The errors also vary with the zenith angle of the incident light field, with the maximum underestimate being approximately 0.06 (equivalent to relative errors from 12 to 17%) for the range of b(b)/a studied here. One implication of this result is that the model could also be used to obtain approximate solutions for the Q factor, defined for a given look angle as the ratio of the upwelling irradiance at the surface to the upwelling radiance at the surface at that angle. This is a quantity that is important in remote-sensing applications of ocean-color models. An advantage of the model discussed here is that its implementation requires inputs that are in principle accessible only in a remote-sensing context.

Do behavior changes herald physical illness in adults with mental retardation?

A longitudinal study of 62 individuals with profound mental retardation was conducted to determine if direct care staff can identify behavior change prior to identifying symptoms of acute illness. Results indicate that staff were able to notice changes in sluggishness prior to the onset of illness. Self-care behavior was of borderline significance and there was no significant change in eight behavior dimensions (vocalizations, peer conflict, stereotypy, aggression, self injurious behavior, restlessness, distractibility, and depression). This finding should alert physicians and caregivers to the importance of prompt response to symptoms. Reliance on behavioral observation of direct care staff is not always sensitive enough to pick up changes in health status in less restrictive residential environments.

A mutation in the ATP binding domain of rho alters its RNA binding properties and uncouples ATP hydrolysis from helicase activity

The Escherichia coli mutant rho201 was originally isolated in a genetic screen for defects in rho-dependent termination. Cloning and sequencing of this gene reveals a single phenylalanine to cysteine mutation at residue 232 in the ATP binding domain of the protein. This mutation significantly alters its RNA binding properties so that it binds trp t', RNA 100-fold weaker than the wild type protein, with a Kd of approximately 1.3 nM. Rho201 binds nonspecific RNA only 3-4-fold less tightly than it binds trp t', while the wild type differential for these same RNAs is 10-20-fold. Curiously, rho201 displays increased secondary site RNA activation, with a Km for ribo(C)10 of 0.6 microM, compared to the wild type value of 3-4 microM. Although rho201 and the wild type protein hydrolyze ATP similarly with poly(C), or trp t' RNA, as cofactors, rho201 has a higher ATPase activity when activated by nonspecific RNA. Physically, rho201 displays an abnormal conformation detectable by mild trypsin digestion. Despite effective ATP hydrolysis, the rho201 mutant is a poor RNA:DNA helicase and terminates inefficiently on trp t'. The single F232C mutation thus appears to uncouple the protein's ATPase activity from its helicase function, so rho can no longer harness available energy for use in subsequent reactions.

Analysis of E. coli rho factor: mutations affecting secondary-site interactions

To define and differentiate primary and secondary RNA binding sites within the linear sequence of the rho protein, we investigated two mutant alleles, rho-115 and rhosuA1. They were first identified as defective in transcription termination in vivo, and later demonstrated to be defective in their interactions with RNA at the primary and secondary sites, respectively. Sequencing of rhosuA1 revealed a single lysine to glutamic acid residue change at position 352 (KE352), while rho-115 carries two mutations, glycine99 to valine (GV99) and a proline235 to histidine (PH235). Proteins carrying single mutations at each of these three positions were purified and their characteristics compared to the wild-type protein. We found both KE352 and GV99 to be defective in secondary-site RNA activation, with Km values for r(C)10 of 100 microM and approximately 650 microM, respectively, compared to the wild-type value of 4 microM. These observed secondary-site defects correlated with decreased helicase and ATPase activities, as well as a loss of transcription termination activity in vitro. By contrast, PH235 was very efficient at interacting with r(C)10 at the secondary site, with a measured Km of 0.5 microM, and displayed the characteristics of a hyperactive rho, as judged by its ATPase, helicase and termination capabilities. Our results show that mutations at three very different locations in the polypeptide can affect secondary-site activation by RNA, and that these interactions play a pivotal role in ATP hydrolysis, helicase activity and transcription termination.

REF2 encodes an RNA-binding protein directly involved in yeast mRNA 3'-end formation

The Saccharomyces cerevisiae mutant ref2-1 (REF = RNA end formation) was originally identified by a genetic strategy predicted to detect decreases in the use of a CYC1 poly(A) site interposed within the intron of an ACT1-HIS4 fusion reporter gene. Direct RNA analysis now proves this effect and also demonstrates the trans action of the REF2 gene product on cryptic poly(A) sites located within the coding region of a plasmid-borne ACT1-lacZ gene. Despite impaired growth of ref2 strains, possibly because of a general defect in the efficiency of mRNA 3'-end processing, the steady-state characteristics of a variety of normal cellular mRNAs remain unaffected. Sequencing of the complementing gene predicts the Ref2p product to be a novel, basic protein of 429 amino acids (M(r), 48,000) with a high-level lysine/serine content and some unusual features. Analysis in vitro, with a number of defined RNA substrates, confirms that efficient use of weak poly(A) sites requires Ref2p: endonucleolytic cleavage is carried out accurately but at significantly lower rates in extracts prepared from delta ref2 cells. The addition of purified, epitope-tagged Ref2p (Ref2pF) reestablishes wild-type levels of activity in these extracts, demonstrating direct involvement of this protein in the cleavage step of 3' mRNA processing. Together with the RNA-binding characteristics of Ref2pF in vitro, our results support an important contributing role for the REF2 locus in 3'-end processing. As the first gene genetically identified to participate in mRNA 3'-end maturation prior to the final polyadenylation step, REF2 provides an ideal starting point for identifying related genes in this event.

A quaternary transcription termination complex. Reciprocal stabilization by Rho factor and NusG protein

The Escherichia coli protein NusG is known to modulate Rho-dependent transcription termination in vivo. We have shown that it can also alter the pattern of Rho-dependent RNA endpoints in vitro, at lower NusG concentrations than can be explained by reported interactions between NusG and Rho or RNA polymerase. Three observations in vitro now suggest a model to account for these effects of NusG on Rho-dependent termination. First, the presence of NusG circumvents the interference with Rho function caused by adding DNA oligonucleotides complementary to particular segments of the Rho binding site. Second, when NusG is added to stalled elongation complexes, the off-rate of Rho from nascent RNA is slowed. Third, NusG associates stably with the elongation complex only when Rho is also present and bound to the nascent RNA. Our observations are consistent with a model in which NusG and Rho participate in an interdependent association with the transcribing RNA polymerase and the nascent RNA to facilitate the recognition and use of termination signals. Common structural and functional features shared with complexes that carry out processive antitermination are discussed.

Effect of the particle-size distribution on the backscattering ratio in seawater

Mie theory is used to model the backscattering ratio (the ratio of the backscattering coefficient to the total scattering coefficient) of marine particles with the assumption that they follow a Junge-type size distribution. Results show that the backscattering ratio is very sensitive to the presence of submicrometer particles and depends strongly on the shape of the size distribution. However, it is not affected significantly by absorption and does not vary with wavelength over the visible range. The implications for modeling of backscattering and ocean color in terms of phytoplankton pigment concentration are discussed.

Rho and RNA: models for recognition and response

Escherichia coli Rho factor is required for termination of transcription at certain sites by RNA polymerase. Binding to unstructured cytosine-containing RNA target sites, subsequent RNA-dependent ATP hydrolysis, and an RNA-DNA helicase activity that presumably facilitates termination, are considered essential for Rho function. Yet the RNA recognition elements have remained elusive, the parameters relating RNA binding to ATPase activation have been obscure, and the mechanistic steps that integrate Rho's characteristics with its termination function in vitro and in vivo have been largely undefined. Recent work offers new insights into these interactions with results that are both surprising and satisfying in the context of Rho's emerging structure. These include the requirements for binding and ATPase activation by a variety of RNA substrates, dynamic analyses of Rho tracking, helicase and termination activity, and the participation of a new factor (NusG) that interacts with Rho. Models for Rho function are considered in the light of these recent revelations.

Detection of phytoplankton pigments from ocean color: improved algorithms

Passive ocean-color data at 32 wavelengths in the visible domain and laser-induced fluorescence line heights of chlorophyll and phycoerythrin, measured simultaneously from an aircraft in the New York Bight area, are used to examine the problem of developing algorithms for pigment retrieval from ocean-color data that would be capable of distinguishing between chlorophyll and phycoerythrin. Using factor analysis, it is shown that it is indeed possible to develop such algorithms. Furthermore, the wavelengths used in the algorithms can be reduced from 32 to 6 (similar to the SeaWiFS channels) without much loss in information. These multiwavelength algorithms yield significantly higher correlation coefficients for chlorophyll compared with the conventional blue-green ratio used for retrieval of this pigment. The Coastal Zone Color Scanner wavelengths appear to be inadequate for quantitative retrieval of the phycoerythrin signal.

Evidence supporting a tethered tracking model for helicase activity of Escherichia coli Rho factor

Transcription termination factor Rho of Escherichia coli has an ATP-dependent RNA.DNA helicase activity that presumably facilitates RNA transcript release from the elongation complex. This helicase activity is unidirectional (5' to 3') and is stoichiometric, with one RNA molecule released per Rho hexamer in vitro. A simple RNA tracking model postulates that after Rho's initial binding, it translocates preferentially toward the 3' end of the RNA. Nitrocellulose filter binding studies combined with RNase H cleavage are inconsistent with this simple tracking model. Instead, they support a model in which Rho forms tight primary binding interactions with the recognition region of the RNA and remains bound there while transient secondary RNA binding interactions coupled to ATP hydrolysis serve to scan along the RNA to contact the RNA.DNA helix. This "tethered tracking" model is consistent with other properties of Rho factor, including the presence of two classes of RNA binding sites on the Rho hexamer and the 1:1 stoichiometry in the Rho helicase assay.

Poly(A) site selection in the yeast Ty retroelement requires an upstream region and sequence-specific titratable factor(s) in vitro

In the Ty retrotransposon of Saccharomyces cerevisiae, as in most retroelements, the polyadenylation site of the 5' long terminal repeat (LTR) is ignored and the one in the 3' LTR is efficiently used. We examine here the contribution to this poly(A) site selection of the region termed 'U3', corresponding to the upstream non-transcribed portion of the 5' LTR. Using an established assay in vitro, we find that 3' processing is accurate and efficient with an RNA substrate corresponding to most of the LTR, whereas none is detectable with a shorter transcript lacking the U3 region, thus explaining why the 5' poly(A) site is ignored in genomic Ty mRNA. When HIS4 coding RNA, representing 'non-specific' sequence, replaces the U3 region, the Ty polyadenylation site is activated to 50% of the wild-type level. Within one specific region (TS1) in U3, 90-95 nt upstream of the poly(A) site, the change of UAGUAU to UCGCAU reduces processing efficiency by half, to the non-specific level provided by other sequences or by a deletion of the TS1 region. Another region (TS2) near the poly(A) site appears to be independently responsible for the remaining half of the processing activity. Alteration of both TS1 and TS2 eliminates processing entirely. In competition assays, excess unlabeled U3, but not its mutated counterparts, reduces the processing of radiolabeled Ty mRNA, suggesting the involvement of some sequence-specific titratable factor(s) in the whole cell extract for U3-specific activation.(ABSTRACT TRUNCATED AT 250 WORDS)

Deletion analysis of the Escherichia coli rho-dependent transcription terminator trp t'

We have analyzed with deletion mutations the Escherichia coli rho-dependent transcription terminator trp t'. This site, 211 nucleotides in length, contains multiple sequence elements that are recognized by rho. Among these multiple elements are two that together appear to be important for full transcription termination efficiency in vitro and are similar to the rutA and rutB sequence elements in the lambda tR1 rho-dependent terminator previously described by Chen and Richardson (1987). The results suggest for the first time that common functionally important elements are shared among rho-dependent terminators. Other regions of trp t' also appear to contribute to its functional efficiency, consistent with the idea that rho-dependent terminators contain dispersed and redundant recognition segments.

Transcriptional arrest of yeast RNA polymerase II by Escherichia coli rho protein in vitro

A promoter-independent assay utilizing poly(dC)-tailed DNA templates has revealed that Saccharomyces cerevisiae whole-cell extracts can be proficient for transcription by the endogenous yeast RNA polymerase II as well as for correct 3'-end RNA processing. Our attempts to examine the fate of polymerase II itself were inconclusive, because only trace transcription products corresponded to the expected size of terminated RNA species. Transcription in our processing-proficient extract was thus insufficient to cause termination. To test our system with a known, albeit heterologous, signal, we examined a dC-tailed template carrying the E. coli rho-dependent termination signal trp t' in the yeast extract. Transcripts from this template were not susceptible to processing, but addition of rho protein resulted in two distinct truncated transcripts that could not be chased by excess unlabeled nucleotides. These RNA species thus represented stably paused or terminated polymerase II products, and their absence when a mutated unresponsive trp t' template was used affirmed that they were due to the effects of rho. E. coli RNA polymerase added to a yeast extract pretreated with alpha-amanitin was also halted by rho at these same two sites. A mutated rho protein, while only partly defective with E. coli polymerase, failed to provoke arrest when transcription was carried out by RNA polymerase II. Thus, functional rho and its cognate site, trp t', appear necessary and sufficient to elicit the production of truncated transcripts by RNA polymerase II in a yeast whole-cell extract. The ability of rho to halt the eukaryotic enzyme strengthens the likelihood that a rho-like helicase may be involved in RNA polymerase II transcription termination.

Selective enrichment of RNA species for tight binding to Escherichia coli rho factor

We have applied the SELEX procedure (systematic evolution of ligands by exponential enrichment) to obtain RNA molecules that bind tightly to the Escherichia coli transcription termination factor rho. The starting pool was a population of RNA molecules 77 nucleotides (nt) long, in which was embedded a cassette of 30 nt of randomized sequence. The apparent dissociation constant of this RNA pool for hexameric rho factor was about 1 microM. After eight rounds of selection by filter binding, with RNA in either 10-fold or 40 to 100-fold excess at each step, the dissociation constant of the selected RNA had dropped by more than 500-fold to about 1 nM. Analysis of 29 clonal isolates from the population revealed that five had KDs substantially weaker than 10 nM (presumably background carryover), 40% were C-rich (as might have been predicted from rho's known substrate binding), and 40% had a strikingly preserved potential hairpin, in most cases of 6 base pairs with a 3 nt CAA loop and preceded by a CCCCA consensus. The rho-dependent trp t' terminator region includes a related potential hairpin structure; however, it is energetically unfavorable. The implications of the sequence findings for elucidating both static and dynamic aspects of rho factor recognition and response to its RNA target site are discussed.

NusG alters rho-dependent termination of transcription in vitro independent of kinetic coupling

To complement the recent discovery that rho-dependent termination in E. coli requires nusG protein in vivo, we have tested the effect of purified nusG protein on rho-dependent termination in vitro. With the well-characterized trp t' terminator of E. coli, and no other proteins than E. coli RNA polymerase and rho factor, nusG causes a proximal shift in the terminated RNA endpoints, compared to the endpoints generated by rho alone. The presence of nusG also enhances rho-mediated termination on partially defective mutant trp t' templates. We rule out explanations such as a change in the kinetic coupling between rho and RNA polymerase or a nusG-mediated increase in the affinity of rho for RNA. We also detect no difference in the helicase rate of rho in the presence of nusG. Even assays with completely stalled and isolated ternary complexes indicate that rho is able to effect the release of RNA with the assistance of nusG at points preceding the most proximal release sites observed in the absence of nusG. Our observations support a model in which nusG acts as a component of the transcription complex, possibly interacting with both rho and RNA polymerase as it governs accessibility to the nascent transcript.

Unusual aspects of in vitro RNA processing in the 3' regions of the GAL1, GAL7, and GAL10 genes in Saccharomyces cerevisiae

A striking feature of the 3'-end regions in polymerase II transcripts of Saccharomyces cerevisiae adjacent to their processing and polyadenylation sites is the lack of well-defined signal elements. Nonetheless, essential signals have seemed to be confined to compact regions in vivo, and we find that a short RNA with only 70 bases of GAL7 sequence upstream and 8 to 10 bases downstream of the poly(A) addition site is processed in vitro, as is an analogous CYC1 pre-RNA. Specific polyadenylation of a precleaved species further delimits the poly(A) signal and rules out obligatory coupling between cleavage and poly(A) addition. Although little proximal and even less distal sequence is required for accurate cleavage with CYC1 and GAL7, we have been unable to identify common features to which processing could be ascribed. We therefore turned to the coregulated set of genes in the galactose cluster (GAL1, GAL7, and GAL10) to assay their corresponding pre-mRNAs in vitro, in hopes of finding a common theme. By contrast to GAL7, short pre-mRNAs corresponding to GAL1 and GAL10 fail to be cleaved detectably, and only much longer transcripts are susceptible to processing. This indicates that signals, even if preserved, are more widely dispersed than the poly(A) addition site, and these results are unchanged whether extracts are from cells grown on glucose or galactose. As a further surprise, RNAs corresponding to the antisense orientation of the 3'-end regions of all three GAL genes are also effective substrates for the processing machinery in vitro. Computer analysis reveals the presence of polydisperse dyad symmetries that might account for these observations.

Effects of decreased cytosine content on rho interaction with the rho-dependent terminator trp t' in Escherichia coli

We have introduced multiple cytosine-to-uracil mutations in the rho-dependent transcription terminator trp t' and have characterized a subset of the resulting mutant derivatives in vitro for termination efficiency, affinity for rho, and stimulation of rho-ATPase activity. No specific cytosine residue appears to be required for termination, and at least 13 of the 28 cytosine residues in the 104 nucleotide trp t' region can be mutated with little effect on termination efficiency. One derivative with 11 mutations is significantly less efficient than other derivatives with a similar number of mutations, implying that the pattern of alterations, as well as the number, can affect termination efficiency. Derivatives with 20 and 28 cytosines mutated are non-functional in termination, consistent with the idea that cytosines are required for rho-dependent termination. Our results are inconsistent, however, with the hypothesis that the termination efficiency is directly related to the cytosine/guanine ratio in the nascent transcript. The results support the idea that neither RNA binding affinity nor ATPase activation per se are accurate predictors of rho-dependent termination efficiency.

Homologous mRNA 3′ end formation in fission and budding yeast

Sequences resembling polyadenylation signals of higher eukaryotes are present downstream of the Schizosaccharomyces pombe ura4+ and cdc10+ coding regions and function in HeLa cells. However, these and other mammalian polyadenylation signals are inactive in S. pombe. Instead, we find that polyadenylation signals of the CYC1 gene of budding yeast Saccharomyces cerevisiae function accurately and efficiently in fission yeast. Furthermore, a 38 bp deletion which renders this RNA processing signal non-functional in S. cerevisiae has the equivalent effect in S. pombe. We demonstrate that synthetic pre-mRNAs encoding polyadenylation sites of S. pombe genes are accurately cleaved and polyadenylated in whole cell extracts of S. cerevisiae. Finally, as is the case in S. cerevisiae, DNA sequences encoding regions proximal to the S. pombe mRNA 3' ends are found to be extremely AT rich; however, no general sequence motif can be found. We conclude that although fission yeast has many genetic features in common with higher eukaryotes, mRNA 3' end formation is significantly different and appears to be formed by an RNA processing mechanism homologous to that of budding yeast. Since fission and budding yeast are evolutionarily divergent, this lower eukaryotic mechanism of mRNA 3' end formation may be generally conserved.

Mutations in an RNP1 consensus sequence of Rho protein reduce RNA binding affinity but facilitate helicase turnover

Escherichia coli rho protein facilitates transcription termination by a mechanism that involves rho binding to the nascent RNA, activation of rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template. The initial step, formation of a rho-RNA complex, is mediated primarily by an RNA binding domain included within the amino-terminal 151 amino acids of rho protein. We have now identified one specific portion of this region that is involved in RNA binding, by photocross-linking and by site-directed mutagenesis. UV irradiation of rho-RNA complexes results in covalent attachment of the RNA to a single peptide in rho that apparently spans amino acids 45-100. Within this peptide is a ribonucleoprotein (RNP1) consensus sequence, Gly-Phe-Gly-Phe, that is present in many RNA-binding proteins. Mutagenesis of the phenylalanine residues in this consensus to leucine or alanine results in mutant proteins that are defective for RNA binding and have altered ATPase and RNA-DNA helicase activities. The weakened affinity but increased salt sensitivity of RNA binding by the mutant proteins suggests that they have lost more than just a set of nonionic interactions and are consistent with a change in the conformation of the RNA binding site. Whatever the changes, they appear localized primarily to the RNA binding domain because the mutants retain much of their RNA-dependent ATPase activity. We infer that the Phe residues themselves do not play a substantial role in the activation of ATP hydrolysis. Our results indicate that several different components of RNA interaction are required for rho activity and support a role for the RNP1 consensus region of rho in at least one specific aspect of RNA binding.

Polymerase chain reaction mapping of yeast GAL7 mRNA polyadenylation sites demonstrates that 3' end processing in vitro faithfully reproduces the 3' ends observed in vivo

In general, synthetic RNA transcripts corresponding to the 3' ends of Saccharomyces cerevisiae genes appear to be accurately cleaved and polyadenylated in vitro under appropriate conditions in yeast cell extracts. Initially, however, the endpoints observed in vitro for the GAL7 gene failed to correlate adequately with those reported in vivo as derived from traditional S1 nuclease protection analyses. This led us to apply an independent method for analyzing mRNA 3' ends, using the polymerase chain reaction, with a first strand primer that incorporated a BamHI restriction site sequence near its 5' end, followed by (dT)17. This proved to be a sensitive and accurate means for determining precisely the major and minor polyadenylation sites of the GAL7 mRNA. Moreover, there was complete agreement between the sites identified with this technique when applied to cellular RNA and those generated in vitro by our 3' end mRNA processing reaction. This provides further support for the likelihood that processing in vitro faithfully reflects the endonucleolytic cleavage and polyadenylation events that occur within the living cell.

A short intervening structure can block rho factor helicase action at a distance

We have characterized the helicase activity of transcription termination factor rho on a variety of substrates. Helicase activity requires specific recognition of a single-stranded region of RNA upstream (5') of the nucleic acid duplex on which rho acts. Spacer sequences of at least 450 nucleotides can be inserted between the rho-binding signals and the duplex region with little effect on activity. RNA-DNA helices of up to 120 base pairs, but not as long as 210 base pairs, can be disrupted efficiently by rho. The stoichiometry of release of substrates with long spacer sequences, as with the standard substrate, approaches a value of one RNA released per rho hexamer; thus cooperative binding by rho does not account for action at a distance. Instead, these results are consistent with a model in which a single rho hexamer binds initially to terminator sequences and then either loops out or tracks along the intervening RNA to reach the duplex region. Results with complex substrates are inconsistent with looping and support the tracking model: under conditions that allow disruption of RNA-DNA, but not RNA-RNA helices (0.4 mM Mg2+), the presence of a short RNA-RNA helix acts as a block to the disruption of an RNA-DNA helix downstream. These findings are discussed in relation to the mechanism of the helicase activity as well as its role in rho-dependent transcription termination.

RNA processing in vitro produces mature 3' ends of a variety of Saccharomyces cerevisiae mRNAs

Ammonium sulfate fractionation of a Saccharomyces cerevisiae whole-cell extract yielded a preparation which carried out correct and efficient endonucleolytic cleavage and polyadenylation of yeast precursor mRNA substrates corresponding to a variety of yeast genes. These included CYC1 (iso-1-cytochrome c), HIS4 (histidine biosynthesis), GAL7 (galactose-1-phosphate uridyltransferase), H2B2 (histone H2B2), PRT2 (a protein of unknown function), and CBP1 (cytochrome b mRNA processing). The reaction processed these pre-mRNAs with varying efficiencies, with cleavage and polyadenylation exceeding 70% in some cases. In each case, the poly(A) tail corresponded to the addition of approximately 60 adenosine residues, which agrees with the usual length of poly(A) tails formed in vivo. Addition of cordycepin triphosphate or substitution of CTP for ATP in these reactions inhibited polyadenylation but not endonucleolytic cleavage and resulted in accumulation of the cleaved RNA product. Although this system readily generated yeast mRNA 3' ends, no processing occurred on a human alpha-globin pre-mRNA containing the highly conserved AAUAAA polyadenylation signal of higher eucaryotes. This sequence and adjacent signals used in mammalian systems are thus not sufficient to direct mRNA 3' end formation in yeast. Despite the lack of a highly conserved nucleotide sequence signal, the same purified fraction processed the 3' ends of a variety of unrelated yeast pre-mRNAs, suggesting that endonuclease cleavage and polyadenylation may produce the mature 3' ends of all mRNAs in S. cerevisiae.

Mutations in the ATP-binding domain of Escherichia coli rho factor affect transcription termination in vivo

Five mutant rho proteins, representing alterations at three different locations in the Escherichia coli rho gene that affect ATP hydrolytic activity but not RNA binding, were examined in vivo for function at the rho-dependent IS2 and bacteriophage lambda tR1 terminators. The altered amino acids in rho are located at highly conserved residues near the beta 1 and beta 4 strands of the hydrophobic ATP-binding pocket that is structurally similar to the F1-type ATPases and adenylate kinase. The RNA-dependent ATPase activities of the mutant rho proteins were previously shown to range from undetectable to a twofold increase over wild-type rho in vitro. Analysis of these proteins within the environment of the cell confirmed that transcription termination in vivo is indeed related to the ability of rho factor to properly hydrolyze nucleoside triphosphates, as would be predicted from results in vitro. The relative efficiency of termination at lambda tR1, as judged by lambda N= plating efficiency and by suppression of polarity of IS2 upstream of galK, was closely linked to the level of RNA-dependent ATPase activity observed in vitro for each protein. Moreover, the termination efficiency of four of the altered rho proteins at IS2 and lambda tR1 in vivo corresponded directly to the effect of these mutations on rho function at the E. coli trp t' terminator in vitro. We conclude that determinations of rho function in vitro accurately reflect its behavior in intracellular termination events.

Specificity and efficiency of rho-factor helicase activity depends on magnesium concentration and energy coupling to NTP hydrolysis

The RNA-DNA helicase activity of Escherichia coli transcription termination factor rho can be significantly enhanced at lower potassium chloride and magnesium acetate concentrations than previously used. Decreasing the potassium chloride concentration from 150 to 50 mM increases the rate of release at least 4-fold, while at lower magnesium concentrations less ATP is required for maximal duplex disruption. For all concentrations tested (between 0.1 and 5 mM), the optimal magnesium and ATP concentrations are interdependent; a roughly equimolar ratio gives the maximal rate of RNA release, although peak height and breadth vary. Surprisingly, rho behaves differently with an RNA-RNA duplex, which cannot be efficiently disrupted at magnesium concentrations below 1 mM. Above 2.0 mM, release does occur efficiently suggesting that Mg2+ promotes some structural transition in the RNA-RNA helix to a rho-susceptible conformation. In addition to Mg2+, helicase activity requires hydrolysis of nucleoside triphosphates, but for all four standard NTPs the rates of NTP hydrolysis do not correlate uniformly with the rates of RNA release. Based on the ratio of the rate of RNA release to the rate of NTP hydrolysis, rho utilizes ATP most efficiently. The 2-4-fold weaker coupling of hydrolysis to duplex disruption for the other three NTPs demonstrates that NTP utilization is not, on its own, sufficient for efficient helicase activity. The less efficient coupling with GTP, CTP, and UTP correlates with conformational differences in the protein complex as probed by mild trypsin digestion. The implications of our findings for substrate specificity and energy coupling in the helicase reaction are discussed.

Sex determination and the Y chromosome: the application of molecular genetic technique to behavioral genetics

In mammals, the Y chromosome mediates both gonadogenesis and spermatogenesis. It is also known to influence such traits as histocompatibility, sperm head morphology, pubertal (but not adult) testosterone level, sexual behavior, and aggressive behavior. An immediate goal in my laboratory is the isolation and characterization of the Y chromosomal gene responsible for initiating differentiation of the primitive bipotential gonads to become testes: the Y chromosomal gonadogenesis gene. Function of this gene initiates a cascade of events involving large numbers of other genes scattered throughout the genome, but it is not responsible for initiating development of all of the male phenotype; where : is XXSxr karyotype males, bearing the Sxr region of the Y chromosome which includes this gene, are sterile. It is not known if this gene influences those behaviors known to be influenced by the Y chromosome. If animals with an XXSxr karyotype, transgenic for specific Y chromosomal genes, could be produced, questions such as this could be answered. The developmental biology of the testis, molecular genetics of the Sxr region of the Y chromosome, and isolation of the testis determination gene from DNA of XXSxr males are discussed. Also discussed are the production of transgenic mice and the prospects for using such animals as coisogenic strains, differing by precisely known DNA sequences, in behavior genetic analysis. Such animals could be used both to test for behavioral phenotype and to dissect out biochemical and neurological mechanisms responsible for the behavior.